Jeffrey GordonCenter for Genome SciencesWashington University, St. Louis, MO jgordon@wustl.edu

The human microbiome project (HMP): The human microbiome project (HMP): extending our view of ourselvesextending our view of ourselves

MarsMarsSpirit rover: sol 008

Extended view of ourselves as a lifeform

• We are composite of species: 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 (~10-100 trillion organisms)

• The aggregate genomes of these gut species (microbiome)may contain >100 fold more genes than our ‘own’ genome

• The microbiome is an integral part of our genetic landscape (‘human metagenome’) and of our genetic evolution

HumanMicrobiome

Project

HMP

Our Human Microbiome: Some Questions to Ponder

• Do we all share an identifiable core microbiota and ‘microbiome’?

• Should differences in our microbiome be viewed, along with our immune and nervous systems, as features of our biology that are profoundly affected by both our human genotypes and by our individual ‘environmental’ exposures?

How is our microbiome evolving (within and between individuals) over varying time scales as

a function of our changing diets, lifestyle, and biosphere?

HumanMicrobiome

Project

HMP

• What affects the diversity of our microbiome: how does diversity impact the robustness of the community and host responses to various physiologic or pathophysiologic states?

• How can we use this knowledge to intentionally manipulate our microbiota to optimize its performance in the context of an individual’s physiology, or the physiology of a population of individuals?

HumanMicrobiome

Project

HMP

Whad’ya Know?

GUT COMMUNITY: 16S rRNA sequence-based studies of the adult

human distal gut microbiota

Eckburg et al., (11,831 sequences); Ley et al, (n=18,348)

Firmicutes Bacteroidetes

Proteobacteria Green Non Sulfur

Planctomycetes Spirochaetes

WS6 Verrucomicrobium

OD1 Cyanobacteria

KSB1_NC5 OP10

GN3 OP5

GN1

OP11 GN4

GN5 GN9

GN10 WS1

GN2 Deinococcus-Thermus

GN7 Haloanaerobiales

GN6 GN11

BRC1 OP8

OS-K GN12

GN13 GN14

Actinobacteria CD16

WS3 GN8

CD13 CD14

CD2 Lentispaerae_CV

OP9 SB1_ZB1

TM6 Unclassified (singles)

Fusobacteria

Microbial mat: 1595 sequences44 divisions

ProteobacteriaActinobacteriaFusobacteriaVerrucomicrobiaCyanobacteriaVadinBE97SpirochaeatesSynergistes

Firmicutes

Bactero

idetes

10 of 70 described divisions of BacteriaMethanobrevibacter smithii(Methanosphaera stadtmanae)

Synergistes

OBESITY: Example of an association between DIVISION-WIDE alterations in gut ecology and host physiology

12 obese adult humansLean controls

FAT-R or CARB-R low calorie diets

% o

f to

tal se

qu

en

ces

HumanMicrobiome

Project

HMP

Microbial community transplant experiments

Measure total body fat content before and after 14-day colonization

HumanMicrobiome

Project

HMP

Some resources are available for sampling

• National Health and Nutrition Examination Survey (NHANES):

1. Estimate the number and percent of persons in the U.S. population and designated subgroups with selected diseases and risk factors,

2. Monitor trends in the prevalence, awareness, treatment and control of selected diseases,

3. Monitor trends in risk behaviors and environmental exposures,

4. Analyze risk factors for selected diseases,

5. Study the relationship between diet, nutrition, and health,

6. Explore emerging public health issues and new technologies,

7. Establish a national probability sample of genetic material for future genetic research,

8. Establish and maintain a national probability sample of baseline information on health and nutritional status.

HumanMicrobiome

Project

HMP

HMP: Some of the Grand Challenges

HumanMicrobiome

Project

HMP

• How can we relate microbial community structure and function at different locales (habitats) on the human body to health and to disease? (measuring similarities and differences in these complex multivariate datasets)

• How should we sample surface-associated communities?

• How many healthy individuals do we need to sample to cover most of the diversity in the human microbiome, both within and between individuals?

• How can we exploit massively parallel sequencing technologies most effectively?

• How can we understand the flow of genes and species into and out of a human microbiota?

HumanMicrobiome

Project

HMP

Experimental systems needed to define how communities operate and interact with their

hosts• Characterize the determinants of robustness

(diversity/modularity)

• Determine whether ecologic principles derived from observations of the macroscopic world apply to the microscopic world that we harbor

• Identify biomarkers to characterize community composition/performance.

• Gnotobiotic models with intentionally designed, simplified microbial consortia to study microbial-microbial and microbial host interactions

• Marriage of gnotobiotics and metagenomics to assay whole community characteristics and their impact on host biology

HumanMicrobiome

Project

HMP

Editorial Comments: one view of a phased implementation of a human microbiome project

• Tier 1 - Initial data acquisition/analysis

– [Pillar 1] - Deep draft assemblies of reference genomes

– [Pillar 2] - Reference microbiome datasets

– [Pillar 3] - Shallower 16S rRNA and community metagenomic datasets from moderate number of samples

• Tier 2 - Choice of individuals that represent different clusters for additional deep sequencing

• Tier 3 - Global human microbiome diversity project

HumanMicrobiome

Project

HMP

Tier 1 Initial datasets [Pillar 1] - Deep draft assemblies of reference

genomes• Select cultured representatives of divisions in targeted

microbial communities

– Based on ‘comprehensive’ 16S rRNA gene-based enumerations: multiple individuals/habitat; multiple habitats/single individual

– Create ‘VIRTUAL MICROBIAL BODY’: a publicly-accessible database of ‘human-associated 16S rRNA-based phylotypes’ (facilitate cross-referencing of diversity within and between habitats; different studies)

– Public input from experts (stakeholders) on choices (include clinicians!)

