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DESCRIPTION
This journal is a peer reviewed scientific forum for the latest advancements in bacteriology research on a wide range of topics including food safety, food microbiology, gut microbiology, biofuels, bioremediation, environmental microbiology, fermentation, probiotics, and veterinary microbiology.TRANSCRIPT
Volume 3, Issue 12013
ISSN: 2159-8967www.AFABjournal.com
2 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 3
Sooyoun Ahn University of Florida, USA
Walid Q. AlaliUniversity of Georgia, USA
Kenneth M. Bischoff NCAUR, USDA-ARS, USA
Debabrata BiswasUniversity of Maryland, USA
Claudia S. Dunkley University of Georgia, USA
Lawrence GoodridgeColorado State University, USA
Leluo GuanUniversity of Alberta, Canada
Joshua GurtlerERRC, USDA-ARS, USA
Yong D. HangCornell University, USA
Divya JaroniOklahoma State University, USA
Weihong Jiang Shanghai Institute for Biol. Sciences, P.R. China
Michael JohnsonUniversity of Arkansas, USA
Timothy KellyEast Carolina University, USA
William R. KenealyMascoma Corporation, USA
Hae-Yeong Kim Kyung Hee University, South Korea
W.K. KimUniversity of Manitoba, Canada
M.B. KirkhamKansas State University, USA
Todd KostmanUniversity of Wisconsin, Oshkosh, USA
Y.M. Kwon University of Arkansas, USA
Maria Luz Sanz MuriasInstituto de Quimica Organic General, Spain
Melanie R. MormileMissouri University of Science and Tech., USA
Rama NannapaneniMississippi State University, USA
Jack A. Neal, Jr.University of Houston, USA
Benedict OkekeAuburn University at Montgomery, USA
John PattersonPurdue University, USA
Toni Poole FFSRU, USDA-ARS, USA
Marcos RostagnoLBRU, USDA-ARS, USA
Roni ShapiraHebrew University of Jerusalem, Israel
Kalidas ShettyNorth Dakota State University, USA
EDITORIAL BOARD
4 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
EDITOR-IN-CHIEFSteven C. RickeUniversity of Arkansas, USA
EDITORSTodd R. CallawayFFSRU, USADA-ARS, USA
Cesar CompadreUniversity of Arkansas for Medical Sciences, USA
Philip G. CrandallUniversity of Arkansas, USA
MANAGING and LAYOUT EDITOREllen J. Van LooGhent, Belgium
TECHNICAL EDITORJessica C. ShabaturaFayetteville, USA
ONLINE EDITION EDITORC.S. ShabaturaFayetteville, USA
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Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 5
Shiga Toxin-Producing Escherichia coli (STEC) Ecology in Cattle and Management Based Options for Reducing Fecal Shedding T. R. Callaway, T. S. Edrington, G. H. Loneragan, M. A. Carr, D. J. Nisbet
39
Can Salmonella Reside in the Human Oral Cavity?S. A. Sirsat
30
Growth of Acetogenic Bacteria In Response to Varying pH, Acetate Or Carbohydrate Concentration
R. S. Pinder, and J. A. Patterson
6
Independent Poultry Processing in Georgia: Survey of Producers’ PerspectiveE. J. Van Loo, W. Q. Alali, S. Welander, C. A. O’Bryan, P. G. Crandall, S. C. Ricke
70
ARTICLES
Greenhouse Gas Emissions from Livestock and PoultryC. S. Dunkley and K. D. Dunkley
17
REVIEW
Instructions for Authors79
Introduction to Authors
The publishers do not warrant the accuracy of the articles in this journal, nor any views or opinions by their authors.
TABLE OF CONTENTS
6 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
www.afabjournal.comCopyright © 2013
Agriculture, Food and Analytical Bacteriology
ABSTRACT
Acetogens have only been isolated in low numbers from ruminal contents, even though the majority
of acetogens isolated from ruminal contents are capable of utilizing both H2 and soluble carbohydrates
present in ruminal fluid (e.g. glucose and cellobiose). The much higher methanogenic affinity for hydro-
gen has been suggested to determine the prevalence of methanogens over acetogens in many ecosys-
tems, suggesting that other environmental factors determine the number of acetogens present in ruminal
fluid. We report the effects of carbohydrate concentration, pH and acetate concentration on the growth of
two ruminal acetogenic isolates (A10 and H3HH). The minimum amount of glucose necessary for growth
(threshold) of A10 (111 μM) and H3HH (56 μM) was greater than the glucose concentration previously de-
tected in bovine ruminal fluid (8-17 μM). However, the threshold of H3HH on cellobiose (14 μM) was much
lower than the actual concentration previously detected in ruminal fluid (110-175 μM), suggesting that this
organism could survive in the rumen using cellobiose as an energy source. Isolate A10 had a sufficiently
high threshold for cellobiose (139 μM) to suggest that, at least for certain periods, the concentration of cel-
lobiose in ruminal contents could be too low to support growth of this isolate. The growth rate of isolate
A10 was decreased by 50 % when the pH of the growth medium was lowered from 6.6 to 5.5. A similar de-
crease in growth rate was observed with isolate H3HH. Increasing the acetate concentration of the growth
medium decreased the growth of both isolates as well. Moreover, the effect of high acetate concentration
was more discernible at lower pH. The present results suggest that pH and volatile fatty acid concentration
may be key factors limiting the growth of acetogens isolated from ruminal contents.
Keywords: acetogens, rumen, hydrogen, pH, carbohydrate concentration
Correspondence: J. A. Patterson, [email protected] Tel: +1 -765-494-4826 Fax: +1-765-494-9347
Growth of Acetogenic Bacteria In Response to Varying pH, Acetate Or Carbohydrate Concentration
R. S.Pinder1,2 and J. A. Patterson1
1Animal Science Dept, Purdue University, West Lafayette, IN 47907-10262Current address; 7855 South 600 East, Brownsburg, IN 46112
Agric. Food Anal. Bacteriol. 3: 6-16, 2013
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 7
INTRODUCTION
Hydrogen produced during microbial degrada-
tion of cellulose in ruminal contents must be elimi-
nated in order to maintain the appropriate condi-
tions for efficient conversion of cellulose to volatile
fatty acids (Zinder, 1993). Normally, methanogens
remove H2 from the rumen through methane produc-
tion from H2/CO2. However, substantial interest ex-
ists to reduce methane emissions from ruminants to
minimize this contribution to global warming. One
potential approach is to use acetogenic bacteria to
produce acetate as an alternate H2 sink. Acetogens
are a diverse group of organisms that are capable
of utilizing H2/CO2 to form acetate, a product use-
ful to the host animal. However, acetogens are typi-
cally isolated in low numbers from ruminal contents
(Morvan et al., 1994; LeVan et al., 1998) despite be-
ing capable of utilizing some of the carbohydrates
glucose, cellobiose) present in ruminal fluid (Bocca-
zzi and Patterson, 2011; Genthner et al., 1981). This
apparent contradiction suggests that other ruminal
environmental factors limit the growth of acetogens
in ruminal contents. Several possibilities exist, in-
cluding: 1) chemical factors (pH and volatile fatty
acid concentration) which interfere with the growth
of acetogens; 2) acetogens are not capable of uti-
lizing carbohydrates at the concentration present in
ruminal fluid; 3) acetogens are not capable of grow-
ing at a pace fast enough to avoid being washed out
of rumen contents; 4) acetogens cannot compete
with methanogens for H2/CO2.
The goal of the research presented herein was to
determine 1) the minimum concentration of glucose,
maltose and cellobiose needed for growth of aceto-
gens, 2 ) the growth rates of acetogens, and 3) the
influence of volatile fatty acid concentrations and pH
on growth of acetogens. We report that the growth
of isolates A10 and H3HH, two acetogenic bacteria
isolated and characterized from ruminal contents
(Boccazzi and Patterson, 2011; Pinder and Patterson,
2011, 2012) may be affected by the carbohydrate
concentrations found in ruminal fluid but that growth
of these organisms is severely influenced by the com-
bination of low pH and high acetate concentration.
MATERIALS AND METHODS
Organisms
Isolates A10 and H3HH, previously described
ruminal isolates (Boccazzi and Patterson, 2011; Pin-
der and Patterson, 2011, 2012) were used in all the
experiments described herein. These organisms
were maintained in acetogenic medium.
Growth medium
The acetogen medium of Boccazzi and Patterson
(2011) was used except where indicated otherwise.
In experiments where the initial concentration of car-
bohydrates was the treatment tested, ruminal fluid
was omitted to reduce the amount of carbohydrates
present in basal medium. In experiments where the
initial pH of the medium was one of the treatments
imposed, the composition of the medium was modi-
fied by eliminating the Na2CO3 which buffered the
medium too strongly for reliable pH adjustment be-
low 6.5. In addition, the medium was gassed with
oxygen-free 100 % N2 rather than 100 % CO2, during
preparation and dispensing. Preliminary experiments
showed that the buffering capacity of this modified
medium was sufficient for short-term (less than 12 h)
experiments with low (0.05 g/L) amounts of carbohy-
drate substrate.
Batch cultures
Glucose, maltose or cellobiose (from 0.2 μ-filter
sterilized stock solutions) were added as indicated to
tubes containing 10 mL of acetogen medium. Tubes
were inoculated with 0.1 mL of an overnight culture,
measured for the initial OD (absorbance at 660 nm)
and placed in a 37°C water bath. The contents of the
tubes were mixed and the OD of the tubes measured
and recorded at intervals as shown. For experiments
where the initial carbohydrate concentration was the
treatment regimen imposed, the growth rate (at each
carbohydrate concentration) was determined and
the threshold of carbohydrate utilization was estimat-
ed as the point where growth rate was greater than
8 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
baseline (without added carbohydrates). For experi-
ments where the pH and acetate concentration of the
media were the treatments imposed, growth rates of
the isolates was estimated by plotting the OD values
for each culture and determining the apparent maxi-
mum growth rate from the steepest portion of the
growth curve.
Continuous cultures
An anaerobic continuous culture system as de-
scribed by Boccazzi and Patterson, (2011) was used.
The growth medium consisted of acetogen medium
supplemented with 1.4 mM glucose. The medium
reservoir and growth vessels were gassed with 100
% CO2 at a flow of approximately 50 mL min-1. After
the system was reduced, the growth vessels (operat-
ing capacity; approximately 215 mL) were inoculated
with 20 mL of an overnight culture. The bacterial
culture was allowed to grow as a batch culture for
6 h after which the medium flow was initiated. The
cultures were allowed at least ten turnovers to reach
steady state conditions before sampling. Turnover
rate was determined by collecting the outflow from
the growth vessels. Sample collection was accom-
plished by diverting the outflow from the growth
vessels for 10 min into ice-cooled collecting vessels.
Aliquots of the outflow were analyzed for volatile
fatty acids (VFA), glucose and bacterial DM as de-
scribed below. Concentrations of volatile fatty acids
in the culture supernatant were determined using a
Hewlett Packard 5890 gas chromatograph (Hewlett
Packard Co., Palo Alto, CA) fitted with a glass column
packed with GP 60/80 carbopack C / 0.3% Carbowax
M / 0.1 % H3PO4 (Supelco, Inc.; Bellefonte, PA). The
injector and detector temperatures were set at 200°C
while the column temperature was set at 135°C. For-
mate concentrations in the culture supernatant were
determined using a formate dehydrogenase assay
(Schaller and Triebig, 1983). The pH of the culture
was measured immediately after sampling for vola-
tile fatty acids with an Ag combination electrode
connected to a Fisher Accumet pH meter (Fisher Sci-
entific, Pittsburg, PA). Glucose concentration in the
culture medium was assayed with a glucose oxidase
kit (Sigma Chemical Co., St. Louis, MO). The initial
glucose concentration was determined on uninocu-
lated control bottles.
After sampling, the media flow to the growth ves-
sels was adjusted to obtain the next dilution rate.
RESULTS
Effect of dilution rate on growth of iso-late A10 and H3HH
Previously, we determined the maximum growth
rate of isolate A10 to be approximately 0.47 h-1 (Pin-
der and Patterson, 2012). Both isolate A10 and isolate
H3HH attached to the surfaces of the growth vessels,
perhaps due to extracellular polysaccharide. The
net result was that apparent maximum growth rates
in continuous culture approached 1.2 h-1 (Figure 1),
This is much higher than the maximum growth rate
estimated in batch culture and is probably a result of
the wall growth continuously inculating the medium.
Similar problems have been reported for Eubacteri-
um limosum, an acetogen also isolated from ruminal
contents, which produces copious amounts of extra-
cellular polysaccharide (Loubiere et al., 1992). Nev-
ertheless, the batch culture experiments provided
sufficient information to obtain an estimate of the
maximum growth rate of isolate H3HH. The highest
growth rate (approximately 0.6 h-1) for isolate H3HH
was obtained when this organism was grown on glu-
cose (42 mM). The maximum growth rate observed
for isolate A10 was approximately 0.5 h-1 in agree-
ment with previous experiments.
Minimum carbohydrate concentration necessary for growth
Boccazzi and Patterson (2011) described the array
of carbohydrates utilized by isolates A10 and H3HH.
The purpose of this series of experiments was to as-
sess the minimum concentration of carbohydrate
necessary for growth of isolates A10 and H3HH. The
approach used in the present experiments was to
determine the growth rate of isolates A10 and H3HH
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 9
Figure 1. Continuous culture of isolate H3HH. A continuous culture system was established as previously described The system was inoculated (approx. 10 % v/v) with an overnight culture and allowed at least ten turnovers to reach steady state conditions. An aliquot of the outflow was collected to determine bacterial mass (●) and acetate content (□). After sampling the media flow rate was adjusted and the cultures were allowed to reach steady state conditions again.
10 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Figure 2. Influence of carbohydrate concentration on the growth rate of isolate H3HH in batch culture. Acetogen media (10 mL) containing various amounts of either glucose (♦), cellobiose (■) or maltose (●) was inoculated (0.1 mL) with an overnight culture of isolate H3HH. The OD (absorbance at 660 nm) was measured at appropriate time intervals. The growth curve of each culture was plotted and the highest growth rate at each carbohydrate concentration was deter-mined. The growth rate not attributable to the carbohydrates added (i.e., growth rate of cultures without added carbohydrates) was subtracted from the other growth rates. The vertical lines drawn on the graph represent the range of glucose and cellobiose concentrations detected in ruminal fluid. Each point is the mean of at least two (but usually three) tubes.
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 11
in acetogen medium containing concentrations of
glucose, maltose and cellobiose that ranged from
very low (10 μM, as found in the rumen) to very high
(> 1 mM, as used in substrate utilization assays). The
apparent maximum growth rates obtained at each
carbohydrate concentration were plotted as a func-
tion of the carbohydrate concentration present at
inoculation. The minimum carbohydrate concen-
tration necessary for growth was estimated as the
carbohydrate concentration below which the growth
rate of the cultures was similar to that of cultures
without added carbohydrate. Using this definition,
H3HH had a lower minimum threshold for maltose
(14 μM) and cellobiose (14 μM) than for glucose
(111 μM) (Figure 2). In contrast, isolate A10 had a
lower minimum threshold for maltose (28 μM) than
for glucose (56 μM) or cellobiose (139 μM) (Figure
3). Furthermore, the concentration of carbohydrates
needed for maximal growth rate of isolate A10 was
one magnitude less than the concentrations needed
by isolate H3HH (1 versus 10 mM).
Effect of pH and acetate concentration on growth
Factors other than growth rate, minimum con-
centration of carbohydrates needed to start growth
may also be involved in maintaining relatively low
numbers of acetogens in rumen contents. Physical
parameters (pH and VFA) have been implicated in
inhibiting growth of a number of bacterial species,
thus, the effects of pH and VFA concentration on the
growth rates of isolates A10 and H3HH were deter-
mined. Because of the growth on the wall of the
growth vessel, continuous culture data was not reli-
able, and only batch culture data is presented. Iso-
late A10 and isolate H3HH were grown in acetogen
medium without ruminal fluid, but with sodium ac-
etate (0, 50 or 100 mM) and initial pH adjusted to 6.6
or 5.5. Ruminal fluid was omitted from the medium
to reduce the basal acetate concentration from ap-
proximately 2 mM to less than 0.1 mM. Both isolate
A10 and isolate H3HH were affected by the initial
pH and acetate concentration of the medium (Table
1). At neutral pH (6.6), there was a small decrease in
growth rate with increasing acetate concentrations.
However, the growth rate of both organisms at pH
5.5 was approximately half of that obtained at pH
6.6 when no acetate was added to the medium. An
Table 1. Growth rate of isolates A10 and H3HH as affected by pH and acetate concentrations1
H3HH A10
Acetate pH 6.6 pH 5.5 pH 6.6 pH 5.5
0 mM 0.309 0.119 0.279 0.126
50 mM 0.260 0.014 0.270 0.023
100 mM 0.278 0.006 0.259 0.005
12 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Figure 3. Influence of initial carbohydrate concentration on the growth rate of isolate A10 in batch culture. Please refer to the legend of Figure 2 for details of this experiment.
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 13
initial acetate concentration of 50 mM was sufficient
to inhibit the growth of both organisms when the pH
of the media was 5.5, and no growth occurred at pH
5.5 when initial acetate concentration was 100 mM.
DISCUSSION
The rumen evolved to provide the appropriate
conditions for microbial degradation of cellulose
and other plant structural carbohydrates (Weimer et
al., 2009). Accordingly, a number of anaerobic, car-
bohydrate-fermenting microbial species grow well
and can be isolated in high numbers from ruminal
fluid (Hungate, 1966; Oshio et al., 1987; Ricke et
al., 1996). However, the rumen is not a hospitable
environment for all microbes. The anaerobiosis, liq-
uid turnover rate, concentration of soluble carbohy-
drates and the chemical (i.e., pH and VFA concentra-
tion) characteristics of the rumen prevent the growth
of a number of bacteria that otherwise should be
able to grow on the substrates in rumen fluid. The
rumen is a highly reduced (Eh = -150 to -350 mV) an-
aerobic environment (Clarke, 1977) and oxygen in-
troduced into ruminal contents through feeding and
drinking is rapidly depleted by facultatively anaero-
bic organisms (Ellis et al., 1989). Many bacterial spe-
cies are unable to tolerate the reduced and anaero-
bic character of ruminal contents. This anaerobic
ecosystem provides the host animal with VFA, which
it can utilize as an energy source (Lin and Luchi, 1991;
Lindley et al., 1990). Although the acetogens used
in these experiments are somewhat tolerant to aero-
bic conditions (Boccazzi and Patterson, 2011), as a
group, acetogens isolated from ruminal contents are
obligate anaerobes.
