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Increasing evidence points to the importance of microbial competition in preventing the colonization of disease-causing pathogens and the spread of AMR. Crucially, the pathogens we target with antibiotics do not exist in isolation but instead compete and interact with the microbial communities that colonize the human body, microbiomes. Here, we therefore argue that the key to approaching the challenge of antibiotic treatment failure is understanding the strategies and mechanisms that microbes use to succeed in microbiomes. We discuss how microbial competition influences the colonization of pathogens and the spread of resistance via horizontal gene transfer. We then discuss how microbial competition may be used to synergize with antibiotic treatment or even replace it. 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Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001856?crawler=true&mimetype=application\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T10:17:19Z","timestamp":1792059439000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.microbiologyresearch.org\/content\/journal\/mgen\/10.1099\/mgen.0.001856"}},"subtitle":["&lt;xhtml:span xmlns:xhtml=\"http:\/\/www.w3.org\/1999\/xhtml\" xml:lang=\"en\"&gt;&lt;p&gt;This article is part of our &lt;span style=\"color: rgb(33, 51, 104);\"&gt;&lt;a href=\"\/content\/emerging-investigators-collection-2025-26\"&gt;Emerging Investigators collection&lt;\/a&gt;&lt;\/span&gt;.&lt;\/p&gt;&lt;p style=\"line-height: 1.2;\"&gt;&lt;img src=\"\/upload\/emerging\/Erik_Bakkeren.png\" alt=\"photograph of Erik Bakkeren\" class=\"ImageBorder img-responsive eb-people fr-fic fr-dib\" style=\"width: 120px; float: left; margin: 0 10px 10px 0;\" \/&gt;&lt;span style=\"font-size: 12px; font-weight: normal;\"&gt;&lt;strong&gt;Erik Bakkeren&amp;#160;&lt;\/strong&gt;is an Assistant Professor at the Department of Biological Sciences, a Tier II Canada Research Chair in the Molecular Genetics for Microbiome Editing, and a CIFAR Azrieli Global Scholar. He trained in infection biology at ETH Zurich in Switzerland for his PhD where he studied the evolution of gut pathogens and the spread of antimicrobial resistance. He then moved to the University of Oxford for his postdoc where he trained in microbial ecology and evolution. Erik then established his research group at the University of Calgary in 2025 where he now works on rationally engineering microbiomes using principles from ecology and evolution, focusing on the human gut microbiome. Ultimately, his goals are to develop guiding principles for the design microbial therapeutics to prevent the colonization of\u2014and even remove\u2014problematic strains from microbiomes.&lt;\/span&gt;&lt;\/p&gt;\n&lt;\/xhtml:span&gt;"],"short-title":[],"issued":{"date-parts":[[2026,10,14]]},"references-count":158,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2026,10,14]]}},"URL":"https:\/\/doi.org\/10.1099\/mgen.0.001856","relation":{},"ISSN":["2057-5858"],"issn-type":[{"value":"2057-5858","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,14]]}}}