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Antibiotics alter microbiota composition and increase infection susceptibility. However, the generalizable effects of antibiotics on and the contribution of environmental variables to gut commensals remain unclear. To address this, we tracked microbiota dynamics with high temporal and taxonomic resolution during antibiotic treatment in a controlled murine system by isolating variables such as diet, treatment history, and housing co-inhabitants. Human microbiotas were remarkably resilient and recovered during antibiotic treatment, with transient dominance of resistant Bacteroides and taxa-asymmetric diversity reduction. In certain cases, in vitro sensitivities were not predictive of in vivo responses, underscoring the significance of host and community context. A fiber-deficient diet exacerbated microbiota collapse and delayed recovery. Species replacement through cross housing after ciprofloxacin treatment established resilience to a second treatment. Single housing drastically disrupted recovery, highlighting the importance of environmental reservoirs. Our findings highlight deterministic microbiota adaptations to perturbations and the translational potential for modulating diet, sanitation, and microbiota composition during antibiotics.
Katharine Michelle Ng
Kerwyn Casey Huang
Katharine Michelle Ng,Andrés Aranda-Díaz,Carolina Tropini,Matthew Ryan Frankel,Willian Van Treuren,Colleen T O'Laughlin,Bryan Douglas Merrill,Feiqiao Brian Yu,Kali M Pruss,Rita Almeida Oliveira,Steven Kyle Higginbottom,Norma F Neff,Michael Andrew Fischbach,Karina Bivar Xavier,Justin Laine Sonnenburg,Kerwyn Casey Huang
Jacob E. Moskowitz, Suzanne Devkota，2019-11-13