Microbial comparative pan-genomics using binomial mixture models

Naturalized soil Escherichia coli populations need to resist common soil desiccation stress in order to inhabit soil environments. In this study, four representative soil E. coli strains and one lab strain, MG1655, were tested for desiccation resistance via die-off experiments in sterile quartz sand under a potassium acetate-induced desiccation condition. The desiccation stress caused significantly lower die-off rates of the four soil strains (0.17 to 0.40 day ؊1 ) than that of MG1655 (0.85 day ؊1 ). Cellular responses, including extracellular polymeric substance (EPS) production, exogenous glycine betaine (GB) uptake, and intracellular compatible organic solute synthesis, were quantified and compared under the desiccation and hydrated control conditions. GB uptake appeared not to be a specific desiccation response, while EPS production showed considerable variability among the E. coli strains. All E. coli strains produced more intracellular trehalose, proline, and glutamine under the desiccation condition than the hydrated control, and only the trehalose concentration exhibited a significant correlation with the desiccation-contributed die-off coefficients (Spearman's ‫؍‬ ؊1.0; P ‫؍‬ 0.02). De novo trehalose synthesis was further determined for 15 E. coli strains from both soil and nonsoil sources to determine its prevalence as a specific desiccation response. Most E. coli strains (14/ 15) synthesized significantly more trehalose under the desiccation condition, and the soil E. coli strains produced more trehalose (106.5 ؎ 44.9 mol/mg of protein [mean ؎ standard deviation]) than the nonsoil reference strains (32.5 ؎ 10.5 mol/mg of protein).T raditionally, Escherichia coli in the environment has been often considered residual cells from recent fecal inputs (46), but this has been contradicted by recent reports of the ubiquitous presence of high levels of E. coli cells in soil samples (5,18,23). Studies using molecular tools have detected unique genotypic compositions of E. coli populations in soil (6,19,23), and the persistence of certain E. coli strains over extended periods of time in soils further supports the notion that certain soil E. coli populations are naturalized members of indigenous soil microbial communities (23). Since soil-sourced E. coli cells may enter nearby waterways in the absence of actual fecal inputs and thus generate false signals of fecal pollution, intense debate has arisen regarding the suitability of E. coli as a fecal indicator in water quality monitoring.To understand the survival and habitation of E. coli in soil, it is important to understand how E. coli resists soil environmental stresses, in particular, the common and unique soil desiccation stress caused by the natural cycles of soil wetting and drying. Studies on traditional soil bacteria have identified numerous cellular mechanisms responsible for enhanced desiccation resistance, including de novo trehalose synthesis (10, 29), production of extracellular polymeric substances (EPS) (36, 38), and uptake of exogenous glycine bet...

Section: Discussionmentioning

confidence: 99%

Correlation of Intracellular Trehalose Concentration with Desiccation Resistance of Soil Escherichia coli Populations

Zhang

Yan

2012

“…GET_HOMOLOGUES defines these compartments empirically, as follows: core, genes contained in all genomes/taxa considered; soft core, genes contained in 95% of the genomes/taxa considered, as in the work of Kaas and collaborators (25); cloud, genes present only in a few genomes/taxa (the cutoff was defined as the most populated noncore cluster class and its immediately neighboring classes); shell, the remaining genes, present in several genomes/taxa. This script will also compute estimates of core and pangenome sizes under the binomial mixture model of Snipen and colleagues (26). If the source genomic data are provided in GenBank format, parse_pangenome_matrix.pl can be asked to plot the clade-specific genes on a linearized genetic map of a reference genome selected from that lineage.…”

