Abstract
We report the draft genome sequence of the strain Lactobacillus hominis CRBIP 24.179T, isolated from a human clinical sample. The total length of the 28 contigs is about 1.9 Mb, with a G+C content of 37% and 1,983 coding sequences.
GENOME ANNOUNCEMENT
Lactobacillus hominis strain 61DT, renamed L. hominis CRBIP 24.179T, was isolated in the early 1960s from a clinical isolate (1). Some species of the genus Lactobacillus have been isolated from clinical patients with a variety of clinical problems (2, 3). Most of those strains (but not all) belong to the species Lactobacillus rhamnosus, Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus plantarum. These species are also among those most frequently found in human intestinal flora. Nevertheless, there is only limited information concerning the risk that is linked to potential virulence factors present in Lactobacillus strains (4).
Here, we report the genome sequence of L. hominis CRBIP 24.179T, obtained using a whole-genome strategy based on Illumina paired-end sequencing, with an insert length of 380 bp (Illumina genome analyzer HiSeq 2000). In order to test assembly de novo tools, quality-filtered reads (116,085,864 reads, 99 bases mean read length, ~5,190-fold coverage) were assembled using two softwares, VelvetOptimiser version 2.2.0 (5) and ABySS version 1.2.6 (6). The resulting contigs were compared using Mauve version 2.3.1 (7). The two scaffolds were somewhat similar (28 Velvet contigs and 37 ABySS contigs, with maximum lengths of 365,062 and 267,206 bases, respectively). Nevertheless, differences related to the number and the maximum length of contigs and Mauve assessment support the de novo assembled contigs obtained using Velvet.
The draft genome consists of 36 contigs, with a total length of 1,927,726 nucleotides (nt) and a G+C content of 37%. The sizes of the contigs were between 701 bases for the shortest and 365,062 bases for the longest. The contigs were annotated with the AGMIAL platform (8), an integrated bacterial genome annotation system. The prediction of coding sequences used the self-training gene detection software SHOW based on hidden Markov models (http://genome.jouy.inra.fr/ssb/SHOW/). tRNAs and rRNAs were detected using tRNAscan-SE (9) and RNAmmer (10) softwares, respectively. There were 1,983 coding sequences (CDSs) predicted (1,938 complete), as well as one rRNA operon with 1 copy each of the 23S, 5S, and 16S genes. Fifty-four tRNA genes were also predicted.
Nucleotide sequence accession numbers.
The strain is publicly available in two European collections under the no. CRBIP 24.179T and DSM 23910T. The draft of this whole-genome sequencing project has been deposited in EMBL under the accession no. CAKE01000001 to CAKE01000036. The version described in this paper is the first version.
ACKNOWLEDGMENTS
We thank N. Joly (Biology IT Center, Institut Pasteur, Paris) for the programs used for the quality filtering of the reads.
This communication is an initiative of the European Consortium of Microbial Resource Centers (EMbaRC), supported by the European Commission’s Seventh Framework Programme (FP7, 2007–2013), Research Infrastructures action under the grant agreement no. FP7-228310.
Footnotes
Citation Cousin S, Creno S, Ma L, Clermont D, Loux V, Bizet C, Bouchier C. 2013. Draft genome sequence of Lactobacillus hominis strain CRBIP 24.179T, isolated from human intestine. Genome Announc. 1(4):e00662-13. doi:10.1128/genomeA.00662-13.
REFERENCES
- 1. Cousin S, Motreff L, Gulat-Okalla ML, Gouyette C, Spröer C, Schumann P, Begaud E, Bouchier C, Clermont D, Bizet C. 2013. Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov. Int. J. Syst. Evol. Microbiol. 63:53–59 [DOI] [PubMed] [Google Scholar]
- 2. Aguirre M, Collins MD. 1993. Lactic acid bacteria and human clinical infection. J. Appl. Bacteriol. 75:95–107 [DOI] [PubMed] [Google Scholar]
- 3. Bourne KA, Beebe JL, Lue YA, Ellner PD. 1978. Bacteriemia due to Bifidobacterium, Eubacterium or Lactobacillus, twenty-one cases and review of the literature. Yale J. Biol. Med. 51:505–512 [PMC free article] [PubMed] [Google Scholar]
- 4. Gasser F. 1994. Safety of lactic acid bacteria and their occurrence in human clinical infections. Bull. Inst. Pasteur 92:45–67 [Google Scholar]
- 5. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. 2009. ABySS: a parallel assembler for short read sequence data. Genome Res. 19:1117–1123 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7. Darling AC, Mau B, Blattner FR, Perna NT. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14:1394–1403 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Bryson K, Loux V, Bossy R, Nicolas P, Chaillou S, van de Guchte M, Penaud S, Maguin E, Hoebeke M, Bessières P, Gibrat JF. 2006. AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res. 34:3533–3545 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25:955–964 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100–3108 [DOI] [PMC free article] [PubMed] [Google Scholar]