- Email: [email protected]
Complete genome sequence of Bifidobacterium bifidum JCM 1255T isolated from feces of a breast-fed infant
Journal of Biotechnology 210 (2015) 66–67
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome announcements
Complete genome sequence of Bifidobacterium bifidum JCM 1255T isolated from feces of a breast-fed infant Hidetoshi Morita a,b,∗,1 , Hidehiro Toh c,1 , Kenshiro Oshima b,d , Akiyo Nakano e , Chie Shindo d , Keiko Komiya d , Kensuke Arakawa a , Wataru Suda d , Kenya Honda b,f , Masahira Hattori d a
Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan c Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan d Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan e Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan f Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan b
a r t i c l e
i n f o
Article history: Received 19 June 2015 Accepted 23 June 2015 Available online 29 June 2015
a b s t r a c t Bifidobacterium bifidum JCM 1255T was isolated from feces of a breast-fed infant. Here we report the complete genome sequence of this organism. © 2015 Elsevier B.V. All rights reserved.
Keywords: Complete genome sequence
Bifidobacterium bifidum is one of the most common probiotic bacteria, which are defined as live microorganisms which when administered in adequate amounts confer a health benefit on the host. For the delivery of viable bifidobacterial cells, B. bifidum is often added in commercial yogurt. B. bifidum form a distinct branch in the phylogenetic tree of the genus Bifidobacterium (Felis and Dellaglio, 2007). B. bifidum JCM 1255T (=DSM 20456T ) was isolated from feces of a breast-fed infant (Miller and Finegold, 1967). We determined the complete genome sequence of B. bifidum JCM 1255T using the whole genome shotgun strategy using Sanger sequencing (ABI 3730xl sequencers). We constructed small-insert (2 kb) genomic DNA libraries, and generated 26,112 sequence reads (8.9-fold coverage) for B. bifidum JCM 1255T from both ends of the genomic clones. Data were assembled with the Phred-Phrap-Consed program. Gap closing and re-sequencing of low-quality regions were conducted by Sanger sequencing to obtain the high-quality finished sequence. The overall accuracy of the finished sequence was estimated to have an error rate of <1 per 10,000 bases (Phrap score of ≥40). An initial set of predicted protein-coding genes was identified
∗ Corresponding author at: Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan. E-mail address: [email protected] (H. Morita). 1 These authors contributed equally to this work. http://dx.doi.org/10.1016/j.jbiotec.2015.06.413 0168-1656/© 2015 Elsevier B.V. All rights reserved.
Table 1 Features of the B. bifidum JCM 1255T genome. Attributes
Value
Genome size (bp) GC content (%) Plasmid Protein coding genes (CDSs) rRNA operons tRNA genes
2,211,039 62.7 0 1,831 2 53
using Glimmer 3.0 (Delcher et al., 2007). Genes consisting of <120 base pairs (bp) and those containing overlaps were eliminated. The tRNA genes were predicted by the tRNAscan-SE (Schattner et al., 2005), and the rRNA genes were detected by BLASTN search using known Bifidobacterium rRNA sequences as queries. The genome sequence of B. bifidum JCM 1255T consists of a circular chromosome of 2,211,039 bp with no plasmid (Table 1). The chromosome contained 1,831 predicted protein-coding genes. We compared the genome of JCM 1255T with publicly available complete genome sequences of B. bifidum strains (PRL2010, S17, and BGN4) (Turroni et al., 2010; Yu et al., 2012; Zhurina et al., 2011). JCM 1255T shared 1,607, 1,575, and 1,612 protein-coding genes with PRL2010, S17, and BGN4, respectively, and then 1,482 protein-coding genes were common to the four strains. JCM 1255T contained genes for glycosyl hydrolases, which were
H. Morita et al. / Journal of Biotechnology 210 (2015) 66–67
less common to other bifidobacterial species, and the genes were classified in GH20, GH33, GH84, GH89, GH101, GH110, and GH112 families using the CAZy database (Lombard et al., 2014). Thirteen of the glycosyl hydrolase genes contained the LPXTG motif (BBBF 0019, BBBF 0199, BBBF 0270, BBBF 0474, BBBF 1004, BBBF 1287, BBBF 1348, BBBF 1434, BBBF 1499, BBBF 1509, BBBF 1524, BBBF 1779, and BBBF 1780), suggesting that these proteins are secreted and anchored to the cell wall. This complete genome sequence will be useful for comparative genome analysis of B. bifidum strains (Duranti et al., 2015). Nucleotide sequence accession number The sequence data for the genome have been deposited in DDBJ/GenBank/EMBL under the accession no. AP012323. Acknowledgement This research was partly supported by “CREST” (research projects pursued by research teams led by research directors) to H.M., K.O., and K.H.
