The Intestinal Mycobiota in Wild Zebrafish Comprises Mainly Dothideomycetes While Saccharomycetes Predominate in Their Laboratory-Reared Counterparts

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.

Seasonal Variations in the Gut Fungal Communities of Hooded Crane (Grus monacha) at Wintering and Stopover Sites in China

“…Ascomycota is the large phylum of the fungi kingdom, as it has been reported in various hosts, predominantly in dogs [ 30 ], cats [ 31 ], mice [ 32 ], fishes [ 33 ], insects [ 34 ], humans [ 35 ], and geese [ 36 ]. It plays an essential role in the physiology, growth, and metabolism mechanisms of host species and produces some crucial enzymes that aid in the digestion of complex carbohydrates [ 37 ]. The dominant classes of phylum Ascomycota found in the gut of the hooded crane across winter, fall, and spring were Sordariomycetes (21.6%), Dothideomycetes (16.6%), and Saccharomycetes (10.7%).…”

Exposure to Yeast Shapes the Intestinal Bacterial Community Assembly in Zebrafish Larvae

“…Genomic DNA from the pooled intestinal samples was extracted using the QIAamp Fast DNA Stool Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, with minor modifications as described in our earlier publication ( Siriyappagouder et al, 2018 ). In addition, we used the QIAamp DNA micro spin column instead of QIAamp column to purify and elute the DNA.…”

Host-environment interplay shapes fungal diversity in mosquitoes

“…Our results are not surprising and can be explained by the ubiquity of Ascomycota and Basidiomycota in freshwater ecosystems as compared to the remaining fungal phyla (34-36). The ITS2 (fITS7 and ITS4) primers we used for amplification are commonly used in mycobiota surveys (37)(38)(39)(40)(41) and readily identify members of the fungal phyla Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota, as demonstrated by our mock fungal community. However, ITS2…”