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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0550

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

5289963-5307396

Substrate

N-acetyl-D-galactosamine

Loci

BcellWH2_04089-BcellWH2_04095

Species

Bacteroides cellulosilyticus/246787

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BcellWH2_04089 ALJ61309.1 0 - 1551 (+) CP012801.1:5289963-5291514 -
pemA_2 BcellWH2_04090 ALJ61310.1 1580 - 2882 (+) CP012801.1:5291543-5292845 3.1.1.11
- BcellWH2_04091 ALJ61311.1 3143 - 6398 (+) CP012801.1:5293106-5296361 -
- BcellWH2_04092 ALJ61312.1 6410 - 8486 (+) CP012801.1:5296373-5298449 -
- BcellWH2_04093 ALJ61313.1 8513 - 10160 (+) CP012801.1:5298476-5300123 -
xyl3A_7 BcellWH2_04094 ALJ61314.1 10365 - 12960 (+) CP012801.1:5300328-5302923 3.2.1.37
todS_24 BcellWH2_04095 ALJ61315.1 12988 - 17434 (-) CP012801.1:5302951-5307397 2.7.13.3

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1551 (+) CAZyme: CE8|PL1|PL1_2 Yes
pemA_2 1581 - 2882 (+) CAZyme: CE8 Yes
- 3144 - 6398 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 6411 - 8486 (+) other Yes
- 8514 - 10160 (+) other Yes
xyl3A_7 10366 - 12960 (+) CAZyme: GH3 Yes
todS_24 12989 - 17434 (-) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607,DBD-SUPERFAMILY|0035607 No

PUL ID

PUL0550

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.