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ERR7738460_bin.115

Identifiers
BioSample: SAMEA13491784; SRA: ERS11093815
Organism
uncultured Propioniciclava sp.
cellular organisms; Bacteria; Bacillati; Actinomycetota; Actinomycetes; Propionibacteriales; Propionibacteriaceae; Propioniciclava; environmental samples
Attributes
collection date2016
broad-scale environmental contextterrestrial biome
local-scale environmental contexthuman-associated habitat
environmental mediumfeces
geographic locationNepal
investigation typemetagenome-assembled genome
isolation sourcehuman feces
project nameMetagenome sequencing of Nepali gut microbiome
reference for biomaterialhttps://doi.org/10.1371/journal.pbio.2005396
sample collection device or methodhttps://doi.org/10.1371/journal.pbio.2005396
sample nameREFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ.115
16S rRNAs recovered0
16S recoveredFALSE
16S recovery softwarebarrnap;0.9;--kingdom bac
23S rRNAs recovered0
5S rRNAs recovered0
CheckM strain heterogeneity18.18
ENA first public2022-04-01
ENA last update2022-04-01
ENA-CHECKLISTERC000011
External IdSAMEA13491784
GTDB r202 classificationd__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Brevilactibacter;s__
INSDC center aliasStanford University School of Medicine
INSDC center namestanford university school of medicine
INSDC first public2022-04-01T08:20:53Z
INSDC last update2022-04-01T08:20:53Z
INSDC statuspublic
MAG coverage depth8.42
MAG coverage softwareReads (ERR7738460) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567617) 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__Nepal_MoBio_Fiber-Hadza-Nepal_J_17_RAJ1013YZ.115
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 ERR7738460 were assembled into contigs (ERZ4567617). The following read sets from this study were the most similar to ERR7738460 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738460,ERR7745346,ERR7745755,ERR7738229,ERR7738144,ERR7745769,ERR7738619,ERR7738258,ERR7738621,ERR7738529. 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 ERZ4567617. 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__Actinomycetales (UID1697)
completeness score67.08
completeness softwareCheckM;1.1.2;lineage_wf
contamination score4.92
contamination screening inputreads
contamination screening parametersAll reads in ERR7738460 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)1400
geographic location (latitude)28.17
geographic location (longitude)84.25
inter-study species representativeERR7738460_bin.115
intra-study species representativeERR7738460_bin.115
metagenomic sourcehuman gut metagenome
nucleic acid extractionhttps://doi.org/10.1371/journal.pbio.2005396
number of standard tRNAs extracted34
reassembly post binningNo
sample derived fromERS9106185
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 Brevilactibacter sp. MAG assembled and binned from ERR7738460.

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

Submission
EBI; 2022-04-02
Accession:
SAMEA13491784
ID:
27213026

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