Schmey T, Auxier B, Krebs S
… +6 more, Patneedi SK, Ploch S, Ahmad F, Thines M, Habig M, Stam R
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42206335
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Alternaria alternata is a globally distributed fungal pathogen with a broad host range, increasingly affecting tomato crops and also infecting wild tomato relatives. The genomic basis of this ecological breadth in A. alt...Alternaria alternata is a globally distributed fungal pathogen with a broad host range, increasingly affecting tomato crops and also infecting wild tomato relatives. The genomic basis of this ecological breadth in A. alternata remains poorly understood. Here we leverage the opportunity of wild pathosystems to study pathogen evolution and diversity beyond agricultural settings. We sampled isolates from wild tomato species across a 2500 km range in South America, producing highly contiguous genomes, to investigate population structure. Our comparative genomics analyses reveal that A. alternata sensu stricto consists of two divergent clades. Strikingly, this divergence is not linked to host species, geography or habitat type. Transposable elements contribute to variation within clades but do not explain their separation. Although some signs of recombination are present, reproductive mode appears stable across clades. Notably, global reference isolates cluster with one clade, while the other, more diverse clade is only found in wild populations. We hypothesize that these wild populations may act as reservoirs of evolutionary potential. These findings challenge prevailing assumptions about the population structure of necrotrophic pathogens and raise new questions about how genetic divergence can persist without ecological or geographic isolation. This article is part of the theme issue 'Wild plant pathosystems'.
Henry L, Rat A, Laderman E
… +6 more, Lion R, Mayjonade B, Team Pathocom, Roux F, Weigel D, Bergelson J
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42206334
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The microbiome often protects plants against pathogens, but most findings are limited to controlled experiments in the lab. In the context of wild populations, one key challenge is to understand sources of variation that...The microbiome often protects plants against pathogens, but most findings are limited to controlled experiments in the lab. In the context of wild populations, one key challenge is to understand sources of variation that impact the commensal microbiome, which in turn shapes the degree of protection. Here, we surveyed both disease symptoms and microbiomes from wild populations of Arabidopsis thaliana over four consecutive seasons (Autumn/Spring) across three different land use types. Land use types varied in the extent of anthropogenic influences and included forest meadows, human-impacted fields adjacent to agriculture or municipal parks and highly disturbed habitats near railroad tracks. By building an integrative map of abiotic and biotic variables, we find that a key predictor of disease was biodiversity across ecological scales. Plant communities with higher diversity were associated with increased microbial diversity and reduced disease burden in A. thaliana populations, particularly in the Spring. However, the diversity-microbiome-disease relationships were all sensitive to season and further modulated by land use. Taken together, our work highlights the importance of anthropogenic change reshaping species interactions across ecological scales to impact disease risk in wild plant populations. This article is part of the theme issue 'Wild plant pathosystems'.
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42206333
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Plants alter soil biotic and abiotic properties with consequences for plant community dynamics at local and global scales, but how plant-soil interactions are affected by other environmental and biotic interactions remai...Plants alter soil biotic and abiotic properties with consequences for plant community dynamics at local and global scales, but how plant-soil interactions are affected by other environmental and biotic interactions remains poorly understood. We performed a fully reciprocal plant-soil feedback (PSF) experiment between two herbaceous plants, Monarda fistulosa and Plantago lanceolata, and tested how PSFs were influenced by drought and foliar powdery mildew pathogen infection. We observed significant negative feedbacks between the two plant species, but only when plants were grown with live soil biota and infected with powdery mildew. The strongest feedback was observed under both foliar infection and drought. High-throughput sequencing of soil fungi and bacteria from the treatment groups with foliar infection and drought revealed that both fungal and bacterial community composition were influenced by soil condition (live versus sterile) and soil training (Monarda versus Plantago). Together, our results indicate that the observed negative PSF was driven by foliar pathogens and plant species-specific soil microbial communities and intensified by drought. Our study suggests that PSF can be sensitive to both aboveground plant-pathogen interactions and climatic factors, improving our understanding of microbial impacts on plant community dynamics. This article is part of the theme issue 'Wild plant pathosystems'.