The turnover rate of rumen contents also can af-
fect which organisms colonize and persist in the ru-
men. For example, fatty acid-degrading bacteria
(e.g., Anerovibrio lipoliticus) have an ample supply
of substrates in ruminal contents. However, these
organisms are unable to propagate in high numbers
in ruminal contents because their maximum growth
rate is less than the liquid turnover rate of ruminal
contents (Hungate, 1966). The result is that VFA are
available for ruminant utilization. The present results
show that maximum growth rate of isolate A10 or
H3HH would not limit establishment of high num-
bers in ruminal contents. Although we were unable
to obtain reliable data from continuous culture ex-
periments, data obtained from batch culture experi-
ments indicated that the maximum growth rate of
these organisms was approximately 0.6 h-1 for isolate
A10 and 0.5 h-1 for isolate H3HH. These generation
times are greater than the liquid turnover rate of
ruminal contents which ranges between 0.05 and 0.1
turnovers/h (Hungate, 1966; Weimer, 1992, Zinder,
1993).
The concentration of soluble carbohydrates in
ruminal fluid may also limit growth of certain bacte-
ria. As an example, Streptococcus bovis, although
routinely isolated from ruminal contents, is not found
in high numbers unless relatively high concentra-
tions of soluble carbohydrates (i.e. maltose) are
present (Russell and Baldwin, 1979). This situation
exists due to the relatively low affinity (> 1 mM) of S.
bovis for carbohydrates. In previous research (Pin-
der et al., 2012), we determined that the concentra-
tion of soluble carbohydrates in rumen fluid of cattle
consuming typical production diets ranges between
8 and 17 μM for glucose, and between 110 and 175
μM for cellobiose. The present results are important
because they indicate that the soluble carbohydrate
concentration of ruminal fluid may be sufficient for
growth by acetogens and other factors may limit
growth.
The low numbers of acetogens in ruminal con-
tents cannot be explained by the anaerobic nature
of the isolates, growth rate, or minimum carbohy-
drate concentration necessarry for growth. Thus,
other factors, such as pH or VFA concentration may
be involved in restricting colonization. The rumen
is an environment with a relatively high concentra-
tion of volatile fatty acids and frequently acidic
conditions (Hungate, 1966; Oshio et al., 1987; Rus-
sell, 1992). The concentration of total fatty acids in
ruminal fluid fluctuates considerably but is usually
within the range of 60-140 mM (Owens and Goetsch,
1988). Many factors (e.g., diet of the animal and time
in relation to feeding) affect ruminal fluid pH and
14 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
VFA concentrations. For example, high concentrate
diets cause an increase in the total concentration
of VFA in ruminal fluid as compared to diets high in
forages (Oshio et al., 1987). Moreover, ruminal VFA
concentrations fluctuate diurnally as a result of feed
ingestion by the animal. Total VFA concentrations
typically start to rise soon after feeding and peak ap-
proximately 6 h post-feeding. Similar to VFA con-
centrations, ruminal fluid pH fluctuates (generally
between pH 5 and 7) in response to diet and time
post-feeding. The pH of ruminal fluid usually is
lower in animals consuming high-concentrate diets
compared to animals consuming high forage diets.
Ruminal fluid typically decreases soon after feeding
and remains low for several h after feeding before
returning to near neutral levels.
Many bacteria (e.g., S. bovis) are capable of tol-
erating the low pH and high VFA concentrations
similar to those often detected in ruminal contents
after feeding (Russell, 1991). However, many other
bacterial species (e.g., Fibrobacter succinogenes, R.
flavefaciens, Salmonella, Veillonella, and Escherichia
coli) are sensitive to decreasing pH, especially as pH
is decreased to values of pH 6.0 and less (Dunkley
et al., 2008; Hollowell and Wolin, 1965; Kwon et al.,
1997; Ricke, 2003; Russell and Dombrowsli, 1980).
Wolin (1969) determined that the growth of E. coli is
markedly inhibited by the high volatile fatty acid con-
centrations of ruminal fluid and that this inhibition
is pH dependent. Although disagreement exists as
to the mechanism by which the presence of volatile
fatty acids in acidic conditions inhibits the growth of
certain bacteria (Russell, 1992), the fact remains that
these low pH and high VFA sensitive bacteria are un-
able to grow in ruminal contents even when specific
enrichment is attempted (Wallace et al., 1989).
The non-ruminal Clostridium thermoaceticum,
is the only acetogen that has been examined re-
garding its ability to tolerate acidic conditions and/
or high VFA concentrations. Clostridium thermo-
aceticum grows faster and produces more acetic
acid when grown at neutral pH than when grown
in acid medium (Schwartz and Keller, 1982; Wang
and Wang, 1984). Furthermore ,when exponentially-
growing cells of C. thermoaceticum were exposed
to pH’s ranging from 7 to 5, the internal pH of the
cells is maintained above 7 until the extracellular pH
dropped below 5.5 (Baronofsky et al., 1984). These
characteristics identify C. thermoaceticum as a neu-
trophile (pH optimum for growth is near 7). One
explanation of the sensitivity of neutrophiles to low
pH conditions, based on the chemiosmotic theory,
proposes that volatile fatty acids act as uncouplers
destroying the H+ gradient across the cell membrane
and are thus capable of dissipating the proton mo-
tive force of cell membranes (Freese et al., 1973;
Sheu et al., 1975; Baronofsky et al., 1984; Salmond et
al., 1984; Wallace et al., 1989). The ability of acido-
philes and acid-tolerant species to resist low pH and
high VFA concentrations is conveyed by the ability to
lower intracellular pH in the face of declining extra-
cellular pH thus maintaining a constant proton mo-
tive force across the cell membrane (Russell, 1992).
The data presented herein show that isolate A10 and
isolate H3HH, are sensitive to the pH of the culture
medium as well as the presence of volatile fatty ac-
ids in an acidic medium. These results suggest that
acetogens isolated from ruminal contents are similar
to C. thermoaceticum, E. coli and other neutrophilic
bacteria which are sensitive to low pH and high VFA
concentrations. It remains to be determined exactly
how these environmental factors (i.e., low pH and
high VFA concentrations) prevent the growth of ace-
togens isolated from ruminal contents.
Although the carbohydrate concentrations in
ruminal fluid may be marginally sufficient for growth
of isolates A10 and H3HH, the inability to grow un-
der low pH and high VFA conditions would sug-
gest that establishment of a high number of these
isolates in ruminal contents (especially with a single
inoculation) would be unlikely. However, we did not
determine if either isolate remains metabolically ac-
tive under low pH and high VFA conditions. If aceto-
gens are metabolically active under low pH and high
VFA conditions, then the possibility of using repeat-
ed (monthly, weekly or daily) inoculations to maintain
high numbers of acetogens in ruminal contents may
be possible. Another, though more difficult, pos-
sibility is to isolate or generate mutants capable of
tolerating low pH and high VFA conditions.
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 15
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Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 17
www.afabjournal.comCopyright © 2013
Agriculture, Food and Analytical Bacteriology
ABSTRACT
In 2008 the Environmental Protection Agency (EPA) estimated that only 6.4% of U.S. greenhouse gas
(GHG) emissions originated from agriculture. Of this amount, 53.5% comes from animal agriculture. Agri-
cultural activities are the largest source of N2O emissions in the U.S. accounting for 69% of the total N2O
emissions for 2009. In animal agriculture, the greatest contributor to methane emissions is enteric fermen-
tation and manure management. Enteric fermentation is the most important source of methane in beef and
dairy production, while most of the methane from poultry and swine production originates from manure.
The main cause of agricultural nitrous oxide emissions is from the application of nitrogen fertilizers and
animal manures. Application of nitrogenous fertilizers and cropping practices are estimated to cause 78%
of total nitrous oxide emissions.
Based on the life cycle assessment of beef cattle, 86.15% of the GHGs are emitted during the production
stage, while 68.51% of emissions take place during the production of pork and 47.82% of GHG emissions
occur during the production stage of broiler chickens. The majority of the emissions from the beef cattle
production comes from enteric fermentation while manure management is the major source during swine
production and propane use during broiler poultry production.
Keywords: greenhouse gas, LCA, poultry emissions, beef emissions
Correspondence: C. S. Dunkley, [email protected]: +1 -229-386-3363 Fax: +1-229-386-3239
REVIEWGreenhouse Gas Emissions from Livestock and Poultry
C. S. Dunkley1 and K. D. Dunkley2
1Department of Poultry Science, University of Georgia, Tifton, GA 2School of Science and Math, Abraham Baldwin Agricultural College, Tifton, GA
Agric. Food Anal. Bacteriol. 3: 17-29, 2013
18 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
INTRODUCTION
The primary greenhouse gases emitted by agri-
cultural activities are carbon dioxide (CO2) methane
(CH4) and nitrous oxide (N2O) (Johnson et al., 2007).
Livestock production contributes GHGs to the atmo-
sphere both directly and indirectly (IPCC, 2006). The
emissions can be classified based on the source of
the emission; 1) Mechanical, and 2) Non-mechanical.
The majority of direct CO2 emissions from animal
agriculture are usually from fossil use, for example;
the use of propane or natural gas in furnaces or in-
cinerators and the use of diesel gas to operate farm
equipment and generators results mostly in CO2
emissions (Dunkley unpublished data), this type of
emission can be described as “mechanical emis-
sions.” The use of electricity on animal production
farms results in indirect emissions since the emis-
sions do not occur on site.
For non-mechanical emissions, direct emissions
can be a by-product of digestion through enteric
fermentation (CH4 emissions). Direct emissions also
occur from the decomposition and nitrification/de-
nitrification of livestock waste (manure and urine)
where CH4 and N2O are emitted. Managed waste
that is collected and stored also emits CH4 and N2O.
Indirect emission of N2O occurs when nitrogen is lost
from the system through volatization as NH3 and Nx.
Also, indirect emissions can result from nitrogen that
is runoff or leached from manure management sys-
tems in a form other than N2O and is later converted
to N2O offsite (IPCC, 2006). Methane from enteric
fermentation and manure management are the main
sources of CH4 emissions from agricultural activities
and of all domestic livestock, dairy and beef cattle
are the largest emitters of CH4. Agricultural activities
are the largest source of N2O emissions in the US
accounting for 69% of the total N2O emissions for
2009 (EPA, 2011). The majority of the N2O emission
from animal agriculture is from manure management
which is the second largest (a far second to crop-
ping practices) N2O emitter in the agricultural sector
(IPCC, 2010). Application of nitrogenous fertilizers
and cropping practices are estimated to cause 78%
of total nitrous oxide emissions according to John-
son et al., (2007).
In 2011 the US Environmental Protection Agency
(EPA) reported that the Agricultural Sector was re-
sponsible for a total of 410.6 Tera gram CO2 equiva-
lents (Tg CO2e in 2005). Enteric fermentation and
manure management contributed a total of 200.4 Tg
CO2e which represented about 48% of the total emis-
sions from the agricultural Sector. During this period
(Figure 1.) enteric fermentation was responsible for
136.5 Tg CO2e and managed manure was respon-
sible for 63.9 Tg CO2e. In 2007, the emissions from
the Agricultural sector were 425.8 Tg CO2e a 3.7%
increase. The emissions from enteric fermentation
during this period were 141 Tg CO2e a 3.3% increase
over the 2005 period, while manure management
emissions increased to 68.8 Tg CO2e a 7.7% increase.
The GHG emissions from agriculture showed a 1.5%
reduction to 419.3 Tg CO2e in 2009 when compared
to 2007. This reduction was reflected slightly in en-
teric fermentation which was down by 0.8% to 139.8
Tg CO2e and a 2% reduction in manure management
emission to 49.5 Tg CO2e (IPCC, 2010).
EMISSIONS BASED OF MANURE MAN-AGEMENT SYSTEMS
The type of manure management system that is
used in livestock production can affect the amount
of emissions and the type of gases that are emitted.
A variety of livestock production systems operates
in the U.S. and different manure management sys-
tems are utilized depending on the type of livestock
or poultry produced (Del Grosso et al., 2008). Among
the manure management systems practiced in the
US are; pit storage, poultry with/without litter (that
is, poultry raised on a bedding material or poultry
raised in cages), dry-lot, anaerobic lagoon, pasture,
etc. (Table 1). Beef cattle can be raised using differ-
ent manure management systems and the amount of
emissions are dependent on how the manure is man-
aged. Beef cattle raised on pasture/range exhibit
relatively high N2O emissions. In this system the ma-
nure and urine from the cattle are deposited directly
on the soil reducing the likelihood of much methane
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 19
emission. When cattle are raised under conditions
where the manure is collected and spread daily and
there is no storage before it is spread onto the soil
there is low CH4 emissions and no N2O emissions.
Dairy cattle and swine reared in liquid/slurry manure
management systems have moderate to high CH4
emissions, while emissions from swine and dairy cat-
tle reared in anaerobic lagoon management systems
have variable CH4 emissions as it is mostly depen-
dent on the duration of time the manure and slurry
are stored in the lagoons. In this system, the waste
can be stored between 30 to 200 days; the longer the
storage time, the more likely the CH4 emissions will
be high. Both the liquid/slurry and anaerobic lagoon
manure systems have low N2O emissions. Poultry
reared in management systems with litter and us-
ing solid storage have relatively high N2O emissions
but low CH4 emissions. This is because the manure is
stock piled under aerobic conditions which limits the
production of CH4 (USAFGGI, 2008). Broiler, pullets,
and to an extent breeders, are reared using these
manure management systems. Commercial layers
are typically reared in high-rise cages or scrape-out/
belt systems. Here the manure is excreted onto the
floor below with no bedding to absorb moisture. The
ventilation system dries the manure as it is stored. In
some broiler breeder houses a part of the manure is
collected under the slats in the houses making it sim-
ilar to the commercial layers. In this type of manure
management system both CH4 and N2O emissions
are relatively low (IPCC, 2000).
The amount of CH4 or N2O that is emitted from
livestock also depends on environmental conditions
(Del Grosso et al., 2008). Methane is emitted under
anaerobic conditions where oxygen is not available
(Palmer and Reeve, 1993). Storage in tanks, ponds
or pits, such as those used with liquid/slurry flushing
systems encourages anaerobic conditions, therefore
more CH4 is produced (USAF 2008). Conversely, sol-
id waste storage in stacks or shallow pits promotes
Figure 1. The distribution of livestock GHG emissions by source in 2005, 2007 and 2009
63.9 68.8 67.4
136.5 141 139.8
0
20
40
60
80
100
120
140
160
2005 2007 2009
Manure Management Enteric Fermentation
Tg C
O2
equi
vale
nt
20 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
aerobic conditions which are more favorable for N2O
emissions. High temperatures and increased storage
time can also increase CH4 emissions (Del Grosso
et al., 2008). Feed characteristics also play a role in
CH4 emissions. Feed, diet, and growth rate have an
effect on the amount and quality of manure an ani-
mal produces (Monteny, 2006). Harper (2000) stated
that there was a large effect on CH4 emissions that
is contingent on the production and use of farmyard
manure. Typically, in an organic system, stock piled
manure is composted, which will increase aeration
limiting anaerobic production of CH4. Higher en-
ergy feeds result in manure with more volatile sol-
ids, which increases the substrates from which CH4
is produced (Del Grosso et al., 2008). Depending on
the species, this impact is somewhat offset because
some higher energy feeds such as that fed to poultry
are more digestible than lower quality forages fed to
ruminant animals and therefore less waste is excret-
ed. The energy content and quality of feed affects
Table 1. Description of livestock waste deposition and storage pathways
Relative Emissions
Manure Management System Description CH4 N2O
Pasture/range/paddock
Ex. beef cattle
Manure and urine from pasture and grazing ani-mals is deposited directly onto soil.
Low High
Daily Spread Manure and urine are collected and spread on fields (little or no storage prior to application).
Low Mini-mal
Solid storage
Ex. poultry
Manure and urine with or without litter are col-lected and stored long term in bulk.
Low High
Dry lot
Ex. Beef cattle
Manure and urine are deposited directly on unpaved feedlots where it is allowed to dry. It is periodically removed.
Low High
Liquid/slurry
Ex. Swine/dairy cattle
Manure and urine are collected and transported in liquid form to tanks for storage. The liquid/slurry may be stored for long periods.
Moderate to high
Low
Anaerobic Lagoon
Ex. Swine/dairy cattle
Manure and slurry are collected using a flush system and transported to lagoons for storage. It remains in lagoons for 30-200 days.
Variable Low
Pit Storage
Ex. Swine/poultry layers
Combined storage of manure and urine in pits below livestock confinements.
Moderate to high
Low
Poultry with litter
Ex. Broiler/pullet/breeders
Enclosed poultry houses utilize bedding material (ex. Wood shavings, peanut hull, rice hulls etc.). The bedding absorbs moisture and dilutes ma-nure. Litter is cleaned out typically once per year.
Low High
Poultry without litter
Ex. Poultry layers/broiler breeders
In high-rise cages or scrape-out/belt systems, manure is excreted onto the floor below with no bedding to absorb moisture. The ventilation system dries the manure as it is stored.
Low Low
Adapted from IPCC (2000) Chapter 4.
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 21
the amount of methane produced in enteric fermen-
tation where lower quality feed and higher quantities
of feed causes greater emissions (USAFGG, 2008).
It was reported by the EPA (2011) that an animals
feed quality and feed intake affects emission rates.
In general, lower feed quality and / or higher feed
intakes lead to higher emissions.The composition
of the waste, the type of bacteria involved, and the
conditions following excretion, all have an effect on
the production of N2O from waste management sys-
tems (EPA, 2010). In order for N2O to be emitted, the
waste must be handled aerobically where NH3 and
organic nitrogen is converted to nitrates and nitrites
(Del Grosso et al., 2008).
EMISSIONS FROM ENTERIC FERMENTA-TION AND MANAGED MANURE FROM 2005 TO 2009
Ninety-one % of emissions from enteric fermenta-
tion and managed livestock manure are in the form
of CH4 (EPA, 2011). When Monteny et al. (2001) com-
pared the distribution of methane emissions from
enteric fermentation among animal types; poultry
had the lowest amount with 0.57 lbs methane/ ani-
mal/ year when compared to dairy cattle with 185 to
271 lbs methane/ animal/ year and swine with 10.5lbs
methane/ animal/ year. In 2005, livestock emissions
from enteric fermentation and manure management
were 200.4 Tg CO2e (Table 2). Of this total, dairy
cattle and beef cattle contributed 99.3 and 30.4 Tg
CO2e respectively from enteric fermentation. Swine
contributed 1.9 Tg CO2e from enteric fermentation
while poultry contributed no emissions from enteric
fermentation. For this same period, dairy cattle were
responsible for 109.6 Tg CO2e from enteric fermen-
tation and managed livestock waste combined; beef
cattle contributed 57.4 Tg CO2e, swine contribut-
ed 22.7 Tg CO2e, while poultry contributed 4.4 Tg
CO2e. The remaining emissions (5.66 Tg CO2e) were
from other livestock animals which were not reared
in large amounts.
