KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Biological Samples | ||
| 25 individual fecal samples | SERA study | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| SM+ buffer (50mM Tris, 5mM NaCl, 8mM MgSO4, 5mM CaCl2, pH = 7, prepare beforehand and filter sterilize) | Duerkop et al., 2016 | N/A |
| DNase buffer (10 mM CaCl2, 50 mM MgCl2) | Shkoporov et al., 2018 | N/A |
| DNase I | Roche | 11284932001 |
| RNase | Roche | 10109134001 |
| proteinase K | Sigma-Aldrich | 1.24568 |
| phage lysis buffer (4.5 M guanidiniumisothiocyanate, 44 mM sodium citrate pH 7.0, 0.88% sarkosyl, 0.72% 2-mercaptoethanol) | Shkoporov et al., 2018 | N/A |
| phenol/chloroform/isoamyl alcohol 25:24:1 | Sigma-Aldrich | P3803 |
| PEG8000 | Fisher BioReagents | BP233 |
| Critical Commercial Assays | ||
| Zymo BashingBead Lysis tube | ZymoResearch | S6012–50 |
| ZymoBIOMICS DNA kit | ZymoResearch | D4303 |
| Ovation Ultralow System v2 | Nugen | 0334 |
| TruSeq Nano DNA Library Prep Kit | Illumina | 20015965 |
| Deposited Data | ||
| Raw virome sequencing data | This paper | PRJEB42612 |
| Raw metagenome sequencing data | This paper | PRJEB42612 |
| 660 curated phage contigs | This paper | PRJEB42612 |
| Oligonucleotides | ||
| Earth Microbiome Project primers 515F and 806R | Caporaso et al., 2011 | N/A |
| Software and Algorithms | ||
| GraphPad Prism v8.4.3 | GraphPad Software | N/A |
| RStudio version 1.2.5001 | RStudio, Inc. | N/A |
| R version 3.6.3 | R Foundation for Statistical Computing | N/A |
| MegaHit assembler v1.2.7 | Li et al., 2016; https://github.com/voutcn/megahit | RRID:SCR_018551 |
| IDBA-UD | Peng et al., 2012; http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ | RRID:SCR_011912 |
| SankeyMATIC | https://github.com/nowthis/sankeymatic | N/A |
| meta-chart | https://www.meta-chart.com/venn | N/A |
| BBtools (BBmap) v38.56 | Bushnell, 2019; http://sourceforge.net/projects/bbmap | RRID:SCR_016965 |
| VIBRANT v1.2.1 | Kieft et al., 2020 | N/A |
| IMG/VR v3.0 | Roux et al., 2020 | N/A |
| tidyverse v1.3.0 | https://cran.r-project.org/package=tidyverse | RRID:SCR_019186 |
| DESeq2 v1.24.0 | Love et al., 2014; https://bioconductor.org/packages/release/bioc/html/DESeq2.html | RRID:SCR_015687 |
| ggplot2 v3.3.3 | https://cran.r-project.org/web/packages/ggplot2/index.html | RRID:SCR_014601 |
| ComplexHeatmap | https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html | RRID:SCR_017270 |
| Pheatmap v1.0.12 | https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap | RRID:SCR_016418 |
| EnhancedVolcano v1.7.16 | https://bioconductor.org/packages/EnhancedVolcano/ | RRID:SCR_018931 |
| corrplot v0.84 | https://github.com/taiyun/corrplot | N/A |
| matrixStats v0.57.0 | https://github.com/HenrikBengtsson/matrixStats | N/A |
| Mothur v1.44.0 | Schloss et al., 2009; http://www.mothur.org/ | RRID:SCR_011947 |