Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli

Ihssen, Julian; Grasselli, Elena; Bassin, Claudio; François, Patrice; Piffaretti, Jean-Claude; Köster, Wolfgang; Schrenzel, Jacques; Egli, Thomas

doi:10.1099/mic.0.2006/002006-0

Cited by 32 publications

(24 citation statements)

References 74 publications

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“…In contrast, the ECOR strains are from a variety of animal sources and geographical locations (Selander et al, 1987), and are thus more representative of the diversity within the E. coli species. Figure 2 indicates that there is, species-wide, a very broad distribution of fitness capabilities and there is no species typical fitness or stress resistance, as suggested previously (Ihssen et al, 2007). Studies of trade-offs in E. coli are beginning to reveal that the SPANC balance, and probably survival multiplication trade-offs generally, are the sum of several mechanistic contributions.…”

Section: Discussionmentioning

confidence: 70%

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A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

Phan

Ferenci

2013

The ISME Journal

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Bacterial species are internally diverse in genomic and multi-locus gene comparisons. The ecological causes of phenotypic and genotypic diversity within species are far less well understood. Here, we focus on the competitive fitness for growth on nutrients within Escherichia coli, an internally rich species. Competition experiments in nutrient-limited chemostats revealed that members of the ECOR collection exhibited a wide continuum of competitive abilities, with some fitter and some less fit than the lab strain MG1655. We observed an inverse relationship between competitiveness and the resistance of strains to detergent and antibiotic, consistent with the notion that membrane permeability and competitive fitness are linked by a trade-off between selfpreservation and nutritional competence (SPANC); high permeability has a postulated cost in antibacterial sensitivity whereas a low permeability has a cost in nutrient affinity. Isolates moved along the markedly nonlinear trade-off curve by mutational adaptation; an ECOR strain sensitive to antibacterials and a good competitor was easily converted by mutation into a mutant with higher resistance but poorer competition in the presence of low antibiotic concentrations. Conversely, a resistant ECOR strain changed into a better competitor after a short period of selection under nutrient limitation. In both directions, mutations can affect porin proteins and outer membrane permeability, as indicated by protein analysis, gene sequencing and an independent assay of outer membrane permeability. The extensive, species-wide diversity of E. coli in ecologically important traits can thus be explained as an evolutionary consequence of a SPANC trade-off driven by antagonistic pleiotropy.

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Section: Discussionmentioning

confidence: 70%

“…A previously reached conclusion is that E. coli isolates all have similar fitness and growth characteristics (Ihssen et al, 2007). This conclusion is not at all borne out by our far more extensive comparisons.…”

Section: Discussionmentioning

confidence: 74%

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

Phan

Ferenci

2013

The ISME Journal

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“…This difference did not affect their growth in common media and also could not be linked to any differential survival in the cow stomach or dung. Finally, the variability across 57 commensal and pathogenic E. coli strains in utilization of carbon and energy sources as well as catabolic and stress protection genes was low, but such variation was clearly found across the different E. coli strains (Ihssen et al, 2007). These results suggest that functions affecting the microorganism's survival and growth, such as those of the central metabolism that determine growth rates, are actually quite broadly shared across the E. coli strains, potentially yielding grossly comparable survival rates in complex natural systems.…”

Section: Presence and Diversity Of An Indigenous Microfloramentioning

confidence: 91%

“…In the light of these challenging conditions, most forms of E. coli seem to have conserved particular key evolutionary adaptations in their core genomes, as indicated by the presence in most strains of import systems, such as siderophore-mediated iron uptake systems (Schubert et al, 2004) or ABC transporters for uptake of amino acids and sugars. This suggests a high ability in E. coli to obtain diverse nutrients, aiding in its survival in open environments (Ihssen et al, 2007).…”

Section: The Lifestyle Of E Coli Is Biphasicmentioning

confidence: 99%

Survival of Escherichia coli in the environment: fundamental and public health aspects

et al. 2010

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In this review, our current understanding of the species Escherichia coli and its persistence in the open environment is examined. E. coli consists of six different subgroups, which are separable by genomic analyses. Strains within each subgroup occupy various ecological niches, and can be broadly characterized by either commensalistic or different pathogenic behaviour. In relevant cases, genomic islands can be pinpointed that underpin the behaviour. Thus, genomic islands of, on the one hand, broad environmental significance, and, on the other hand, virulence, are highlighted in the context of E. coli survival in its niches. A focus is further placed on experimental studies on the survival of the different types of E. coli in soil, manure and water. Overall, the data suggest that E. coli can persist, for varying periods of time, in such terrestrial and aquatic habitats. In particular, the considerable persistence of the pathogenic E. coli O157:H7 is of importance, as its acid tolerance may be expected to confer a fitness asset in the more acidic environments. In this context, the extent to which E. coli interacts with its human/animal host and the organism's survivability in natural environments are compared. In addition, the effect of the diversity and community structure of the indigenous microbiota on the fate of invading E. coli populations in the open environment is discussed. Such a relationship is of importance to our knowledge of both public and environmental health.

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“…The functional category(s) of each gene was determined by using RAST subsystem annotations (http://rast.nmpdr.org) of the uploaded genome sequences, supplemented by MG-RAST (http://metagenomics.anl.gov) for gene features, for which subsystem assignments were lacking from RAST. Genes linked to uptake/catabolism of carbon substrates and stress response are of specific interest for the culture conditions applied and detailed analysis focusing on those features was performed based on the study by Ihssen et al (2007).…”

Section: Discussionmentioning

confidence: 99%

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

et al. 2014

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Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.

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Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-)physiological properties are highly conserved in the species Escherichia coli

Cited by 32 publications

References 74 publications

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

Survival of Escherichia coli in the environment: fundamental and public health aspects

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

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