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Going With Your Gut: The Microbiome and You

Robert T. Schooley, MDProfessor of Medicine

University of California San DiegoSan Diego, California

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Learning Objectives

After attending this presentation, learners will be able to: ▪ Describe basic concepts of the microbiome and its

relationship with human health▪ Delineate factors that destabilize the human

microbiome▪ Describe changes in the microbiome associated with

HIV infection

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The Microbiome: Definitions

• Microbiota: ecological community of commensal, symbiotic and pathogenic microorganisms

• The human microbiome (or human microbiota) is the collection of microorganisms which live on us. They live on the skin, in the saliva and mouth, in the eyes, and in the gut and the rest of the gastrointestinal tract.

• Relative number of human and bacterial cells in each of us• Humans are composed of ~ 37 trillion cells• We carry 100 trillion individual bacteria

Lederberg and McCray, Scientist, 2001

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What has Accounted for the Explosion of Knowledge about the Microbiome?

We could only identify what we could grow

Metagenomics

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Technical advance: Inexpensive high-throughput shotgun sequencing

Deep sequencing/next generation sequencing

• Cost has decreased dramatically

• Number and length of reads improved

• Sequence communities or single cells

• Bioinformatics• Massive and cumulative data

basis allow analysis and cataloguing of sequences

Log

scal

e!

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Constant and Variable Regions of 16s RNA

Constant

Variable

Cui, et. al., Annals. ATS 11: S4, 2014

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Technical advance: PCR-based 16S rRNA gene sequencing

Extract DNA Amplify 16S rRNA genes

Sequence rRNA amplicon

Data analysis

Bioinformatics: community profile

• 16S rRNA most highly conserved bacterial gene• But conserved and variable regions within gene

VC C

Universal primers

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New terminology

• Phylotype: Environmental DNA sequence or group of sequences sharing more than an arbitrarily chosen level of similarity based on a specific marker

• Most commonly based on rRNA gene

• Operational taxonomic unit (OTU)• Cluster of microorganisms grouped by >97% DNA

similarity (rRNA gene)• OTU=≠species

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Metagenomics

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Metagenomics has improved how we classify microorganisms

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Metrics Used to Describe a Microbial Community

Cui, et. al., Annals. ATS 11: S4, 2014

Low Diversity High Diversity

Obesity/IBD Bacterial vaginosis

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NIH Human Microbiome Project

• How many microbes on our body, spatio-temporal issues?

• How do they differ between site and/or between individuals?

• How do they change over time or in response to environmental changes?

• Is there a conserved “core” microbiome?

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Methods

• 300 healthy subjects• 15 or 18 body sites• >11,000 primary specimens• 1,900 reference strains

Proctor, Cell Host Microbe (2011) 10, 287

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The Microbiome of the Skin

Grice and Segre, Nat Rev Microbiol, 2011

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Clustering by Organizational Taxonomic Unit

Human Microbiome Consortium,Nature, 2013

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Microbial Diversity In a Given Site Is Greater Between Individuals than Between Visits

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Intrapersonal Variation Between Sites is Greater than Interpersonal Variation at the Same Site

Class

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The Microbiome of the Gut• Established in early life – differs in infants born by C-section vs. vaginal birth.• In murine models, transfer of “obese” microbiome affects the growth

characteristics of the mouse for life• Drastically altered acutely by antibiotic administration• In farm animals (and mice), antibiotic exposure early in life promotes

microbiota associated with high coloric efficiency. • There is some evidence that early exposure to antibiotics affects humans the

same way.• After cessation of antibiotics, the antibiotic “footprint” remains; e.g., the

microbiome reverts toward but does not reach pre-antibiotic richness/diversity.

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Microbiome of the Gut: Four Major Phyla

• Firmicutes – gram positive organisms, including sporulating gram positive rods (ex: Staphylococcus, Micrococcus, Streptococcus and Lactobacillus)

• Bacteroidetes – three large classes of Gram-negative, non-spore forming, anaerobic or aerobic, rod-shaped bacteria (ex: Bacterioides)

• Actinobacteria – primarily gram positive bacteria (including those that are acid fast) (Ex: M. tuberculosis and Gardnerella)

• Proteobacteria – primarily gram negative rods (Ex: E coli, Salmonella)

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Shaping of Our Microbiome begins Before Conception

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• Controlled reconstitution of gut microbiome• Instill microbiota from different groups or pure cultures, feed

controlled diet

Gnotobiotic (germ-free) mice: Animal model to study microbiome

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Microbiome Can Modulate Obesity

No change in daily caloric intake, body fat increased by 60% in 2 weeks and developed insulin resistance

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Microbiome is altered in lean vs obese mice and humans

Ley et al. Nature. 2006Ley et al PNAS 2005

Humans on diets

Turnbaugh et al, Nature 2009Komaroff, JAMA, 2017

Mice

Lean humans: diverse microbiome, altered gene representation

Firmicutes generate more harvestable energy

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The Microbiome of the Gut• Established in early life – differs in infants born by C-section vs. vaginal birth.• In murine models, transfer of “obese” microbiome affects the growth

characteristics of the mouse for life• Drastically altered acutely by antibiotic administration• In farm animals (and mice), antibiotic exposure early in life promotes

microbiota associated with high coloric efficiency. • There is some evidence that early exposure to antibiotics affects humans the

same way.• After cessation of antibiotics, the antibiotic “footprint” remains; e.g., the

microbiome reverts toward but does not reach pre-antibiotic richness/diversity.

