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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0347

PubMed

24581150, BMC Genomics. 2014 Mar 1;15(1):170. doi: 10.1186/1471-2164-15-170.

Characterization method

gene deletion mutant and growth assay,RT-PCR

Genomic accession number

CP006712.1

Nucelotide position range

1904821-1922254

Substrate

sorbitol

Loci

B7017_1838-B7017-1850

Species

Bifidobacterium breve/1685

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- B7017_1838 AHJ18068.1 0 - 309 (-) CP006712.1:1904821-1905130 -
- B7017_1839 AHJ18069.1 811 - 1531 (+) CP006712.1:1905632-1906352 -
- B7017_1840 AHJ18070.1 1954 - 2782 (+) CP006712.1:1906775-1907603 -
- B7017_1841 AHJ18071.1 2982 - 5706 (-) CP006712.1:1907803-1910527 -
- B7017_1842 AHJ18072.1 6114 - 7062 (-) CP006712.1:1910935-1911883 -
- B7017_1843 AHJ18073.1 7142 - 8183 (-) CP006712.1:1911963-1913004 -
- B7017_1844 AHJ18074.1 8294 - 9632 (-) CP006712.1:1913115-1914453 -
- B7017_1845 AHJ18075.1 9852 - 11001 (+) CP006712.1:1914673-1915822 -
- B7017_1846 AHJ18076.1 11080 - 11479 (-) CP006712.1:1915901-1916300 -
- B7017_1847 AHJ18077.1 11552 - 12926 (-) CP006712.1:1916373-1917747 -
- B7017_1848 AHJ18078.1 13111 - 14116 (-) CP006712.1:1917932-1918937 -
- B7017_1849 AHJ18079.1 14411 - 16859 (+) CP006712.1:1919232-1921680 -
- B7017_1850 AHJ18080.1 16942 - 17434 (-) CP006712.1:1921763-1922255 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 309 (-) CDS No
- 812 - 1531 (+) CDS No
- 1955 - 2782 (+) CDS No
- 2983 - 5706 (-) CDS No
- 6115 - 7062 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 No
- 7143 - 8183 (-) CDS No
- 8295 - 9632 (-) TC: gnl|TC-DB|O52718|2.A.1.18.1 Yes
- 9853 - 11001 (+) TF: DBD-Pfam|MarR,DBD-SUPERFAMILY|0044258 Yes
- 11081 - 11479 (-) STP: STP|Glyoxalase Yes
- 11553 - 12926 (-) TC: gnl|TC-DB|O52717|2.A.1.18.2 Yes
- 13112 - 14116 (-) other Yes
- 14412 - 16859 (+) CAZyme: CBM48|GH13_11 Yes
- 16943 - 17434 (-) CDS No

PUL ID

PUL0347

PubMed

24581150, BMC Genomics. 2014 Mar 1;15(1):170. doi: 10.1186/1471-2164-15-170.

Title

Comparative genomics of the Bifidobacterium breve taxon.

Author

Bottacini F, O'Connell Motherway M, Kuczynski J, O'Connell KJ, Serafini F, Duranti S, Milani C, Turroni F, Lugli GA, Zomer A, Zhurina D, Riedel C, Ventura M, van Sinderen D

Abstract

BACKGROUND: Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina. RESULTS: In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol. CONCLUSIONS: Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.