The Microbiome and Immune System in Environmental Risk of Infectious Disease

Rodney Dietert

Cornell University

Appreciation

• To the workshop organizers for my inclusion in the program

• To my editor and wife, Janice Dietert

Disclosures

Recent and Current Positions Held and Financial Support:

• Professor of Immunotoxicology at Cornell University

(Now Professor Emeritus)

• Consultant – in Education and Translational Research for Seed (a 2018 start-up company)

• Author at Dutton Penguin Random House

Disappearing Dogmas of the 20th Century

1. The newborn is fully prepared immunologically to fight all diseases.- (The newborn must postnatally co-mature with the microbiome to be

immunologically balanced and prepared to fight diseases).

2. Species barriers are chromosomally gene driven.- (Immune-microbiome incompatibility can also determine species barriers)

3. Most microbes are a threat to human health.

- (Some microbes are required for human health.)

4. The human mammal is the target of environmental health risk assessments (e.g., toxicological safety).

- (The human superorganism is the most relevant target for assessment/evaluation/safety determinations).

The Complete Human: Three Domains of Life

Eukaryota

Archaea

Bacteria

Majority-Microbial Humans

(based on cell and gene numbers)

Domains of Life Genomes

First~ 25,000 genes

Approximately 57%-90% microbial

by cell number

Second ~ 10 million genes

Superorganism

Mammalian

MicrobialEukaryotes

Adapted from: Dietert and DietertHealthcare 3(1), 100-129; 2015.

~ 3.3. million microbial genes in a individual

Routes of Exposure, Portals of Entry, and Microbiome Sites Converge

Main Toxicological Routes of Exposure

See: Damalas and Koutroubas,

Toxics 2016, 4(1), 1; doi:10.3390/toxics4010001;.

Skin Break Urogenital

Infectious Agents - Major Portals of Entry

InhalationDermal Oral

Major Body Sites for the Microbiome

Hologenomic Speciation Determined by the Microbiome and Immune System

See: Brucker, R. M. & Bordenstein, S. R. Science 2013; 341 (6146): 667-669Flintoft, L. Nature Reviews Genetics 2013; 14: 598 (Photo : Bordenstein Lab)Wang et al. Nature Comm 2015; 6, Article number: 6440 doi:10.1038/ncomms7440Sutherland et al. Immunol Rev. 2016 Mar;270(1):20-31. doi: 10.1111/imr.12384

Nasonia sp. wasp House Mouse in Europe

(note: generalized wasp depicted)

Postnatal Immune Maturation(Note: 1,000 day concept on postnatal developmental windows)

• Environmental exposures and adaptations are required for full immune maturation (the newborn does not equal adult immunologically). The prenatal environment has a Th2 preferential bias).

• Gut microbes at mucosal surfaces drive the newborn’s stereotypic immune development. Microbial dysbiosis impairs immune maturation.

• Some aspects of inflammation must be ramped down and others made more selective as per innate immune responses. Macrophage polarization and regulation must be altered to better protect the infant from infections (e.g., via cell signaling factors - IRF5).

• Peripheral T cell helper and regulatory populations must change for balanced responses

• B cell, Natural killer cell, and dendritic cell maturation is affected during first 3 months of life

• Specialized innate immune populations (e.g., microglia, invariant NKT cells) must mature, expand, contract in tissues to provide immune homeostasis

See: Olin et al. Cell 174: 1277–1292. 2018

Lenz and Nelson, Front. Immunol., 13 April 2018 | https://doi.org/10.3389/fimmu.2018.00698

Zeissig and Blumberg, FEBS Lett 588(22): 4188-4194. 2014

Schneider et al. Front. Immunol., 11 July 2018 | https://doi.org/10.3389/fimmu.2018.01597

Examples of Neonatal “Critical Windows”Involving the microbiome and immune system

•Modulation of proliferative burst of invariant Natural Killer T cells (iNKT cells) in the gut –(determines risk of G.I. inflammatory disease)

(An et al. Scharschmidt et al. Immunity 43, 1011–1021, 2015)

•Neonatal timed influx of FoxP3+ T regulatory cells (Tregs) into the skin (determines tolerance to skin commensals)

(Scharschmidt et al. Immunity 43, 1011–1021, 2015)

