Unlocking bacterial potential to reduce farmland N2O emissions.

Farmed soils contribute substantially to global warming by emitting N2O (ref. 1), and mitigation has proved difficult2. Several microbial nitrogen transformations produce N2O, but the only biological sink for N2O is the enzyme NosZ, catalysing the reduction of N2O to N2 (ref. 3). Although strengthening the NosZ activity in soils would reduce N2O emissions, such bioengineering of the soil microbiota is considered challenging4,5. However, we have developed a technology to achieve this, using organic waste as a substrate and vector for N2O-respiring bacteria selected for their capacity to thrive in soil6-8. Here we have analysed the biokinetics of N2O reduction by our most promising N2O-respiring bacterium, Cloacibacterium sp. CB-01, its survival in soil and its effect on N2O emissions in field experiments. Fertilization with waste from biogas production, in which CB-01 had grown aerobically to about 6 × 109 cells per millilitre, reduced N2O emissions by 50-95%, depending on soil type. The strong and long-lasting effect of CB-01 is ascribed to its tenacity in soil, rather than its biokinetic parameters, which were inferior to those of other strains of N2O-respiring bacteria. Scaling our data up to the European level, we find that national anthropogenic N2O emissions could be reduced by 5-20%, and more if including other organic wastes. This opens an avenue for cost-effective reduction of N2O emissions for which other mitigation options are lacking at present.

Spillover of highly pathogenic avian influenza H5N1 virus to dairy cattle.

The highly pathogenic avian influenza (HPAI) H5N1 virus clade 2.3.4.4b has caused the death of millions of domestic birds and thousands of wild birds in the USA since January 2022 (refs. 1-4). Throughout this outbreak, spillovers to mammals have been frequently documented5-12. Here we report spillover of the HPAI H5N1 virus to dairy cattle across several states in the USA. The affected cows displayed clinical signs encompassing decreased feed intake, altered faecal consistency, respiratory distress and decreased milk production with abnormal milk. Infectious virus and viral RNA were consistently detected in milk from affected cows. Viral distribution in tissues via immunohistochemistry and in situ hybridization revealed a distinct tropism of the virus for the epithelial cells lining the alveoli of the mammary gland in cows. Whole viral genome sequences recovered from dairy cows, birds, domestic cats and a raccoon from affected farms indicated multidirectional interspecies transmissions. Epidemiological and genomic data revealed efficient cow-to-cow transmission after apparently healthy cows from an affected farm were transported to a premise in a different state. These results demonstrate the transmission of the HPAI H5N1 clade 2.3.4.4b virus at a non-traditional interface, underscoring the ability of the virus to cross species barriers.

Ageing threatens sustainability of smallholder farming in China.

Rapid demographic ageing substantially affects socioeconomic development1-4 and presents considerable challenges for food security and agricultural sustainability5-8, which have so far not been well understood. Here, by using data from more than 15,000 rural households with crops but no livestock across China, we show that rural population ageing reduced farm size by 4% through transferring cropland ownership and land abandonment (approximately 4 million hectares) in 2019, taking the population age structure in 1990 as a benchmark. These changes led to a reduction of agricultural inputs, including chemical fertilizers, manure and machinery, which decreased agricultural output and labour productivity by 5% and 4%, respectively, further lowering farmers' income by 15%. Meanwhile, fertilizer loss increased by 3%, resulting in higher pollutant emissions to the environment. In new farming models, such as cooperative farming, farms tend to be larger and operated by younger farmers, who have a higher average education level, hence improving agricultural management. By encouraging the transition to new farming models, the negative consequences of ageing can be reversed. Agricultural input, farm size and farmer's income would grow by approximately 14%, 20% and 26%, respectively, and fertilizer loss would reduce by 4% in 2100 compared with that in 2020. This suggests that management of rural ageing will contribute to a comprehensive transformation of smallholder farming to sustainable agriculture in China.

Global trends of cropland phosphorus use and sustainability challenges.

