characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738550) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560050) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_B_9_1942.333

characteristic: Submitter Id

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

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738550 were assembled into contigs (ERZ4560050). The following read sets from this study were the most similar to ERR7738550 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738550,ERR7746411,ERR7745823,ERR7745335,ERR7745994,ERR7738959,ERR7738626,ERR7738565,ERR7738643,ERR7738602. 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 ERZ4560050. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738550 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Prevotella sp. MAG assembled and binned from ERR7738550.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Prevotella sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Prevotella sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


status: PUBLIC

tag: attribute

characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251295

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738586) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567843) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_E_6_1527.184

tag: Namespace:Stanford University School of Medicine

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738586 were assembled into contigs (ERZ4567843). The following read sets from this study were the most similar to ERR7738586 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738586,ERR7746321,ERR7738242,ERR7738559,ERR7738659,ERR7738660,ERR7746365,ERR7745896,ERR7738561,ERR7747394. 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 ERZ4567843. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: o__Bacteroidales (UID2716)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738586 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Prevotella sp. MAG assembled and binned from ERR7738586.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: number of standard tRNAs extracted

text: uncultured Prevotella sp.

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Prevotella sp.

text: Illumina NovaSeq 6000

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738167) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559455) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_B_9_2646.100

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738167 were assembled into contigs (ERZ4559455). The following read sets from this study were the most similar to ERR7738167 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738167,ERR7738616,ERR7746767,ERR7738594,ERR7747394,ERR7738622,ERR7738584,ERR7746349,ERR7738552,ERR7738611. 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 ERZ4559455. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738167 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Prevotella sp. MAG assembled and binned from ERR7738167.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: most complete 5S rRNA recovered

characteristic: nucleic acid extraction

text: uncultured Prevotella sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Prevotella sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745414) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560961) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_L_5_1538.17

characteristic: Submitter Id

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

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7745414 were assembled into contigs (ERZ4560961). The following read sets from this study were the most similar to ERR7745414 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745414,ERR7745989,ERR7738149,ERR7738213,ERR7738240,ERR7737956,ERR7745937,ERR7745397,ERR7738556,ERR7738957. 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 ERZ4560961. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7745414 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Prevotella sp. MAG assembled and binned from ERR7745414.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Prevotella sp.

characteristic: organism

text: No

text: uncultured Prevotella sp.

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002251295

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738596) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561093) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_D_21_1577.192

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738596 were assembled into contigs (ERZ4561093). The following read sets from this study were the most similar to ERR7738596 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738596,ERR7738228,ERR7738602,ERR7738557,ERR7738643,ERR7737970,ERR7745924,ERR7746030,ERR7738570,ERR7738531. 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 ERZ4561093. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: o__Bacteroidales (UID2716)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738596 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Prevotella sp. MAG assembled and binned from ERR7738596.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: most complete 23S rRNA recovered

characteristic: nucleic acid extraction

text: uncultured Prevotella sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Prevotella sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738177) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561804) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_I_4_1118.132

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738177 were assembled into contigs (ERZ4561804). The following read sets from this study were the most similar to ERR7738177 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738177,ERR7745588,ERR7738254,ERR7745759,ERR7738271,ERR7738245,ERR7746094,ERR7738594,ERR7738150,ERR7738151. 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 ERZ4561804. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738177 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Prevotella sp. MAG assembled and binned from ERR7738177.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: number of standard tRNAs extracted

text: uncultured Prevotella sp.

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Prevotella sp.

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__51-20;s__51-20 sp900542055

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7803603) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (NA) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K127_MEGAHIT__Hadza_MoBio_hadza-A-D_C_6_1128.549

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7803603 were assembled into contigs (NA). The following read sets from this study were the most similar to ERR7803603 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7803603,ERR7746411,ERR7738959,ERR7747394,ERR7745335,ERR7738264,ERR7746688,ERR7745816,ERR7747255,ERR7738628. 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 NA. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: k__Bacteria (UID2565)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7803603 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Alphaproteobacteria bacterium MAG assembled and binned from ERR7803603.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-239;g__CAG-495;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745859) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567976) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_PheChl_Fiber-Hadza-Nepal_A_4_1166.273

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7745859 were assembled into contigs (ERZ4567976). The following read sets from this study were the most similar to ERR7745859 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745859,ERR7738581,ERR7746101,ERR7747255,ERR7747394,ERR7745947,ERR7738569,ERR7745335,ERR7747324,ERR7745890. 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 ERZ4567976. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7745859 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Alphaproteobacteria bacterium MAG assembled and binned from ERR7745859.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: organism

text: No

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7747426) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559945) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_I_19_2477.62

