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_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_447_length_73649_cov_7.086473

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Podoviridae virus assembled from ERR7738569.

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 (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured podovirus

characteristic: organism

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)

characteristic: reference database(s)

text: uncultured podovirus

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

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

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


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 (ERR7738569) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4567755) 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_PheChl_Fiber-Hadza-Nepal_C_10_2277__NODE_700_length_58320_cov_21.503786

tag: Namespace:Stanford University School of Medicine

characteristic: Submitter Id

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

characteristic: assembly quality

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

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738569.

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 (elevation)

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 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

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: 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; Siphoviridae


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) 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_F_21_1974__NODE_1_length_727939_cov_35.613056_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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 ERR7738570.

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

characteristic: geographic location (country and/or sea)

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-488;s__CAG-488 sp900539465

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-E-H_F_21_1974__NODE_1461_length_53771_cov_51.209390_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

characteristic: environment (feature)

text: feces

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (elevation)

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 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__RF39;f__UBA660;g__CAG-1000;s__CAG-1000 sp900768345

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


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_F_21_1974__NODE_2308_length_38813_cov_12.219486_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

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

text: human-associated habitat

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger;s__Gemmiger sp900540775

characteristic: taxonomy of predicted host

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

characteristic: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_F_21_1974__NODE_43_length_296908_cov_43.645125_1_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

characteristic: geographic location (elevation)

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 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;c__Bacilli;o__RF39;f__UBA660;unk;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


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 (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) 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_F_21_1974__NODE_630_length_88339_cov_10.841370_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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 ERR7738570.

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 (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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oribacterium;s__Oribacterium sp900772695

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

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


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_F_21_1974__NODE_958_length_70335_cov_16.696376_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Caudovirales provirus assembled from ERR7738570.

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

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: uncultured Caudovirales phage

text: non-segmented

text: dsDNA

text: Human gut UViGs

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

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Caudovirales phage

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 sp003447235

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: 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: 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_F_21_1974__NODE_1203_length_60684_cov_49.721319

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 Spbetavirus virus assembled from ERR7738570.

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

text: human-associated habitat

characteristic: environment (feature)

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

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

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B

characteristic: taxonomy of predicted host

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

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


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) 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_F_21_1974__NODE_1617_length_49727_cov_19.567533

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 ERR7738570.

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)

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 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__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella;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: 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_F_21_1974__NODE_2078_length_41786_cov_6.159030

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Caudovirales virus assembled from ERR7738570.

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

characteristic: reference database(s)

text: uncultured Caudovirales phage

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

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


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_F_21_1974__NODE_2411_length_37794_cov_31.172177

characteristic: Submitter Id

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

characteristic: assembly quality

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

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Myoviridae virus assembled from ERR7738570.

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 (country and/or sea)

characteristic: geographic location (elevation)

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

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 (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) 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_F_21_1974__NODE_2833_length_34012_cov_7.942626

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738570.

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 (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

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

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

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

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia_A;o__Christensenellales;f__CAG-74;g__Firm-10;s__

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-E-H_F_21_1974__NODE_3518_length_29206_cov_17.170140

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

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 for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

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

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E;s__Ruminococcus_E bromii_B

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: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_F_21_1974__NODE_4196_length_25537_cov_4.768775

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

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

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

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

characteristic: viral identification software


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738570) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560092) 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_F_21_1974__NODE_5248_length_21722_cov_6.125387

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

characteristic: description

text: independent sequence (UViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

characteristic: environment (feature)

text: feces

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

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

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

characteristic: taxonomic classification

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

characteristic: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU representative

characteristic: vOTU sequence comparison approach


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

characteristic: MAG coverage software

characteristic: Number of BLAST hits supporting host taxonomy

characteristic: Number of CRISPR spacer hits supporting host taxonomy

characteristic: SRA accession

text: Hadza_MoBio_hadza-E-H_F_21_1974__NODE_6969_length_17438_cov_8.049191

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738570.

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

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

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

characteristic: nucleic acid extraction

text: Siphoviridae environmental samples

characteristic: organism

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

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

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus

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

text: Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) 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_H_2_1640__NODE_1067_length_70336_cov_128.322137_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae provirus assembled from ERR7738571.

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)

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 for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

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

characteristic: taxonomic classification

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;s__RC9 sp900541925

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: 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_H_2_1640__NODE_1551_length_55192_cov_10.240298_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 (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 provirus assembled from ERR7738571.

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

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

characteristic: reference database(s)

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__Prevotellamassilia;s__Prevotellamassilia sp900543155

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

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: 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_H_2_1640__NODE_207_length_170799_cov_7.301695_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

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

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

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 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

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1781;unk;unk

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

text: Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) 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_H_2_1640__NODE_41_length_310743_cov_17.256678_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

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 ERR7738571.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

characteristic: environment (biome)

text: human-associated habitat

text: feces

characteristic: feature prediction

text: Tanzania

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

text: 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__Paludibacteraceae;g__RF16;s__RF16 sp900556095

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_H_2_1640__NODE_706_length_90988_cov_18.922804_1

characteristic: Submitter Id

characteristic: Viral contig found in MAG

characteristic: assembly quality

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

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Caudovirales provirus assembled from ERR7738571.

characteristic: description

text: provirus (UpViG)

characteristic: detection type

text: terrestrial biome

text: human-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: Tanzania

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

text: uncultivated viral genomes

text: human feces

text: human gut metagenome

text: uncultured Caudovirales phage

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Caudovirales phage

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 sp000436035

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_H_2_1640__NODE_11488_length_11770_cov_12.233473

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Salasmaviridae virus assembled from ERR7738571.

