2024-12-11
ENA first public
ERC000047
ENA-CHECKLIST
CMR
INSDC center name
public
INSDC status
ERS22273769
SRA accession
SRP278969_co1_36
Submitter Id
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly quality
metaSPAdes;3.15.4;default
assembly software
coverage and kmer
binning parameters
MetaBAT2;2.15;default
binning software
host
broad-scale environmental context
2018-10-12
collection date
59.77
%
completeness score
CheckM2;1.0.2;default
completeness software
1.46
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs SRR12529037,SRR12529044 of study SRP278969.
description
host
environmental medium
not provided
geographic location (country and/or sea)
not provided
DD
geographic location (latitude)
not provided
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
gut metagenome
isolation_source
gut biome
local environmental context
gut metagenome
metagenomic source
uncultured Candidatus Saccharibacteria bacterium
organism
Gastrointestinal tract (GIT) microbiomes in ruminant play major roles in host health and thus animal production. However, an integrated characterization of microbial community structure and function is yet to be obtained as prior studies are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, we generated shotgun metagenomic data from 370 samples that represent 10 GIT regions of seven ruminant species. Our analyses reconstructed a GIT microbial reference catalog with >154 million nonredundant gene, and identified 8,745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrate spatial associations between the microbiome and physiological adaptations, and 8,745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly microbiomes from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improves our understanding concerning methane production and feed efficiency in ruminants. Overall, our study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution, and offers clues for improving ruminant livestock production in the future. Having access to comprehensive gene catalog and collections of microbial genomes provide the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production.
project name
SAMN15829918,SAMN15829912
sample derived from
uncultured Candidatus Saccharibacteria bacterium
scientific_name
Illumina NovaSeq 6000
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: SRP278969_co1_36
title