Longitudinal effects of antibiotics and fecal transplant on lemur gut microbiota structure, associations, and resistomes

Abstract

Antibiotics alter the diversity, structure, and dynamics of host-associated microbial consortia, including via development of antibiotic resistance; however, patterns of recovery from dysbiosis and methods to mitigate negative effects, remain poorly understood. We applied an ecological framework via long-term, integrated study of community structure, across scales, to improve understanding of host-microbe symbiosis during dysbiosis and recovery. We experimentally administered a broad-spectrum antibiotic alone or with subsequent fecal transfaunation to healthy, male ring-tailed lemurs (Lemur catta) and longitudinally tracked the diversity, composition, associations, and resistomes of their gut microbiota. Whereas microbial diversity recovered rapidly in lemurs, antibiotics caused long-term instability in community composition - effects that were attenuated by fecal transfaunation. Antibiotic resistance genes, which were universally present, including in treatment-naive subjects, increased during and persisted after antibiotic treatment. Long-term, integrated study post antibiotic-induced dysbiosis revealed differential, metric-dependent evidence of recovery, beneficial effects of fecal transfaunation, and negative consequences to lemur resistomes.