ISME 13 Day 1
Time to finally break the 9 month digital silence. I’ve had many posts in the works in my head, including the publication of progressiveMauve and it’s coverage in genomeweb, surprising bugs in progressiveMauve (to be continued), reviews of papers I’ve read, neat software engineering tricks I’ve learned, and various hypocrisies of science that seem to abound.
That will all have to wait, because today I’m posting my notes from the ISME 13 conference. ISME is an acronym for International Society for Microbial Ecology and the society meeting occurs every two years, this time in Seattle. I wasn’t planning to attend ISME, but Jenna Morgan has a poster here for work on which I’m a coauthor and she couldn’t make it so I’m presenting the work on her behalf. Last time I attended the meeting in Cairns I thoroughly enjoyed it, and yesterday’s talks and posters did not disappoint either.
Without further ado, here are some notes…
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AmpliconNoise
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I only caught about a third of this one.
Rare biosphere seems to be a sequencing artifact created by protocol noise and the 3% OTU cutoff
Open source software method to clean up 16S pyrotag data:
http://code.google.com/p/ampliconnoise/
YAY! open source
Substantially reduces inferred OTU counts, makes that pesky rare biosphere disappear.
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Tal Dagan talk on Lateral Gene Transfer
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60% of genes have lgt
analyzed about 650 genomes
directed network gains/losses
origins inferred using codon bias
non-homologous end joining proteins
200 genomes encode both subunits
nhej positive organisms appear to acquire from more distant organisms
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widespread HR in Streptomyces
Daniel H Buckley
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defines LGT to be allelic replacement
Fraser 2006 rates decline log-linearly with seq similarity based on MLSA analysis
some organisms very clonal, others recombining wildly at the tips of the tree
now let’s look at wild isolates
Streptomyces soil organism, wet dirt smells like Streptomyces B.O.
Half of antibiotics coming from Streptomyces
Sporulating — exospore. hyphae grows from spore, dna replicates during hyphae growth. hyphae form mycelium.
Streptomyces can do dsDNA exchange. depends on traB, atp dependent dsDNA translocator.
traB localizes at tips of hyphae, speculates traB might mobilize entire chromosomes during hyphae fusions
Someone designed MLST for Strepto
Six loci, not a single pair of congruent trees.
Used RDP to infer some recombination events. Signal looks a bit blurry.
ClonalFrame tree of Streptomyces trees
> 40% of genes impacted by HGT
HGT gene pairs have average 6% divergence — events are probably old.
did some sampling of S. flavogriseus pratensis from around eastern half of US.
samples are 99.8% identical on average
within “species” rho/theta = 27
cross species rho/theta < 1.
suggests cohesion
forward time simulation under a neutral model
estimates of divergence and rho/theta from Vos and Didelot approximately match the neutral speciation model predictions
Konstantinidis 2008 “valley of genetic discontinuity” — lack of reads recruiting at 86-92% identity
Fred Cohan asked a question or rather, made a statement about recombination driven cohesion and ecotypes. It seemed like he was suggesting that ecotypes exist only in the niche-specifying genes, and the recombining core genes don’t give the data necessary to identify the ecotype. So the ecotype model gets pushed further into the margins of the genome and we now have something Jeffrey Lawrence might call “ecotypes in pieces” (for the unfamiliar, that’s a reference to Lawrence’s species in pieces work).
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Broad host range plasmids LGT in bacteria
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How frequently do bacteria swap DNA and plasmids with each other?
What is the host range of particular plasmids?
How do those plasmids evolve over time?
Use a model plasmid: IncP-1
simplified the plasmid by removing various transfer genes
Use Shewanella oneidensis Mr-1 as a host
Ancestral plasmid unstable, but can naturalize into a new host over 1000 generations.
How did they adapt?
Can they adapted plasmids be moved to yet another new host? Not always.
many mutations localized in the replication protein TrfA1
evolved plasmid genes have copy-number amplification
conclusions: drug resistance plasmids can rapidly adapt to new hosts
single gene changes can facilitate host shifts
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GeneFish
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create a recombinant E. coli to capture environmental DNA
environmental DNA ends up on plasmid
Simplify metagenome protocol by getting environmental DNA directly into the cloning vector.
avoid DNA extraction bias, other biasing steps. (but isn’t cloning a bias??)
get env DNA into plasmid, select for it using colE3 relF toxin system, grow on plates.
selectable recombination seems to increase recomb frequency by 4-5 log units.
Now looking to test the system.
Use NarG gene. design homologous regions to narG gene for the plasmid
use 500bp homologous region
recombination frequency 10^-6
toxin selection effectiveness 25-50%?
tolerates 80-100% divergence from homologous region
not very good??
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Hinsby Cadillo, Sulfolobus sympatric species
disclaimer: I am a collaborator on this project
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S. islandicus genomes from the same location
39 strains from Mutnovsky formation, Kamchakta
MLSA some large clonal complexes, a few rare groups, some intermediate strains.
ClonalFrame infers presence of some recombination
12 genomes from M16 spring
2.285Mbp core genome, build a phylogeny based on core genome
ClonalOrigin analysis
higher than expected rates of exchange among closely related organisms, lower than expected exchange among more divergent organisms
geographically isolated populations do not recombine much at all
Recombination could be mediated by pili in S. solfataricus
respiratory nitrate reductase has a presence/absence pattern consistent with the phylogeny
gene content specified niche separation, within-niche cohesion by homologous recombination