By 2007 (Table 3), the total amount of GHG emis-
sions from enteric fermentation and managed live-
stock waste had increased by 4.69% from emission
levels in 2005 to 209.8 Tg CO2e. This was as a result
of increases in enteric fermentation from dairy cattle
(101.6 Tg CO2e), beef cattle (32.4 Tg CO2e) swine (2.1
Tg CO2e) and horses. There were also increases in
emissions from managed livestock waste in all the
major livestock categories. Overall, during the two
year period from 2005 to 2007, dairy cattle had a
2.5% increase in emissions (112.4 Tg CO2e), beef cat-
tle had the highest percentage increase of 8.7% up
to 62.4 Tg CO2e. Swine had an increase of 6.6% up to
24.3 Tg CO2e, while poultry had a 4.5% increase (4.6
Tg CO2e) during the 2005 to 2007 period (EPA, 2011).
In 2009 (Table 4), a reduction in emissions of 1.28%
from the 2007 levels was observed even though these
emissions were not as low as in 2005. The emissions
from enteric fermentation from the major livestock
categories showed a reduction in enteric fermenta-
tion from dairy cattle (99.6 Tg CO2e), while beef cat-
tle showed an increase (33.2 Tg CO2e). Enteric fer-
mentation emissions from swine remained the same
as in 2007. For the major livestock categories overall
reductions in emissions from enteric fermentation
and managed livestock waste combined were ob-
served in all with the exception of beef cattle. Dairy
cattle had a 2% reduction down to 110.1 Tg CO2e
from the 2007 levels of 112.4 Tg CO2e. Beef cattle
had a 1.7% increase up to 63.5 Tg CO2e, swine had a
reduction of 4.9% (23.1 Tg CO2e) while poultry had a
6.5% reduction in the emissions from 2007. Of all the
major livestock categories (dairy, beef cattle, swine
and poultry) only poultry had an overall reduction
(2.2%) in emissions from 2005 to 2009 (EPA, 2011).
The emission estimates reported here were adapted
from the EPA’s 2011 report. Several modifications
to the estimates relative to the previous estimates
had an effect on the emission estimates. The modi-
fications included; the average weight assumed for
mature dairy cows from 1550 pounds used in pre-
vious inventories to 1500 pounds. There were also
slight modifications from the 2008 numbers in the
populations of calves, beef replacement and feedlot
cattle. Swine populations were also modified so that
the categories “<60 pounds” and “60- 119pounds”
changed to “<50 pounds” and “50-119 pounds”.
22 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Table 2. Greenhouse gas emissions by livestock category and source in 2005
Enteric Fermentation Managed Livestock Waste
CH4 CH4 N2OTotal
Animal Type Tg CO2 equivalent
Dairy Cattle 99.3 2.8 7.5 109.6
Beef Cattle 30.4 21.4 5.6 57.4
Swine 1.9 19.0 1.8 22.7
Horses 3.5 0.06 0.3 3.86
Poultry 0.00 2.7 1.7 4.4
Sheep 1.0 0.1 0.4 1.5
Goats 0.30 0.00 0.0 0.3
Total 136.5 46.6 17.3 200.4
Table 3. Greenhouse gas emissions by livestock category and source in 2007
Enteric Fermentation Managed Livestock Waste
CH4 CH4 N2OTotal
Animal Type Tg CO2 equivalent
Dairy Cattle 101.6 2.9 7.9 112.4
Beef Cattle 32.4 24.2 5.8 62.4
Swine 2.1 20.3 1.9 24.3
Horses 3.6 0.6 0.6 4.8
Poultry 0.00 2.8 1.8 4.6
Sheep 1.0 0.1 0.1 1.2
Goats 0.3 0.0 0.0 0.3
Total 141.0 50.7 18.1 209.8
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 23
These changes attributed to an average reduction
in emissions from dairy cattle of 11.5 Gg or 0.8% per
year and beef cattle emissions decreased an aver-
age of 0.13 Gg or less that 0.01% per year over the
entire time series relative to the previous inventory
(EPA, 2011).
Of course, in order to discuss emissions from
enteric fermentation one must consider the size
(weight) of the livestock and the number of each
type of livestock grown each year. Larger animals will
produce more methane than smaller animals and
the amount of methane emitted is increased with in-
creasing number of animals grown (Del Grosso et al.,
2011). The type of digestive system will also deter-
mine the amount of methane produced. Cattle are
ruminant animals with a four compartment stomach.
Their digestive tract is designed for microbial fer-
mentation of fibrous, high cellulose materials. One
of the by-products of microbial fermentation is meth-
ane (Stevens and Hume, 1998). Poultry and swine
are mono-gastric animals with a simple stomach and
little microbial fermentation taking place; therefore
they have less enteric methane production (Frédéric
et al., 2007). The feed quality also plays a role in the
amount of CH4 that is emitted, poorer quality high-
fiber diets will likely result in greater CH4 emissions
than higher quality diets that contains more pro-
tein (Del Grosso et al., 2011). Typically, CH4 is usu-
ally produced following the degradation of carbon
components during digestion of feed and manure
(Monteny et al., 2006). Husted (1994) stated that the
rumen was the most important site of methane pro-
duction in ruminants (breath), while in monogastric
animals such as swine and poultry, methane is usu-
ally produced in the large intestines. The manner in
which animal manure are stored whether indoors in
sub-floor pits or outdoors are also relevant sources
of CH4 production (Husted, 1994). Enteric fermen-
tation is the most important source of methane in
the dairy industry, while, the majority of CH4 emis-
sions from the pig and poultry industries originates
from manures (Monteny et al., 2006). There is also
a range in the total emissions in dairy cows that is
caused by differences in diet and housing systems.
For example; there are lower emission rates for ty-
ing stalls and higher rates for cubicle houses (Groot
Koerkamp and Uenk, 1997).
Table 4. Greenhouse gas emissions by livestock category and source in 2009
Enteric Fermentation Managed Livestock Waste
CH4 CH4 N2OTotal
Animal Type Tg CO2 equivalent
Dairy Cattle 99.6 2.7 7.8 110.1
Beef Cattle 33.2 24.5 5.8 63.5
Swine 2.1 19.0 2.0 23.1
Horses 3.6 0.5 0.3 4.4
Poultry 0.0 2.7 1.6 4.3
Sheep 1.0 0.1 0.3 1.4
Goats 0.3 0.0 0.0 0.3
Total 139.8 49.5 17.9 207.2
24 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
FARM-GATE AND LIFE CYCLE ASSESS-MENT EMISSIONS
Greenhouse gas emission from the different live-
stock categories can also be evaluated based on
“Life Cycle Assessment” (LCA). This involves not
only the farm-gate emissions but also an inventory
of the material and energy inputs and the emissions
associated with each stage of production. The LCA
looks at the “cradle to grave” energy use (Guinee
et al., 2001). This assessment could include; fertil-
izer production and transportation, crop production
and transportation, feed additive manufacturing and
transportation, animal production facilities, trans-
portation to processing plants, processing, distribu-
tion to retail markets, consumer use of the product
and disposal of packaging (Guinee et al., 2001). This
can be a very complex process and researchers have
used different boundaries when approaching the
LCA for different livestock. The Environmental Work-
ing Group (2011) examined GHG emissions from
beef cattle and poultry, based on “farm-gate” emis-
sions and showed that each of the livestock category
assessed displayed differences in various areas of
production (Figure 2). Farm-gate emissions here are
based on the emissions that occur within the bounds
of the farm plus the feed production and did not in-
clude processing of the meat. The EWG reported
that the majority (7.51 kg CO2e) of GHGs was emit-
ted to produce 1 kg beef at the farm-gate was as a
result of enteric fermentation. In poultry production
the majority (1.26 kg CO2e) of GHGs emissions was
from feed production and no GHGs emissions from
enteric fermentation. To produce 1 kg of edible beef
at the farm-gate resulted in the emissions of 1.75 kg
CO2e of N2O from manure, while 0.28 kg CO2e N2O
was emitted from manure to produce 1 kg edible
chicken meat. Emissions of GHGs from energy use
at the farm-gate can also be compared for different
livestock categories. On-farm energy use to produce
1 kg of beef at the farm-gate resulted in the emission
of 0.23 kg CO2e, while to produce 1 kg chicken meat
at the farm-gate resulted in the emission of 0.26 kg
CO2e GHGs. It was also reported that 4.8 kg CO2e
was generated to produce 1 kg of edible eggs. The
majority of the emissions from the production of ed-
ible eggs occurs at the farmgate (Figure 3) and as
with chicken meat production, these emissions came
from feed production, on-farm energy use, N2O from
poultry litter and fuel combustion (EWG, 2011). The
Environmental Working Group (2011) also report-
ed LCAs from dairy production, reporting yogurt,
cheese and 2% milk LCAs. The production of whole
milk at the farm-gate resulted in 1.02 CO2e per Kg
of edible whole milk, while only 0.67 kg CO2e was
emitted per kg of edible 2% milk. Domestic cheese
production at the farm-gate resulted in the emission
of 9.09 kg per kg of edible cheese (Figure 3). For yo-
gurt production, the majority of emissions occurred
post-farm gate (1.03 kg CO2e per kg yogurt). Meth-
ane emissions from enteric fermentation were the
primary source of pre-farm-gate GHGs for cheese,
milk and yogurt production (EWG, 2011).
A number of different GHG emission values from
LCA have been published for different livestock cat-
egories (Table 4). Based on these publications the
emissions from beef production at the farm-gate
ranged from 14.8 to 20 kg CO2e/kg of product at
the farm-gate with an average of 16.25 kg CO2e/kg
of product at the farm-gate. The figures for swine
ranged from 3.4 to 6.4 kg CO2e/kg of product at
the farm-gate with an average of 4.82 kg CO2e/kg
of product at the farm-gate, while the emissions
for poultry ranged from 2.33 to 4.6 kg CO2e/kg of
product at the farm-gate with an average of 3.09 kg
CO2e/kg of product at the farm-gate. According to
reports by EWG (2011), beef cattle LCA emissions in
kg CO2e/kg of consumed food was 27 kg. They also
reported that the LCA for pork was 12.1 kg CO2e/kg
of consumed food, while chicken had an LCA of 6.9
kg CO2e/kg of consumed food (Figure 3).
The LCA emissions that were calculated by the
EWG included the production emissions. This in-
cluded the emissions before the product left the
farm plus all avoidable and unavoidable waste. Cal-
culations were also done to include post-production
emissions which included processing, transport, re-
tail, cooking and waste disposal (EWG, 2011). Of the
27 kg CO2e emitted to produce 1 kg of beef (con-
sumed) only 3.73 kg CO2e was post farm-gate emis-
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 25
Figure 2. Sources of beef and poultry production emissions
Figure 3. LCA production and post-production emissions of beef and dairy cattle, swine and poultry
7.51
4.67
1.75
0.590.23
0
1.26
0.280
0.26
0
1
2
3
4
5
6
7
8
Enteric Fermentation CH4
Feed Production Manure N20 Manure CH4 On-farm Energy Use
kg CO2e/kg
edible meat
at farm-gate
Beef Cattle Poultry
Farmgate Emissions per kg consumed meat
23.27
11.778.29
3.3 3.631.17 0.92
3.73
1.7 3.81
3.61.17
1.03 0.98
0
5
10
15
20
25
30
Beef Cattle Cheese Swine Poultry Eggs Yogurt Milk (2%)
kg C
O2e
/kg
cons
umed
mea
t
Production Emissions Post-production Emissions
LCA Emissions for Beef Cattle, Dairy, Swine and Poultry
26 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
sions (Figure 3). A total of 3.81 kg CO2e was emitted
post farm-gate to produce 1 kg of consumed pork,
while 3.3 kg CO2e from the total 6.9 kg emitted to
produce 1 kg chicken (consumed) was post farm-
gate.
From the LCA emissions it is clear that the major-
ity (86%) of the emissions from beef cattle produc-
tion occur during the production stage while only
14% of the LCA emissions occur post-production
(Figure 4). This is similar to swine where the major-
ity (69%) of emissions was also observed during the
production stage. A different scenario was observed
for the poultry LCA where 48% of the emissions were
observed during the production stage.
CONCLUSIONS
Of the major livestock animals reared, emissions
from poultry production systems generate the low-
est levels of emissions to produce one kg CO2e/kg
meat at farm-gate while dairy cattle produce the
lowest levels of emissions to produce one kg CO2e/
kg product at farm-gate. Dairy cattle emit the high-
est levels of GHG per animal followed by beef cattle
and swine. The majority of the emissions from beef
production come from enteric fermentation and
feed production with the cow to calf and the steer
calf stages generating more than 65% of the total
GHG emissions from this livestock category. In all the
stages of beef production, high levels of CH4 from
enteric fermentation are generated. For dairy cattle,
the majority of emissions are from enteric fermen-
tation, similar to beef cattle production. Methane
emission from manure storage and feed production
Figure 4. Percent production and post-production emissions for beef and dairy cattle, swine and poultry LCA
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
Beef Cattle Cheese Swine Poultry Eggs Yogart Milk (2%)
Production Emissions Post-production Emissions
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 27
in dairy cattle production also contributes to high
levels of GHGs. Swine production emits GHGs pri-
marily from manure management and fuel combus-
tion. Only a small amount of CH4 is emitted during
digestion when compared to ruminants. At least one
third of GHG emitted from swine production is from
post farm-gate activities. The largest contributor
to GHG emissions from poultry production is feed
production. The highest emissions from poultry on-
farm activities are from fuel combustion from energy
use and manure management. In broiler production
post farm-gate emission makes up more than half
of all the emission, while post farm-gate emissions
from egg farm operations accounts for less than one
quarter of the total emissions.
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30 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
www.afabjournal.comCopyright © 2013
Agriculture, Food and Analytical Bacteriology
ABSTRACT
The oral cavity is a dynamic environment with several niches for attachment of a variety of flora. The
dominant flora in the mouth are comprised of anaerobic Gram-positive bacteria. Salmonella is a Gram-
negative bacterium which, according to the literature, is found very rarely in the parotid gland of the mouth
of humans. One of the most important characteristics of bacteria in the oral cavity is their ability to attach
to the mucosal cells. Salmonella has displayed ability to attach to the epithelial cells of the intestine and
have a variety of fimbiral lectins, type I fimbriae, and flagella which aid attachment to a variety of cells. This
review details the ability of Salmonella to cause disease and the potential of Salmonella as a pathogen in
the oral cavity of humans.
Keywords: Salmonella, dental, oral cavity
INTRODUCTION
Salmonella is a facultative intracellular Gram-neg-
ative pathogen transmitted by the ingestion of con-
taminated food and water. Depending on the spe-
cies, Salmonella may cause either typhoid fever or
enteritis. S. Typhi causes typhoid fever which is a se-
rious systemic infection. S. Typhimurium causes gas-
troenteritis which is localized infection in the intes-
Correspondence:Sujata A. Sirsat, [email protected]: +1 -713-743-2624 Fax: +1-713-743-3696
tines of humans (Takaya et al., 2005). The incidence
of illness due to salmonellosis has risen in the past
three decades. Foods such as eggs, poultry, peanut
butter, raw sprouts and most commonly implicated
in foodborne Salmonella outbreaks (Maki, 2009).
One of the largest outbreak of Salmonella Ty-
phimurium occurred in Chicago in 1984 when
200,000 people acquired the pathogen via pasteur-
ized milk contaminated with non-pasteurized milk
(Tafazoli et al., 2003). Salmonella outbreaks in foods
can be prevented by proper food handling practices
and thorough cooking of poultry and eggs. Improv-
REVIEWCan Salmonella Reside in the Human Oral Cavity?
Sujata A. Sirsat1
1 Conrad N. Hilton College of Hotel and Restaurant Management, University of Houston, Houston, TX 77204-3028
Agric. Food Anal. Bacteriol. 3: 30-38, 2013
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 31
ing standards of quality testing and animal rearing
practices will also be advantageous (Tafazoli et al.,
2003). However, contaminated ready-to-eat (RTE)
foods pose a challenge since these are not pro-
cessed before consumption (Koo et al., 2012). More
recently, Salmonella outbreaks have occurred in
ground beef, mangoes, cantaloupe, and pet food
(CDC, 2012a; CDC, 2012b; CDC, 2012c; CDC, 2013).
The evidence of Salmonella in the oral cavity
dates back to 430 BC (Sulonen et al., 2007). There
have been a few cases reported of Salmonella infec-
tion in the parotid gland of the mouth (Sulavik et al.,
1997; Suárez and Rüssmann, 1998; Stern et al., 2001;
Sulakvelidze et al., 2001; Stone 2002; Sturny et al.,
2003; Strindelius et al., 2004; Stern et al., 2005; Stern
et al., 2006). The parotid gland is the salivary gland in
humans that facilitates the early digestion of starch
and swallowing (Thesleff et al., 1988).These cases are
most often caused by Salmonella due to secondary
infections (Stern et al., 2001). As will be discussed in
the following sections, Salmonella has a tremendous
ability of attach to epithelial cells of the intestine of
the host. The focus of this review is to discuss the
potential ability of Salmonella to survive and attach
to the oral mucosa and propose possible methods
to study this interaction.
GENETICS OF SALMONELLA PATHO-GENESIS
It is believed that Salmonella virulence has
evolved as a result of horizontal gene transfer (John-
ston et al., 1996). This concept is supported by the
fact that large numbers of virulence genes are clus-
tered within its chromosome. The five Salmonella
Pathogenicity Islands (SPI) identified in Salmonella
are located in various regions on the chromosomes
and contain sets of virulence genes (Foster and
Spector, 1995). Invasion is believed to be controlled
by genetic and environmental regulators. Envi-
ronmental signals such as high pH (Cheung et al.,
1999), low osmolarity (Darwin and Miller, 1999) and
low oxygen (Cirillo et al., 1998) are believed to in-
crease invasion of Salmonella in the host. This has
been proven by testing the effects of these factors
on Salmonella strains containing lacZ fusions in the
invasion genes and performing ß–galactosidase as-
says and improved invasion of Salmonella in tissue
culture cell lines (Cheung et al., 1999; Davidson and
Harrison, 2002). In addition, (Sirsat et al., 2011) dem-
onstrated that sublethal heat stress may increase the
attachment ability of Salmonella in Caco-2 cells. SPI-
1 encodes a type III secretion system (TTSS) which is
essential for the process of cell invasion. The protein
forms a secretory “needle complex” which spans the
inner and outer bacterial membrane (Jones, 2005).
Control of invasion genes leads to the formation of
the type III secretion apparatus at the point of infec-
tion (Bowe et al., 1998). This secretion system is used
by microorganisms to translocate virulence-associat-
ed effector proteins into the cytoplasm of the host
cells resulting in a cross-talk which leads to down
stream responses such as membrane ruffling on the
surface of the host cell followed by the formation
of phagosomes which may internalize the bacteria
(Lucas and Lee, 2000; Liu et al.,2008). SPI-1 specifi-
cally codes for transcriptional regulators such as hilA
(Davidson and Harrison, 2002), hilC (Chenoweth et
al., 2007), and hilD (Chatfield et al., 1992). The hilA
gene has been shown to be required for the expres-
sion of three other invasion genes: invF, sspC, and
orgA (Davidson and Harrison, 2002). The gene invF is
a transcriptional regulator (Enoch, 2007), sspC codes
for an invasion protein (Libby et al., 1994), and orgA
product is a component of an export machinery
system (Leverentz et al., 2001). PhoPQ is a regula-
tory two-component system, which is not contained
within SPI-1 but is crucial for invasion phenotype of
Salmonella (Liljemark and Gibbons, 1972; Lichten-
steiger and Vimr, 2003). This two-component system
responds to extracellular cation levels (Lillard, 1980).
