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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0129

PubMed

30356154, Nat Microbiol. 2018 Nov;3(11):1274-1284. doi: 10.1038/s41564-018-0225-4. Epub 2018 Oct 24.

Characterization method

enzyme activity assay

Genomic accession number

Ga0139390_150

Nucelotide position range

30256-49978

Substrate

beta-mannan

Loci

2703759865_27-2703759865_38

Species

gut metagenome/749906

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - 2703759865_27 30256 - 31410 (-) Ga0139390_150:60512-61666 -
- - 2703759865_28 31443 - 32606 (-) Ga0139390_150:61699-62862 -
- - 2703759865_29 32624 - 34189 (-) Ga0139390_150:62880-64445 -
- - 2703759865_30 34208 - 36667 (-) Ga0139390_150:64464-66923 -
- - 2703759865_31 36687 - 38117 (-) Ga0139390_150:66943-68373 -
- - 2703759865_32 38141 - 39913 (-) Ga0139390_150:68397-70169 -
- - 2703759865_33 39930 - 43223 (-) Ga0139390_150:70186-73479 -
- - 2703759865_34 43511 - 44866 (+) Ga0139390_150:73767-75122 -
- - 2703759865_35 44928 - 46064 (+) Ga0139390_150:75184-76320 -
- - 2703759865_36 46092 - 47282 (+) Ga0139390_150:76348-77538 -
- - 2703759865_37 47334 - 48674 (+) Ga0139390_150:77590-78930 -
- - 2703759865_38 48671 - 49978 (+) Ga0139390_150:78927-80234 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 30256 - 31410 (-) CAZyme: GH5|GH5_4|GH26 Yes
- 31443 - 32606 (-) CAZyme: GH26 Yes
- 32624 - 34189 (-) CAZyme: GH5|GH5_4 Yes
- 34208 - 36667 (-) other Yes
- 36687 - 38117 (-) other Yes
- 38141 - 39913 (-) other Yes
- 39930 - 43223 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 43511 - 44866 (+) CAZyme: CE7 Yes
- 44928 - 46064 (+) CAZyme: CE7|GH26 Yes
- 46092 - 47282 (+) CAZyme: GH130 Yes
- 47334 - 48674 (+) TC: gnl|TC-DB|P31435|2.A.2.3.4 Yes
- 48671 - 49978 (+) CDS No

PUL ID

PUL0129

PubMed

30356154, Nat Microbiol. 2018 Nov;3(11):1274-1284. doi: 10.1038/s41564-018-0225-4. Epub 2018 Oct 24.

Title

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem.

Author

Solden LM, Naas AE, Roux S, Daly RA, Collins WB, Nicora CD, Purvine SO, Hoyt DW, Schuckel J, Jorgensen B, Willats W, Spalinger DE, Firkins JL, Lipton MS, Sullivan MB, Pope PB, Wrighton KC

Abstract

Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack a holistic view of the microbial food web responsible for carbon processing in this ecosystem. Here, we sampled rumen-fistulated moose, allowing access to rumen microbial communities actively degrading woody plant biomass in real time. We resolved 1,193 viral contigs and 77 unique, near-complete microbial metagenome-assembled genomes, many of which lacked previous metabolic insights. Plant-derived metabolites were measured with NMR and carbohydrate microarrays to quantify the carbon nutrient landscape. Network analyses directly linked measured metabolites to expressed proteins from these unique metagenome-assembled genomes, revealing a genome-resolved three-tiered carbohydrate-fuelled trophic system. This provided a glimpse into microbial specialization into functional guilds defined by specific metabolites. To validate our proteomic inferences, the catalytic activity of a polysaccharide utilization locus from a highly connected metabolic hub genome was confirmed using heterologous gene expression. Viral detected proteins and linkages to microbial hosts demonstrated that phage are active controllers of rumen ecosystem function. Our findings elucidate the microbial and viral members, as well as their metabolic interdependencies, that support in situ carbon degradation in the rumen ecosystem.