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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0788

PubMed

39892338, Food Chem. 2025 May 1;473:143109. doi: 10.1016/j.foodchem.2025.143109. Epub 2025 Jan 27.

Characterization method

RNA-seq,reducing-sugar assay,growth assay

Genomic accession number

NZ_CP012938.1

Nucelotide position range

5761137-5810545

Substrate

pectic polysaccharide

Loci

Bovatus_RS25580-Bovatus_RS21805

Species

Bacteroides ovatus strain ATCC 8483/28116

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- Bovatus_RS25045 WP_074726648.1 0 - 101 (-) NZ_CP012938.1:5761137-5761238 -
- Bovatus_RS25580 WP_004301589.1 0 - 276 (-) NZ_CP012938.1:5761137-5761413 -
- Bovatus_RS21685 WP_032848700.1 272 - 521 (-) NZ_CP012938.1:5761409-5761658 -
- Bovatus_RS21690 WP_004301592.1 681 - 2286 (-) NZ_CP012938.1:5761818-5763423 -
- Bovatus_RS21695 WP_004301593.1 2305 - 5437 (-) NZ_CP012938.1:5763442-5766574 -
- Bovatus_RS21700 WP_004320945.1 5648 - 6527 (-) NZ_CP012938.1:5766785-5767664 -
- Bovatus_RS21705 WP_004301596.1 6659 - 9623 (-) NZ_CP012938.1:5767796-5770760 3.2.1.-
- Bovatus_RS21710 WP_004301597.1 9822 - 14160 (-) NZ_CP012938.1:5770959-5775297 2.7.13.3
- Bovatus_RS21715 WP_004320943.1 14297 - 16199 (-) NZ_CP012938.1:5775434-5777336 -
- Bovatus_RS21720 WP_004301602.1 16419 - 17883 (+) NZ_CP012938.1:5777556-5779020 3.2.1.-
- Bovatus_RS21725 WP_004301607.1 18395 - 19940 (+) NZ_CP012938.1:5779532-5781077 -
- Bovatus_RS21730 WP_004301610.1 19986 - 20421 (+) NZ_CP012938.1:5781123-5781558 -
- Bovatus_RS21740 WP_004301612.1 20714 - 22025 (+) NZ_CP012938.1:5781851-5783162 3.2.1.-
- Bovatus_RS21745 WP_004301613.1 22327 - 24757 (+) NZ_CP012938.1:5783464-5785894 -
- Bovatus_RS21750 WP_004301615.1 24930 - 26622 (+) NZ_CP012938.1:5786067-5787759 4.2.2.-
- Bovatus_RS21755 WP_004301617.1 26648 - 28922 (+) NZ_CP012938.1:5787785-5790059 -
- Bovatus_RS21760 WP_004301619.1 28934 - 32201 (+) NZ_CP012938.1:5790071-5793338 -
- Bovatus_RS21765 WP_004301622.1 32214 - 33762 (+) NZ_CP012938.1:5793351-5794899 -
- Bovatus_RS21770 WP_032846044.1 33778 - 35512 (+) NZ_CP012938.1:5794915-5796649 -
- Bovatus_RS21775 WP_004301626.1 35519 - 37199 (+) NZ_CP012938.1:5796656-5798336 -
- Bovatus_RS21780 WP_004301631.1 37219 - 40360 (+) NZ_CP012938.1:5798356-5801497 -
- Bovatus_RS21785 WP_004301633.1 40362 - 42036 (+) NZ_CP012938.1:5801499-5803173 -
- Bovatus_RS21790 WP_004301639.1 42159 - 44271 (+) NZ_CP012938.1:5803296-5805408 -
- Bovatus_RS21795 WP_004301641.1 44287 - 47551 (+) NZ_CP012938.1:5805424-5808688 -
- Bovatus_RS21800 WP_004301643.1 47586 - 48996 (+) NZ_CP012938.1:5808723-5810133 3.2.1.-
- Bovatus_RS21805 WP_004301645.1 49028 - 49409 (+) NZ_CP012938.1:5810165-5810546 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 101 (-) CDS No
- 1 - 276 (-) CDS No
- 273 - 521 (-) CDS No
- 682 - 2286 (-) TC: gnl|TC-DB|C6Y217|8.A.46.1.3 Yes
- 2306 - 5437 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 5649 - 6527 (-) other Yes
- 6660 - 9623 (-) CAZyme: GH2 Yes
- 9823 - 14160 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 14298 - 16199 (-) CAZyme: PL11 Yes
- 16420 - 17883 (+) CAZyme: GH28 Yes
- 18396 - 19940 (+) CAZyme: PL9_1 Yes
- 19987 - 20421 (+) other Yes
- 20715 - 22025 (+) CAZyme: GH28 Yes
- 22328 - 24757 (+) CAZyme: CE20|GH105 Yes
- 24931 - 26622 (+) CAZyme: PL1_2 Yes
- 26649 - 28922 (+) other Yes
- 28935 - 32201 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 32215 - 33762 (+) other Yes
- 33779 - 35512 (+) other Yes
- 35520 - 37199 (+) other Yes
- 37220 - 40360 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 40363 - 42036 (+) other Yes
- 42160 - 44271 (+) other Yes
- 44288 - 47551 (+) other Yes
- 47587 - 48996 (+) CAZyme: GH28 Yes
- 49029 - 49409 (+) TF: DBD-Pfam|GerE No

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PUL ID

PUL0788

PubMed

39892338, Food Chem. 2025 May 1;473:143109. doi: 10.1016/j.foodchem.2025.143109. Epub 2025 Jan 27.

Title

In vitro fermentation of a purified fraction of polysaccharides from the root of Brassica rapa L. by human gut microbiota and its interaction with Bacteroides ovatus.

Author

Yi W, Shi J, Zhou W, Wei J, Sun Y, Zeng X, Wang W

Abstract

In this study, the physicochemical properties, in vitro fermentation, and interaction with Bacteroides ovatus of a purified fraction of polysaccharides from the root of Brassica rapa (BRP2-2) were investigated. It was demonstrated with an in vitro anaerobic fermentation model that BRP2-2 significantly increased (p < 0.05) the relative abundance of Bacteroides spp. After 24 h incubation of BRP2-2 with Bacteroides ovatus alone, 10.24 +/- 0.69, 8.76 +/- 0.48 and 3.37 +/- 0.26 mM of acetate, propionate and isovalerate were produced, respectively. Moreover, transcriptome analysis of B. ovatus showed that 143 genes were up-regulated by BRP2-2, including five discrete polysaccharide utilization loci and two carbohydrate-active enzyme clusters. Based on the annotation of carbohydrate enzyme function, we speculate that BRP2-2 is a pectic polysaccharide containing homogalacturonan, rhamnogalacturonan I and rhamnogalacturonan II domains. These results suggested that BRP2-2 was degraded by B. ovatus, which produced metabolites with beneficial effects on host health.