Age and Early Life Adversity in the Wild Baboon Gut Microbiome

Mammalian gut microbiomes are highly individualized, dynamic microbial communities. They serve essential functions for their hosts by breaking down complex carbohydrates, producing vitamins, training the immune system, and resisting pathogens. These communities also change substantially throughout life in response to host environment, diet, and sociality. Age and early life experiences have also been shown to influence the composition of the gut microbiome in cross-sectional studies. These changes are proposed to be important markers of individual development and senescence. However, to date, scientific understanding of host-microbe dynamics is hampered by the fact that most microbiome research is cross-sectional. Without fine-grained longitudinal data on microbiome composition across the host's life, we do not know how gut microbiomes change in individuals over time, what factors drive variation in gut microbiome development and aging, or whether these changes serve as markers of maturational milestones or mortality risk.

To address this gap, my PhD research leverages long-term, longitudinal data from a wild population of baboons (Papio cynocephalus) monitored by the Amboseli Baboon Research Project (ABRP) in Kenya. My dissertation objective was to characterize how the gut microbiome changes in response to early life experiences and age across the lifespan, understand what host and environmental factors predict these changes, and determine whether microbial changes are linked to host maturation and survival. To accomplish this objective, I combine the ABRP’s 50 years of demographic, environmental, social, and genetic data with a corresponding gut microbiome data set consisting of over 17,000 16S gut microbial profiles collected from 601 known individually-known, wild baboons over a 14-year period. Using a subset of these data, I have shown that the gut microbiome changes predictably with age and found that individuals who were socially low-ranked exhibit faster rates of microbial aging relative to high-ranked peers. Next, I found that individuals who aged faster attain certain maturational milestones earlier. Last, I discovered that specific types of early life adversity are correlated with changes in microbial composition or decreased stability late in life. Together, my research improves our understanding of how the gut microbiome adapts to and influences its mammalian host’s life course.