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Linking Gut Viral Populations to bacterial colonization patterns and malnutrition
Laura Carolina Camelo Valera, Corinne F Maurice
Malnutrition is one of the leading causes of mortality of infants under the age of five. Its prevalence is highest in low- and middle-income countries due to food supply limitations, where it can lead to stunting and wasting. Stunting is a multifactorial condition with long-lasting effects such as cognitive and growth impairment as well as delayed bacterial colonization patterns leading to increased susceptibility to enteric infections. Changes in bacterial abundances are intrinsically linked to their viral predators, called bacteriophages or phages. Previous in vitro work in our lab showed that phages contribute to shaping a malnourished gut microbiome by exacerbating gut bacterial pathogen loads in stunted children. However, further work is needed to understand fundamental phage-host ecology patterns that can only be seen at fine-level resolution and how these dynamics serve to modulate bacterial communities in malnutrition. We explored the links between viral population dynamics and nutritional health status in a cohort of 232 children from Zimbabwe sampled monthly from 30 to 650 days after birth, including stunted and non-stunted controls. We developed a framework to assess macro- and micro-diversity patterns in the infant gut. So far, we found that there is a natural gap at 99.5% ANI and 95% coverage suggesting sequence discrete viral populations (vPOPs). These vPOPs show high individuality (86% of the vOTUs are found in < 10 infants), consistent with previous reports at the genus level. Still, we found 249 vPOPs present in at least 50% of the children, some of which were persistent and others sporadic (only present at a certain age period). Phage prevalence also differed with respect to nutritional status, likely depending on bacterial host availability. Overall, these findings provide essential information to understand the eco-evolutionary patterns of viral communities in the human gut and their links to malnutrition. The framework we developed offers a robust strategy for other researchers to explore viral populations at a high resolution, facilitating a deeper understanding of microbiome dynamics. Understanding phage dynamics at sub-species level in the infant gut may enable us to study their influence on gut bacterial communities during early colonization.