Arnold KMH, Bugay MJ, Fox Q
… +15 more, Morris CM, Hutson WD, Durant A, Basta A, Tomera C, Pierce SE, Armstrong GZ, Chen D, Chertow DJ, Hofstra RL, Talbert K, Johnson C, Wallace K, Wassel A, Penczykowski RM
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42206332
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Understanding how urbanization affects plant interactions with pathogens and herbivores is important for clarifying how changes in land use, climate and biodiversity affect ecological and evolutionary processes, and for...Understanding how urbanization affects plant interactions with pathogens and herbivores is important for clarifying how changes in land use, climate and biodiversity affect ecological and evolutionary processes, and for managing urban plants to maximize ecosystem services. We performed a systematic literature review of relationships between urbanization and pathogens or pests of wild and cultivated plants. We identified k = 171 relationships from n = 54 studies in which pathogen or pest abundance was quantified in both urban and non-urban areas and summarized their distribution across taxa, geographic regions and directions and mechanisms of effects proposed by the authors. Most studies featured tree hosts and their arthropod pests or fungal pathogens. Grasses and forbs were the next most commonly studied hosts, followed by crops and shrubs. We then performed a meta-analysis limited to trees, which had the most studies with sufficient statistical information (k = 55 relationships, n = 14 studies). In that meta-analysis, we found no overall effect of urbanization on tree pest or pathogen abundance. However, there was a significant effect of pest/pathogen, with arthropod pests trending towards lower abundance in urban areas and fungal pathogens trending towards higher abundance. Drawing on literature from the broader fields of urban ecology, disease ecology and plant pathology, we synthesize our findings and offer insights into mechanisms by which urbanization influences disease and herbivory in wild and cultivated plants. We conclude by identifying research gaps, with the goal of informing management strategies that prioritize food security, environmental health and global biodiversity. This article is part of the theme issue 'Wild plant pathosystems'.
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42206331
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Wild plant diseases impact host fitness and ecosystem functions, threatening food security and ecological integrity. Fungal and oomycete pathogens differ in nutrient acquisition strategies (i.e. biotroph versus necrotrop...Wild plant diseases impact host fitness and ecosystem functions, threatening food security and ecological integrity. Fungal and oomycete pathogens differ in nutrient acquisition strategies (i.e. biotroph versus necrotroph), and these strategies shape pathogen reproduction, infection patterns and host defences. While existing reviews have outlined these differences, a unifying framework leveraging these nutrient acquisition strategies to explain disease patterns across diverse abiotic and biotic drivers is lacking. To address this, we explore how these strategies determine pathogen responses to abiotic and biotic factors and associated disease risks. Biotrophic pathogens typically show a unimodal relationship with temperature and precipitation, with optimal ranges for each. Necrotrophic pathogen infections usually increase under high temperature, drought or excessive precipitation. Nitrogen additions generally elevate disease risk for both, although biotrophs may benefit more owing to reliance on host nutrients. Biodiversity loss exacerbates the disease load, particularly for diseases caused by biotrophic pathogens. Herbivory suppresses biotrophic but promotes necrotrophic pathogens, whereas arbuscular mycorrhizal fungi reduce necrotrophic rather than biotrophic pathogens. We propose that incorporating data on pathogen nutrient acquisition strategy into plant disease models will improve predictions of fungal and oomycete disease outbreaks under future climate scenarios and support the development of targeted management policies. This article is part of the theme issue 'Wild plant pathosystems'.
