COS 87-2 - Colonization and transmission after antibiotic perturbation in the human gut microbiome

Abstract: Humans constantly encounter new microbes, but few of these introduced microbes become long-term residents of the gut microbiome. Ecological perturbations like antibiotic treatment can disrupt the gut microbiome and provide opportunities for new microbes to colonize, but the role of colonization in shaping community recovery remains unclear. Here, we tracked the dynamics of gut microbiome colonization in a longitudinal cohort of 22 households over two months, during which one subject in each household underwent a controlled perturbation with the antibiotic ciprofloxacin. Colonization was rare in control subjects, who did not take antibiotics, and in most antibiotic-taking subjects, who experienced only transient disruptions in microbiome composition. However, about a quarter of antibiotic-taking subjects displayed lasting shifts in gut microbiome composition, reaching alternative states that persisted for weeks or months after antibiotics. In these subjects, colonization was limited in the first month after antibiotic perturbation despite major losses of community diversity, and strains rarely recolonized from cohabiting subjects, suggesting that highly perturbed, post-antibiotic communities maintain substantial colonization resistance. During up to two years of follow-up sampling, however, colonization substantially reshaped the post-antibiotic alternative states, with some subjects displaying elevated rates of colonization for more than a year after the initial perturbation. Though colonization was the main force driving recovery from post-antibiotic alternative states, one subject underwent a rapid switch between alternative states that was driven primarily by the re-emergence of pre-antibiotic strains. These results show that gut microbiomes continue to display substantial colonization resistance even after major ecological perturbations and suggest that factors like priority effects may slow community recovery.