Electronic Thesis and Dissertation Repository

Thesis Format



Master of Arts



Collaborative Specialization

Environment and Sustainability


Dr. Jay Stock


Human microbiome research has rapidly developed over the past two decades yet absent from most research is the composition and dynamics of microbiomes within human populations. Given the limitations in longitudinal studies which requires decades of repeated microbe taxonomic testing of a population sample, an alternative option is to examine microbiomes and their influences via proxies using pre-existing health datasets. This research demonstrates preliminary associations between presumed disrupted and supportive microbiomes dynamics proxied by antibiotic and breastmilk exposure respectively. Using health record data across the life span from approximately 500,000 U.K. participants, this research demonstrates variable altered growth and health outcomes in antibiotic and breastfed exposure groups evaluated by anthropometric measures and health diagnosis occurrences via T-test, ANOVA, and Chi-square statistical testing. While preliminary, these results indicate microbial modification can produce detectable population associations. These potential trends may allow biological anthropologists an indirect method of examining ancient microbiome dynamics and its influences.

Summary for Lay Audience

The human microbiome is a growing area of interest for researchers across several fields. Comprised of all microorganisms (microbes) on and in the human body, the microbiome is a complex realm of interaction between microbes (bacteria, fungi, viruses, archaea, and protists) and human tissues often resulting in benefits for those involved. While some of these interactions may become detrimental to humans, the majority of interactions are beneficial playing important roles in digestion, nutrient synthesis, and immune system defense.

The bulk of microbiome research centers on contemporary populations, though some inquiries into ancient microbiomes have been completed. Part of the limited ancient microbiome research is due to the microbiome’s poor preservation within the archaeological record. Currently, direct genetic analysis of ancient microbiomes comes from three primary sources: dental plaque (which traps the oral microbiome of an individual), coprolites (fossilized faeces which captures the gut microbiome of a group), and preserved soft tissues (mummified or medical specimens which may contain the microbiome of the respective body/component).

Poor preservation creates an issue for ancient microbiome research as direct access is limited. One way to circumvent this issue is to indirectly study ancient microbiomes through their influences on human growth and health outcomes in contemporary populations. Some factors have been demonstrated to alter microbiome dynamics such as antibiotics (in a negative) and breastfeeding (in a positive) manner. By examining groups exposed to one or both of these factors and their respective growth and health outcomes, associations between microbiome dynamics and growth and health outcomes can be established and applied to past populations.

To examine the idea, this research used health record data from approximately 500,000 United Kingdom participants grouping them in exposed and unexposed groups for three variables: breastfed, antibiotic, and breastfed and antibiotic. Through statistical analysis testing, this study determined each exposure did influence several growth and health outcomes to varying degrees.

The correlation of microbiome establishment factors associating with altered growth and health outcomes in one population may indicate that trends derived from contemporary populations could be used indirectly to view microbiome associated influences in other populations.