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Conflicts of interest: none
ILSI/ILSI North America Annual Meeting 24 January 2012, Phoenix, Arizona
Studying the human microbiome using high‐throughput meta‐omics data
Marie Joossens for
Jeroen Raes
VIB – VUB
Belgium
jeroen.raes@vib‐vub.be
Last 7y: developing approaches to study microbial population variation and its functional impact from meta‐omics data
Raes et al., Genome Biology 2007
Foerstner et al. EMBO reports 2005
Von Mering et al., Science 2007
Harrington et al., PNAS 2007
Raes et al., Curr Opin Microbiol 2007
Gianoulis*, Raes* PNAS 2008
Raes et al., MSB 2011
Data handling is tough, interpretation is difficult: many technical and biological factors influence the end result
Raes and Bork, Nat Rev Microbiol, 2008
MareNostrum supercomputer Barcelona
Comparative metagenomics as a tool to compare microbial communities as a whole
What’s the functional difference between sample A and B?
What’s the phylogenetic difference between sample A and B?
Comparing total gene pool of diverse environments
Same environments
(human intestine), different hosts
e.g. patient vs. reference
Same host,
different timepoints
MetaHIT – European partners in the international human microbiome consortium
Metagenomics of the human intestinal tract
• Creation of a reference gut gene and genome pool
• Determining metagenomic variation within the European population, investigation of determining factors
• Studying microbiome variation in disease (Inflammatory Bowel Disease, Obesity)
• Functional follow‐up studies of disease –
related genes and species
MetaHIT partners
CBS‐DTU, Denmark
EMBL, Germany (now +VIB/VUB)
HUVH, Spain
IEO, Italy
INRA, France
SDU, Denmark
WU, The Netherlands
Sanger centre, UK
Genoscope, France
Bejing Genome Centre, China
Danone research
Novo Nordisk, Denmark
UCB Pharma, Spain
124 individuals
3.3 mio genes
Ultra‐deep Illumina sequencing (BGI, Shenzen) allows almost complete coverage
580 Gbases
(~200 human genomes!)
First ultra‐short read
metagenome
+unknown genes (grand total: ~19.000 gene families)
+known genes with unknown functions
Known functions
Qin, Li, Raes et al. Nature 2010
Substantial overlap in gut microbiota composition between individuals
• 1/3rd of species present in almost all individuals
• 1500 species total
• 160 species/ individual
Gut gene core (minimal metagenome ‐ present in all individuals) +‐ 6000 gene families ‐ housekeeping genes for general bacterial survival, but also specific functionalities rare in currently sequenced genomes (+unknowns!)
Qin, Li, Raes et al. Nature 2010
What determines the microbiota composition? Comparing nationalities shows very little influence of ethnicity
Quantitative species composition comparison based on phylomarkers
(40 universal single copy genes)
Blue: danish
Red: french
Orange: italian
Yellow: japanese
Each individuals’ gut microbiota can be classified in a limited number of cross‐national ‘enterotypes’
85 Illumina danish metagenomes
33 international sanger metagenomes
155 US 16S rRNA pyrosequencing
Arumugam*, Raes* et al. Nature 2011
Enterotypes are stable constellations of co‐occurring species, with 3 main drivers
“ecosystem optima”
What do they mean?
‐No correlation to measured host properties (age, sex, BMI, nationality)
‐Functional composition (e.g. vitamin production pathways, metabolism)
‐Many unknowns or unclear trends,
maybe factors we haven’t taken into
account yet?
Confirmation: Morotomi et al Biol Pharm Bull 2011
Clustering based on functional content
Long term dietary patterns?
Short term dietary intervention ‐> no effect
Wu et al Science 2011
Rare biomarkers correlate with host properties, proof of principle for future disease studies
Method pool see Gianoulis*, Raes* et al. PNAS 2009 & Raes et al Mol Sys Biol 2010; Arumugam*, Raes* et al. Nature 2011
Gut‐specific pathway modules:
a powerful tool for gut meta‐omics data annotation, interpretation and metabolic modeling
•Advantage 1: Interpretation improvement
“Butyrate metabolism is down and H2S production + mucus degradation is up” vs. long lists of genes, species and orthologous groups
•Advantage 2: Sensitivity & Specificity increase
•Less multiple testing issues
•Pathways as they occur in gut, not as they are in KEGG
“You see what you need to see”
Extending “cellular level”‐systems biology to whole ecosystems (“eco‐systems biology”)
metagenomics, metatranscriptomics,
meta‐metabolomics
Computational integration will be main challenge
Raes and Bork, Nat Rev Microbiol 2008
Metagenomics and ‐transcriptomics indicate that small
intestine microbiota is tuned for fast carbohydrate uptake
Zoetendal*, Raes* et al., ISME 2012
Eco‐systems biology of the human intestinal microbiota in Crohn’s disease
NIH HMP concordant/discordant twin study Janet Jansson (Berkeley), Claire Fraser (U.Maryland), Robert Hettich (Oak Ridge National Lab)
Metaproteomics
Metagenomics
Ecosystem network reconstruction and its variation in disease Meta‐metabolomics
454‐tag phylotyping
Wrap up: Gut microbiota for personalized medicine
•Microbiota is characterizable using meta‐omics combined with dedicated computational tools
•Microbiota is linked to disease, interpretation through specific metabolic models
•Specific diagnostic & prognostic markers for disease are possible
•Enterotype‐based diagnosis (“bad” enterotypes?)
•Enterotype‐specific drug treatment (different metabolism of chemical compounds)
Your genome matters ‐ your microbiome even more!
Functional diversity of the human gut microbiome
Plateau is not reached yet – new cohorts add more (unknown) gene families
+unknown genes +known genes with unknown functions
known functions
Spanish + Danish cohort, 124 individuals
Data from Qin, Li, Raes et al Nature 2010
Same, + 73 individuals from Chinese (diabetes) cohort
(collab w. Junjie Qin, Wang Jun, BGI)
Acknowledgments
Raes lab @ VIB, Brussels
The MetaHIT consortium
Falk Hildebrand
EMBL
Dusko Ehrlich
Youssef Darzi
Peer Bork
Wang Jun/Junjie Qin (BGI)
Gwen Falony
Mani Arumugam
Joel Dore (INRA)
Gipsi Lima‐Mendez …and many others
…and many others
Karoline Faust
Shujiro Okuda
Ugent
HMP
Anh Nguyen
Peter Vandenabeele
Curtis Huttenhower (Harvard)
Roberto Garcia
Wim Declerq
Dirk Gevers (Broad)
Sara Vieira‐Silva
Jacques Izard (Forsyth)
Samuel Chaffron
Universiteit Wageningen
Marie Joossens
Erwin Zoetendal
Michiel Kleerebezem
Berkeley/U. Maryland/Oak Ridge
Willem De Vos
Janet Jansson
Claire Fraser‐Ligget
Robert Hettich
Thanks for your attention
Positions available: [email protected]