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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0294

PubMed

29310579, BMC Genomics. 2018 Jan 8;19(1):33. doi: 10.1186/s12864-017-4388-9.

Characterization method

gene trait matching exercise

Genomic accession number

PJEE01000011.1

Nucelotide position range

293988-308944

Substrate

xylooligosaccharide

Loci

APC1464_1419-APC1464_1430

Species

Bifidobacterium longum/216816

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- APC1464_1419 PKD09594.1 0 - 345 (+) PJEE01000011.1:293988-294333 -
- APC1464_1420 PKD09792.1 607 - 790 (-) PJEE01000011.1:294595-294778 -
- APC1464_1421 PKD09793.1 980 - 2960 (-) PJEE01000011.1:294968-296948 -
- APC1464_1422 PKD09794.1 3022 - 3655 (-) PJEE01000011.1:297010-297643 -
- APC1464_1423 PKD09795.1 3727 - 5500 (-) PJEE01000011.1:297715-299488 -
- APC1464_1424 PKD09796.1 5576 - 7196 (-) PJEE01000011.1:299564-301184 -
- APC1464_1425 PKD09797.1 7311 - 8208 (-) PJEE01000011.1:301299-302196 -
- APC1464_1426 PKD09798.1 8204 - 9257 (-) PJEE01000011.1:302192-303245 -
- APC1464_1427 PKD09799.1 9350 - 10664 (-) PJEE01000011.1:303338-304652 -
- APC1464_1428 PKD09595.1 11002 - 12043 (+) PJEE01000011.1:304990-306031 -
- APC1464_1429 PKD09800.1 12051 - 13251 (-) PJEE01000011.1:306039-307239 -
- APC1464_1430 PKD09801.1 13607 - 14957 (-) PJEE01000011.1:307595-308945 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 345 (+) CDS No
- 608 - 790 (-) CDS No
- 981 - 2960 (-) CAZyme: GH120 Yes
- 3023 - 3655 (-) other Yes
- 3728 - 5500 (-) CAZyme: GH43|GH43_12 Yes
- 5577 - 7196 (-) CAZyme: GH43_11|GH43 Yes
- 7312 - 8208 (-) TC: gnl|TC-DB|Q72H66|3.A.1.1.25 Yes
- 8205 - 9257 (-) TC: gnl|TC-DB|Q72H67|3.A.1.1.25 Yes
- 9351 - 10664 (-) TC: gnl|TC-DB|Q9L027|3.A.1.1.21 Yes
- 11003 - 12043 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 No
- 12052 - 13251 (-) CDS No
- 13608 - 14957 (-) CDS No

PUL ID

PUL0294

PubMed

29310579, BMC Genomics. 2018 Jan 8;19(1):33. doi: 10.1186/s12864-017-4388-9.

Title

Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains.

Author

Arboleya S, Bottacini F, O'Connell-Motherway M, Ryan CA, Ross RP, van Sinderen D, Stanton C

Abstract

BACKGROUND: Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. RESULTS: We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). CONCLUSIONS: The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.