Human Microbiome Project

Transcription

1 Human Microbiome Project

2 Definitions Microbiome: the collective genomes of the community of organisms that share our space Metagenome: culture independent study of genomes of many organisms in order to understand microbial communities as intact systems, usually involving direct DNA sequencing from natural environment Metabolome: complete set of small molecule metabolites in a biological sample Transcriptome, Proteome, other omics

3 16s rrna 16S rrna gene present in all Bacteria and Archaea Gene contains highly conserved and more variable regions amplify 16S rrna genes using primers directed at conserved regions but flanking variable regions align gene sequences, resolve phylogenetic relationships at different depths Most 16S rrna sequences come from previously undescribed microbes taxa operationally defined based on sequence similarity: e.g., members of a species share 97% 16S rrna sequence identity Fierer et al., PNAS 105:17994 (2008)

4 16s RNA

5 Analysis of diversity Alpha diversity (how many types of sequences in a sample) or Beta diversity (how different types are distributed among samples) Qualitative or quantitative Phylogenetic or taxon-based

6 Humans as a supra-organism Our microbial census exceeds the total number of our own human cells by ~10 fold Our largest collection of microbes resides in the intestine (~ trillion organisms) The aggregate genomes of these species = microbiome The microbiome is an integral part of our genetic landscape (our human meta-genome ) [Jeffrey Gordon]

7 Microbial composition at different body sites in healthy humans [Spor, 2011]

8 Microbiota of the hands Surprising degree of diversity >150 species level phylotypes/palm; 4742 unique phylotypes observed Pronounced intra- and interpersonal variation Hands from same individual share only 17% of species-level phylotypes Women have higher diversity than men Community composition significantly affected by handedness, time after handwashing Study illustrates challenges inherent in defining what constitutes a healthy bacterial community [Fierer, PNAS, 2008]

9 Intestinal microbiota 100 trillion per human >1,000 species 99.9% anaerobic 1.5 Kg biomass Metabolic organ equal to liver Contributes 10% of caloric intake to humans Largest mass of microbial antigens and adjuvants encountered by the host Epithelial turnover, maturation, integrity Development of the mucosal and systemic immune system Development of enteric nervous system Development of gut vasculature Provision of energy, metabolites, vitamins

10 Beneficial effects of the microbiota Vitamin production Food degradation Colonization resistance Terminal differentiation of mucosa Education of innate immune defense Epithelial homeostasis Energy harvesting

11 Gut microbiome 10 of 70 described divisions of bacteria, plus a few archae.

12 Bacteroides Gram negative, non spore forming Anaerobic Rod shaped Multiple operons for degrading complex carbohydrates Bacteroides thetaiotaomicron- genome 40% unknown function

13 Firmicutes Gram positive, low-g & C group Anaerobic; cocci and bacilli; many sporulate >270 genera Bacilli, Lactobacilli, Clostridia, Mollicutes Bacillus subtilis Genome: 50% unknown function A4 Lachnospiracea Genome: 80% unknown function

14 Firmicute; A4 Lachnospiracea

15 Firmicute: A4 Lachnospiracea genome 6853 genes

16 Proteobacteria Gram negative Facultative or obligate anaerobes Six classes: alpha, beta, gamma, delta, epsilon, zeta Pathogens include Salmonella, Vibrio, Shigella, Helicobacter, some E. coli E. coli Genome: 50% unknown function

17 Actinobacteria Gram positive Common in soil and freshwater Notables: Bifidobacteria, actinomycetes (Streptomyces) Bifidobacteria infantis (Align Probiotic)

18 Verrucomicrobia Common in environment In gut a single genus and species, Akkermansia mucinophila Influences calorie harvesting Deficient in obesity and DM type 2; feeding it reversed high fat diet induced metabolic syndrome [Everard, PNAS, 2013]

19 Microbiota Fingerprint [O Doherty, The Scientist, 2012]

20 Different species assemblages lead to similar functional profiles in the gut 6 MZ twin pairs and their mothers

21 Enterotypes of the human gut microbiome [Arumugam, Nature, 2011]

22 Changes in the microbiota with age [Palmer, Plos Biol 2007]

23 Panorganismal Gut Microbiome- Host Metabolic Crosstalk [Martin, J Proteome Res, 2009]

24 The gut-associated lymphoid tissue establishes perinatal host-microbiota mutualism in the intestine. [Maynard, Nature, 2012]

25 How do host cells know the microbiota are there? Toll like receptors NOD receptors Arylhydrocarbon receptor (AHR) G protein coupled receptors fatty acids GPR43 acetate, proprionate GPR109a- butyrate Nuclear receptors Neurotransmitter receptors

26 Our Microbiome May Be Looking Out For Itself Diet selectively alters the microbiota Microbes can manipulate host behavior Microbes can alter mood that changes feeding behavior Microbes can influence host via neurohormones Microbes can influence host via vagus signaling [Alcock, Bioessays, 2014] [Carl Zimmer, New York Times, Aug 14, 2014]

27 Layers of Response to the intestinal microbiota [Saleh & Elson, Immunity, 2011]

28 ILC3 stimulates fucosylation of IEC and protects against salmonella infection [Goto, Science, 2014]

29 [Alexander, Immunol Rev, 2014] T effector : Treg balance in the gut IgA Flagellated bacteria Nonflagellated bacteria TLR and its ligand SFB Clostridia XIVa IEC IEL M cell SAA SCFAs T effector cells SFB SAA TLR9 signals- microbial DNA TLR5 signaling Teff T cell Treg Regulatory T cells Clostridia cluster XIVa Increased TGF-β SCFAs B.Fragilis (PSA)

30 Dysbiosis and Disease Antibiotics [Arrieta and Finlay Frontiers Immunol 2012]

31 Microbiome and Disease [Kinross, Genome Med, 2011]

32 [Flint, Nature,2012] Low dose antibiotics early in life results in adiposity

33 Gut microbiota in infants prior to onset of type 1 diabetes [Kostic, Cell Host Microbe, 2015]

34 Xenobiotics shape the active gut microbiome [Maurice, Cell, 2013]

35 Components of the Virome and Their Relationship to the Genotype/Phenotype Relationship [Virgin, Cell, 2015]

36 Virome in IBD [Norman, Cell, 2015]

37 Virome in IBD The enteric virome is abnormal in multiple inflammatory bowel disease patient cohorts The enteric virome richness increases in Crohn s disease and ulcerative colitis Decreases in bacterial diversity and richness in IBD do not explain virome changes Virome changes in Crohn s disease and ulcerative colitis are disease specific

38 The gut mycobiome [Iliev, Science, 2012]

39 Response to the gut mycobiome [Mukherjee, Nat Rev Gastro Hep, 2015]

40 it is now becoming crucial for immunologists to consider the effects of the gut microbiota on every animal experiment [Gill & Finlay, Nat Rev Immunol, 2012]