Article
Multidisciplinary Sciences
Andrew Digby, Daryl Eason, Alejandro Catalina, Michael Lierz, Stephanie Galla, Lara Urban, Marissa F. Le Lec, Joseph Guhlin, Tammy E. Steeves, Peter K. Dearden, Tineke Joustra, Caroline Lees, Tane Davis, Deidre Vercoe
Summary: Hand-rearing can negatively impact the reproductive fertility of male birds, while the fertility of females is not affected. However, having multiple mates and copulations can increase fertility. These findings have significant implications for the conservation management of threatened bird species.
Article
Genetics & Heredity
Yasmin Foster, Ludovic Dutoit, Stefanie Grosser, Nicolas Dussex, Brodie J. Foster, Ken G. Dodds, Rudiger Brauning, Tracey Van Stijn, Fiona Robertson, John C. McEwan, Jeanne M. E. Jacobs, Bruce C. Robertson
Summary: Events of inbreeding are inevitable in critically endangered species due to reduced population sizes and unique life-history traits, leading to declines in fitness and increased risk of extinction. Investigating levels of inbreeding in a critically endangered flightless parrot, the kakapo, researchers found correlations between measures of inbreeding and significant differences among descendants of the two founding populations.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Annie G. West, Andrew Digby, Anna W. Santure, Joseph G. Guhlin, Peter Dearden, Kakapo Recovery Team, Michael W. Taylor, Lara Urban
Summary: Gut microbiota play a crucial role in conserving threatened wildlife, influenced by factors such as diet, medication, and habitat. In this study, the interaction between host genomic diversity and gut microbiota of the critically endangered kakapo was comprehensively analyzed. The research identified the impact of host genomic diversity, as well as factors like diet, antibiotics, disease, and habitat, on the kakapo gut microbiota. These findings provide valuable insights for kakapo conservation and disease prevention.
Review
Biochemistry & Molecular Biology
Ivana Cibulkova, Veronika Rehorova, Jan Hajer, Frantisek Duska
Summary: The human gut microbiota is a dynamic ecosystem consisting of bacteria, archaea, fungi, and viruses that play a crucial role in maintaining human health. Dysbiosis, or disruption of the gut microbiota, can increase susceptibility to various diseases, leading to rapid overgrowth of pathogenic bacteria in critically ill patients. Restoring a healthy microbiota through fecal microbiota transplantation is a promising concept, especially in intensive care settings, but further research is needed to fully understand its potential benefits and safety in various clinical conditions.
Article
Veterinary Sciences
Li Gao, Li Liu, Chao Du, Qiangchuan Hou
Summary: The study revealed differences in the gut microbial composition and diversity among six bird species, suggesting that dietary habits and living environment may play a role. This provides a theoretical basis for bird protection, including disease prevention and control.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Microbiology
Adrian Low, Melissa Soh, Sou Miyake, Henning Seedorf
Summary: The lifelong relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Microbiome composition throughout the life span of a host remains largely understudied. The fecal microbiota of conventionally raised C57BL/6J male mice was characterized throughout almost the entire adult life span. Microbiota changes occur throughout life but are more pronounced in maturing to middle-age mice than in mice later in life. The Bacteroidota-to-Firmicutes ratio shifts in favor of Firmicutes in old and very old mice. More Firmicutes amplicon sequence variants (ASVs) were transient with varying successional patterns than Bacteroidota ASVs. Age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies. The sensitivity of the age prediction to dietary perturbations was tested. The predicted age for the western diet-fed animals was older than that of standard diet-fed animals. The study sheds light on the temporal changes within the gut microbiota of laboratory mice over their life span and may inform researchers on the appropriate mouse age for their research.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biodiversity Conservation
J. L. Savage, J. M. S. Crane, N. Hemmings
Summary: Reproductive failure is a major obstacle to recovery in many endangered species, including the critically endangered kakapo bird. Recent studies show that fertilization failure is rare in non-threatened bird species, but distinguishing between causes of fertilization failure and embryo death is crucial for conservation management. This study on kakapo eggs found that the majority were fertilized, providing a more accurate estimate of fertility in a wild population, and also demonstrated that artificial insemination can result in more sperm reaching the egg in a wild bird species.
