microbial systems: the human microbiome and probiotics

MICROBIAL SYSTEMS: THE HUMAN MICROBIOME AND PROBIOTICS

SYSTEMS THEORY• From reductionism to synthesis: leaps in modern science and theory• Evolution – the study of inherited phenotypic change in organisms over successive

generations; Darwin noted: more offspring are produced than survive, traits vary among individual offspring = different rates of survival and reproduction, traits are inherited

• Evolution is not “progress,” it is change by adaptation; natural selection drives adaptation• Punctuated equilibrium – Gould• Endosymbiosis – Lynn Margulis• Gaia – Lovelock

• In short, modern scientific investigation increasingly reveals cooperation and symbiosis as adaptive in many circumstances

EMERGING SYSTEMS SCIENCE• Modern environmental conditions lead us to recognize the interconnected

nature of human and non-human communities, of ecology and economy, and of psychology and consciousness…

• Ecological and biological sciences have increasingly exposed the importance of systems, networks, and interconnected (often cooperative) relationships

• Are you a solitary organism or a feature of a great holistic network of living things?

• …the map “is” not the terrain…

THE HUMAN MICROBIOME• The ecological community of

commensal, symbiotic, and pathogenic microorganisms that share our body

• Remember… You are made of 10x more microbial cells than human cells

• Typical adult microbiome weighs between 200 and 1,400 grams, with 400-500 species of intestinal microflora

• Modern genetic analysis in the 1990’s led to the discovery of microbiome; its impact on human health is only beginning to be understood

POSSIBLE EFFECTS OF THE MICROBIOME

• Roles in auto-immune diseases like diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, fibromyalgia, some cancers and obesity

• Regulation of mood through the production of neurotransmitters involved in schizophrenia, depression, bipolar disorder and other neuro-chemical imbalances

• The microbes being discussed are generally non-pathogenic (do not cause disease unless they grow abnormally); they exist in harmony and symbiotically with their hosts

• Much of the human microbiome is composed of archaea

MICROBIOME EXPERIMENTAL EVIDENCE

• Germ free mice have an exaggerated stress response and reduced expression of brain-derived neurotrophic factor in the cortex and hippocampus

• Treating maternally separated mice with a probiotic culture of Bifodobacterium infantis minimizes weight loss, causes mice to swim longer and increases the serotonin precursor tryptophan

• Human patients with depression are less able to properly digest fructose, which is also associated with a reduction in tryptophan production

• Eliminating fructose from their diet improved depression in human test subjects

HOLOGENOME THEORY OF EVOLUTION

• All animals and plants establish symbiotic relationships with microorganisms• Different host species contain different symbiont populations; individuals of the

same species may contain different symbiont populations• Host organism + microbial community relationships affect both the host and its

microbiota • Genetic info encoded by microorganisms can change under environmental

demands more rapidly and diversely than the genes encoded by the host organism

• The host genome can act in harmony with the genomes of the associated symbiotic microorganisms to create a hologenome

• The holobiont with its hologenome should be considered as the unit of natural selection in evolution

• If a given holobiont is to be considered a unit of natural selection the hologenome must be heritable from generation to generation

SOCIETY AND SCIENCE• The cultural significance of evolutionary theory

- most modern cultures have abandoned creationism/religious explanations for life; scientific theory often guides society

- If life is about “survival of the fittest” in terms of competitive behavior, what behaviors will individuals adopt? What are the social and systemic results?

Beijing, China 2014: Attempting to co-opt biophila with aTechnological “solutions”

• “…the hologenome theory of evolution focuses on the holobiont as a single dynamic entity in which a vast amount of the genetic information and variability is contributed by the microorganisms. Evolution of the holobiont can occur by changes in the host genome and/or in any of the associated microbial genomes, and relies on cooperation between the genomes within the holobiont, as much as on competition with other holobionts.” – Rosenberg et al

COEVOLUTION OF THE HOLOBIONT

• Holobiont = host + symbiotic microbiota

• Coral reefs are examples of holobionts – Oculina patagonia – Mediterranean coral infected by Vibrio bacteria – coral developed resistance by adaptive changes in microbiota, not immune response by O. patagonia

• The microbiome coevolves with the immune system and controls it – “germ free animals” possess severely underdeveloped immune systems

WHAT ARE PROBIOTICS?• Dietary supplements or food products with viable microbe populations to alter the

microflora of the host with potential beneficial health effects

• 1877 – Pasteur – antagonistic relationships between bacteria suggested non-pathogenic microbes could be used to control pathogens

• 1907 - Elie Metchnikoff noticed lactic acid fermentation of milk stopped spoilage; introduced the idea of eating lactic acid bacteria (LAB) to promote health; attributed the longevity/health of populations in the Balkans to bacteria in their traditional yogurt

• 1950’s researchers confirm the effects of antibiotics on beneficial intestinal microbes

• Fermentation effects are known to: improve digestion, produce amino acids and vitamins, but the actual health benefits of probiotics are somewhat uncertain

