To tackle these issues, we reconstructed complete metabolic pathways by analyzing the representation of 565 curated metabolic functional roles (transporters, CAZymes, downstream catabolic enzymes, transcriptional regulators) (9/)
Genomic studies often focus only on CAZymes, mainly glycoside hydrolases (GHs), whereas glycan transporters are frequently overlooked. This approach can lead to false positive predictions, especially when the cellular localization of GHs is not taken into account (8/)
Another interesting example of gut microbes able to metabolically degrade a drug, in this case Bacteroides salyersiae (with a few identified CAZymes) and chondroitin sulfate, used to prevent osteoarthritis. microbiomejournal.biomedcentral.com/articles/10....
They’re really damn good at it. Anaerobic fungi, of the phylum Neocallimastigomycota, are so good at it that the number and diversity of CAZymes in their genomes outstrips everything else on the tree of life and they’re also the only organisms in the gut that break down plants mechanically. 8/?
What are they fermenting? All that delicious plant matter their hosts are eating. Rumen bacteria, fungi, and protozoa are equipped with an arsenal of carbohydrate-active enzymes (CAZymes) to break down plant biomass. They ferment it anaerobically to gain energy. 5/?
That's neat! and maybe also just running dbcan on the scaffolds and/or bins if cazymes are especially of interest github.com/linnabrown/r...
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes. - GitHub - linnabrown/run_dbcan: Run_dbcan V4, usi...
However, we found that the expression profiles of genes related to polysaccharide and protein degradation and nutrient transport notably varied between and within the fungal guilds, suggesting niche adaptation. Image: Transcript levels for CAZymes in saprotrophic and ectomycorrhizal fungi
