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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0299

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_PJDX01000003.1

Nucelotide position range

147509-164237

Substrate

fucosyllactose

Loci

APC1477_RS01575-APC1477_RS01635

Species

Bifidobacterium longum/216816

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- APC1477_RS01575 WP_100967851.1 0 - 2844 (+) NZ_PJDX01000003.1:147509-150353 -
- APC1477_RS01580 WP_100967852.1 2978 - 4022 (-) NZ_PJDX01000003.1:150487-151531 -
- APC1477_RS01585 WP_100967853.1 4378 - 5290 (+) NZ_PJDX01000003.1:151887-152799 -
- APC1477_RS01590 WP_033501883.1 5289 - 6267 (+) NZ_PJDX01000003.1:152798-153776 -
- APC1477_RS01595 WP_081962303.1 6364 - 7777 (+) NZ_PJDX01000003.1:153873-155286 -
- APC1477_RS01600 WP_033501881.1 7868 - 9146 (+) NZ_PJDX01000003.1:155377-156655 -
- APC1477_RS01605 WP_100967854.1 9161 - 9953 (+) NZ_PJDX01000003.1:156670-157462 -
- APC1477_RS01610 WP_100967855.1 9963 - 10785 (+) NZ_PJDX01000003.1:157472-158294 -
- APC1477_RS01615 WP_100967856.1 10781 - 11678 (+) NZ_PJDX01000003.1:158290-159187 -
fucU APC1477_RS01620 WP_100967857.1 11713 - 12151 (+) NZ_PJDX01000003.1:159222-159660 5.1.3.29
- APC1477_RS01625 WP_100967858.1 12170 - 13607 (+) NZ_PJDX01000003.1:159679-161116 -
- APC1477_RS01630 WP_100967859.1 13621 - 15973 (+) NZ_PJDX01000003.1:161130-163482 -
rsmD APC1477_RS01635 WP_080770942.1 16108 - 16729 (+) NZ_PJDX01000003.1:163617-164238 2.1.1.171

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2844 (+) CDS No
- 2979 - 4022 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 No
- 4379 - 5290 (+) TC: gnl|TC-DB|D6ZW63|3.A.1.1.48 Yes
- 5290 - 6267 (+) TC: gnl|TC-DB|D6ZW62|3.A.1.1.48 Yes
- 6365 - 7777 (+) STP: STP|SBP_bac_1 Yes
- 7869 - 9146 (+) other Yes
- 9162 - 9953 (+) other Yes
- 9964 - 10785 (+) other Yes
- 10782 - 11678 (+) other Yes
fucU 11714 - 12151 (+) other Yes
- 12171 - 13607 (+) CAZyme: GH29 Yes
- 13622 - 15973 (+) CAZyme: GH95 Yes
rsmD 16109 - 16729 (+) CDS No

PUL ID

PUL0299

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.