In conditions of low cation concentration, sensor
kinase PhoQ phospohorylates the regulator PhoP
which activates pag transcription. Induction and ex-
pression of pag genes are required for the survival of
the bacteria in the macrophage (Lewis et al., 2009).
Other pathogenicity islands, SPI-2 and SPI-5, encode
genes which are responsible for pathogenesis of Sal-
monella after invasion of the host (Shumway, 1990).
32 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Salmonella attachment to epithelial cells is de-
pendent on lectin-like adhesions which recognize
specific glycoconjugate receptors on the host cells.
Salmonella has several types of fimbrial lectins in-
cluding SEF14. SEF17, and SEF21 (Teplitski et al.,
2003). Other fimbriae such as plasmid-encoded
fimbriae (PEF) and long polar fimbriae (LPF) of Sal-
monella are also believed to be involved in the ad-
hesion of the bacteria to villus of the small intestine
and the Peyers patches (Terai et al., 2005; Mihaljevic
et al., 2007). Studies done by (Teplitski et al., 2003)
have shown that flagella also play an important role
in the attachment of Salmonella to epithelial cells of
the host by functioning to move to appropriate sites.
The next section discusses host immune reaction to
combat virulent Salmonella.
IMMUNE REACTION TO COMBAT SAL-MONELLA
Salmonella enters the host via contaminated food
or water (Threlfall, 2006). The pathogen exhibits in-
creased acid-tolerance response when exposed to
the low pH of the stomach (Leistner and Gorris, 1995).
Following this, Salmonella enters the small intestine
and moves towards and adheres to the intestinal ep-
ithelium due to expression of several fimbriae genes
(Leistner, 2000). Cytoskeletal rearrangements occurs
once the bacteria adhere to the epithelial surface
causing host membrane ruffling which leads to en-
closing adherent bacteria in vesicles (Li et al., 2002).
Salmonella invasion into epithelial cells leads to
recruitment of neutrophils into the intestinal lumen.
One of the significant factors that lead to neutrophil
recruitment is the secretion of IL-8 by the epithelial
cells (Takaya et al., 2005). Following this, Salmonella
enters the macrophages leading to the activation of
its virulence mechanisms which further leads to its
survival and replication in the host. In some cases
Salmonella may enter the blood and cause second-
ary infections colonizing in various organs of the
body (Lewis et al., 2009).
Salmonella also has the potential to activate the
adaptive immune system. Activation of cytokines
leads to downstream activation of both the T helper
(Th) and T cytotoxic (Tc) cells (Thomson et al., 1977;
Testerman et al., 2002). Tc cells either kill the intra-
cellular bacteria or release live bacteria when they
lyse. Th cells activate B cells which may produce an-
tibodies which could aid in opsonizing the bacteria
(Thomson et al.,1977; Testerman et al., 2002). Mice
studies have shown that the depletion of Th cells
had a more pronounced effect than the depletion
of Tc cells. Transfer of Th cells to naïve recipients
induced more effective vaccination compared to
transfer of Tc cells. The following section discusses
the microbial ecology of the mouth (Mittrucker and
Kaufmann, 2000).
ORAL MICROBIAL ECOLOGY
Bacteria have been found in the mouths of infants
shortly after birth. Organisms such as Escherichia
coli are transient microorganisms. Others such as S.
salivarius and lactobacilli are more characteristic of
adult flora and are found within a few days (Takaya
et al., 2002). Studies have shown that maternal sa-
liva may act as a source of some Gram-negative
anaerobes in the oral microflora of infants even be-
fore tooth eruption (Könönen et al., 2007). Oral flora
rapidly changes once teeth erupt in the mouth since
teeth provide an additional unique surface for bacte-
rial colonization. Saliva is another common environ-
mental influence in the mouth since it washes away
non-adherent bacteria and has inherent buffering
properties (Russell and Melville, 1978). Additionally,
other factors such as diet, oral hygiene, and general
health also influence the nature of oral flora (Tatusov
et al., 2003).
The mouth contains several different types of
bacteria. This could be because of the availability
of several different niches available for bacterial at-
tachment. These surfaces are the teeth, mucosal epi-
thelial cells, and the bacterial layers that constitute
the plaque on the teeth (Whittaker et al.,1996). This
topic has been extensively reviewed by (Tafazoli et
al., 2003; Takaya et al., 2004). The majority of bacteria
belong to streptococci genus which is a Gram-posi-
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 33
tive filamentous organism. In particular, Streptococ-
cus mutans are especially important as they cause
dental caries (Gibbons and Houte, 1975; Gibbons,
1984). S. mitis and S. sanguis are other streptococ-
ci that are present in lower numbers (Liljemark and
Gibbons, 1972). Other Gram-positive rods such as
those belonging to the Actinomyces species are also
present. These are involved in some periodontal dis-
eases. Gram-negative organisms such as Neisseria
and Veillonella may be also present on the oral cav-
ity. Most of these bacteria are anaerobic and include
members of Bacteroides, Fusobacterium, and Vibrio
(Gibbons, 1984).
The indigenous oral flora exerts competition to-
ward bacteria found elsewhere in the human body
and hence it is rare to isolate Salmonella, E. coli or
Staphylococcus aureus from the mouth. This is be-
cause all the attachment sites are taken up by the
indigenous flora and their numbers are a lot higher
as compared to the potential pathogenic bacteria
(Tavazoie et al., 1999).
There are several forces that regulate the coloni-
zation of bacteria in the mouth. The most important
factor however is bacterial adherence to surfaces
in the mouth. Attachment properties are especially
crucial for microorganisms since there is a risk of be-
ing washed out of the oral cavity entirely (Tafazoli et
al., 2003). The mouth has proven to be a particularly
interesting model for studying adhesion between
host and pathogens since it has several different mi-
crocosms which can be easily sampled. Additionally,
there is increased interest to study these interactions
because microorganisms cause periodontal diseas-
es. It has been demonstrated that dietary sucrose
is required for accumulation of microorganisms on
teeth surfaces (Taitt et al., 2004).
SALMONELLA IN THE ORAL CAVITY
Evidence of Salmonella in the oral cavity has been
seen as far back as 430 BC when (Sulonen et al.,
2007) set out to determine the probable cause of
the “Plague of Athens” using skeleton dental pulp
from the mass burial site. The researchers performed
polymerase chain reaction (PCR) and screened six
different pathogens using specific DNA primers.
They concluded that the pathogen in the dental
pulp of the skeletons was Salmonella or a pathogen
very closely related to Salmonella.
The parotid gland is the salivary gland that is of-
ten affected due to inflammation (Takaya et al., 2004;
Takaya et al., 2005). Parotitis usually manifests in in-
fants, elderly persons, and the immunocompromised
(Takaya et al., 2005). The most common pathogen
that is associated with bacterial parotitis is Staphylo-
coccus aureus (Takaya et al., 2005). Other organisms
such as Haemophilus influenzae, Klebsiella pneu-
monia, and Salmonella spp. are not as frequently
isolated (Takaya et al., 2004). Nine cases of parotid
abscess due to Salmonella has been reported in the
literature to date (Sulavik et al., 1997; Suárez and
Rüssmann, 1998; Stern et al., 2001; Sulakvelidze et
al., 2001; Stone 2002; Sturny et al., 2003; Strindelius
et al., 2004; Stern et al., 2005; Stern et al., 2006).
As described in the previous sections, Salmonella
causes these types of infections after it enters the
gastrointestinal tract and is disseminated into the
bloodstream. The secondary areas of colonization
are usually diseased tissue and trauma sites (Stern et
al., 2001). (Stern et al., 2001) presented a case study
of a 50-year old patient who had parotid abscess.
This individual may have been infected orally or it
could have been a result of a secondary infection
due to Salmonella. However, the patient did not
show symptoms of gastroenteritis and hence may
have been a carrier of the pathogen eventually re-
sulting in Salmonella spreading to the bloodstream
and the manifestation of parotid abscess.
Saliva contains the enzymes lysozyme and lac-
toferrin (Tafazoli et al., 2003) and Gram-negative
pathogens such as Salmonella and E. coli have been
shown to be sensitive toward lactoferrin as it acts
as an antimicrobial (Takaya et al., 2002). In addition,
these antimicrobial enzymes interact with each other
in a synergistic or additive manner (Tenovuo, 1998).
Lysozyme acts on Gram-negative bacteria by hydro-
lyzing 1,4-beta-linkages in the bacterial cell walls
(Proctor et al., 1988). Lactoferrin interacts with the
lipolysacharide of the Gram negative cell membrane
34 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
(Appelmelk et al., 1994). This may explain why such
few cases of Salmonella persistence are evident in
the oral cavity. Independent studies have found that
specific Salmonella mutations may lead to resistance
against lysozyme (Sanderson et al., 1974).
POTENTIAL STUDIES
As discussed in previous sections, the key to bac-
terial presence and survival in the mouth is attach-
ment to various sites in the oral cavity. This is espe-
cially challenging in the mouth due to the constant
washing of non-adherent bacteria by saliva. Also,
saliva contains lysozyme which has been shown to
be effective against Gram-negative organisms such
as Salmonella and E. coli (Takaya et al., 2002). One of
the initial studies to examine Salmonella in the oral
cavity would be to test the effect of saliva on the vi-
ability of Salmonella. This would give investigators
an indication if the concentration of lysozyme in sa-
liva is inhibitory to Salmonella. This can be done by
collecting saliva from humans and adding cultures of
Salmonella grown overnight and testing viability by
the plate count method.
Tenor et al. (2004) prepared epithelial cell suspen-
sions to test the adherence of bacteria to the cells of
oral cavity and similar studies could be performed
for Salmonella to test its capability of adherence to
these types of cells. A flow-chart of the method is
Figure 1. Flow chart of an experimental method to test the ability of bacterial attachment to hu-man epithelial cells from the oral cavity
Collect human epithelial cells by scraping oral cavity with wooden
stick
Wash cells to remove unattached bacteria and diluted to 105 cells/ml
Mix cell suspensions with bacteria
and incubate at 35°C for 30 min
Wash cells to removed unattached bacteria
Stain bacteria and enumerate under the microscope
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 35
demonstrated in Figure 1. The method can be de-
scribed briefly as follows. The researchers collected
human epithelial cells by scraping oral mucosal cells
with a wooden stick and twirled the applicator in
saline to dislodge the cells. The cells were subse-
quently washed free of unattached bacteria and ad-
justed with saline to 105 cells/mL. Following this, the
authors tested the ability of various bacteria to ad-
here to the epithelial cells. This was done by mixing
cell suspensions of the bacteria with cell suspensions
of the epithelial cells and incubating the mixture at
35°C for 30 min. The epithelial cells were washed to
remove non-adherent bacteria. The bacteria were
stained in order to observe and enumerate the cells
under the microscope. A more quantitative method
would involve conducting viable bacteria studies by
recovering cells as petri plate counts and assessing
the number of Salmonella that adhere to the human
epithelial cells. This study would offer the means for
assessing the capability of Salmonella to compete
with the normal flora of the human oral cavity. Also,
the results may indicate whether Salmonella has the
necessary mechanisms to attach to surfaces of the
mouth.
Tenor et al. (2004) performed electron microscopy
studies after mixing bacterial cultures and epithelial
cells to observe the adherence property of bacteria.
Similar studies could be performed with Salmonella
and human epithelial cells. The electron microscopy
analyses would be particularly useful in demonstrat-
ing visually, the ability of Salmonella to adhere to
these cells in the presence of other bacterial com-
petition.
CONCLUSIONS
The ability to adhere to a variety of surfaces avail-
able in the oral cavity of the mouth is of utmost
important to the flora that primarily resides in the
mouth. Salmonella has been observed in some cas-
es of parotid gland infection; however, this type of
infection is often secondary in nature and extremely
rare. Lysozyme and lactoferrin, key enzymes in the
saliva may act as antimicrobial agents against Sal-
monella; however, some strains may be resistant to
these enzymes. Additional studies are needed to
understand the implications of Salmonella in the
oral cavity and complications that may results down-
stream. The proposed experiments may be able to
identify whether Salmonella possesses gene(s) that
encodes for the necessary fimbrial lectins to attach
to surfaces of the oral cavity.
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Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 39
www.afabjournal.comCopyright © 2013
Agriculture, Food and Analytical Bacteriology
ABSTRACT
Cattle can be naturally colonized with foodborne pathogenic bacteria such as Shiga Toxin-producing E.
coli (STEC) in their gastrointestinal tract. While these foodborne pathogens are a threat to food safety, they
also cause human illnesses via cross contamination of other foods and the water supply, as well as via direct
animal contact. In order to further curtail these human illnesses and ensure a safe and wholesome food
supply, research into preharvest pathogen reduction controls and interventions has grown in recent years.
This review addresses the ecology of STEC in cattle and potential controls and interventions that have been
proposed or implemented to reduce STEC in cattle. We focus in this review on the use of management
practices and the effects of diet and water management. Implementation of preharvest strategies will not
eliminate the need for good sanitation procedures in the processing plant and during food preparation
and consumer handling. Instead, live-animal management interventions must be implemented as part of
a multiple-hurdle approach that complements the in-plant interventions, so that the reduction in pathogen
entry to the food supply can be maximized.
Keywords: E. coli O157:H7, EHEC, cattle, management
INTRODUCTION
One of the largest food safety (and economic) im-
pacts on the cattle industry has been the emergence
Correspondence: Todd Callaway, [email protected]: +1-979-260-9374 Fax: +1-979-260-9332.
of Shiga Toxin-producing Escherichia coli (STEC)
bacteria, which are part of the natural reservoir in ru-
minant animals such as cattle (Karmali et al., 2010).
STEC-caused illnesses cost the American economy
more than $1 billion each year in direct and indirect
costs from more than 175,000 human illnesses (Scal-
lan et al., 2011; Scharff, 2010). Furthermore, since
the emergence of the “poster child” of STEC, E. coli
REVIEWShiga Toxin-Producing Escherichia coli (STEC) Ecology in Cattle
and Management Based Options for Reducing Fecal Shedding
T. R. Callaway1, T. S. Edrington1, G. H. Loneragan2, M. A. Carr3, D. J. Nisbet1
1Food and Feed Safety Research Unit, USDA/ARS, 2881 F&B Rd., College Station, TX 778452Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX 79409
3Research and Technical Services, National Cattlemen’s Beef Association, Centennial, CO 80112
Proprietary or brand names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies neither approval of the product, nor exclusion of others that
may be suitable.
Agric. Food Anal. Bacteriol. 3: 39-69, 2013
40 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
O157:H7, more than $2 billion dollars have been
spent by the cattle industry to combat STEC in pro-
cessing plants (Kay, 2003).
While post-harvest pathogen-reduction strate-
gies have been largely successful at reducing direct
foodborne illness, these processing interventions
have not been perfect (Arthur et al., 2007; Barkocy-
Gallagher et al., 2003), in large part because avenues
of human exposure include indirect routes (LeJeune
and Kersting, 2010; Nastasijevic, 2011). In order to
further curtail human illnesses and ensure a safe and
wholesome food supply, research into preharvest
pathogen reduction controls and interventions has
grown in recent years (Callaway et al., 2004; LeJeune
and Wetzel, 2007; Oliver et al., 2008; Sargeant et al.,
2007).
The impact of using pathogen reduction strate-
gies focused on the environmental contamination
and exposure routes at the live animal stage are like-
ly to have large impacts on resulting human illnesses
(Rotariu et al., 2012; Smith et al., 2012). Reduction
of STEC can also yield public health improvements
in rural communities (LeJeune and Kersting, 2010)
and amongst attendees of agricultural fairs, ro-
deos and open farms (Keen et al., 2006; Lanier et
al., 2011). Thus, the logic underlying focusing on
reducing foodborne pathogenic bacteria in live
cattle is straightforward: 1) reducing the amount of
pathogens entering processing plants will reduce
the burden on the plants and render the in-plant
interventions more effective; 2) reducing horizontal
pathogen spread from infected animals (especially
in “supershedders”) in transport and lairage; 3) will
reduce the pathogenic bacterial burden in the envi-
ronment and wastewater streams; and 4) will reduce
the direct risk to those in direct contact with animals
via petting zoos, open farms, rodeos and to animal
workers. This review addresses the microbial ecol-
ogy of STEC colonization of cattle and controls and
interventions that have been proposed or imple-
mented to reduce STEC in live cattle in the areas
of: 1) Management practices and transport, and 2)
Cattle water and feed management.
EHEC, STEC, VTEC AND NON-O157:H7’S: A PRIMER
Although the relatively recent (1982) emergence
of E. coli O157:H7 into public view makes it seem
that this organism is a new arrival in the food chain,
data indicates that this organism is far more ancient,
having arisen between 400 and 70,000 years ago
(Law, 2000; Riley et al., 1983; Wick et al., 2005; Zhou
et al., 2010). Although a variety of acronyms have
been applied to the “hamburger bug”, they belong
to a single group that acquired toxin genes from Shi-
gella via a gene transfer event (Kaper et al., 2004;
Karmali et al., 2010; Wick et al., 2005). Research-
ers refer to these pathogens often interchangeably
as Enterohemorrhagic E. coli (EHEC), Shiga toxin-
producing E. coli (STEC), or Verotoxin-producing E.
coli (VTEC). While E. coli O157:H7 was the first of
the STEC’s to be recognized as a major food safety
threat, recently the other “non O157:H7 STEC” have
been increasingly implicated in human illness out-
breaks (Bettelheim, 2007; Fremaux et al., 2007). Be-
cause of this linkage, the “gang of six” non-O157 se-
rogroups (O26, O45, O103, O111, O121, and O145)
have joined O157:H7 as being classified as adulter-
ants in beef (USDA/FSIS, 2012). Since this declara-
tion, focus has shifted on understanding the general-
ized STEC ecology, rather than simply focusing on E.
coli O157:H7 (Gill and Gill, 2010).
For years, researchers (including the present au-
thors) assumed that in general, all of the non-O157
STEC would behave similarly to O157:H7 in a physi-
ological and ecological sense. However, recent
research has found that in addition to the genetic
divergence seen in O157:H7 lineages (Zhang et al.,
2007), there appear to be significant physiological
differences between and within non-O157 STEC
which may play a role in the ecological niche occu-
pied in the ruminant gastrointestinal tract by these
non-O157 serotypes (Bergholz and Whittam, 2007;
Free et al., 2012; Fremaux et al., 2007). While these
and other physiological differences need to be inves-
tigated further, and their roles in the gastrointestinal
microbial population must be determined, it appears
that the O157:H7 serotype is well adapted to survive
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 41
in cattle (García et al., 2010; O’Reilly et al., 2010) and
that other STEC serotypes can also live in the gastro-
intestinal tract of cattle (Arthur et al., 2002; Chase-
Topping et al., 2012; Joris et al., 2011; Monaghan et
al., 2011; Polifroni et al., 2012; Thomas et al., 2012),
and be transferred into ground beef (Bosilevac and
Koohmaraie, 2011; Fratamico et al., 2011).
