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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0300

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_PJDO01000018.1

Nucelotide position range

15593-34141

Substrate

arabinoxylan

Loci

DPC6321_RS09575-DPC6321_RS09635

Species

Bifidobacterium longum/216816

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- DPC6321_RS09575 WP_011068669.1 0 - 333 (-) NZ_PJDO01000018.1:15593-15926 -
- DPC6321_RS09580 WP_007052908.1 639 - 1566 (-) NZ_PJDO01000018.1:16232-17159 -
- DPC6321_RS09585 WP_007052909.1 1562 - 2516 (-) NZ_PJDO01000018.1:17155-18109 -
- DPC6321_RS09590 WP_069483955.1 2651 - 3971 (-) NZ_PJDO01000018.1:18244-19564 -
- DPC6321_RS09595 WP_011068667.1 4388 - 5423 (-) NZ_PJDO01000018.1:19981-21016 -
- DPC6321_RS09600 WP_007055574.1 5687 - 6632 (+) NZ_PJDO01000018.1:21280-22225 -
- DPC6321_RS09605 WP_007052913.1 6743 - 7802 (-) NZ_PJDO01000018.1:22336-23395 -
- DPC6321_RS09610 WP_059280450.1 7917 - 10050 (-) NZ_PJDO01000018.1:23510-25643 -
- DPC6321_RS09615 WP_007054128.1 10165 - 11761 (+) NZ_PJDO01000018.1:25758-27354 -
- DPC6321_RS09620 WP_100985299.1 11917 - 13663 (+) NZ_PJDO01000018.1:27510-29256 -
- DPC6321_RS09625 WP_058060998.1 13816 - 14029 (-) NZ_PJDO01000018.1:29409-29622 -
- DPC6321_RS09630 WP_081040118.1 14012 - 16484 (-) NZ_PJDO01000018.1:29605-32077 -
- DPC6321_RS09635 WP_058060996.1 16740 - 18549 (-) NZ_PJDO01000018.1:32333-34142 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 72 (+) CDS No
- 1 - 333 (-) CDS No
- 640 - 1566 (-) TC: gnl|TC-DB|Q93J92|3.A.1.1.36 Yes
- 1563 - 2516 (-) TC: gnl|TC-DB|Q93J93|3.A.1.1.36 Yes
- 2652 - 3971 (-) STP: STP|SBP_bac_1 Yes
- 4389 - 5423 (-) CAZyme: GH43_26|GH43 Yes
- 5688 - 6632 (+) other Yes
- 6744 - 7802 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 7918 - 10050 (-) CAZyme: GH43_27|GH43 Yes
- 10166 - 11761 (+) CAZyme: GH43_4 Yes
- 11918 - 13663 (+) CAZyme: GH43_4 Yes
- 13817 - 14029 (-) other Yes
- 14013 - 16484 (-) CAZyme: GH51 Yes
- 16741 - 18549 (-) TC: gnl|TC-DB|Q8G7R7|3.A.1.106.3 Yes

PUL ID

PUL0300

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.