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42206330
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The plant's microbiome is influenced by the plant species and biotic factors such as infection by pathogens. Pathogen-microbiome interactions are relevant for disease progression since both can compete within the host. W...The plant's microbiome is influenced by the plant species and biotic factors such as infection by pathogens. Pathogen-microbiome interactions are relevant for disease progression since both can compete within the host. We hypothesize that pathogens specialized to different hosts have distinct, direct and indirect influence on the host microbiome. We focused on the host-specific leaf pathogens Zymoseptoria tritici and Zymoseptoria passerinii. By using microbiome metabarcoding and coculture interactions, we evaluated the influence of virulent (wild host-infecting pathogen) and avirulent (domesticated host-infecting pathogen) Zymoseptoria isolates on the leaf microbiome of the wild grasses Aegilops cylindrica and Hordeum murinum, which are hosts to virulent lineages of Z. tritici and Z. passerinii, respectively. Our microbiome analysis showed that the fungal communities were affected by virulent lineages, while the avirulent lineages had the most negative correlations with bacteria. Both virulent and avirulent pathogens had a similar spectrum of interactions when experimentally cocultured with bacteria. The intensity of pathogen-induced growth enhancement on bacteria differed between Z. tritici isolates. We demonstrated that the pathogen-secreted invertases can be a determinant of bacterial growth enhancement. Our study illustrates the extent of specificity in pathogen-microbe coexistence and suggests an interaction mechanism that may influence in planta interactions. This article is part of the theme issue 'Wild plant pathosystems'.
Del Ponte EM, Mikaberidze A, Bebber DP
… +2 more, Halliday FW, Cunniffe NJ
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42206329
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Plant diseases occurring across wild and crop plants present modelling and management challenges. Wild plant and crop pathosystems differ in ecological structure, evolutionary dynamics and responsiveness to human interve...Plant diseases occurring across wild and crop plants present modelling and management challenges. Wild plant and crop pathosystems differ in ecological structure, evolutionary dynamics and responsiveness to human intervention. At the interface, pathogens may spill over, spill back, persist or evolve, shaped by host diversity, dispersal processes and landscape connectivity. The potential importance of factors including pathogen dispersal, host life history and spatial configuration are examined through a qualitative comparison of case studies: Puccinia graminis, Phakopsora pachyrhizi, Xylella fastidiosa, Pyricularia oryzae Triticum lineage and Austropuccinia psidii. These examples illustrate how wild hosts may function as reservoirs, recombination partners or spillover targets, and how their role influences management efficacy and evolutionary risk. We explore the consequences of this wild-crop interface through two central questions: (i) how should plant diseases involving wild and cultivated pathosystems be managed, and (ii) what proportion of management effort should be allocated to each system? We show the principles underpinning answers to these questions via a conceptual framework based on a generic compartmental model incorporating asymmetric transmission and system-specific interventions, thereby accounting for key aspects of pathogen spread within and between wild host and crop populations. Finally, we identify critical data needs and modelling directions to better inform disease management on the wild plant-crop interface and argue for a more integrative approach bridging ecological and anthropogenic drivers of epidemics. This article is part of the theme issue 'Wild plant pathosystems'.
Htet MK, Nurfadilah M, Ramsteijn AS
… +11 more, Angelin TC, Ameline AS, Momo Kadia B, Gabain IL, Davies-Kershaw H, Calvo-Urbano B, Webster JP, Ferguson EL, Allen S, Walker AW, Fahmida U
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132035
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Previous studies have compared the microbiota profiles of stunted and non-stunted children. However, how these profiles interact with dietary patterns is not completely understood. To assess differences in microbial dive...Previous studies have compared the microbiota profiles of stunted and non-stunted children. However, how these profiles interact with dietary patterns is not completely understood. To assess differences in microbial diversity, composition and bacteria taxa between stunted and non-stunted children and how the consumption of food groups influence the gut microbiota of stunted children, this matched case-control study was conducted among 150 pairs of stunted and non-stunted children of between 18-23 months old in East Lombok, Indonesia. Anthropometry