The host diet and the gut microbiota are directly related. In humans, intestinal bacteria ferment a portion of ingested dietary fiber to produce short-chain fatty acids (SCFAs), including butyrate, propionate and acetate. These bacteria are also capable, through putrefaction, of producing branched-chain fatty acids (BCFAs) from branched-chain amino acids (BCAAs). In this study we investigated the influence of the concentration of these fibers on the production rate of SCFAs and the possibility of using waste stream products from milling to produce these same fatty acids. We also analyzed the production of BCFAs from BCAAs. We observed that the concentration of dietary fiber seems to influence the rate of production of some SCFAs, such as acetic acid. We also found that milling waste increases the production of SCFAs, and amino acids increase the production of specific BCFAs but also SCFAs. These studies could be continued and expanded by analyzing more samples and varying the fiber, waste, and amino acids studied.