Scalable metabolic reconstruction for metagenomic data and the human microbiome
1 / 26

Scalable metabolic reconstruction for metagenomic data and the human microbiome - PowerPoint PPT Presentation

  • Uploaded on

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,

I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
Download Presentation

PowerPoint Slideshow about 'Scalable metabolic reconstruction for metagenomic data and the human microbiome' - mrinal

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.

- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
Scalable metabolic reconstruction for metagenomic data and the human microbiome

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
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
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
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
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 reconstruction1
HMP: Metabolic reconstruction

Pathway coverage

Pathway abundance

Humann validating gene and pathway abundances on synthetic data
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.) complexity Even 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
Functional modules in 741 HMP samples

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

  • Zero microbes are core among individuals

  • 19 (of ~220) pathways are present in every sample

  • 53 pathways are present in 90%+ samples








← Samples →


← Pathways→


  • Only 31 (of 1,110) pathways are present/absent from exactly one body site

  • 263 pathways are differentially abundant in exactly one body site

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

Pathway coverage

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

Hmp penetrance of species otus across the population
HMP population?: Penetrance of species (OTUs)across the population

Data from Pat Schloss

Hmp penetrance of genera phylotypes across the population
HMP population?: Penetrance of genera (phylotypes)across the population

Data from Pat Schloss

Hmp penetrance of pathways across the population
HMP population?: 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 dictated primarily 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 these functions are implemented

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

Population summary statistics population biology
Population summary statistics population? 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 class comparison and explanation
LEfSe population?: Metagenomic classcomparison and explanation


LDA +Effect Size

Nicola Segata

Lefse evaluation on synthetic data
LEfSe population?: Evaluation on synthetic data

Their FP rate

Our FP rate

Microbes characteristic of the oral and gut microbiota
Microbes characteristic of the population?oral and gut microbiota

Aerobic microaerobic and anaerobic communities
Aerobic, population?microaerobic and anaerobic communities

  • High oxygen: skin, nasal

  • Mid oxygen: vaginal, oral

  • Low oxygen: gut

Lefse the truc murine colitis microbiota
LEfSe population?: The TRUC murine colitis microbiota

With Wendy Garrett

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

Thanks! population?

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 Birren Mark Daly

Doyle Ward Eric Alm

Ashlee Earl Lisa Cosimi

Levi Waldron


Interested? We’re recruiting graduate students and postdocs!