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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0787

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

5695360-5755102

Substrate

pectic polysaccharide

Loci

Bovatus_RS21500-Bovatus_RS21650

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_RS21500 WP_004301549.1 0 - 2766 (-) NZ_CP012938.1:5695360-5698126 -
- Bovatus_RS21505 WP_004301550.1 2762 - 4166 (-) NZ_CP012938.1:5698122-5699526 3.2.1.-
- Bovatus_RS21510 WP_004320955.1 4162 - 4765 (-) NZ_CP012938.1:5699522-5700125 -
- Bovatus_RS21515 WP_004301552.1 4715 - 6251 (-) NZ_CP012938.1:5700075-5701611 3.2.1.-
- Bovatus_RS21520 WP_004301553.1 6299 - 7538 (-) NZ_CP012938.1:5701659-5702898 -
- Bovatus_RS21525 WP_004320954.1 7667 - 10544 (-) NZ_CP012938.1:5703027-5705904 -
- Bovatus_RS21530 WP_004301555.1 10786 - 13144 (+) NZ_CP012938.1:5706146-5708504 -
- Bovatus_RS21535 WP_004301556.1 13175 - 15326 (+) NZ_CP012938.1:5708535-5710686 3.2.1.23
- Bovatus_RS21540 WP_004301557.1 15364 - 15730 (+) NZ_CP012938.1:5710724-5711090 -
- Bovatus_RS21545 WP_004301558.1 15774 - 17160 (+) NZ_CP012938.1:5711134-5712520 3.2.1.-
- Bovatus_RS21550 WP_004301559.1 17248 - 17935 (+) NZ_CP012938.1:5712608-5713295 -
- Bovatus_RS21555 WP_004301560.1 18036 - 20118 (-) NZ_CP012938.1:5713396-5715478 -
- Bovatus_RS21560 WP_004301561.1 20142 - 23274 (-) NZ_CP012938.1:5715502-5718634 -
- Bovatus_RS21565 WP_052588036.1 23777 - 24956 (-) NZ_CP012938.1:5719137-5720316 -
- Bovatus_RS21570 WP_157452186.1 25355 - 26369 (+) NZ_CP012938.1:5720715-5721729 -
- Bovatus_RS21575 WP_004301565.1 26414 - 28040 (+) NZ_CP012938.1:5721774-5723400 -
- Bovatus_RS21580 WP_004301566.1 28099 - 31279 (+) NZ_CP012938.1:5723459-5726639 -
- Bovatus_RS21585 WP_004301567.1 31300 - 33313 (+) NZ_CP012938.1:5726660-5728673 -
- Bovatus_RS21590 WP_004301568.1 33359 - 36410 (+) NZ_CP012938.1:5728719-5731770 -
- Bovatus_RS21595 WP_004301569.1 36431 - 38153 (+) NZ_CP012938.1:5731791-5733513 -
- Bovatus_RS21600 WP_004301570.1 38233 - 40318 (+) NZ_CP012938.1:5733593-5735678 -
- Bovatus_RS21605 WP_004301571.1 40499 - 43898 (+) NZ_CP012938.1:5735859-5739258 -
- Bovatus_RS21610 WP_004301572.1 43878 - 45639 (-) NZ_CP012938.1:5739238-5740999 -
- Bovatus_RS21615 WP_004301576.1 46351 - 47986 (-) NZ_CP012938.1:5741711-5743346 -
- Bovatus_RS21620 WP_004301577.1 48115 - 49258 (-) NZ_CP012938.1:5743475-5744618 -
- Bovatus_RS21625 WP_004301578.1 49502 - 51344 (+) NZ_CP012938.1:5744862-5746704 -
- Bovatus_RS21630 WP_004301579.1 51347 - 52757 (+) NZ_CP012938.1:5746707-5748117 3.2.1.-
rhaM Bovatus_RS21635 WP_004301580.1 52775 - 53090 (+) NZ_CP012938.1:5748135-5748450 5.1.3.32
- Bovatus_RS21640 WP_004301581.1 53180 - 57464 (+) NZ_CP012938.1:5748540-5752824 2.7.13.3
- Bovatus_RS21645 WP_004301582.1 57630 - 58599 (+) NZ_CP012938.1:5752990-5753959 -
- Bovatus_RS21650 WP_032848694.1 58612 - 59743 (+) NZ_CP012938.1:5753972-5755103 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2766 (-) CAZyme: GH106 Yes
- 2763 - 4166 (-) CAZyme: GH28 Yes
- 4163 - 4765 (-) other Yes
- 4716 - 6251 (-) CAZyme: GH28 Yes
- 6300 - 7538 (-) CAZyme: CE12 Yes
- 7668 - 10544 (-) CAZyme: GH2 Yes
- 10787 - 13144 (+) CAZyme: GH43_18|GH43_34 Yes
- 13176 - 15326 (+) CAZyme: GH42 Yes
- 15365 - 15730 (+) other Yes
- 15775 - 17160 (+) CAZyme: GH28 Yes
- 17249 - 17935 (+) other Yes
- 18037 - 20118 (-) other Yes
- 20143 - 23274 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 23778 - 24956 (-) other Yes
- 25356 - 26369 (+) other Yes
- 26415 - 28040 (+) other Yes
- 28100 - 31279 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 31301 - 33313 (+) other Yes
- 33360 - 36410 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 36432 - 38153 (+) other Yes
- 38234 - 40318 (+) CAZyme: PL11_1 Yes
- 40500 - 43898 (+) CAZyme: PL26 Yes
- 43879 - 45639 (-) other Yes
- 46352 - 47986 (-) CAZyme: CE12|CE12 Yes
- 48116 - 49258 (-) CAZyme: GH105 Yes
- 49503 - 51344 (+) CAZyme: PL11_1 Yes
- 51348 - 52757 (+) CAZyme: GH105 Yes
- 52776 - 53090 (+) other Yes
- 53181 - 57464 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 57631 - 58599 (+) CAZyme: CE4 Yes
- 58613 - 59743 (+) CAZyme: GH105 Yes

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PUL ID

PUL0787

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.