Grand Challenges in Environmental Health

Research Could the microbiome be

the missing link?

Andrew D. Patterson Penn State University adp117@psu.edu

“It is now recognized that the metabolism of both exogenous and endogenous compounds by conventional animals can be attributed not only to the enzyme of the host but also to the enzyme of the host’s bacterial microflora.” - Peter Goldman, Mark Peppercorn, Barry Goldin The American Journal of Clinical Nutrition November 1974 Vol 27 Number 11

http://www.issx.org/?page=RTWilliams

“Thus it must be emphasized that our conception of the flora is greatly dependent on the techniques used and also that our present knowledge may be both limited and somewhat misleading.” - Ronald R. Scheline Journal of Pharmaceutical Sciences December 1968 Vol 57 Number 12

MICROBIAL

COMMUNITY

STRUCTURE ? METABOLIC

ACTIVITY

HEALTH

DISEASE

Cell Metabolism 2014

MICROBIAL METABOLISM

GI TRANSIT

TIME

ABSORPTION AND

ENTEROHEPATIC

CIRCULATION IMMUNE

SYSTEM

HOST

GENOTYPE

HOST

METABOLISM

CHEMICAL STABILITY

IN THE STOMACH

DIETARY INTAKE

MICROBIAL

INTERACTIONS MICROBIAL GENOTYPE

(STRAIN-LEVEL VARIATION) ENVIRONMENTAL CHEMICALS

???

Cell Metabolism 2014 Nov 20(5) 761-8

Symbiont Evidence for Environmental Chemical Interaction with the Gut

Microbiota

BEAN BUG Riptortus pedestris

PNAS 2012 May 109(22) 8618-22

Fenitrothion degradation by Burkholderia spp.

Symbiont Evidence for Environmental Chemical Interaction with the Gut

Microbiota

COFFEE BERRY BORER Hypothenemus hanpei

Nature Communications 2015 Vol 6 Article 7618

Caffeine degradation by Pseudomonas fulva

(source of Nitrogen and Carbon)

Image: Georg Goergen/IITA Insect Museum, Cotonou, Benin

Intersection of Environmental Chemicals, the Microbiome, and

Human Health

Impact on

Health

Personal Care Products

Persistent Environmental Contaminants

Heavy Metals

Environmental Human

Penn State’s Living Filter

Photo: Emily Woodward

Environmental Contaminants, the Microbiome, and Human Health

Chlorpyrifos (pesticide) • SHIME studies reveal dysbiosis • Intestinal bacteria important for

degradation

Pesticides can interact with and modify the intestinal microbiota

Enviro Sci Pollut Res 2013 Vol 20: 2726-2734; Biotech 2013 Vol 3: 137-142

Environmental Contaminants, the Microbiome, and Human Health

Arsenic (heavy metal) • In vitro cultured human gut

microbiota can metabolize Arsenic to methylated arsenicals and thioarsenicals

Intestinal microbiota can metabolize heavy metals and contribute to presystemic

metabolism

EHP 2010 Vol 118 No 7

EHP 2012 Vol 120 No 3

A - alter absorption via changes in barrier function or transport systems

D - altered distribution via bacterial metabolism

M – contribute to pre-systemic metabolism

E – alter enterohepatic circulation

Environmental Contaminants, the Microbiome, and Human Health

DOSE

EHP 2014 Vol 122 Number 8

FOOD

PESTICIDES

COSMETICS

POLLUTANTS

DRUGS

XEN

OB

IOTI

C

MET

AB

OLI

SM

END

OG

ENO

US

M

ETA

BO

LISM

EXPOSOME

GUT MICROBIOTA

Reconsider What Dose Means?