To meet the growing food demand while addressing the multiple challenges of exacerbating phosphorus (P) pollution and depleting P rock reserves1-15, P use efficiency (PUE, the ratio of productive P output to P input in a defined system) in crop production needs to be improved. Although many efforts have been devoted to improving nutrient management practices on farms, few studies have examined the historical trajectories of PUE and their socioeconomic and agronomic drivers on a national scale1,2,6,7,11,16,17. Here we present a database of the P budget (the input and output of the crop production system) and PUE by country and by crop type for 1961-2019, and examine the substantial contribution of several drivers for PUE, such as economic development stages and crop portfolios. To address the P management challenges, we found that global PUE in crop production must increase to 68-81%, and recent trends indicate some meaningful progress towards this goal. However, P management challenges and opportunities in croplands vary widely among countries.

From Amish farm dust to bacterial lysates: The long and winding road to protection from allergic disease.

Allergic diseases typically begin in early life and can impose a heavy burden on children and their families. Effective preventive measures are currently unavailable but may be ushered in by studies on the "farm effect", the strong protection from asthma and allergy found in children born and raised on traditional farms. Two decades of epidemiologic and immunologic research have demonstrated that this protection is provided by early and intense exposure to farm-associated microbes that target primarily innate immune pathways. Farm exposure also promotes timely maturation of the gut microbiome, which mediates a proportion of the protection conferred by the farm effect. Current research seeks to identify allergy-protective compounds from traditional farm environments, but standardization and regulation of such substances will likely prove challenging. On the other hand, studies in mouse models show that administration of standardized, pharmacological-grade lysates of human airway bacteria abrogates allergic lung inflammation by acting on multiple innate immune targets, including the airway epithelium/IL-33/ILC2 axis and dendritic cells whose Myd88/Trif-dependent tolerogenic reprogramming is sufficient for asthma protection in adoptive transfer models. To the extent that these bacterial lysates mimic the protective effects of natural exposure to microbe-rich environments, these agents might provide an effective tool for prevention of allergic disease.

Crop yields fail to rise in smallholder farming systems in sub-Saharan Africa.

Drawing on a harmonized longitudinal dataset covering more than 55,000 smallholder farms in six African countries, we analyze changes in crop productivity from 2008 to 2019. Because smallholder farmers represent a significant fraction of the world's poorest people, agricultural productivity in this context matters for poverty reduction and for the broader achievement of the UN Sustainable Development Goals. Our analysis measures productivity trends for nationally representative samples of smallholder crop farmers, using detailed data on agricultural inputs and outputs which we integrate with detailed data on local weather and environmental conditions. In spite of government commitments and international efforts to strengthen African agriculture, we find no evidence that smallholder crop productivity improved over this 12-y period. Our preferred statistical specification of total factor productivity (TFP) suggests an overall decline in productivity of -3.5% per year. Various other models we test also find declining productivity in the overall sample, and none of them finds productivity growth. However, the different countries in our sample experienced varying trends, with some instances of growth in some regions. The results suggest that major challenges remain for agricultural development in sub-Saharan Africa. They complement previous analyses that relied primarily on aggregate national statistics to measure agricultural productivity, rather than detailed microdata.

Emergence and spread of SARS-CoV-2 variants from farmed mink to humans and back during the epidemic in Denmark, June-November 2020.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) not only caused the COVID-19 pandemic but also had a major impact on farmed mink production in several European countries. In Denmark, the entire population of farmed mink (over 15 million animals) was culled in late 2020. During the period of June to November 2020, mink on 290 farms (out of about 1100 in the country) were shown to be infected with SARS-CoV-2. Genome sequencing identified changes in the virus within the mink and it is estimated that about 4000 people in Denmark became infected with these mink virus variants. However, the routes of transmission of the virus to, and from, the mink have been unclear. Phylogenetic analysis revealed the generation of multiple clusters of the virus within the mink. Detailed analysis of changes in the virus during replication in mink and, in parallel, in the human population in Denmark, during the same time period, has been performed here. The majority of cases in mink involved variants with the Y453F substitution and the H69/V70 deletion within the Spike (S) protein; these changes emerged early in the outbreak. However, further introductions of the virus, by variants lacking these changes, from the human population into mink also occurred. Based on phylogenetic analysis of viral genome data, we estimate, using a conservative approach, that about 17 separate examples of mink to human transmission occurred in Denmark but up to 59 such events (90% credible interval: (39-77)) were identified using parsimony to count cross-species jumps on transmission trees inferred using Bayesian methods. Using the latter approach, 136 jumps (90% credible interval: (117-164)) from humans to mink were found, which may underlie the farm-to-farm spread. Thus, transmission of SARS-CoV-2 from humans to mink, mink to mink, from mink to humans and between humans were all observed.

