Defining the Distinct Skin and Gut Microbiomes of the Northern Pike (Esox lucius)

Abstract

The microbiome of freshwater fish has important implications for both commercial and recreational fishing because it can have significant impacts on host heath, spoilage rates, and susceptibility to disease. The aqueous environment serves as a possible avenue for continuous introduction of microbes to an animal host, but little is known about how the surrounding microbiota contribute to piscine microbiomes. To better understand the composition of the fish microbiome exposed to the natural environment, we profiled the microbial composition of the gut and the skin mucosal surface (SMS) of northern pike (Esox lucius) and the surrounding river water. We collected fish samples from eight sites along a single river in southwestern Quebec, Canada and analyzed the microbial composition via 16S rRNA sequencing. Our results reveal robust taxonomic differences between the SMS and the gut, indicating a divergence between the microbiomes. The gut community was characterized by a lower alpha diversity compared to the SMS and a large proportion of Cetobacterium, a genus previously linked to carnivorous species. On the other hand, the SMS was more similar to the water than the gut at the family level but divergent at lower taxonomic levels, with fewer than 30% of amplicon sequence variants (ASVs) shared between the SMS and water. In total, our results suggest the establishment of distinct communities across the two fish sites, as well as a clear separation from the microbes in surrounding waters. These data indicate that despite continuous exposure to water, pike are able to establish and maintain unique microbial communities.

Effects of Full Replacement of Dietary Fishmeal with Insect Meal from Tenebrio Molitor on Rainbow Trout Gut and Skin Microbiota.

“…Regardless of the diet type, marked differences in terms of alpha diversity were found between gut and skin microbiota, being the latter characterized by higher microbial diversity and richness. Previous studies on trout and other fresh water species displayed a similar trend with a lower alpha diversity in the gut than in the skin mucosal surface [22,41,42]. Unfortunately, in contrast to high number of studies focused on sh gut microbiome, the skin mucus microbiome remains largely underexplored.…”

“…Initially, sh skin is colonized by bacteria present in the water, but over time, the super cial mucus harbors an increasingly divergent microbial community [41,43]. Like in intestine, the balance between members of skin microbial community, i.e., commensals, symbionts or pathogenic bacterial strains, collectively forming skin microbiome, is important to preserve sh health.…”

Characterization of the skin and gill microbiomes in farmed seabass and seabream across different age groups

“…The water microbiome of shponds were signi cantly distinct and more diverse than the skin and gill microbiomes of both sh, regardless of their age. It is known that free-living microbial communities retain higher richness than host-associated communities [31], with many studies showing a higher bacterial diversity in water relative to sh skin [28,30,36,[58][59][60], gills [14,36], gut [7,15,18,21,61], stomach [36], hindgut [36] and whole larvae [22]. Although some studies in sh have shown that the microbial communities found in the water tend to be recovered in the larval gut microbiome [17,21], others have also shown that water microbiomes do not in uence directly the microbiomes of sh mucosa [7, 8, 13-15, 18, 19, 22, 28, 30, 34, 36, 58-60, 62, 63].…”

“…Previous sh studies of skin and gill microbiomes [e.g. 7,8,36,61], including seabass and seabream [71], have shown remarkable differences in microbial composition and structure across host species and tissues. Additionally, a previous study by our group [72] showed that disease and antibiotic treatment in seabass leads to asymmetrical shifts in skin and gill microbial communities.…”

Effects of aging on the skin and gill microbiota of farmed seabass and seabream

“…The water microbiota of shponds were signi cantly distinct and more diverse than the skin and gill microbiota of both sh, regardless of their age. It is known that free-living microbial communities retain higher richness than host-associated communities [31], with many studies showing a higher bacterial diversity in water relative to sh skin [28,30,36,[66][67][68], gills [14,36], gut [7,15,18,21,69], stomach [36], hindgut [36] and whole larvae [22]. Although some studies in sh have shown that the microbial communities found in the water tend to be recovered in the larval gut microbiota [17,21], others have also shown that water microbiota do not in uence directly the microbiota of sh mucosa [7, 8, 13-15, 18, 19, 22, 28, 30, 34, 36, 66-68, 70, 71].…”