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_9_CHE0002SZ__NODE_555_length_77005_cov_84.579009_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 Bacteroides phage F2 provirus assembled from ERR7738938.

characteristic: description

text: provirus (UpViG)

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)

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 Caudovirales phage

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: uncultured Caudovirales phage

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;unk;unk;unk

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

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

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; Bacteroides phage F2


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 (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) using Bowtie2 v2.3.4 (--very-sensitive -X 1000). Coverage was calculated using jgi_summarize_bam_contig_depths (default parameters) from MetaBAT2 v2.15.

characteristic: MAG coverage software

characteristic: SRA accession

text: Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1068_length_53028_cov_8.394044

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; 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 Siphoviridae virus assembled from ERR7738938.

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

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

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

characteristic: reference database(s)

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

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

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

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_9_CHE0002SZ__NODE_1396_length_43805_cov_71.435510

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; DTR (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

text: feces

characteristic: feature prediction

text: Nepal

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: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk

characteristic: taxonomy of predicted host

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

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: Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1582_length_40101_cov_16.716895

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 Lambdavirus virus assembled from ERR7738938.

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: Nepal

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

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

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: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU representative

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


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 (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) 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_9_CHE0002SZ__NODE_1676_length_38445_cov_5.261129

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 ERR7738938.

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 (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

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

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

characteristic: taxonomy of predicted host

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

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

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: Nepal_MoBio_Fiber-Hadza-Nepal_B_9_CHE0002SZ__NODE_1850_length_36068_cov_23.605568

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; HMM-based (lower-bound)

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: Nepal

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: Myoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

characteristic: reference database(s)

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;unk;unk;unk

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


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_9_CHE0002SZ__NODE_2032_length_33769_cov_80.878933

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

text: This sample represents an uncultured Bacteroides phage F2 virus assembled from ERR7738938.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

text: Nepal

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: uncultured Caudovirales phage

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: uncultured Caudovirales phage

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__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp002265625

characteristic: taxonomy of predicted host

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

characteristic: vOTU sequence comparison approach

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Bacteroides phage F2


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 (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) 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_9_CHE0002SZ__NODE_2609_length_27650_cov_603.983951

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 ERR7738938.

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: Nepal

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

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__Erysipelatoclostridiaceae;g__Catenibacterium;unk;unk

characteristic: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU representative

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

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_9_CHE0002SZ__NODE_3214_length_23191_cov_36.536428

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

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: Nepal

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: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

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_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_C;s__Ruminococcus_C sp000433635

characteristic: taxonomy of predicted host

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

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

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: 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_9_CHE0002SZ__NODE_359_length_96675_cov_94.034814

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; 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 crAssphage cr131_1 virus assembled from ERR7738938.

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: Nepal

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

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

characteristic: reference database(s)

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: tRNA extraction software

characteristic: taxonomic classification

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella sp900543975

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: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses; UAG-readthrough crAss clade; crAssphage cr131_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

text: Reads (ERR7738938) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567102) 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_9_CHE0002SZ__NODE_4154_length_18573_cov_4.491458

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 Lambdavirus virus assembled from ERR7738938.

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 (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: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

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

characteristic: taxonomy of predicted host

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

characteristic: vOTU sequence comparison approach

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


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_9_CHE0002SZ__NODE_6393_length_12536_cov_5.538413

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 unclassified Astrithrvirus virus assembled from ERR7738938.

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: Nepal

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: uncultured podovirus

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

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__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter faecis

characteristic: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU representative

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

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; Podoviridae; Astrithrvirus; unclassified Astrithrvirus


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 (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) 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-A-D_F_2_1628__NODE_1034_length_64695_cov_119.830171_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

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 ERR7738957.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: 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

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

characteristic: percent of BLAST hits supporting viral taxonomy

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)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

characteristic: taxonomy of predicted host

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

characteristic: vOTU sequence comparison approach

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

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-A-D_F_2_1628__NODE_1666_length_50017_cov_18.765579_1

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: 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

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

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: species-level group of predicted host

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;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia;s__

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


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-A-D_F_2_1628__NODE_230_length_135960_cov_32.828735_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

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: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae 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

characteristic: taxonomy of predicted host

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

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

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: 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 (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) 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-A-D_F_2_1628__NODE_40_length_273788_cov_15.197234_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

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: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

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__RF39;f__UBA660;g__CAG-460;s__CAG-460 sp000437315

characteristic: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU representative


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-A-D_F_2_1628__NODE_628_length_85860_cov_29.635837_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

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 (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 provirus assembled from ERR7738957.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

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

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

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E;s__Ruminiclostridium_E siraeum

characteristic: taxonomy of predicted host

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


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-A-D_F_2_1628__NODE_961_length_67301_cov_277.661906_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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 Myoviridae provirus assembled from ERR7738957.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

text: human-associated habitat

text: feces

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Myoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

characteristic: reference database(s)

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

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__Bacteroidota;c__Bacteroidia;o__Bacteroidales;unk;unk;unk;unk

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

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 (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) 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-A-D_F_2_1628__NODE_1431_length_54881_cov_47.550270

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 Caudovirales virus assembled from ERR7738957.

