Abstract
Anaerobic microbial communities have immense waste-degrading potential, but further characterization is necessary to understand and utilize these consortia. Cultivating microbial communities is valuable for product generation and for evaluating waste degradation, but challenges exist for both natural microbial
communities derived from environmental samples and synthetic communities established by growing isolated microbial strains together. Natural microbial consortia lack characterization and are less controllable; these communities are complex with many diverse microbial members, but with the vast number of undefined members, it is difficult to restrict these communities to the particular metabolic processes of interest. On the other hand, synthetic microbial consortia can be more restricted to certain metabolic processes since only specific isolated strains are employed. However, loss of microbial members often occurs over time (or early on) in these communities. 

 

This research focuses on characterizing microbial members of degradative anaerobic environments, with cultivation as a way of enriching less abundant strains that may be missed by sequencing directly from environmental samples. We utilized amplicon sequencing and whole-genome shotgun sequencing to characterize microbial communities, and genomic and transcriptomic sequencing to characterize a novel fungal isolate. Many microbial members in these environments were identified to possess numerous genes predicted to encode carbohydrate active enzymes that are involved in the breakdown of recalcitrant substrates. 

 

Synthetic microbial communities were also engineered in this research based on pairings naturally found in the guts of large herbivores. Namely, anaerobic gut fungi and chain-elongating bacteria were combined in vitro to convert lignocellulose into short- and medium-chain fatty acids. In coculture, Pseudoramibacter alactolyticus and Neocallimastix spp. can be stable and metabolically active (based on consistent metabolic output over time and bacterial RNA sequencing data in coculture compared to monoculture). This system, both in terms of its design based on flow of metabolites in a natural system and methods used for cocultivation, provides a basis for designing stable, synthetic, fully anaerobic microbial communities for consolidated bioprocessing of lignocellulose to short- and medium-chain fatty acids.