67
References Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679. Duranti, S., Milani, C., Lugli, G.A., Turroni, F., Mancabelli, L., Sanchez, B., Ferrario, C., Viappiani, A., Mangifesta, M., Mancino, W., Gueimonde, M., Margolles, A., van Sinderen, D., Ventura, M., 2015. Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum. Environ. Microbiol., http:// dx.doi.org/10.1111/1462-2920.12743 Felis, G.E., Dellaglio, F., 2007. Taxonomy of Lactobacilli and Bifidobacteria. Curr. Issues Intest. Microbiol. 8, 44–61. Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P.M., Henrissat, B., 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–495. Miller, L.G., Finegold, S.M., 1967. Antibacterial sensitivity of Bifidobacterium (Lactobacillus bifidus). J. Bacteriol. 93, 125–130. Schattner, P., Brooks, A.N., Lowe, T.M., 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, W686–W689. Turroni, F., Bottacini, F., Foroni, E., Mulder, I., Kim, J.H., Zomer, A., Sánchez, B., Bidossi, A., Ferrarini, A., Giubellini, V., Delledonne, M., Henrissat, B., Coutinho, P., Oggioni, M., Fitzgerald, G.F., Mills, D., Margolles, A., van Sinderen, Kelly. D, Ventura, D., 2010. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc. Natl. Acad. Sci. U. S. A. 107, 19514–19519. Yu, D.S., Jeong, H., Lee, D.H., Kwon, S.K., Song, J.Y., Kim. B, K., Park, M.S., Ji, G.E., Oh, T.K., Kim, J.F., 2012. Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4. J. Bacteriol. 194, 4757–4758. Zhurina, D., Zomer, A., Gleinser, M., Brancaccio, V.F., Auchter, M., Waidmann, M.S., Westermann, C., van Sinderen, D., Riedel, C.U., 2011. Complete genome sequence of Bifidobacterium bifidum S17. J. Bacteriol. 193, 301–302.
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome announcements
Complete genome sequence of Bifidobacterium bifidum JCM 1255T isolated from feces of a breast-fed infant Hidetoshi Morita a,b,∗,1 , Hidehiro Toh c,1 , Kenshiro Oshima b,d , Akiyo Nakano e , Chie Shindo d , Keiko Komiya d , Kensuke Arakawa a , Wataru Suda d , Kenya Honda b,f , Masahira Hattori d a
Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan c Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan d Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan e Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan f Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan b
a r t i c l e
i n f o
Article history: Received 19 June 2015 Accepted 23 June 2015 Available online 29 June 2015
a b s t r a c t Bifidobacterium bifidum JCM 1255T was isolated from feces of a breast-fed infant. Here we report the complete genome sequence of this organism. © 2015 Elsevier B.V. All rights reserved.
Keywords: Complete genome sequence
Bifidobacterium bifidum is one of the most common probiotic bacteria, which are defined as live microorganisms which when administered in adequate amounts confer a health benefit on the host. For the delivery of viable bifidobacterial cells, B. bifidum is often added in commercial yogurt. B. bifidum form a distinct branch in the phylogenetic tree of the genus Bifidobacterium (Felis and Dellaglio, 2007). B. bifidum JCM 1255T (=DSM 20456T ) was isolated from feces of a breast-fed infant (Miller and Finegold, 1967). We determined the complete genome sequence of B. bifidum JCM 1255T using the whole genome shotgun strategy using Sanger sequencing (ABI 3730xl sequencers). We constructed small-insert (2 kb) genomic DNA libraries, and generated 26,112 sequence reads (8.9-fold coverage) for B. bifidum JCM 1255T from both ends of the genomic clones. Data were assembled with the Phred-Phrap-Consed program. Gap closing and re-sequencing of low-quality regions were conducted by Sanger sequencing to obtain the high-quality finished sequence. The overall accuracy of the finished sequence was estimated to have an error rate of <1 per 10,000 bases (Phrap score of ≥40). An initial set of predicted protein-coding genes was identified
∗ Corresponding author at: Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan. E-mail address: [email protected] (H. Morita). 1 These authors contributed equally to this work. http://dx.doi.org/10.1016/j.jbiotec.2015.06.413 0168-1656/© 2015 Elsevier B.V. All rights reserved.
