BA_Helicobacter_hepaticus_01

Identifiers: BioSample: SAMEA115430780; SRA: ERS18592580

Organism: Helicobacter hepaticus
cellular organisms; Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales; Helicobacteraceae; Helicobacter

Attributes

broad-scale environmental context	host associated gut microbiome
collection date	2017-02-14
environmental medium	host associated gut microbiome
geographic location	Germany
isolation source	mouse colon contents
project name	Baseline aging (BA); Aging-associated loss of metabolic host-microbiome-interactions in mice
sample name	ena-SAMPLE-TAB-22-03-2024-10:43:23:851-115543
16S recovery software	barrnap (version 0.9)
16s recovered	No
23s recovered	no
5s recovered	no
ENA first public	2024-03-27
ENA-CHECKLIST	ERC000047
GC content	36.1
INSDC center name	CAU
INSDC status	public
MAG coverage software	Bowtie (version 2.2.5) with jgi_summarize_bam_contig_depths script from MetaBAT (version 2.12.1)
Submitter Id	ena-SAMPLE-TAB-22-03-2024-10:43:23:851-115543
assembly quality	Many fragments with little to no review of assembly other than reporting of standard assembly statistics
assembly software	metaSPAdes hybrid (SPAdes version 3.13.1)
binning parameters	coverage 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 software	MetaBAT (version 2.12.1), CONCOCT (version 1.1.0), MaxBin (version 2.2.4), DASTool (version 1.1.2)
completeness score	93.9
completeness software	CheckM (version 1.1.2)
contamination score	4.8
geographic location (latitude)	50.9
geographic location (longitude)	11.6
local environmental context	host associated gut microbiome
metagenomic source	mouse gut metagenome
number of standard tRNAs extracted	20
sample derived from	ERS18444878,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_name	Helicobacter hepaticus
tRNA extraction software	tRNAscan-SE (version 2.0.9)
taxonomic classification	GTDB-Tk, r214
taxonomic identity marker	multi-marker approach

Description: MAG_BA_Helicobacter_hepaticus_01: 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:: SAMEA115430780
ID:: 41667944

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