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ERR7738187_bin.123

Identifiers
BioSample: SAMEA13499014; SRA: ERS11101035
Organism
uncultured Lachnospiraceae bacterium
cellular organisms; Bacteria; Bacillati; Bacillota; Clostridia; Lachnospirales; Lachnospiraceae; environmental samples
Attributes
collection date2014-01-26
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-A-D_P_11_1507.123
16S rRNAs recovered0
16S recoveredFALSE
16S recovery softwarebarrnap;0.9;--kingdom bac
23S rRNAs recovered0
5S rRNAs recovered0
CheckM strain heterogeneity0
ENA first public2022-04-01
ENA last update2022-04-01
ENA-CHECKLISTERC000011
External IdSAMEA13499014
GTDB r202 classificationd__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1;s__COE1 sp900753305
INSDC center aliasStanford University School of Medicine
INSDC center namestanford university school of medicine
INSDC first public2022-04-01T08:25:32Z
INSDC last update2022-04-01T08:25:32Z
INSDC statuspublic
MAG coverage depth14.22
MAG coverage softwareReads (ERR7738187) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4562246) 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-A-D_P_11_1507.123
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 ERR7738187 were assembled into contigs (ERZ4562246). The following read sets from this study were the most similar to ERR7738187 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738187,ERR7745953,ERR7746793,ERR7747522,ERR7745559,ERR7738222,ERR7738239,ERR7746094,ERR7745438,ERR7738251. 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 ERZ4562246. 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: f__Lachnospiraceae (UID1255)
completeness score98.74
completeness softwareCheckM;1.1.2;lineage_wf
contamination score1.25
contamination screening inputreads
contamination screening parametersAll reads in ERR7738187 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 representativeGUT_GENOME110833
intra-study species representativeERR7738187_bin.123
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 extracted38
reassembly post binningNo
sample derived fromERS2585763
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 extracted16
Description

This sample represents an uncultured Lachnospiraceae bacterium MAG assembled and binned from ERR7738187.

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

Submission
EBI; 2022-04-02
Accession:
SAMEA13499014
ID:
27220144

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