Genomic perspectives on human dispersals during the Holocene.

Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. Here, we provide an overview of Holocene dispersals in the light of genomic evidence and conclude that they have a complex history. Even when there is a demonstrated connection between a demographic expansion of people, the spread of agriculture, and the spread of a particular language family, the outcome in the results of contact between expanding and resident groups is highly variable. Further research is needed to identify the factors and social circumstances that have influenced this variation and complex history.

Large-scale land acquisitions exacerbate local farmland inequalities in Tanzania.

Land inequality stalls economic development, entrenches poverty, and is associated with environmental degradation. Yet, rigorous assessments of land-use interventions attend to inequality only rarely. A land inequality lens is especially important to understand how recent large-scale land acquisitions (LSLAs) affect smallholder and indigenous communities across as much as 100 million hectares around the world. This paper studies inequalities in land assets, specifically landholdings and farm size, to derive insights into the distributional outcomes of LSLAs. Using a household survey covering four pairs of land acquisition and control sites in Tanzania, we use a quasi-experimental design to characterize changes in land inequality and subsequent impacts on well-being. We find convincing evidence that LSLAs in Tanzania lead to both reduced landholdings and greater farmland inequality among smallholders. Households in proximity to LSLAs are associated with 21.1% (P = 0.02) smaller landholdings while evidence, although insignificant, is suggestive that farm sizes are also declining. Aggregate estimates, however, hide that households in the bottom quartiles of farm size suffer the brunt of landlessness and land loss induced by LSLAs that combine to generate greater farmland inequality. Additional analyses find that land inequality is not offset by improvements in other livelihood dimensions, rather farm size decreases among households near LSLAs are associated with no income improvements, lower wealth, increased poverty, and higher food insecurity. The results demonstrate that without explicit consideration of distributional outcomes, land-use policies can systematically reinforce existing inequalities.

The impact of farming on prehistoric culinary practices throughout Northern Europe.

To investigate changes in culinary practices associated with the arrival of farming, we analysed the organic residues of over 1,000 pottery vessels from hunter-gatherer-fisher and early agricultural sites across Northern Europe from the Lower Rhine Basin to the Northeastern Baltic. Here, pottery was widely used by hunter-gatherer-fishers prior to the introduction of domesticated animals and plants. Overall, there was surprising continuity in the way that hunter-gatherer-fishers and farmers used pottery. Both aquatic products and wild plants remained prevalent, a pattern repeated consistently across the study area. We argue that the rapid adaptation of farming communities to exploit coastal and lagoonal resources facilitated their northerly expansion, and in some cases, hunting, gathering, and fishing became the most dominant subsistence strategy. Nevertheless, dairy products frequently appear in pottery associated with the earliest farming groups often mixed with wild plants and fish. Interestingly, we also find compelling evidence of dairy products in hunter-gatherer-fisher Ertebølle pottery, which predates the arrival of domesticated animals. We propose that Ertebølle hunter-gatherer-fishers frequently acquired dairy products through exchange with adjacent farming communities prior to the transition. The continuity observed in pottery use across the transition to farming contrasts with the analysis of human remains which shows substantial demographic change through ancient DNA and, in some cases, a reduction in marine consumption through stable isotope analysis. We postulate that farmers acquired the knowledge and skills they needed to succeed from local hunter-gatherer-fishers but without substantial admixture.

Diversified farms bolster forest-bird populations despite ongoing declines in tropical forests.

