organism: uncultured Cardiobacterium sp.
description: This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR13061542 of study SRP292586.
attributes.tag: INSDC center name
attributes.value: EMG
attributes.tag: Submitter Id
attributes.value: SRR13061542_bin.2_MetaWRAP_v1.3_MAG
attributes.tag: assembly quality
attributes.value: Many fragments with little to no review of assembly other than reporting of standard assembly statistics
attributes.tag: assembly software
attributes.value: metaspades v3.15.3
attributes.tag: binning parameters
attributes.value: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
attributes.tag: binning software
attributes.value: MetaWRAP v1.3
attributes.tag: broad-scale environmental context
attributes.value: human digestive system
attributes.tag: broker name
attributes.value: EBI-EMG
attributes.tag: collection date
attributes.value: 2018-01
attributes.tag: completeness score
attributes.value: 55.17
attributes.tag: completeness software
attributes.value: CheckM
attributes.tag: contamination score
attributes.value: 3.45
attributes.tag: environmental medium
attributes.value: saliva
attributes.tag: geographic location (country and/or sea)
attributes.value: Denmark
attributes.tag: geographic location (latitude)
attributes.value: 55.67
attributes.tag: geographic location (longitude)
attributes.value: 12.57
attributes.tag: investigation type
attributes.value: metagenome-assembled genome
attributes.tag: isolation_source
attributes.value: oral metagenome
attributes.tag: local environmental context
attributes.value: oral cavity
attributes.tag: metagenomic source
attributes.value: oral metagenome
attributes.tag: project name
attributes.value: The purpose of the present investigation was to use the oral cavity as an in-vivo model to study the impact of internal and external perturbations on bacterial biofilm communities. We tested the hypotheses that bacterial gene expression of the healthy microbiota reflects habituation to site-specific ecological perturbations, and that the perturbation effect of chronic inflammation, periodontitis, impacts bacterial gene expression not only locally, but also at other sites of the oral cavity. Oral microbial samples were collected from three oral sites plaque, tongue and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterisation of taxonomic composition and to determine species specific bacterial activity as expressed by the ratio of messenger RNA to the corresponding genomic DNA.
attributes.tag: sample derived from
attributes.value: SAMN16796851
attributes.tag: sample name
attributes.value: SRR13061542_bin.2_MetaWRAP_v1.3_MAG
attributes.tag: scientific_name
attributes.value: uncultured Cardiobacterium sp.
attributes.tag: sequencing method
attributes.value: Illumina HiSeq 2500
attributes.tag: taxonomic classification
attributes.value: The taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Cardiobacteriales;f__Cardiobacteriaceae;g__Cardiobacterium;s__
attributes.tag: taxonomic identity marker
attributes.value: multi-marker approach