The first steps of adaptation of Escherichia coli to the gut are  dominated by soft sweeps

João Barroso-Batista; Ana Sousa; Marta Lourenço; Marie-Louise Bergman; Jocelyne Demengeot; Karina B. Xavier; Isabel Gordo

Publication

The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps

2014-03-06Journal article

dc.contributor.author	João Barroso-Batista
dc.contributor.author	Ana Sousa
dc.contributor.author	Marta Lourenço
dc.contributor.author	Marie-Louise Bergman
dc.contributor.author	Jocelyne Demengeot
dc.contributor.author	Karina B. Xavier
dc.contributor.author	Isabel Gordo
dc.date.accessioned	2015-09-28T16:38:13Z
dc.date.available	2015-09-28T16:38:13Z
dc.date.issued	2014-03-06
dc.description.abstract	The accumulation of adaptive mutations is essential for survival in novel environments. However, in clonal populations with a high mutational supply, the power of natural selection is expected to be limited. This is due to clonal interference - the competition of clones carrying different beneficial mutations - which leads to the loss of many small effect mutations and fixation of large effect ones. If interference is abundant, then mechanisms for horizontal transfer of genes, which allow the immediate combination of beneficial alleles in a single background, are expected to evolve. However, the relevance of interference in natural complex environments, such as the gut, is poorly known. To address this issue, we studied the invasion of beneficial mutations responsible for Escherichia coli's adaptation to the mouse gut and demonstrate the pervasiveness of clonal interference. The observed dynamics of change in frequency of beneficial mutations are consistent with soft sweeps, where a similar adaptive mutation arises repeatedly on different haplotypes without reaching fixation. The genetic basis of the adaptive mutations revealed a striking parallelism in independently evolving populations. This was mainly characterized by the insertion of transposable elements in both coding and regulatory regions of a few genes. Interestingly in most populations, we observed a complete phenotypic sweep without loss of genetic variation. The intense clonal interference during adaptation to the gut environment, here demonstrated, may be important for our understanding of the levels of strain diversity of E. coli inhabiting the human gut microbiota and of its recombination rate.	pt_PT
dc.description.sponsorship	Howard Hughes Medical Institute (HHMI-55007436), LAO/ITQB, FCT Grants: FRH/BD/80257/2011 and SFRH/BPD/14299/2003.	pt_PT
dc.identifier	10.1371/journal.pgen.1004182
dc.identifier.citation	Barroso-Batista J, Sousa A, Lourenço M, Bergman M-L, Sobral D, Demengeot J, et al. (2014) The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps. PLoS Genet 10(3): e1004182. doi:10.1371/journal.pgen.1004182	pt_PT
dc.identifier.doi	10.1371/journal.pgen.1004182
dc.identifier.doi	10.1371/journal.pgen.1004182
dc.identifier.uri	http://hdl.handle.net/10400.7/319
dc.language.iso	eng	pt_PT
dc.peerreviewed	yes	pt_PT
dc.publisher	PLOS	pt_PT
dc.relation	Microbial adaptation within ecosystems
dc.relation	Adaptation of commensal bacteria to the mammalian gut
dc.relation.publisherversion	http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004182	pt_PT
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	pt_PT
dc.subject	Quantitative Biology - Populations and Evolution	pt_PT
dc.subject	Cloning	pt_PT
dc.title	The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps	pt_PT
dc.type	journal article
dspace.entity.type	Publication
oaire.awardTitle	Microbial adaptation within ecosystems
oaire.awardTitle	Adaptation of commensal bacteria to the mammalian gut
oaire.awardURI	info:eu-repo/grantAgreement/EC/FP7/260421/EU
oaire.awardURI	info:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-EVF%2F118075%2F2010/PT
oaire.citation.endPage	12	pt_PT
oaire.citation.issue	3	pt_PT
oaire.citation.startPage	1	pt_PT
oaire.citation.title	PLOS GENETICS	pt_PT
oaire.citation.volume	10	pt_PT
oaire.fundingStream	FP7
oaire.fundingStream	3599-PPCDT
project.funder.identifier	http://doi.org/10.13039/501100008530
project.funder.identifier	http://doi.org/10.13039/501100001871
project.funder.name	European Commission
project.funder.name	Fundação para a Ciência e a Tecnologia
rcaap.rights	openAccess	pt_PT
rcaap.type	article	pt_PT
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