Climate Change Metagenomic Record Index

    Metagenomic analyses of Rumen microbiomes reveals the functional isoforms driving microbial niche differentiation for nutrient acquisition and use

    MGnify Record MGYS00005452

    Description
    Metagenomics has provided insights into the species composition and function of microbial communities and revealed that many species even in highly competitive environments seem to share the same sets of genes for acquiring and utilising nutrients. This questions whether niche differentiation between microbes under competitive stress exists and if so, how it is maintained. Rumen microbes exist in a highly competitive, anaerobic environment, and compete for access to the limited nutrients available in the biomass consumed by the host. The rumen microbiome affects the efficiency and health of the host, and has been mined for novel enzymes and anti microbial peptides and is known as a potent contributor to greenhouse gas emissions. A better understanding of the structure and function of this community has large potential benefits. We generated separate metagenomic libraries from 14 Limousin cows. Following assembly, gene prediction and taxonomic assignment, SNPs were identified and functional isoform diversity (pN/pS) was calculated for each gene. The independent calculations from each sample were used to calculate confidence intervals for testing for diversity of function between microbes, a signature of niche differentiation. We identified significant differences in functional diversity between competing organisms in genes involved in carbon, amino-sugar and nucleotide sugar metabolism, suggesting adaptation to utilizing different routes for nutrient acquisition in the rumen. This suggests that a greater understanding of the rumen microbiome and considering macro-ecological concepts, such as successional change and adaptation, are likely to improve strategies for increasing the efficiency and health of the host and reducing greenhouse gas emissions.

    Related Publications

    Pubmed Record 28085156

    Abstract Text
    Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.