Whole genome sequencing of Bifidobacterium adolescentis ATCC15703

2006 Fiscal Year Final Research Report Summary

• Project/Area Number: 17510164
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Applied genomics
• Research Institution: Gifu University
• Principal Investigator: SUZUKI Tohru Gifu University, Life Science Research Center, Associate Professor, 生命科学総合研究支援センター, 准教授 (20235972)
• Co-Investigator(Kenkyū-buntansha): SUGA Haruhisa Gifu University, Life Science Research Center, Assistant Professor, 生命科学総合研究支援センター, 助教 (20283319)
• Project Period (FY): 2005 – 2006
• Keywords: Bifidobacterium / Probiotics / Tailor-made probiotics / genome analysis / genomics / microflora

Research Abstract

Bifidobacterium adolescentis is one of most predominant species in adult human large intestine. To investigate its physiological function and probiotic effect, we have analyzed whole genome sequence of the type-strain, B. adolescentis ATCC15703, by the whole genome shot-gun method.
About 40,000 reads of plasmid clone which carried ca. 2 kb of the genomic DNA flagment were assembled by Phred/Phrap/Consed. We also constructed Fosmid library with ca. 40 kb insert. About 1000 pair of the fosmid reads also added to generate the supercontig. There are 70 parts of high GC% palindromic regions at the each end of the contig which are unreadable by the cycle sequencing. We tried transcriptional sequencing using CUGA system to read these points and finally obtained single circular contig.
The genome consists of 2,089,645 by circular DNA, with 59 % GC content. We found 1631 CDSs, 54 tRNAs, 5 rRNA operons. Conparing to B. longum NCC2705 genome, 1203 CDSs were common and 428 CDSs were specific to B. adolescentis. There are seven long stretch (>50 kb) of low GC (about 50%) portion. We also found 88 times of 33bp length repeat, called Clustered Regularly Interspaced Short Parindrome Reapeats (CRISPR) and its related genes in its flanking region, which has not found in the genomes of other Bifidobacteria. These evidences reviealed B. adolescentis accepted long forign genomes and caused some genomic rearrangement in its past evolution.
Lacto-N-biose phosphorylase, 1,2-α-L-fucosidase and endo-α-N-acethyl galactosamidase gene, which found in B.longum, B.bifidum, and thought that association with host-bacterial interaction, were not exist in the B. adolescentis genome. These data suggested that B. adolescentis has alternative strategy to interact with host large intestinal tract.
The geome sequence was deposited to DDBJ/NCBI/EMBL database with accession no. AP009256.