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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0532

PubMed

23976882, PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20.

Characterization method

RNA-Seq

Genomic accession number

CP012801.1

Nucelotide position range

925123-954278

Substrate

arabinan,pectin

Loci

BcellWH2_00920-BcellWH2_00935

Species

Bacteroides cellulosilyticus/246787

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BcellWH2_00920 ALJ58182.1 0 - 204 (-) CP012801.1:925123-925327 -
- BcellWH2_00921 ALJ58183.1 209 - 2168 (-) CP012801.1:925332-927291 3.2.1.55
- BcellWH2_00922 ALJ58184.1 2218 - 3706 (-) CP012801.1:927341-928829 3.2.1.99
tmoS_2 BcellWH2_00923 ALJ58185.1 3826 - 8149 (+) CP012801.1:928949-933272 2.7.13.3
- BcellWH2_00924 ALJ58186.1 8544 - 11739 (+) CP012801.1:933667-936862 -
- BcellWH2_00925 ALJ58187.1 11778 - 13530 (+) CP012801.1:936901-938653 -
- BcellWH2_00926 ALJ58188.1 13559 - 15353 (+) CP012801.1:938682-940476 -
abn-ts_1 BcellWH2_00927 ALJ58189.1 15434 - 17330 (+) CP012801.1:940557-942453 3.2.1.99
mro_2 BcellWH2_00928 ALJ58190.1 17498 - 18638 (+) CP012801.1:942621-943761 5.1.3.3
sglT_1 BcellWH2_00929 ALJ58191.1 18663 - 20358 (+) CP012801.1:943786-945481 -
- BcellWH2_00930 ALJ58192.1 20456 - 21137 (+) CP012801.1:945579-946260 -
ulaF BcellWH2_00931 ALJ58193.1 21140 - 21824 (+) CP012801.1:946263-946947 5.1.3.4
araA BcellWH2_00932 ALJ58194.1 21866 - 23375 (+) CP012801.1:946989-948498 5.3.1.4
xylB_1 BcellWH2_00933 ALJ58195.1 23377 - 24976 (+) CP012801.1:948500-950099 2.7.1.17
hypBA1_1 BcellWH2_00934 ALJ58196.1 25228 - 27577 (+) CP012801.1:950351-952700 3.2.1.185
abf2 BcellWH2_00935 ALJ58197.1 27611 - 29156 (+) CP012801.1:952734-954279 3.2.1.55
- BcellWH2_00936 ALJ58198.1 29032 - 29156 (-) CP012801.1:954155-954279 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 204 (-) CDS No
- 210 - 2168 (-) CAZyme: GH51 Yes
- 2219 - 3706 (-) CAZyme: GH43_4|GH43 Yes
tmoS_2 3827 - 8149 (+) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
- 8545 - 11739 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 11779 - 13530 (+) other Yes
- 13560 - 15353 (+) other Yes
abn-ts_1 15435 - 17330 (+) CAZyme: GH43_4|GH43 Yes
mro_2 17499 - 18638 (+) other Yes
sglT_1 18664 - 20358 (+) TC: gnl|TC-DB|Q8AAV7|2.A.21.3.19 Yes
- 20457 - 21137 (+) STP: STP|NUDIX Yes
ulaF 21141 - 21824 (+) other Yes
araA 21867 - 23375 (+) other Yes
xylB_1 23378 - 24976 (+) other Yes
hypBA1_1 25229 - 27577 (+) CAZyme: GH146 Yes
abf2 27612 - 29156 (+) CAZyme: GH51 Yes
- 29033 - 29156 (-) CDS No

PUL ID

PUL0532

PubMed

23976882, PLoS Biol. 2013;11(8):e1001637. doi: 10.1371/journal.pbio.1001637. Epub 2013 Aug 20.

Title

Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome.

Author

McNulty NP, Wu M, Erickson AR, Pan C, Erickson BK, Martens EC, Pudlo NA, Muegge BD, Henrissat B, Hettich RL, Gordon JI

Abstract

The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities.