Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF

Background

Enterococcus faecalis has emerged as a major hospital pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF, which is commonly used for molecular manipulation and virulence studies.

Results

The 2,739,625 base pair chromosome of OG1RF was found to contain approximately 232 kilobases unique to this strain compared to V583, the only publicly available sequenced strain. Almost no mobile genetic elements were found in OG1RF. The 64 areas of divergence were classified into three categories. First, OG1RF carries 39 unique regions, including 2 CRISPR loci and a new WxL locus. Second, we found nine replacements where a sequence specific to V583 was substituted by a sequence specific to OG1RF. For example, the iol operon of OG1RF replaces a possible prophage and the vanB transposon in V583. Finally, we found 16 regions that were present in V583 but missing from OG1RF, including the proposed pathogenicity island, several probable prophages, and the cpsCDEFGHIJK capsular polysaccharide operon. OG1RF was more rapidly but less frequently lethal than V583 in the mouse peritonitis model and considerably outcompeted V583 in a murine model of urinary tract infections.

Conclusion

E. faecalis OG1RF carries a number of unique loci compared to V583, but the almost complete lack of mobile genetic elements demonstrates that this is not a defining feature of the species. Additionally, OG1RF's effects in experimental models suggest that mediators of virulence may be diverse between different E. faecalis strains and that virulence is not dependent on the presence of mobile genetic elements.     

Microbial communities in semi-consolidated carbonate sediments of the Southwest Indian Ridge

White semi-consolidated carbonate sediments attached to black ferromanganese oxide films were collected approximately 50 km west of a newly discovered hydrothermal field near the Southwest Indian Ridge (SWIR). The biodiversity of the prokaryotic communities within the field was examined using clone library-based culture-independent analysis of the exterior black oxides and the interior white carbonates. Subsequent 16S rRNA gene analysis suggested that Gamma-proteobacteria, Acidobacteria, and Thaumarchaeota members dominated the bacterial and archaeal clone libraries. To further characterize the metabolic processes within the microbial community, analyses of the amoA (coding the alpha subunit of the ammonia monooxygenase for Archaea) and aprA (coding the alpha subunit of the dissimilatory adenosine-5′-phosphosulfate reductase for the sulfate-reducing and sulfur-oxidizing prokaryotes) functional genes were conducted. The functional gene analysis results suggested that Thaumarchaeota and Alphaproteobacteria members were the potential players that participated in N and S cycles in this marine carbonate sedimentary environment. This paper is the first to describe the microbial communities and their potential metabolic pathways within the semi-consolidated carbonate sediments of the SWIR.