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7747426 were assembled into contigs (ERZ4559945). The following read sets from this study were the most similar to ERR7747426 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7747426,ERR7738608,ERR7738179,ERR7746779,ERR7738143,ERR7738569,ERR7738568,ERR7738552,ERR7746184,ERR7745815. 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 ERZ4559945. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7747426 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Alphaproteobacteria bacterium MAG assembled and binned from ERR7747426.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-977;g__UBA2903;s__UBA2903 sp900768875

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7747084) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561533) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_K_14_1158.280

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7747084 were assembled into contigs (ERZ4561533). The following read sets from this study were the most similar to ERR7747084 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7747084,ERR7738537,ERR7745890,ERR7747426,ERR7738624,ERR7738608,ERR7738604,ERR7738630,ERR7745582,ERR7738571. 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 ERZ4561533. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: o__Rhodospirillales (UID3754)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7747084 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Alphaproteobacteria bacterium MAG assembled and binned from ERR7747084.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__RF32;f__CAG-977;g__UBA11549;s__UBA11549 sp900768185

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746101) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561613) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_K_22_1166.112

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7746101 were assembled into contigs (ERZ4561613). The following read sets from this study were the most similar to ERR7746101 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746101,ERR7738581,ERR7745859,ERR7738215,ERR7738271,ERR7745759,ERR7746767,ERR7746440,ERR7738588,ERR7738230. 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 ERZ4561613. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7746101 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Alphaproteobacteria bacterium MAG assembled and binned from ERR7746101.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__SFHR01;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7747324) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560480) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_A_18_1822.173

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7747324 were assembled into contigs (ERZ4560480). The following read sets from this study were the most similar to ERR7747324 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7747324,ERR7745859,ERR7745335,ERR7745994,ERR7745823,ERR7745906,ERR7738581,ERR7746051,ERR7746688,ERR7747394. 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 ERZ4560480. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: c__Betaproteobacteria (UID3971)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7747324 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Rhodocyclaceae bacterium MAG assembled and binned from ERR7747324.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: number of standard tRNAs extracted

text: uncultured Rhodocyclaceae bacterium

characteristic: organism

text: No

text: uncultured Rhodocyclaceae bacterium

text: Illumina NovaSeq 6000

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansia muciniphila

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738162) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560186) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_F_8_2217.68

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738162 were assembled into contigs (ERZ4560186). The following read sets from this study were the most similar to ERR7738162 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738162,ERR7745429,ERR7738537,ERR7738552,ERR7738593,ERR7745890,ERR7738661,ERR7738612,ERR7738170,ERR7738568. 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 ERZ4560186. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: k__Bacteria (UID2982)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738162 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Akkermansia sp. MAG assembled and binned from ERR7738162.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Akkermansia sp.

text: Metagenome sequencing of Hadza gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Akkermansia sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738567) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561222) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_D_14_1620.13

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738567 were assembled into contigs (ERZ4561222). The following read sets from this study were the most similar to ERR7738567 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738567,ERR7745335,ERR7747394,ERR7738569,ERR7745823,ERR7746184,ERR7745947,ERR7738158,ERR7738959,ERR7745994. 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 ERZ4561222. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: collection date

text: CheckM marker lineage: o__Burkholderiales (UID4000)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738567 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Oxalobacter sp. MAG assembled and binned from ERR7738567.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

text: uncultured Oxalobacter sp.

characteristic: organism

text: No

text: uncultured Oxalobacter sp.

text: Illumina NovaSeq 6000

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: TRUE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalobacter;s__Oxalobacter sp900760095

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738630) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561632) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_D_12_1182.316

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738630 were assembled into contigs (ERZ4561632). The following read sets from this study were the most similar to ERR7738630 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738630,ERR7745423,ERR7738624,ERR7745890,ERR7738537,ERR7746349,ERR7747084,ERR7738584,ERR7738604,ERR7738622. 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 ERZ4561632. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738630 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Oxalobacter sp. MAG assembled and binned from ERR7738630.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: most complete 16S rRNA recovered

characteristic: most complete 23S rRNA recovered

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Oxalobacter sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Oxalobacter sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732;s__UBA9732 sp001940825

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738143) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559842) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_K_3_2480.87

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738143 were assembled into contigs (ERZ4559842). The following read sets from this study were the most similar to ERR7738143 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738143,ERR7746779,ERR7738179,ERR7738608,ERR7747426,ERR7738569,ERR7738200,ERR7738610,ERR7738203,ERR7746184. 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 ERZ4559842. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: k__Bacteria (UID2495)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738143 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Sphaerochaetaceae sp. MAG assembled and binned from ERR7738143.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: most complete 5S rRNA recovered

characteristic: number of standard tRNAs extracted

text: uncultured Spirochaetales bacterium

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Spirochaetales bacterium

text: Illumina NovaSeq 6000

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: TRUE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745588) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561767) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_A_4_1104.91

