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Scalable metabolic reconstruction for metagenomic data and the human microbiome. Sahar Abubucker , Nicola Segata , Johannes Goll , Alyxandria Schubert, Beltran Rodriguez-Mueller, Jeremy Zucker , the Human Microbiome Project Metabolic Reconstruction team, the Human Microbiome Consortium,

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Scalable metabolic reconstruction for metagenomic data and the human microbiome

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Scalable metabolic reconstructionfor metagenomic dataand the human microbiome

SaharAbubucker, Nicola Segata, Johannes Goll,Alyxandria Schubert, Beltran Rodriguez-Mueller, Jeremy Zucker,

the Human Microbiome Project Metabolic Reconstruction team,the Human Microbiome Consortium,

Patrick D. Schloss, Dirk Gevers, MakedonkaMitreva,Curtis Huttenhower


Harvard School of Public Health

Department of Biostatistics

What’s metagenomics?

Total collection of microorganisms within a community

Also microbial communityormicrobiota

Total genomic potential of a microbial community

Study of uncultured microorganisms from the environment, which can include humans or other living hosts

Total biomolecular repertoire of a microbial community

The Human Microbiome Project for a normal population

Multifaceted analyses

Multifaceted data

300 People/15(18) Body Sites

  • >12,000 samples

  • >50M 16S seqs.

  • 4.6Tbp uniquemetagenomicsequence

  • >1,900 referencegenomes

  • Full clinicalmetadata

  • Human population

  • Microbial population

  • Novel organisms

  • Biotypes

  • Viruses

  • Metabolism

2 clin. centers, 4 seq. centers, data generation,technology development, computational tools, ethics…

15+ Demonstration Projects for microbial communities in disease




  • Obesity

  • Crohn’s disease

  • Ulcerative colitis

  • Autoimmunity

  • Cancer

  • Necrotizing enterocolitis

  • Psoriasis

  • Acne

  • Atopic dermatitis

  • Bacterialvaginosis

  • STDs

  • Reproductive health

All include additional subjects and technology development

What to do with your metagenome?

Reservoir of gene and protein functional information

Comprehensive snapshot of microbial ecology and evolution

Who’s there?

What are they doing?

What do functional genomic data tell us about microbiomes?

What can our microbiomes tell us about us?


Public health tool monitoring population health and interactions

Diagnostic or prognostic biomarker for host disease

Metabolic/Functional Reconstruction: The Goal





Biological story?

Independent sample

Batch effects?




Taxon abundances

Enzyme family abundances

Pathway abundances


Niches &Phylogeny

Test forcorrelates


Featureselectionp >> n


HMP: Metabolic reconstruction

Functional seq.



300 subjects

1-3 visits/subject

~6 body sites/visit

10-200M reads/sample

100bp reads


HUMAnN:HMP UnifiedMetabolic AnalysisNetwork



BLAST → Genes

Genes → Pathways

MinPath(Ye 2009)

WGS reads


Taxonomic limitation

Rem. paths in taxa < ave.





Distinguish zero/low(Rodriguez-Mueller in review)

Gap filling

c(g) = max( c(g), median )

HMP: Metabolic reconstruction

Pathway coverage

Pathway abundance

HUMAnN: Validating gene and pathwayabundances on synthetic data

Individual gene families

  • Validated on individual gene families, module coverage, and abundance

  • 4 synthetic communities:Low (20 org.) and high (100 org.) complexityEven and lognormal abundances

  • Few false negatives: short genes (<100bp),taxonomically rare pathways

  • Few false positives: large andmulticopy(not many in bacteria)


Functional modules in 741 HMP samples

  • Zero microbes (of ~1,000)are core among body sites

  • Zero microbes are coreamong individuals

  • 19 (of ~220) pathways arepresent in every sample

  • 53 pathways are present in90%+ samples








← Samples →


← Pathways→


  • Only 31 (of 1,110) pathwaysare present/absent fromexactly one body site

  • 263 pathways aredifferentially abundant inexactly one body site

A portrait of the human microbiome:Who’s there?

With Jacques Izard, Susan Haake, Katherine Lemon

A portrait of the human microbiome:What are they doing?

