Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.

The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.

Four ways blue foods can help achieve food system ambitions across nations.

Blue foods, sourced in aquatic environments, are important for the economies, livelihoods, nutritional security and cultures of people in many nations. They are often nutrient rich1, generate lower emissions and impacts on land and water than many terrestrial meats2, and contribute to the health3, wellbeing and livelihoods of many rural communities4. The Blue Food Assessment recently evaluated nutritional, environmental, economic and justice dimensions of blue foods globally. Here we integrate these findings and translate them into four policy objectives to help realize the contributions that blue foods can make to national food systems around the world: ensuring supplies of critical nutrients, providing healthy alternatives to terrestrial meat, reducing dietary environmental footprints and safeguarding blue food contributions to nutrition, just economies and livelihoods under a changing climate. To account for how context-specific environmental, socio-economic and cultural aspects affect this contribution, we assess the relevance of each policy objective for individual countries, and examine associated co-benefits and trade-offs at national and international scales. We find that in many African and South American nations, facilitating consumption of culturally relevant blue food, especially among nutritionally vulnerable population segments, could address vitamin B12 and omega-3 deficiencies. Meanwhile, in many global North nations, cardiovascular disease rates and large greenhouse gas footprints from ruminant meat intake could be lowered through moderate consumption of seafood with low environmental impact. The analytical framework we provide also identifies countries with high future risk, for whom climate adaptation of blue food systems will be particularly important. Overall the framework helps decision makers to assess the blue food policy objectives most relevant to their geographies, and to compare and contrast the benefits and trade-offs associated with pursuing these objectives.

Environmental performance of blue foods.

Fish and other aquatic foods (blue foods) present an opportunity for more sustainable diets1,2. Yet comprehensive comparison has been limited due to sparse inclusion of blue foods in environmental impact studies3,4 relative to the vast diversity of production5. Here we provide standardized estimates of greenhouse gas, nitrogen, phosphorus, freshwater and land stressors for species groups covering nearly three quarters of global production. We find that across all blue foods, farmed bivalves and seaweeds generate the lowest stressors. Capture fisheries predominantly generate greenhouse gas emissions, with small pelagic fishes generating lower emissions than all fed aquaculture, but flatfish and crustaceans generating the highest. Among farmed finfish and crustaceans, silver and bighead carps have the lowest greenhouse gas, nitrogen and phosphorus emissions, but highest water use, while farmed salmon and trout use the least land and water. Finally, we model intervention scenarios and find improving feed conversion ratios reduces stressors across all fed groups, increasing fish yield reduces land and water use by up to half, and optimizing gears reduces capture fishery emissions by more than half for some groups. Collectively, our analysis identifies high-performing blue foods, highlights opportunities to improve environmental performance, advances data-poor environmental assessments, and informs sustainable diets.

Aquatic foods to nourish nations.

Despite contributing to healthy diets for billions of people, aquatic foods are often undervalued as a nutritional solution because their diversity is often reduced to the protein and energy value of a single food type ('seafood' or 'fish')1-4. Here we create a cohesive model that unites terrestrial foods with nearly 3,000 taxa of aquatic foods to understand the future impact of aquatic foods on human nutrition. We project two plausible futures to 2030: a baseline scenario with moderate growth in aquatic animal-source food (AASF) production, and a high-production scenario with a 15-million-tonne increased supply of AASFs over the business-as-usual scenario in 2030, driven largely by investment and innovation in aquaculture production. By comparing changes in AASF consumption between the scenarios, we elucidate geographic and demographic vulnerabilities and estimate health impacts from diet-related causes. Globally, we find that a high-production scenario will decrease AASF prices by 26% and increase their consumption, thereby reducing the consumption of red and processed meats that can lead to diet-related non-communicable diseases5,6 while also preventing approximately 166 million cases of inadequate micronutrient intake. This finding provides a broad evidentiary basis for policy makers and development stakeholders to capitalize on the potential of aquatic foods to reduce food and nutrition insecurity and tackle malnutrition in all its forms.

Characterizing pathways of seafood access in small island developing states.

