Metagenome-assembled genome: ERR1135178_bin.57_CONCOCT_v1.1_MAG
uncultured Campylobacter sp.
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR1135178 of study ERP013165.
ENA-FIRST-PUBLIC
2023-01-03
ENA-LAST-UPDATE
2023-01-03
External Id
SAMEA14080446
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
ERR1135178_bin.57_CONCOCT_v1.1_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaSPAdes version 3.10.139
binning parameters
Default
binning software
CONCOCT v1.1
broker name
EMG broker account, EMBL-EBI
collection date
2012-01-01
completeness score
98.63
completeness software
CheckM
contamination score
1.34
environment (biome)
Host-associated
environment (feature)
Mammals
environment (material)
Digestive system
geographic location (country and/or sea)
France
geographic location (latitude)
16.20735
geographic location (longitude)
-61.648144
investigation type
metagenome-assembled genome
isolation_source
gut metagenome
metagenomic source
gut metagenome
project name
Pig is a main species for livestock and biomedicine. The pig genome sequence was recently reported. To boost research, we established a catalogue of the genes of the gut microbiome based on faecal samples of 287 pigs from France, Denmark and China. More than 7.6 million non-redundant genes representing 719 metagenomic species were identified by deep metagenome sequencing, highlighting more similarities with the human than with the mouse catalogue. The pig and human catalogues share only 12.6 and 9.3 % of their genes, respectively, but 70 and 95% of their functional pathways. The pig gut microbiota is influenced by gender, age and breed. Analysis of the prevalence of antibiotics resistance genes (ARGs) reflected antibiotics supplementation in each farm system, and revealed that non-antibiotics-fed animals still harbour ARGs. The pig catalogue creates a resource for whole metagenomics-based studies, highly valuable for research in biomedicine and for sustainable knowledge-based pig farming.
sample derived from
SAMEA3663005
sample name
ERR1135178_bin.57_CONCOCT_v1.1_MAG
scientific_name
uncultured Campylobacter sp.
sequencing method
Illumina HiSeq 2000
taxonomic identity marker
multi-marker approach