and dietary data were collected by trained enumerators. Microbiome data were generated by sequencing the V4 hypervariable region of the 16S rRNA gene. No between-group differences in alpha and beta diversity were observed. Exploratory analysis identified that Agathobacter, Coprococcus, Dorea, Hominimerdicola, Lawsonibacter and Ruminococcoides were more proportionally abundant among non-stunted children and Peptostreptococcus among stunted children. However, there was no association between food group consumption and abundance of these taxa. Breastfeeding significantly shaped the microbiota profiles. Future research on the association between microbiota profiles and complementary feeding should incorporate approaches such as diet modelling to capture the combined contributions of food groups and dietary components, alongside longitudinal study designs. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132034
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As of 2025, an estimated 150.2 million children under 5 years globally were stunted-falling more than two standard deviations below the World Health Organization (WHO) Child Growth Standards median. Helminth infections r...As of 2025, an estimated 150.2 million children under 5 years globally were stunted-falling more than two standard deviations below the World Health Organization (WHO) Child Growth Standards median. Helminth infections represent a potentially significant yet under-addressed contributor to childhood stunting. Our aim was to elucidate the potential causal relationship between helminth infections and childhood stunting, including the mediating role of low birth weight (LBW). Three causal directed acyclic graphs (DAGs) were constructed using evidence synthesis for constructing DAGs (ESC-DAGs) methodology: (i) maternal infection, (ii) infant infection during exclusive breastfeeding (<6 months old), and (iii) child infection post-weaning (6-24 months old). Minimally sufficient adjustment sets (MSAS) were derived from our DAGs. All three DAG models included core adjustments for geographical location, healthcare access and water, sanitation and hygiene factors. The maternal infection model additionally incorporated maternal age, socioeconomic status (SES) and maternal education as key confounders. For the child models, both age groups included adjustments for child sex, age, birth weight and parental education. The model for infants <6 months of age additionally incorporated breastfeeding status, while the model for children post-weaning (6-24 months of age) included SES alongside the other shared variables. These MSAS provide researchers with standardized confounder adjustment frameworks, helping to resolve inconsistencies in prior literature stemming from incomplete confounder control and advancing methodologically rigorous causal inference. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Htet MK, Nurfadilah M, Angelin TC
… +10 more, Momo Kadia B, Gabain IL, Ramsteijn AS, Davies-Kershaw H, Calvo-Urbano B, Webster JP, Walker AW, Ferguson EL, Allen S, Fahmida U
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132033
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Poor gut health, characterized by persistent immune activation and increased intestinal permeability, is considered a significant underlying cause of impaired child growth. This study aimed to investigate effects of envi...Poor gut health, characterized by persistent immune activation and increased intestinal permeability, is considered a significant underlying cause of impaired child growth. This study aimed to investigate effects of environmental enteric dysfunction (EED) and systemic inflammation on plasma insulin-like growth factor (IGF)-1 and linear growth among Indonesian infants. In this longitudinal cohort study (Action Against Stunting Hub), faecal and plasma samples were collected at six months of age, and anthropometry assessment was conducted at six and twelve months of age. EED markers included faecal myeloperoxidase, alpha-1 antitrypsin and plasma intestinal fatty acid binding protein (IFABP). Systemic inflammation markers included C-reactive protein, alpha-1 acid glycoprotein and cluster of differentiation-14 (CD14). IGF-1 was measured as a growth biomarker. Correlation and multivariable regression analyses assessed association with length-for-age z-score (LAZ). Structural equation modelling explored potential pathways. Elevated EED markers were common among the infants (>80%). Maternal height, birth weight and IGF-1 were significant determinants of LAZ at 12 months. Pathway analysis showed IGF-1 was negatively associated with CD14, whereas CD14 was positively associated with IFABP. EED influences linear growth indirectly through systemic inflammation and altered growth signalling. Studies to further address gut integrity and systemic inflammation to improve linear growth are recommended. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Hlongwa N, Rich K, Kelly P
… +7 more, Ngobeni-Nyambi R, Stone W, von Fintel M, Schenck C, Swart R, Makhalanyane T, Burger R
