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West AG, DeLaunay A, Marsh P, Perry EK, Jolly M, Gartrell BD, Pas A, Digby A, Taylor MW. Gut microbiota of the threatened takahē: biogeographic patterns and conservation implications. Anim Microbiome 2022; 4:11. [PMID: 35078539 PMCID: PMC8790836 DOI: 10.1186/s42523-021-00158-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Aotearoa New Zealand takahē (Porphyrio hochstetteri), once thought to be extinct, is a nationally threatened flightless rail under intensive conservation management. While there has been previous research into disease-related microbes in takahē, little is known about the microbes present in the gastrointestinal tract. Given the importance of gut-associated microbes to herbivore nutrition and immunity, knowledge of these communities is likely to be of considerable conservation value. Here we examined the gut microbiotas of 57 takahē at eight separate locations across Aotearoa New Zealand. RESULTS Faecal samples, taken as a proxy for the hindgut bacterial community, were subjected to 16S rRNA gene amplicon sequencing using Illumina MiSeq. Phylogenetic analysis of > 2200 amplicon sequence variants (ASVs) revealed nine main bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Campilobacterota, Firmicutes, Fusobacteriota, Planctomycetota, Proteobacteria, and Verrucomicrobiota) that accounted for the majority of sequence reads. Location was a significant effect (p value < 0.001, 9999 permutations) that accounted for 32% of the observed microbiota variation. One ASV, classified as Lactobacillus aviarius, was present in all samples at an average relative abundance of 17% (SD = 23.20). There was strong evidence (p = 0.002) for a difference in the abundance of the genus Lactobacillus between locations. A common commensal bacterium previously described in takahē, Campylobacter spp., was also detected in most faecal samples. CONCLUSIONS Location plays a pivotal role in the observed variation among takahē gut bacterial communities and is potentially due to factors such as supplemental feeding and medical treatment experienced by birds housed in captivity at one of the eight sampled sites. These data present a first glimpse of the previously unexplored takahē gut microbiota and provide a baseline for future microbiological studies and conservation efforts.
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Affiliation(s)
- Annie G West
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Anne DeLaunay
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Phil Marsh
- Takahē Recovery Programme, Department of Conservation, Lakefront Drive, Te Anau, New Zealand
| | - Elena K Perry
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Megan Jolly
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Brett D Gartrell
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - An Pas
- New Zealand Centre for Conservation Medicine, Auckland Zoo, Auckland, New Zealand
| | - Andrew Digby
- Takahē Recovery Programme, Department of Conservation, Lakefront Drive, Te Anau, New Zealand
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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Cornelius AJ, Huq M, On SLW, French NP, Vandenberg O, Miller WG, Lastovica AJ, Istivan T, Biggs PJ. Genetic characterisation of Campylobacter concisus: Strategies for improved genomospecies discrimination. Syst Appl Microbiol 2021; 44:126187. [PMID: 33677170 DOI: 10.1016/j.syapm.2021.126187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 02/08/2023]
Abstract
Although at least two genetically distinct groups, or genomospecies, have been well documented for Campylobacter concisus, no phenotype has yet been identified for their differentiation and thus formal description as separate species. C. concisus has been isolated from a variety of sites in the human body, including saliva and stool samples from both healthy and diarrhoeic individuals. We evaluated the ability of a range of whole genome-based tools to distinguish between the two C. concisus genomospecies (GS) using a collection of 190 C. concisus genomes. Nine genomes from related Campylobacter species were included in some analyses to provide context. Analyses incorporating sequence analysis of multiple ribosomal genes generated similar levels of C. concisus GS discrimination as genome-wide comparisons. The C. concisus genomes formed two groups; GS1 represented by ATCC 33237T and GS2 by CCUG 19995. The two C. concisus GS were separated from the nine genomes of related species. GS1 and GS2 also differed in G+C content with medians of 37.56% and 39.51%, respectively. The groups are consistent with previously established GS and are supported by DNA reassociation results. Average Nucleotide Identity using MUMmer (ANIm) and Genome BLAST Distance Phylogeny generated in silico DNA-DNA hybridisation (isDDH) (against ATCC 33237T and CCUG 19995), plus G+C content provides cluster-independent GS discrimination suitable for routine use. Pan-genomic analysis identified genes specific to GS1 and GS2. WGS data and genomic species identification methods support the existence of two GS within C. concisus. These data provide genome-level metrics for strain identification to genomospecies level.
