U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Metagenome-Assembled Genome: SRR13061536_bin.4_MetaWRAP_v1.3_MAG

Identifiers
BioSample: SAMEA114449075; SRA: ERS16435719
Organism
Prevotella melaninogenica
cellular organisms; Bacteria; Pseudomonadati; FCB group; Bacteroidota/Chlorobiota group; Bacteroidota; Bacteroidia; Bacteroidales; Prevotellaceae; Prevotella
Attributes
broad-scale environmental contexthuman digestive system
collection date2018-01
environmental mediumsaliva
geographic locationDenmark
investigation typemetagenome-assembled genome
isolation sourceoral metagenome
project nameThe 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.
sample nameSRR13061536_bin.4_MetaWRAP_v1.3_MAG
ENA-CHECKLISTERC000047
INSDC center nameEMG
Submitter IdSRR13061536_bin.4_MetaWRAP_v1.3_MAG
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaspades v3.15.3
binning parametersMaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.
binning softwareMetaWRAP v1.3
broker nameEBI-EMG
completeness score69.14
completeness softwareCheckM
contamination score0.34
geographic location (latitude)55.67
geographic location (longitude)12.57
local environmental contextoral cavity
metagenomic sourceoral metagenome
sample derived fromSAMN16796826
scientific_namePrevotella melaninogenica
sequencing methodIllumina HiSeq 2500
taxonomic classificationThe taxonomy of this Metagenome-Assembled Genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__Prevotella melaninogenica
taxonomic identity markermulti-marker approach
Description

This sample represents a Third Party Annotation (TPA) metagenome-assembled genome assembled from the metagenomic run SRR13061536 of study SRP292586.

BioProject
PRJEB65451
Retrieve all samples from this project

Submission
EBI; 2023-09-29
Accession:
SAMEA114449075
ID:
37600301

BioProject Nucleotide

Supplemental Content

Related information

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
You are here: NCBI > DNA & RNA > BioSample
Support Center