Discovering the Role of the Microbiome in Human Health through the Power of Metagenomics. Tanya Yatsunenko Second Genome
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1 Discovering the Role of the Microbiome in Human Health through the Power of Metagenomics Tanya Yatsunenko Second Genome
2 The microbiome is implicated in the biggest public health threats Ridaura et al, Science, 2013
3 Our view of the microbiome is evolving SANITIZER/
4 Incidence of Crohn s disease around the world
5 Global view on the gut microbiome USA 94 families: 312 people, 1mo-55 y/o Amerindians (Venezuela) 2 villages: 19 families: 98 people, 1mo 73 y/o Malawi 1 fecal sample per person 16S rrna 1.8 mln sequences/sample Shotgun sequencing of 110 microbiomes 150,000 sequences/sample 4 regions: 34 families: 114 people, 3 wks 35 y/o Yatsunenko et al, Nature, 2012
6 Analysis of microbial communities Composition 16S rrna gene surveys Functional potential (microbiome) Metagenomics
7 Analysis of composition of microbial communities (16S rrna) 4 biological samples
8 Comparison of microbial communities OR Taxon Gene Sample1 Sample2 Sample3 Sample4 A B C D E F Distance matrix 0 = min distance 1 = max distance Sample1 Sample2 Sample3 Sample4 Sample Sample Sample Sample4 0 Cluster microbiomes: Principal Coordinate Analysis Or Hierarchical Clustering OR UniFrac: Lozupone et al, 2005
9 USA microbiomes differ from Malawians and Amerindians at all sampled ages UniFrac PCoA of adults
10 What factors influence the microbiome? Environment Diet Genetics
11 Role of diet: mammals 60 phylogenetically diverse mammals Animals consuming similar diets have similar microbiomes Amino acid metabolism differentiates herbivorous vs carnivorous gut microbiomes UniFrac PCoA Ley et al, Science, 2008; Muegge et al, Science, 2011
12 Role of diet: humans 10 subjects Plant Animal Different from baseline Dramatic shifts on animal diet Genus Prevotella decreased Changes mirror differences Similar to baseline between herbivorous and carnivorous animals Increase in bile-tolerant microbes (Alistepes, Bilophila, Bacteroides) David et al, Nature, 2013
13 Analysis of microbiomes - metagenomics Genomic DNA or mrna Databases of sequenced genomes Gene Sample1 Sample2 Sample3 Sample4 A B C D E F
14 Functional annotation Example of pathway/genome database (BioCyc) >BTHE226 GJXV-2161 Na+-driven multidrug pump Bacteroides thetaiotaomicron VPI-5482 MADDKKIIFSMVGVSKAFQPNKNVLKDIYLSFFYGAKIGIIGLNGSGKSTLLKIIAGLEK SYQGEVVFSPGYSVGYLAQEPYLDDTKTVKEVVMEGVQPIVDALAEYEEINQKFGLPEYY EDQDKMDILFARQGELQDIIDATDAWNLDSKLERAMDALRCPPEDQPVVNLSGGERRRVA LCRLLLQKPDILLLDEPTNHLDAESIDWLEQHLQQYEGTVIAVTHDRYFLDHVAGWILEL >FP226 GJXV-1205 GTP cyclohydrolase Faecalibacterium prausnitzii M-65 MTGQKTPTALGTEKIGKLLMQYAIPAIIAMTASSLYNMVDSIFIGHGVGAMAISGLALTF PLMNLAAAFGSLVGVGAATLVSVKLGQKDYDTAQRVLGNVLVLNIIIGLAFTVLTLIFLD