• Pre-systemic (first pass elimination) vs absorbed dose

• Route of exposure and impact on the microbiome

Antibiotics

Low, Chronic Dose • Promote inflammation,

altered host metabolism, weight gain

• Critical timing window

High, Acute Dose • Improve fatty liver

• Reduce progression of liver cancer ( DCA)

VEHICLE ANTIBIOTICS

JCI 2015 125(1): 386-402 Nature 2013 499(7456):97-101

MOUSE MODELS Conventional and Germ Free

-300

-200

-100

0

100

200

300

-400 -200 0 200 400

t[2

]

t[1]SIMCA-P+ 12.0.1 - 2012-08-07 18:46:17 (UTC-5)

METABOLOMICS NMR, LC-MS, GC-MS

SMALL MOLECULE CHATTER BETWEEN

HOST AND MICROBIOTA

Need Tools Used to Uncover and Decipher Host Gut Interactions

16S rRNA Amplicon Sequencing,

Metagenomics, and Metatranscriptomics

Microbial “Small Molecule” Chatter

Who is listening?

GR MR AR PR ER, VDR TR, RAR,

PPAR, LXR, FXR PXR CAR RXR, HNF4,

ARP-1 COUP-TF EAR2 SCP46 REVERB, SF-1 LRH-1 NGFI-B NURR1 TR2 TR4 RZR, ERR1 Others………

STEROID METABOLIC SENSORS ORPHANS

6 Families 26 Subfamilies > 50 genes

Nuclear Receptor Superfamily

ARYL HYDROCARBON RECEPTOR (AHR)

*not a nuclear receptor but shares many

features*

Aryl Hydrocarbon Receptor

• Xenobiotic Sensor • TCDD

• Dibenzofurans

• Benzo[a]pyrene

• Dietary Sensor • Flavoniods

• Indoles

• Gut Microbiome Sensor • Bacterial Phenazines

• Tryptophan Catabolites

• 7-ketocholesterol

Ve

hi c

l e

TC

DF

0 . 0

0 . 1

0 . 2

0 . 3

0 . 4

Fir

mic

ut

es

/Ba

ct

er

oid

et

es

p = 0 . 0 1 3

Ah

r -/-

Veh

icle

Ah

r -/-

TC

DF

0 .0 0

0 .0 5

0 .1 0

0 .1 5

0 .2 0

Fir

mic

ute

s/B

ac

tero

ide

tes

N S

TCDF Effect

Ahr Effect

16S rRNA Gene Sequencing

AHR Activation Significantly Modulates Gut Microbota Community Structure

ACTIVATION AND GENOTYPE INFLUENCE ON THE GUT

MICROBIOTA

Microbial “Small Molecule” Chatter

Can we tap their line?

Metabolomics

Identification of the chemical fingerprints that biological processes leave behind

Chemical fingerprint is significantly “contaminated” with metabolites of bacterial origin • Indole-containing compounds • Glycine-conjugated compounds • Bile acids (co-metabolites)

Antibiotic Treatment Causes Pronounced Changes in Gut Microbiota Metabolism

p-Cresol glucuronide Antibiotic

p-Cresol sulfate

Vehicle

Anti-Oxidant Tempol Alters the Cecal Community Structure

Genus: Lactobacillus

Tempol kills Lactobacillus spp.

Secondary bile acids – Metabolites produced in the intestine by bacterial enzymes

Lactobacillus

BSH

Deconjugation

TMCA MCA

Dehydroxylation and Deconjugation

β-MCA DCA

γ-MCA CDCA

T-β-MCA

TCA TUDCA

TCDCA

Unconjugated Bile Acids Depleted

Conjugated Bile Acids Enriched

Bile Acid Profiling Fecal Bile Acids Small Intestine Bile Acids

Disruption of Lactobacillus spp. Bile Salt Hydrolase Activity Impacts the Farnesoid X

Receptor (Bile Acid Receptor)

Repression of FXR target genes

Shp (FXR target gene) induction in hepatocytes

TβMCA is an FXR Antagonist

Sayin et al Cell Metabolism 2013

Li et al Nature

Communications 2013

Reducing FXR Activity ( BSH Activity) Can Promote Weight Loss in Mice

Summary Questions

1. Should our considerations of dose include the microbiota? Timing, duration, and route of exposure?

2. How do we best monitor and interpret changes (structural, functional) in the microbiota?

3. How do we assess the “health” of the microbiota?