Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates

Abstract

Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.

The Discovery of a Multidomain Mannanase Containing Dual-Catalytic Domain of the Same Activity: Biochemical Properties and Synergistic Effect

“…By searching for homologous sequences through BLAST, potential homologues of Man26/5 were mostly derived from the Paludibacteraceae, a group of microorganisms found in the guts of homeothermic animals, especially the rumen of ruminants. They play an important role in the degradation of hemicellulose . When GH26, GH5_8, and CBM35 coexist, most sequences exhibit a structure similar to Man26/5 (Figure B), namely, GH26-CBM35-GH5_8.…”

“…They play an important role in the degradation of hemicellulose. 28 When GH26, GH5_8, and CBM35 coexist, most sequences exhibit a structure similar to Man26/5 (Figure 1B), namely, GH26-CBM35-GH5_8. Only one homologous sequence appears in the CBM35-GH26-GH5_8 series.…”

Biological Interactions Mediate Soil Functions by Altering Rare Microbial Communities

“…This positive association suggests the potential occurrence of anthropogenic synthetic chemical contamination within the agricultural soil and highlights the remarkable metabolic competence of SM1A02 in effectively metabolizing complex organic compounds. 55 A large number of genes encoding carbohydrate-active enzymes was identified within the genomic composition of the phylum Planctomycetota, to which the genus SM1A02 belongs, 56 indicating their profound metabolic capabilities even at low relative abundance. Furthermore, functional genes nirK1, narG, and nirS1 related to the denitrification with Epsilon-Caprolactam were significantly associated with ASV12413.…”

Rumen biogeographical regions and their impact on microbial and metabolome variation

“…The identification and higher prevalence of Verrucomicrobiota in both the epimural and planktonic microbial communities is infrequent. Verrucomicrobiota have been examined in a lignocellulosic forage studies, where bacteria in this phylum have carbohydrate active enzymes, sulfatases, and peptidases (Gharechahi et al, 2022) which facilitate carbohydrate polysaccharide metabolism and may aid in lignocellulose breakdown within the rumen. In general, having a major phylum in the planktonic community being involved in cellulose degradation is not uncommon (Schären et al, 2017;Tan et al, 2021;Zhou et al, 2021), but it is more unexpected for the epimural community where Proteobacteria are typically detected at greater abundances (De Mulder et al, 2016;Sbardellati et al, 2020;Pacifico et al, 2021;Zhou et al, 2021).…”