Going With Your Gut: The Microbiome and You

Transcription

1 Going With Your Gut: The Microbiome and You Robert T. Schooley, MD Professor of Medicine University of California San Diego San Diego, California 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 Slide 3 of 39 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 Slide 4 of 39 Lederberg and McCray, Scientist, 2001

2 Slide 5 of 39 What has Accounted for the Explosion of Knowledge about the Microbiome? We could only identify what we could grow Metagenomics 16s RNA Technical advance: PCR-based 16S rrna gene sequencing 16S rrna most highly conserved bacterial gene But conserved and variable regions within gene Universal primers C V C Data analysis Extract DNA Amplify 16S rrna genes Sequence rrna amplicon Bioinformatics: community profile Slide 6 of 39 Technical advance: Inexpensive high-throughput shot-gun sequencing Deep sequencing/next generation sequencing Cost has decreased dramatically Number and length of reads improved Sequence communities or single cell Bioinformatics Massive and cumulative data basis allow analysis and cataloguing of sequences Log scale! Slide 7 of 39

3 Slide 8 of 39 Metagenomics Metagenomics has improved how we classify microorganisms Slide 9 of 39 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 Slide 10 of 39

4 Slide 11 of 39 NIH Human Microbiome Project How many microbes on our body, spatiotemporal 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 Methods Slide 12 of healthy subjects 15 or 18 body sites >11,000 primary specimens 1,900 reference strains Proctor, Cell Host Microbe (2011) 10, 287 The Microbiome of the Skin Slide 13 of 39 Grice and Segre, Nat Rev Microbiol, 2011

5 Slide 14 of 39 Organizational Taxonomic Unit Human Microbiome Consortium, Nature, 2013 The Microbiome of the Skin: A Close Up Slide 15 of 39 Grice and Segre, Nat Rev Microbiol, 2011 Microbial Diversity Within and Between Individuals Slide 16 of 39

6 Slide 17 of 39 Intrapersonal variation > interpersonal variation Class Shaping of Our Microbiome begins Before Conception Slide 18 of 39 Gnotobiotic (germ-free) mice: Animal model to study microbiome Controlled reconstitution of gut microbiome Instill microbiota from different groups or pure cultures, feed controlled diet Slide 19 of 39

7 Slide 20 of 39 Microbiome can modulate obesity No change in daily caloric intake, body fat increased by 60% in 2 weeks and developed insulin resistance Microbiome is altered in lean vs obese mice and humans Firmicutes generate more harvestable energy Humans on diets Mice Lean humans: diverse microbiome, altered gene representation Slide 21 of 39 Ley et al. Nature Ley et al PNAS 2005 Turnbaugh et al, Nature 2009 Komaroff, JAMA, 2017 The Gut Microbiome and Host Defense Slide 22 of 39 McKenney and Pamer, 2015

8 Slide 23 of 39 HIV and the Microbiome Changes in the Microbiome in Association with HIV Infection The Vaginal Microbiome and Risk of HIV Acquisition The Vaginal Microbiome and PrEP The Gut Microbiome is Less Diverse in HIV Infected Persons Slide 24 of 39 Metlu, et. al. PLoS Pathogens 2014 Gut Bacterial Populations Differ in HIV Infected and Un-infected Persons Slide 25 of 39 Metlu, et. al. PLoS Pathogens 2014

9 Slide 26 of 39 HIV Transmission and the Microbiome: A Meta-analysis McClelland, et. al., Lancet ID, 2018 Vaginal Microbiome and Risk of HIV Acquisition Slide 27 of 39 McClelland, et. al., Lancet ID, 2018 The Vaginal Microbiome and PrEP Slide 28 of 39

10 Slide 29 of 39 TDF PrEP in Women Van Damme L et al. N Engl J Med 2012;367: Women Fail to Adhere Slide 30 of 39 Koss et. al., AIDS Res Hum Retroviruses, 2017 The Microbiome and HIV Infection Slide 31 of 39 Klatt, et. al., Science 2017

11 Slide 32 of 39 Bacterial Vaginosis and the Vaginal Microbiome Healthy State Bacterial Vaginosis Minimal Diversity Lactobacillus Dominated Increased Diversity Gardnerella dominated Vaginal Flora in Women Participating in CAPRISA Topical TDF Study Community groups Slide 33 of 39 Klatt, et. al., Science 2017 Influence of Vaginal Microbiome on TDF Efficacy Slide 34 of 39 Klatt, et. al., Science 2017

12 Slide 35 of 39 Gardnerella vaginalis Degrades TDF Klatt, et. al., Science 2017 Gardnerella vaginalis Metabolizes TDF to Adenine Slide 36 of 39 Klatt, et. al., Science 2017 Depletion of TDF Prevents Accumulation of Intracellular Tenofovir diphosphate Slide 37 of 39 Klatt, et. al., Science 2017

13 Slide 38 of 39 The Human Microbiome: It Takes a 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 Environmental factors including food and antibiotics have profound 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 Stay tuned there is a lot to learn Question-and-Answer Slide 39 of 39