characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_C_4_7003__NODE_2004_length_40089_cov_11.867040

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;unk;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90


status: PUBLIC

tag: attribute

characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_C_4_7003__NODE_2406_length_34319_cov_1804.528678

tag: Namespace:Stanford University School of Medicine

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Myoviridae virus assembled from ERR7738546.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Myoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_C_4_7003__NODE_3262_length_26092_cov_58.953335

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Myoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_C_4_7003__NODE_524_length_97634_cov_8.582808

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Spbetavirus virus assembled from ERR7738546.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: feature prediction

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelatoclostridiaceae;g__Faecalibacillus;s__Faecalibacillus intestinalis

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738546) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558884) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_C_4_7003__NODE_716_length_82643_cov_10.610615

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Phage DP SC_6_H4_2017 virus assembled from ERR7738546.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: USA

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Myoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A;s__Methanobrevibacter_A smithii_A

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Phage DP SC_6_H4_2017


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_1055_length_61781_cov_21.377399_1

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Myoviridae provirus assembled from ERR7738547.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Myoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_1555_length_46764_cov_4.038919_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae provirus assembled from ERR7738547.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: USA

characteristic: geographic location (country and/or sea)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: species-level group of predicted host

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I;s__Eubacterium_I ramulus

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_2119_length_36585_cov_23.411335_1

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;unk;unk;unk;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

characteristic: viral identification software


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_634_length_87967_cov_14.533098_1

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: USA

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_78_length_230989_cov_6.994015_1

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: CheckV; HMM-based (lower-bound)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Spbetavirus provirus assembled from ERR7738547.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_1318_length_52638_cov_6.739046

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738547.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;unk;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738547) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558876) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_1743_length_42564_cov_45.906842

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: 95% ANI;85% AF;greedy, centroid-based

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

characteristic: viral identification software


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_2294_length_33896_cov_6.164109

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured unclassified Moineauvirus virus assembled from ERR7738547.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: species-level group of predicted host

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Streptococcus;s__Streptococcus thermophilus

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Moineauvirus; unclassified Moineauvirus


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: SRA accession

text: Pilot_MoBio_Fiber_G_11_1024__NODE_4512_length_16928_cov_7.724316

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: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Podoviridae virus assembled from ERR7738547.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured podovirus

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

text: uncultured podovirus

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae

characteristic: viral taxonomy


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738548) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567341) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_200_length_74673_cov_12.439957_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae provirus assembled from ERR7738548.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Nepal

characteristic: geographic location (country and/or sea)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: species-level group of predicted host

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira;s__Lachnospira sp900545725

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_1170_length_23316_cov_4.629330

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Podoviridae virus assembled from ERR7738548.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Nepal

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured podovirus

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: uncultured podovirus

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Dialisteraceae;g__Dialister;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_B_17_RAU1026YZ__NODE_651_length_37130_cov_19.787736

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: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738548.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: feature prediction

text: Nepal

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Mitsuokella;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: viral identification software


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_N_24_7019__NODE_1585_length_35661_cov_5.502585_1

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae provirus assembled from ERR7738549.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.

text: d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium infantis

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_N_24_7019__NODE_638_length_71119_cov_7.196546_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: USA

characteristic: geographic location (country and/or sea)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster;s__Enterocloster sp000431375

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_N_24_7019__NODE_1098_length_48567_cov_15.182759

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

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: CheckV; DTR (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Myoviridae virus assembled from ERR7738549.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Myoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_N_24_7019__NODE_1344_length_41492_cov_35.619872

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: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Winogradskyella phage Peternella_1 virus assembled from ERR7738549.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: USA

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Myoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Winogradskyella phage Peternella_1


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_N_24_7019__NODE_1779_length_32227_cov_20.823950

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Spbetavirus virus assembled from ERR7738549.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;s__Faecalibacterium sp900539945

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_N_24_7019__NODE_2294_length_25978_cov_34.215320

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738549.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: USA