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132032
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The causes of childhood stunting remain debated, with emerging evidence highlighting the complexity of poverty-related mechanisms. While nutrition, healthcare and sanitation have traditionally been viewed as the primary...The causes of childhood stunting remain debated, with emerging evidence highlighting the complexity of poverty-related mechanisms. While nutrition, healthcare and sanitation have traditionally been viewed as the primary drivers of stunting, new research highlights the physiological mediators linking poverty to impaired growth. Chronic exposure to unsanitary environments may lead to environmental enteric dysfunction, a subclinical gut condition that may impair the development of the gut microbiome. Stunted children frequently exhibit an immature and dysbiotic gut microbiome, which is linked to higher levels of gut inflammation, reduced nutrient assimilation and increased susceptibility to infections. Here, we examine how poverty-related factors, including poor diet and hygiene, affect gut health and early neurodevelopment, with a particular focus on the gut-brain axis. Understanding this 'physiology of poverty' reveals that effective interventions must extend beyond food provision to integrate improvements in water, sanitation, hygiene (WASH) and microbiome support (e.g. via probiotics or prebiotics). A holistic strategy targeting environmental and biological factors in early life is critical to disrupting the intergenerational cycle of stunting and poverty. We identify key evidence gaps and stress the need for multidisciplinary, context-specific approaches to mitigate stunting's long-term association with health and human capital. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132031
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Linear growth stunting increases a child's risk for mortality and lifelong morbidities. Understanding and preventing the causes of childhood stunting is a global health priority. The leading contributors to stunting are...Linear growth stunting increases a child's risk for mortality and lifelong morbidities. Understanding and preventing the causes of childhood stunting is a global health priority. The leading contributors to stunting are undernutrition and infection. Schistosomiasis, a neglected tropical disease, has long been associated with childhood stunting, but there are limited reviews summarizing the evidence. This narrative review examines cross-sectional associations between infection and linear growth, longitudinal impacts of schistosomiasis treatment on growth and the influence of schistosomiasis on the endocrine system, specifically the growth hormone (GH) and insulin-like growth factor 1 (IGF-1) axis. After reviewing more than 60 years of research, there is evidence for an association between schistosomiasis infection and linear growth measures but mixed results relating to stunting, a categorical outcome based on low height-for-age measures. This may be due to limitations in study design or the length of time required to induce stunting. The reports also support the theory that schistosomiasis disrupts the GH/IGF-1 axis, resulting in reduced IGF-1 and impaired linear growth. These findings reinforce the need for early treatment interventions for children living in schistosomiasis-endemic regions and encourage research to include stunting risk factors and endocrine measures in future schistosomiasis study designs. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132030
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Malnutrition still affects millions of children in Africa. Changes in the gut microbiome have been implicated in malnutrition, but there has been inconsistent nomenclature of microbes. This meta-analysis reviews the micr...Malnutrition still affects millions of children in Africa. Changes in the gut microbiome have been implicated in malnutrition, but there has been inconsistent nomenclature of microbes. This meta-analysis reviews the microbiome literature using natural language processing (NLP) methods. We searched PubMed for gut microbiome studies of undernourished children living in low- and middle-income countries (LMICs). The primary analysis focused on continental coverage and study characteristics of microbiome research in sub-Saharan Africa (ss-Africa). We also used an NLP tool for normalizing primary data from full-text publications in ss-Africa compared with other LMICs, and between diseased and healthy children. We identified 16 studies. Most studies were conducted in Malawi and characterized the faecal microbiome using 16S rRNA sequencing. For comparison, 18 studies conducted in Bangladesh, India, Pakistan and Peru were included. With this, we identified frequently reported microbes that were distinctly identified in ss-Africa and highlighted possible signatures of an undernourished faecal microbiome across the globe. The consistent associations between elevated Pseudomonadota levels and severe acute malnutrition provide new insights into host-microbiome interactions in African contexts. However, the overlap between taxa associated with healthy and stunting underscores the need for further research to better inform potential targeted interventions in Africa. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Mweetwa MN, Ashan K, Kung V
