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Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr


Gut microbiota of wild Baltic salmon (a sub-population of Atlantic salmon Salmo salar L.) parr was first analyzed using microbial profiling of the 16S rRNA gene (V3–V4 region) and high taxonomic richness was revealed. At the phylum level, the gut microbiota was dominated by Firmicutes, Actinobacteria, and Proteobacteria, the most numerous of which were Firmicutes. The phylum Tenericutes (mainly assigned to Mycoplasmataceae), which is common both in wild North- and East- Atlantic salmon parr, was not detected in Baltic salmon parr. Across all samples, unique amplicon sequence variants (ASVs) belonging to the unclassified Bacilli, Actinomycetales, and Rhizobiales were identified as the major taxa. Fifteen ASVs at the family level were found in all gut samples of Baltic salmon parr, the majority of which were Mycobacteriaceae, Cryptosporangiaceae, Microbacteriaceae, and Planctomycetaceae. At the genus level, Mycobacterium, Clostridium sensu stricto, and Hyphomicrobium were dominant but at low levels in all gut samples. Our study has revealed that the gut microbial community of wild Baltic salmon parr differs from those of wild North- and East-Atlantic salmon parr. This can be due to biogeographical differences or host-selective pressures, as the Baltic salmon population is believed to have split from the Atlantic salmon population in the Ancylian period.

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Correspondence to Vesta Skrodenytė-Arbačiauskienė.

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All animal work was conducted on public land and waterways and complied with relevant national and international guidelines and legislation. Permits to perform sampling of salmon specimens (Council Directive 92/43/EEC Annex II species) at the rivers Žeimena, Neris, and Siesartis were issued to the Nature Research Centre (NRC) by The Environmental Protection Agency under the Ministry of the Environment of the Republic of Lithuania. The following permits were issued: Permit No. 044 in 2018, Permit No. 021 in 2019, and Permit No. 025 in 2020. All applicable international, national, and institutional guidelines for the care and use of animals were followed (Directive 2010/63/EU; LT 61-13-005).

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Skrodenytė-Arbačiauskienė, V., Virbickas, T., Lukša, J. et al. Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr. Microb Ecol 84, 1294–1298 (2022).

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  • Salmo salar
  • Gut microbiome
  • Next-generation sequencing
  • Microbial ecology