Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts

peer-reviewedBackground: The genus Lactobacillus is characterized by an extraordinary degree of phenotypic and genotypic diversity, which recent genomic analyses have further highlighted. However, the choice of species for sequencing has been non-random and unequal in distribution, with only a single representative genome from the L. salivarius clade available to date. Furthermore, there is no data to facilitate a functional genomic analysis of motility in the lactobacilli, a trait that is restricted to the L. salivarius clade. Results: The 2.06 Mb genome of the bovine isolate Lactobacillus ruminis ATCC 27782 comprises a single circular chromosome, and has a G+C content of 44.4%. In silico analysis identified 1901 coding sequences, including genes for a pediocin-like bacteriocin, a single large exopolysaccharide-related cluster, two sortase enzymes, two CRISPR loci and numerous IS elements and pseudogenes. A cluster of genes related to a putative pilin was identified, and shown to be transcribed in vitro. A high quality draft assembly of the genome of a second L. ruminis strain, ATCC 25644 isolated from humans, suggested a slightly larger genome of 2.138 Mb, that exhibited a high degree of synteny with the ATCC 27782 genome. In contrast, comparative analysis of L. ruminis and L. salivarius identified a lack of long-range synteny between these closely related species. Comparison of the L. salivarius clade core proteins with those of nine other Lactobacillus species distributed across 4 major phylogenetic groups identified the set of shared proteins, and proteins unique to each group. Conclusions: The genome of L. ruminis provides a comparative tool for directing functional analyses of other members of the L. salivarius clade, and it increases understanding of the divergence of this distinct Lactobacillus lineage from other commensal lactobacilli. The genome sequence provides a definitive resource to facilitate investigation of the genetics, biochemistry and host interactions of these motile intestinal lactobacilli

Effect of Lactobacillus salivarius Bacteriocin Abp118 on the Mouse and Pig Intestinal Microbiota

Lactobacilli are Gram-positive bacteria that are a subdominant element in the human gastrointestinal microbiota, and which are commonly used in the food industry. Some lactobacilli are considered probiotic, and have been associated with health benefits. However, there is very little culture-independent information on how consumed probiotic microorganisms might affect the entire intestinal microbiota. We therefore studied the impact of the administration of Lactobacillus salivarius UCC118, a microorganism well characterized for its probiotic properties, on the composition of the intestinal microbiota in two model animals. UCC118 has anti-infective activity due to production of the bacteriocin Abp118, a broad-spectrum class IIb bacteriocin, which we hypothesized could impact the microbiota. Mice and pigs were administered wild-type (WT) L. salivarius UCC118 cells, or a mutant lacking bacteriocin production. The microbiota composition was determined by pyrosequencing of 16S rRNA gene amplicons from faeces. The data show that L. salivarius UCC118 administration had no significant effect on proportions of major phyla comprising the mouse microbiota, whether the strain was producing bacteriocin or not. However, L. salivarius UCC118 WT administration led to a significant decrease in Spirochaetes levels, the third major phylum in the untreated pig microbiota. In both pigs and mice, L. salivarius UCC118 administration had an effect on Firmicutes genus members. This effect was not observed when the mutant strain was administered, and was thus associated with bacteriocin production. Surprisingly, in both models, L. salivarius UCC118 administration and production of Abp118 had an effect on Gram-negative microorganisms, even though Abp118 is normally not active in vitro against this group of microorganisms. Thus L. salivarius UCC118 administration has a significant but subtle impact on mouse and pig microbiota, by a mechanism that seems at least partially bacteriocin-dependent

Comparative Genomic Analysis of Pathogenic and Probiotic Enterococcus faecalis Isolates, and Their Transcriptional Responses to Growth in Human Urine

Urinary tract infection (UTI) is the most common infection caused by enterococci, and Enterococcus faecalis accounts for the majority of enterococcal infections. Although a number of virulence related traits have been established, no comprehensive genomic or transcriptomic studies have been conducted to investigate how to distinguish pathogenic from non-pathogenic E. faecalis in their ability to cause UTI. In order to identify potential genetic traits or gene regulatory features that distinguish pathogenic from non-pathogenic E. faecalis with respect to UTI, we have performed comparative genomic analysis, and investigated growth capacity and transcriptome profiling in human urine in vitro. Six strains of different origins were cultivated and all grew readily in human urine. The three strains chosen for transcriptional analysis showed an overall similar response with respect to energy and nitrogen metabolism, stress mechanism, cell envelope modifications, and trace metal acquisition. Our results suggest that citrate and aspartate are significant for growth of E. faecalis in human urine, and manganese appear to be a limiting factor. The majority of virulence factors were either not differentially regulated or down-regulated. Notably, a significant up-regulation of genes involved in biofilm formation was observed. Strains from different origins have similar capacity to grow in human urine. The overall similar transcriptional responses between the two pathogenic and the probiotic strain suggest that the pathogenic potential of a certain E. faecalis strain may to a great extent be determined by presence of fitness and virulence factors, rather than the level of expression of such traits

Transcriptional Regulator PerA Influences Biofilm-Associated, Platelet Binding, and Metabolic Gene Expression in Enterococcus faecalis

Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections, traits facilitated by the ability to quickly acquire and transfer virulence determinants. A 150 kb pathogenicity island (PAI) comprised of genes contributing to virulence is found in many enterococcal isolates and is known to undergo horizontal transfer. We have shown that the PAI-encoded transcriptional regulator PerA contributes to pathogenicity in the mouse peritonitis infection model. In this study, we used whole-genome microarrays to determine the PerA regulon. The PerA regulon is extensive, as transcriptional analysis showed 151 differentially regulated genes. Our findings reveal that PerA coordinately regulates genes important for metabolism, amino acid degradation, and pathogenicity. Further transcriptional analysis revealed that PerA is influenced by bicarbonate. Additionally, PerA influences the ability of E. faecalis to bind to human platelets. Our results suggest that PerA is a global transcriptional regulator that coordinately regulates genes responsible for enterococcal pathogenicity

Identification et caractérisation d'Ers, régulateur transcriptionnel impliqué dans la virulence d'Enterocccus faecalis

Ers a été identifié comme un régulateur transcriptionnel chez Enterococcus faecalis, une bactérie lactique responsable d infections nosocomiales. Cette protéine fait partie de la branche PrfA des régulateurs de la famille Crp/Fnr et serait, chez E. faecalis, l homologue de PrfA, régulateur majeur de la virulence chez Listeria monocytogenes. Elle possède en effet des similitudes structurales avec les protéines de cette famille et en particulier avec PrfA. De plus, on retrouve une séquence similaire de la boîte PrfA dans la région promotrice d ers. Celle-ci a été montrée comme étant incluse dans le segment d ADN reconnu par Ers. D autre part, cette protéine est impliquée dans la survie de la bactérie au stress oxydatif et dans les macrophages. Un mutant deltaers est, de plus, moins virulent que la souche sauvage dans un modèle murin de péritonite. Ers joue également un rôle dans le métabolisme de l arginine, du citrate et du glycérol. Les membres actuellement connus du régulon Ers sont les gènes ef0082 (codant un transporteur du glycérol), arcABC (codant des enzymes du métabolisme de l arginine), ef1459 (codant une protéine hypothétique), citF (codant la sous-unité alpha de la citrate lyase), ace (codant une adhésine impliquée dans la virulence) et enfin glpKOF (codant des protéines jouant un rôle dans le catabolisme du glycérol). L ensemble de ces résultats révèle qu Ers est un régulateur pléiotrope impliqué dans la virulence et le métabolisme cellulaire chez E. faecalis.Ers is a transcriptional regulator of Enterococcus faecalis, a lactic acid bacterium more and more involved in hospital acquired infection. It is part of the PrfA branch of the Crp/Fnr family regulators and may exert a PrfA-like activity in E. faecalis. This protein shares strong structural homologies with proteins of this family including PrfA, the major regulator of virulence in Listeria monocytogenes. Moreover, a sequence similar to the PrfA-box is found in the promoter regions of ers and it has been shown to be included in the DNA segment recognized by Ers. Furthermore, this protein is important for the survival of this opportunistic pathogen towards oxidative stress and within macrophages. In addition, in a mouse peritonitis model of virulence, the deltaers mutant appeared significantly less lethal than the JH2-2 wild type strain. Ers is also involved in the arginine, citrate and glycerol metabolism. At the present time, the Ers regulon is composed of ef0082 encoding a glycerol transporter, arcABC, encoding enzymes of the arginine deiminase system, ef1459 encoding a hypothetical protein, citF, encoding the alpha subunit of the citrate lyase involved in the citrate catabolism, ace, an adhesin involved in virulence and finally glpKOF, encoding two glycerol degradation enzymes, GlpK and GlpO, and a glycerol uptake facilitator, GplF. Taken together, these results indicate that the regulator Ers has a pleiotropic effect, especially in the cellular metabolism and in the virulence of E. faecalisCAEN-BU Sciences et STAPS (141182103) / SudocSudocFranceF

Ers Controls Glycerol Metabolism in Enterococcus faecalis

International audienceErs is a pleiotropic transcriptional regulator in Enterococcus faecalis, an opportunistic bacterium. The authors have already shown that this protein is important for survival against oxidative stress and within macrophages as well as for survival of mice, and that Ers also is involved in the regulation of citrate and arginine metabolisms. The current study highlights the involvement of Ers also in the regulation of glycerol metabolism. The results suggest that EF0082, a known member of the Ers regulon encoding a major facilitator family transporter, may be able to transport glycerol. Moreover, the study demonstrates that Ers acts as a positive regulator of the glpKOF operon encoding glycerol kinase, glycerol-3-phosphate oxidase, and glycerol transport facilitator proteins

Enterococcus faecalis Maltodextrin Gene Regulation by Combined Action of Maltose Gene Regulator MalR and Pleiotropic Regulator CcpA

International audienceEnterococcus faecalis represents a leading cause of hospital-acquired infections worldwide. Several studies highlighted the importance of carbohydrate metabolism in the infection process of this bacterium. The genes required for maltodextrin metabolism are particularly induced during mouse infection and, therefore, should play an important role for pathogenesis. Since no data were hitherto available concerning the regulation of expression of the maltodextrin operons, we have conducted experiments to study the underlying mechanisms