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The Gut Microbiome in HIV-1 Infection

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Metlu, et. al, Plos Pathogens 2013

Colonic Microbiome in HIV-Infected Persons

• 56 samples from HIV-1 infected persons and 65 samples from 22 healthy controls undergoing elective colonoscopy (primarily for cancer screening)

• Age and sex-matched

• HIV-1 infected population• Mean CD4 cell count: 425 cells/mm3• VL <75 IU/mL in 17/21 participants

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The Gut Microbiome is Less Diverse in HIV Infected Persons

Metlu, et. al. PLoS Pathogens 2014

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Gut Bacterial Populations Differ in HIV Infected and Uninfected Persons

Metlu, et. al. PLoS Pathogens 2014

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Certain Organisms were More Common in Healthy Individuals

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…and Others were more Common in the HIV-1 Infected Participants

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UPGMA Dendrogram based on Bray-Curtis Similarity

HIV Infected had moreCampylobacter, Escherechia and otherUnclassified Enterobacteriaciae,Fusobacteria, Prevotella, (and others)

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The Gut Microbiome and Host Defense

McKenney and Pamer, 2015

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The Promaltia Study: Pre- and Probiotics

Serrano-Villar, CID, 2018

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Promaltia Study: CD4 and CD8 Cell Counts vs. Time


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The Promaltia Study: Intermediary Biomarkers not Affected

• No differences in microbiome diversity at 48 weeks between treatment and placebo groups

• Some enrichment of unclassified bacteria from the Lachnospiraceae and Victivallaceae families and depletion of Blautia spp. in treatment group compared to placebo

• No differences in inflammatory markers between treatment and placebo groups


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The Vaginal Microbiome in HIV-1 Infection

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Stability of the Vaginal Microbiome over Time

Jespers, et. al., Sci Rep, 2017

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Increased Microbiome Diversity in Those Bacterial Vaginosis

Jespers, et. al., Sci Rep, 2017

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Bacterial Vaginosis and the Vaginal Microbiome

Minimal DiversityLactobacillus Dominated

Healthy State Bacterial Vaginosis

Increased DiversityGardnerella dominated

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The Healthy Vaginal Microbiome• Unlike in the gut, the healthy microbiome in the vagina is less diverse

and dominated by a single species: Lactobacilli• Lactobacilli are decreased in population with sexual intercourse (as

assessed by the presence of prostate specific antigen [PSA] in the sample.

• Lactobacilli are decreased in amenorrhoeic women while inflammatory mediators (IL-8, IL-12 and MIP-1b) are increased

• The presence of inflammatory mediators was also increased in the presence of PSA

of 39McClelland, et. al., Lancet ID, 2018

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HIV Acquisition Risk is Increased with Vaginal Dysbiosis

McClelland, et. al., Lancet ID, 2018

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HIV Acquisition is Increased with More Vaginal Bacterial Diversity


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Vaginal Microbiome and Risk of HIV Acquisition


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The Vaginal Microbiome and PrEP

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TDF PrEP in Women

Van Damme L et al. N Engl J Med 2012;367:411-422.

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Women “Fail” to Adhere

Koss et. al., AIDS Res Hum Retroviruses, 2017

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The Microbiome and HIV Infection

Klatt, et. al., Science 2017

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Vaginal Flora in Women Participating in CAPRISA Topical TDF Study


Community groups

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Influence of Vaginal Microbiome on TDF Efficacy


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Gardnerella vaginalis Degrades TDF


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Gardnerella vaginalis Metabolizes TDF to Adenine


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Depletion of TDF Prevents Accumulation of Intracellular Tenofovir diphosphate


of 39 Klatt CROI 2018Slide 27 of 36

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Not yet a “done deal”: The Partners Study

Heffron, et. al. Lancet HIV 2017

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PrEP Efficacy not Reduced in those with Bacterial Vaginosis

Heffron, et. al. Lancet HIV 2017

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The Human Microbiome: It is “Family”• Humans live in concert with an immense array of microbial organisms

from birth to death• The microbiome differs from body site to body site and from person to

person but is reasonably stable over time – unless it is disturbed by antibiotics

• Other environmental factors including food and those with whom we associate also have direct effects on the microbiome

• The microbiome influences gut metabolism, systemic immunity and susceptibility to disease

• The microbiome changes in health and disease – including HIV Infection• We are only now beginning to unravel carts and horses.

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Can we Alter the Microbiome?• Yes….but with the elegance of a meat cleaver.• Antibiotics are the most dramatic way we affect the human

microbiome• Usually for the worse, e.g., C. difficile, Salmonella infection

• Other approaches• Probiotics• Prebiotics• Fecal transplantation• Bacteriophage therapy

powerpoint presentation · ppt file · web view2018-06-05 · slide of 39. what has accounted ......

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