While some agricultural landscapes can support wildlife in the short term, it is uncertain how well they can truly sustain wildlife populations. To compare population trends in different production systems, we sampled birds along 48 transects in mature forests, diversified farms, and intensive farms across Costa Rica from 2000 to 2017. To assess how land use influenced population trends in the 349 resident and 80 migratory species with sufficient data, we developed population models. We found, first, that 23% of species were stable in all three land use types, with the rest almost evenly split between increasing and decreasing populations. Second, in forest habitats, a slightly higher fraction was declining: 62% of the 164 species undergoing long-term population changes; nearly half of these declines occurred in forest-affiliated invertivores. Third, in diversified farms, 49% of the 230 species with population changes were declining, with 60% of these declines occurring in agriculture-affiliated species. In contrast, 51% of the species with population changes on diversified farms showed increases, primarily in forest-affiliated invertivores and frugivores. In intensive farms, 153 species showed population changes, also with similar proportions of species increasing (50%) and decreasing (50%). Declines were concentrated in agriculture-affiliated invertivores and forest-affiliated frugivores; increases occurred in many large, omnivorous species. Our findings paint a complex picture but clearly indicate that diversified farming helps sustain populations of diverse, forest-affiliated species. Despite not fully offsetting losses in forest habitats, diversified farming practices help sustain wildlife in a critical time, before possible transformation to nature-positive policies and practices.

Developing the agroecological niche in Nicaragua: The roles of knowledge flows and intermediaries.

Supporting transitions to sustainable, resilient agri-food systems is important to ensure stable food supply in the face of growing climate extremes. Agroecology, or diversified farming systems based on ecological principles, can contribute to such systems. Based on a qualitative case study of Nicaragua, a forerunner in agroecology, this paper unpacks an ongoing transition to agroecology, focusing on how the transition has been shaped by knowledge flows and intermediary actors. Using a niche development framework based on knowledge processes, we analyze the growth of the agroecological niche in Nicaragua over three phases of niche development. The findings show how knowledge processes' emphases have shifted over time, as have functions enacted by intermediaries. Dedicated, diversified intermediaries have been key in creating momentum for agroecology, as have individual actors moving between niche and regime. Agency in niche development has come from both niche and regime actors. Finally, we find that Nicaragua's transition to agroecology has been ambiguous: While the niche has succeeded in changing the mainstream selection environment to its favor in some arenas, transition dynamics lag in others. Drawing lessons from this ambiguity, we suggest entry points for broader systems change, such as market stimulation, value chain development, phase-out policies, and supportive policy in related arenas. We also point out possible actions for niche actors such as integration of financial and commercial actors into niches and creation of dedicated market-focused intermediaries. Our results provide evidence of an ongoing transition and action points for supporting niche development in (sustainable agri-food) transitions around the globe.

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs.

The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized.

Biodiversity and pollination benefits trade off against profit in an intensive farming system.

Agricultural expansion and intensification have boosted global food production but have come at the cost of environmental degradation and biodiversity loss. Biodiversity-friendly farming that boosts ecosystem services, such as pollination and natural pest control, is widely being advocated to maintain and improve agricultural productivity while safeguarding biodiversity. A vast body of evidence showing the agronomic benefits of enhanced ecosystem service delivery represent important incentives to adopt practices enhancing biodiversity. However, the costs of biodiversity-friendly management are rarely taken into account and may represent a major barrier impeding uptake by farmers. Whether and how biodiversity conservation, ecosystem service delivery, and farm profit can go hand in hand is unknown. Here, we quantify the ecological, agronomic, and net economic benefits of biodiversity-friendly farming in an intensive grassland-sunflower system in Southwest France. We found that reducing land-use intensity on agricultural grasslands drastically enhances flower availability and wild bee diversity, including rare species. Biodiversity-friendly management on grasslands furthermore resulted in an up to 17% higher revenue on neighboring sunflower fields through positive effects on pollination service delivery. However, the opportunity costs of reduced grassland forage yields consistently exceeded the economic benefits of enhanced sunflower pollination. Our results highlight that profitability is often a key constraint hampering adoption of biodiversity-based farming and uptake critically depends on society's willingness to pay for associated delivery of public goods such as biodiversity.

Farmland practices are driving bird population decline across Europe.

