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BA_Enterousia_03

Identifiers
BioSample: SAMEA115430792; SRA: ERS18592592
Organism
uncultured Alphaproteobacteria bacterium
cellular organisms; Bacteria; Pseudomonadota; Alphaproteobacteria; environmental samples
Attributes
broad-scale environmental contexthost associated gut microbiome
collection date2017-02-14
environmental mediumhost associated gut microbiome
geographic locationGermany
isolation sourcemouse colon contents
project nameBaseline aging (BA); Aging-associated loss of metabolic host-microbiome-interactions in mice
sample nameena-SAMPLE-TAB-22-03-2024-10:43:23:853-115555
16S recovery softwarebarrnap (version 0.9)
16s recoveredYes
23s recoveredyes
5s recoveredno
ENA first public2024-03-27
ENA-CHECKLISTERC000047
GC content44.5
INSDC center nameCAU
INSDC statuspublic
MAG coverage softwareBowtie (version 2.2.5) with jgi_summarize_bam_contig_depths script from MetaBAT (version 2.12.1)
Submitter Idena-SAMPLE-TAB-22-03-2024-10:43:23:853-115555
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly softwaremetaSPAdes hybrid (SPAdes version 3.13.1)
binning parameterscoverage depth and k-mer binning. Scaffolds were filtered for min. length 1000bp and min. coverage 7.7815. Quality-controlled metagenomic reads were mapped back to the filtered scaffolds with Bowtie (version 2.2.5); the insert size was 0–1000 bp in very sensitive, non-deterministic, “fr” stranded mode with end-to-end alignment. Non-unique mappings and unaligned reads were discarded. The scaffold coverage depth was determined with the jgi_summarize_bam_contig_depths script from MetaBAT (version 2.12.1). Scaffolds were broken into 10 kbp chunks for CONCOCT.
binning softwareMetaBAT (version 2.12.1), CONCOCT (version 1.1.0), MaxBin (version 2.2.4), DASTool (version 1.1.2)
completeness score85.7
completeness softwareCheckM (version 1.1.2)
contamination score0.0
geographic location (latitude)50.9
geographic location (longitude)11.6
local environmental contexthost associated gut microbiome
metagenomic sourcemouse gut metagenome
number of standard tRNAs extracted20
sample derived fromERS18444878,ERS18444879,ERS18444880,ERS18444881,ERS18444882,ERS18444883,ERS18444884,ERS18444885,ERS18444886,ERS18444887,ERS18444888,ERS18444889,ERS18444890,ERS18444891,ERS18444892,ERS18444893,ERS18444894,ERS18444895,ERS18444896,ERS18444897,ERS18444898,ERS18444899,ERS18444900,ERS18444901,ERS18444902,ERS18444903,ERS18444904,ERS18444905,ERS18444906,ERS18444907,ERS18444908,ERS18444909,ERS18444910,ERS18444911,ERS18444912,ERS18444913,ERS18444914,ERS18444915,ERS18444916,ERS18444917,ERS18444918,ERS18444919,ERS18444920,ERS18444921,ERS18444922,ERS18444923,ERS18444924,ERS18444925,ERS18444926,ERS18444927,ERS18444928,ERS18444929,ERS18590020,ERS18590021,ERS18590022,ERS18590023,ERS18590024,ERS18590025,ERS18590026,ERS18590027
scientific_nameuncultured Alphaproteobacteria bacterium
tRNA extraction softwaretRNAscan-SE (version 2.0.9)
taxonomic classificationGTDB-Tk, r214
taxonomic identity markermulti-marker approach
Description

MAG_BA_Enterousia_03: Metagenomic assembled genome (MAG) from colon contents of n=52, untreated, wild-type, male C57BL/6J/Ukj mice, aged 2-30 months. Full cohort assembly of all metagenomic samples assembled together from short and long read sequencing with metaSpades hybrid. Coverage and k-mer binning with MetaBAT (version 2.12.1), CONCOCT (version 1.1.0), and MaxBin (version 2.2.4) produced 252 bins which were refined into 181, high to medium quality MAGs via DASTool.

BioProject
PRJEB73981 Baseline Aging
Retrieve all samples from this project

Submission
EBI; 2024-06-04
Accession:
SAMEA115430792
ID:
41667955

BioProject Nucleotide

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