PILYFFGGSEATVGYARDYMVVILWGNVITHLYLGLNAVLRSAGHPQKAMYATIATVVIN >ASP232 GHWE-1493 orf Acidovorax sp.js42 MKKLVALAMLAASASPLWATTQSVTLSVPDMNCATCPITVKKALTKVSGVSKIDVNLDRR EAKVTFDDTKANVEVLTRATRNAGYPATVLGDAK >ASP232 GHWE-1158 orf Acidovorax sp.js42 MSVNHPIAFLCRLLTTAAFCCLVALGVTLARSTPWDANLVYSLTIGLVSWFTVDLGRMAL TRHSAIPWPRRPWGAVLIFAGTAMGFVSGSVVGHLYNGGALGDLAWLRGHEAVSTLVVTI AASASISFFFHSRGKARFLQARVAQVQRDAAEARLKLLETQLEPHMMFNTLANLRVLVAT DPPRAQEMLDHFIAYLRATLGASRAALHPLADEFARLQDYLALMAVRMGPRLDYTLELPE PSPDCRG FP226 Genome ID GJXV-1205 Gene ID GTP cyclohydrolase - Gene name Faecalibacterium prausnitzii M-65 Strain name
15 Functional annotation Query Sequence from Sample1: KDYDTAQRVLGNVLVLNIIIGLAFTVLTLIFLD >BTHE226 GJXV-2161 Na+-driven multidrug pump Bacteroides thetaiotaomicron VPI-5482 MADDKKIIFSMVGVSKAFQPNKNVLKDIYLSFFYGAKIGIIGLNGSGKSTLLKIIAGLEK SYQGEVVFSPGYSVGYLAQEPYLDDTKTVKEVVMEGVQPIVDALAEYEEINQKFGLPEYY EDQDKMDILFARQGELQDIIDATDAWNLDSKLERAMDALRCPPEDQPVVNLSGGERRRVA LCRLLLQKPDILLLDEPTNHLDAESIDWLEQHLQQYEGTVIAVTHDRYFLDHVAGWILEL >FP226 GJXV-1205 GTP cyclohydrolase Faecalibacterium prausnitzii M-65 MTGQKTPTALGTEKIGKLLMQYAIPAIIAMTASSLYNMVDSIFIGHGVGAMAISGLALTF PLMNLAAAFGSLVGVGAATLVSVKLGQKDYDTAQRVLGNVLVLNIIIGLAFTVLTLIFLD PILYFFGGSEATVGYARDYMVVILWGNVITHLYLGLNAVLRSAGHPQKAMYATIATVVIN >ASP232 GHWE-1493 orf Acidovorax sp.js42 MKKLVALAMLAASASPLWATTQSVTLSVPDMNCATCPITVKKALTKVSGVSKIDVNLDRR EAKVTFDDTKANVEVLTRATRNAGYPATVLGDAK 100% ID, Exact match to 2 nd sequence Add count to genes and genomes table Genes 1 2 GJXV-1205, GTP cyclohydrolase 1 0 GJXV-2161, Na+-driven multidrug pump 0 10 Genomes 1 2 Faecalibacterium prausnitzii M Acidovorax sp.js42 0 1
16 Functional annotation Genes -> Enzymes -> Pathways Genes 1 2 GJXV-1205, GTP cyclohydrolase 1 0 GJXV-2161, Na+-driven multidrug pump 0 10 Gene GJXV-1205 encodes an enzyme ENZRXNJXV-1763, which is part of the Lipopolysaccharide-Biosynthesis Pathway Enzymes 1 2 ENZRXNJXV ENZRXNJXV Pathways 1 2 NAGLIPASYN-PWY 1 0 PWY
17 Functional annotation Genes -> Enzymes -> Pathways and Strains 1 Query Sequence from Sample1: KDYDTAQRVLGNVLVLNIIIGLAFTVLTLIFLD Functional assignments Genes 1 2 GJXV-1205, GTP cyclohydrolase 1 0 GJXV-2161, Na+-driven multidrug pump 0 10 Bacterial strain assignments Strains 1 2 Faecalibacterium prausnitzii M Acidovorax sp.js Enzymes 1 2 ENZRXNJXV ENZRXNJXV Pathways 1 2 NAGLIPASYN-PWY 1 0 PWY
18 The function of most microbial genes is still not fully understood Escherichia coli K-12 Faecalibacterium prausnitzii Total # genes 4,273 3,553 Protein coding genes connected to MetaCyc Pathways 31% 16%
19 Differences between adult microbiomes could be related to diet USA Malawi Amerindians Amino acid metabolism Carbohydrate metabolism Vitamin metabolism Other functions USA microbiome enriched in: Catabolism of amino acids Catabolism of simple sugars Biosynthesis of vitamins Metabolism of bile salts