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7745588 were assembled into contigs (ERZ4561767). The following read sets from this study were the most similar to ERR7745588 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745588,ERR7746094,ERR7745432,ERR7745425,ERR7745759,ERR7746793,ERR7738230,ERR7738253,ERR7745577,ERR7746440. 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 ERZ4561767. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7745588 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Sphaerochaetaceae sp. MAG assembled and binned from ERR7745588.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: most complete 16S rRNA recovered

characteristic: most complete 23S rRNA recovered

characteristic: nucleic acid extraction

text: uncultured Spirochaetales bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Spirochaetales bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745759) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561840) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-A-D_A_10_1110.276

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745759 were assembled into contigs (ERZ4561840). The following read sets from this study were the most similar to ERR7745759 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745759,ERR7746411,ERR7745408,ERR7745881,ERR7745743,ERR7746748,ERR7738168,ERR7746094,ERR7745588,ERR7745432. 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 ERZ4561840. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7745759 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Sphaerochaetaceae sp. MAG assembled and binned from ERR7745759.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: most complete 5S rRNA recovered

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: number of standard tRNAs extracted

text: uncultured Spirochaetales bacterium

characteristic: organism

text: No

text: uncultured Spirochaetales bacterium

text: Illumina NovaSeq 6000

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA9732;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7745329) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559348) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_G_24_2613.96

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7745329 were assembled into contigs (ERZ4559348). The following read sets from this study were the most similar to ERR7745329 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7745329,ERR7746440,ERR7747125,ERR7745759,ERR7738271,ERR7747128,ERR7745845,ERR7738604,ERR7738594,ERR7746219. 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 ERZ4559348. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: k__Bacteria (UID203)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7745329 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Sphaerochaetaceae sp. MAG assembled and binned from ERR7745329.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Spirochaetales bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Spirochaetales bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Sphaerochaetales;f__Sphaerochaetaceae;g__UBA5920;s__UBA5920 sp002406055

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738661) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560067) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_P_7_2143.157

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738661 were assembled into contigs (ERZ4560067). The following read sets from this study were the most similar to ERR7738661 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738661,ERR7738643,ERR7738537,ERR7745890,ERR7738552,ERR7745963,ERR7747426,ERR7738624,ERR7738569,ERR7738584. 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 ERZ4560067. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: k__Bacteria (UID2495)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738661 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Sphaerochaetaceae sp. MAG assembled and binned from ERR7738661.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: most complete 5S rRNA recovered

characteristic: number of standard tRNAs extracted

text: uncultured Spirochaetales bacterium

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Spirochaetales bacterium

text: Illumina NovaSeq 6000

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738150) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560197) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_F_10_2221.14

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738150 were assembled into contigs (ERZ4560197). The following read sets from this study were the most similar to ERR7738150 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738150,ERR7738151,ERR7745963,ERR7738552,ERR7738568,ERR7745890,ERR7738197,ERR7738537,ERR7745582,ERR7738271. 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 ERZ4560197. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738150 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Sphaerochaetaceae sp. MAG assembled and binned from ERR7738150.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: nucleic acid extraction

text: uncultured Spirochaetales bacterium

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Spirochaetales bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D;s__

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738662) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567250) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Nepal_MoBio_Fiber-Hadza-Nepal_F_3_RAJ1020YZ.146

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738662 were assembled into contigs (ERZ4567250). The following read sets from this study were the most similar to ERR7738662 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738662,ERR7738583,ERR7745908,ERR7745760,ERR7738535,ERR7738513,ERR7745858,ERR7738352,ERR7745755,ERR7738451. 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 ERZ4567250. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: f__Pasteurellaceae (UID4932)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738662 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Haemophilus sp. MAG assembled and binned from ERR7738662.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Nepal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: most complete 5S rRNA recovered

characteristic: number of standard tRNAs extracted

text: uncultured Haemophilus sp.

characteristic: organism

text: Metagenome sequencing of Nepali gut microbiome

text: No

text: uncultured Haemophilus sp.

text: Illumina NovaSeq 6000

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D;s__Haemophilus_D parainfluenzae_K

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738145) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559588) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_J_24_2316.42

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738145 were assembled into contigs (ERZ4559588). The following read sets from this study were the most similar to ERR7738145 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738145,ERR7738148,ERR7738169,ERR7747615,ERR7745922,ERR7746344,ERR7745948,ERR7745675,ERR7738172,ERR7737973. 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 ERZ4559588. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738145 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Haemophilus sp. MAG assembled and binned from ERR7738145.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Haemophilus sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Haemophilus sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: GTDB-TK v1.7.0, r202 database, default parameters

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746144) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560517) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-E-H_K_12_1914.138

