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J Bacteriol. Jan 2009; 191(2): 678–679.
Published online Nov 14, 2008. doi:  10.1128/JB.01515-08
PMCID: PMC2620821
Genome Sequence of the Probiotic Bacterium Bifidobacterium animalis subsp. lactis AD011 [down-pointing small open triangle]
Jihyun F. Kim,1,2* Haeyoung Jeong,1 Dong Su Yu,1,3 Sang-Haeng Choi,1 Cheol-Goo Hur,1 Myeong-Soo Park,4,6 Sung Ho Yoon,1 Dae-Won Kim,1 Geun Eog Ji,5,6 Hong-Seog Park,1,2* and Tae Kwang Oh1,7
Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 305-806, Korea,1 Korea University of Science and Technology (UST), 113 Gwahangno, Yuseong, Daejeon 305-333, Korea,2 Chungnam National University, 79 Daehangno, Yuseong, Daejeon 305-764, Korea,3 Anyang Technical College, Anyang, Gyeonggi-do 430-749, Korea,4 Department of Food and Nutrition, Research Institute of Human Ecology, Seoul National University, Seoul 151-742, Korea,5 Bifido Inc., Gangwon-do 250-804, Korea,6 21C Frontier Microbial Genomics and Applications Center, Yuseong, Daejeon 305-806, Korea7
*Corresponding author. Mailing address: 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Korea. Phone for Jihyun F. Kim: 82 42 860 4412. Fax: 82 42 879 8595. E-mail: jfk/at/kribb.re.kr. Phone for Hong-Seog Park: 82 42 879 8132. Fax: 82-42-879-8139. E-mail: hspark/at/kribb.re.kr
These authors contributed equally to this work.
Received October 27, 2008; Accepted October 31, 2008.
Abstract
Bifidobacterium animalis subsp. lactis is a probiotic bacterium that naturally inhabits the guts of most mammals, including humans. Here we report the complete genome sequence of B. animalis subsp. lactis AD011 that was isolated from an infant fecal sample. Biological functions encoded in a single circular chromosome of 1,933,695 bp, smallest among the completely sequenced bifidobacterial genomes, are suggestive of their probiotic functions, such as utilization of bifidogenic factors and a variety of glycosidic enzymes and biosynthesis of polysaccharides.
A plethora of microorganisms thriving in the human intestine are known to play vital roles in supporting and maintaining human health (4). Among them, bifidobacterial species form a phylogenetically distinct group with characteristic biochemical and probiotic properties (2, 9). Bifidobacterium animalis and Bifidobacterium lactis, both frequently utilized as probiotics, are described as being two subspecies of B. animalis according to a recent polyphasic taxonomic study (10). Isolated from the fecal sample of a healthy, breast-fed infant, B. animalis subsp. lactis AD011 showed a high level of immunomodulatory activity (7) as well as a tolerance to gastric acid and bile acids (data not shown).
The complete genome sequence of strain AD011 was determined by the traditional Sanger pair-ended sequencing of plasmid and fosmid libraries. Shotgun sequences were base called and were assembled into contigs using the Phred/Phrap/Consed software package (http://www.phrap.org). Sequencher (Gene Codes Corp., Ann Arbor, MI) was used for processing of the finishing reads from custom primer walks and manual validation. Protein-coding genes, predicted by Glimmer (3) and CRITICA (1), were assigned functions by the transitive annotation implemented in AutoFACT (8). Artemis (11) was used for final verification of the annotation results.
B. animalis subsp. lactis AD011 has one circular chromosome of 1,933,695 bp (60.49% G+C), without any plasmids. This genome size is smaller than the other completely sequenced genomes in the Bifidobacteriales that are Bifidobacterium adolescentis ATCC 15703 (2.09 Mb; NC_008618), Bifidobacterium longum DJO10A (2.38 Mb; NC_010816), and B. longum NCC2705 (2.26 Mb; NC_004307 [13]). The AD011 genome codes for 1,528 coding sequences, two rRNA operons, and 52 tRNA genes. No functional prophages were identified from the genome sequence, except for a couple of phage-related genes, including integrases.
Comparative genome analysis with the other completely sequenced bifidobacteria disclosed the “bifid shunt” carbohydrate degradation strategy with an incomplete citric acid cycle. A dozen glycosylases that can degrade various plant- or milk-derived oligosaccharides were identified from the genome sequence. A modular glycosyl hydrolase cluster consisting of hydrolase genes, a transcriptional regulator, and an ABC transporter (BLA_1513 to BLA_1524) was also found. Additionally, genome analysis revealed the fos gene cluster that is involved in the processing of health-promoting fructooligosaccharides, called bifidogenic factors, and that is highly similar to the gene cluster described from Bifidobacterium breve UCC2003 (12).
A significant portion of the AD011 genome (22.1%) is computationally predicted to be genomic islands (15). Among them, the largest island with a low G+C content encompasses the 732- to ~787-kb region and appears to be dedicated to polysaccharide biosynthesis. Polysaccharides produced by gut microbes are thought to be potential candidates for probiotic factors.
