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
FIN