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: 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: uncultured Caudovirales phage

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: uncultured Caudovirales phage

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__UBA4334;s__

characteristic: taxonomy of predicted host

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

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

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

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


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: Hadza_MoBio_hadza-A-D_F_2_1628__NODE_17643_length_8656_cov_25.145122

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 Siphoviridae virus assembled from ERR7738957.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: environment (material)

characteristic: feature prediction

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

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

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

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

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: viral identification software

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

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

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-A-D_F_2_1628__NODE_2006_length_44505_cov_28.602458

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 Podoviridae virus assembled from ERR7738957.

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

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: uncultured podovirus

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

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)

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)

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__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;s__Prevotella copri

characteristic: taxonomy of predicted host

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

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 (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) 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-A-D_F_2_1628__NODE_247_length_131579_cov_12.514585

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; DTR (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: Tanzania

characteristic: geographic location (country and/or sea)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

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: 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: 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-A-D_F_2_1628__NODE_29154_length_5610_cov_3.430508

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 (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 Microviridae sp. virus assembled from ERR7738957.

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: 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

characteristic: nucleic acid extraction

text: uncultured Microviridae

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: ssDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: uncultured Microviridae

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-110;s__CAG-110 sp900549705

characteristic: taxonomy of predicted host

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

text: Viruses; Monodnaviria; Sangervirae; Phixviricota; Malgrandaviricetes; Petitvirales; Microviridae; unclassified Microviridae; Microviridae sp.


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-A-D_F_2_1628__NODE_3952_length_28292_cov_15.937693

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 Myoviridae virus assembled from ERR7738957.

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: Tanzania

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

text: Myoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

characteristic: reference database(s)

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;unk;unk;unk

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: 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

text: Reads (ERR7738957) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4561272) 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-A-D_F_2_1628__NODE_5078_length_23434_cov_8.604273

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 ERR7738957.

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 (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

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

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: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4;unk;unk

characteristic: taxonomy of predicted host

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

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-A-D_F_2_1628__NODE_6360_length_19715_cov_5.068031

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

characteristic: description

text: independent sequence (UViG)

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

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference database(s)

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__Fusicatenibacter;unk;unk

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

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: SRA accession

text: Hadza_MoBio_hadza-A-D_F_2_1628__NODE_9514_length_14523_cov_7.135678

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 unclassified Astrithrvirus virus assembled from ERR7738957.

characteristic: description

text: independent sequence (UViG)

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 (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

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

characteristic: nucleic acid extraction

text: uncultured podovirus

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: uncultured podovirus

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

characteristic: viral identification software

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

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 (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) 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_D_4_2182__NODE_125_length_210428_cov_6.592980_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 (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 provirus assembled from ERR7738959.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

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

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

characteristic: reference database(s)

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__Oscillospirales;f__Acutalibacteraceae;g__;s__

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: 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_D_4_2182__NODE_181_length_179431_cov_25.295148_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 (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: 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

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

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: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465;s__CAG-465 sp000433755

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

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_D_4_2182__NODE_247_length_152864_cov_68.626807_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

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 Roseburia phage Jekyll provirus assembled from ERR7738959.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial 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

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: uncultured virus

text: non-segmented

text: uncharacterized

text: Human gut UViGs

characteristic: reference database(s)

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured virus

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

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

text: Viruses; unclassified bacterial viruses; Roseburia phage Jekyll


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 (ERR7738959) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560159) 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_D_4_2182__NODE_2965_length_40479_cov_8.084229_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

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

characteristic: percent of BLAST hits supporting viral taxonomy

text: non-segmented

characteristic: predicted genome structure

text: dsDNA

characteristic: predicted genome type

text: Human gut UViGs

characteristic: project name

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA1777;unk;unk

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

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: Hadza_MoBio_hadza-E-H_D_4_2182__NODE_4398_length_30604_cov_6.136830_1

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 (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 provirus assembled from ERR7738959.

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: Tanzania

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: Siphoviridae environmental samples

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

characteristic: reference database(s)

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__Oribacterium;s__Oribacterium sp900772695

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