Research Article: Microbiome sharing between children, livestock and household surfaces in western Kenya

Date Published: February 2, 2017

Publisher: Public Library of Science

Author(s): Emily Mosites, Matt Sammons, Elkanah Otiang, Alexander Eng, Cecilia Noecker, Ohad Manor, Sarah Hilton, Samuel M. Thumbi, Clayton Onyango, Gemina Garland-Lewis, Douglas R. Call, M. Kariuki Njenga, Judith N. Wasserheit, Jennifer A. Zambriski, Judd L. Walson, Guy H. Palmer, Joel Montgomery, Elhanan Borenstein, Richard Omore, Peter M. Rabinowitz, Peter E. Larsen.


The gut microbiome community structure and development are associated with several health outcomes in young children. To determine the household influences of gut microbiome structure, we assessed microbial sharing within households in western Kenya by sequencing 16S rRNA libraries of fecal samples from children and cattle, cloacal swabs from chickens, and swabs of household surfaces. Among the 156 households studied, children within the same household significantly shared their gut microbiome with each other, although we did not find significant sharing of gut microbiome across host species or household surfaces. Higher gut microbiome diversity among children was associated with lower wealth status and involvement in livestock feeding chores. Although more research is necessary to identify further drivers of microbiota development, these results suggest that the household should be considered as a unit. Livestock activities, health and microbiome perturbations among an individual child may have implications for other children in the household.

Partial Text

The various taxa comprising the gut microbiome perform metabolic, signaling and immune functions in people and animals [1–3]. The maturation and structure of the gut microbiome can therefore have a long-term impact on health, and gut microbiome dysbiosis has been associated with various disease states, including malnutrition [4–10]. In order to promote health among young children, it is necessary to understand the environmental influences of gut microbiome development.

In this study, we describe the microbial constituents of the gut from young children in western Kenya, the gut of their household livestock, and their household environment. Overall, we found that the gut microbiome of children is more likely to be shared with other children within the household compared to children from different households. Overall, we did not observe significantly greater microbiome sharing between children and livestock or surfaces in the same households than between households. Further research will be necessary to determine the characteristics of households that show higher microbial overlap between host species.

In rural villages, the gut microbiome of children appears to be shared between children within the same household. Some children may also share microbiome components with nearby animals, although this effect does not appear to be consistent across the population. Microbiome diversity of children varied with wealth status and livestock contact. Because the gut microbiome plays a critical role in child health, our findings suggest that the health of household members should be considered linked, and that antibiotic use and livestock interactions among a single child in a household can have implications for the microbiome of other children in the home.




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