Ensuring healthy and sustainable food systems in increasing social, economic, and ecological change is a key global priority to protect human and environmental health. Seafood is an essential component of these food systems and a critical source of nutrients, especially in coastal communities. However, despite rapid transformations in aquatic food systems, and our urgent need to understand them, there is a dearth of data connecting harvested food production to actualized food consumption. Many analyses suggest institutional, legal, or technological innovations to improve food systems, but few have analyzed the pathways through which people already gain access to nutritious food. Here, using a random forest model and cluster analysis of a nationally representative data set from Kiribati, we operationalize access theory to trace the flows of consumptive benefit in a fisheries-based food system. We demonstrate that the market access mechanism is the key mechanism mediating seafood access in Kiribati, but importantly, the highest seafood consumption households showed lower market access, pointing to the importance of non-market acquisition (e.g., home production and gifting). We reveal six distinct household strategies that employ different sets of access mechanisms to ensure high levels of local seafood consumption in different contexts. We demonstrate the impacts of these strategies on the composition of household seafoods consumed, stressing the need to support these existing successful strategies. Finally, we point to key policy and management insights (e.g., improved infrastructure, shifts in species management) that may be more effective in reinforcing these existing pathways than commonly proposed food system interventions.

Applying an evolutionary mismatch framework to understand disease susceptibility.

Noncommunicable diseases (NCDs) are on the rise worldwide. Obesity, cardiovascular disease, and type 2 diabetes are among a long list of "lifestyle" diseases that were rare throughout human history but are now common. The evolutionary mismatch hypothesis posits that humans evolved in environments that radically differ from those we currently experience; consequently, traits that were once advantageous may now be "mismatched" and disease causing. At the genetic level, this hypothesis predicts that loci with a history of selection will exhibit "genotype by environment" (GxE) interactions, with different health effects in "ancestral" versus "modern" environments. To identify such loci, we advocate for combining genomic tools in partnership with subsistence-level groups experiencing rapid lifestyle change. In these populations, comparisons of individuals falling on opposite extremes of the "matched" to "mismatched" spectrum are uniquely possible. More broadly, the work we propose will inform our understanding of environmental and genetic risk factors for NCDs across diverse ancestries and cultures.

The future of food from the sea.

Global food demand is rising, and serious questions remain about whether supply can increase sustainably1. Land-based expansion is possible but may exacerbate climate change and biodiversity loss, and compromise the delivery of other ecosystem services2-6. As food from the sea represents only 17% of the current production of edible meat, we ask how much food we can expect the ocean to sustainably produce by 2050. Here we examine the main food-producing sectors in the ocean-wild fisheries, finfish mariculture and bivalve mariculture-to estimate 'sustainable supply curves' that account for ecological, economic, regulatory and technological constraints. We overlay these supply curves with demand scenarios to estimate future seafood production. We find that under our estimated demand shifts and supply scenarios (which account for policy reform and technology improvements), edible food from the sea could increase by 21-44 million tonnes by 2050, a 36-74% increase compared to current yields. This represents 12-25% of the estimated increase in all meat needed to feed 9.8 billion people by 2050. Increases in all three sectors are likely, but are most pronounced for mariculture. Whether these production potentials are realized sustainably will depend on factors such as policy reforms, technological innovation and the extent of future shifts in demand.

A habitat stronghold on the precipice: A call-to-action for supporting lemur conservation in northeast Madagascar.

The northeast of Madagascar is as diverse as it is threatened. The area bordering the Analanjirofo and SAVA regions contains six protected areas and at least 22 lemur species. Many applied research and conservation programs have been established in the region with the aim of ensuring both wildlife and people thrive in the long term. While most of the remaining humid evergreen forest of northeast Madagascar is formally protected, the local human population depends heavily on the land, and unsustainable natural resource use threatens this biodiversity hotspot. Drawing from our collective experiences managing conservation activities and research programs in northeast Madagascar, we discuss the major threats to the region and advocate for eight conservation activities that help reduce threats and protect the environment, providing specific examples from our own programs. These include (1) empowering local conservation actors, (2) ensuring effectively protected habitat, (3) expanding reforestation, (4) establishing and continuing long-term research and monitoring, (5) reducing food insecurity, (6) supporting environmental education, (7) promoting sustainable livelihoods, and (8) expanding community health initiatives. Lastly, we provide a list of actions that individuals can take to join us in supporting and promoting lemur conservation.

Neo-Traditional and Industrialized Dietary Patterns Coexist and Are Differentially Associated with Cardiometabolic Health among Adults in Puerto Rico.