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;unk;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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 (ERR7738549) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4558860) 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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_N_24_7019__NODE_471_length_84657_cov_30.630965

characteristic: Submitter Id

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Phage DP SC_6_H4_2017 virus assembled from ERR7738549.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: USA

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Myoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides uniformis

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Phage DP SC_6_H4_2017


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Pilot_MoBio_Fiber_N_24_7019__NODE_918_length_55459_cov_46.113286

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: USA

characteristic: geographic location (country and/or sea)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

text: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_B_9_1942__NODE_1422_length_57121_cov_5.986677_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae provirus assembled from ERR7738550.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

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: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

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

text: 95% ANI;85% AF;greedy, centroid-based

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_B_9_1942__NODE_261_length_151304_cov_17.989155_1

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: CheckV; AAI-based (medium-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Spbetavirus provirus assembled from ERR7738550.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

characteristic: vOTU sequence comparison approach

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae; Spbetavirus


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_B_9_1942__NODE_3432_length_29673_cov_5.170766_1

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__;unk

text: 95% ANI;85% AF;greedy, centroid-based

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_B_9_1942__NODE_685_length_95026_cov_28.229513_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs.

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: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae provirus assembled from ERR7738550.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

text: Taxonomic predictions from VPF-Class (https://github.com/biocom-uib/vpf-tools, c8422bc, default params) and from DIAMOND (v2.0.9, --sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5) vs NCBI GenBank database compiled using INPHARED v1.6 (run 27 Feb 2022) were aggregated and the lowest agreeing taxonomy was used.

characteristic: taxonomic classification

text: d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_B_9_1942__NODE_937_length_77029_cov_14.087600_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

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: Siphoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__VUNA01;s__;unk

text: 95% ANI;85% AF;greedy, centroid-based

text: CheckV;0.8.1;end-to-end,>=medium-quality; MGV_viral_detection(https://github.com/snayfach/MGV);95c2d4d;defaults


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_B_9_1942__NODE_143_length_194270_cov_26.422636

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; DTR (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Podoviridae virus assembled from ERR7738550.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Tanzania

text: CRISPR spacer matches (PILER-CR;v1.06 or CRT;v1.2; blastn;2.10.1+ -dust no -word_size 18, allowing <=1 gap or mismatch over 95% of spacer length) and >=1kb+>=96% identity BLAST hits (hs-blastn max_target_seqs 25000 -perc_identity 96 -evalue 1e-180) were used to identify connections between each viral contig and all non-viral contigs in the UHGG v1 (286,997 genomes) and this study (54,779 genomes). The predicted host for each viral contig is the lowest taxonomic rank with >70% agreement among all CRISPR+BLAST connections, as described previously (https://doi.org/10.1038/s41564-021-00928-6).

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: uncultured podovirus

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured podovirus

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: species-level group of predicted host

characteristic: tRNA extraction software

characteristic: taxonomic classification

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

characteristic: taxonomy of predicted host

characteristic: title

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU classification approach

text: MGV (https://doi.org/10.1038/s41564-021-00928-6);1.0

characteristic: vOTU database

characteristic: vOTU representative

text: blastn;2.10.1+;-max_target_seqs 25000 -perc_identity 90

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_B_9_1942__NODE_1938_length_45579_cov_53.519582

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; AAI-based (high-confidence)

characteristic: completeness approach

characteristic: completeness score

text: CheckV;0.8.1;end-to-end, database v1.0

characteristic: completeness software

text: This sample represents an uncultured Myoviridae virus assembled from ERR7738550.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: Myoviridae environmental samples

characteristic: organism

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: NCBI GenBank downloaded using INPHARED v1.6 (27 Feb 2022)

characteristic: reference database(s)

text: Myoviridae environmental samples

text: Illumina NovaSeq 6000

text: diamond;2.0.9;--sensitive -k 10 --query-cover 50 --subject-cover 50 --evalue 1e-5

text: metagenome (not viral targeted)

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;unk;unk

text: 95% ANI;85% AF;greedy, centroid-based

characteristic: vOTU sequence comparison approach

characteristic: viral identification software

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae