Multiple generations of antibiotic exposure and isolation influence host fitness and the microbiome in a model zooplankton species

Reilly O. Cooper, Sarah Tjards, Jessica Rischling, David T. Nguyen, Clayton E. Cressler

Research output: Contribution to journalArticlepeer-review


Chronic antibiotic exposure impacts host health through changes to the microbiome. The detrimental effects of antibiotic perturbation on microbiome structure and function after one host generation of exposure have been well-studied, but less is understood about multigenerational effects of antibiotic exposure and subsequent recovery. In this study, we examined microbiome composition and host fitness across five generations of exposure to antibiotics in the model zooplankton host Daphnia magna. By utilizing a split-brood design where half of the offspring from antibiotic-exposed parents were allowed to recover and half were maintained in antibiotics, we examined recovery and resilience of the microbiome. Unexpectedly, we discovered that isolation of single host individuals across generations exerted a strong effect on microbiome composition, with microbiome diversity decreasing over generations regardless of treatment, while host body size and cumulative reproduction increased across generations. Though antibiotics did cause substantial changes to microbiome composition within a generation, recovery generally occurred in one generation regardless of the number of prior generations spent in antibiotics. Our results demonstrate that isolation of individual hosts leads to stochastic extinction of less abundant taxa in the microbiome, suggesting that these taxa are likely maintained via transmission in host populations.

Original languageEnglish (US)
Article numberfiac082
JournalFEMS microbiology ecology
Issue number10
StatePublished - Oct 1 2022


  • Daphnia–microbiota interactions
  • antibiotics
  • invertebrate microbiome
  • recovery
  • transmission

ASJC Scopus subject areas

  • Microbiology
  • Ecology
  • Applied Microbiology and Biotechnology


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