While we understand much of how E. coli O157:H7
behaves in the gastrointestinal tract and farm envi-
ronment, we know very little about the ecology of
other STEC in those environments (Monaghan et al.,
2011; Polifroni et al., 2012). Thus this review focuses
on pre-harvest pathogen interventions based upon
E. coli O157:H7 data. We hypothesize that non-
O157:H7 STEC will largely behave in a broadly simi-
lar fashion to E. coli O157:H7 in the gastrointestinal
and farm environment; however this is an educated
assumption and that imposed limitation must be un-
derstood. Thus readers must be aware that most of
the research referred to in this review is based upon
E. coli O157:H7 specifically, and may or may not ap-
ply to all STEC.
ECOLOGY OF STEC AND GASTROIN-TESTINAL COLONIZATION
Because E. coli O157:H7 (and to some degree
non-O157 STEC) co-evolved along with its host it is
uniquely well-fitted to survive in the gastrointestinal
tract of cattle as a commensal type organism (Law,
2000; Wick et al., 2005). While E. coli O157:H7 can
live in the rumen of cattle (Rasmussen et al., 1999),
the site of primary colonization is the terminal rec-
tum (Naylor et al., 2003; Smith et al., 2009a). This
organism produces a potent cytotoxin (Shiga toxin)
that does not seriously impact its preferred host (cat-
tle) because they lack toxin receptors (Pruimboom-
Brees et al., 2000), but this same toxin causes serious
illness in humans colonized by E. coli O157:H7 (Kar-
mali et al., 2010; O’Brien et al., 1992). Unfortunately,
this means that the natural commensal-type relation-
ship between STEC (including O157 and non-O157)
and cattle ensures that this organism can be passed
on to meat products and consumers of beef (Fe-
rens and Hovde, 2011). This transmission most fre-
quently occurs during summer months, and is linked
to a summer increase in the prevalence of E. coli
O157:H7 in cattle (Edrington et al., 2006a; Lal et al.,
2012; Naumova et al., 2007; Ogden et al., 2004; Wells
et al., 2009), not just an increase in consumption or
a change of cooking habits by consumers (Money et
al., 2010; Williams et al., 2010a). It has been sug-
gested that neuroendocrine factors may play a role
in E. coli O157:H7 (Edrington et al., 2006a; Green et
al., 2004), as may signaling between host and intes-
tinal microbial populations or within STEC popula-
tions via quorum-sensing (Edrington et al., 2009b;
Sperandio, 2010; Sperandio et al., 2001). Further
possible interactions within the microbial ecosystem
of the rumen are demonstrated in the preferential
consumption of E. coli O157:H7 by ruminal protozoa
(Epidinium), and increased populations in the pres-
ence of Dasytricha (Stanford et al., 2010).
Because of the nature of STEC survival in the
ruminant gut, it is no surprise that it persists in fe-
cal deposits (Dargatz et al., 1997; Jiang et al., 2002;
Maule, 2000; Yang et al., 2010) and in soils (Bolton
et al., 2011; Semenov et al., 2009; Van Overbeek et
al., 2010). This allows E. coli O157:H7 to cycle within
pens and farms in a fecal-oral route (Russell and Jar-
vis, 2001), recirculating within groups or individual
animals (Arthur et al., 2010). The presence of super-
shedding cattle (Chase-Topping et al., 2008) in the
population can further enhance this horizontal trans-
mission within a herd or a pen of cattle (Arthur et
al., 2010; Arthur et al., 2009; Cobbold, 2007; LeJeune
and Kauffman, 2006). However, the host/dietary/mi-
crobial factors underlying the “supershedder” status
of cattle remains unknown, as do factors that allow
simple gut colonization by E. coli O157:H7. Thus it
is apparent that the farm/pen/facility environment
plays an important role in STEC colonization and re-
circulation, as well as via direct and indirect transmis-
sion to human farm workers/visitors and consumers
(Ihekweazu et al., 2012; LeJeune and Kersting, 2010;
Smith et al., 2012; Stacey et al., 2007; Strachan et al.,
2006).
42 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
MANAGEMENT PRACTICES AND TRANSPORTATION
Good management of cattle is critical for efficient
animal production, but to date no typical “manage-
ment” procedures have been shown to affect colo-
nization or shedding of foodborne pathogens (Ellis-
Iversen et al., 2008; Ellis-Iversen and Van Winden,
2008; LeJeune and Wetzel, 2007), some practices
may reduce horizontal transmission and recirculation
of STEC within a herd of cattle (Ellis-Iversen and Wat-
son, 2008). However, the use of management tools
like the squeeze chute (crush) to process cattle has
been shown to increase the odds of hide contami-
nation with E. coli O157(Mather et al., 2007). Yet, in
spite of this lack of evidence regarding impacts on
food safety, good management practices are criti-
cal to ensuring animal health and welfare (Morrow-
Tesch, 2001).
Bedding and pen surfaces
E. coli O157:H7 can live for a long period of time
in manure, soil and other organic materials (Jiang
et al., 2002; Maule, 2000; Winfield and Groisman,
2003) and can be transmitted successively through
their environment (Semenov et al., 2010; Semenov
et al., 2009). Cattle, especially dairy cows, are bed-
ded on materials that are largely chosen on animal
health and welfare grounds. Unfortunately, bedding
material can harbor bacteria that are responsible for
mastitis, as well as foodborne pathogenic bacteria
that can be spread between cattle (Davis et al., 2005;
Oliver et al., 2005; Richards et al., 2006; Wetzel and
LeJeune, 2006). Researchers have shown that urine
increases growth of E. coli O157:H7 on bedding, po-
tentially by providing substrate for growth (Davis et
al., 2005). Modeling research has shown that an in-
crease in bedding cleaning frequency would increase
the death rate of E. coli O157:H7 (Vosough Ahmadi
et al., 2007). Further studies have demonstrated that
the use of very dry bedding reduced E. coli O157:H7
prevalence on farms (Ellis-Iversen et al., 2008; Ellis-
Iversen and Van Winden, 2008). Researchers have
shown that sand bedding reduced transmission of E.
coli O157:H7 between dairy cows, resulting in lower
populations of E. coli O157:H7 in cattle bedded on
sand compared to sawdust (LeJeune and Kauffman,
2005; Westphal et al., 2011). It is suspected that this
difference was due to desiccation or reduced nutri-
ent availability.
Feedlot surfaces were thought to contain ma-
nure-like bacterial populations, but recent molecular
studies have indicated that the bacterial communi-
ties of feedlot surfaces are complex, yet utterly dis-
tinct from fecal bacterial populations (Durso et al.,
2011). This suggests that traits that favor survival
in the gastrointestinal tract (anaerobic, warm, dark)
do not favor survival on the feedlot surface (aerobic,
cooler, sunlit). Surfaces such as pond ash do not im-
pact survival of E. coli O157 (Berry et al., 2010), how-
ever studies and anecdotal evidence indicates that a
greater number of cattle shed E. coli O157:H7 when
housed in muddy pen conditions than cattle from
pens in normal condition and that the condition of
the pen floor may influence the prevalence of cat-
tle shedding the organism and the ability of E. coli
O157:H7 to survive dry conditions (Berry and Miller,
2005; Smith et al., 2001; Smith et al., 2009b). Studies
have recently demonstrated that sunlight can reduce
E. coli O157:H7 populations on pen surfaces (Berry
and Wells, 2012) and in water systems (Jenkins et
al., 2011). Overall, bedding or pen cleaning will not
eliminate E. coli O157:H7 from any farm or feedlot
environment, but it may slow spread within a herd or
between penmates.
Manure Management
E. coli O157:H7 and other STEC survive in manure
and can persist for a lengthy period of time (up to
21 months) (Bolton et al., 2011; Fremaux et al., 2007;
Hutchison et al., 2005; Kudva et al., 1998; Varel et
al., 2008). Although there are differences amongst
STEC strains in their ability to persist in manure,
these appear to be related to the oxidative capacity
of each strain (Franz et al., 2011). The presence of
a native bacterial population in manure reduces E.
coli O157:H7 survival in soils (Van Overbeek et al.,
2010). The amendation of manure in soil can result in
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 43
STEC uptake directly by plants, including food crops
(Franz and Van Bruggen, 2008; Jiang et al., 2002; Se-
menov et al., 2010; Semenov et al., 2009). Rainfall
events can also wash STEC from cattle feces (stored
or in fields) into drinking or irrigation water supplies
(Anonymous, 2000; Cook et al., 2011; Ferguson et al.,
2007; Oliveira et al., 2012; Pachepsky et al., 2011). As
the mean temperature of manure rises during stor-
age the survival of E. coli O157:H7 is reduced (Se-
menov et al., 2007), indicating that composting can
enhance manure safety, thus reducing human illness-
es (Graham and Nachman, 2010; Kelley et al., 1999).
There have been few studies that have isolated
STEC consistently from cattle waste lagoons (Purdy
et al., 2010). This is potentially due to the oxidized
nature of the lagoon, or the presence of a native mi-
crobial population. In waste water lagoons, there are
protozoa that preferentially consume E. coli O157:H7
(Ravva et al., 2010), possibly explaining at least some
of the difference between E. coli O157:H7 survival in
manure with that of limited survival in dairy lagoons
(Ravva et al., 2006). Research has demonstrated that
the addition of chemical oxidants to wastewater
lagoons can reduce pathogen populations (Luster-
Teasley et al., 2011).
Biosecurity
Farm biosecurity is critical for animal health and
welfare, especially in regard to animal diseases, but
to date there has been little direct impact demon-
strated on foodborne pathogenic bacteria such as
E. coli O157:H7 (Ellis-Iversen and Van Winden, 2008).
Research has shown that other animal species, ro-
dents, insects and birds and boars can carry STEC at
least transiently (Branham et al., 2005; Cernicchiaro
et al., 2012; French et al., 2010; Rice et al., 2003; Sán-
chez et al., 2010; Wetzel and LeJeune, 2006). Mix-
ing of sheep with cattle has been shown to increase
the risk of cattle shedding STEC (Stacey et al., 2007),
and a positive correlation between cattle and sheep
density was found, at least in the UK (Strachan et al.,
2001). Other diverse factors such as the presence
of dogs, pigs, or wild geese on the farm have been
linked to an increased risk of E. coli O157:H7 shed-
ding (Gunn et al., 2007; Synge et al., 2003). Ruminant
animals other than cattle do carry E. coli O157:H7
(French et al., 2010; Hussein et al., 2000; Sargeant
et al., 1999), and this includes sheep and deer that
often share the same pasture, feed bunks and wa-
ter supplies (Bolton et al., 2012; Branham et al.,
2005). Other researchers have found that flies and
other insects on farms can carry STEC from one loca-
tion to another (Ahmad et al., 2007; Hancock et al.,
1998; Keen et al., 2006; Talley et al., 2009). Further-
more, wild migratory birds such as starlings (Carlson
et al., 2011a; Carlson et al., 2011b; Cernicchiaro et
al., 2012; Wallace et al., 1997; Wetzel and LeJeune,
2006), cowbirds and egrets (Callaway, unpublished
data) can carry STEC (and other foodborne patho-
gen) between pens, and even between farms long
distances apart. While these effects are probably
minimal in their direct impact on food safety within a
farm, they represent vectors for pathogens to move
between “clean” groups of cattle or farms.
Cattle grouping
Many farms are closed to entry by animals from
other farms to prevent animal disease transmission.
Closed herds prevent spread of E. coli O157:H7 (and
other pathogens) from one farm to another (Ellis-
Iversen et al., 2008; Ellis-Iversen and Van Winden,
2008; Ellis-Iversen and Watson, 2008). However
some studies have shown that a closed farm does
not impact E. coli O157:H7 incidence on farms (Cob-
baut et al., 2009). The results of this study suggest
that E. coli O157:H7 should be considered common
to groups of feedlot cattle housed together in pens
(Smith et al., 2001), thus keeping groups together
throughout their time on a farm, or in a feedlot, with-
out introducing new members to groups appears to
reduce horizontal transmission between animals.
A further benefit of grouping cattle involves the
use of age as a segregating factor. Young cattle (es-
pecially heifers) shed more E. coli O157:H7 than do
older cattle (Cobbaut et al., 2009; Cray and Moon,
1995; Smith et al., 2001). While it is not possible
to segregate calves from cows in the beef indus-
try, there is potential benefit to keeping same-age
44 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
groups of calves together as they are transported
and enter backgrounding or feedlot operations to
prevent horizontal transmission between groups.
Off-site rearing of dairy heifers may be an important
solution to reducing foodborne pathogens, as has
been shown in regard to Salmonella (Hegde et al.,
2005), and the risk of transmission back to the farm
by heifers returning from an off-site facility was found
to be low (Edrington et al., 2008).
Animal density may also play a role in the horizon-
tal spread of E. coli O157:H7 and other foodborne
pathogens (Vidovic and Korber, 2006) as well as the
vertical spread to humans (Friesema et al., 2011b).
Densely packed animals have a great chance of con-
tamination with fecal spread. However increased an-
imal density reduces the physical footprint and may
allow for more efficient and effective waste handling.
It has been shown that higher animal density can be
linked to an increased risk of carriage of some STEC,
including O157:H7 (Frank et al., 2008; Vidovic and
Korber, 2006). Other European studies have also
found an effect of animal density on human STEC
illnesses (Friesema et al., 2011a; Haus-Cheymol et
al., 2006), yet Canadian researchers found a variable
impact (Pearl et al., 2009). Further studies found
that increased stocking density increased shedding
of STEC, independent of group size (Stacey et al.,
2007; Strachan et al., 2006).
The issue of “supershedders” complicates re-
search into effects of animal density and pathogen
shedding (Arthur et al., 2009; Cernicchiaro et al.,
2010; Chen et al., 2012; LeJeune and Kauffman, 2006;
Stanford et al., 2005). If supershedders do exist long
term, rather than simply being a transient phase of
infection, then there are interactive effects of animal
density and pathogen density in the animal that must
be accounted for (Matthews et al., 2006; Matthews et
al., 2009). The role of super-shedding animals (even
if a transient phenomenon) cannot be discounted
in the contamination of hides during transport and
lairage, especially in dense conditions (Arthur et al.,
2010; Arthur et al., 2009).
Transportation and lairage
Handling and transport to processing plants or
feedlots or other farms causes stress (see below) and
may spread E. coli O157:H7 due to physical contact
or fecal contamination, and trailers used may spread
pathogens between lots or loads of cattle (Mather
et al., 2007). Studies have indicated that transport
did not affect STEC populations in cattle, however
in these studies E. coli O157:H7 populations were
very low initially (Barham et al., 2002; Minihan et
al., 2003; Reicks et al., 2007; Schuehle Pfeiffer et al.,
2009). However, other studies have found that trans-
port caused an increase in fecal shedding of E. coli
O157:H7 (Bach et al., 2004). Researchers found that
transporting cattle more than 100 miles doubled the
risk of having positive hides at slaughter compared to
cattle shipped a short distance, though the question
of time in close-confinement versus being in transit
was not examined (Dewell et al., 2008). In another
study, longer transport times were correlated with
increased levels of fecal shedding of E. coli O157:H7
(Bach et al., 2004). It was also demonstrated that a
combination of transport and lairage did not lead to
an increase in the number or prevalence of E. coli
O157:H7 from cattle (Fegan et al., 2009).
The presence of a high shedding animal in a
trailer has been shown to increase the odds of other
animals within the load being hide-positive for E.
coli O157:H7 (Arthur et al., 2010; Arthur et al., 2009;
Fox et al., 2008). However, it should be noted that
both low- and high-shedding cattle can be respon-
sible for the spread within and between truckloads
(Dodd et al., 2010). Cattle trailers can be important
fomites of E. coli O157:H7 to uninfected cattle and
are frequently positive for E. coli O157:H7 when
sampled (Barham et al., 2002; Cuesta Alonso et al.,
2007; Reicks et al., 2007). It has been shown that the
incidence of E. coli O157:H7 in transport trailers in-
creases the risk of transmission to farms and feedlots
from cattle on these trailers (Cuesta Alonso et al.,
2007). To date however, the washing of trailers has
only been shown to be effective against Salmonella
contamination in swine (Rajkowski et al., 1998), yet it
is an intuitive, feasible solution to prevent some de-
gree of cross-contamination of cattle during a stress-
ful period.
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 45
Lairage and holding facilities are further locations
that can impact the prevalence and concentration of
E. coli O157:H7 on hides of cattle, which is an impor-
tant route of entry to the food supply (Arthur et al.,
2007). Studies have shown that the transfer of E. coli
O157:H7 to hides that occurs in lairage at processing
plants accounted for more of the hide and carcass
contamination than did the population of cattle leav-
ing the feedlot (Arthur et al., 2008). Furthermore, the
presence of supershedding cattle in these pens can
increase the spread of E. coli O157:H7 between ani-
mals from different farms or feedlots (Arthur et al.,
2010; Cernicchiaro et al., 2010). The exact role of
lairage and transport/trailers in the spread of E. coli
O157:H7 (and other pathogens) in cattle is unclear,
and is likely time- and animal density-dependent,
and may also be affected by stress.
Stress
While we understand stress intuitively, any dis-
cussion of “stress” in animals is fraught with anthro-
pomorphism and complexity (Rostagno, 2009; Ver-
brugghe et al., 2012). Long-term stress may depress
immune function in cattle (Carroll and Forsberg,
2007; Kelley, 1980; Salak-Johnson and McGlone,
2007), making them more susceptible to coloniza-
tion, but the short term effects of stress from wean-
ing, handling or transport on immune status are un-
known. Catecholamines rise when animals are under
stress, and catecholamines (along with other hor-
mones) have been demonstrated to have an effect
on the microbial population, including pathogens
(Freestone and Lyte, 2010; Lyte, 2010; Walker and
Drouillard, 2012). To date the effect of stress on col-
onization or shedding of E. coli O157:H7 is unclear.
Weaning is stressful to calves, and was shown to
increase colonization with STEC (Herriott et al., 1998)
and E. coli O157:H7 (Chase-Topping et al., 2007). In
other studies however, these researchers demon-
strated that weaning does not affect the likelihood of
shedding (Synge et al., 2003). Interestingly, calving
was seen to reduce the likelihood of E. coli O157:H7
shedding (Synge et al., 2003). Further studies found
that weaning stresses alone did not impact shedding
of E. coli O157:H7 in dairy calves (Edrington et al.,
2011). Other stresses such as movement have been
identified as playing a role in E. coli O157:H7 shed-
ding in Scottish cattle (Chase-Topping et al., 2007),
but this has not been clearly defined in U.S. cattle
systems.
When calves were preconditioned to transport
stress, they were found to be less susceptible to in-
fection from the environment than were calves not
preconditioned to this stressor (Bach et al., 2004).
