Trophic diversification and parasitic invasion as ecological niche modulators for gut microbiota of a sympatric pair of whitefish

Abstract

The impact of parasites on gut microbiota of the host is well documented, but the role of the relationship between the parasite and the host in the formation of the microbiota is poorly understood. Using 16S amplicon sequencing and newly developed methodological approaches, we characterize the gut microbiota of the sympatric pair of whitefish Coregonus lavaretus complex and the associated microbiota of cestodes parasitizing their intestine. The essence of the proposed approaches is, firstly, to use the method of successive washes of the microbiota from the cestode’s surfaces to analyze the degree of bacterial association to the tegument of the parasite. Secondly, to use a method combining the sampling of intestinal content and mucosa with the wash-out procedure from the mucosa to understand the real structure of the fish gut microbiota. Our results demonstrate that the trophic diversification of a sympatric pair of whitefish predetermines a segregation by ecological niches of their respective microbial communities within their intestine. Additional environmental niches for settlement of bacteria in the intestine are formed by the parasitic helminths that caused the restructuring of the bacterial community in infected fish compared to those uninfected. Using the desorption method in Ringer’s solution, we have demonstrated that Proteocephalus sp. cestodes possess their own microbial community which is put together from “surface” bacteria received from the host, bacteria which are weakly and strongly associated with the tegument, and microbiota obtained after removal of the tegument from the cestodes.

Mucus-associated microbiotas among different body sites of wild tuna from the South China Sea

“…recruit and assemble organ-specific symbionts for long-term coevolution. It is necessary to point out that the microbiome of hindgut in this paper was from the content of the hindgut instead of its surface mucus and there might be difference of biodiversity and abundance of microbiota between gut mucus layer and the content (Kashinskaya et al, 2017). The aim in this study is to compare the mucus-associated microbiota from different body sites in tuna.…”

An insight into gill microbiome of Eastern Mediterranean wild fish by applying next generation sequencing

“…It was suggested by de Bruijn et al (2018) (Louca et al, 2017) that the functional characteristics of greatest importance would be the protection of the fish against pathogens, and that this could be achieved by research of gene clusters involved in biosynthesis and production of proteins and metabolites, and studying these genes' frequency, diversity and transcription (Lynn and De Leenheer, 2019). Also, parallel investigation of both phylogeny and function is likely to help cut to a minimum the over-or underrepresentation of certain bacterial families, due to bias resulting from DNA extraction methods (Kashinskaya et al, 2017) and PCR, when relying solely on rRNA amplicon sequencing (Chakravorty et al, 2007;Sinclair et al, 2015;Stoddard et al, 2015).…”