A Systems Biology Unit: the Microimmunosome

Adapted from Dietert, Reprod. Toxicol. 2017

Microbes

Barrier

Specialized

Immune Cells

Barrier integrity and

bi-directional

communication

leading

to immune

homeostasis is critical

2/3rds of

your

immune

cells are

in the gut

near the

gut barrier

Responses of the Microbiota to Environmental Exposures

Environmentalpollutants

(e.g., metals, organics)DrugsDiet

1. Sequestration2. Avoidance/Exclusion3. Metabolism4. Specific Signaling5. Selective Microbe Death6. Selective Microbe Expansion7. Translocation

Adapted from: Dietert R. The microbiome in early life: self-completion and microbiota protection as health priorities. Birth Defects Res. Part B. 101(4): 333-340, 2014.

Gut Microbiota and Xenobiotics

• Increase or decrease drug available for absorption

• Directly metabolize drug

• Inhibit detoxification

• Biotransform common food components, drugs, and xenobiotics

• Generate aryl-hydrocarbon receptor agonists

• Convert a pro-drug into an active drug

• Respond to one drug/xenobiotic by inactivating host enzymes for an unrelated drug

• Regulate host metabolism

From: Klaassen and Cui, Drug Metab Disp. 2015; 43(10): 1505-1521

See: Clayton et al. Proc Natl Acad Sci U S A. 2016 Sep 13; 113(37): 10376–10381;

Lekshmi et al., Microorganisms 2017, 5, 11; doi:10.3390/microorganisms5010011;

Kristensen K1, Henriksen L, J Allergy Clin Immunol. 2016 Feb;137(2):587-90; Kristensen et al.

Pediatr Infect Dis

J. 2015 Feb;34(2):145-8.

Captivity

Reduced

microbiota

diversity

Humanized

microbiome

- from animal

handlers

Microbiome Destruction – What happens next?

Elective Cesarean delivery

More hospital-

associated

microbes

seeding the

neonatal gut

Altered

infant

cytokine

production

Howler monkeys

(Food and lifestyle restricted)

Prophylactic use of antibiotics

for growth promotion

in food-producing animals

Increased antimicrobial

resistance

and zoonotic risk from

pathogens (e.g.,

Campylobacter spp.,

Salmonella spp.,

Escherichia coli and

Staphylococcus aureus)

Elevated risk for several

diseases associated with

the mucosal immune

system

From:

National Research Council,

Environ Health Perspect,

74: 3-9, 1987

Current Biomarkers Model for Health Risk Assessment (1987)

The Microbiome Filters Virtually All Exposuresand Directly Participates in Epigenetic Alterations

Proposed New Environmental Health Assessment Model

Adapted from: Dietert and Silbergeld, Toxicol. Sci. 2015 Apr;144(2):208-16.

Microbiome

Colonization ResistanceGeneral factors: competitive exclusion (Gauses’ Law in ecology, Nurmi Concept), host gut motility, mucus layer regulation, epithelial barrier integrity

Specific processes: Inter-bacterial interactions

• Nutrient limitation (e.g., need to block simple sugar availability for pathogens)

• Including blocking inflammation-associated nutrient shifts (e.g., nitric oxide)

• Bile salts metabolism (secondary bile salt inhibition of pathogens)

• Short chain fatty acid (SCFAs) production (note: loss of butyrate production triggers increased oxygen and nitrate release in the lumen)

• Bacteriocin production

• Cell-cell contact-dependent inhibition

• Type VI secretion systems (e.g., B. fragilis blocks enterotoxigenic B. fragilis)

• LgX proteins

See: Sobara and Pamer, Mucosal Immunology 12: 1-19 (2019)

Nurmi and Schneitz, Int J Food Microbiol. 15(3-4): 237-240.

Wiles et al. PLoS Biol. 2016 Jul; 14(7): e1002517.

Cornick et al. Tissue Barriers. 2015; 3(1-2): e982426.

Importance of Commensal Microbes to Block Pathogens

Information adapted from: Keith and Pamer, J. Exp Med.DOI: 10.1084/jem.20180399 Published October 11, 2018

Treg

cell

Barrier structural and

functional integrity

Inner mucus layer

Outer mucus layer

B. fragilis + opportunistic pathogen

Immune population

mix and status

Exposure to

environmental

chemicals,

drugs,

stress, and/or

dietary changes

Loss of inhibition

capacity –

increase in

susceptibility

Barrier

damage

likely

LPS signal

to underlying immune cellsInflammatory

attack

Pathogens: Minimum Microbiota Necessary for Effective Competitive Resistance

• Metagenomic tools were used to construct a minimum consortium of gut microbiota that would protect mice from infection with the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm).