BACKGROUND: An increasingly industrialized food system has marginalized local, traditional food cultures in Puerto Rico (PR). Recent efforts to decolonize diets have promoted local food intake; however, how resulting dietary patterns may influence cardiometabolic disease remains unknown. OBJECTIVES: This study aimed to 1) identify dietary patterns in PR and 2) determine their associations with metabolic syndrome (MetS) and its components. METHODS: Data were obtained from participants (30-75 y) in PROSPECT (PR Observational Study of Psychosocial, Environmental, and Chronic Disease Trends; n = 989). Dietary patterns were derived using partial least squares analysis with food frequency questionnaire data, using nutrients associated with local food purchasing (dietary fiber, magnesium, saturated fat) as response variables. MetS was classified using harmonized criteria from clinical and laboratory measures and medication use. Fully adjusted generalized linear models tested associations between tertiles of dietary patterns and MetS. RESULTS: Approximately half (52%) of the participants were classified with MetS. Four dietary patterns were revealed: conventional (legumes, coffee, and dairy), industrialized starch and meat-centric (red/processed meats, pasta, and starchy roots), industrialized sugar-centric (rice, sugary beverages, and refined grains), and neo-traditional (local plants and seafood). Individuals in the highest (compared with lowest) tertile of the industrialized starch and meat-centric dietary pattern had higher mean waist circumference (102 compared with 99 cm) (P = 0.01), fasting glucose (106 compared with 98 mg/dL) (P = 0.019), and systolic blood pressure (123 compared with 119 mmHg) (P = 0.022). Individuals in the highest (compared with lowest) tertile of the neo-traditional diet were 0.69 (0.49, 0.97) times less likely to have MetS (P = 0.035) and had 4.1 cm lower mean waist circumference (P = 0.002). CONCLUSIONS: Promoting a neo-traditional diet and curbing industrialized starch and meat-centric diets may improve cardiometabolic health in PR. Results can guide local food promotion as a healthful, decolonizing approach in island settings.

Fine-scale variation in malaria prevalence across ecological regions in Madagascar: a cross-sectional study.

BACKGROUND: Large-scale variation in ecological parameters across Madagascar is hypothesized to drive varying spatial patterns of malaria infection. However, to date, few studies of parasite prevalence with resolution at finer, sub-regional spatial scales are available. As a result, there is a poor understanding of how Madagascar's diverse local ecologies link with variation in the distribution of infections at the community and household level. Efforts to preserve Madagascar's ecological diversity often focus on improving livelihoods in rural communities near remaining forested areas but are limited by a lack of data on their infectious disease burden. METHODS: To investigate spatial variation in malaria prevalence at the sub-regional scale in Madagascar, we sampled 1476 households (7117 total individuals, all ages) from 31 rural communities divided among five ecologically distinct regions. The sampled regions range from tropical rainforest to semi-arid, spiny forest and include communities near protected areas including the Masoala, Makira, and Mikea forests. Malaria prevalence was estimated by rapid diagnostic test (RDT) cross-sectional surveys performed during malaria transmission seasons over 2013-2017. RESULTS: Indicative of localized hotspots, malaria prevalence varied more than 10-fold between nearby (< 50 km) communities in some cases. Prevalence was highest on average in the west coast region (Morombe district, average community prevalence 29.4%), situated near protected dry deciduous forest habitat. At the household level, communities in southeast Madagascar (Mananjary district) were observed with over 50% of households containing multiple infected individuals at the time of sampling. From simulations accounting for variation in household size and prevalence at the community level, we observed a significant excess of households with multiple infections in rural communities in southwest and southeast Madagascar, suggesting variation in risk within communities. CONCLUSIONS: Our data suggest that the malaria infection burden experienced by rural communities in Madagascar varies greatly at smaller spatial scales (i.e., at the community and household level) and that the southeast and west coast ecological regions warrant further attention from disease control efforts. Conservation and development efforts in these regions may benefit from consideration of the high, and variable, malaria prevalences among communities in these areas.

Variation in Anopheles distribution and predictors of malaria infection risk across regions of Madagascar.