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Affiliation(s)
- Angela J Cornelius
- Institute of Environmental Science and Research Ltd, P.O. Box 29181, Christchurch 8540, New Zealand.
| | - Mohsina Huq
- School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia
| | - Stephen L W On
- Lincoln University, P.O. Box 85084, Lincoln 7647, New Zealand
| | - Nigel P French
- Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Olivier Vandenberg
- National Reference Centre for Campylobacter, Laboratoire Hospitalier Universitaire de Bruxelles, 322 rue Haute, 1000 Brussels, Belgium; School of Public Health, Campus Erasme - Bâtiment A, Route de Lennik 808 - CP591, Université Libre de Bruxelles, 1070 Bruxelles, Belgium
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, United States Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA
| | - Albert J Lastovica
- University of Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Taghrid Istivan
- School of Science, RMIT University, G.P.O. Box 2476, Bundoora, Victoria 3001, Australia
| | - Patrick J Biggs
- Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
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Phiri BJ, French NP, Biggs PJ, Stevenson MA, Reynolds AD, Garcia-R JC, Hayman DTS. Microbial contamination in drinking water at public outdoor recreation facilities in New Zealand. J Appl Microbiol 2020; 130:302-312. [PMID: 32639595 DOI: 10.1111/jam.14772] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/30/2023]
Abstract
AIM The aim of our study was to assess the presence and risk of waterborne pathogens in the drinking water of outdoor facilities in New Zealand and track potential sources of microbial contamination in water sources. METHODS AND RESULTS A serial cross-sectional study with a risk-based sample collection strategy was conducted at 15 public campgrounds over two summer seasons (2011-2012 and 2012-2013). Drinking water supplied to these campgrounds was not compliant with national standards, based on Escherichia coli as an indicator organism, in more than half of the sampling occasions. Campylobacter contamination of drinking water at the campgrounds was likely to be of wild bird origin. Faecal samples from rails (pukeko and weka) were 35 times more likely to return a Campylobacter-positive result compared to passerines. Water treatment using ultraviolet (UV) irradiation or a combination of filtration and UV irradiation or chemicals was more likely to result in water that was compliant with the national standards than water from a tap without any treatment. The use of filters alone was not associated with the likelihood of compliance. CONCLUSIONS Providing microbiologically safe drinking water at outdoor recreational facilities is imperative to avoid gastroenteritis outbreaks. This requires an in-depth understanding of potential sources of contamination in drinking water sources and the installation of adequate water treatment facilities. SIGNIFICANCE AND IMPACT OF THE STUDY Our study provides evidence that drinking water without treatment or filter-only treatment in public campgrounds is unlikely to comply with national standards for human consumption and extra water treatment measures such as UV irradiation or chemical treatment are needed.
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Affiliation(s)
- B J Phiri
- mEpiLab, Hopkirk Research Institute, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - N P French
- mEpiLab, Hopkirk Research Institute, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - P J Biggs
- mEpiLab, Hopkirk Research Institute, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - M A Stevenson
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Sciences, the University of Melbourne, Parkville, Vic, Australia
| | - A D Reynolds
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | - J C Garcia-R
- mEpiLab, Hopkirk Research Institute, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
| | - D T S Hayman
- mEpiLab, Hopkirk Research Institute, School of Veterinary Sciences, Massey University, Palmerston North, New Zealand
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Affiliation(s)
- Graham P. Wallis
- Department of Zoology, University of Otago, Dunedin, New Zealand
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Abstract
Our knowledge of diseases in New Zealand wildlife has expanded rapidly in the last two decades. Much of this is due to a greater awareness of disease as a cause of mortality in some of our highly threatened species or as a limiting factor to the successful captive rearing of intensely managed species such as hihi (Notiomystis cincta), kiwi (Apteryx spp.) and kakapo (Strigops habroptilus). An important factor contributing to the increase of our knowledge has been the development of new diagnostic techniques in the fields of molecular biology and immunohistochemistry, particularly for the diagnosis and epidemiology of viral and protozoan diseases. Although New Zealand remains free of serious exotic viruses there has been much work on understanding the taxonomy and epidemiology of local strains of avipox virus and circoviruses. Bacterial diseases such as salmonellosis, erysipelas and tuberculosis have also been closely investigated in wildlife and opportunist mycotic infections such as aspergillosis remain a major problem in many species. Nutritional diseases such as hyperplastic goitre due to iodine deficiency and metabolic bone disease due to Ca:P imbalance have made significant impacts on some captive reared birds, while lead poisoning is a problem in some localities. The increasing use of wildlife translocations to avoid the extinction of threatened species has highlighted the need for improved methods to assess the disease risks inherent in these operations and other intensive conservation management strategies such as creching young animals. We have also become more aware of the likelihood of inbreeding suppression as populations of many species decrease or pass through a genetic bottleneck. Climate change and habitat loss, however, remain the greatest threats to biodiversity and wildlife health worldwide. Temperature changes will affect our wildlife habitats, alter the distribution of disease vectors and wildlife predators, or directly harm threatened species in vulnerable localities.
