Genome Sequence of Enterococcus faecalis Strain CG_E.

Enterococcus faecalis CG_E is a Gram-positive, lactic acid-producing coccus. The draft genome of E. faecalis strain CG_E comprises 2,969,881 bp and exhibits a G+C content of 37.34%. The genome encodes 2,848 predicted protein-encoding and 97 RNA genes.

GENOME ANNOUNCEMENT

Enterococcus faecalis was isolated from peritoneal fluid in 1906 as a Streptococcus species (1), a designation which was revised in 1989 by Coykendall (2). This strain is known as a commensal bacterium that inhabits the gastrointestinal tract of humans and other mammals (3). Other studies also showed that 16S rRNA gene sequences of Enterococcus are also present in low abundances in biogas reactors (4).

E. faecalis strain CG_E was isolated from biogas reactor content and initially designated E. faecalis CG01 (5). Maize silage and cattle as well as poultry dry manure were the main substrates supplied to the reactor, which is located in Troisdorf, Germany (6).

Genomic DNA was isolated from E. faecalis CG_E cells cultured in RCM liquid medium (Oxoid Ltd., Basingstoke, Hampshire, United Kingdom) at 37°C under an N2 and CO2 (80% + 20%) atmosphere. For genome sequencing, we used an approach that combined both the Titanium chemistry of the 454 GS-FLX pyrosequencing system (Roche Life Sciences) and the Genome Analyzer IIx (2- × 112-bp paired-end sequencing; Illumina). Shotgun sequencing libraries were generated from the extracted genomic DNA according to the instructions of the manufacturers (Illumina, San Diego, CA, USA; Roche Life Science). Sequencing resulted in 10,316,210 paired-end Illumina reads (112 bp) that were trimmed using Trimmomatic 0.32 (7) and 76,327 454 pyrosequencing reads. For the hybrid de novo assembly performed with the Mira v 3.4 (8), four million quality-filtered Illumina reads and all 454 reads were used. This resulted in a draft genome consisting of 79 contigs with an average coverage of 152-fold. The genome of E. faecalis CG_E consists presumably of a single chromosome (2,969,881 bp) with a G+C content of 37.34%. For automatic gene prediction, the software tool Prodigal (9) was used. Genes coding for rRNA and tRNA were identified using RNAmmer (10) and tRNAscan (11), respectively. The Integrated Microbial Genomes–Expert Review (IMG-ER) system (12) was applied for automatic annotation followed by manual curation using the Swiss-Prot, TrEMBL, and InterPro databases (13).

The draft genome encodes three rRNAs and 47 tRNAs. The genome harbors 2,101 predicted protein-encoding genes with deduced functions and 747 (26.23%) coding for hypothetical proteins.

In silico pairwise average nucleotide identity (ANI) (14) using version 4.540 deposited on an IMG/ER system (12) was used to analyze the genetic identity of the genome sequence of E. faecalis strain CG_E with E. faecalis ATCC 19433T (ASDA00000000), the type strain of this species. This analysis yielded 99.04% sequence similarity of both genome sequences, which clearly showed that the isolate CG_E belongs to the species Enterococcus faecalis. Genome inspection also revealed that a gene encoding a fructose-1,6-bisphosphate aldolase, the key enzyme for homofermentative lactic acid fermentation, is present. We also identified several phosphotransferase systems specific for several sugars such as fructose, glucose, maltose, sucrose, trehalose, mannose, and cellobiose and also for mannitol, sorbitol, and galactitol as well as for N-acetyl-d-glucosamine and N-acetyl-galactosamine. The genome harbors genes encoding a mannose-6-phosphate isomerase, an l-rhamnose-isomerase, and an l-rhamnose mutarotase as well as a mannitol-1-phosphate-5-dehydrogenase.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession no. MIQF00000000. The version described in this paper is version MIQF01000000.