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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0786

PubMed

38890895, Foods. 2024 May 26;13(11):1666. doi: 10.3390/foods13111666.
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,high performance gel permeation chromatography,gas chromatography,RNA-seq,differential gene expression

Genomic accession number

NZ_CP012938.1

Nucelotide position range

686700-736482

Substrate

pectic polysaccharide

Loci

Bovatus_RS02815-Bovatus_RS02940

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_RS02815 WP_055167753.1 0 - 3327 (+) NZ_CP012938.1:686700-690027 -
- Bovatus_RS02820 WP_004300467.1 3345 - 4923 (+) NZ_CP012938.1:690045-691623 -
- Bovatus_RS02825 WP_004300468.1 4955 - 6020 (+) NZ_CP012938.1:691655-692720 -
- Bovatus_RS02830 WP_004300469.1 6042 - 7254 (+) NZ_CP012938.1:692742-693954 -
- Bovatus_RS02835 WP_004300470.1 7277 - 8243 (+) NZ_CP012938.1:693977-694943 -
- Bovatus_RS02840 WP_081015842.1 8407 - 10609 (+) NZ_CP012938.1:695107-697309 -
- Bovatus_RS02845 WP_004300472.1 10707 - 12036 (+) NZ_CP012938.1:697407-698736 -
- Bovatus_RS02850 WP_004318517.1 12052 - 13021 (+) NZ_CP012938.1:698752-699721 2.4.1.320
- Bovatus_RS02855 WP_004300474.1 13028 - 15302 (+) NZ_CP012938.1:699728-702002 3.2.1.-
- Bovatus_RS02860 WP_004300475.1 15456 - 17118 (+) NZ_CP012938.1:702156-703818 -
- Bovatus_RS02865 WP_004300476.1 17417 - 18311 (+) NZ_CP012938.1:704117-705011 -
- Bovatus_RS02870 WP_004300477.1 18482 - 20006 (+) NZ_CP012938.1:705182-706706 -
- Bovatus_RS02875 WP_004300478.1 20036 - 23423 (+) NZ_CP012938.1:706736-710123 -
- Bovatus_RS02880 WP_004300479.1 23435 - 25649 (+) NZ_CP012938.1:710135-712349 -
- Bovatus_RS02885 WP_004300480.1 25854 - 27594 (+) NZ_CP012938.1:712554-714294 -
- Bovatus_RS02890 WP_004300481.1 27596 - 28265 (+) NZ_CP012938.1:714296-714965 -
- Bovatus_RS02895 WP_004300482.1 28470 - 29394 (+) NZ_CP012938.1:715170-716094 -
- Bovatus_RS02900 WP_004300483.1 29425 - 32746 (+) NZ_CP012938.1:716125-719446 -
- Bovatus_RS02905 WP_004300484.1 33037 - 35872 (+) NZ_CP012938.1:719737-722572 -
- Bovatus_RS02910 WP_004306223.1 36072 - 37425 (+) NZ_CP012938.1:722772-724125 3.2.1.-
- Bovatus_RS02915 WP_004300486.1 37521 - 39486 (+) NZ_CP012938.1:724221-726186 -
- Bovatus_RS02920 WP_004300487.1 39718 - 40606 (-) NZ_CP012938.1:726418-727306 1.1.1.-
- Bovatus_RS02925 WP_004300489.1 40719 - 44580 (-) NZ_CP012938.1:727419-731280 -
- Bovatus_RS02930 WP_004300490.1 44611 - 46078 (-) NZ_CP012938.1:731311-732778 -
- Bovatus_RS02935 WP_004300491.1 46098 - 47301 (-) NZ_CP012938.1:732798-734001 3.2.1.-
- Bovatus_RS02940 WP_004300492.1 47314 - 49783 (-) NZ_CP012938.1:734014-736483 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 3327 (+) TC: gnl|TC-DB|Q8A8X1|1.B.14.6.13 Yes
- 3346 - 4923 (+) TC: gnl|TC-DB|Q8A0N7|8.A.46.2.2 Yes
- 4956 - 6020 (+) CAZyme: GH18 Yes
- 6043 - 7254 (+) other Yes
- 7278 - 8243 (+) other Yes
- 8408 - 10609 (+) CAZyme: GH163 Yes
- 10708 - 12036 (+) other Yes
- 12053 - 13021 (+) CAZyme: GH130_2 Yes
- 13029 - 15302 (+) CAZyme: GH92 Yes
- 15457 - 17118 (+) other Yes
- 17418 - 18311 (+) other Yes
- 18483 - 20006 (+) other Yes
- 20037 - 23423 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 23436 - 25649 (+) other Yes
- 25855 - 27594 (+) CAZyme: PL1_2 Yes
- 27597 - 28265 (+) other Yes
- 28471 - 29394 (+) CAZyme: GH43_18 Yes
- 29426 - 32746 (+) CAZyme: GH143|GH142 Yes
- 33038 - 35872 (+) CAZyme: CBM67|GH78 Yes
- 36073 - 37425 (+) CAZyme: GH28 Yes
- 37522 - 39486 (+) CAZyme: CE19 Yes
- 39719 - 40606 (-) other Yes
- 40720 - 44580 (-) CAZyme: CBM67|GH78|GH33 Yes
- 44612 - 46078 (-) CAZyme: GH140 Yes
- 46099 - 47301 (-) CAZyme: GH105 Yes
- 47315 - 49783 (-) CAZyme: GH95 Yes

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PUL ID

PUL0786

PubMed

38890895, Foods. 2024 May 26;13(11):1666. doi: 10.3390/foods13111666.

Title

The Utilization by Bacteroides spp. of a Purified Polysaccharide from Fuzhuan Brick Tea.

Author

Shi J, Zhou W, Chen G, Yi W, Sun Y, Zeng X

Abstract

In the present study, four Bacteroides species that could degrade Fuzhuan brick tea polysaccharide-3 (FBTPS-3) were isolated from human feces and identified to be Bacteroides ovatus, B. uniformis, B. fragilis and B. thetaiotaomicron. The four Bacteroides species showed growth on FBTPS-3 as the carbon source, and B. ovatus showed the best capability for utilizing FBTPS-3 among the four species since B. ovatus could utilize more FBTPS-3 during 24 h fermentation. Moreover, the four Bacteroides species could metabolize FBTPS-3 and promote the production of acetic, propionic and isovaleric acids. Transcriptome analysis of B. ovatus revealed that 602 genes were up-regulated by FBTPS-3, including two carbohydrate-active enzyme clusters and four polysaccharide utilization loci (PULs). The PUL 1 contained GH28 family that could hydrolyze rhamnogalacturonan and other pectic substrates, which was in line with our previous work that rhamnose and galacturonic acid were the main component monosaccharides of FBTPS-3. Collectively, the results suggested that FBTPS-3 could be utilized by Bacteroides spp., and it might be developed as a promising prebiotic targeting Bacteroidetes in intestinal environment.

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.