Gut microbiome, enteric infections and child growth across a rural urban gradient

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Animals are ubiquitous in both urban and rural communities in low- and middle-income countries, and recent evidence suggests that animal exposure is an important, yet often overlooked factor shaping infant gut health and development. While connections between animal exposure and the gut microbiome are increasingly recognized, the health impacts of these associations are unclear. The goal of this study is to understand if and how animal exposures affect gut characteristics and health outcomes of infants enrolled in an ongoing cohort study in northern Ecuador. Our proposed mixed methods approach will result in a comprehensive understanding of infant exposure to animals and animal-sourced contamination, and how this varies along an urban-rural gradient. We will collect rich and nuanced data on household and infant animal interactions and exposures from this proposal and leverage the extensive health and microbiome data being collected within our ongoing cohort study to examine the implications of exposures to animals on the infant gut microbiome and health outcomes during the first two years of life. Through this competing revision proposal we thus substantially expand the scope of our existing study to characterize a potentially key pathway for infant exposure to enteropathogens and other microorganisms. Our specific aims are: SA1) To characterize infant exposure to animals and animal feces using environmental microbiology, qualitative, and survey-based methods. We will use environmental microbiology methods to quantify and differentiate human- and animal- specific fecal contamination in study households (SA1a), and use qualitative methods to understand the conditions under which children are exposed to animals and animal-sourced contamination, and to gain insights into feasible strategies for managing health risks associated with animal exposure (SA1b). We will integrate these data to develop complementary microbial and survey-based indices of animal exposure, that will be used as exposure variables measures in subsequent analyses. SA2) To test the association between animal exposure and infant gut microbiome characteristics. We will use microbiome sequencing data generated in the parent study to examine associations between animal exposure and gut microbiome of cohort children (SA2a). We will also look for evidence of zoonotic transmission of microorganisms between infants and animals by testing for the presence of animal-specific sequences within the microbiomes of highly exposed children (SA2b). SA3) To test the association between animal exposure and infant gut health. We will use health outcome data from the parent study to examine associations between animal exposure and diarrhea, enteropathogen infections, infant growth, and environmental enteric dysfunction, adjusting for key covariates (SA3a). This project integrates additional interdisciplinary expertise into our study team (qualitative, measurement development, and microbial source tracking methods), provides substantive additional training opportunities for our Ecuadorian team, and increases the translational aspects of our research.