My current work in the Archie Lab at the University of Notre Dame focuses on understanding how the gut microbiome changes with age, developmental stage, early life environmental conditions, and the consequences of these changes on host health and fitness. In order to answer my research questions, I am using data collected from a wild population of well-studied baboons in Amboseli National Park, Kenya.
How does the gut microbiome change over host lifespan?
Host-associated microbiomes are highly individualized, dynamic ecosystems that fluctuate over time. However, most of these findings come from cross-sectional data; indeed, longitudinal data on gut microbiome dynamics—especially in adulthood and old age—are rare (Yatsunenko et al. 2012; Odamaki et al. 2016; Mueller et al. 2006; McDonald et al. 2015). Accordingly, our understanding of how the microbiome changes across a host’s life, from birth to death is very limited. Specifically, I am testing the hypothesis that the gut microbiome exhibits predictable age-related changes in composition, diversity, and stability, analogous to “successional” stages that correlate with host age. Understanding how the microbiome ages with the host, and what markers are informative of this aging, will be important for understanding how functionality shifts with age.
Do Early life events leave a mark on the gut microbiome?
Harsh conditions in early life have been shown to have marked, long-term effects on an individual’s behavior, cognition, and physiology (Chaby 2016; Lindström 1999). However, relatively little is known about the role of host life history and, specifically, early life adversity on the composition of the gut microbiome over time. To this end, I am specifically testing whether sources of early life adversity, including both nutritional limitation and social isolation, will exert long term changes on the gut microbiome.
how does variation in the gut microbiome relate to variation in darwinian fitness?
Metrics of gut microbial diversity, composition, and stability are often proposed to be important markers of healthy microbiomes and even overall host health and fitness (Bäckhed et al. 2012; Trosvik et al. 2015; Hollister et al. 2014; Gerber 2014). However, whether any general features of microbiome composition, diversity, and stability can serve as common, reliable predictors of “healthy microbiomes” and/or host fitness is completely unknown. In order to fill this gap in our understanding, I will test whether gut microbial diversity, composition, and stability predict biodemographic markers of health, including the timing of maturity, fertility, and survival.