This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR899286 of study ERP010550.
ENA-FIRST-PUBLIC
2022-10-13T12:29:00Z
ENA-LAST-UPDATE
2022-10-13T12:29:00Z
External Id
SAMEA111463628
INSDC center name
EMG
INSDC first public
2022-10-13T12:29:00Z
INSDC last update
2022-10-13T12:29:00Z
INSDC status
public
Submitter Id
ERR899286_bin.29_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
EBI-EMG
collection date
not provided
completeness score
85.31
completeness software
CheckM
contamination score
1.52
environmental medium
feces
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
mouse gut metagenome
local environmental context
digestive tube
metagenomic source
mouse gut metagenome
project name
The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess changes to both bacterial community structure and transcriptional activity in a mouse model of colitis. Gene families involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase, were transcriptionally up-regulated in colitis, implicating a role for increased oxygen tension in gut microbiota modulation. Transcriptional profiling of the host gut tissue and host RNA in the gut lumen revealed a marked increase in the transcription of genes with an activated macrophage and granulocyte signature, suggesting the involvement of these cell types in influencing microbial gene expression. Down-regulation of host glycosylation genes further supports a role for inflammation-driven changes to the gut niche that may impact the microbiome. We propose that members of the bacterial community react to inflammation-associated increased oxygen tension by inducing genes involved in oxidative stress resistance. Furthermore, correlated transcriptional responses between host glycosylation and bacterial glycan utilisation support a role for altered usage of host-derived carbohydrates in colitis.
sample derived from
SAMEA3403101
sample name
ERR899286_bin.29_metawrap_v1.3_MAG
scientific_name
Eubacterium plexicaudatum
sequencing method
Illumina HiSeq 2000
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__Eubacteriaceae;g__Eubacterium;s__Eubacterium plexicaudatum
taxonomic identity marker
multi-marker approach