Declines in European bird populations are reported for decades but the direct effect of major anthropogenic pressures on such declines remains unquantified. Causal relationships between pressures and bird population responses are difficult to identify as pressures interact at different spatial scales and responses vary among species. Here, we uncover direct relationships between population time-series of 170 common bird species, monitored at more than 20,000 sites in 28 European countries, over 37 y, and four widespread anthropogenic pressures: agricultural intensification, change in forest cover, urbanisation and temperature change over the last decades. We quantify the influence of each pressure on population time-series and its importance relative to other pressures, and we identify traits of most affected species. We find that agricultural intensification, in particular pesticides and fertiliser use, is the main pressure for most bird population declines, especially for invertebrate feeders. Responses to changes in forest cover, urbanisation and temperature are more species-specific. Specifically, forest cover is associated with a positive effect and growing urbanisation with a negative effect on population dynamics, while temperature change has an effect on the dynamics of a large number of bird populations, the magnitude and direction of which depend on species' thermal preferences. Our results not only confirm the pervasive and strong effects of anthropogenic pressures on common breeding birds, but quantify the relative strength of these effects stressing the urgent need for transformative changes in the way of inhabiting the world in European countries, if bird populations shall have a chance of recovering.

Spatial distribution of poultry farms using point pattern modelling: A method to address livestock environmental impacts and disease transmission risks.

The distribution of farm locations and sizes is paramount to characterize patterns of disease spread. With some regions undergoing rapid intensification of livestock production, resulting in increased clustering of farms in peri-urban areas, measuring changes in the spatial distribution of farms is crucial to design effective interventions. However, those data are not available in many countries, their generation being resource-intensive. Here, we develop a farm distribution model (FDM), which allows the prediction of locations and sizes of poultry farms in countries with scarce data. The model combines (i) a Log-Gaussian Cox process model to simulate the farm distribution as a spatial Poisson point process, and (ii) a random forest model to simulate farm sizes (i.e. the number of animals per farm). Spatial predictors were used to calibrate the FDM on intensive broiler and layer farm distributions in Bangladesh, Gujarat (Indian state) and Thailand. The FDM yielded realistic farm distributions in terms of spatial clustering, farm locations and sizes, while providing insights on the factors influencing these distributions. Finally, we illustrate the relevance of modelling realistic farm distributions in the context of epidemic spread by simulating pathogen transmission on an array of spatial distributions of farms. We found that farm distributions generated from the FDM yielded spreading patterns consistent with simulations using observed data, while random point patterns underestimated the probability of large outbreaks. Indeed, spatial clustering increases vulnerability to epidemics, highlighting the need to account for it in epidemiological modelling studies. As the FDM maintains a realistic distribution of farm location and sizes, its use to inform mathematical models of disease transmission is particularly relevant for regions where these data are not available.

Farm vehicles approaching weights of sauropods exceed safe mechanical limits for soil functioning.

Mechanization has greatly contributed to the success of modern agriculture, with vastly expanded food production capabilities achieved by the higher capacity of farm machinery. However, the increase in capacity has been accompanied by higher vehicle weights that increase risks of subsoil compaction. We show here that while surface contact stresses remained nearly constant over the course of modern mechanization, subsoil stresses have propagated into deeper soil layers and now exceed safe mechanical limits for soil ecological functioning. We developed a global map for delineating subsoil compaction susceptibility based on estimates of mechanization level, mean tractor size, soil texture, and climatic conditions. The alarming trend of chronic subsoil compaction risk over 20% of arable land, with potential loss of productivity, calls for a more stringent design of farm machinery that considers intrinsic subsoil mechanical limits. As the total weight of modern harvesters is now approaching that of the largest animals that walked Earth, the sauropods, a paradox emerges of potential prehistoric subsoil compaction. We hypothesize that unconstrained roaming of sauropods would have had similar adverse effects on land productivity as modern farm vehicles, suggesting that ecological strategies for reducing subsoil compaction, including fixed foraging trails, must have guided these prehistoric giants.

Complex agricultural landscapes host more biodiversity than simple ones: A global meta-analysis.

