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ERR7738269_bin.183

Identifiers
BioSample: SAMEA13485403; SRA: ERS11087443
Organism
uncultured Eubacteriales bacterium
cellular organisms; Bacteria; Bacillati; Bacillota; Clostridia; Eubacteriales; environmental samples
Attributes
collection date2014-08-14
broad-scale environmental contextterrestrial biome
local-scale environmental contexthuman-associated habitat
environmental mediumfeces
geographic locationTanzania
investigation typemetagenome-assembled genome
isolation sourcehuman feces
project nameMetagenome sequencing of Hadza gut microbiome
reference for biomaterialhttps://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
sample collection device or methodhttps://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
sample nameREFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_N_14_2337.183
16S rRNAs recovered0
16S recoveredFALSE
16S recovery softwarebarrnap;0.9;--kingdom bac
23S rRNAs recovered0
5S rRNAs recovered0
CheckM strain heterogeneity0
ENA-CHECKLISTERC000011
ENA-FIRST-PUBLIC2022-12-02
ENA-LAST-UPDATE2022-12-02
External IdSAMEA13485403
GTDB r202 classificationd__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__UMGS902;s__
INSDC center aliasStanford University School of Medicine
INSDC center namestanford university school of medicine
INSDC first public2022-12-02T04:25:13Z
INSDC last update2022-12-02T04:25:13Z
INSDC statuspublic
MAG coverage depth10.95
MAG coverage softwareReads (ERR7738269) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559654) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.
Submitter IdREFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_N_14_2337.183
assembly qualityMany fragments with little to no review of assembly other than reporting of standard assembly statistics.
assembly softwaremetaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz
binning parametersReads from ERR7738269 were assembled into contigs (ERZ4559654). The following read sets from this study were the most similar to ERR7738269 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738269,ERR7745412,ERR7738185,ERR7745403,ERR7738166,ERR7738201,ERR7745388,ERR7738171,ERR7738159,ERR7737968. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 10 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4559654. Depth information for all 10 mapped samples was utilized by MetaBAT2 2.15 for genome binning. Contigs flagged by any module in MAGpurify 2.1.0 (--weighted mode for gc_content, tetra_freq, and coverage modules; conspecific database augmented by high-quality MAGs from this study) were removed from the bin.
binning softwareMetaBAT2 v2.15; MAGpurify v2.1.0
completeness approachCheckM marker lineage: o__Clostridiales (UID1212)
completeness score80.69
completeness softwareCheckM;1.1.2;lineage_wf
contamination score0
contamination screening inputreads
contamination screening parametersAll reads in ERR7738269 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).
geographic location (elevation)1287
geographic location (latitude)-3.55
geographic location (longitude)-34.58
inter-study species representativeERR7745994_bin.72
intra-study species representativeERR7745994_bin.72
metagenomic sourcehuman gut metagenome
nucleic acid extractionhttps://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
number of standard tRNAs extracted34
reassembly post binningNo
sample derived fromERS2586207
sequencing methodIllumina NovaSeq 6000
tRNA extraction softwaretRNAscan-SE;2.0.9;-B
taxonomic classificationGTDB-TK v1.7.0, r202 database, default parameters
taxonomic identity markermulti-marker approach
unique standard tRNAs extracted17
Description

This sample represents an uncultured Eubacteriales bacterium MAG assembled and binned from ERR7738269.

BioProject
PRJEB49206 Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Microbes
Retrieve all samples from this project

Submission
EBI; 2022-12-03
Accession:
SAMEA13485403
ID:
32019264

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