AbstractSprouts are popular for health conscious and vegetarian consumers; however, this produce item has been associated with frequent foodborne outbreaks. To understand the influence of the sprouting environment on the microbiota colonizing the sprout, microbial populations of both sprouting seeds and sprouts were characterized using terminal fragment length polymorphism analysis. The dominant microbial populations on mung bean, alfalfa, and broccoli seeds over the course of germination were compared to the microbiota of commercially grown sprouts that were grown from seeds from the same distributer. Regardless of the initial population, similar organismal families were found on all final sprout varieties and was primarily composed of Pseudomonadaceae. Commercially germinated sprout varieties had lower abundances of Pseudomonadaceae for all three varieties, and housed more diverse microbial families, such as Bacillaceae, Sphingomonadaceae, Phyllobacteriacae, and Lactobacillaceae.Practical applicationsObservations from this manuscript can be used to better understand the impact the sprouting environment has on the microbial population of the final sprout product. The microbiota of sprout varieties, as described in this manuscript, may help understand microbial spoilage factors of sprout products. By understanding the microbial populations of sprouts, the observed benefits of sprouting seeds/beans in previously used sprout water and the use of competitive exclusion techniques can progress forward.