… +7 more, McNulty NP, Besa E, Barratt MJ, Posma J, Amadi B, Gordon JI, Kelly P
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132029
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Childhood malnutrition is linked to gut microbiome changes; however, most studies focus on faecal samples, while less is known about the small intestinal microbiome. Here, we characterized the duodenal microbiota of chil...Childhood malnutrition is linked to gut microbiome changes; however, most studies focus on faecal samples, while less is known about the small intestinal microbiome. Here, we characterized the duodenal microbiota of children in Zambia with severe acute malnutrition (SAM) and stunting and compared the microbiomes of stunted children living across the globe. To do this, duodenal aspirates from only stunted (i.e. not concurrently wasted) (n = 53) and SAM (n = 24) Zambian children were analysed by 16S rRNA gene amplicon sequencing. Associations between bacterial composition, clinical features and biomarkers of enteropathy were explored. Comparison of duodenal 16S rRNA gene datasets from malnourished children in different countries was also performed using publicly available datasets to assess the impact of age and geography on microbial diversity and composition. The duodenal microbiota in both stunted and SAM children was dominated by Streptococcus, Granulicatella, Gemella and Klebsiella. Children with SAM had lower α-diversity than stunted children. Meta-analysis revealed similarities in the bacterial composition of age-matched children in different countries, but relative abundances and their association with nutritional status differed. This study offers insight into the duodenal microbiota in children with different states of malnutrition, highlighting the potential influence of geography and age in shaping the proximal small intestine. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Hlaing LM, Htet MK, Gibson R
… +3 more, Utomo B, Firmansyah A, Fahmida U
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132028
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Iron deficiency, with or without anemia, remains a major public health concern among young children in Myanmar. While iron supplementation is widely recommended, its potential adverse effects on growth and gut microbiota...Iron deficiency, with or without anemia, remains a major public health concern among young children in Myanmar. While iron supplementation is widely recommended, its potential adverse effects on growth and gut microbiota warrant investigation, particularly in contexts of poor complementary feeding. To assess the effects of iron supplementation, with or without complementary feeding recommendations (CFRs), on micronutrient status, linear growth and gut microbiota composition among Myanmar children aged 12-23 months, a 24-week randomized controlled trial was conducted in Ayeyarwady Region of Myanmar. Fourteen clusters (villages/wards) were randomized to receive CFRs or not, and children within the clusters were randomized to receive daily aqueous iron or placebo, creating four arms: Placebo (n = 104), CFR (n = 112), Fe (n = 105) and CFRFe (n = 112) totalling 433 children. All intervention groups (CFR, Fe, CFRFe) improved haemoglobin and reduced anaemia risk compared with Placebo (AOR = 0.31 (0.15-0.62), 0.15 (0.07-0.32), 0.14 (0.07-0.31), respectively). CFR and CFRFe also improved zinc status. However, iron-alone (Fe) increased the stunting risk (AOR= 2.74 (1.04-7.23)), while CFRFe did not. No significant effects were observed on gut microbiota composition. Aqueous iron supplementation may impair linear growth when diets are not optimized; combining supplements with optimized complementary feeding may support healthier outcomes. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Osakunor DNM, Pfavayi LT, Mduluza T
… +1 more, Mutapi F
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132027
