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ERR7745922_bin.3

Identifiers
BioSample: SAMEA13486569; SRA: ERS11088607
Organism
uncultured Candidatus Melainabacteria bacterium
cellular organisms; Bacteria; Bacillati; Cyanobacteriota/Melainabacteria group; Candidatus Melainabacteria; environmental samples
Attributes
collection date2014-08-20
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-I-L_O_10_2644.3
16S rRNAs recovered0
16S recoveredFALSE
16S recovery softwarebarrnap;0.9;--kingdom bac
23S rRNAs recovered0
5S rRNAs recovered1
CheckM strain heterogeneity0
ENA first public2022-04-01
ENA last update2022-04-01
ENA-CHECKLISTERC000011
External IdSAMEA13486569
GTDB r202 classificationd__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag1;s__
INSDC center aliasStanford University School of Medicine
INSDC center namestanford university school of medicine
INSDC first public2022-04-01T08:25:59Z
INSDC last update2022-04-01T08:25:59Z
INSDC statuspublic
MAG coverage depth45.47
MAG coverage softwareReads (ERR7745922) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559426) 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-I-L_O_10_2644.3
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 ERR7745922 were assembled into contigs (ERZ4559426). The following read sets from this study were the most similar to ERR7745922 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745922,ERR7745948,ERR7746344,ERR7737973,ERR7738172,ERR7745675,ERR7745384,ERR7745389,ERR7738210,ERR7738182. 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 ERZ4559426. 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: k__Bacteria (UID1453)
completeness score88.55
completeness softwareCheckM;1.1.2;lineage_wf
contamination score0.85
contamination screening inputreads
contamination screening parametersAll reads in ERR7745922 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 representativeERR7746344_bin.28
intra-study species representativeERR7746344_bin.28
metagenomic sourcehuman gut metagenome
most complete 5S rRNA recovered0.8571428571428571
nucleic acid extractionhttps://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103
number of standard tRNAs extracted45
reassembly post binningNo
sample derived fromERS2586348
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 extracted20
Description

This sample represents an uncultured Candidatus Gastranaerophilales sp. MAG assembled and binned from ERR7745922.

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

Submission
EBI; 2022-04-02
Accession:
SAMEA13486569
ID:
27207901

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