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Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe

  • Host Microbe Interactions
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Abstract

Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations.

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Acknowledgments

This study was funded by the Allan Wilson Centre. We would like to thank L. Howe, A. Reynolds, P. Marsh, J. Marshall, D. Wilkinson, G. Greaves, A. Wilson, B. Jackson, the friends of Tiritiri Matangi for assistance, Department of Conservation and the Maori community for their support.

Author information

Authors and Affiliations

  1. Allan Wilson Centre for Molecular Ecology and Evolution, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand

    Zoë L. Grange, Brett D. Gartrell, Patrick J. Biggs & Nigel P. French

  2. mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand

    Zoë L. Grange, Patrick J. Biggs & Nigel P. French

  3. Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand

    Zoë L. Grange & Brett D. Gartrell

  4. Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand

    Nicola J. Nelson

  5. Allan Wilson Centre for Molecular Ecology and Evolution, New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand

    Marti Anderson

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  1. Zoë L. Grange
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Correspondence to Zoë L. Grange.

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Ethical Approval

All applicable international, national and/or institutional guidelines for the care and use of animals were followed. 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. This article does not contain any studies with human participants performed by any of the authors.

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The authors declare that they have no conflict of interest.

Electronic Supplementary Material

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Online resource 1

Online resource 1 contains the list of publically available Campylobacter spp. genomes used (Appendix S1), PERMANOVA results (Appendix S2 and 3), MDS plots (Appendix S4 and 5) and results of the independence test comparing clades and locations (Appendix S6). (DOCX 247 kb)

Online resource 2

Tables of factors, cofactors, allelic profiles and distance matrices are available in online resource 2. (XLSX 165 kb)

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Grange, Z.L., Gartrell, B.D., Biggs, P.J. et al. Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe. Microb Ecol 71, 1020–1029 (2016). https://doi.org/10.1007/s00248-015-0721-5

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  • DOI: https://doi.org/10.1007/s00248-015-0721-5

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