Aaron P. Jenkins

Mobile genes in the human microbiome are structured from global to individual scales

Recent work has underscored the importance of the microbiome in human health, and has largely attributed differences in phenotype to differences in the species present among individuals. However, mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with those of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes found in Fijian individuals. Notably, we also observed differences between the mobile gene pools of neighbouring Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviours provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important for colonizing specific human populations.

Spatial and seasonal patterns in freshwater ichthyofaunal communities of a tropical high island in Fiji

We surveyed freshwater ichthyofaunal communities in streams of Vanua Levu, Fiji, under a range of land cover to assess differential, seasonal effects on fish abundance and diversity. We collected fish from 32 families, 19 genera and 87 species, representing approximately 50% of the known Fijian freshwater and estuarine fish fauna. Position in reach was the strongest overall factor influencing fish abundance and diversity, particularly in the larger, steeper catchments. However, fish communities exhibited strong seasonal specificity with over half (55%) of species observed in only one season. There were greater numbers of estuarine and marine migrants and fishes with poor swimming ability in the dry season, with more schooling species, large predators and fish that prefer muddy benthos in the wet. In the more pristine catchments of Kubulau District, higher species abundance and diversity were observed in the wet season and were associated with significantly greater flow, pH and dissolved oxygen. We observed the opposite pattern for fish diversity and abundance from the more degraded catchments of Macuata Province. These results suggest that the wet season is having a net positive effect on habitable space for fishes in Kubulau and a net negative effect in Macuata, as species may be lost due to increased runoff from heavily cleared and cultivated catchments. Integrated water resource management across the full range of habitats utilized by Fiji’s freshwater fishes is recommended in order to maintain species diversity and abundance.

Exploring Ecosystems and Health by Shifting to a Regional Focus: Perspectives from the Oceania EcoHealth Chapter.

This article highlights contributions that can be made to the public health field by incorporating “ecosystem approaches to health” to tackle future environmental and health challenges at a regional level. This qualitative research reviews attitudes and understandings of the relationship between public health and the environment and the priorities, aspirations and challenges of a newly established group (the Oceania EcoHealth Chapter) who are attempting to promote these principles. Ten semi-structured interviews with Oceania EcoHealth Chapter members highlighted the important role such groups can play in informing organisations working in the Oceania region to improve both public health and environmental outcomes simultaneously. Participants of this study emphasise the need to elevate Indigenous knowledge in Oceania and the role regional groups play in this regard. They also emphasis that regional advocacy and ecosystem approaches to health could bypass silos in knowledge and disciplinary divides, with groups like the Oceania EcoHealth Chapter acting as a mechanism for knowledge exchange, engagement, and action at a regional level with its ability to bridge the gap between environmental stewardship and public health.

Health at the Sub-catchment Scale: Typhoid and Its Environmental Determinants in Central Division, Fiji.

The impact of environmental change on transmission patterns of waterborne enteric diseases is a major public health concern. This study concerns the burden and spatial nature of enteric fever, attributable to Salmonella Typhi infection in the Central Division, Republic of Fiji at a sub-catchment scale over 30-months (2013–2015). Quantitative spatial analysis suggested relationships between environmental conditions of sub-catchments and incidence and recurrence of typhoid fever. Average incidence per inhabited sub-catchment for the Central Division was high at 205.9/100,000, with cases recurring in each calendar year in 26% of sub-catchments. Although the numbers of cases were highest within dense, urban coastal sub-catchments, the incidence was highest in low-density mountainous rural areas. Significant environmental determinants at this scale suggest increased risk of exposure where sediment yields increase following runoff. The study suggests that populations living on large systems that broaden into meandering mid-reaches and floodplains with alluvial deposition are at a greater risk compared to small populations living near small, erosional, high-energy headwaters and small streams unconnected to large hydrological networks. This study suggests that anthropogenic alteration of land cover and hydrology (particularly via fragmentation of riparian forest and connectivity between road and river networks) facilitates increased transmission of typhoid fever and that environmental transmission of typhoid fever is important in Fiji.

Public health guide to field developments linking ecosystems, environments and health in the Anthropocene

The impacts of global environmental change have precipitated numerous approaches that connect the health of ecosystems, non-human organisms and humans. However, the proliferation of approaches can lead to confusion due to overlaps in terminology, ideas and foci. Recognising the need for clarity, this paper provides a guide to seven field developments in environmental public health research and practice: occupational and environmental health; political ecology of health; environmental justice; ecohealth; One Health; ecological public health; and planetary health. Field developments are defined in terms of their uniqueness from one another, are historically situated, and core texts or journals are highlighted. The paper ends by discussing some of the intersecting features across field developments, and considers opportunities created through such convergence. This field guide will be useful for those seeking to build a next generation of integrative research, policy, education and action that is equipped to respond to current health and sustainability challenges.