• An installed combination of 15 specific gut bacterial strains were equivalent to a complete microbiome in effective colonization resistance.

From: Brigiroux et al. Nat. Microbiol. 2:16215 · November 2016

Utility of BiomarkersFrom Altered Microbiota to Disease

Clinical Disease

Altered

Gut Microbiota

Loss of

Colonization

Resistance

Physiological

System/

Immune

Dysbiosis

Infectious Disease

Non-communicable Disease

Barrier

Function

(Is it useful to Flip this information?)

Arsenic Presystemic Metabolism via the Microbiome• Sulfate-reducing colon microbiota can thiolate methylated arsenic producing

highly toxic metabolites.

• There is individual human variation in the presence of these bacteria potentially affecting individual risk.

• Arsenic exposure can also change gut microbiome composition and microbial genes.

• Arsenic exposure is associated with increased risk of certain human infections (e.g., hep B). - NHANES

• Infections can change both microbiome composition and arsenic metabolism (mouse study).

• Components of the gut microbiome can protect the immune system from arsenic toxicity (mouse study)

See: Rubin et al. Environ Health Perspect. 2014 Aug; 122(8): 817–822.

Luk et al. Chem Res Toxicol. 2013 Dec 16;26(12):1893-903.

Gokulan et al. MBio. 2018 Aug 14;9(4). pii: e01418-18. doi: 10.1128/mBio.01418-18.

Chi et al. Toxicol Sci. 2017 Dec 1;160(2):193-204.

Coryell et al. Nat Commun. 2018 Dec 21;9(1):5424.

Zhang et al. Curr Med Sci. 2018 Aug;38(4):610-617.

Arsenic “Ages” the Immune System

1. Prenatal and early childhood arsenic

exposure is inversely associated with telomere length and

signal joint T- cell receptor excision circle (sjTREC)

at 9 years of age. Fewer naive T cells with aging.

Immunosenesence - Mannan et al. Associations of Arsenic Exposure

With Telomere Length and Naïve T Cells in Childhood-

A Birth Cohort Study.

Toxicol Sci. 2018 Aug 1;164(2):539-549.

2. Low to moderate levels of arsenic disrupt T cell development.

Both genotoxic (oxidation) and non-genotoxic

(IL-7 signaling are involved) processes are involved.

The earliest T cells are the least capable of pumping

out arsenic and are at the greatest risk. - Xu et al.

Toxicity of environmentally-relevant concentrations of arsenic on

developing T lymphocyte.

Environ Toxicol Pharmacol. 2018 Sep;62:107-113.

Case Scenario for Cumulative Environmental Health RisksChildhood Incompleteness of the Microbiome

Bereavement

Maternal stress

Environmental tobacco smoke

Air pollution/

PAHs, others

F1 immune programmingReduced Tregs

Antibioticsadministered

Cesareandelivery

Reduced microbial seeding

Depletedmicrobiome

Altered metabolites& Immune development

BPA, heavy metals, certain food additives

Improper control of inflammation;Inadequateinnate

immune training

Inflammatorypromotionof

metabolic syndrome& carcinogenesis

Elevated risk of allergy,autoimmunity, obesity,CVD

Formula feeding

Missing prebioticsand microbes

urbanization

Reduced colonization resistance;Increased risk of infectionAdapted from:

Dietert, R. NeoReviews 2018 19(2):e78-e88.

Summary

• The microbiome is the lens through which we see our external environment (chemicals and pathogens). It is also our first line of defense from external threats and it is malleable.

• The microbiome and immune system must be sufficiently matched and must co-mature together to ensure host integrity and effective immune function (e.g., self tolerance and host defense against infectious diseases). The immune system, absent a “healthy” microbiome, is a disease inflictor rather than a protector.

• Optimizing colonization resistance is a key to improved health protection even as we work to reduce external health threats (chemical and microbiological).

• Managing the microbiome-immune interface should be a significant part of future preventative and therapeutic health.