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Microbiol."},{"key":"10.1016\/j.chom.2024.09.004_bib74","doi-asserted-by":"crossref","DOI":"10.1016\/j.micpath.2022.105556","article-title":"Phage resistance mutation triggered by OmpC deficiency in Klebsiella pneumoniae induced limited fitness costs","volume":"167","author":"Cai","year":"2022","journal-title":"Microb. Pathog."},{"key":"10.1016\/j.chom.2024.09.004_bib75","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2022.104146","article-title":"Rehabilitation of a misbehaving microbiome: phages for the remodeling of bacterial composition and function","volume":"25","author":"Baaziz","year":"2022","journal-title":"iScience"},{"key":"10.1016\/j.chom.2024.09.004_bib98","doi-asserted-by":"crossref","DOI":"10.1186\/1756-0500-7-13","article-title":"Capsule deletion via a \u03bb-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578","volume":"7","author":"Huang","year":"2014","journal-title":"BMC Res. 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Biol."},{"key":"10.1016\/j.chom.2024.09.004_bib79","doi-asserted-by":"crossref","DOI":"10.1186\/s13073-021-00858-2","article-title":"A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch","volume":"13","author":"S\u00e1nchez-Bus\u00f3","year":"2021","journal-title":"Genome Med."},{"key":"10.1016\/j.chom.2024.09.004_bib82","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btac776","article-title":"Pharokka: a fast scalable bacteriophage annotation tool","volume":"39","author":"Bouras","year":"2023","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2024.09.004_bib93","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1128\/JB.02347-14","article-title":"TfoX-based genetic mapping identifies Vibrio fischeri Strain-Level differences and reveals a common lineage of laboratory strains","volume":"197","author":"Brooks","year":"2015","journal-title":"J.\u00a0Bacteriol."},{"key":"10.1016\/j.chom.2024.09.004_bib107","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. 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Immun."},{"key":"10.1016\/j.chom.2024.09.004_bib109","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0011147","article-title":"Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement","volume":"5","author":"Darling","year":"2010","journal-title":"PLoS One"},{"key":"10.1016\/j.chom.2024.09.004_bib104","series-title":"Vegan: Community Ecology Package","author":"Oksanen","year":"2024"},{"key":"10.1016\/j.chom.2024.09.004_bib102","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. 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Commun."},{"key":"10.1016\/j.chom.2024.09.004_bib83","doi-asserted-by":"crossref","first-page":"4537","DOI":"10.1093\/bioinformatics\/btz265","article-title":"PHANOTATE: a novel approach to gene identification in phage genomes","volume":"35","author":"McNair","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.chom.2024.09.004_bib84","doi-asserted-by":"crossref","first-page":"9077","DOI":"10.1093\/nar\/gkab688","article-title":"TRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes","volume":"49","author":"Chan","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2024.09.004_bib85","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1093\/nar\/gkh152","article-title":"ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences","volume":"32","author":"Laslett","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2024.09.004_bib86","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-8-209","article-title":"CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats","volume":"8","author":"Bland","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/j.chom.2024.09.004_bib87","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.chom.2024.09.004_bib88","article-title":"PHROG: families of prokaryotic virus proteins clustered using remote homology","volume":"3","author":"Terzian","year":"2021","journal-title":"NAR Genom. Bioinform."},{"key":"10.1016\/j.chom.2024.09.004_bib89","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: a reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2024.09.004_bib90","first-page":"D517","article-title":"CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database","volume":"48","author":"Alcock","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.chom.2024.09.004_bib91","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"10.1016\/j.chom.2024.09.004_bib92","first-page":"214","article-title":"INfrastructure for a phage REference database: identification of large-scale biases in the current collection of cultured phage genomes","volume":"2","author":"Cook","year":"2021","journal-title":"Phage (New Rochelle)"},{"key":"10.1016\/j.chom.2024.09.004_bib94","doi-asserted-by":"crossref","DOI":"10.1038\/msb4100050","article-title":"Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection","volume":"2","author":"Baba","year":"2006","journal-title":"Mol. 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