Skin and intestinal microbial diversity of Herzensteinia microcephalus determined by high-throughput sequencing

Abstract:

[Objective] To reveal the microbiota structure and diversity in different parts of Herzensteinia microcephalus and predict the functions of the microbiota.[Methods] High-throughput sequencing of 16S rRNA gene was performed to reveal the microbiota structure. Tax4Fun was employed to predict the functions of the microbiota. [Results] The microbiota in skin mucosa had the highest alpha diversity, with the Shannon index higher than that of the microbiota in intestinal mucosa (P<0.05) and intestinal content (P<0.001). Moreover, the microbiota in skin mucosa can be significantly distinguished from that in intestinal mucosa and intestinal content by principal co-ordinates analysis. Actinobacteria, Proteobacteria, Firmicutes, Chloroflexi, and Cyanobacteria were the top 5 phyla accounting for more than 75% of the total microbiota. Among them, Actinobacteria in intestinal content had higher relative abundance (46.53%) than that in intestinal mucosa (29.23%, P<0.05) and skin mucosa (25.83%, P<0.01). The relative abundance of Proteobacteria in intestinal mucosa (40.33%) was higher than in intestinal content (26.10%, P<0.05). The top 10 families and genera in each part were further analyzed, which showed that skin mucosa and intestinal content had more different microorganisms, including 6 families (e.g., Microbacteriaceae, Burkholderiaceae, and JG30-KF-CM45) and 9 different genera (e.g., Cryobacterium, Carnobacterium, and Arthrobacter). The genera with higher abundance in skin mucosa were associated with organic material degradation and bacterial inhibition. The microbiota in the three parts showed different functional characteristics on pathway level 3 as predicted by Tax4Fun. Specifically, the microbiota in skin mucosa were mainly involved in ABC transporters and histidine metabolism pathway, that in intestinal mucosa in a two-component system and glycerophospholipid metabolism pathway, and that in intestinal content in fatty acid biosynthesis and terpenoid backbone biosynthesis pathway.[Conclusion] The microbiota structures in different parts of H. microcephalus were related to the environment. The skin mucosa had the highest microbial diversity among the three parts, and the intestinal mucosa and intestinal content had similar microbial diversity. In addition, the microorganisms related to the environment, those associated with the host’s physiological characteristics, immunity, and digestion were identified. Revealing the characteristics of microbial distribution in different parts will provide basic data and a scientific basis for the protection and the living environment improvement of fish in the plateau regions.