Section: Methodsmentioning

confidence: 99%

GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

Contreras‐Moreira

Vinuesa

2013

757

657

GET_HOMOLOGUES is an open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians. It can cluster homologous gene families using the bidirectional best-hit, COGtriangles, or OrthoMCL clustering algorithms. Clustering stringency can be adjusted by scanning the domain composition of proteins using the HMMER3 package, by imposing desired pairwise alignment coverage cutoffs, or by selecting only syntenic genes. The resulting homologous gene families can be made even more robust by computing consensus clusters from those generated by any combination of the clustering algorithms and filtering criteria. Auxiliary scripts make the construction, interrogation, and graphical display of core genome and pangenome sets easy to perform. Exponential and binomial mixture models can be fitted to the data to estimate theoretical core genome and pangenome sizes, and high-quality graphics can be generated. Furthermore, pangenome trees can be easily computed and basic comparative genomics performed to identify lineage-specific genes or gene family expansions. The software is designed to take advantage of modern multiprocessor personal computers as well as computer clusters to parallelize time-consuming tasks. To demonstrate some of these capabilities, we survey a set of 50 Streptococcus genomes annotated in the Orthologous Matrix (OMA) browser as a benchmark case. The package can be downloaded at http://www.eead.csic.es/compbio/soft/gethoms.php and http://maya.ccg.unam.mx/soft/gethoms.php. The ever-growing number of sequenced genomes in public databases such as GenBank has prompted the development of tools aimed at comparing the gene repertoires of species. Such comparisons include the identification of orthologous genes, assumed to diverge from a common ancestor after a speciation event and more likely to conserve their functions across organisms than paralogues (1). For this reason, orthologues are key elements in genome annotation and evolutionary studies (2, 3). Among bacteria, which are being sequenced faster than any other domain of life (4), a popular heuristic recipe for detecting orthologous sequences is simply looking for reciprocal BLAST hits (5, 6), and different software choices are available for this task (7). By combining these tools with a growing number of genomic sequences, several recent studies have provided evidence suggesting that bacterial genomes are actually mosaics that include genes shared by all isolates of a group of interest (core genome) as well as strainspecific/partially shared genes (8). The sum of the core genome and the remaining genes within the group is defined as the pangenome (9).Here we present GET_HOMOLOGUES, an open-source software package released under the GNU General Public License, specifically designed and tested for the pangenomic and comparative-genomic analysis of bacterial strains at different phylogenetic distances on Linux/Mac OS X computer systems. ...

“…Based on the 22 complete genome sequences of E. coli that are currently available, the E. coli pangenome (the complete complement of noncore genes distributed within individuals within the species) has been estimated to comprise at least 42,500 gene families (51), significantly more than the human genome. Studies have revealed enormous diversity in E. coli populations in primary and various secondary habitats.…”

Section: Vol 76 2010 Distribution and Diversity Of E Coli In A Watmentioning

confidence: 99%

Distribution and Diversity of Escherichia coli Populations in the South Nation River Drainage Basin, Eastern Ontario, Canada

Lyautey

Lü

Lapen

et al. 2010

We investigated the prevalence and diversity of Escherichia coli strains isolated from surface waters from multiple watersheds within the South Nation River basin in eastern Ontario, Canada. The basin is composed of mixed but primarily agricultural land uses. From March 2004 to November 2007, a total of 2,004 surface water samples were collected from 24 sampling sites. E. coli densities ranged from undetectable to 1.64 ؋ 10 5 CFU 100 ml ؊1 and were correlated with stream order and proximity to livestock production systems. The diversity of 21,307 E. coli isolates was characterized using repetitive extragenic palindromic PCR (rep-PCR), allowing for the identification of as many as 7,325 distinct genotypes, without capturing all of the diversity. The community was temporally and spatially dominated by a few dominant genotypes (clusters of more than 500 isolates) and several genotypes of intermediary abundance (clustering between 10 and 499 isolates). Simpson diversity indices, assessed on a normalized number of isolates per sample, ranged from 0.050 to 0.668. Simpson indices could be statistically discriminated on the basis of year and stream order, but land use, discharge, weather, and water physical-chemical properties were not statistically important discriminators. The detection of Campylobacter species was associated with statistically lower Simpson indices (greater diversity; P < 0.05). Waterborne E. coli isolates from genotypes of dominant and intermediary abundance were clustered with isolates obtained from fecal samples collected in the study area over the same period, and 90% of the isolates tested proved to share genotypes with fecal isolates. Overall, our data indicated that the densities and distribution of E. coli in these mixed-use watersheds were linked to stream order and livestock-based land uses. Waterborne E. coli populations that were distinct from fecal isolates were detected and, on this basis, were possibly naturalized E. coli strains.Escherichia coli is ubiquitously distributed in fecal material from humans and warm-blooded animals (38). The detection of E. coli in water is an implicit indicator of recent fecal contamination and therefore of the risk of cooccurrence of enteric pathogens that can cause illness in susceptible populations (62). Many jurisdictions evaluate and mandate compliance with drinking and recreational water quality standards on the basis of the presence and abundance of E. coli (14,44). For example, Canadian recreational water quality standards stipulate that E. coli densities in excess of a geometric mean of 200 CFU per 100 ml indicate that the water is unsuitable for swimming and bathing (23).In a background of increasing occurrence of microbial contamination of surface water, a variety of methods for elucidating the sources of fecal contamination have been developed, and these microbial source tracking (MST) methods are recommended components of fecal pollution abatement strategies (16,57). So-called library-dependent MST methods compare environmental isolates to co...