is microbial ecology driven by roaming genes?

http://commons.wikimedia.org/wiki/File:Bison_herd_at_Genesee_Park-2012_03_10_0601.jpg

Microbial communities

http://upload.wikimedia.org/wikipedia/commons/2/2d/Bacteria_%28251_31%29_Airborne_microbes.jpg

Profiling the microbiome

Marker genes(e.g., 16S rRNA gene)

Metagenomics:Functions predicted via similarity to known genes

Marker-gene survey:Identify best matching relative from a database

nifA

ppk

spo

vanR

www.jisponline.com

Supragingival plaque

Subgingival plaque

Patterns in microbial ecology

Species 1: 23%

Species 1: 38%

Subgingival Supragingival

Jessie Ning

Characteristic groups

??

Pairwise dissimilarity (beta-diversity)

1

2

D1,2

What to do with a distance matrix

Hierarchical clustering Ordination (e.g. PCA, PCoA)

Parks and Beiko,MBE (2012)

Arumugam et al. (2011) Nature

“Enterotypes”*

Oral sample data from the Human Microbiome ProjectNing and Beiko (in preparation)

Oral sample data from the Human Microbiome ProjectNing and Beiko (in preparation)

Lawley et al., PLoS Pathog (2012)

Wu et al., Nature (2009)

Phylogenetic approaches to diversity

UniFrac (Lozupone and Knight, 2007)

Similar Communities Maximally Different Communities

UniFrac Distance Measure = (------) / (------ + ------)

D1,2 = ?

There’s more than one way to do it

Parks and Beiko, ISME J (2013)

*

But…

There is a critical assumption in phylogenetic beta diversity:

Microbial FUNCTION and ECOLOGY are intertwined with PHYLOGENY

Is this true?

Dagan et al. (2008) PNAS

Maybe not.

Apologies to Brock, 7th ed.

Example:Mycobacterium abscessus – Segniliparus rotundus

Unexpectedly similar!

Smith et al. (2012) PLoS ONE

TetR transcriptional regulators

Also:non-ribosomal peptide synthetasesoligopeptide transportersMmpL / MmpS membrane proteins

Silvia Smith

LGT patterns for Clostridium

Whidden et al., 2014 Chris Whidden

Smillie et al. (2011) Science

LGT by habitat type~5% of all comparedgenes?

Butyrate production – a crucialfunction, subject to LGT

Different candidate “species” trees -All REJECTED!!

Meehan and Beiko (2014) GBE

LGT matters in the microbiome!

“…not only the bacterial taxa, but also their plasmids, are defined by the ecological niche.”

PN

AS, 2

01

3

PN

AS, 2

01

2

“…pathogen-driven inflammatory responses in the gut can generate transient enterobacterialblooms in which conjugative transfer occurs at unprecedented rates.”

PLo

SB

iol, 2

00

7

“…lateral gene transfer, mobile elements, and gene amplification have played important roles in affecting the ability of gut-dwelling Bacteroidetes to vary their cell surface, sense their environment, and harvest nutrient resources present in the distal intestine.”

The point.

•Microbial ecology (whether community comparisons or something more explicit) can benefit from understanding the relatedness of taxonomic groups

•But PHYLOGENY may not capture the whole story

• If we want to better exploit this relatedness, the best approach may be to explore different ways in which genomes and also genes may interact

LachnoZilla

http://en.wikipedia.org/wiki/File:Godzilla_%2754_design.jpg

From ecology of organisms

To ecology of genes

And maybe, just maybe,

back again

Photo courtesy of Dr.Emma Allen Vercoe, University of Guelph

Lachnospiraceae bacterium 3-1-57FAA-CT1

Lachno

PATRIC taxonomy

(http://patricbrc.vbi.vt.edu)

Meehan and Beiko (2014) Genome Biol Evol

0 1000 2000 3000 4000 5000 6000 7000 8000

Number of Protein-Coding Genes

Sizes of Assembly and Draft Genomes of Class Clostridia

Zilla

What makes LachnoZilla

LachnoZilla ?

C. difficileC. bolteae….

“Virulence-associated protein”Recombinase / resolvaseConjugation proteinsTransposases, transposases,

transposases

Extremely good matches toother genomes (> 95% ID, > 95% coverage)

LZ & friends:Clostridium sp. KLE 1755Clostridiales bacterium VE202-29Clostridiales bacterium VE202-27

C. hathewayi

C. bolteae

C. clostridioforme

Eubacterium

*

*

*

*

***

*

* 279 genomesBrutal / no taxonomy

Conserved marker-gene tree

Close relative

Distant relative

Another distant relative

Genome-centric graphs

Edge weights are proportional to shared genesOther people who have done this kind of thing: Gipsi Lima-Mendes, Eric Bapteste, Tal Dagan

P. aeruginosaP. fluorescensP. lePewtidaP. syringaeP. entomophilaP. stutzeriP. mendocina

Catherine Holloway

“Plume”

Holloway and Beiko, 2010

LachnoZilla (and friends)best-hit graph

!

Close relative(expected)

Distant relative(not so expected)

Selective sharing

Gene-centric graphs

Edge weights are proportional to similarity of distribution

LZGenome

1Genome

2Genome

3Genome

4Genome

5Genome

6

Gene 1 × ×

Gene 2 ×

Gene 3 × ×

Gene 4 × × ×

Gene 2

Gene 3

Gene 1

Gene 4

Legionaminic acidAcetylneuraminic acid

(pathogen associated)

Bacteroides pectinophilusButyrivibrio proteoclasticusEubacterium plexicaudatumRoseburiaNeighborsWeirdly named isolates

Mystery isolate #1(made-up example)

Mystery isolate #2(made-up example)

Genome ecology

•Adapts existing techniques developed for deer and microbial populations

•Can identify modules that may be shared and reused, and overlay other information:• Microbial community structure

• Phylogenetic trees

•Construction is agnostic to microbial habitat and role, and to putative gene functions• Since we don’t know a lot of this (hypothetical protein /

Lachnospiraceae protein blah blah blah)

• It may not work very well (techniques fail or teach us nothing new)

So…

• There are connections between distant relatives that almost certainly play a role in pathogenesis and other ecological roles

• Our ability to understand these systems is limited for several reasons:• Most microorganisms are not understood or even described at all

• Many genes lack reliable functional predictions

• So…many…genes…

• So…much…diversity…

• An ecology of genomes may help us establish linkages and shared properties of genes and microorganisms, which we might then map up to the microbial community

Thanks!Microbial ecology

• Donovan Parks

• Jessie Ning

LachnoZilla• Emma Allen-Vercoe

• Ben Wright

• Eyre Nomi

LGT stories• Catherine Holloway

• Rob Eveleigh, John Archibald

• Silvia Smith, Darren Martin

• Conor Meehan

• Chris Whidden, Norbert Zeh

• Beiko, Blouin labs

• CGEB people

FEMS Microbiology Reviews, 2013

Funding: NSERC, CIHR, Killam Trusts, CGEB, CFI, NSHRF, Computer Science

Fin

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