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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0297

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

NZ_PJEG01000006.1

Nucelotide position range

13106-25205

Substrate

galactan

Loci

APC1461_RS02130-APC1461_RS0270

Species

Bifidobacterium longum/216816

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- APC1461_RS02130 WP_007055690.1 0 - 1350 (+) NZ_PJEG01000006.1:13106-14456 -
- APC1461_RS02135 WP_007055699.1 1568 - 2531 (+) NZ_PJEG01000006.1:14674-15637 -
- APC1461_RS02140 WP_007055725.1 2533 - 3541 (+) NZ_PJEG01000006.1:15639-16647 -
- APC1461_RS02145 WP_008782890.1 3727 - 5860 (+) NZ_PJEG01000006.1:16833-18966 -
- APC1461_RS02150 WP_008782891.1 5903 - 6959 (+) NZ_PJEG01000006.1:19009-20065 -
- APC1461_RS02155 WP_011068390.1 7154 - 9848 (+) NZ_PJEG01000006.1:20260-22954 -
- APC1461_RS02160 WP_003831698.1 10025 - 10415 (-) NZ_PJEG01000006.1:23131-23521 -
- APC1461_RS02165 WP_013140277.1 10483 - 11353 (+) NZ_PJEG01000006.1:23589-24459 -
- APC1461_RS02170 WP_075662544.1 11416 - 12100 (+) NZ_PJEG01000006.1:24522-25206 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1350 (+) STP: STP|SBP_bac_1 No
- 1569 - 2531 (+) TC: gnl|TC-DB|D6ZW63|3.A.1.1.48 Yes
- 2534 - 3541 (+) TC: gnl|TC-DB|D6ZW62|3.A.1.1.48 Yes
- 3728 - 5860 (+) CAZyme: GH42 Yes
- 5904 - 6959 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 7155 - 9848 (+) CAZyme: GH53|CBM61 Yes
- 10026 - 10415 (-) CDS No
- 10484 - 11353 (+) CDS No
- 11417 - 12100 (+) CDS No

PUL ID

PUL0297

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.