Natural Disasters, Health and Wetlands: A Pacific Small Island Developing State Perspective

Natural disasters in the context of public health continue to be a challenge for small island developing states (SIDS) of the Pacific. Pacific SIDS are particularly sensitive to disaster risk given geographic isolation, developing economies, lack of adaptive capacity and the interaction of climate variability with rapid environmental change. Health risks are amplified by the high levels of dependence on wetland resources and population concentration along low-lying floodplains and coastal margins. Thus, the health consequences of disasters cannot be considered in isolation from their wetland ecosystem settings. Wetlands provide protective and essential provisioning services in disasters, yet can also become vehicles for poor health outcomes. In this chapter we review the direct and indirect health consequences of interruptions to wetland ecosystem services associated with disaster events and emphasize how longer-term health effects of natural disasters can be exacerbated when wetland services are lost. We examine patterns of ill health for those populations in Pacific SIDS that are associated with wetlands and provide examples of how wetlands can either mitigate or contribute to these health outcomes. Finally, we identify opportunities and examples of improved management of wetland ecosystems for human health benefits under local to regional-scale management frameworks. Greater understanding at the interface of wetland ecology and disaster epidemiology is needed to strengthen existing models of disaster risk management and wetland conservation. We suggest applying principles of Integrated Island Management (IIM) as regionally appropriate means to guide those seeking to build this understanding.

Freshwater ichthyofauna of the Pacific-Asia Biodiversity Transect (PABITRA) Gateway in Viti Levu, Fiji

The freshwater ichthyofauna of the Fiji islands remained poorly documented before the establishment of the Pacific-Asia Biodiversity Transect (PABITRA) network. The PABITRA approach assesses biodiversity along ocean-to-mountain transects and promotes sustainable land use on islands across the Pacific. Multiple surveys of freshwater fish species along the Viti Levu PABITRA transect have contributed six new occurrence records and one new species to the known freshwater fishes of Fiji since 2002. In total, 21 indigenous species of fish (9% endemic) from 10 families and no introduced fishes were found in the three PABITRA sites. Diversity was highest (16 species) at Savura forest reserve and decreased further inland into Sovi and Wabu. The assemblage found is dominated by highly migratory species (95%) that traverse the different aquatic habitats (marine, estuarine, lowland and upland streams) covered by the PABITRA transect. This high degree of connectivity highlights several growing issues affecting aquatic fauna on the high island of Viti Levu. The reduction in forest cover along the gateway transects, especially in the terminal reaches, and infrastructure development such as dams and weirs have deleterious effects on the migration routes of the Fijian ichthyofauna. Several species collected are important food sources and have cultural totemic importance to local inhabitants along the vertical transect. This paper documents the ichthyofauna of the Fiji gateway transect, ecological characteristics of this assemblage, IUCN Redlist conservation assessment status and highlights factors affecting the fragility and resilience of these communities, particularly focusing on the importance of life-history patterns and watershed conditions.

Redescription of Yirrkala gjellerupi, a Poorly Known Freshwater Indo-Pacific Snake Eel (Anguilliformes: Ophichthidae)

ABSTRACT Yirrkala gjellerupi (Weber & de Beaufort, 1916), unknown since the brief and unfigured original description of the holotype from New Guinea, is herein diagnosed, described, and illustrated, based on specimens recently captured in a Fijian freshwater stream. Other eels collected there and nearby include Anguilla megastoma, A. obscura, Lamnostoma kampeni, and an unidentified moringuid. Living far from the sea is very atypical for an adult ophichthid.

Corrigendum: Mobile genes in the human microbiome are structured from global to individual scales

This corrects the article DOI: 10.1038/nature18927

Where ecosystems, people and health meet: academic traditions and emerging fields for research and practice

Human-driven environmental change has brought attention to the importance of ecosystems in sustaining human health and well-being. There are various schools of thought and fields of inquiry and action that seek to understand health in relation to linked social and ecological phenomena. We describe 18 such fields and outline common elements and incongruities among them. They converge around the application of systems thinking and crossing disciplinary boundaries, while differences are found in methodologies, research foci and problem framing. Although fields encourage sustainable and equitable pathways for health promotion, depoliticized and ahistorical approaches continue to be standard practice. Future research calls for a deeper commitment to examining ourselves as political actors, making space for conversations around power dynamics, and (re)centering participants in research methodologies.Human-driven environmental change has brought attention to the importance of ecosystems in sustaining human health and well-being. There are various schools of thought and fields of inquiry and action that seek to understand health in relation to linked social and ecological phenomena. We