Abstract
Microbial communities regulate essential ecological and metabolic processes across both engineered and host-associated ecosystems. Although these systems differ substantially in composition and function, they are governed by common ecological principles including community succession, resilience, species interactions, and responses to environmental and biological perturbations. This dissertation investigates how perturbations influence microbiome structure, function, and stability through three complementary studies spanning anaerobic digestion and the human gut microbiome. First, the effects of an extremophilic biological pretreatment using Caldicellulosiruptor bescii were evaluated in industrial-scale anaerobic digesters treating dairy manure. High- temperature pretreatment substantially altered microbial community composition, with bacterial populations remaining metabolically active while acetoclastic methanogens were greatly diminished and failed to recover following anaerobic digestion. In contrast, hydrogenotrophic methanogens survived pretreatment and persisted throughout digestion despite being poorly suited to utilize the acetate-rich products generated during pretreatment. These findings suggest that restoring acetoclastic methanogens may improve methane production in biologically pretreated systems. Second, the ecological role of bacteriophage was investigated across fifteen commercial anaerobic digesters processing chicken, cattle, and swine manure. Phage and microbial abundance were strongly influenced by feedstock type, demonstrating that viral and microbial populations respond to common environmental drivers. Viral genomes encoded auxiliary metabolic genes involved in pyruvate metabolism, and cobalamin biosynthesis, indicating that phages contribute directly to metabolic processes supporting anaerobic digestion while simultaneously influencing bacterial and archaeal community structure through host interactions. Finally, gut microbiome development was characterized in infants and toddlers with elevated likelihood of autism spectrum disorder (ASD). Distinct microbial community compositions were observed between children with and without autistic siblings across the first three years of life. Prevotella species were associated with elevated ASD likelihood and behavioral assessment scores. The difference in microbiome species provides encouragement for future ASD microbiome studies designed for diagnostic markers. Collectively, these studies demonstrate that microbiome responses to environmental and biological perturbations are governed by shared ecological principles across engineered and host- associated ecosystems. By examining microbial resilience, viral-host interactions, and community succession, this dissertation advances understanding of the mechanisms that shape microbiome function and provides insight into strategies for improving anaerobic digestion performance and informing future investigations of early-life microbiome development and human health.
Degree
PhD
College and Department
Life Sciences; Microbiology and Molecular Biology
Rights
https://lib.byu.edu/about/copyright/
BYU ScholarsArchive Citation
Nipko, Maliea AnnHolden, "From Anaerobic Digesters to the Human Gut: Ecological Responses of Microbiomes to Environmental and Biological Perturbations" (2026). Theses and Dissertations. 11436.
https://scholarsarchive.byu.edu/etd/11436
Date Submitted
2026-07-29
Document Type
Dissertation
Keywords
microbiome, human gut, anaerobic digestion, metagenomics
Language
english