20 Amerindians Malawi Cassava Corn- nsyma Ants!
21 Role of environment USA year old twins Fathers are as similar to their children as mothers in adulthood Shared features of microbial communities among household members extends to husband and wife True for skin and oral microbiota Dog ownership increases the exchange of microbes Yatsunenko et al, Nature, 2012; Song et al, elife, 2013
22 Role of host genetics: twins Malawi 0-3 year old USA 0-1 year old Identical twins are as similar to each other as fraternal twins in all sampled countries and ages USA year old More similar Less similar Yatsunenko et al, Nature, 2012
23 Gut microbiota evolves toward adult-like in the first 3 years of life Less similar to adults 0.96 More similar to adults UniFrac Distance Average distance from Malawian child to all unrelated adults from Malawi Malawi Amerindians USA Age, years Yatsunenko et al, Nature, 2012
24 GTP Formamidopyrimidine nucleoside triphosphate 2,5-Diaminopyrimidine nucleoside triphosphate ,5-Diamino-6-(5 -triphosphoryl- 3,4 -trihydroxy-2 -oxopentyl)- amino-4-oxopyrimidine Representation of genes involved in folate biosynthesis is higher in infant microbiomes; those involved in folate metabolism are higher in adult microbiomes 2-Amino-4-hydroxy- 6-(erythro-1,2,3-trihydroxypropyl)- dihydropteridine triphosphate Dihydroneopterin Dihydroneopterin phosphate De novo biosynthesis 4-Amino- 4-deoxychorismate 4-aminobenzoate Chorismate ,8-Dihydropteroate Amino-4-hydroxy- 6-hydromethyl- 7,8-dihydropteridine 2-Amino-4-hydroxy- 6-hydromethyl- 7,8-dihydropteridine-P ? Higher dietary intake of folate in adults? Metabolism of tetrahydrofolate 7,8-dihydrofolate (DHF) 5-Formyl-THF Folate ,6,7,8-tetrahydrofolate (THF) Formyl-THF ,10-Methenyl-THF ,10-Methylene- THF EC Breast-fed babies THF-L-glutamate Formimino-THF Methyl- THF EC Adults THF-L-polyglutamate L-methionine B12 L-Homocysteine
25 5-Aminolevulinate Porphobilinogen Hydroxymethylbilane Uroporphyrinogen III Heme, Chlorophyll synthesis Glutamate-1- semialdehyde (Anaerobic pathway) Sirohydrochlorin Siroheme Precorrin Co-Sirohydrochlorin Co-Factor 3 Co-Precorrin 3 Co-Precorrin 4 Co-Precorrin 5A Co-Precorrin 6B Co-Precorrin Co-Precorrin 8X (Aerobic pathway) Precorrin 3A... Precorrin 3B Precorrin 4 Precorrin Precorrin 6B Precorrin 8X Biosynthesis of B12 is higher in adults Correlates with published reports indicating that blood levels of folate decrease and vitamin B12 increase as babies age Glycine, threonine metabolism (R)-1-Aminopropan-2-ol Cobinamide Adenosyl cobinamide (R)-1-Aminopropan-2-yl L-Threonine phosphate phosphate Adenosyl cobinamide phosphate L-Threonine Dimethyl benzimidazole α Ribazole-5 -P α Ribazole Adenosine-GDPcobinamide Cobyrinate Cob(II)yrinate a,c diamide Cob(I)yrinate a,c diamide Hydrogenobyrinate a,c diamide Adenosyl cobyrinate a,c diamide Adenosyl cobyrinate hexaamide Microbes that are abundant in babies do not have genes encoding B12 biosynthesis! Higher in the microbiomes of adults Vitamin B12 coenzyme Vitamin B12s
26 Hypothesis: B12 microbiome Intrinsic Factor secretion increases with age Yuriko et al, J of Ped Gastro, 2002
27 Our view of the microbiome is evolving SANITIZER/
28 Questions?
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