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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0256

PubMed

23996813, Biotechnol Bioeng. 2014 Jan;111(1):165-73. doi: 10.1002/bit.24994. Epub 2013 Jul 30.

Characterization method

gene chips

Genomic accession number

AE015928.1

Nucelotide position range

734869-758273

Substrate

capsule polysaccharide

Loci

BT_0595-BT_0613

Species

Bacteroides thetaiotaomicron/818

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BT_0595 AAO75702.1 0 - 957 (+) AE015928.1:734869-735826 -
- BT_0596 AAO75703.1 1306 - 1885 (+) AE015928.1:736175-736754 -
- BT_0597 AAO75704.1 1892 - 2246 (+) AE015928.1:736761-737115 -
- BT_0598 AAO75705.1 2299 - 4225 (+) AE015928.1:737168-739094 -
- BT_0599 AAO75706.1 4259 - 5576 (+) AE015928.1:739128-740445 -
- BT_0600 AAO75707.1 5580 - 6645 (+) AE015928.1:740449-741514 -
- BT_0601 AAO75708.1 6844 - 8056 (+) AE015928.1:741713-742925 -
- BT_0602 AAO75709.1 8075 - 9299 (+) AE015928.1:742944-744168 -
- BT_0603 AAO75710.1 9442 - 10555 (+) AE015928.1:744311-745424 -
- BT_0604 AAO75711.1 10556 - 11744 (+) AE015928.1:745425-746613 -
- BT_0605 AAO75712.1 11745 - 13191 (+) AE015928.1:746614-748060 -
- BT_0606 AAO75713.1 13251 - 14472 (+) AE015928.1:748120-749341 -
- BT_0607 AAO75714.1 14478 - 15054 (+) AE015928.1:749347-749923 -
- BT_0608 AAO75715.1 15150 - 16230 (+) AE015928.1:750019-751099 -
- BT_0609 AAO75716.1 16761 - 17901 (+) AE015928.1:751630-752770 -
- BT_0610 AAO75717.1 17922 - 19113 (+) AE015928.1:752791-753982 -
- BT_0611 AAO75718.1 20333 - 20927 (+) AE015928.1:755202-755796 -
- BT_0612 AAO75719.1 20954 - 22229 (+) AE015928.1:755823-757098 -
- BT_0613 AAO75720.1 22451 - 23405 (+) AE015928.1:757320-758274 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 957 (+) CDS No
- 1307 - 1885 (+) CDS No
- 1893 - 2246 (+) CDS No
- 2300 - 4225 (+) TC: gnl|TC-DB|Q6MMD5|9.B.18.2.1 Yes
- 4260 - 5576 (+) other Yes
- 5581 - 6645 (+) other Yes
- 6845 - 8056 (+) other Yes
- 8076 - 9299 (+) other Yes
- 9443 - 10555 (+) other Yes
- 10557 - 11744 (+) other Yes
- 11746 - 13191 (+) other Yes
- 13252 - 14472 (+) other Yes
- 14479 - 15054 (+) other Yes
- 15151 - 16230 (+) CAZyme: GT4 Yes
- 16762 - 17901 (+) CAZyme: GT4|GT94 Yes
- 17923 - 19113 (+) other Yes
- 20334 - 20927 (+) TC: gnl|TC-DB|917585193|9.B.18.1.3 Yes
- 20955 - 22229 (+) other Yes
- 22452 - 23405 (+) TC: gnl|TC-DB|A5FN23|1.B.18.3.3 Yes

PUL ID

PUL0256

PubMed

23996813, Biotechnol Bioeng. 2014 Jan;111(1):165-73. doi: 10.1002/bit.24994. Epub 2013 Jul 30.

Title

Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats.

Author

TerAvest MA, He Z, Rosenbaum MA, Martens EC, Cotta MA, Gordon JI, Angenent LT

Abstract

Bacteroides thetaiotaomicron is a prominent member of the human distal gut microbiota that specializes in breaking down diet and host-derived polysaccharides. While polysaccharide utilization has been well studied in B. thetaiotaomicron, other aspects of its behavior are less well characterized, including the factors that allow it to maintain itself in the gut. Biofilm formation may be a mechanism for bacterial retention in the gut. Therefore, we used custom GeneChips to compare the transcriptomes of biofilm and planktonic B. thetaiotaomicron during growth in mono-colonized chemostats. We identified 1,154 genes with a fold-change greater than 2, with confidence greater than or equal to 95%. Among the prominent changes observed in biofilm populations were: (i) greater expression of genes in polysaccharide utilization loci that are involved in foraging of O-glycans normally found in the gut mucosa; and (ii) regulated expression of capsular polysaccharide biosynthesis loci. Hierarchical clustering of the data with different datasets, which were obtained during growth under a range of conditions in minimal media and in intestinal tracts of gnotobiotic mice, revealed that within this group of differentially expressed genes, biofilm communities were more similar to the in vivo samples than to planktonic cells and exhibited features of substrate limitation. The current study also validates the use of chemostats as an in vitro "gnotobiotic" model to study gene expression of attached populations of this bacterium. This is important to gut microbiota research, because bacterial attachment and the consequences of disruptions in attachment are difficult to study in vivo.