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"last-update": "2020-05-22T08:17:23",
"secondary-accession": "ERP114152",
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"study-abstract": "The Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJEB8939. This project includes samples from the following biomes: root:Host-associated:Mammals:Digestive system:Stomach:Rumen.",
"study-name": "EMG produced TPA metagenomics assembly of the PRJEB8939 data set (Metagenomic analyses of Rumen microbiomes reveals the functional isoforms driving microbial niche differentiation for nutrient acquisition and use).",
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"last-update": "2020-05-22T03:08:26",
"secondary-accession": "ERP009980",
"centre-name": "ABERSYTWYTH UNIVERSITY",
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"study-abstract": "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.",
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