characteristics: ERC000047
characteristics: ENA-CHECKLIST
characteristics: 2022-10-13T12:29:00Z
characteristics: ENA-FIRST-PUBLIC
characteristics: 2022-10-13T12:29:00Z
characteristics: ENA-LAST-UPDATE
characteristics: SAMEA111463702
characteristics: External Id
characteristics: EMG
characteristics: INSDC center name
characteristics: 2022-10-13T12:29:00Z
characteristics: INSDC first public
characteristics: 2022-10-13T12:29:00Z
characteristics: INSDC last update
characteristics: public
characteristics: INSDC status
characteristics: ERS13557732
characteristics: SRA accession
characteristics: ERR899291_bin.89_metawrap_v1.3_MAG
characteristics: Submitter Id
characteristics: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
characteristics: assembly quality
characteristics: metaSPAdes v3.15.3
characteristics: assembly software
characteristics: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
characteristics: binning parameters
characteristics: metawrap v1.3
characteristics: binning software
characteristics: mouse digestive system
characteristics: broad-scale environmental context
characteristics: EBI-EMG
characteristics: broker name
characteristics: not provided
characteristics: collection date
characteristics: 98.82
characteristics: %
characteristics: completeness score
characteristics: CheckM
characteristics: completeness software
characteristics: 0.57
characteristics: %
characteristics: contamination score
characteristics: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run ERR899291 of study ERP010550.
characteristics: description
characteristics: feces
characteristics: environmental medium
characteristics: not provided
characteristics: geographic location (country and/or sea)
characteristics: not provided
characteristics: DD
characteristics: geographic location (latitude)
characteristics: not provided
characteristics: DD
characteristics: geographic location (longitude)
characteristics: metagenome-assembled genome
characteristics: investigation type
characteristics: mouse gut metagenome
characteristics: isolation_source
characteristics: digestive tube
characteristics: local environmental context
characteristics: mouse gut metagenome
characteristics: metagenomic source
characteristics: uncultured Lachnospiraceae bacterium
characteristics: organism
characteristics: 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.
characteristics: project name
characteristics: SAMEA3403117
characteristics: sample derived from
characteristics: uncultured Lachnospiraceae bacterium
characteristics: scientific_name
characteristics: Illumina HiSeq 2000
characteristics: sequencing method
characteristics: 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__
characteristics: taxonomic classification
characteristics: multi-marker approach
characteristics: taxonomic identity marker
characteristics: Metagenome-assembled genome: ERR899291_bin.89_metawrap_v1.3_MAG
characteristics: title