A gene (for BLA_1379) encoding the bile salt hydrolase (EC 3.5.1.24), 99.7% identical to that of B. animalis subsp. lactis KL612 (6), was uncovered from the genome sequence and may be responsible for this bacterium's tolerance to bile acids. Bile tolerance is considered to be mediated by specific hydrolases or exclusion systems (5).
Though their biological significance as health-promoting commensal microorganisms in human intestines is being emphasized, complete genome sequence information for bifidobacteria is still scarce (14). Our work thus may lead to genome-based biotechnological applications in the health care and food industries that utilize B. animalis subsp. lactis and related bacteria.
Nucleotide sequence accession number.
The genome sequence and annotation of the AD011 chromosome, deposited in GenBank under accession number CP001213, are also available from the Genome Encyclopedia of Microbes (GEM; http://www.gem.re.kr).
Acknowledgments
We thank the GEM members, including the KRIBB sequencing and informatics teams, for technical assistance.
J.F.K., G.E.J., and T.K.O. conceived the project; M.-S.P. and G.E.J. isolated and characterized the bacterium; S.-H.C., D.-W.K., and H.-S.P. carried out shotgun sequencing and finishing; D.S.Y. annotated the genome sequence; C.-G.H. maintained a genome database; H.J., D.S.Y., S.H.Y., and J.F.K. analyzed the genome information; and H.J. and J.F.K. wrote the manuscript.
This work was funded by the 21C Frontier Microbial Genomics and Applications Center Program of the Ministry of Education, Science, and Technology (to J.F.K.).
Footnotes
[down-pointing small open triangle]Published ahead of print on 14 November 2008.
1. Badger, J. H., and G. J. Olsen. 1999. CRITICA: coding region identification tool invoking comparative analysis. Mol. Biol. Evol. 16512-524. [PubMed]
2. Biavati, B., and P. Mattarelli. 2006. The family Bifidobacteriaceae, p. 538-604. In M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer, and E. Stackebrandt (ed.), The prokaryotes: a handbook on the biology of bacteria, 3rd ed., vol. 3. Springer, New York, NY.
3. Delcher, A. L., K. A. Bratke, E. C. Powers, and S. L. Salzberg. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23673-679. [PMC free article] [PubMed]
4. Guarner, F., and J.-R. Malagelada. 2003. Gut microflora in health and disease. Lancet 360512-519. [PubMed]
5. Gunn, J. S. 2000. Mechanisms of bacterial resistance and response to bile. Microbes Infect. 2907-913. [PubMed]
6. Kim, G. B., and B. H. Lee. 2008. Genetic analysis of a bile salt hydrolase in Bifidobacterium animalis subsp. lactis KL612. J. Appl. Microbiol. 105778-790. [PubMed]
7. Kim, J. Y., Y. O. Choi, and G. E. Ji. 2008. Effect of oral probiotics (Bifidobacterium lactis AD011 and Lactobacillus acidophilus AD031) administration on ovalbumin-induced food allergy mouse model. J. Microbiol. Biotechnol. 181393-1400. [PubMed]
8. Koski, L. B., M. W. Gray, B. F. Lang, and G. Burger. 2005. AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics 6151. [PMC free article] [PubMed]
9. Leahy, S. C., D. G. Higgins, G. F. Fitzgerald, and D. van Sinderen. 2005. Getting better with bifidobacteria. J. Appl. Microbiol. 981303-1315. [PubMed]
10. Masco, L., M. Ventura, R. Zink, G. Huys, and J. Swings. 2004. Polyphasic taxonomic analysis of Bifidobacterium animalis and Bifidobacterium lactis reveals relatedness at the subspecies level: reclassification of Bifidobacterium animalis as Bifidobacterium animalis subsp. animalis subsp. nov. and Bifidobacterium lactis as Bifidobacterium animalis subsp. lactis subsp. nov. Int. J. Syst. Evol. Microbiol. 541137-1143. [PubMed]
11. Rutherford, K., J. Parkhill, J. Crook, T. Hornell, P. Rice, M. A. Rajandream, and B. Barrell. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16944-945. [PubMed]
12. Ryan, S. M., G. F. Fitzgerald, and D. van Sinderen. 2005. Transcriptional regulation and characterization of a novel β-fructofuranosidase-encoding gene from Bifidobacterium breve UCC2003. Appl. Environ. Microbiol. 713475-3482. [PMC free article] [PubMed]
13. Schell, M. A., M. Karmirantzou, B. Snel, D. Vilanova, B. Berger, G. Pessi, M. C. Zwahlen, F. Desiere, P. Bork, M. Delley, R. D. Pridmore, and F. Arigoni. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA 9914422-14427. [PubMed]
14. Ventura, M., M. O'Connell-Motherway, S. Leahy, J. A. Moreno-Munoz, G. F. Fitzgerald, and D. van Sinderen. 2007. From bacterial genome to functionality; case bifidobacteria. Int. J. Food Microbiol. 1202-12. [PubMed]
15. Yoon, S. H., C.-G. Hur, H.-Y. Kang, Y. H. Kim, T. K. Oh, and J. F. Kim. 2005. A computational approach for identifying pathogenicity islands in prokaryotic genomes. BMC Bioinformatics 6184. [PMC free article] [PubMed]
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