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Genome Announc. 2017 September; 5(36): e00675-17.
Published online 2017 September 7. doi:  10.1128/genomeA.00675-17
PMCID: PMC5589521

Draft Genome Sequence of Lactobacillus brevis Strain 3M004, a Probiotic with Potential Quorum-Sensing Regulation


We present here the draft genome sequence of Lactobacillus brevis strain 3M004, a probiotic that has potential for regulating quorum sensing. The strain was obtained from a type of aquafeed. The assembly consists of 2,459,326 bp and contains 33 contigs, with a G+C content of 45.10%.


Lactobacillus brevis strain 3M004 was obtained from a type of aquafeed. Some strains of this species have been reported to act against influenza in elementary schoolchildren and have anti-inflammatory effects on periodontal disease (1, 2). This strain could degrade acyl-homoserine lactones (AHLs) as quorum-sensing (3) signaling molecules efficiently, and the strain does not produce AHLs, which indicates that it has potential for regulating quorum sensing.

A TIANamp bacterial DNA kit (DP302-02, TIANGEN Biotech Co, Ltd, Beijing, China) was used to extract genomic DNA from L. brevis strain 3M004. A paired-end library with an insert size of 350 bp was constructed and sequenced using the Illumina HiSeq platform with a PE150 strategy. Then, the high-quality reads, without PCR adapter sequences, were assembled with SOAPdenovo (4, 5) to generate scaffolds, and all reads were used for further gap closure. A total of 667 Mb of high-quality sequence data were obtained, and the resulting assembly consisted of 2,459,326 bp comprising 33 contigs (the longest was 435,481 bp; N50 was 299,821 bp) with a G+C content of 45.10%. With gene prediction, a total of 2,410 genes in the genome assembly of L. brevis strain 3M004 were found by GeneMarkS (6) with integrated and heuristic model parameters. Gene annotation was performed with BLAST (7) searches (E value less than 1e−5 and minimal alignment length larger than 40%) against four databases; as a result, 1,325, 1,704, 2,350, and 1,664 functional genes were annotated from KEGG (8), COG (9), NR, and GO (10), respectively.

Accession number(s).

The genome sequence of L. brevis strain 3M004 was deposited at DDBJ/ENA/GenBank under the accession number NFZZ00000000. The version described in this paper is the first version, NFZZ01000000.


This work, including the efforts of Yan Liang, was funded by the Foundation of Shenzhen Strategic Emerging Industries Development (JSKF20150831171545604) and the Shenzhen Technology Development Project (CXZZ20150529144041624).


Citation Li Q, Pan Y, Ding L, Hong H, Yan S, Wu B, Liang Y. 2017. Draft genome sequence of Lactobacillus brevis strain 3M004, a probiotic with potential quorum-sensing regulation. Genome Announc 5:e00675-17.


1. Waki N, Matsumoto M, Fukui Y, Suganuma H 2014. Effects of probiotic Lactobacillus brevis KB290 on incidence of influenza infection among schoolchildren: an open-label pilot study. Lett Appl Microbiol 59:565–571. doi:.10.1111/lam.12340 [PMC free article] [PubMed] [Cross Ref]
2. Della Riccia DN, Bizzini F, Perilli MG, Polimeni A, Trinchieri V, Amicosante G, Cifone MG 2007. Anti-inflammatory effects of Lactobacillus brevis (CD2) on periodontal disease. Oral Dis 13:376–385. doi:.10.1111/j.1601-0825.2006.01291.x [PubMed] [Cross Ref]
3. Federle MJ, Bassler BL 2003. Interspecies communication in bacteria. J Clin Invest 112:1291–1299. doi:.10.1172/JCI20195 [PMC free article] [PubMed] [Cross Ref]
4. Li R, Li Y, Kristiansen K, Wang J 2008. SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714. doi:.10.1093/bioinformatics/btn025 [PubMed] [Cross Ref]
5. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272. doi:.10.1101/gr.097261.109 [PubMed] [Cross Ref]
6. Besemer J, Lomsadze A, Borodovsky M 2001. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618. doi:.10.1093/nar/29.12.2607 [PMC free article] [PubMed] [Cross Ref]
7. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ 1990. Basic local alignment search tool. J Mol Biol 215:403–410. doi:.10.1016/S0022-2836(05)80360-2 [PubMed] [Cross Ref]
8. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280. doi:.10.1093/nar/gkh063 [PMC free article] [PubMed] [Cross Ref]
9. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41. doi:.10.1186/1471-2105-4-41 [PMC free article] [PubMed] [Cross Ref]
10. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G 2000. Gene ontology: tool for the unification of biology. Nat Genet 25:25–29. doi:.10.1038/75556 [PMC free article] [PubMed] [Cross Ref]

Articles from Genome Announcements are provided here courtesy of American Society for Microbiology (ASM)