Baseline microbiome composition impacts resilience to and recovery following antibiotics
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Abstract
The gut microbiome of healthy individuals naturally undergoes temporal changes linked to the dynamics of its community components 1 . These dynamics are only observable in longitudinal studies; they are particularly relevant to understanding ecosystem responses to external environment disturbances. External exposures, such as antibiotic treatment, significantly reshape the gut microbiome, impacting both pathogen and commensal microbes 2 . The gut microbiome plays pivotal roles in digestion, nutrient absorption, and mental health, influencing immune systems, obesity, and various diseases 3-6 . Consequently, beyond the short-term effects on the host gut microbiome dynamics, alterations resulting from antibiotic exposure also have enduring repercussions on human health and physiological equilibrium 7 . Therefore, enhancing gut microbiome resilience during antibiotic treatment is essential, with the goal of mitigating prolonged adverse effects. Here, we explored the impact of pre-antibiotic microbial and functional profiles on resilience, suggesting that specific baseline features exhibit greater resilience to antibiotics-induced changes. Our results identified an uncultured Faecalibacterium prausnitzii taxon as a species at baseline associated with diminished resilience. We demonstrated that this association could be linked to the role of this F. prausnitzii taxon as a keystone species. Additionally, we observed the influence of other commensal bacteria, such as Bifidobacterium animalis and Lactobacillus acidophilus , as well as functional modules, such as multidrug resistance efflux pump, on resilience. This lays the foundations for designing targeted strategies to promote a resilient gut microbiome before antibiotic treatment, alleviating possible prolonged effects on human health.
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- last seen: 2026-05-20T01:45:00.602351+00:00