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In this work, we investigate the elusive phage\u2013bacterium interface in M. bovis by integrating comparative genomics of 200 isolates from infected animals with molecular analyses of M. bovis-positive environmental samples. Despite employing diverse and complementary approaches, we found no evidence of active or recent phage infections: no novel prophages beyond the conserved phiRv1, no expansion of CRISPR arrays, and no cooccurrence of M. bovis and mycobacteriophages in host tissues or environmental matrices. Intriguingly, we identified multiple independent excision events of phiRv1 across closely related lineages, suggesting recent prophage mobilization driven by unidentified ecological or genomic triggers. These findings echo previous observations in M. tuberculosis and point toward a stable, phage-scarce landscape across MTBC members. Our results raise compelling questions about the barriers to phage predation in M. bovis, the functionality of its CRISPR-Cas system, and the selective pressures underlying prophage retention and loss. By shedding light on these underexplored dynamics, our study reveals critical gaps in the ecological understanding of M. bovis and highlights opportunities for phage-based innovation in TB control.<\/jats:p>","DOI":"10.1093\/femsec\/fiaf072","type":"journal-article","created":{"date-parts":[[2025,7,4]],"date-time":"2025-07-04T07:54:09Z","timestamp":1751615649000},"source":"Crossref","is-referenced-by-count":0,"title":["Genomic survey reveals no detectable bacteriophage activity in <i>Mycobacterium bovis<\/i> across a large population"],"prefix":"10.1093","volume":"101","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2405-8755","authenticated-orcid":false,"given":"Daniela","family":"Pinto","sequence":"first","affiliation":[{"name":"Pathogen Biology and Global Health Research Group, Centre for Ecology, Evolution and Environmental Changes (cE3c) and CHANGE \u2013 Global Change and Sustainability Institute, Faculdade de Ci\u00eancias, Universidade de Lisboa , Lisboa, 1749-016 ,","place":["Portugal"]},{"name":"Phage Biology Research and Infection Control (PhaBRIC), Research Institute for Medicines (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa , Lisboa, 1649-003 ,","place":["Portugal"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"In\u00eas","family":"Mendes","sequence":"additional","affiliation":[{"name":"Pathogen Biology and Global Health Research Group, Centre for Ecology, Evolution and Environmental Changes (cE3c) and CHANGE \u2013 Global Change and Sustainability Institute, Faculdade de Ci\u00eancias, Universidade de Lisboa , Lisboa, 1749-016 ,","place":["Portugal"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0401-0276","authenticated-orcid":false,"given":"M\u00f3nica V","family":"Cunha","sequence":"additional","affiliation":[{"name":"Pathogen Biology and Global Health Research Group, Centre for Ecology, Evolution and Environmental Changes (cE3c) and CHANGE \u2013 Global Change and Sustainability Institute, Faculdade de Ci\u00eancias, Universidade de Lisboa , Lisboa, 1749-016 ,","place":["Portugal"]},{"name":"Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ci\u00eancias, Universidade de Lisboa , Lisboa, 1749-016 ,","place":["Portugal"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,7,4]]},"reference":[{"key":"2025071705564003200_bib1","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00446-23","article-title":"The heterogenous and diverse population of prophages in Mycobacterium genomes","volume":"8","author":"Abad","year":"2023","journal-title":"mSystems"},{"key":"2025071705564003200_bib2","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","author":"Afgan","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025071705564003200_bib3","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"article-title":"FastQC: a quality control tool for high throughput sequence data","year":"2010","author":"Andrews","key":"2025071705564003200_bib4"},{"key":"2025071705564003200_bib5","doi-asserted-by":"publisher","first-page":"1263","DOI":"10.1099\/00207713-49-3-1263","article-title":"Mycobacterium tuberculosis subsp. 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