Stratified reconstruction of ancestral Escherichia coli diversification

González-Alba, José Marı́a; Baquero, Fernando; Galán, Juan Carlos

doi:10.1186/s12864-019-6346-1

Cited by 26 publications

(27 citation statements)

References 49 publications

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“…Interestingly, the phylogroups D and F, which are not close in the species tree, cluster together in terms of gene repertoires. This may explain the conflicting results of our phylogenetic analysis, which places with high confidence the phylogroup D in the same partition of A and B1, and works based on ancestral gene repertoires that place them as a basal group in the tree (not far from F and G) [49]. Hence, phylogroups differ in terms of their gene repertoires and in their rates of genetic diversification, but while some are quite similar (A and B1), others (B2) stand aside from the remaining phylogroups.…”

Section: Plos Geneticsmentioning

confidence: 78%

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

et al. 2020

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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.

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Section: Plos Geneticsmentioning

confidence: 78%

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

et al. 2020

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“…This means that the complexity of ancestor niches was either simpler, or at least relatively simpler, that is, dominated by a few powerful conditions, or were simply insufficiently dug up, exploited and far from their carrying capacity. The search for cores by using stratified phylogenies in successive supraspecific and subspecific taxons supports such a hypothesis ( Gonzalez-Alba et al, 2019 ).…”

Section: Niche Variability Core Genomes and Accessory Genomesmentioning

confidence: 95%

The Origin of Niches and Species in the Bacterial World

et al. 2021

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Niches are spaces for the biological units of selection, from cells to complex communities. In a broad sense, “species” are biological units of individuation. Niches do not exist without individual organisms, and every organism has a niche. We use “niche” in the Hutchinsonian sense as an abstraction of a multidimensional environmental space characterized by a variety of conditions, both biotic and abiotic, whose quantitative ranges determine the positive or negative growth rates of the microbial individual, typically a species, but also parts of the communities of species contained in this space. Microbial organisms (“species”) constantly diversify, and such diversification (radiation) depends on the possibility of opening up unexploited or insufficiently exploited niches. Niche exploitation frequently implies “niche construction,” as the colonized niche evolves with time, giving rise to new potential subniches, thereby influencing the selection of a series of new variants in the progeny. The evolution of niches and organisms is the result of reciprocal interacting processes that form a single unified process. Centrifugal microbial diversification expands the limits of the species’ niches while a centripetal or cohesive process occurs simultaneously, mediated by horizontal gene transfers and recombinatorial events, condensing all of the information recovered during the diversifying specialization into “novel organisms” (possible future species), thereby creating a more complex niche, where the selfishness of the new organism(s) establishes a “homeostatic power” limiting the niche’s variation. Once the niche’s full carrying capacity has been reached, reproductive isolation occurs, as no foreign organisms can outcompete the established population/community, thereby facilitating speciation. In the case of individualization-speciation of the microbiota, its contribution to the animal’ gut structure is a type of “niche construction,” the result of crosstalk between the niche (host) and microorganism(s). Lastly, there is a parallelism between the hierarchy of niches and that of microbial individuals. The increasing anthropogenic effects on the biosphere (such as globalization) might reduce the diversity of niches and bacterial individuals, with the potential emergence of highly transmissible multispecialists (which are eventually deleterious) resulting from the homogenization of the microbiosphere, a possibility that should be explored and prevented.

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“…Thus, the distribution of pipolins limited to phylogroups A, B1, C and D may be due to the restricted mobility beyond those groups. In line with this, these phylogenetic groups have been proposed to belong to different ancient lineages 24 , downplaying a strict vertical transmission of pipolins throughout the evolutionary diversification of E. coli phylogroups.…”

Section: Resultsmentioning

confidence: 83%

High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains

Flament-Simon

Toro

Chuprikova

et al. 2020

Sci Rep

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Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus-host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB). We have now surveyed the presence of pipolins in a collection of 2,238 human and animal pathogenic Escherichia coli strains and found that, although detected in only 25 positive isolates (1.1%), they are present in E. coli strains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belong to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring genomes from GenBank database spanning strains from diverse origin, further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons. In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulating E. coli and possibly also among other pathogenic bacteria. Mobile genetic elements (MGE), comprising bacteriophages, transposons, plasmids, and insertion sequences, contribute to the great plasticity of the bacterial genome, resulting in an extremely large pangenomes that, in the case of Escherichia coli, can amount to more than 16,000 genes 1. Thus, MGEs dynamics is the main source of horizontal gene transfer, which leads to the spread of antimicrobial resistance (AR) among both E. coli and other commensals, thereby enlarging the spectrum of resistance (the resistome) among circulating strains 2. Pipolins constitute a recently reported new group of integrative MGEs widespread among diverse bacterial phyla and also identified in mitochondria as circular plasmids 3. The hallmark feature of the pipolins is a gene encoding for a replicative family B DNA polymerases (PolB) with an intrinsic de novo primer synthesis capacity,

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Stratified reconstruction of ancestral Escherichia coli diversification

Cited by 26 publications

References 49 publications

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

The Origin of Niches and Species in the Bacterial World

High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains

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