Metagenome-assembled genome: ERR833046_bin.35_CONCOCT_v1.1_MAG
uncultured Prevotellaceae bacterium
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR833046 of study ERP009980.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14080671
INSDC center alias
EBI
INSDC center name
European Bioinformatics Institute
INSDC first public
2023-01-03T00:33:01Z
INSDC last update
2023-01-03T00:33:01Z
INSDC status
public
Submitter Id
ERR833046_bin.35_CONCOCT_v1.1_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaspadesv3.12.0
binning parameters
Default
binning software
CONCOCT v1.1
broker name
EMG broker account, EMBL-EBI
collection date
not provided
completeness score
97.52
completeness software
CheckM
contamination score
1.57
environment (biome)
Host-associated
environment (feature)
Mammals
environment (material)
Digestive system
geographic location (country and/or sea)
not provided
geographic location (latitude)
not provided
geographic location (longitude)
not provided
investigation type
metagenome-assembled genome
isolation_source
gut metagenome
metagenomic source
gut metagenome
project name
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.
sample derived from
SAMEA3312790
sample name
ERR833046_bin.35_CONCOCT_v1.1_MAG
scientific_name
uncultured Prevotellaceae bacterium
sequencing method
Illumina Genome Analyzer IIx
taxonomic identity marker
multi-marker approach