BACKGROUND: Deforestation and land use change is widespread in Madagascar, altering local ecosystems and creating opportunities for disease vectors, such as the Anopheles mosquito, to proliferate and more easily reach vulnerable, rural populations. Knowledge of risk factors associated with malaria infections is growing globally, but these associations remain understudied across Madagascar's diverse ecosystems experiencing rapid environmental change. This study aims to uncover socioeconomic, demographic, and ecological risk factors for malaria infection across regions through analysis of a large, cross-sectional dataset. METHODS: The objectives were to assess (1) the ecological correlates of malaria vector breeding through larval surveys, and (2) the socioeconomic, demographic, and ecological risk factors for malaria infection in four ecologically distinct regions of rural Madagascar. Risk factors were determined using multilevel models for the four regions included in the study. RESULTS: The presence of aquatic agriculture (both within and surrounding communities) is the strongest predictive factor of habitats containing Anopheles larvae across all regions. Ecological and socioeconomic risk factors for malaria infection vary dramatically across study regions and range in their complexity. CONCLUSIONS: Risk factors for malaria transmission differ dramatically across regions of Madagascar. These results may help stratifying current malaria control efforts in Madagascar beyond the scope of existing interventions.

Two new phlebotomine sandflies (Diptera: Psychodidae) from the forest edge in Madagascar: the anthropophilic Phlebotomus artemievi sp. nov. and Sergentomyia maroantsetra ensis sp. nov.

A few data are related to the anthropophily of Malagasy Phlebotomine sandflies. Prior studies focussed mainly to inventories and description of new species. Our goal was to emphasize the anthropophily of Malagasy Phlebotomine sandflies. We worked in the Makira region, using two simultaneous methods: human landing catches (HLC) and CDC light traps. We collected sandflies in three rural communities adjacent to the Makira Natural Park. In each community, three different biotopes were sampled: within community settlements; at the edge of forest, typically in agricultural land; and within the forest. We collected 61 sandflies belonging to two new species presently described: Phlebotomus artemievi sp. nov. and Sergentomyia maroantsetraensis sp. nov. These sandflies were caught exclusively in the forest edge biotope. None were captured within communities or within forests. HLC provided 97% of the collected sandflies, corresponding to a human-biting rate of 15 females per human per night. CDC provided only two females. Ph. artemievi sp. nov. was predominantly captured by HLC and appears to be highly anthropophilic. Here, we update the behavioural ecology of sandflies and describe two new species. Further research is required to understand their vector competence and their ability to transmit arboviruses and other pathogens such as Leishmania.

Population viability and harvest sustainability for Madagascar lemurs.

Subsistence hunting presents a conservation challenge by which biodiversity preservation must be balanced with safeguarding of human livelihoods. Globally, subsistence hunting threatens primate populations, including Madagascar's endemic lemurs. We used population viability analysis to assess the sustainability of lemur hunting in Makira Natural Park, Madagascar. We identified trends in seasonal hunting of 11 Makira lemur species from household interview data, estimated local lemur densities in populations adjacent to focal villages via transect surveys, and quantified extinction vulnerability for these populations based on species-specific demographic parameters and empirically derived hunting rates. We compared stage-based Lefkovitch with periodic Leslie matrices to evaluate the impact of regional dispersal on persistence trajectories and explored the consequences of perturbations to the timing of peak hunting relative to the lemur birth pulse, under assumptions of density-dependent reproductive compensation. Lemur hunting peaked during the fruit-abundant wet season (March-June). Estimated local lemur densities were roughly inverse to body size across our study area. Life-history modeling indicated that hunting most severely threatened the species with the largest bodies (i.e., Hapalemur occidentalis, Avahi laniger, Daubentonia madagascariensis, and Indri indi), characterized by late-age reproductive onsets and long interbirth intervals. In model simulations, lemur dispersal within a regional metapopulation buffered extinction threats when a majority of local sites supported growth rates above the replacement level but drove regional extirpations when most local sites were overharvested. Hunt simulations were most detrimental when timed to overlap lemur births (a reality for D. madagascariensis and I. indri). In sum, Makira lemurs were overharvested. Regional extirpations, which may contribute to broad-scale extinctions, will be likely if current hunting rates persist. Cessation of anthropogenic lemur harvest is a conservation priority, and development programs are needed to help communities switch from wildlife consumption to domestic protein alternatives.

Seasonal trends of nutrient intake in rainforest communities of north-eastern Madagascar.