ANIMAL CONSERVATION
(2022)
Article
Ecology
Daniel T. Nugent, David J. Baker-Gabb, Steve W. J. Leonard, John W. Morgan
Summary: Livestock grazing is an important management tool for biodiversity conservation in native grasslands. In semiarid grasslands of Australia, different grazing species have varying effects on the habitat and breeding activity of the plains-wanderer. Therefore, sheep and cattle grazing can be substitutable as a habitat management tool, but their effectiveness may depend on climate conditions.
ECOLOGICAL APPLICATIONS
(2022)
Article
Biology
Diana A. Robledo-Ruiz, Han Ming Gan, Parwinder Kaur, Olga Dudchenko, David Weisz, Ruqayya Khan, Erez Lieberman Aiden, Ekaterina Osipova, Michael Hiller, Hernan E. Morales, Michael J. L. Magrath, Rohan H. Clarke, Paul Sunnucks, Alexandra Pavlova
Summary: The study assembled the chromosome-length genome of the helmeted honeyeater and obtained high-density linkage maps, providing valuable resources for evolutionary studies and guiding conservation efforts for this endangered bird species.
Article
Ecology
Alexander P. Boast, Jamie R. Wood, Nicola Bolstridge, George L. W. Perry, Janet M. Wilmshurst
Summary: Threatened animal species often cannot be found in their original habitats, making it difficult to fully understand their ecological niche using contemporary data alone. However, by analyzing DNA from scats and coprolites, it is possible to identify past and present species interactions of these animals. In this study, the dietary plants of the critically endangered kakapo were analyzed using DNA metabarcoding and palynological analysis. The results revealed previously unknown plant species in the kakapo's diet, indicating that contemporary data may underestimate the dietary breadth of threatened species and highlighting the potential value of coprolite analysis in conservation biology.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Annie G. West, Andrew Digby, Gavin Lear, Michael W. Taylor
Summary: This study analyzed the fecal samples of kakapo chicks and the nest litter to understand the development of their gut microbiota. The results showed that the age and hand rearing conditions of the chicks had a significant impact on the bacterial communities in their excrement. The microbiota of the nest litter also changed over time since the chick was placed in the nest.
Article
Zoology
Annie G. West, Andrew Digby, Michael W. Taylor
Summary: This study examined the impact of Aspergillus infection and management practices on the fungal communities in the gut of kakapo chicks. The results showed that neither the disease nor management practices had a significant effect on the fungal communities, but age and time were associated with variation in the mycobiotas of chicks and nests. This study provides important information and future research directions for the conservation of the critically endangered kakapo.
NEW ZEALAND JOURNAL OF ZOOLOGY
(2023)
Article
Biodiversity Conservation
Katherine A. Farquharson, Elspeth A. McLennan, Adrian Wayne, Michael Smith, Emma Peel, Katherine Belov, Carolyn J. Hogg
Summary: The study on woylie in Australia demonstrates the benefits of generating a large number of SNPs for providing conservation recommendations, while also highlighting the significant differences between observed and expected heterozygosity. It is shown that conservation recommendations are broadly similar between microsatellite and SNP data sets.
GLOBAL ECOLOGY AND CONSERVATION
(2021)
Article
Evolutionary Biology
Elin Videvall, Hanna M. Bensch, Anel Engelbrecht, Schalk Cloete, Charlie K. Cornwallis
Summary: Coprophagy, a behavior observed in various species including birds and mammals, involves the consumption of feces. This study investigates the effects of ostrich chicks ingesting adult feces on their gut microbiota development, growth, feeding behavior, pathogen abundance, and mortality. The results show that coprophagy leads to significant changes in the juvenile gut microbiota, promotes growth, alters feeding behavior, reduces a common gut pathogen, and lowers mortality associated with gut disease.
