Metagenome-assembled genome: SRR19390405_bin.2_metawrap_v1.3_MAG
This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR19390405 of study SRP376910.
ENA-FIRST-PUBLIC
2022-11-14
ENA-LAST-UPDATE
2022-11-14
External Id
SAMEA111557510
INSDC center alias
EMG
INSDC center name
EMG
INSDC first public
2022-11-14T15:53:31Z
INSDC last update
2022-11-14T15:53:31Z
INSDC status
public
Submitter Id
SRR19390405_bin.2_metawrap_v1.3_MAG
assembly quality
Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software
metaSPAdes v3.15.3
binning parameters
MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning software
metawrap v1.3
broad-scale environmental context
mouse digestive system
broker name
EMG broker account, EMBL-EBI
collection date
2019-12-05
completeness score
66.87
completeness software
CheckM
contamination score
1.68
environmental medium
feces
geographic location (country and/or sea)
USA
geographic location (latitude)
34.7455
geographic location (longitude)
-92.288
investigation type
metagenome-assembled genome
isolation_source
mouse gut metagenome
local environmental context
digestive tube
metagenomic source
mouse gut metagenome
project name
In humans and animal models, Cesarean section (C-section) has been associated with alterations in the taxonomic structure of the gut microbiome. These changes in microbiota populations are hypothesized to impact immune, metabolic, and behavioral/neurologic systems and others. It is not clear if birth mode inherently changes the microbiome, or if C-section effects are context-specific and involve interactions with environmental and other factors. To address this and control for potential confounders, cecal microbiota from ~3 wk old mice born by C-section (n=16) vs. natural birth (n=23) were compared under matched conditions for housing, cross-fostering, diet, sex and genetic strain.
sample derived from
SAMN28591019
sample name
SRR19390405_bin.2_metawrap_v1.3_MAG
sequencing method
NextSeq 500
taxonomic classification
The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__;s__
taxonomic identity marker
multi-marker approach