Pathway coverage

HMP: How do microbes vary within each body site across the population?

HMP: How do body sites compare between individuals across the population?

HMP: Penetrance of species (OTUs)across the population

Data from Pat Schloss

HMP: Penetrance of genera (phylotypes)across the population

Data from Pat Schloss

HMP: Penetrance of pathwaysacross the population

KEGG Metabolic modules

M00001: Glycolysis (Embden-Meyerhof)

M00002: Glycolysis, core module

M00003: Gluconeogenesis

M00004: Pentose phosphate cycle

M00007: Pentose phosphate (non-oxidative)

M00049: Adenine biosynthesis

M00050: Guanine biosynthesis

M00052: Pyrimidine biosynthesis

M00053: Pyrimidinedeoxyribonuleotide biosynthesis

M00120: Coenzyme A biosynthesis

M00126: Tetrahydrofolate biosynthesis

M00157: F-type ATPase, bacteria

M00164: ATP synthase

M00178: Ribosome, bacteria

M00183: RNA polymerase, bacteria

M00260: DNA polymerase III complex, bacteria

M00335: Sec (secretion) system

M00359: Aminoacyl-tRNA biosynthesis

M00360: Aminoacyl-tRNA biosynthesis, prokaryotes

M00362: Nucleotide sugar biosynthesis, prokaryotes

M00006: Pentose phosphate (oxidative)

M00051: Uridinemonophosphate biosynthesis

M00125: Riboflavin biosynthesis

M00008: Entner-Doudoroff pathway

M00239: Peptides/nickel transport system

M00018: Threonine biosynthesis

M00168: CAM (Crassulacean acid metabolism), dark

M00167: Reductive pentose phosphate cycle

  • Human microbiome functional structure dictatedprimarily by microbial niche, not host (in health)

  • Huge variation among hosts in who’s there;small variation in what they’re doing

  • Note: definitely variation in how thesefunctions are implemented

  • Does not yet speak in detail to hostenvironment (diet!), genetics, or disease

Population summary statistics population biology

← Individuals →

Posterior fornix, ref. genomes

Lactobacillus iners

Lactobacillus crispatus


Lactobacillus jensenii

Lactobacillus gasseri

← Species →

Posterior fornix, functional modules

Essential amino acids

Basic biology, sugar transport

← Pathways →

Urea cycle, amines, aromatic AAs

LEfSe: Metagenomic classcomparison and explanation


LDA +Effect Size

Nicola Segata

LEfSe: Evaluation on synthetic data

Their FP rate

Our FP rate

Microbes characteristic of theoral and gut microbiota

Aerobic, microaerobic and anaerobic communities

  • High oxygen:skin, nasal

  • Mid oxygen:vaginal, oral

  • Low oxygen:gut

LEfSe: The TRUC murine colitis microbiota

With Wendy Garrett

Microbial biomolecular function and biomarkers in the human microbiome: the story so far?

  • Who’s there changes

    • What they’re doing doesn’t (as much)

    • How they’re doing it does

  • The data so far only scratch the surface

    • Only 1/3 to 2/3 of the reads/sample map to cataloged gene families

    • Only 1/3 to 2/3 of these gene families have cataloged functions

    • Very much in line with MetaHIT study of gut microbiota

    • Job security!

  • Looking forward to functional reconstruction…

    • In environmental communities

    • With respect to host environment + genetics

    • With respect to host disease


Human Microbiome Project

George Weinstock

Jennifer Wortman

Owen White


Erica Sodergren

Mihai Pop


Jane Peterson

Lita Proctor


Yuzhen Ye

Beltran Rodriguez-Mueller

Jeremy Zucker



Brandi Cantarel

Maria Rivera

Barbara Methe

Bill Klimke

Daniel Haft

Dirk Gevers

Jacques Izard

Nicola Segata


Ramnik Xavier

HMP Metabolic Reconstruction

Wendy Garrett

Bruce BirrenMark Daly

Doyle WardEric Alm

Ashlee EarlLisa Cosimi

Levi Waldron


Interested? We’re recruiting graduate students and postdocs!

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