Article
Microbiology
Caiquan Zhao, Li Liu, Li Gao, Lige Bai
Summary: This study compared the fecal microbiota of different ecological groups of wild birds in the Yellow River National Wetland in Baotou, China. The results showed significant differences in microbiota composition and interaction patterns between the bird groups. The fecal bacterial microbiota of all bird groups were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes, with distinct bacterial genera differences among the groups. Additionally, functional analysis predicted enrichment of antibiotic biosynthesis in all three bird groups.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Eleonora Chiri, Chris Greening, Rachael Lappan, David W. Waite, Thanavit Jirapanjawat, Xiyang Dong, Stefan K. Arndt, Philipp A. Nauer
Article
Multidisciplinary Sciences
Anna Vesty, Kim Gear, Sharon Boutell, Michael W. Taylor, Richard G. Douglas, Kristi Biswas
SCIENTIFIC REPORTS
(2020)
Article
Otorhinolaryngology
Michael Hoggard, Richard G. Douglas, Michael W. Taylor, Kristi Biswas
INTERNATIONAL FORUM OF ALLERGY & RHINOLOGY
(2020)
Article
Immunology
Brett Wagner Mackenzie, Annie G. West, David W. Waite, Christian A. Lux, Richard G. Douglas, Michael W. Taylor, Kristi Biswas
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2020)
Article
Microbiology
Carmen Astudillo-Garcia, James J. Bell, Jose M. Montoya, Lucas Moitinho-Silva, Torsten Thomas, Nicole S. Webster, Michael W. Taylor
ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Microbiology
Christian A. Lux, Brett Wagner Mackenzie, James Johnston, Melissa Zoing, Kristi Biswas, Michael W. Taylor, Richard G. Douglas
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Immunology
Michael Hoggard, Bincy Jacob, David Wheeler, Melissa Zoing, Kevin Chang, Kristi Biswas, Martin Middleditch, Richard G. Douglas, Michael W. Taylor
Summary: This study utilized multiomics-based time-series assessment of nasal polyp biopsies from chronic rhinosinusitis patients, revealing pathways associated with inflammation and apoptosis. Results showed natural variation in certain transcripts and proteins over time, as well as significant responses of some transcripts to corticosteroid therapy.
IMMUNITY INFLAMMATION AND DISEASE
(2021)
Article
Multidisciplinary Sciences
Eleonora Chiri, Philipp A. Nauer, Rachael Lappan, Thanavit Jirapanjawat, David W. Waite, Kim M. Handley, Philip Hugenholtz, Perran L. M. Cook, Stefan K. Arndt, Chris Greening
Summary: Organoheterotrophs are dominant in most soils, but termite mounds feature a unique community dominated by diverse hydrogenotrophic Actinobacteriota and Dormibacterota. These bacteria efficiently consume termite-derived H2 emissions and act as net sinks of atmospheric H2, while also releasing small amounts of methane. The availability of H2 shapes microbial communities and activities, highlighting a unique arthropod-bacteria interaction dependent on H2 transfer.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Lia W. Liefting, David W. Waite, Jeremy R. Thompson
Summary: The adoption of Oxford Nanopore Technologies (ONT) sequencing in plant virology has been slow, but its promise of real-time generation of long nucleotide sequences makes it an attractive method for both low- and high-scale virus diagnostics. The portability of the MinION and Flongle platforms, combined with lower costs and improved read accuracy, highlight ONT's feasibility as a valuable component to diagnostician's toolkit.
Article
Immunology
Christian A. Lux, James J. Johnston, Sharon Waldvogel-Thurlow, Camila Dassi, Richard G. Douglas, Do-Yeon Cho, Michael W. Taylor, Kristi Biswas
Summary: This study successfully developed chronic rhinosinusitis in a rabbit model without pathogen inoculation by inducing bilateral sinonasal mucosal inflammation through unilateral sinus blockage. Results demonstrated diverse bacterial community and inflammatory response in different time points and sides, providing insights into the pathogenesis of CRS.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Brett Wagner Mackenzie, Melissa Zoing, Fiona Clow, David W. Waite, Fiona J. Radcliff, Michael W. Taylor, Kristi Biswas, Richard G. Douglas
Summary: The role of Staphylococcus aureus in chronic rhinosinusitis is still uncertain. Analysis showed no significant differences in S. aureus strain-level diversity between patients with and without CRS. Additionally, there may be an antagonistic interaction between S. aureus and D. pigrum.