Managing agricultural landscapes to support biodiversity conservation requires profound structural changes worldwide. Often, discussions are centered on management at the field level. However, a wide and growing body of evidence calls for zooming out and targeting agricultural policies, research, and interventions at the landscape level to halt and reverse the decline in biodiversity, increase biodiversity-mediated ecosystem services in agricultural landscapes, and improve the resilience and adaptability of these ecosystems. We conducted the most comprehensive assessment to date on landscape complexity effects on nondomesticated terrestrial biodiversity through a meta-analysis of 1,134 effect sizes from 157 peer-reviewed articles. Increasing landscape complexity through changes in composition, configuration, or heterogeneity significatively and positively affects biodiversity. More complex landscapes host more biodiversity (richness, abundance, and evenness) with potential benefits to sustainable agricultural production and conservation, and effects are likely underestimated. The few articles that assessed the combined contribution of linear (e.g., hedgerows) and areal (e.g., woodlots) elements resulted in a near-doubling of the effect sizes (i.e., biodiversity level) compared to the dominant number of studies measuring these elements separately. Similarly, positive effects on biodiversity are stronger in articles monitoring biodiversity for at least 2 y compared to the dominant 1-y monitoring efforts. Besides, positive and stronger effects exist when monitoring occurs in nonoverlapping landscapes, highlighting the need for long-term and robustly designed monitoring efforts. Living in harmony with nature will require shifting paradigms toward valuing and promoting multifunctional agriculture at the farm and landscape levels with a research agenda that untangles complex agricultural landscapes' contributions to people and nature under current and future conditions.

Biodiversity effects of food system sustainability actions from farm to fork.

Diet shifts and food waste reduction have the potential to reduce the land and biodiversity footprint of the food system. In this study, we estimated the amount of land used to produce food consumed in the United States and the number of species threatened with extinction as a result of that land use. We predicted potential changes to the biodiversity threat under scenarios of food waste reduction and shifts to recommended healthy and sustainable diets. Domestically produced beef and dairy, which require vast land areas, and imported fruit, which has an intense impact on biodiversity per unit land, have especially high biodiversity footprints. Adopting the Planetary Health diet or the US Department of Agriculture (USDA)­recommended vegetarian diet nationwide would reduce the biodiversity footprint of food consumption. However, increases in the consumption of foods grown in global biodiversity hotspots both inside and outside the United States, especially fruits and vegetables, would partially offset the reduction. In contrast, the USDA-recommended US-style and Mediterranean-style diets would increase the biodiversity threat due to increased consumption of dairy and farmed fish. Simply halving food waste would benefit global biodiversity more than half as much as all Americans simultaneously shifting to a sustainable diet. Combining food waste reduction with the adoption of a sustainable diet could reduce the biodiversity footprint of US food consumption by roughly half. Species facing extinction because of unsustainable food consumption practices could be rescued by reducing agriculture's footprint; diet shifts and food waste reduction can help us get there.

Farm animal exposure, respiratory illnesses, and nasal cell gene expression.

BACKGROUND: Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development. OBJECTIVE: We hypothesized that children raised in farm environments have a lower incidence of respiratory illnesses over the first 2 years of life than nonfarm children. We also analyzed whether farm exposures or respiratory illnesses were related to patterns of nasal cell gene expression. METHODS: The Wisconsin Infant Study Cohort included farm (n = 156) and nonfarm (n = 155) families with children followed to age 2 years. Parents reported prenatal farm and other environmental exposures. Illness frequency and severity were assessed using illness diaries and periodic surveys. Nasopharyngeal cell gene expression in a subset of 64 children at age 2 years was compared to farm exposure and respiratory illness history. RESULTS: Farm versus nonfarm children had nominally lower rates of respiratory illnesses (rate ratio 0.82 [95% CI, 0.69, 0.97]) with a stepwise reduction in illness rates in children exposed to 0, 1, or ≥2 animal species, but these trends were nonsignificant in a multivariable model. Farm exposures and preceding respiratory illnesses were positively related to nasal cell gene signatures for mononuclear cells and innate and antimicrobial responses. CONCLUSIONS: Maternal and infant exposure to farms and farm animals was associated with nonsignificant trends for reduced respiratory illnesses. Nasal cell gene expression in a subset of children suggests that farm exposures and respiratory illnesses in early life are associated with distinct patterns of mucosal immune expression.