• Phylotypes culled from existing culture collections (public and ‘private’; consent to deposit data in public domain)

• Improve technology for culturing the ‘unculturable’

HumanMicrobiome

Project

HMP

Tier 1 Initial datasets [Pillar 1] - Deep draft assemblies of reference

genomes

• Select subset of ‘species’ for additional sequencing of ‘strains’ (pan-genome studies; defining niches; create better tools for detecting LGT). ?Sequencing strategies versus those used for de novo projects

• Insure dataflow to, anddata capture by, structural genomicscommunity

• Deposit sequenced isolates together with information about habitat of origin, conditions for growth, phenotypes, in public CULTURE REPOSITORY capable of maintaining and distributing material

HumanMicrobiome

Project

HMP

Tier 1 - Initial datasets [Pillar 2] - Reference microbiome datasets

• Issues: – What degree of genetic relatedness/place in human

family structure; age

– Other demographic, social-cultural considerations

– What phenotypic parameters are needed about the host (definition of ‘health’); about host habitat?

– Barriers to obtaining samples/metadata?

– Sample collection and handling: DNA-, protein- and metabolite-level data can be obtained/compared/archived

– What type of comparisons are needed or desired: e.g., between-habitat comparisons within a given individual; between habitat comparisons of other family members; between different family units?

HumanMicrobiome

Project

HMP

Tier 1 - Initial datasets [Pillar 2] - Reference microbiome datasets

• Young adult monozygotic and dizygotic twin pairs, plus their mothers (gene-by-gene; gene-by-environment). Host DNA for whole genome association studies

• Benefits/drawbacks of different sequencing platforms

• Preliminary characterization of alpha and beta diversity. Develop/optimize tools for comparing 16S rRNA and WGS microbiome datasets to one another: feedback to pipeline characterizing cultured/retrieved representatives of habitat-associated communities*

• Establish specimen and data archives with distribution capabilities: determine resources needed to support their maintenance/growth; what are the deliverables?*

• Large insert microbiome libraries for present and future functional metagenomic screens, for structural genomics, etc.*

*establish coordinating council involving thought leaders in environmental metagenomics initiatives so that resource/tool developmental efforts can be reinforced and shared

HumanMicrobiome

Project

HMP

Tier 1 - Initial datasets [Pillar 3] - ‘Shallower’ 16S rRNA and metagenomic

datasets from ‘moderate’ number of samples

• Within USA - expand family sampling (fathers, siblings, children of MZ and DZ twins); expand age range; explore demographic, socio-economic/cultural variables; what sort of metadata?

e.g., Hawaii (Native Hawaiians on Niihau; Filipino, Chinese and Japanese all more or less mixed,or not mixed); islands have different population sizes

• Outside of USA - begin to establish global sample collection network - target countries undergoing rapid transformation of social

structures, technology, lifestyles (IRB, IP issues)

HumanMicrobiome

Project

HMP

Tier 1 - Initial datasets [Pillar 3] - Shallower 16S rRNA and metagenomic

datasets from moderate number of samples

• Tools for transcriptome, proteome and metabolome analyses using biospecimens employed for DNA-level characterization, computational tools and metrics for comparing these diverse multivariate datasets

– Higher throughput analyses (e.g., DNA-based microbiome arrays designed based on functionality)

• Further characterize alpha and beta diversity, and other ecological parameters

– What can we learn from island biogeography, neutral theories of community assembly, and other centerpieces of community ecology for large organisms?

HumanMicrobiome

Project

HMP

Tier 2 - Choice of individuals that represent different clusters for additional deep

sequencing

• Estimate of sampling depth and number of individuals needed to characterize ‘full’ human microbiome

– granularity of the characterization has to match the data

• Search for relatives of species and gene lineages in other mammalian communities and in other environments for additional genome sequencing (search for niches; feedback to Tier 1)

• Tie-in to structural genomics initiatives (benchmarking outputs from Tier 1)

HumanMicrobiome

Project

HMP

Tier 3 - Human microbiome diversity project

• Shallow sequencing of a large sample (?) of geographically, demographically, and culturally diverse individuals

• Choice of individuals with different clinical ‘parameters’ for association studies and biomarker panning

• Large-scale sequencing of reservoirs of microbes and genes (e.g., soils and water sources) to relate the fluxes of energy, materials, genes, and microbial lineages into the human microbiome (microbial observatories and human observatories)

• Expand/enhance global sampling networks; user-friendly databases containing biomedical and environmental metagenomic datasets; data-mining capabilities

• Outreach: applications (diagnostic/therapeutic; global food chain); educational

HumanMicrobiome

Project

HMP

Education

• Public education: ending the war metaphor about human-microbial interactions; issues related to sustainability of our planet

• Educating governments: sampling on a global scale; exchange of materials; intellectual property issues

• Educating scientists: Programs to support/sustain/attract those who are, will and/or need to work in this area