Unique pool of carbohydrate-degrading enzymes in novel bacteria assembled from cow and buffalo rumen metagenomes

• Published in: Applied microbiology and biotechnology Vol. 106; no. 12; pp. 4643 - 4654
• Main Authors: Bohra, Varsha, Tikariha, Hitesh, Purohit, Hemant J., Dafale, Nishant A.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.06.2022; Springer; Springer Nature B.V
• Subjects: Bacteria; Bacteroidetes; Biofuels; Biomass; Biomedical and Life Sciences; Biotechnology; Buffalo; Carbohydrates; Cattle; Enzymes; Genes; Genetic aspects; Genomes; Genomics; Glycosidases; Glycoside hydrolase; High frequencies; Hydrolase; Life Sciences; Metabolism; Microbial Genetics and Genomics; Microbiology; Microorganisms; Nucleotides; Physiological aspects; Plant biomass; Proteomics; Rumen; Transcriptomics; Water buffalo; Hong Kong; Binning; Genome; CAZyme; Metagenome-assembled genomes (MAGs); Bacteroidetes; Firmicutes
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-022-12020-y

Reconstruction of genomes from environmental metagenomes offers an excellent prospect for studying the metabolic potential of organisms resilient to isolation in laboratory conditions. Here, we assembled 12 high-quality metagenome-assembled genomes (MAGs) with an estimated completion of ≥ 90% from cow and buffalo rumen metagenomes. Average nucleotide identity (ANI) score-based screening with an existing database suggests the novelty of these genomes. Gene prediction led to the identification of 30,359 protein-encoding genes (PEGs) across 12 genomes, of which only 44.8% were annotated against a specific functional attribute. Further analysis revealed the presence of 985 carbohydrate-active enzymes (CAZymes) from more than 50 glycoside hydrolase families, of which 90% do not have a proper match in the CAZy database. Genome mining revealed the presence of a high frequency of plant biomass deconstructing genes in Bacteroidetes MAGs compared to Firmicutes . The results strongly indicate that the rumen chamber harbors high numbers of deeply branched and as-yet uncultured microbes that encode novel CAZymes, candidates for prospective usage in plant biomass-hydrolyzing and biofuels industries. Key points • Genome binning plays a crucial role in revealing the metabolic potential of uncultivable microbes . • Assembled 12 novel genomes from cow and buffalo rumen metagenome datasets . • High frequency of plant biomass deconstructing genes identified in Bacteroidetes MAGs .