Cattle with excitable temperaments were less like-
ly to shed E. coli O157:H7 than were “calm” cattle
(Brown-Brandl et al., 2009; Schuehle Pfeiffer et al.,
2009). In studies with pigs, it was found that the so-
cial stress/excitement of mixing penmates increased
fecal shedding of Salmonella (Callaway et al., 2006),
but this has not been shown to date in cattle, how-
ever this implies a potential role of social stresses in
cattle during lairage.
Heat stress (and methods to alleviate it) can have
effects on animal health and productivity (Brown-
Brandl et al., 2003), as well as shedding of E. coli
O157:H7 and Salmonella (Callaway et al., 2006).
Water sprinkling to alleviate heat stress in cattle
increased measures of animal well-being and de-
creased E. coli O157:H7 populations on the hides of
cattle, but did not affect fecal populations (Morrow
et al., 2005). In another study with dairy cattle, re-
searchers found that heat stress had no impact on
STEC shedding, but Salmonella shedding was in-
creased (Edrington et al., 2004). Other researchers
have also found that heat stress did not impact E.
coli O157:H7 shedding in cattle (Brown-Brandl et al.,
2009).
CATTLE WATER AND FEED MANAGE-MENT
Diet and water supplies can be used to reduce
horizontal transmission of STEC between animals on
the same farm or in the same feedlot pen. The un-
derlying biology behind these effects has not been
elucidated to this point, but it has been suggested
that difference could be due to increased fecal pH or
46 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
intermediate endproducts of the yeast fermentation
(e.g., vitamins, organic acids, L-lactic acid), however
these suggestions remain hypothetical (Wells et al.,
2009). While the magnitude of the dietary impacts
effects is relatively small, it underlines the point that
dietary composition can potentially significantly im-
pact E. coli O157:H7 populations in the gut of cattle.
Drinking Water treatments
Cattle water troughs can harbor E. coli O157:H7
for long periods of time (Hancock et al., 1998;
LeJeune et al., 2001a; LeJeune et al., 2001b; Mu-
rinda et al., 2004; Polifroni et al., 2012; Wetzel and
LeJeune, 2006), and as many as 25% of cattle farm
water samples have been shown to contain E. coli
O157:H7 (Sanderson et al., 2006). These results sug-
gest that these common-use troughs can be vectors
for horizontal transmission of E. coli O157:H7 within
a group of animals. The organic material in the wa-
ter troughs tends to harbor and protect the STEC,
and modeling research has shown that an increase
in water trough cleaning frequency would increase
the death rate of E. coli O157:H7 (Vosough Ahmadi
et al., 2007) as well as exposure to sunlight (Jenkins
et al., 2011). Chlorination of water supplies has long
been used to reduce bacterial populations in mu-
nicipal water supplies, and this also can be used in
cattle water troughs to reduce E. coli O157:H7 pop-
ulations. However, sunlight and organic material in
the water reduces the effectiveness of chlorination
over time, as has been seen in real world chlorina-
tion studies with cattle water troughs (LeJeune et al.,
2004). Electrolyzed oxidizing (EO) water has been
shown to reduce STEC populations as high as 104
CFU/mL (Stevenson et al., 2004), and can be used as
an in-plant hide cleaning strategy (Bosilevac et al.,
2005). Other treatments such as cinnamaldehyde
and sodium caprylate addition to water supplies
have been shown to reduce STEC populations, but
the effects on palatability are not currently known
(Amalaradjou et al., 2006; Charles et al., 2008).
Fasting
Cattle can be fasted for up to 48 h before and dur-
ing their transport to slaughter, which can affect the
prevalence of E. coli O157:H7 (Pointon et al., 2012).
Ruminal and intestinal VFA concentrations limit the
proliferation of E. coli because of toxicity of the VFA
to the bacteria (Hollowell and Wolin, 1965; Russell
and Diez-Gonzalez, 1998; Wolin, 1969). This has cre-
ated the demand for the use of organic acids/VFA
as methods to alter the ruminal fermentation and to
reduce pathogen populations in the gut (Ohya et al.,
2000; Prohaszka and Baron, 1983; Van Immerseel et
al., 2006). However, fasting causes levels of VFA to
decline rapidly (Harmon et al., 1999).
Fasting increased E. coli, Enterobacter and total
anaerobic bacterial populations throughout the in-
testinal tract of cattle (Buchko et al., 2000b; Greg-
ory et al., 2000), and increased Salmonella and E.
coli populations in the rumen (Brownlie and Grau,
1967; Grau et al., 1969). More recent research has
demonstrated that fasting can cause “apparently
E. coli (O157:H7) negative animals to become posi-
tive” (Kudva et al., 1995). Fasting made calves more
susceptible to colonization by inoculated E. coli
O157:H7 (Cray et al., 1998). Cattle fasted for 48 h
prior to slaughter contained significantly greater
E. coli populations throughout the gut than cattle
fed forage (Gregory et al., 2000). In contrast, it was
demonstrated that a fasting period had no effect
on E. coli O157:H7 shedding (Harmon et al., 1999).
When culled dairy cows were reconditioned through
feeding high energy diets for 28 d before harvest,
the prevalence of E. coli O157:H7 declined from
14% to 6% (Maier et al., 2011). In general, studies
examining the intestinal environment have repeat-
edly indicated that low pH and high concentrations
of short chain VFA result in lower STEC populations
(Bach et al., 2002a; Bach et al., 2005b; Cobbold and
Desmarchelier, 2004; Pointon et al., 2012; Shin et al.,
2002). Thus the bulk of research supports the con-
cept that fasting increases shedding or population
concentrations, or makes cattle more susceptible to
colonization due to decreased short chain VFA and
increased pH in the gastrointestinal tract. Because
feed withdrawal and/or starvation results in de-
creased VFA concentrations in the gut, it has been
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 47
suggested that this shift plays a role in the effects of
transport and/or lairage on the shedding of STEC.
Feed types
The first dietary practice shown in early studies
to significantly increase the risk of STEC shedding
among heifers was feeding corn silage (Herriott et
al., 1998). In adult cows, the inclusion of animal by-
products in the diet (currently discontinued) was
shown to increase STEC shedding (Herriott et al.,
1998). Other studies linked feeding whole cotton-
seed with reduced E. coli O157 shedding (Garber et
al., 1995; Hancock et al., 1994). Fecal samples from
cattle fed dry rolled corn, high-moisture corn and
wet corn gluten feed did not contain different popu-
lations of generic E. coli, or extreme acid-resistant E.
coli during a limit-feeding period (Scott et al., 2000).
However, feces from cattle fed wet corn gluten ad
libitum contained significantly higher concentrations
of extreme acid resistant E. coli (resistant to an acid
shock simulating passage through the human stom-
ach) than did feces of cattle fed dry-rolled or high
moisture corn (Scott et al., 2000).
Barley is often fed to cattle and is ruminally fer-
mented more rapidly than corn by the commensal
microbial population. More starch is fermented in
the lower gut of corn-fed cattle than in barley-fed
cattle, resulting in barley-fed cattle having higher fe-
cal pH and lower VFA concentrations compared with
corn-fed animals (Bach et al., 2005a; Berg et al., 2004;
Buchko et al., 2000a). Barley feeding was linked (al-
beit at a low correlation) to increased E. coli O157:H7
shedding (Dargatz et al., 1997); and in experimen-
tal infection studies barley feeding was again asso-
ciated with increased shedding of E. coli O157:H7
by feedlot cattle (Buchko et al., 2000a). Survival of
E. coli O157:H7 in manure from corn-and barley fed
cattle is approximately equal, therefore simple sur-
vival in the feces is not responsible for the increased
prevalence of E. coli O157:H7 in barley-fed cattle
(Bach et al., 2005b).
Distiller’s grains
The industrial fermentation of corn to produce
ethanol has increased more than 4-fold between
2001 and 2007, and its use doubled by 2010 (Rich-
man, 2007). Thus, an economic incentive to increase
the utilization of distillers grains (DG) by-product
feeds in the cattle industry has increased dramati-
cally in recent years, especially given DG’s role as
cost-effective feed supplements for finishing and
lactating cattle (Firkins et al., 1985). The inclusion
DG into cattle rations has been shown to be an ef-
fective replacement for common feedstuffs and has
demonstrated an increased daily gain in beef cattle
(Al-Suwaiegh et al., 2002) and milk yield and feed ef-
ficiency in dairy cows (Kleinschmit et al., 2006). This
improvement is likely due to the fact that DG alters
the population structure and function of the micro-
bial ecosystem of the rumen and throughout the
gastrointestinal tract (Callaway et al., 2010a; Durso
et al., 2012; Williams et al., 2010b). Cattle fed 40%
corn wet distiller’s grains (WDG) were very different
than the fecal populations in cattle fed a non DG-
containing diet, and populations of generic E. coli
were higher in their feces (Durso et al., 2012), and in
previous studies the survival of E. coli O157:H7 in fe-
ces was increased by increasing levels of DG supple-
mentation (Varel et al., 2008).
Unfortunately, research has suggested a potential
association between DG feeding and an increased
prevalence and fecal shedding of the foodborne
pathogen E. coli O157:H7 in cattle (Jacob et al.,
2008a; Jacob et al., 2008b; Yang et al., 2010). Distill-
ers grains were shown to increase the shedding of
E. coli O157:H7 in cow-calf operations in Scotland
(Synge et al., 2003). Other researchers found that
feeding a related product (brewers grain) to cattle
was also associated with increased E. coli O157
shedding, and increased the odds of shedding by
more than 6-fold (Dewell et al., 2005). The individual
animal prevalence of feedlot cattle shedding E. coli
O157 on d 122 (but not d 136) was higher in cattle
fed 25% wet distiller’s grain compared to control di-
ets lacking WDG (Jacob et al., 2008b), but the pen-
level shedding was unaffected by WDG feeding.
Pen floor fecal sample prevalence of E. coli O157 was
significantly higher across a 12 week finishing period
48 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
in cattle fed 25% DDG and either 15% or 5% corn
silage compared with cattle fed 0% DDG and 15%
corn silage (Jacob et al., 2008a). However, follow-up
studies found no differences in E. coli O157:H7 fe-
cal shedding in cattle fed DG (Edrington et al., 2010;
Jacob et al., 2009), with no indications of why this
difference in results was observed. In a further study
utilizing both dry and wet-distillers grains, research-
ers found that higher levels (40% of the ration) of DG
inclusion did increase fecal E. coli O157:H7 shedding
(Jacob et al., 2010). When cattle were fed 40% wet
DG, they had higher populations of E. coli O157:H7
as well as higher pH values and lower concentra-
tions of L-lactate (Wells et al., 2009). Further studies
found that the DG-associated increase in fecal E. coli
O157:H7 populations could be mitigated by reduc-
ing WDG concentrations to 15% or less for 56 d prior
to slaughter (Wells et al., 2011). When corn or wheat
DDG were supplemented into cattle on a primarily
barley-based diet, there was no difference in impact
of DDG supplementation, likely because barley in-
clusion had already increased the E. coli O157:H7
populations through some complementary mecha-
nism (Hallewell et al., 2012). Interestingly, research-
ers found that the numbers of E. coli O157:H7 were
greater in fecal in vitro incubations that contained
corn DG than with wheat DG (Yang et al., 2010).
Grain form
Other scientists have examined the form of corn
included in cattle rations can impact E. coli O157:H7.
In feedlot cattle, steam-flaked grains increased E.
coli O157 shedding in feces compared to diets com-
posed of dry-rolled grains (Fox et al., 2007). This
difference was theorized to be due to dry rolling al-
lowing the passage of more starch to the hindgut
where it was fermented to produce VFA thereby kill-
ing E. coli O157 (Fox et al., 2007). This theory is sup-
ported by the fact that post-ruminal starch infusion
increased generic E. coli populations in the lower
gut numerically (Van Kessel et al., 2002). However, to
date studies have shown no effect on E. coli O157:H7
populations of increasing starch concentrations in
the diet (Nagaraja, T. G., personal communication)
or by increasing fecal starch concentrations (Depen-
busch et al., 2008).
Forage feeding
Escherichia coli can and does thrive in the lower
gut of animals fed forage diets (Hussein et al., 2003a;
Hussein et al., 2003b; Jacobson et al., 2002). Com-
paring grain-fed to forage-fed cattle indicates that
more E. coli (including O157:H7) are present in the
feces of cattle fed grain diets. The effects of high
grain or high forage diets on the duration or shed-
ding of fecal E. coli O157:H7 populations in experi-
mentally inoculated calves have been examined. In
these studies the calves that consistently shed the
highest concentrations of E. coli O157:H7 were fed
a high concentrate (grain) diet (Tkalcic et al., 2000).
Ruminal fluid collected from steers fed a high-forage
diet allowed E. coli O157:H7 to proliferate to higher
populations in vitro than did ruminal fluid from high-
grain fed steers (Tkalcic et al., 2000). This was pos-
sibly due to differences in VFA concentrations be-
tween the ruminal fluids.
Other researchers found that feeding forage ac-
tually increased the shedding of E. coli O157:H7 in
cattle (Van Baale et al., 2004). When cattle were fed
forage E. coli O157:H7 was shed for 60 d compared
to 16 d for cattle on a grain-based diet (Van Baale et
al., 2004). Studies examining the effects of forage
on survival of E. coli O157:H7 in manure found that
low quality forages caused a faster rate of death of
E. coli O157 populations (Franz et al., 2005), indicat-
ing a possible role of forage chemical or secondary
plant components (such as tannins, see below) in fe-
cal shedding (Min et al., 2007). Feces from cattle fed
grain had higher VFA concentrations and lower pH
which allowed E. coli O157:H7 populations to survive
longer than feces from grass-fed cattle (Lowe et al.,
2010). Other studies have found that feeding forage
rich secondary compounds such as sainfoin, might
be a method to manipulate fecal populations of E.
coli O157:H7 to a limited extent (Aboaba et al., 2006;
Berard et al., 2009).
Although E. coli O157:H7 populations are gen-
erally lower in cattle fed forage diets, it must be
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 49
emphasized that STEC are still isolated from cattle
solely fed forage, so forage feeding should not be
viewed as a magic bullet (Hussein et al., 2003b; Thran
et al., 2001). Many outlets have claimed that grass-
fed cattle contain fewer pathogens than do cattle
fed grain; however this has not been demonstrated
scientifically. Researchers have found no difference
in food safety parameters of beef from grass-fed cat-
tle versus grain fed cattle (Zhang et al., 2010). Fur-
thermore, research into organic versus conventional
rearing systems have demonstrated no difference in
the incidence of E. coli O157:H7 shedding (Jacob et
al., 2008c; Reinstein et al., 2009).
Dietary shifts
A sudden shift from grain to hay appears to cause
a severe, widespread disruption in the gut microbial
flora population, much like an earthquake in a mac-
robiological environment (Fernando et al., 2010).
Thus the effects of rapid dietary shifts on the micro-
bial population in regards to E. coli O157:H7 popula-
tions have been examined. Early studies investigat-
ing (generic) E. coli and dietary effects indicated that
a sudden decrease in hay intake by cattle increased
fecal E. coli populations (Brownlie and Grau, 1967).
Other studies using experimentally infected sheep
found a sudden switch from an alfalfa pellet diet or
a corn/alfalfa ration to a poor-quality forage diet
increased E. coli O157:H7 shedding (Kudva et al.,
1995; 1997).
Cattle fed feedlot-type ration contained (generic)
E. coli populations that were 1000-fold higher than
cattle fed a 100% good-quality hay diet (Diez-Gon-
zalez et al., 1998). When these cattle were abruptly
switched from a 90% grain finishing ration to a 100%
hay diet, fecal E. coli populations declined 1000-fold
within 5 d (Diez-Gonzalez et al., 1998). However,
it is important to note that in this study no E. coli
O157:H7 were detected. Based on these results
the authors suggested that feedlot cattle could be
switched from high grain diets to hay for 5 days prior
to slaughter to reduce E. coli contamination entering
the abattoir (Diez-Gonzalez et al., 1998). Research
indicated that a brief (5 d) period of hay-feeding did
not impact carcass characteristics; however, when
cattle were fed hay during the final portion of the fin-
ishing period, they had lower dry matter intake and
lost 2.2 lb/head/d (Stanton and Schutz, 2000). Hay
feeding did not significantly impact carcass weight,
dressing percentage, carcass grades, or quality pa-
rameters, but significantly reduced total coliform
counts and (generic) E. coli counts (Stanton and
Schutz, 2000), but the impact was not as large as that
reported by Diez-Gonzalez et al. (1998). Cattle fed
hay for a 48 h period immediately prior to transport
to slaughter did not lose more weight during trans-
port than fasted or pasture fed animals (Gregory et
al., 2000). Cattle with a natural E. coli O157:H7 in-
fection (53%) were divided into two groups and one
was fed grain and the other abruptly switched to
hay, 52% of the grain-fed controls remained E. coli
O157:H7 positive, but only 18% of the hay-fed cattle
continued to shed E. coli O157:H7; but this switch re-
sulted in a BW decrease of 1.25 lb/hd/d compared to
controls (Keen et al., 1999). Other researchers found
that cattle fed a high-concentrate diet and switched
to a diet containing 50/50% corn silage/alfalfa hay
diet had lower E. coli counts (0.3 log10) after just 4
days (Jordan and McEwen, 1998). Cattle that were
fed an 80% barley ration, fasted for 48 h and then
subsequently switched to 100% alfalfa silage did
not exhibit any change in E. coli O157:H7 shedding
(Buchko et al., 2000b). However, when these same
animals were again fasted for 48 h and re-fed alfalfa
silage, the prevalence of E. coli O157:H7 shedding
increased significantly (Buchko et al., 2000b). Re-
searchers found that experimentally-infected cattle
fed hay shed E. coli O157:H7 significantly longer
than did grain-fed cattle (42 d vs. 4 d), but E. coli
O157:H7 populations shed were similar between
diets (Hovde et al., 1999). Cattle abruptly switched
from a finishing diet that contained wet corn gluten
feed to alfalfa hay for 5 d showed an increase in co-
lonic pH and total E. coli populations decreased ap-
proximately 10-fold (Scott et al., 2000).
Conversely, it was found that when cattle were
switched from forage-type diets to a high grain fin-
ishing ration, fecal and ruminal generic E. coli con-
centrations increased (Berry et al., 2006). In another
50 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
study slightly outside of the “normal” dietary switch
structure, switching cattle from pasture to hay for 48
h prior to slaughter significantly reduced the E. coli
population throughout the gut (Gregory et al., 2000).
Gregory et al., found that hay feeding increased in-
testinal Enterococci populations that are capable of
inhibiting E. coli populations in a fashion similar to
that of a competitive exclusion culture. However,
the effects of high grain versus forage diets were not
examined in this New Zealand-based study (Greg-
ory et al., 2000). Based on their data, the authors
concluded, “the most effective way of manipulating
gastro-intestinal counts of E. coli was to feed hay”
(Gregory et al., 2000).
