We employ next generation sequencing to investigate microbial populations in the milk and manure of farm animals. We have surveyed the microbial populations in the milk and manure of dairy cows on commercial dairies in California. Work in ongoing to identify microbial communities in manure and milk and their contributions to nitrogen cycling and milk quality, respectively. We also use genetic information to study how goat casein genotypes are related to milk production parameters. Allelic variants of the a_s1-casein gene are being studied to determine if genotype is related to the amount of protein in milk. This information will be of great interest to producers as animals could be selected for cheese making or fluid milk production based on the alleles present as genetic variants which produce low levels of protein may be associated with the “non-allergenic” response, or ease of digestion some individuals experience ingesting goat milk, and those which produce high levels of protein correlate with greater cheese yield.