Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with specific habitats. After a while, the divergence of gene repertoires becomes linear with phylogenetic distance, presumably reflecting the continuous turnover of mobile element and the occasional acquisition of adaptive genes. Surprisingly, the phylogroups with smallest genomes have the highest rates of gene repertoire diversification and fewer but more diverse mobile genetic elements. This suggests that smaller genomes are associated with higher, not lower, turnover of genetic information. Many of these genomes are from freshwater isolates and have peculiar traits, including a specific capsule, suggesting adaptation to this environment. Altogether, these data contribute to explain why epidemiological clones tend to emerge from specific phylogenetic groups in the presence of pervasive horizontal gene transfer across the species.
A collection of 266 faecal isolates of Escherichia coli from humans was assayed for the production of mitomycin C-inducible bacteriocins and screened using a PCR-based method for the presence of eleven colicins and seven microcins. Eight different colicins were detected and all seven microcins. Of the strains examined, 38 % produced a bacteriocin, 24 % produced a colicin and 20 % produced a microcin. Of the 102 bacteriocin-producing strains, 42 % produced one type of bacteriocin, 41 % produced two, 16 % produced three and one strain was found to produce four different bacteriocins. Strains producing more than one bacteriocin were more likely to be members of E. coli genetic group B2 and less likely to belong to genetic groups A or D. Several of the bacteriocins were found to co-occur in a strain more often than would be expected by chance: microcins H47 and M; colicin Ia and microcin V; colicins B and M; colicins E1 and M; colicins E1 and Ia. No bacteriocins released as a consequence of cell lysis were found to co-associate more often than expected by chance. Three non-mutually exclusive hypotheses are presented that might explain the high frequency of multiple bacteriocin production in E. coli strains: (1) expanded killing range, (2) expanded receptor repertoire and (3) fitness benefits in different environments.
The gut microbiota is important in maintaining human health, but numerous factors have the potential to alter its composition. Our aim was to examine the impact of a standard bowel preparation on the intestinal microbiota using two different techniques. Fifteen subjects undergoing colonoscopy consumed a bowel preparation comprised of 10 mg bisacodyl and 2 L polyethylene glycol. The microbiota of stool samples, collected one month before, one week before (pre-colonoscopy), and one week, one month, and three to six months after colonoscopy (post-colonoscopy) was evaluated. Two samples were taken three to six months apart from five healthy subjects who did not undergo colonoscopy. Universal primers targeting the V2–V3 region of the 16S rRNA gene were used to PCR amplify all samples for denaturing gradient gel electrophoresis (PCR-DGGE). Pre- and post-colonoscopy samples were compared using Dice’s similarity coefficients. Three samples from ten subjects who underwent colonoscopy, and both samples from the five subjects who didn’t, were used for high-throughput sequencing of the V1–V3 region of the 16S rRNA gene. Samples were curated and analysed in Mothur. Results of the DGGE analyses show that the fecal microbiota of a small number of subjects had short-term changes. High-throughput sequencing results indicated that the variation between the samples of subjects who underwent colonoscopy was no greater than the variation observed between samples from subjects who did not. We conclude that bowel preparation does not have a lasting effect on the composition of the intestinal microbiota for the majority of subjects.
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