Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| Dh5α | Thermo Fisher Scientific | Cat# 16512160 |
| BL21-AI | Thermo Fisher Scientific | Cat# C607003 |
| ECOR7, ECOR8, ECOR19, ECOR25, ECOR35, ECOR49, ECOR52, ECOR64, ECOR66, ECOR70 | Fagenbank | N/A |
| All bacteriophages are listed and described in Table S4 | N/A | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Agar | Formedium | Cat# AGA04 |
| Agarose | Melford | Cat# A20090 |
| Ampicillin | Melford | Cat# A40040-10.0 |
| Arabinose | Melford | Cat# A51000-100.0 |
| Gibson assembly Master Mix | New England Biolabs | Cat# E2611L |
| Glycerol | Melford | Cat# G1345-5L |
| Chloramphenicol | Acros Organics | Cat# A0414716 |
| Kanamycin | Gibco | Cat# 11815024 |
| Lysogeny Broth (LB) | Formedium | Cat# LBX0103 |
| Nuclease free water | New England Biolabs | Cat# B1500L |
| OneTaq 2X MasterMix with Standard Buffer | New England Biolabs | Cat# M0486S |
| Q5 DNA polymerase | New England Biolabs | Cat# M0491L |
| TAE 50X | Melford | Cat# T60015-1000.0 |
| Critical commercial assays | ||
| DNA Clean & Concentrator Kit | Zymo Research | Cat# D4029 |
| GeneJET Genomic DNA Purification Kit | Thermo Fisher Scientific | Cat# K0722 |
| NucleoSpin Plasmid QuickPure Kit | Thermo Fisher Scientific | Cat# 11902422 |
| Mix&Go! E. coli Transformation Kit (Zymo) | Zymo Research | Cat# T3001 |
| Qubit™ 1X dsDNA High Sensitivity (HS) Kit | Invitrogen | Cat# Q33231 |
| Zymoclean Gel DNA Recovery Kit | Zymo Research | Cat# D4002 |
| BacTiter-Glo™ Microbial Cell Viability Assay | Promega | Cat# G8230 |
| Deposited data | ||
| Code and raw experimental data | This study | https://github.com/garushyants/synergy_bacterial_immune_systems/ and https://zenodo.org/doi/10.5281/zenodo.1 0075783 |
| Oligonucleotides | ||
| All DNA oligonucleotides are listed in Table S6 | IDT | N/A |
| Recombinant DNA | ||
| All plasmids are listed and described in Table S5 | N/A | N/A |
| Software and algorithms | ||
| Adobe Illustrator 24.2 | Adobe | N/A |
| BioRender | BioRender | N/A |
| BWA v0.7.17 | (Li 2013) | https://github.com/lh3/bwa |
| bcl-convert v3.9.3 | N/A | https://support.illumina.com/downloads/bcl-convert-v4-0-3-installer.html |
| Cactus v2.4.4 | (Armstrong et al. 2020) | https://github.com/ComparativeGenomicsToolkit/cactus |
| CheckM | (Parks et al. 2015) | https://github.com/Ecogenomics/CheckM |
| DefenseFinder version 1.0.8 | (Tesson et al. 2022) | https://github.com/rndmparis/defense-finder |
| gatk v4.2.6.1 | (van der Auwera and O’Connor 2020) | https://github.com/broadinstitute/gatk/releases |
| ggtree for R | (Yu et al. 2017) | https://github.com/YuLab-SMU/ggtree |
| GraphPad Prism 9.2.0 | GraphPad | N/A |
| Jupyter v4.6.3 | N/A | https://github.com/jupyter/notebook/ |
| Mash v2.3 | (Ondov et al. 2016) | https://github.com/rnarbl/Mash/releases/tag/v2.3 |
| PADLOC version 1.1.0 with database version 1.4.0 | (Payne et al. 2021) | https://github.com/padlocbio/padloc |
| phytools for R | (Revell 2012) | https://github.com/liamrevell/phytools |
| Phigaro version 2.2.6 | (Starikova et al. 2020) | https://github.com/bobeobibo/phigaro |
| Platon version 1.6 | (Schwengers et al. 2020) | https://www.uni-giessen.de/fbz/fb08/Inst/bioinformatik/software/platon |
| Python v3.7 | N/A | https://www.python.org/downloads/release/pvthon-370/ |
| R version 4.1.2 | (R Core Team 2018) | https://cran.r-project.org |
| RapidNJ | (Simonsen et al. 2008) | https://github.com/somme89/rapidNJ |
| TreeShrink v1.3.9 | (Mai and Mirarab 2018) | https://github.com/uym2/TreeShrink |
| Other | ||
| FLUOstar OPTIMA plate reader | BMG LABTECH | Cat# 0413B0001J |
| Nanodrop 2000 | Thermo Fisher Scientific | Cat# ND2000 |
| Qubit 2.0 Fluorometer | Invitrogen | Cat# Q32866 |