Abstract
As an integral part of the resident microbial community of fish intestinal tract, the mycobiota is expected to play important roles in health and disease resistance of the host. The composition of the diverse fungal communities, which colonize the intestine, is greatly influenced by the host, their diet and geographic origin. Studies of fungal communities are rare and the majority of previous studies have relied on culture-based methods. In particular, fungal communities in fish are also poorly characterized. The aim of this study was to provide an in-depth overview of the intestinal mycobiota in a model fish species (zebrafish, Danio rerio) and to determine differences in fungal composition between wild and captive specimens. We have profiled the intestinal mycobiota of wild-caught (Sharavati River, India), laboratory-reared (Bodø, Norway) and wild-caught-laboratory-kept (Uttara, India) zebrafish by sequencing the fungal internal transcribed spacer 2 region on the Illumina MiSeq platform. Wild fish were exposed to variable environmental factors, whereas both laboratory groups were kept in controlled conditions. There were also differences in husbandry practices at Bodø and Uttara, particularly diet. Zebrafish from Bodø were reared in the laboratory for over 10 generations, while wild-caught-laboratory-kept fish from Uttara were housed in the laboratory for only 2 months before sample collection. The intestine of zebrafish contained members of more than 15 fungal classes belonging to the phyla Ascomycota, Basidiomycota, and Zygomycota. Fungal species richness and diversity distinguished the wild-caught and laboratory-reared zebrafish communities. Wild-caught zebrafish-associated mycobiota comprised mainly Dothideomycetes in contrast to their Saccharomycetes-dominated laboratory-reared counterparts. The predominant Saccharomycetes in laboratory-reared fish belonged to the saprotrophic guild. Another characteristic feature of laboratory-reared fish was the significantly higher abundance of Cryptococcus (Tremellomycetes) compared to wild fish. This pioneer study has shed light into the differences in the intestinal fungal communities of wild-caught and laboratory-reared zebrafish and the baseline data generated will enrich our knowledge on fish mycobiota.
Highlights
Next-generation sequencing (NGS) has revolutionized microbial metagenomics and it has revealed diverse and complex microbial associations between hosts and resident microbes
A total of 1,899,708 high quality sequences were assigned to 334 phylotypes; 199 of which were assigned to genus and/or species level and the remaining ones were identified at higher taxonomic levels
The dominant fungal phylum in the intestine of zebrafish was Ascomycota, which accounted for 87.5% of the total identified sequences
Summary
Next-generation sequencing (NGS) has revolutionized microbial metagenomics and it has revealed diverse and complex microbial associations between hosts and resident microbes. Most of the gut microbe studies had focused their attention only on the bacterial communities, without giving importance to other microorganisms like fungi. Numerous fungal species have been identified in gastrointestinal sections and fecal samples of human, mice, and dog (Foster et al, 2013; Underhill and Iliev, 2014; Luan et al, 2015; Qiu et al, 2015), and intestinal mycobiota are usually studied using laboratoryreared animals, mainly mouse (Iliev et al, 2012; Dollive et al, 2013). The fungal community in murine gut has been associated with husbandry conditions (Dollive et al, 2013)
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