The Rise of the Microbiome:

Challenges and Opportunities

ACHJ15

Jonathan A. Eisen

@phylogenomics

University of California, Davis

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Pubmed “Microbiome” Hits

The Rise of the Microbiome

microBIOME or microbiOME

• microbi-OME

collection of genomes of microbes from a

community (emphasis on OME)

• micro-BIOME

a community of microbes (emphasis on

BIOME)

• see http://tinyurl.com/definemicrobiome

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Why Now?

Why Now I: Appreciation of Microbial Diversity

Functional Diversity

Diversity of Form

Phylogenetic Diversity

MICROBES

RUN THE

PLANET

Why Now II: Post Genome Blues

The Microbiome

Transcriptome

VariomeEpigenome

Overselling the Human Genome?

<<<<

Culturing Observation

CountCount

http://www.google.com/url?sa=i&rct=j&q=&

esrc=s&source=images&cd=&docid=rLu5s

L207WlE1M&tbnid=CRLQYP7d9d_TcM:&

ved=0CAUQjRw&url=http%3A%2F%2Fw

ww.biol.unt.edu%2F~jajohnson%2FDNA_

sequencing_process&ei=hFu7U_TyCtOqs

QSu9YGwBg&psig=AFQjCNG-8EBdEljE7-

yHFG2KPuBZt8kIPw&ust=140487395121

1424

DNA

Why Now III: CSI-Microbiology Advances

Why Now IV: Sequencing Has Gone Crazy

Turnbaugh et al Nature. 2006 444(7122):1027-31.

Why Now V: Microbiome Functions

Challenge 1: Complexity

Microbial Diversity

Microbial Diversity2 Fragmented Data

Host Variation

http://bit.ly/HumanMicrobiome

Functional

Diversity

Challenge 1: Complexity

Host Variation

http://bit.ly/HumanMicrobiome

TranscriptomeSNPs, CNVs

Epigenetics

Environment

Challenge 2: Public Understanding

Germophobia Microbiomania

Opportunity 1: Better Reference Data

Opportunity 2: Better Methods

PhylOTU rRNA Copy # Correction Metagenomic PD

Genome TreePhyloSift PhyEco Markers

SFAMs Meta HiC Linking Taxa and Function

Opportunity 3: Model Systems (e.g., Rice)

Edwards et al. 2015. Structure, variation,

and assembly of the root-associated

microbiomes of rice. PNAS

Variation w/in Plant

Cultivation Site Effects

Rice Genotype Effects

Function x Genotype

Time Series

Mom The Microbes We Eat

PetsBuilt

Environment

Other People

Many Taxa

Opportunity 4: Whole Systems

Opportunity 6: Education & Outreach

http://microBE.net

http://gut-check.net

Opportunity 7: Citizen Science

Kitty Microbiome

Acknowledgements

DOE JGI GBMF

DARPA

Aaron Darling

Russell

Neches

Rob KnightTanja Woyke

Jessica

Green

Darlene

Cavalier

Eddy Rubin

Dongying Wu

Phil HugenholtzSundar

Srijak

Bhatnagar

Jennifer Gardy

Holly Ganz