Real-time genomics for One Health.

The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.

Whole genome sequencing of Penicillium and Burkholderia strains antagonistic to the causal agent of kauri dieback disease (Phytophthora agathidicida) reveals biosynthetic gene clusters related to antimicrobial secondary metabolites.

Phytophthora agathidicida is a virulent soil pathogen of Aotearoa New Zealand's iconic kauri tree species (Agathis australis (D. Don) Lindl.) and the primary causal agent of kauri dieback disease. To date, only a few control options are available to treat infected kauri that are expressing symptoms of dieback disease. Previous research has identified strains of Penicillium and Burkholderia that inhibited the mycelial growth of P. agathidicida in vitro. However, the mechanisms of inhibition remain unknown. By performing whole genome sequencing, we screened the genomes of four Penicillium and five Burkholderia strains to identify secondary metabolite encoding biosynthetic gene clusters (SM-BGCs) that may be implicated in the production of antimicrobial compounds. We identified various types of SM-BGCs in the genome of each strain, including polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs), and terpenes. Across all four of the Penicillium strains, five SM-BGCs were detected that encoded the biosynthesis of napthopyrone, clavaric acid, pyranonigrin E, dimethyl coprogen and asperlactone. Across all five of the Burkholderia strains, three SM-BGCs were detected that encoded the biosynthesis of ornibactin, pyochelin and pyrrolnitin. Our analysis detected numerous SM-BGCs which could not be characterised. Further efforts should be made to identify the compounds encoded by these SM-BGCs so that we can explore their antimicrobial potential. The potential inhibitory effects of the compounds encoded by the SM-BGCs identified in this study may be worthy of further investigation for their effect on the growth and virulence of P. agathidicida.

Internal Transcribed Spacer and 16S Amplicon Sequencing Identifies Microbial Species Associated with Asbestos in New Zealand.

Inhalation of asbestos fibres can cause lung inflammation and the later development of asbestosis, lung cancer, and mesothelioma, and the use of asbestos is banned in many countries. In most countries, large amounts of asbestos exists within building stock, buried in landfills, and in contaminated soil. Mechanical, thermal, and chemical treatment options do exist, but these are expensive, and they are not effective for contaminated soil, where only small numbers of asbestos fibres may be present in a large volume of soil. Research has been underway for the last 20 years into the potential use of microbial action to remove iron and other metal cations from the surface of asbestos fibres to reduce their toxicity. To access sufficient iron for metabolism, many bacteria and fungi produce organic acids, or iron-chelating siderophores, and in a growing number of experiments these have been found to degrade asbestos fibres in vitro. This paper uses the internal transcribed spacer (ITS) and 16S amplicon sequencing to investigate the fungal and bacterial diversity found on naturally-occurring asbestos minerals, asbestos-containing building materials, and asbestos-contaminated soils with a view to later selectively culturing promising species, screening them for siderophore production, and testing them with asbestos fibres in vitro. After filtering, 895 ITS and 1265 16S amplicon sequencing variants (ASVs) were detected across the 38 samples, corresponding to a range of fungal, bacteria, cyanobacterial, and lichenized fungal species. Samples from Auckland (North Island, New Zealand) asbestos cement, Auckland asbestos-contaminated soils, and raw asbestos rocks from Kahurangi National Park (South Island, New Zealand) were comprised of very different microbial communities. Five of the fungal species detected in this study are known to produce siderophores.

Soil microbial diversity in adjacent forest systems - contrasting native, old growth kauri (Agathis australis) forest with exotic pine (Pinus radiata) plantation forest.

Globally, the conversion of primary forests to plantations and agricultural landscapes is a common land use change. Kauri (Agathis australis) is one of the most heavily impacted indigenous tree species of New Zealand with <1% of primary forest remaining as fragments adjacent to pastoral farming and exotic forest plantations. By contrasting two forest systems, we investigated if the fragmentation of kauri forests and introduction of pine plantations (Pinus radiata) are significantly impacting the diversity and composition of soil microbial communities across Waipoua kauri forest, New Zealand. Using next generation based 16S rRNA and ITS gene region sequencing, we identified that fungal and bacterial community composition significantly differed between kauri and pine forest soils. However, fungal communities displayed the largest differences in diversity and composition. This research revealed significant shifts in the soil microbial communities surrounding remnant kauri fragments, including the loss of microbial taxa with functions in disease suppression and plant health. Kauri dieback disease, caused by Phytophthora agathidicida, currently threatens the kauri forest ecosystem. Results from this research highlight the need for further investigations into how changes to soil microbial diversity surrounding remnant kauri fragments impact tree health and disease expression.

Metagenome Profiling Identifies Potential Biocontrol Agents for Selaginella kraussiana in New Zealand.

Metagenomics can be used to identify potential biocontrol agents for invasive species and was used here to identify candidate species for biocontrol of an invasive club moss in New Zealand. Profiles were obtained for Selaginella kraussiana collected from nine geographically disjunct locations in Northern New Zealand. These profiles were distinct from those obtained for the exotic club moss Selaginella moellendorffii and the native club mosses Lycopodium deuterodensum and Lycopodium volubile also collected in Northern New Zealand. Fungi and bacteria implicated elsewhere in causing plant disease were identified on plants of Selaginella that exhibited signs of necrosis. Most notably, high densities of sequence reads from Xanthomonas translucens and Pseudomonas syringae were associated with some populations of Selaginella but not Lycopodium. Since these bacteria are already in use as biocontrol agents elsewhere, further investigation into their potential as biocontrol of Selaginella in New Zealand is suggested.

Effect of insulating existing houses on health inequality: cluster randomised study in the community.

OBJECTIVE: To determine whether insulating existing houses increases indoor temperatures and improves occupants' health and wellbeing. DESIGN: Community based, cluster, single blinded randomised study. SETTING: Seven low income communities in New Zealand. PARTICIPANTS: 1350 households containing 4407 participants. INTERVENTION: Installation of a standard retrofit insulation package. MAIN OUTCOME MEASURES: Indoor temperature and relative humidity, energy consumption, self reported health, wheezing, days off school and work, visits to general practitioners, and admissions to hospital. RESULTS: Insulation was associated with a small increase in bedroom temperatures during the winter (0.5 degrees C) and decreased relative humidity (-2.3%), despite energy consumption in insulated houses being 81% of that in uninsulated houses. Bedroom temperatures were below 10 degrees C for 1.7 fewer hours each day in insulated homes than in uninsulated ones. These changes were associated with reduced odds in the insulated homes of fair or poor self rated health (adjusted odds ratio 0.50, 95% confidence interval 0.38 to 0.68), self reports of wheezing in the past three months (0.57, 0.47 to 0.70), self reports of children taking a day off school (0.49, 0.31 to 0.80), and self reports of adults taking a day off work (0.62, 0.46 to 0.83). Visits to general practitioners were less often reported by occupants of insulated homes (0.73, 0.62 to 0.87). Hospital admissions for respiratory conditions were also reduced (0.53, 0.22 to 1.29), but this reduction was not statistically significant (P=0.16). CONCLUSION: Insulating existing houses led to a significantly warmer, drier indoor environment and resulted in improved self rated health, self reported wheezing, days off school and work, and visits to general practitioners as well as a trend for fewer hospital admissions for respiratory conditions.