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Insights into the Gut and Skin Microbiome of Freshwater Fish, Smelt (Hypomesus nipponensis)

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Abstract

Freshwater smelt (Hypomesus nipponensis) is a planktivorous fish found in the river of South Korea, Japan, China, and Russia. Because of its specific characteristics living in the cold temperature, this species is economically valuable in the various countries that held winter festival. The body size of the smelt is too small, so people consumed raw smelt during the winter festival sometimes. However, the microbial studies of smelt are nonexistent. Here, we characterized and compared the bacterial communities in the gut and skin of freshwater smelts. We amplified, sequenced, and analyzed the V4 regions of bacterial 16S rRNA genes from freshwater smelts. The microbial diversity in the skin (375 OTUs) was much greater than that in the gut (250 OTUs). At the phylum level, Proteobacteria (gut: 51.5%; skin: 52.9%), Firmicutes (gut: 30.6%; skin: 25.4%), Bacteroidetes (gut: 7.7%; skin: 14.7%), and Actinobacteria (gut: 5.2%; skin: 3.8%) were predominant in both organs. At the genus level, Sphingomonas (gut: 24.9%; skin: 4.4%, P < 0.01) was more abundant in the gut, whereas Acinetobacter (gut: 0.8%; skin: 11.8%, P = 0.02) and Pseudomonas (gut: 0.3%; skin: 2.1%, P = 0.01) were more abundant in the skin. Both beneficial (Lactobacillus) and harmful (Staphylococcus and Streptococcus) bacteria were detected in both organs, even under freshwater conditions. These results revealed that smelts have their own unique microbial communities in the gut and skin. Our findings broaden the understanding of planktivorous freshwater fish microbiomes and provide new insights into fish microbiomes for ensuring food safety.

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Data Availability

All data generated and analyzed in this study are included in this published article. Obtained sequences were deposited in GenBank with the Accession Number PRJNA636637.

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Acknowledgements

This study was supported by the Collaborative Genome Program of the Korea Institute of Marine Science and Technology Promotion (KIMST) funded by the Ministry of Oceans and Fisheries (MOF) (No. 20180430) and supported by the BK21 Plus Program from Ministry of Education.

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Authors and Affiliations

  1. Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Kangwon-do, Republic of Korea

    Jongbin Park & Eun Bae Kim

  2. Department of Animal Life Science, College of Animal Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea

    Eun Bae Kim

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  1. Jongbin Park
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  2. Eun Bae Kim
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EBK contributed to conceptualization, funding acquisition, project administration, resources, and supervision. JP was involved in data curation, investigation, and visualization. JP and EBK contributed to formal analysis, methodology, software, validation, writing––original draft, and writing––review and editing.

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Correspondence to Eun Bae Kim.

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All experimental procedures were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) of Kangwon National University (Approval No. KW-181022–1).

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Park, J., Kim, E.B. Insights into the Gut and Skin Microbiome of Freshwater Fish, Smelt (Hypomesus nipponensis). Curr Microbiol 78, 1798–1806 (2021). https://doi.org/10.1007/s00284-021-02440-w

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