THE MICROBIAL ECOSYSTEM OF THE HUMAN GI TRACT

• Complexity and access of GI tract makes research on probiotics difficult

• Human GI tract – 400 + species of bacteria

• Acidity of stomach destroys many potential probiotics; acid/bile resistant strains of Lactobacillus acidophilus and Bifidobacterium have been isolated from humans and used in yogurt cultures

COMMON PROBIOTIC GENERA• Bifidobacterium – genus of non-motile, gram-positive anaerobes found in

human mouth, colon, and GI tract; common and ubiquitous human endosymbiotic bacteria

• Some introduced through breastfeeding; babies with Bifidobacterium as intestinal microflora were observed to suffer less from GI disorders

• Lactobacillus – Gram-positive facultative anaerobic or microaerophilic rod-shaped bacteria

• Streptococcus • Saccharomyces

PROBIOTICSMANY POTENTIAL USES

• Infectious diarrhea and day care related illness• Antibiotic Associated Diarrhea

• Clostridium difficile• Inflammatory bowel disease• Traveler’s diarrhea• Prevention of NEC (necrotizing enterocolitus)• Allergy• Irritable Bowel Syndrome

Yogurt (364)

Yogurt+L. casei

(360)

P-value

Children with diarrhea 87

(22%)61 (16%) 0.029

Duration of diarrhea (days) 3.95 3.53 0.24Rotavirus positive stool 2.2% 0.3%

Prevention of Diarrheal Illness18 Week Therapy in French Children (6-24 months) in Day

Care

CA Pedone, et al. Int J Clin Pract 54(9):568-71, 2000

Controls (60)

B. lactis (73)

L. reuteri (68)

P-value

Days with diarrhea 0.59 0.37 0.15 <0.00

1Episodes of diarrhea

0.31 0.13 0.02 <0.001

Clinic visits 0.55 0.51 0.23 0.002Absences 0.43 0.41 0.14 0.015

Prevention of Diarrheal Illness12 Week Therapy in Israeli Infants (4-10 months) in Day

Care

Z Weizman, et al. Pediatrics 115:5-9, 2005

Control (19)

L. reuteri/L.

rhamnosus (24)

P-value

Duration of diarrhea (hours) 115.7 75.9 0.05Duration of watery diarrhea 37 38.1 0.94Duration of fever (days) 1.1 1.4 0.59Diarrhea after 120 hours 7 2 0.03

Treatment of Acute Diarrhea5 Day Therapy in Danish Children (9 to 44 months) in Day Care with

Acute Diarrhea

V Rosenfeldt, et al. Pediatr Infect Dis J 21:417-9, 2002

Whole Study Group

PROBIOTIC TREATMENT IN CASES OFINFECTIOUS DIARRHEA

• Experiment conducted with children up to 2 years of age in chronic care facility

• Subjects were randomized to receive B. bifidum and S. thermophilus or placebo

• Probiotic supplement resulted in statistically less diarrhea (7% vs 31%)

• Statistically less rotavirus shedding (10% vs 39%) with probioticsSaavedra et al, Lancet 1994

PROBIOTICS IN ANTIBIOTIC ASSOCIATED DIARRHEA

• Diarrhea is a common side effect of antibiotic therapy

• Up to 40% of children receiving broad spectrum antibiotic therapy

• Likely due to altered microbial flora• Leads to altered metabolism of osmotically active

substances

PREBIOTICS AND SYNBIOTICS

• Prebiotics: Non-digestable food ingredients with positive effects on endogenous microbiota

• Stimulate the growth and activity of one or more species of beneficial microbiota; usually confer benefits to a range of beneficial microblora, especially Bifidobacterium and LAB

• Prebiotic examples: Inulin (a dietary fiber found in some plants/roots), oligosaccharides (polymers of simple sugars found in cell membranes)

• Synbiotics – a probiotic combined with its own, specific prebiotic food – improves survival rate of probiotics through the GI tract

TOP 10 FOODS CONTAINING PREBIOTICS

Food Prebiotic Fiber Content by WeightRaw Chicory Root 64.6%Raw Jerusalem Artichoke 31.5%Raw Dandelion Greens 24.3%Raw Garlic 17.5%Raw Leek 11.7%Raw Onion 8.6%Cooked Onion 5%Raw Asparagus 5%Raw Wheat bran 5%Whole Wheat flour, Cooked 4.8%Raw Banana 1%

PROBIOTICSPRACTICAL ISSUES

• Correctly purified strains of bacteria?• Must be selected for ability to:

• Survive acid/bile in upper GI tract• Colonize• Adhere

• Must have shelf viability• Should have quality control• Not FDA regulated

PROBIOTICSPRACTICAL ISSUES

• Typically $1 to $3 per day• VSL3: $56 for 20 day supply• Culturelle (LGG): $55 for 30 day supply• Custom Probiotics CP-1: $40 for 30 day supply

• May need several months of therapy to see an effect • Likely stop working after discontinued• Concentration (dose) highly variable