SCIENTIFIC REPORTS
(2021)
Article
Microbiology
David T. J. Broderick, David W. Waite, Robyn L. Marsh, Carlos A. Camargo, Paul Cardenas, Anne B. Chang, William O. C. Cookson, Leah Cuthbertson, Wenkui Dai, Mark L. Everard, Alain Gervaix, J. Kirk Harris, Kohei Hasegawa, Lucas R. Hoffman, Soo-Jong Hong, Laurence Josset, Matthew S. Kelly, Bong-Soo Kim, Yong Kong, Shuai C. Li, Jonathan M. Mansbach, Asuncion Mejias, George A. O'Toole, Laura Paalanen, Marcos Perez-Losada, Melinda M. Pettigrew, Maxime Pichon, Octavio Ramilo, Lasse Ruokolainen, Olga Sakwinska, Patrick C. Seed, Christopher J. van der Gast, Brandie D. Wagner, Hana Yi, Edith T. Zemanick, Yuejie Zheng, Naveen Pillarisetti, Michael W. Taylor
Summary: In this study, a meta-analysis of individual participant data from 20 studies involving 2624 children revealed that respiratory diseases were associated with decreased bacterial diversity in nasal and lower airway samples, as well as higher abundance of specific nasal taxa including Streptococcus and Haemophilus. Machine learning showed varying success rates in assigning samples to diagnostic groupings depending on the anatomical site, with positive predictive value ranging from 43 to 100 and sensitivity ranging from 8 to 99%.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Virology
David W. Waite, Lia Liefting, Catia Delmiglio, Anastasia Chernyavtseva, Hye Jeong Ha, Jeremy R. Thompson
Summary: The field of biosecurity has greatly benefited from high-throughput sequencing technologies, but the bioinformatics tools designed for rapid analysis of these sequencing datasets are not developed with biosecurity applications in mind. Many current virus-detection pipelines are not adequate for identifying plant- and animal-infecting viruses. Our work demonstrated that several methods provide sensitive and specific detection of agriculturally important viruses in a timely manner, providing a key piece of ground truthing for method development in this space.
Review
Virology
Catia Delmiglio, David W. W. Waite, Sonia T. T. Lilly, Juncong Yan, Candace E. E. Elliott, Julie Pattemore, Paul L. L. Guy, Jeremy R. R. Thompson
Summary: To protect New Zealand's ecosystems and primary industries, robust and rapid techniques such as polymerase chain reaction (PCR) and high-throughput sequencing are being employed to monitor imported plant materials at the border for high-threat pathogens. Point-of-Use (PoU) technologies, such as recombinase polymerase amplification (RPA) and loop-mediated amplification (LAMP), are also gaining popularity due to their cost-effectiveness and comparable sensitivity to PCR. Efforts are being made nationally and internationally to improve plant virus biosecurity infrastructure and integrate new virus diagnostic technologies.
Article
Plant Sciences
Annelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Z. A. Gaafar, Oscar P. Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovsek, Marie Lefebvre, Martha Malapi, Irena Mavric Plesko, Serkan Onder, Jean-Sebastien Reynard, Ferran Salavert Pamblanco, Olivier Schumpp, Kristian Stevens, Chandan Pal, Lucie Tamisier, Cigdem Ulubas Serce, Inge van Duivenbode, David W. Waite, Xiaojun Hu, Heiko Ziebell, Sebastien Massart
Summary: High-throughput sequencing of plant tissues is a crucial tool for plant virologists to detect plant viruses. However, during the analysis of the data, researchers often neglect sequences without homologies to viruses, which may contain traces of other pathogens. In this study, we re-analyzed RNA-seq datasets and found non-viral plant pathogens, including fungi, insects, and mites. This highlights the potential of using total RNA-seq data for detecting various plant pathogens.