Metagenome-assembled genome: ERR1278103_bin.189_CO... - BioSample

Metagenome-assembled genome: ERR1278103_bin.189_CONCOCT_v1.1_MAG

Identifiers: BioSample: SAMEA14080494; SRA: ERS11683750

Organism: uncultured Candidatus Saccharibacteria bacterium
cellular organisms; Bacteria; Bacteria incertae sedis; Bacteria candidate phyla; Candidatus Saccharibacteria; environmental samples

Attributes

collection date	2011-10-01
broad-scale environmental context	Host-associated
local-scale environmental context	Mammals
environmental medium	Digestive system
geographic location	Sweden
investigation type	metagenome-assembled genome
isolation source	gut metagenome
project name	The moose (Alces alces) manages to utilize energy from fiber-rich lignocellulose material through enzymes produced by the microbes in its rumen. Some of these specialized enzymes may outperform cellulases and hemicellulases that are used in bio-refinery processes today. Shotgun metagenomics offers a method to study microbial communities in detail and to capture the gene sequences coding for enzymes that can be produced in the laboratory. We applied the technique on rumen material from moose. Through a binning approach, a large number of metagenome-assembled genomes (MAGs) from single species and strains were isolated and characterized based on taxonomy and carbohydrate active enzyme (CAZY) profile. Most of the 99 MAGs were classified to the bacterial phyla Bacteriodetes and Firmicutes, which is in agreement with previous studies of rumen from moose and other herbivores. Phylogenomic analysis of MAGs revealed novel clades within Bacteriodetes with no related previously characterized genome. In addition, new genomes that were closely related to the recently described Melainabacteria, newly proposed candidate divisions SR1 and TM7 and previously uncharacterized Alphaproteobacteria were also retrieved. Putative cellulolytic functions were observed in several clades of Bacteroidetes and for MAGs of genus Ruminococcus, Fibrobacteres, and Treponema. Cellulosome components were present in MAGs of Ruminococcus but also in certain clades of Bacteroidetes. Cellulosomes are generally described in the Firmicutes family Clostridiales. Multiple putative cellulases were identified within species from several phyla. At a general level, the most frequently occurring polysaccharide-degrading enzymes targeted hemicellulose, starch and pectin. This study describes the first shotgun-metagenomic characterization of moose rumen and the high number of reconstructed genomes provides a valuable link between phylogeny and cellulolytic role.
sample name	ERR1278103_bin.189_CONCOCT_v1.1_MAG
ENA-CHECKLIST	ERC000047
ENA-FIRST-PUBLIC	2023-01-03
ENA-LAST-UPDATE	2023-01-03
External Id	SAMEA14080494
INSDC center alias	EBI
INSDC center name	European Bioinformatics Institute
INSDC first public	2023-01-03T00:33:02Z
INSDC last update	2023-01-03T00:33:02Z
INSDC status	public
Submitter Id	ERR1278103_bin.189_CONCOCT_v1.1_MAG
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	spadesv3.11.1
binning parameters	Default
binning software	CONCOCT v1.1
broker name	EMG broker account, EMBL-EBI
completeness score	62.96
completeness software	CheckM
contamination score	0.85
geographic location (latitude)	56.752724
geographic location (longitude)	16.688232
metagenomic source	gut metagenome
sample derived from	SAMEA3878206
scientific_name	uncultured Candidatus Saccharibacteria bacterium
sequencing method	Illumina HiSeq 2500
taxonomic identity marker	multi-marker approach

Description: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1278103 of study ERP014306.

BioProject: PRJEB51895 Large-scale analysis of novel cellular microbes from the mammal gut biome
Retrieve all samples from this project

Submission: EBI; 2023-01-04

Accession:: SAMEA14080494
ID:: 32558182

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Metagenome-assembled genome: ERR1278103_bin.189_CONCOCT_v1.1_MAG

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