OBJECTIVE: We collected dietary records over the course of nine months to comprehensively characterize the consumption patterns of Malagasy people living in remote rainforest areas of north-eastern Madagascar. DESIGN: The present study was a prospective longitudinal cohort study to estimate dietary diversity and nutrient intake for a suite of macronutrients, micronutrients and vitamins for 152 randomly selected households in two communities. SETTING: Madagascar, with over 25 million people living in an area the size of France, faces a multitude of nutritional challenges. Micronutrient-poor staples, especially rice, roots and tubers, comprise nearly 80 % of the Malagasy diet by weight. The remaining dietary components (including wild foods and animal-source foods) are critical for nutrition. We focus our study in north-eastern Madagascar, characterized by access to rainforest, rice paddies and local agriculture. PARTICIPANTS: We enrolled men, women and children of both sexes and all ages in a randomized sample of households in two communities. RESULTS: Although the Household Dietary Diversity Score and Food Consumption Score reflect high dietary diversity, the Minimum Dietary Diversity-Women indicator suggests poor micronutrient adequacy. The food intake data confirm a mixed nutritional picture. We found that the median individual consumed less than 50 % of his/her age/sex-specific Estimated Average Requirement (EAR) for vitamins A, B12, D and E, and Ca, and less than 100 % of his/her EAR for energy, riboflavin, folate and Na. CONCLUSIONS: Malnutrition in remote communities of north-eastern Madagascar is pervasive and multidimensional, indicating an urgent need for comprehensive public health and development interventions focused on providing nutritional security.

Climate Change and Global Food Systems: Potential Impacts on Food Security and Undernutrition.

Great progress has been made in addressing global undernutrition over the past several decades, in part because of large increases in food production from agricultural expansion and intensification. Food systems, however, face continued increases in demand and growing environmental pressures. Most prominently, human-caused climate change will influence the quality and quantity of food we produce and our ability to distribute it equitably. Our capacity to ensure food security and nutritional adequacy in the face of rapidly changing biophysical conditions will be a major determinant of the next century's global burden of disease. In this article, we review the main pathways by which climate change may affect our food production systems-agriculture, fisheries, and livestock-as well as the socioeconomic forces that may influence equitable distribution.

Genetic evidence that the Makira region in northeastern Madagascar is a hotspot of malaria transmission.

BACKGROUND: Encouraging advances in the control of Plasmodium falciparum malaria have been observed across much of Africa in the past decade. However, regions of high relative prevalence and transmission that remain unaddressed or unrecognized provide a threat to this progress. Difficulties in identifying such localized hotspots include inadequate surveillance, especially in remote regions, and the cost and labor needed to produce direct estimates of transmission. Genetic data can provide a much-needed alternative to such empirical estimates, as the pattern of genetic variation within malaria parasite populations is indicative of the level of local transmission. Here, genetic data were used to provide the first empirical estimates of P. falciparum malaria prevalence and transmission dynamics for the rural, remote Makira region of northeastern Madagascar. METHODS: Longitudinal surveys of a cohort of 698 total individuals (both sexes, 0-74 years of age) were performed in two communities bordering the Makira Natural Park protected area. Rapid diagnostic tests, with confirmation by molecular methods, were used to estimate P. falciparum prevalence at three seasonal time points separated by 4-month intervals. Genomic loci in a panel of polymorphic, putatively neutral markers were genotyped for 94 P. falciparum infections and used to characterize genetic parameters known to correlate with transmission levels. RESULTS: Overall, 27.8% of individuals tested positive for P. falciparum over the 10-month course of the study, a rate approximately sevenfold higher than the countrywide average for Madagascar. Among those P. falciparum infections, a high level of genotypic diversity and a high frequency of polygenomic infections (68.1%) were observed, providing a pattern consistent with high and stable transmission. CONCLUSIONS: Prevalence and genetic diversity data indicate that the Makira region is a hotspot of P. falciparum transmission in Madagascar. This suggests that the area should be highlighted for future interventions and that additional areas of high transmission may be present in ecologically similar regions nearby.

Human health impacts of ecosystem alteration.

Human activity is rapidly transforming most of Earth's natural systems. How this transformation is impacting human health, whose health is at greatest risk, and the magnitude of the associated disease burden are relatively new subjects within the field of environmental health. We discuss what is known about the human health implications of changes in the structure and function of natural systems and propose that these changes are affecting human health in a variety of important ways. We identify several gaps and limitations in the research that has been done to date and propose a more systematic and comprehensive approach to applied research in this field. Such efforts could lead to a more robust understanding of the human health impacts of accelerating environmental change and inform decision making in the land-use planning, environmental conservation, and public health policy realms.