This study demonstrates how bioinformatics tools, such as metagenome functional prediction from 16S rRNA genes, can help understand biological systems and reveal microbial interactions in controlled systems (e.g., bioreactors). Results obtained from controlled systems are easier to interpret than those from human/animal studies because observed changes may be specifically attributed to the design conditions imposed on the system. Bioinformatics analysis allowed us to identify potential butyrogenic phylotypes and associated butyrate metabolism pathways when we systematically varied the PH 2 in a carefully controlled fermentation system. Our insights may be adapted to butyrate production studies in biohydrogen systems and gut models, since butyrate is a main product and a crucial fatty acid in human/animal colon health.