Table 1 Features of the B. bifidum JCM 1255T genome. Attributes
Value
Genome size (bp) GC content (%) Plasmid Protein coding genes (CDSs) rRNA operons tRNA genes
2,211,039 62.7 0 1,831 2 53
using Glimmer 3.0 (Delcher et al., 2007). Genes consisting of <120 base pairs (bp) and those containing overlaps were eliminated. The tRNA genes were predicted by the tRNAscan-SE (Schattner et al., 2005), and the rRNA genes were detected by BLASTN search using known Bifidobacterium rRNA sequences as queries. The genome sequence of B. bifidum JCM 1255T consists of a circular chromosome of 2,211,039 bp with no plasmid (Table 1). The chromosome contained 1,831 predicted protein-coding genes. We compared the genome of JCM 1255T with publicly available complete genome sequences of B. bifidum strains (PRL2010, S17, and BGN4) (Turroni et al., 2010; Yu et al., 2012; Zhurina et al., 2011). JCM 1255T shared 1,607, 1,575, and 1,612 protein-coding genes with PRL2010, S17, and BGN4, respectively, and then 1,482 protein-coding genes were common to the four strains. JCM 1255T contained genes for glycosyl hydrolases, which were
H. Morita et al. / Journal of Biotechnology 210 (2015) 66–67
less common to other bifidobacterial species, and the genes were classified in GH20, GH33, GH84, GH89, GH101, GH110, and GH112 families using the CAZy database (Lombard et al., 2014). Thirteen of the glycosyl hydrolase genes contained the LPXTG motif (BBBF 0019, BBBF 0199, BBBF 0270, BBBF 0474, BBBF 1004, BBBF 1287, BBBF 1348, BBBF 1434, BBBF 1499, BBBF 1509, BBBF 1524, BBBF 1779, and BBBF 1780), suggesting that these proteins are secreted and anchored to the cell wall. This complete genome sequence will be useful for comparative genome analysis of B. bifidum strains (Duranti et al., 2015). Nucleotide sequence accession number The sequence data for the genome have been deposited in DDBJ/GenBank/EMBL under the accession no. AP012323. Acknowledgement This research was partly supported by “CREST” (research projects pursued by research teams led by research directors) to H.M., K.O., and K.H.
67
References Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679. Duranti, S., Milani, C., Lugli, G.A., Turroni, F., Mancabelli, L., Sanchez, B., Ferrario, C., Viappiani, A., Mangifesta, M., Mancino, W., Gueimonde, M., Margolles, A., van Sinderen, D., Ventura, M., 2015. Insights from genomes of representatives of the human gut commensal Bifidobacterium bifidum. Environ. Microbiol., http:// dx.doi.org/10.1111/1462-2920.12743 Felis, G.E., Dellaglio, F., 2007. Taxonomy of Lactobacilli and Bifidobacteria. Curr. Issues Intest. Microbiol. 8, 44–61. Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P.M., Henrissat, B., 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. 42, D490–495. Miller, L.G., Finegold, S.M., 1967. Antibacterial sensitivity of Bifidobacterium (Lactobacillus bifidus). J. Bacteriol. 93, 125–130. Schattner, P., Brooks, A.N., Lowe, T.M., 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 33, W686–W689. Turroni, F., Bottacini, F., Foroni, E., Mulder, I., Kim, J.H., Zomer, A., Sánchez, B., Bidossi, A., Ferrarini, A., Giubellini, V., Delledonne, M., Henrissat, B., Coutinho, P., Oggioni, M., Fitzgerald, G.F., Mills, D., Margolles, A., van Sinderen, Kelly. D, Ventura, D., 2010. Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging. Proc. Natl. Acad. Sci. U. S. A. 107, 19514–19519. Yu, D.S., Jeong, H., Lee, D.H., Kwon, S.K., Song, J.Y., Kim. B, K., Park, M.S., Ji, G.E., Oh, T.K., Kim, J.F., 2012. Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4. J. Bacteriol. 194, 4757–4758. Zhurina, D., Zomer, A., Gleinser, M., Brancaccio, V.F., Auchter, M., Waidmann, M.S., Westermann, C., van Sinderen, D., Riedel, C.U., 2011. Complete genome sequence of Bifidobacterium bifidum S17. J. Bacteriol. 193, 301–302.