Cattle rumen microbiome RUG RUG11014 uncultured Elusimicrobium sp.

assembly software

IDBA-UD; v1.1.3; --num_threads 16 --pre_correction --min_contig 300

environment (material)

bodily fluid

collection date

not collected

sample derived from

ERS3611110

geographic location (longitude)

-3.206493

binning parameters

tetra-nucleotide frequencies and abundance

contamination score

0

reference for biomaterial

Stewart RD, Auffret MD, Warr A, Walker AW, Roehe R, Watson M. Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. (2019) Nat Biotechnol. 37(8):953-961. doi: 10.1038/s41587-019-0202-3.

ENA-FIRST-PUBLIC

2019-11-13

ENA-LAST-UPDATE

2019-11-01

completeness software

CheckM

environment (biome)

Bos taurus

environment (feature)

stomach

geographic location (country and/or sea)

United Kingdom

ENA-CHECKLIST

ERC000047

binning software

MetaBAT2

organism

uncultured Elusimicrobium sp.

assembly quality

Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs

taxonomic identity marker

multi-marker approach - MAGpy - Stewart RD, Auffret MD, Snelling TJ, Roehe R, Watson M. (2019) MAGpy: a reproducible pipeline for the downstream analysis of metagenome-assembled genomes (MAGs). Bioinformatics. 35(12):2150-2152. doi: 10.1093/bioinformatics/bty905

completeness score

96.63

geographic location (latitude)

55.861398

scientific_name

uncultured Elusimicrobium sp.

investigation type

metagenome

metagenomic source

bovine gut metagenome

project name

Metagenomic sequencing of the rumen of 240 cattle from Scotland

sequencing method

Illumina HiSeq 4000

isolation_source

cattle rumen

Cattle rumen microbiome bin 10674_0036_idba_bin.39

assembly software

IDBA-UD; v1.1.3; --num_threads 16 --pre_correction --min_contig 300

environment (material)

bodily fluid

collection date

not collected

sample derived from

ERS3190196

geographic location (longitude)

-3.206493

binning parameters

tetra-nucleotide frequencies and abundance

contamination score

0

ENA-FIRST-PUBLIC

2019-08-02

ENA-LAST-UPDATE

2019-07-31

completeness software

checkm

environment (biome)

Bos taurus

environment (feature)

stomach

geographic location (country and/or sea)

United Kingdom

ENA-CHECKLIST

ERC000050

binning software

MetaBAT2

organism

uncultured bacterium

assembly quality

Many fragments with little to no review of assembly other than reporting of standard assembly statistics

taxonomic identity marker

multi-marker approach (checkm)

completeness score

96.63

geographic location (latitude)

55.861398

scientific_name

uncultured bacterium

investigation type

metagenome

metagenomic source

bovine gut metagenome

project name

Metagenomic sequencing of the rumen of 240 cattle from Scotland

sequencing method

Illumina HiSeq 4000

isolation_source

cattle rumen

Cattle rumen microbiome. breed:AAx; sex:M; age:609

ENA-CHECKLIST

ERC000013

environment (material)

bodily fluid

organism

bovine gut metagenome

collection date

not collected

geographic location (longitude)

-3.206493

host taxid

9913

geographic location (latitude)

55.861398

scientific_name

bovine gut metagenome

investigation type

metagenome

host body habitat

gut

host common name

cow

host body product

rumen fluid

host body site

rumen

host sex

male

subspecific genetic lineage

AAx

host-associated environmental package

host-associated

ENA-FIRST-PUBLIC

2019-03-11

project name

Metagenomic sequencing of the rumen of 240 cattle from Scotland

sequencing method

Illumina HiSeq 4000

ENA-LAST-UPDATE

2019-05-31

host age

609 days

environment (biome)

Bos taurus

environment (feature)

stomach

geographic location (country and/or sea)

United Kingdom

Metadata as EBI XML

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      <LIBRARY_CONSTRUCTION_PROTOCOL>TruSeq Nano</LIBRARY_CONSTRUCTION_PROTOCOL>
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