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7746144 were assembled into contigs (ERZ4560517). The following read sets from this study were the most similar to ERR7746144 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746144,ERR7738599,ERR7738577,ERR7738242,ERR7738574,ERR7738613,ERR7738595,ERR7738605,ERR7738936,ERR7738569. 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 ERZ4560517. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7746144 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Haemophilus sp. MAG assembled and binned from ERR7746144.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: most complete 5S rRNA recovered

text: https://doi.org/10.1126/science.aan4834; https://doi.org/10.1080/19490976.2018.1494103

characteristic: number of standard tRNAs extracted

text: uncultured Haemophilus sp.

characteristic: organism

text: Metagenome sequencing of Hadza gut microbiome

text: No

text: uncultured Haemophilus sp.

text: Illumina NovaSeq 6000

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_D;s__Haemophilus_D parainfluenzae

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7746692) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561431) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_C-REDO_B_7_1518.57

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7746692 were assembled into contigs (ERZ4561431). The following read sets from this study were the most similar to ERR7746692 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7746692,ERR7745433,ERR7745411,ERR7738195,ERR7738200,ERR7745362,ERR7738242,ERR7738244,ERR7738556,ERR7738184. 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 ERZ4561431. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: f__Pasteurellaceae (UID4932)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7746692 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Haemophilus sp. MAG assembled and binned from ERR7746692.

text: terrestrial biome

text: human-associated habitat

text: feces

text: Tanzania

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Haemophilus sp.

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Haemophilus sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;s__Klebsiella pneumoniae

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738664) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4559409) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_TOP10_CONTIGS_1500_ASSEMBLY_K77_MERGED__Hadza_MoBio_hadza-I-L_K_16_2625.138

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes;3.13.1;-k 21,33,55,77 --merged BBMerge.fq.gz -1 R1.fq.gz -2 R2.fq.gz

characteristic: assembly software

text: Reads from ERR7738664 were assembled into contigs (ERZ4559409). The following read sets from this study were the most similar to ERR7738664 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738664,ERR7745545,ERR7738599,ERR7746111,ERR7738569,ERR7738613,ERR7746048,ERR7738936,ERR7738577,ERR7738605. 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 ERZ4559409. 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

text: CheckM marker lineage: f__Enterobacteriaceae (UID5121)

characteristic: completeness approach

characteristic: contamination score

text: reads

characteristic: contamination screening input

text: All reads in ERR7738664 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

characteristic: contamination screening parameters

text: This sample represents an uncultured Klebsiella sp. MAG assembled and binned from ERR7738664.

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human feces

text: human gut metagenome

characteristic: most complete 5S rRNA recovered

characteristic: number of standard tRNAs extracted

text: uncultured Klebsiella sp.

characteristic: organism

text: No

text: uncultured Klebsiella sp.

text: Illumina NovaSeq 6000

characteristic: tRNA extraction software

text: multi-marker approach


characteristic: 16S rRNAs recovered

text: FALSE

characteristic: 16S recovered

text: barrnap;0.9;--kingdom bac

characteristic: 16S recovery software

characteristic: 23S rRNAs recovered

characteristic: 5S rRNAs recovered

characteristic: CheckM strain heterogeneity

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli

characteristic: GTDB r202 classification

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738562) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558868) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: REFINED_METABAT215_SUBJECT_CONTIGS_1500_ASSEMBLY_K77_MERGED__Pilot_MoBio_Fiber_G_23_1002.51

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: Reads from ERR7738562 were assembled into contigs (ERZ4558868). The following read sets from this study were the most similar to ERR7738562 as determined by MASH (-r -m 2 -s 100000 -k 32): ERR7738562,ERR7738597. Following processing using BBMerge (rem k=62 extend2=50 ecct vstrict), reads from each of these 2 samples were mapped using bowtie2 v2.3.4 (--very-sensitive -X 1000) onto contigs >=1500bp from ERZ4558868. Depth information for all 2 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.

characteristic: binning parameters

text: MetaBAT2 v2.15; MAGpurify v2.1.0

characteristic: binning software

characteristic: collection date

text: CheckM marker lineage: f__Enterobacteriaceae (UID5124)

characteristic: completeness score

characteristic: completeness software

text: reads

text: All reads in ERR7738562 failed to map to hg19 (with custom masking) using BBMap v38.86 (minid=0.95 maxindel=3 bwr=0.16 bw=12 minhits=2).

text: This sample represents an uncultured Escherichia sp. MAG assembled and binned from ERR7738562.

text: terrestrial biome

text: human-associated habitat

text: feces

text: USA

characteristic: inter-study species representative

characteristic: intra-study species representative

text: metagenome-assembled genome

characteristic: investigation type

text: human feces

characteristic: isolation source

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured Escherichia sp.

text: Metagenome sequencing of Californian gut microbiome

characteristic: project name

text: No

characteristic: reassembly post binning

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Escherichia sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: GTDB-TK v1.7.0, r202 database, default parameters

characteristic: taxonomic classification

text: multi-marker approach