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Stunting (low height-for-age > 2 s.d. below the WHO child growth standards median) is a key indicator of chronic malnutrition and is influenced by poor nutrition, infections, chronic inflammation and impaired gut health....Stunting (low height-for-age > 2 s.d. below the WHO child growth standards median) is a key indicator of chronic malnutrition and is influenced by poor nutrition, infections, chronic inflammation and impaired gut health. In sub-Saharan Africa, stunting frequently occurs in regions where schistosomiasis is endemic. Our previous research in Zimbabwean preschool children (≤ 5 years) found that Schistosoma haematobium infection alone could account for up to one-third of stunting cases. Using epidemiological, gut microbiome and metabolomic analyses, we investigated how this parasitic infection contributes to poor growth. Infected children showed significantly altered gut microbiome profiles compared to uninfected peers, indicating potential microbiome disruption linked to disease and impaired development. Metabolomic profiling revealed that S. haematobium infection elevated energy- and purine-related metabolites, reflecting metabolic stress associated with malnutrition. Early treatment with praziquantel did not significantly alter the microbiome but did restore normal metabolic profiles, aligning with observed catch-up growth. Here, we synthesize findings from our studies and others to highlight opportunities for intervention and key research gaps, supporting the inclusion of praziquantel in early health programmes and integrated strategies combining treatment with nutrition. Further research, particularly longitudinal studies, is needed to confirm causality and optimize child health outcomes in endemic areas. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Häsler B, Kumar Ramachandrappa N, Rotta S
… +14 more, Konapur A, Ravichandran T, Dominguez-Salas P, Foster D, Claron M, Grace D, Validandi V, Moodley A, Ochieng L, Bosire C, Augustine LF, Heffernan C, Kumar Banjara S, Kulkarni B
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132026
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Bovine milk has shown a positive association with child growth rates, but access in Hyderabad, India, is variable and milk-borne hazards are of concern. The aim of this study was to investigate how milk value chains (VCs...Bovine milk has shown a positive association with child growth rates, but access in Hyderabad, India, is variable and milk-borne hazards are of concern. The aim of this study was to investigate how milk value chains (VCs) in urban Hyderabad influence microbiological and toxicological milk safety and their intersection with child stunting. A mixed-methods approach was used, encompassing a thematic reflexive analysis of qualitative interviews conducted with 12 VC key informants and risk-based sampling of 42 milk, 24 animal feed and 20 water samples that were subjected to microbiological and aflatoxin testing. Key themes identified were financial instability, trust-based processes, milk safety concerns and power imbalances in the VCs. The microbiological analysis showed contamination in unpasteurized milk at various nodes, with high levels of total colony count, faecal coliforms, Staphylococcus aureus and yeast/mould, while water used in the VCs also showed microbial contamination. A total of 67% of dairy feed samples tested positive for total aflatoxins; all of them were within Indian regulatory limits. Opportunities for safer and more nutritious milk that could help to reduce child stunting include improved food safety practices, enhanced awareness of milk-borne hazards, institutional accountability and increased agency of VC actors. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.
Rosenbaum J, Abariga S, Wang Y
… +1 more, Wallach T
Philos Trans R Soc Lond B Biol Sci
· 2026 May · PMID 42132025
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Early childhood nutrition determines cognitive development and physical health throughout the life course. Prior work has suggested protein deficiency, in particular tryptophan, may be a major driver of stunted growth. W...Early childhood nutrition determines cognitive development and physical health throughout the life course. Prior work has suggested protein deficiency, in particular tryptophan, may be a major driver of stunted growth. We evaluated the association between the consumption of animal versus plant protein sources and anthropometric z-scores using Multiple Indicator Cluster Surveys for children aged 1-4 years: Central African Republic 2010 (n = 7843), Ghana 2011 (n = 5887), Mali 2009 (n = 17 496) and Sierra Leone 2017 (n = 9254). In the past 24 h, 72% had consumed any animal-sourced foods (fish, dairy, egg, meat, liver, milk, yogurt, cheese) and 45% had consumed legumes. We used a doubly robust regression that reduced confounding using three-moment entropy balancing on survey parameters, demographics (age, gender) and socioeconomic status (urban residence, mother's education, wealth quintile), followed by survey-weighted multivariable linear regression with outcomes interviewer-measured height-for-age and weight-for-age z-scores. Height-for-age and weight-for-age z-scores were greater for children who had consumed animal-source food (0.134 (0.082, 0.186) and 0.075 (0.029, 0.120)); children who had consumed legumes had higher weight (0.056 (0.021, 0.091)) but not height (0.015 (-0.028, 0.059)). Our findings align with biomedical research implicating essential amino acids as key mediators of growth and intestinal function, and suggest a role for complete protein and essential amino acid deficiency as a driver of environmental enteric dysfunction. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.