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Affiliation(s)
- M R Alley
- a Wildbase, School of Veterinary Science , Massey University , Private Bag 11-222, Palmerston North 4442 , New Zealand
| | - B D Gartrell
- a Wildbase, School of Veterinary Science , Massey University , Private Bag 11-222, Palmerston North 4442 , New Zealand
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Grange ZL, Biggs PJ, Rose SP, Gartrell BD, Nelson NJ, French NP. Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation. MICROBIAL ECOLOGY 2017; 74:735-744. [PMID: 28361266 DOI: 10.1007/s00248-017-0959-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
Translocation and isolation of threatened wildlife in new environments may have unforeseen consequences on pathogen transmission and evolution in host populations. Disease threats associated with intensive conservation management of wildlife remain speculative without gaining an understanding of pathogen dynamics in meta-populations and how location attributes may determine pathogen prevalence. We determined the prevalence and population structure of an opportunistic pathogen, Salmonella, in geographically isolated translocated sub-populations of an endangered New Zealand flightless bird, the takahe (Porphyrio hochstetteri). Out of the nine sub-populations tested, Salmonella was only isolated from takahe living on one private island. The apparent prevalence of Salmonella in takahe on the private island was 32% (95% CI 13-57%), with two serotypes, Salmonella Mississippi and Salmonella houtenae 40:gt-, identified. Epidemiological investigation of reservoirs on the private island and another island occupied by takahe identified environmental and reptile sources of S. Mississippi and S. houtenae 40:gt- on the private island. Single nucleotide polymorphism analysis of core genomes revealed low-level diversity among isolates belonging to the same serotype and little differentiation according to host and environmental source. The pattern observed may be representative of transmission between sympatric hosts and environmental sources, the presence of a common unsampled source, and/or evidence of a recent introduction into the ecosystem. This study highlights how genomic epidemiology can be used to ascertain and understand disease dynamics to inform the management of disease threats in endangered wildlife populations.
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Affiliation(s)
- Zoë L Grange
- Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
- Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand.
- One Health Institute, University of California Davis, Davis, CA, USA.
| | - Patrick J Biggs
- Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Shanna P Rose
- Allan Wilson Centre, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Brett D Gartrell
- Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
- Wildbase, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - Nicola J Nelson
- Allan Wilson Centre, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Nigel P French
- Allan Wilson Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
- mEpiLab, Infectious Disease Research Centre, Hopkirk Research Institute, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
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O’Dea MA, Jackson B, Jackson C, Xavier P, Warren K. Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa). PLoS One 2016; 11:e0165209. [PMID: 27828982 PMCID: PMC5102451 DOI: 10.1371/journal.pone.0165209] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/07/2016] [Indexed: 12/17/2022] Open
Abstract
A respiratory disease syndrome has been observed in large numbers of wild shingleback lizards (Tiliqua rugosa) admitted to wildlife care facilities in the Perth metropolitan region of Western Australia. Mortality rates are reportedly high without supportive treatment and care. Here we used next generation sequencing techniques to screen affected and unaffected individuals admitted to Kanyana Wildlife Rehabilitation Centre in Perth between April and December 2015, with the resultant discovery of a novel nidovirus significantly associated with cases of respiratory disease according to a case definition based on clinical signs. Interestingly this virus was also found in 12% of apparently healthy individuals, which may reflect testing during the incubation period or a carrier status, or it may be that this agent is not causative in the disease process. This is the first report of a nidovirus in lizards globally. In addition to detection of this virus, characterisation of a 23,832 nt segment of the viral genome revealed the presence of characteristic nidoviral genomic elements providing phylogenetic support for the inclusion of this virus in a novel genus alongside Ball Python nidovirus, within the Torovirinae sub-family of the Coronaviridae. This study highlights the importance of next generation sequencing technologies to detect and describe emerging infectious diseases in wildlife species, as well as the importance of rehabilitation centres to enhance early detection mechanisms through passive and targeted health surveillance. Further development of diagnostic tools from these findings will aid in detection and control of this agent across Australia, and potentially in wild lizard populations globally.
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Affiliation(s)
- Mark A. O’Dea
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- * E-mail:
| | - Bethany Jackson
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Carol Jackson
- Kanyana Wildlife Rehabilitation Centre, 120 Gilchrist Rd, Lesmurdie, WA, Australia
| | - Pally Xavier
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Kristin Warren
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
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