Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)


Civil and Environmental Engineering

First Advisor

Matthew Scarborough


Microbiomes have benefited humans for as long as humans have existed. In addition to the microbiomes that inhabit the human body, microbiomes have been used to ferment and preserve food and beverages since prehistoric times. As science and technology emerged, microbiomes have been employed for more intricate processes and for treating wastes. Despite humankind’s shared history with microbiomes, underlying drivers of microbiome function, stability, and resilience are still unknown. As humans work to combat global climate change, microbiome-based processes are a potential tool for both reducing greenhouse gas emissions directly and producing chemicals currently derived from fossil fuels. Therefore, improved understanding of microbiome-based conversion processes can help humans reduce impacts on the environment. This work assessed the production of beneficial chemicals through fermentation by self-assembled microbiomes. Three different feedstocks were studied - a mixture of glucose and xylose, glucose, and food waste - for the anaerobic production of medium-chain carboxylic acids (MCCAs). For all feedstocks, the microbial communities that emerged were comprised of only a few abundant taxa contained within the Bacillota and Actinobacteria phyla. So called “chain elongating” organisms that produced MCCAs were identified through metagenomic and metatranscriptomic approaches. These organisms were supported by flanking communities performing simpler fermentations to produce acetate and lactate. In experiments with glucose as the sole carbon source, augmentation with hydrogen gas increased MCCA production. Further, when transitioning from a synthetic medium containing glucose to a real food waste, the abundant taxa remained the same. Lastly, metabolic networks for MCCA production were reconstructed based on evidence from metagenomic and metatranscriptomic analyses and suggest energetic drivers for MCCA production.



Number of Pages

193 p.

Available for download on Thursday, April 17, 2025