Home Repository Download Help About Statistics Taxonomy Blastx
Links
PULDB
CAZy
dbCAN2
dbCAN-seq
run_dbcan
CAZypedia
PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0140

PubMed

30306201, Appl Microbiol Biotechnol. 2018 Dec;102(24):10645-10663. doi: 10.1007/s00253-018-9413-7. Epub 2018 Oct 10.

Characterization method

sequence homology analysis

Genomic accession number

CP028460

Nucelotide position range

622448-639066

Substrate

xylose

Loci

CNCMI4602_0516-CNCMI4602_0526

Species

Bifidobacterium animalis subsp. animalis/302912

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- CNCMI4602_0516 AYN23376.1 0 - 1353 (+) CP028460.1:622448-623801 -
- CNCMI4602_0517 AYN23377.1 1782 - 3465 (+) CP028460.1:624230-625913 -
- CNCMI4602_0518 AYN23378.1 3629 - 4646 (-) CP028460.1:626077-627094 -
- CNCMI4602_0519 AYN23379.1 4977 - 6255 (+) CP028460.1:627425-628703 -
- CNCMI4602_0520 AYN23380.1 6362 - 7421 (+) CP028460.1:628810-629869 -
- CNCMI4602_0521 AYN23381.1 7422 - 8292 (+) CP028460.1:629870-630740 -
- CNCMI4602_0522 AYN23382.1 8369 - 9995 (+) CP028460.1:630817-632443 -
- CNCMI4602_0523 AYN23383.1 9997 - 12028 (+) CP028460.1:632445-634476 -
- CNCMI4602_0524 AYN23384.1 12264 - 13428 (+) CP028460.1:634712-635876 -
- CNCMI4602_0525 AYN23385.1 13440 - 15000 (-) CP028460.1:635888-637448 -
- CNCMI4602_0526 AYN23386.1 15089 - 16619 (-) CP028460.1:637537-639067 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1353 (+) CDS No
- 1783 - 3465 (+) CAZyme: GH43|GH43_12 Yes
- 3630 - 4646 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 4978 - 6255 (+) STP: STP|SBP_bac_1 Yes
- 6363 - 7421 (+) TC: gnl|TC-DB|Q72H67|3.A.1.1.25 Yes
- 7423 - 8292 (+) TC: gnl|TC-DB|Q8RJU8|3.A.1.1.18 Yes
- 8370 - 9995 (+) CAZyme: GH43|GH43_11 Yes
- 9998 - 12028 (+) other Yes
- 12265 - 13428 (+) other Yes
- 13441 - 15000 (-) CAZyme: GH43_10 Yes
- 15090 - 16619 (-) CDS No

PUL ID

PUL0140

PubMed

30306201, Appl Microbiol Biotechnol. 2018 Dec;102(24):10645-10663. doi: 10.1007/s00253-018-9413-7. Epub 2018 Oct 10.

Title

Staying alive: growth and survival of Bifidobacterium animalis subsp. animalis under in vitro and in vivo conditions.

Author

Egan M, Bottacini F, O'Connell Motherway M, Casey PG, Morrissey R, Melgar S, Faurie JM, Chervaux C, Smokvina T, van Sinderen D

Abstract

Members of the Bifidobacterium genus are widely used as probiotics in fermented milk products. Bifidobacterium animalis subsp. animalis CNCM I-4602 grows and survives poorly in reconstituted skimmed milk (RSM). Availing of genome and transcriptome information, this poor growth and survival phenotype in milk was substantially improved by the addition of certain compounds, such as yeast extract, uric acid, glutathione, cysteine, ferrous sulfate, and a combination of magnesium sulfate and manganese sulfate. Carbohydrate utilization of CNCM I-4602 was also investigated, allowing the identification of several carbohydrate utilization gene clusters, and highlighting this strain's inability to utilize lactose, unlike the type strain of this subspecies, B. animalis subsp. animalis ATCC25527 and the B. animalis subsp. lactis subspecies. In addition, the ability of B. animalis subsp. animalis CNCM I-4602 to colonize a murine model was investigated, which showed that this strain persists in the murine gut for a period of at least 4 weeks. Associated in vivo transcriptome analysis revealed that, among other genes, a gene cluster encoding a predicted type IVb tight adherence (Tad) pilus was upregulated, indicating that this extracellular structure plays a role in the colonization/adaptation of the murine gastrointestinal tract by this strain.