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Insights into the microbiome of farmed Asian sea bass (Lates calcarifer) with symptoms of tenacibaculosis and description of Tenacibaculum singaporense sp. nov.

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Abstract

Outbreaks of diseases in farmed fish remain a recurring problem despite the development of vaccines and improved hygiene standards on aquaculture farms. One commonly observed bacterial disease in tropical aquaculture of the South-East Asian region is tenacibaculosis, which is attributed to members of the genus Tenacibaculum (family Flavobacteriaceae, phylum Bacteroidetes), most notably Tenacibaculum maritimum. The impact of tenacibaculosis on the fish microbiota remains poorly understood. In this study, we analysed the microbiota of different tissues of commercially reared Asian seabass (Lates calcarifer) that showed symptoms of tenacibaculosis and compared the microbial communities to those of healthy and experimentally infected fish that were exposed to diseased farmed fish. The relative abundance of Tenacibaculum species in experimentally infected fish was significantly lower than in commercially reared diseased fish and revealed a higher prevalence of different Tenacibaculum species. One isolated strain, TLL-A2T, shares 98.7% 16S rRNA gene identity with Tenacibaculum mesophilum DSM 13764T. The genome of strain TLL-A2T was sequenced and compared to that of T. mesophilum DSM 13764T. Analysis of average nucleotide identity and comparative genome analysis revealed only 92% identity between T. mesophilum DSM 13764T and strain TLL-A2T and differences between the two strains in predicted carbohydrate activating enzymes respectively. Phenotypic comparison between strain TLL-A2T and T. mesophilum DSM 13764T indicated additional differences, such as growth response at different salt concentrations. Based on molecular and phenotypic differences, strain TLL-A2T (=DSM 106434T, KCTC 62393T) is proposed as the type strain of Tenacibaculum singaporense sp. nov.

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Acknowledgements

We thank Daniela Moses at the Singapore Centre for Environmental Life Sciences Engineering for performing the PacBio sequencing, and Amit Anand and Muhammad Khairillah Bin Nanwi at TLL biocomputing for bioinformatics support. This work was funded by Temasek Life Sciences Laboratory.

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Author notes

  1. László Orbán

    Present address: Frontline Fish Genomics Research Group, Department of Animal Sciences, Georgikon Faculty, University of Pannonia, Keszthely, 8360, Hungary

  2. Si Yan Ngoh

    Present address: Marine Aquaculture Center, Agri-Food and Veterinary Authority of Singapore, Singapore, Republic of Singapore

Authors and Affiliations

  1. Temasek Life Sciences Laboratory, 1 Research Link, Singapore, 117604, Republic of Singapore

    Sou Miyake, Melissa Soh, Muhamad Nursyafiq Azman, Si Yan Ngoh, László Orbán & Henning Seedorf

  2. Centre for Comparative Genomics, Murdoch University, Murdoch, Australia

    László Orbán

  3. Department of Biological Sciences, National University of Singapore, Singapore, 117558, Republic of Singapore

    Henning Seedorf

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Contributions

S.M., S.N., M.S., L.O. and H.S. designed experiments, S.M., M.S. and S.N. performed sample collection. S.M., M.S. and M.A. processed samples for DNA sequencing. M.S. conducted cultivation-based analysis of strains. S.N. isolated the novel Tenacibaculum strain. S.M., M.S., analysed data with input from S.N., L.O. and H.S. S.M., M.S., and H.S. wrote the manuscript with input from all other authors.

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Correspondence to Henning Seedorf.

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The authors declare that they have no conflict of interest.

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All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted (Temasek Life Sciences Laboratory IACUC protocol TLL(F)-14–004).

Accession numbers

The de-multiplexed, pair-matched amplicon sequences are deposited in NCBI SRA under the accession number PRJNA493496. The assembled T. singaporense DSM 106434T genome has been deposited in GenBank under accession number GCA_003867015.1.

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Miyake, S., Soh, M., Azman, M.N. et al. Insights into the microbiome of farmed Asian sea bass (Lates calcarifer) with symptoms of tenacibaculosis and description of Tenacibaculum singaporense sp. nov.. Antonie van Leeuwenhoek 113, 737–752 (2020). https://doi.org/10.1007/s10482-020-01391-9

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