Collectively, these results emphasize that while
dietary manipulations such as shifting cattle from
a high grain to forage ration could be a power-
ful method to reduce E. coli/STEC populations in
cattle prior to harvest, the mechanism remains un-
known and the effect is very inconsistent. It appears
that a factor in this inconsistency involves forage
quality and type, but this remains a hypothesis. It
does appear that the presence of endproducts of
fermentation (e.g., VFA) and some secondary plant
compounds in forages play some role in pathogen
population levels. While a dietary switch to forage
in feedlots is not advocated due to feasibility, weight
loss and other logistical issues, other high fiber feed-
stuffs (e.g., soy hulls, cottonseed meal) or feedstuffs
rich in phenolics or essential oils (see below), may be
a more feasible alternative strategy to decrease in E.
coli O157:H7 populations.
Tannins, phenolics, and essential oils
Plants contain phenolic and polyphenolic com-
pounds, such lignin and tannins, that can affect the
microbial ecosystem of the gastrointestinal tract
through antimicrobial action (Berard et al., 2009;
Cowan, 1999; Hristov et al., 2001; Jacob et al., 2009;
Patra and Saxena, 2009). It is theorized that some of
these compounds may penetrate biofilms and have
an anti-quoroum-sensing effect, which may play a
role in STEC colonization (Edrington et al., 2009b;
Kociolek, 2009; Sperandio, 2010). Tannins have been
demonstrated to significantly inhibit the growth of E.
coli O157:H7 in vitro and generic E. coli populations
in cattle (Berard et al., 2009; Cueva et al., 2010; Min
et al., 2007; Wang et al., 2009). Other researchers
have found that the phenolic acids that comprise lig-
nin also demonstrated antimicrobial activity against
E. coli O157:H7 in fecal slurries, and highly lignified
forages showed a reduced period of E. coli O157:H7
shedding compared with cattle fed only corn silage
(Wells et al., 2005). Phenolic compounds in cranber-
ry extract and sorrel are also effective against E. coli
O157:H7 growth in vitro (Caillet et al., 2012; Fullerton
et al., 2011), also the anthocyanins/proanthocyani-
dins from lowbush blueberries demonstrated in vitro
potential to inhibit E. coli O157:H7 growth (Lacombe
et al., 2012).
Essential oils are most often associated with aro-
matic compounds in various plants used as spices
or extracts (Barbosa et al., 2009). Many of these es-
sential oils exhibit antimicrobial acitivity (Dusan et
al., 2006; Fisher and Phillips, 2006; Kim et al., 1995;
Pattnaik et al., 1996; Reichling et al., 2009; Turgis et
al., 2009), often through the mode of action of dis-
solving bacterial membranes (Di Pasqua et al., 2007;
Turgis et al., 2009). As a result, many plant prod-
ucts have been used for centuries for the preserva-
tion and extension of the shelf life of foods (Dab-
bah et al., 1970). Essential oils have been proposed
as potential modifiers of the ruminal fermentation
(Benchaar et al., 2008; Benchaar et al., 2007; Boadi
et al., 2004; Patra and Saxena, 2009) and to reduce
E. coli O157:H7 in the live animal via in vitro studies
(Benchaar et al., 2008; Jacob et al., 2009). Some es-
sential oils have been shown to penetrate biofilms
and kill E. coli O157:H7 (Pérez-Conesa et al., 2011),
which could potentially play a role in reducing colo-
nization in the rumen and/or terminal rectum.
Seaweed (Tasco)
Brown seaweed (Tasco-14) is a feed additive that
has been included in cattle diets to improve carcass
quality characteristics and shelf life, increase anti-
oxidants and to improve ruminal fermentation ef-
ficiency (Anderson et al., 2006; Braden et al., 2007;
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 51
Leupp et al., 2005). In vitro studies have indicated
that Tasco-14 can reduce populations of E. coli and
Salmonella (Callaway, unpublished data), and more
recent results have linked this antipathogen activity
to presence of phlorotannins in the brown seaweed
(Wang et al., 2009). The phlorotannin anti- E. coli
activity was greater than that found in other studies
with terrestrial tannin sources (Min et al., 2007; Wang
et al., 2009). Studies in vivo found that Tasco-14
feeding reduced fecal and hide prevalence of E. coli
O157 in cattle (Braden et al., 2004). Because Tas-
co-14 is currently available in the market place, this
is a product that can be included in cattle rations;
however the extent of anti-pathogen activity in vivo
is still not clear, therefore the cost of addition must
be weighed carefully by the producer.
Citrus products
Orange peel and citrus pulp have excellent nutri-
tional characteristics for cattle and have been includ-
ed as low-cost ration ingredients in dairy and beef
cattle rations for many years (Arthington et al., 2002).
Citrus fruits contain a variety of compounds, includ-
ing essential oils and phytophenols that exhibit an-
timicrobial activity against foodborne pathogens
(Friedly et al., 2009; Mkaddem et al., 2009; Nannapa-
neni et al., 2008; Viuda-Martos et al., 2008). Other
studies have found that limonids from grapefruit
may play a role in inhibiting secretion and intercel-
lular communication by E. coli O157:H7 (Vikram et
al., 2010).
Research has demonstrated that the addition of >
1% orange peel and pulp reduced populations of E.
coli O157:H7 and Salmonella Typhimurium in mixed
ruminal fluid fermentations in the laboratory (Calla-
way et al., 2008; Nannapaneni et al., 2008). Further
studies have demonstrated that feeding orange peel
and pulp reduced intestinal populations of diarrhea-
genic E. coli in weaned swine (Collier et al., 2010).
In ruminants, researchers demonstrated that feeding
of orange peel and citrus pellets (a 50/50 mixture)
at levels up to 10% DM reduced artificially inoculat-
ed populations of E. coli O157:H7 and Salmonella
Typhimurium in sheep (Callaway et al., 2011a; b).
When studies were performed using only dried pel-
leted orange peel, the reduction in pathogen popu-
lations disappeared (Farrow et al., 2012), likely due
to the inactivation of essential oils (limonene and
terpeneless fraction) during the pelleting process.
Continuing studies have demonstrated that orange
oils offer a potential method for reducing both STEC
and Salmonella on beef carcasses as well (Pendleton
et al., 2012; Pittman et al., 2011). To date, orange
peel feeding has not been examined in large-scale
feeding studies, but retains promise as a potential
on farm strategy to reduce the burden of pathogens
on the farm, reducing environmental contamination
and re-infection.
Organic acids
Organic acids have been used in animal nutrition
to modify the ruminal fermentation by providing
some members of the microbial ecosystem a com-
petitive advantage, and by inhibiting other species
(Grilli et al., 2010; Martin and Streeter, 1995; Nisbet
and Martin, 1993; Piva et al., 2007). Some organic
acids (such as lactate, acetate, propionate, malate)
have been shown to have antimicrobial activity
against E. coli O157:H7 (Harris et al., 2006; Sagong
et al., 2011; Vandeplas et al., 2010; Wolin, 1969).
These acids have been used on hide and carcass
washes to reduce pathogen populations, but only
recently has interest in using organic acids to reduce
pathogens in live animals received interest (Callaway
et al., 2010b; Nisbet et al., 2009). Preliminary results
do show some success in inhibiting pathogens in the
lower intestinal tract of animals (unpublished data),
however, further research needs to be performed to
be able to release the appropriate organic acid and
concentration in the appropriate intestinal location
to reduce populations of E. coli O157:H7 in cattle.
Ractopamine
ß-agonists, such as ractopamine, are used in
cattle to improve animal performance and carcass
leanness. In vitro, ractopamine showed no effect on
growth parameters of E. coli O157:H7 (Edrington et
52 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
al., 2006c); but when used in sheep, the fecal shed-
ding and cecal populations of E. coli O157:H7 were
increased (Edrington et al., 2006c). When feedlot
cattle were fed ractopamine, the numbers of cattle
shedding E. coli O157:H7 were decreased (Edring-
ton et al., 2006b). In a follow-up study, researchers
demonstrated a negligible effect of ß-agonist (rac-
topamine and zilpaterol) treatment on fecal shed-
ding of E. coli O157:H7 in cattle (Edrington et al.,
2009a; Paddock et al., 2011). Taken as a whole, these
results indicate that the effects of ß-agonist feeding
are minimal or non-existent. Interestingly however,
in an in vitro swine model norepinephrine was shown
to increase E. coli O157:H7 adherence (Green et al.,
2004), though further research is obviously needed
to determine if this applies to cattle colonization.
Ionophores
Ionophores, such as monensin and lasalocid, are
antimicrobial compounds included in most feedlot
and dairy rations to inhibit gram-positive bacteria,
thereby improving feed:gain ratios and production
efficiency (Callaway et al., 2003). Because these feed
additives affect the gram-positive portion of the mi-
crobial population, possibly giving gram-negative
bacteria (such as E. coli) a competitive advantage,
they have been investigated as to their role in the
spread of E. coli O157:H7 in cattle. Because E. coli
O157:H7 has a true gram-negative membrane physi-
ology ionophores did not affect the growth of this
pathogen in vitro when added at concentrations up
to 3 fold higher than those normally found in the ru-
men (Bach et al., 2002b; Van Baale et al., 2004).
Early studies demonstrated a marginal increase of
STEC shedding by heifers fed ionophores (Herriott et
al., 1998), but other studies found no effect (Dargatz
et al., 1997). Further studies examining the effect of
ionophoric feed additives (monensin, lasalocid, laid-
lomycin and bambermycin) on E. coli O157:H7 dem-
onstrated no effect of these additives in vitro (Edring-
ton et al., 2003b), or on fecal shedding or intestinal
populations in experimentally-inoculated lambs in a
short-term (12 d) trial (Edrington et al., 2003a). In an
in vivo study using cattle, it was found that cattle fed
a forage ration that included monensin shed E. coli
O157:H7 for a shorter period of time than forage-fed
cattle not supplemented with monensin, but monen-
sin had no effect on shedding when cattle were fed
a corn-based ration (Van Baale et al., 2004). In an in
vitro study, it was found that monensin and the co-
approved antibiotic tylosin (tylan) treatment reduced
E. coli O157:H7 populations up to 2 log10 CFU/mL
in ruminal fermentations from cows fed forage, but
this did not extend to E. coli O157:H7 populations
in ruminal fluid from cows fed corn (McAllister et al.,
2006). These researchers later found that the inclu-
sion of monensin and tylosin did not alter fecal shed-
ding of experimentally-inoculated E. coli O157:H7
when included in barley (grain)-based diet fed to
cattle (McAllister et al., 2006). These results suggest
there may a potential interaction between diet and
ionophore inclusion in the effects on E. coli O157:H7
populations. Further studies found that monensin
decreased E. coli O157:H7 prevalence when fed at
44 mg/kg of feed, compared to the typical 33 mg/kg
dosing (Paddock et al., 2011).
CONCLUSIONS
While STEC of many serotypes can be viewed as
a commensal organism in the gastrointestinal tract
cattle, they represent a significant threat to human
consumers and public health. Pre-harvest controls in
cattle hold great potential to reduce STEC dissemi-
nation on farms, in the environment, and entering
the food chain. However, none of the on farm man-
agement-based controls discussed herein will com-
pletely eliminate STEC from cattle and will certainly
not eliminate the need for proper procedures in the
processing plant. Instead the live-animal manage-
ment controls must be installed in a complementary
fashion to reduce pathogens in a multiple-hurdle
approach (Nastasijevic, 2011) that complements the
in-plant interventions as well, so that the reduction
in pathogen entry to the food supply can be maxi-
mized.
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 53
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70 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
www.afabjournal.comCopyright © 2013
Agriculture, Food and Analytical Bacteriology
ABSTRACT
A survey was presented to Georgia independent poultry farmers to evaluate current processing options
as well as desired future changes. A total of 82 Georgia farmers participated in the survey, 31 of whom
were raising broilers at the time of the survey. Most of the farmers surveyed who were growing broilers at
the time (81%) processed on-farm, but these were also the farmers who processed less than 1000 birds per
year. The larger independent Georgia farmers processed off-farm in South Carolina and Kentucky, where
there were processors that served small-scale farmers and provided USDA inspection. These out of state
processing trips took place between 4 and 30 times per year for an average of 391 miles round trip. For
farmers’ future needs, similar numbers of farmers wanted only on-farm or only off-farm drop off processing
(22% and 25% respectively), but 40% of the farmers surveyed were open to more than one processing op-
tion. The farmers were also asked to evaluate the importance of several attributes of processing facilities,
and they chose quality of service to be the most important processing facility attribute, followed by cost of
processing, distance from the farm, and USDA inspection.
Keywords: Poultry processing, independent growers, pastured poultry, mobile processing units,
on-farm processing
INTRODUCTION
The U.S. broiler industry produced more than 8.6
billion broilers in 2009, estimated at a retail equiva-
lent of $45 billion (ERS, 2011). Georgia is the number
one broiler production state producing 1.3 billion
Correspondence: Steven C. Ricke, [email protected]: +1-479-575-4678 Fax: +1-479-575-6936
broilers in 2009, accounting for 15% of the total U.S.
broiler production (ERS, 2011). Federal laws exempt
farms processing fewer than 20,000 birds per calen-
dar year from USDA bird-by-bird inspection (USDA,
2006). However, some states have laws that are strict-
er and prohibit this exemption, which is the case in
Georgia. The small-scale poultry industry in Georgia
is limited in growth due to challenges it faces im-
posed by the strict state rules. Without the exemp-
Independent Poultry Processing in Georgia: Survey of Producers’ Perspective
E. J. Van Loo1,2, W. Q. Alali3, S. Welander4, C. A. O’Bryan1, P. G. Crandall1, S. C. Ricke1
1Department of Food Science and Center for Food Safety, University of Arkansas, Fayetteville, AR2Present address: Department of Agricultural Economics, Faculty of Bioscience Engineering,
Ghent University, Ghent, Belgium3Center for Food Safety and Department of Food Science & Technology,
University of Georgia, Griffin, GA4Georgia Organics, 200-A Ottley Drive, Atlanta, GA
Agric. Food Anal. Bacteriol. 3: 70-77, 2013
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 71
tion, small farmers who process more than 1,000
birds/year have to meet the federal inspection re-
quirements for commercial processors. Procedures
and practices need to be well-documented and in-
clude documents such as Standard Operating Pro-
cedures and Hazard Analysis Critical Control Point
(HACCP) plans. Complying with these regulations
to meet federal inspection standards is costly but is
manageable for large commercial processors. How-
ever, it is too costly for small farmers and the farmers
may also need help in developing all the required
documentation (Geering, 2011a,b).
The poultry industry in the U.S. is strongly verti-
cally integrated, leaving limited options for off-farm
processing for small-scale poultry farms. At the time
of conducting the survey in Georgia, the only avail-
able processing facilities were owned by the large
poultry companies, and there were no independent
federally inspected processing facilities. Thus, the
Georgia farmers who processed more than 1,000
birds/year had to travel to other states such as South
Carolina and Kentucky to process their birds. This
results in additional travel and accommodation ex-
penses, requires additional time and results in a tre-
mendous reduction in profitability for the grower.
This lengthy transportation also increases the envi-
ronmental impact of the locally grown poultry prod-
ucts and may have negative effects on the animal
welfare which are both important to many of the lo-
cal poultry product consumers.
The local Georgia poultry farmers’ community is
in need of safe and legal processing options, both
on- and off-farm, that provide both easy access to
poultry processing for farms throughout the state
and ensure a safe product for the Georgia consum-
ers. The purpose of this survey was to evaluate pro-
cessing options for the independent local poultry
farms in Georgia for small-scale poultry processing
that would (1) ensure safe products for Georgia con-
sumers, (2) meet farmer needs for various safe pro-
cessing options, both on- and off-farm, (3) provide
easily accessible poultry processing options, (4) lay
the foundation for future growth of pastured poultry
production in Georgia.
MATERIALS AND METHODS
Notice of the survey was posted in the Georgia
Organics print newsletter, and in an electronic news-
letter, as well as by a targeted email to a list of in-
terested parties amassed based on connections
Georgia Organics made at conferences and meet-
ings. The link to the survey was also posted on Geor-
gia Organics’ website. A total of 82 Georgia farm-
ers took the survey between September of 2008
and July of 2010. The survey consisted of questions
about (i) current processing methods; (ii) interest in
other processing options; (iii) importance of different
processing facilities attributes; (iv) demographics of
the farm. Farmers were asked to rate importance of
attributes on a Likert scale from 1 (not important) to
7 (very important). Table 1 contains the questions
and possible answers. Frequency tables, mean val-
ues and standard deviations were determined using
JMP (release 9.0.0: SAS Institute, Inc.).
RESULTS AND DISCUSSION
Current Processing Methods
A total of 82 Georgia farmers participated in the
survey, of which 31 farmers were raising broilers at the
time of the survey totaling 37,642 birds/year. Most
of the farmers who were currently growing broilers
(28 of the 31) processed on-farm but grew only 43%
of the total pastured birds produced by the respon-
dents in Georgia each year (Figure 1, Figure 2). The
majority (60%) of the 28 farmers that processed on-
farm produced less than 500 birds/year.
Pastured poultry is actually not a new concept;
until the 1950’s, all poultry was raised outdoors (Sus-
tainable Agriculture Network, 2006). The renewed
interest in pastured poultry has served to highlight
the lack of suitable processing available to small pro-
ducers. With the vertical integration of the industry,
poultry processing is highly consolidated and not
available to independent producers (Heffernan and
Hendrickson, 2002). This lack of processing is a real
barrier and greatly restricts the ability of pastured
72 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Table 1. Farmers survey questions and possible answers
1. Indicate the number of broilers you are currently processing per year at the different processing sites
listed. a) On-farm b) USDA-inspected facility in South Carolina c) USDA-inspected facility in Kentucky d)
Other off-farm processing facility (please describe) e) Not currently processing (enter 0)
2. If you currently process birds off-farm, please answer the following questions: (Enter your response in
numbers only, with no dollar signs. Decimal points are ok.) a) Roundtrip driving miles to the facility b) Num-
ber of trips made per year c) Average # of birds processed per visit c) Approximate processing cost per bird
charged by facility
3. Please indicate the annual number of broilers that you would like to raise under the following processing
scenarios. Please enter your response in numbers only. a) Processing on-farm b) Shared-use facility with USDA
inspection c) Drop Off/Pick Up facility with USDA inspection d) Contract grower
4. Do you want to sell your poultry direct to consumers, under your own farm’s label? a) Yes, I want to di-
rect market my own processed poultry b) No, I want to raise pastured poultry but have someone else sell it to
the consumer c) I want to pursue both options d) Not sure e) I am not interested in raising pastured poultry at
this time.
5. What is the maximum distance you would be willing to drive for processing?
6. Rate the importance of the following items in considering a Georgia based processing facility where 7 =
Very important, and 1 = Not important at all. Distance from farm, Processing price, Quality of service, Cer-
tified organic, USDA Inspection, Marketing services
7. If you were paying a facility to process your chickens for you (Drop off/pick up arrangement), at what
price per bird processed would this service be a) Absolutely too expensive to ever use? b) Getting expensive?
c) Inexpensive? d) A great value for the money? e) So cheap I would not trust what was happening in there.
