Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs
That antibiotics alter microbiota composition and increase infection susceptibility is well known, but their generalizable effects on the gut commensal community and dependence on environmental variables remain open questions. Here, we systematically compared antibiotic responses in gnotobiotic and conventional mice across antibiotics, microbiotas, diets, and housing status. We identify remarkable resilience, whereby a humanized microbiota recovers before drug administration ends, with transient dominance of resistant Bacteroides and taxa-asymmetric reduction in diversity. In other cases, in vitro sensitivities were not predictive of in vivo responses, underscoring the significance of host and community contexts. A fiber-deficient diet exacerbated collapse of the microbiota and delayed recovery, despite the presence of a similar core community across diets at the point of maximal disturbance. Resilience to a second ciprofloxacin treatment was observed via response reprogramming, in which species replacement after ciprofloxacin treatment established resilience to a second treatment, and also through cross housing transmission. Single-housing drastically disrupted recovery, highlighting the importance of environmental microbial reservoirs and suggesting sanitation may exacerbate the duration of antibiotic-mediated disruption. Our findings highlight the ability of the commensal microbiota to deterministically adapt to large perturbations, and the translational potential for modulating diet, sanitation, and microbiota composition during antibiotics.
This repository contains the raw sequencing data contained in this paper.
|Type of resource
|November 13, 2019
|16S amplicon sequencing
|whole genome sequencing
|Ng, K.T., et al. "Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs." Cell Host & Microbe, vol. 26, issue 5 pp 650-665. doi:10.1016/j.chom.2019.10.011 https://doi.org/10.1016/j.chom.2019.10.011
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- Preferred Citation
- Ng, Katharine. (2019). Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs. Stanford Digital Repository. Available at: https://purl.stanford.edu/rm696bw4911
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