Microbiome disruption and recovery in the fish <em>Gambusia affinis</em> following exposure to broad-spectrum antibiotic

Abstract

Antibiotics are a relatively common disturbance to the normal microbiota of humans and agricultural animals, sometimes resulting in severe side effects such as antibiotic-associated enterocolitis. Gambusia affinis was used as a vertebrate model for effects of a broad-spectrum antibiotic, rifampicin, on the skin and gut mucosal microbiomes. The fish were exposed to the antibiotic in the water column for 1 week, and then monitored during recovery. As observed via culture, viable counts from the skin microbiome dropped strongly yet returned to pretreatment levels by 1.6 days and became >70% resistant. The gut microbiome counts dropped and took longer to recover (2.6 days), and became >90% drug resistant. The resistance persisted at ~20% of skin counts in the absence of antibiotic selection for 2 weeks. A community biochemical analysis measuring the presence/absence of 31 activities observed a 39% change in results after 3 days of antibiotic treatment. The antibiotic lowered the skin and gut microbiome community diversity and altered taxonomic composition, observed by 16S rRNA profiling. A 1-week recovery period did not return diversity or composition to pretreatment levels. The genus Myroides dominated both the microbiomes during the treatment, but was not stable and declined in abundance over time during recovery. Rifampicin selected for members of the family Comamonadaceae in the skin but not the gut microbiome. Consistent with other studies, this tractable animal model shows lasting effects on mucosal microbiomes following antibiotic exposure, including persistence of drug-resistant organisms in the community.

Effects of Life Stage, Site, and Species on the Dragonfly Gut Microbiome

“…Nymphs collected from sites with the greatest level of human impact, the Shelby Farms site downstream from a horse farm, and the Wolf River Greenway downstream from a hospital, tended to have a less rich gut microbiome than nymphs from sites less likely to suffer disturbance. The gut microbial communities of aquatic organisms can shift when exposed to environmental contamination or pollution [33][34][35], and environmental disturbance was found to decrease the overall diversity of the oyster gut microbiome, primarily through the loss of rare phylotypes [36]. These studies and ours suggest that the gut microbiomes of invertebrates may be sensitive to anthropogenic disturbance of the environment, and hosts collected from sites subject to greater human impacts may harbor gut microbiomes that are less diverse than those from less impacted sites.…”

Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs’ gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods

“…Therefore, even though samples cluster mostly by environment, thus suggesting this factor overpasses genetic origin in controlling gut microbiota composition, it also suggests that genetic origin is still exerting a minimal control on bacteria recruitment. At last, sanitary management in hatcheries, due to high density, impairs microbial environment and gut microbiota (Carlson, Leonard, Hyde, Petrosino, & Primm, ; Nakayama et al., ), thus amplifying microbiota divergence between hatchery‐ and wild‐born parrs.…”

Characterization of the skin and gill microbiomes of the farmed seabass (Dicentrarchus labrax) and seabream (Sparus aurata)

“…Each sample was amplified for the V4 hypervariable region of the 16S rRNA gene (~250 bp), which has been widely used to characterize microbiomes from vertebrates (Earth Microbiome Project, Gilbert et al, 2014), including fish (e.g. Carlson et al, 2017;Llewellyn et al, 2015;Nielsen et al, 2017;Wang et al, 2017). Amplicon libraries were sequenced in a single run of the Illumina MiSeq sequencing platform.…”