PRJNA362181
Fish metagenome Targeted loci environmental
Prophylactic antibiotics in the aquaculture industry are intended to prevent disease and provide an alternative to vaccination. Research in mice and humans suggests antibiotics may disturb microbiome communities and decrease microbiome-mediated disease resistance, also known as 'biotic resistance'. If antibiotics impact fish as they do mice and humans, prophylactic administrations on aquaculture farms may increase downstream disease susceptibility in target hosts, despite short-term pathogen control benefits. We tested the effects of antibiotics on mortality after a pathogen challenge in the Poecilia sphenops black molly, and subsequently tested if probiotic treatments could reverse any antibiotic-induced losses of disease resistance. We found antibiotics significantly increased mortality. We further found that two candidate probiotic bacterial species, Phaeobacter inhibens S4Sm and Bacillus pumilus RI06-95, were able to colonize black molly microbiomes and reverse the negative impacts of antibiotics, suggesting they may have restored microbiome biotic resistance. Despite their positive impact on survival, colonization by probiotics did not influence overall microbiome community structure or diversity, suggesting minor alterations to microbiome composition alone can drastically influence biotic resistance. Our results have immediate implications both for the aquaculture industry but also more broadly for future research on the role of diversity in microbiome function.