8. Are you interested in participating in a co-op of producers to explore: a) processing options? b) Other
infrastructure issues? c) What other issues/comments do you have?
9. Where is your farm located? Please provide answers to at least two of the following options. State:
County: City/Town:
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 73
Figure 1. Percentages of current place of processing for 31 Georgia (GA) pastured poultry farm-ers
81%
16%3%
On-farm in GA
Off-farm SC
Off-farm KY
Figure 2. Percentage of current poultry processing of 31 Georgia farmers by total broiler pro-cessed per year (total 37,642 broilers/year)
43%
50%
7%
On-farm in GA
Off-farm SC
Off-farm KY
74 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Figure 3. Type of processing preferred by Georgia pastured poultry farmers (n=82) when pre-sented with multiple choice options: 1) on-farm, 2) shared-use/rental facility, 3) drop off/pick up, 4) contract grower facility. Farmers had the choice to select/be interested in some of the 4 or all 4 processing options.
0
10
20
30
40
50
60
On-farm Shared-use Drop-off Contract
# Fa
rmer
s
All 4 methods
Shared-use + drop-off + contract
On-farm + shared-use + drop-off
On-farm + shared-use
Contract + drop-off
Shared + drop-off
On-farm + drop-off
Only this method
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 75
poultry producers to sell and market their products;
if a farmer wants to slaughter more than 1,000 birds a
year, they must meet stringent inspection standards
established by the U.S. Department of Agriculture
for large-scale poultry processing operations. Farm-
ers raising up to 1,000 birds per year may slaughter
on their own farms and sell the whole birds on site
directly to consumers, or sell frozen birds directly to
consumers at farmers markets, provided they have
a mobile vehicle license. These on farm processors
generally consist of family members, are able to pro-
cess about 50 to 100 birds per day, and the work is
very labor intensive (Fanatico, 2003).
Some of the Georgia farmers (19% of the 31 grow-
ing broilers at the time of the survey) processed off-
farm in South Carolina and Kentucky, where there
were processors that serve small-scale farmers and
provide USDA inspection (Figure 1). These were the
larger farms that processed more than 1,000 birds/
year each, and raised 57% of the total amount of
birds raised each year (Figure 2). These farmers trav-
eled between 4 and 30 times per year for an aver-
age of 391 miles round trip to processing facilities
out of state. Not only do the long travel times and
distances cost farmers’ time and money, it may also
adversely affect the survival or quality of the birds
themselves. Vecerek et al. (2006) found that mortality
was higher in broilers transported up to 185 mi com-
pared those transported up to 30 mi (0.9% v. 0.2%).
Warriss et al. (1992) examined the effects of time
of transport and found higher mortality for broilers
transported for 9 h as compared to 4 h (0.3% v. 0.2%).
These last findings, when taken together with those
of Bayliss and Hinton (1990), indicate that it is the
time of transport and stationary waiting time that
affects mortality, rather than distance driven. More
bruising has been seen on carcasses with increasing
transport duration (Scholtyssek and Ehinger, 1977).
Ehinger and Gschwindt (1981) found that meat pH
measured post mortem decreased with duration of
transport, and live weight has been found to de-
crease as much as 3% with transport duration of 4.5
h (Scholtyssek et al., 1977). Blood corticosterone is
an indication of stress in broilers and has been found
to be higher in broilers following transport for 4 h
compared to 2 h duration (Freeman, 1984).
Interest in Potential Processing Options and Importance of Different Processing Facilities Attributes
Interest in on-farm and three different off-farm
processing options was evaluated with a multiple
choice question which was answered by all 82 re-
spondents (Figure 3). Off-farm processing options
included: (1) shared-use facility where the farmers
do the processing, and sell their birds under their
own farm label, (2) drop off/pick up facility where the
facility processes as a service to the farmer, and the
farmer sells the birds under their own label and (3)
Table 2. Importance of processing facility attributes to Georgia pastured poultry farmers (average Likert scale value with 1 = Not important and 7 = Very important)
Processing facilities’ attributesMean Likert scale value
St. dev.
Quality of service 6.42 0.96
Processing price 6.09 1.18
Distance from farm 5.95 1.20
USDA inspection 4.76 2.06
Certified organic 3.64 2.04
Marketing services 2.92 1.80
76 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
contract grower facility where the farmer sells the
live birds to the facility, and the facility processes and
sells the birds under the facility’s label.
A similar number of farmers wanted only on-farm
processing (22%) or only off-farm drop off process-
ing (24%). However, 40% of the farmers were more
flexible and were open to more than one processing
option. The off-farm drop-off scored the best with
49 farmers (60%) being interested. This was followed
by on-farm processing (43 farmers or 52%), off-farm
rental (27 farmers or 33%), and contract growers (11
farmers or 13%). Overall, off-farm processing (includ-
ing drop-off, shared use and contract growers) was
more popular than on-farm processing. Comparing
the three off-farm processing options, drop-off was
the preferred off-farm processing option. Availabil-
ity of off-farm processing has potential to signifi-
cantly increase the volume of pastured birds raised
in Georgia. Based on the reported volumes that the
farmers would like to produce, an off-farm drop-off
facility has the potential to increase the total small-
scale poultry production from 37,642 birds/year to
232,205 birds/year, a potential 6-fold increase. How-
ever, it may be difficult to find a location for one sin-
gle processing facility to be conveniently located for
all interested farmers.
The farmers evaluated the importance of several
attributes of processing facilities. The farmers re-
ported quality of service to be the most important
processing facility attribute (Table 2), followed by
the processing price, the distance from the farm and
USDA inspection. It was less important if the pro-
cessing plant was certified organic and if the market-
ing services were provided by the processing plant.
Small-scale farmers in Georgia were having diffi-
culties catching up with demand for local or pasture
raised poultry due to the processing regulations in
Georgia. Georgia is not alone in the need to ad-
dress these issues; many other states are innovating
processing solutions to address the chronic need
for small-scale slaughter facilities in rural communi-
ties while protecting and preserving the health and
safety of the food supply. The production of small-
scale poultry producers is insufficient to justify long
trips to processors and additional fees, and thus is
there a need to find a solution in order to keep small
poultry production as a profitable business. Off-farm
processing, in particular drop-off facilities might of-
fer an efficient solution; however, determination of
the location might be an issue as distance to the pro-
cessing facility is an important factor for many farm-
ers. Of course, these services need to be offered at
an affordable processing price and the quality of the
service is very important to the farmers.
The second preferred processing option, on-farm
processing, also offers some opportunities. One in-
novative solution that is already being used in sev-
eral other states is mobile processing. These consist
essentially of small trailers equipped with everything
needed to process poultry, and travel to the farm
for processing, providing necessary infrastructure
and less environmental impact than a fixed facility.
Several mobile processing units have shown to be
successful in other states (eXtension, 2011), such
as Kentucky (Skelton, 2011). These mobile process-
ing units have the advantages compared to a fixed
processing unit including lower processing costs, re-
duced stress on animals, lower capital investment,
and less resistance from municipalities and neigh-
bors (Simon, 2008).
With a rising consumer interest and awareness in
local and sustainable foods, it will be increasingly
important to make local food products more widely
available in the U.S. food market. Different solutions
exist to help the small local farmers with limited re-
sources to gain profits and make the local poultry
production as a viable industry.
ACKNOWLEDGEMENTS
This research was funded by SARE grant LS11-245
(WQA, PGC and SCR) and USDA-NIFSI grant #2008-
51110-04339 (SCR and PGC) and a farm aid grant
(SW and Georgia Organics, Atlanta, GA).
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Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 79
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The purpose of this section will be to discuss, cri-
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expressed in this viewpoint is the authors alone and
does not necessarily represent the opinion of AFAB
or the editorial board.
COPYRIGHT AGREEMENT
The copyright form is published in AFAB as space
permits and is available online (www.afabjournal.com).
82 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
AFAB grants to the author the right of re-publication
in any book of which he or she is the author or edi-
tor, subject only to giving proper credit to the original
journal publication of the article by AFAB. AFAB re-
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PEER REVIEW PROCESS
Authors will be requested to provide the names
and complete addresses including emails of five (5) potential reviewers who have expertise in the research
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Except for manuscripts designated as Rapid Commu-
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PRODUCTION OF PROOFS
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Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 83
MANUSCRIPT CONTENT REQUIREMENTS
Preparing the Manuscript File
Manuscripts must be written in grammatically
correct English. AFAB offers a fee based language
service upon request ([email protected]).
Manuscripts should be typed double-spaced, with
lines and pages numbered consecutively. All docu-
ments must be submitted in Microsoft Word (.doc or
.docx, PC or Mac). All special characters (e.g., Greek,
math, symbols) should be inserted using the sym-
bols palette available in this font. Tables and figures
should be placed in separate sections at the end of
the manuscript (not placed in the text). Failure to fol-
low these instructions will cause delays of the pro-
cessing and review of the manuscript.
Title Page
At the very top of the title page, include a title of
not more than 100 characters. Format the title with
the first letter of each word capitalized. No abbre-
viations should be used. Under the title, the authors
names are listed. Use the author’s initials for both first
and middle names with a period (full-stop) between
initials (e.g., W. A. Afab). Underneath the authors, a
list affiliations must be listed. Please use numerical
superscripts after the author’s names to designate
affiliation. If an authors address has changed since
the research was completed, this new information
must be designated as “Current address:”. The cor-
responding author should be indicated with an aster-
isk e.g., * Corresponding author. The title page shall
include the name and full address of the correspond-
ing author. Telephone and e-mail address must also
be provided for the corresponding author, and email-addresses must be provided for all authors.
Editing
Author-derived abbreviations should be defined
at first use in the abstract and again in the body of
the manuscript. If abbreviations are extensive au-
thors may need to provide a list of abbreviations
at the beginning of the manuscript. In vivo, in vitro
and bacterial names must be italicized (obligatory).
Authors must avoid single sentence paragraphs and
merge such paragraphs appropriately. Authors must
not begin sentences with “Figure or Table shows…”
as these are inanimate objects and cannot “show”
anything. When number are reported in text or in ta-
bles, always put a zero in front of decimal numbers:
“0.10” instead of “.10”.
MANUSCRIPT SECTIONS
Abstract
The abstract provides an abridged version of the
manuscript. Please submit your abstract on a sepa-
rate page after the title page. The abstract should
provide a justification of your work, objectives, meth-
ods, results, discussion and implications of study or
review findings . Your abstract must consist of com-
plete sentences without references to other work or
footnotes and must not exceed 250 words. On the
same page as your abstract, please provide at least ten (10) keywords to be used for linking and index-
ing. Ideally, these keywords should include signifi-
cant words from the title.
Introduction
The introduction should clearly present the foun-
dation of the manuscript topic and what makes the
research or the review unique. The introduction
should validate why this topic is important based on
previously published literature, and the relevance of
the current research. Overall goals and project ob-
jectives must be clearly stated in the final sentence
of the last paragraphs of the introduction.
Materials and Methods
Information on equipment and chemicals used
must include the full company name, city, and state
(country if outside the United States or Province if
in Canada) [i.e., (Model 123, ACME Inc., Afab, AR)].
84 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Variability, Replication, and Statistical Analysis
To properly assess biological systems indepen-
dent replication of experiments and quantification
of variation among replicates is required by AFAB.
Reviewers and/or editors may request additional
statistical analysis depending on the nature of the
data and it will be the responsibility of the authors
to respond appropriately. Statistical methods com-
monly used in the bacteriology do not need to be
described in detail, but an adequate description
and/or appropriate references should be provided.
The statistical model and experimental unit must
be designated when appropriate. The experimen-
tal unit is the smallest unit to which an individual
treatment is imposed. For bacterial growth stud-
ies, the average of replicate tubes per single study
per treatment is the experimental unit; therefore,
individual studies must be replicated. Repeated
time analyses of the same sample usually do not
constitute independent experimental units. Mea-
surements on the same experimental unit over time
are also not independent and must not be consid-
ered as independent experimental units. For analy-
sis of time effects, assess as a rate of change over
time. Standard deviation refers to the variability
in the biological response being measured and is
presented as standard deviation or standard error
according to the definitions described in statistical
references or textbooks.
Results
Results represent the presentation of data in
words and all data should be described in same
fashion. No discussion of literature is included in
the results section.
Discussion
The discussion section involves comparing the
current data outcomes with previously published
work in this area without repeating the text in the
results section. Critical and in-depth dialogue is
encouraged.
Results and Discussion
Results and discussion can be under combined or
separate headings.
Conclusions
State conclusions (not a summary) briefly in one
paragraph.
Acknowledgments
Acknowledgments of individuals should include
institution, city, and state; city and country if not U.S.;
and City or Province if in Canada. Copies being re-
viewed shall have authors’ institutions omitted to re-
tain anonymity.
References
a) Citing References In Text
Authors of cited papers in the text are to be pre-
sented as follows: Adams and Harry (1992) or Smith
and Jones (1990, 1992). If more than two authors of
one article, the first author’s name is followed by the
abbreviation et al. in italics. If the sentence structure
requires that the authors’ names be included in pa-
rentheses, the proper format is (Adams and Harry,
1982; Harry, 1988a,b; Harry et al., 1993). Citations to a
group of references should be listed first alphabeti-
cally then chronologically. Work that has not been
submitted or accepted for publication shall be listed
in the text as: “G.C. Jay (institution, city, and state,
personal communication).” The author’s own un-
published work should be listed in the text as “(J.
Adams, unpublished data).” Personal communica-
tions and unsubmitted unpublished data must not
be included in the References section. Two or more
publications by the same authors in the same year
must be made distinct with lowercase letters after
the year (2010a,b). Likewise when multiple author ci-
tations designated by et al. in the text have the same
first author, then even if the other authors are differ-
ent these references in the text and the references
section must be identified by a letter. For example
Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013 85
“(James et al., 2010a,b)” in text, refers to “James,
Smith, and Elliot. 2010a” and “James, West, and Ad-
ams. 2010b” in the reference section.
b) Citing References In Reference Section
In the References section, references are listed in
alphabetical order by authors’ last names, and then
chronologically. List only those references cited in the
text. Manuscripts submitted for publication, accepted
for publication or in press can be given in the refer-
ence section followed by the designation: “(submit-
ted)”, “(accepted)’, or “(In Press), respectively. If the
DOI number of unpublished references is available,
you must give the number. The year of publication fol-
lows the authors’ names. All authors’ names must be
included in the citation in the Reference section. Jour-
nals must be abbreviated. First and last page num-
bers must be provided. Sample references are given
below. Consult recent issues of AFAB for examples
not included in the following section.
Journal manuscript:
Examples:
Chase, G., and L. Erlandsen. 1976. Evidence for a
complex life cycle and endospore formation in the
attached, filamentous, segmented bacterium from
murine ileum. J. Bacteriol. 127:572-583.
Jiang, B., A.-M. Henstra, L. Paulo, M. Balk, W. van
Doesburg, and A. J. M. Stams. 2009. A typical
one-carbon metabolism of an acetogenic and
hydrogenogenic Moorella thermioacetica strain.
Arch. Microbiol. 191:123-131.
Book:
Examples:
Hungate, R. E. 1966. The rumen and its microbes
Academic Press, Inc., New York, NY. 533 p.
Book Chapter:
Examples:
O’Bryan, C. A., P. G. Crandall, and C. Bruhn. 2010.
Assessing consumer concerns and perceptions
of food safety risks and practices: Methodologies
and outcomes. In: S. C. Ricke and F. T. Jones. Eds.
Perspectives on Food Safety Issues of Food Animal
Derived Foods. Univ. Arkansas Press, Fayetteville,
AR. p 273-288.
Dissertation and thesis:
Maciorowski, K. G. 2000. Rapid detection of Salmo-
nella spp. and indicators of fecal contamination
in animal feed. Ph.D. Diss. Texas A&M University,
College Station, TX.
Donalson, L. M. 2005. The in vivo and in vitro effect
of a fructooligosacharide prebiotic combined with
alfalfa molt diets on egg production and Salmo-
nella in laying hens. M.S. thesis. Texas A&M Uni-
versity, College Station, TX.
Van Loo, E. 2009. Consumer perception of ready-to-
eat deli foods and organic meat. M.S. thesis. Uni-
versity of Arkansas, Fayetteville, AR. 202 p.
Web sites, patents:
Examples:
Davis, C. 2010. Salmonella. Medicinenet.com.
http://www.medicinenet.com/salmonella /article.
htm. Accessed July, 2010.
Afab, F. 2010, Development of a novel process. U.S.
Patent #_____
Author(s). Year. Article title. Journal title [abbreviated].
Volume number:inclusive pages.
Author(s) [or editor(s)]. Year. Title. Edition or volume (if
relevant). Publisher name, Place of publication. Number
of pages.
Author(s) of the chapter. Year. Title of the chapter. In:
author(s) or editor(s). Title of the book. Edition or vol-
ume, if relevant. Publisher name, Place of publication.
Inclusive pages of chapter.
Author. Date of degree. Title. Type of publication, such
as Ph.D. Diss or M.S. thesis. Institution, Place of institu-
tion. Total number of pages.
86 Agric. Food Anal. Bacteriol. • AFABjournal.com • Vol. 3, Issue 1 - 2013
Abstracts and Symposia Proceedings:
Fischer, J. R. 2007. Building a prosperous future in
which agriculture uses and produces energy effi-
ciently and effectively. NABC report 19, Agricultural
Biofuels: Tech., Sustainability, and Profitability. p.27
Musgrove, M. T., and M. E. Berrang. 2008. Presence
of aerobic microorganisms, Enterobacteriaceae and
Salmonella in the shell egg processing environment.
IAFP 95th Annual Meeting. p. 47 (Abstr. #T6-10)
Vianna, M. E., H. P. Horz, and G. Conrads. 2006. Op-
tions and risks by using diagnostic gene chips. Pro-
gram and abstracts book , The 8th Biennieal Con-
gress of the Anaerobe Society of the Americas. p.
86 (Abstr.)
Data Presentation in Tables and Figures
Figures and tables to be published in AFAB must
be constructed in such a fashion that they are able
to “stand alone” in the published manuscript. This
means that the reader should be able to look at
the figure or table independently of the rest of the
manuscript and be able to comprehend the experi-
mental approach sufficiently to interpret the data.
Consequently, all statistical analyses should be very
carefully presented along with variation estimates
and what constitutes an independent replication
and the number of replicates used to calculate the
averages presented in the table or figure.
Each table and figure must be on a separate
page in the submitted paper. In addition, you will
need to submit all data for charts, tables and
figures in native format when possible (e.g., Mi-
crosoft Excel, Powerpoint). Photographs should
be submitted as high-resolution (600 dpi) .jpg or
tif. files. All figures should be clearly presented with
well defined axis and units of measurement. Sym-
bols, lines, and bars must be made distinct as “stand
alone” black and white presentations. Stippling,
dashed lines etc. are encouraged for multiple com-
parison but shades of gray are discouraged. Color
images, micrographs, pictures are recommended
and there is no additional fee for their submission.
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