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Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.ORCID iD: 0000-0001-7068-2017
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.ORCID iD: 0000-0001-6582-3452
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen K, Denmark.
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2019 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 2, p. 484-502Article in journal (Refereed) Published
Abstract [en]

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro-organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterize the skin microbiome and investigate how host social and geographical factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographical factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology.

Place, publisher, year, edition, pages
John Wiley & Sons, 2019. Vol. 28, no 2, p. 484-502
Keywords [en]
Orcinus orca, Cetacea, contamination, metagenomics, microbiota
National Category
Zoology
Identifiers
URN: urn:nbn:se:uu:diva-374203DOI: 10.1111/mec.14860ISI: 000459345000024PubMedID: 30187987OAI: oai:DiVA.org:uu-374203DiVA, id: diva2:1280384
Funder
EU, European Research Council, ERCStGā€336536EU, Horizon 2020, 663830Swedish Research Council Formas, 2016-00835
Note

These authors contributed equally to this work: Rebecca Hooper, Jaelle C. Brealey, Katerina Guschanski, Andrew D. Foote

Available from: 2019-01-18 Created: 2019-01-18 Last updated: 2019-08-01Bibliographically approved

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Brealey, Jaelle C.van der Valk, TomWolf, Jochen B. W.Guschanski, Katerina

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