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 (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

characteristic: reference database(s)

text: uncultured Caudovirales phage

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__Lachnospirales;f__Lachnospiraceae;g__Agathobacter;s__Agathobacter rectalis

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

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


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 (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) 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_H_2_1640__NODE_14325_length_9659_cov_5.578689

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 ERR7738571.

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 (country and/or sea)

characteristic: geographic location (elevation)

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 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

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes;s__Anaerostipes hadrus

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


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_H_2_1640__NODE_182_length_180922_cov_16.677691

characteristic: Submitter Id

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

characteristic: assembly quality

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

characteristic: assembly software

text: CheckV; DTR (high-confidence)

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

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 (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: 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)

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

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

characteristic: vOTU sequence comparison approach

characteristic: viral identification software

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_H_2_1640__NODE_2277_length_42284_cov_84.539674

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; DTR (high-confidence)

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

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)

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 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__;s__

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


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_H_2_1640__NODE_2501_length_39491_cov_7.205663

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

characteristic: environment (material)

characteristic: feature prediction

text: Tanzania

characteristic: geographic location (country and/or sea)

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

characteristic: reference database(s)

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

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

text: 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

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 (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) 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_H_2_1640__NODE_28069_length_5238_cov_8.188529

characteristic: Submitter Id

characteristic: assembly quality

characteristic: assembly software

text: CheckV; DTR (high-confidence)

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Microviridae sp. virus assembled from ERR7738571.

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)

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: uncultured Microviridae

text: non-segmented

text: ssDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Microviridae

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__Fusicatenibacter;s__Fusicatenibacter sp900772675

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

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_H_2_1640__NODE_3389_length_31799_cov_8.670859

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 ERR7738571.

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 (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

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

characteristic: nucleic acid extraction

text: 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

characteristic: reference database(s)

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: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-170;unk;unk

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

characteristic: vOTU sequence comparison approach

characteristic: viral identification software

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


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_H_2_1640__NODE_4623_length_24769_cov_3.685607

characteristic: Submitter Id

characteristic: assembly quality

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

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Siphoviridae virus assembled from ERR7738571.

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 (elevation)

characteristic: geographic location (latitude)

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 for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: Siphoviridae environmental samples

text: Illumina NovaSeq 6000

characteristic: sequencing method

characteristic: similarity search method

text: metagenome (not viral targeted)

characteristic: source of UViGs

characteristic: tRNA extraction software

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

characteristic: taxonomic classification

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

characteristic: taxonomy of predicted host

characteristic: title

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

characteristic: vOTU classification approach

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

characteristic: vOTU database

characteristic: vOTU representative

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


characteristic: BACPHLIP temperate score

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Stanford University School of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: MAG coverage depth

text: Reads (ERR7738571) were merged using BBMerge (rem k=62 extend2=50 ecct vstrict) and then mapped to assembled contigs >=1500bp (ERZ4560598) 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_H_2_1640__NODE_562_length_104136_cov_28.299628

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

text: This sample represents an uncultured crAss-like viruses virus assembled from ERR7738571.

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

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

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

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

characteristic: number of standard tRNAs extracted

characteristic: number of unique standard tRNAs extracted

text: 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

characteristic: reference database(s)

text: uncultured podovirus

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

text: d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__RC9;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

text: Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Podoviridae; crAss-like viruses


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_H_2_1640__NODE_6994_length_17801_cov_235.385837

characteristic: Submitter Id

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

characteristic: assembly quality

characteristic: assembly software

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

characteristic: completeness approach

characteristic: completeness score

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

characteristic: completeness software

text: This sample represents an uncultured Salasmaviridae virus assembled from ERR7738571.

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)

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: uncultured Caudovirales phage

text: non-segmented

text: dsDNA

text: Human gut UViGs

characteristic: reference for biomaterial

characteristic: sample collection device or method

characteristic: sample derived from

text: uncultured Caudovirales phage

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

characteristic: taxonomic classification

text: d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;unk;unk;unk

characteristic: taxonomy of predicted host

characteristic: title

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

characteristic: vOTU classification approach

characteristic: vOTU database

characteristic: vOTU representative

characteristic: viral identification software

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


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_H_2_1640__NODE_8961_length_14486_cov_8.607953

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 Pectobacterium phage DU_PP_III virus assembled from ERR7738571.

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 (longitude)

characteristic: host prediction approach

text: uncultivated viral genomes

characteristic: investigation type

text: human feces

text: human gut metagenome

characteristic: metagenomic source

characteristic: nucleic acid extraction

text: uncultured podovirus

characteristic: organism

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)

characteristic: reference database(s)

text: uncultured podovirus

text: Illumina NovaSeq 6000

text: metagenome (not viral targeted)

characteristic: species-level group of predicted host

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

text: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UBA738;s__UBA738 sp003522945

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

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

characteristic: vOTU sequence comparison approach

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