The brewing process differs slightly in craft breweries as compared to industrial breweries, as there are fewer control points. This affects the microbiota of the final product. Beer contains several antimicrobial properties that protect it from pathogens, such as low pH, low oxygen and high carbon dioxide content, and the addition of hops. However, these hurdles have limited power controlling spoilage organisms. Contamination by these organisms can originate in the raw materials, persist in the environment, and be introduced by using flavoring ingredients later in the process. Spoilage is a prominent issue in brewing, and can cause quality degradation resulting in consumer rejection and product waste. For example, lactic acid bacteria are predominately associated with producing a ropy texture and haze, along with producing diacetyl which gives the beer butter flavor notes. Other microorganisms may not affect flavor or aroma, but can retard fermentation by consuming nutrients needed by fermentation yeast. Quality control in craft breweries today relies on culturing methods to detect specific spoilage organisms. Using media can be beneficial for detecting the most common beer spoilers, such as Lactobacillus and Pediococci. However, these methods are time consuming with long incubation periods. Molecular methods such as community profiling or high throughput sequencing are better used for identifying entire populations of beer. These methods allow for detection, differentiation, and identification of taxa.

Consumption of fermented food has long been associated with health benefits, but there is still limited knowledge on the bacterial dynamics in plant‐based food fermentation outside of culture‐based studies. Different fermented plant‐based products were assessed for the presence of Archaea and their microbiota bacterial dynamics during the fermentation. Archaea were consistently detected in the brine of the vegetables, and constant increase in gene copy number throughout the fermentation of kraut indicated that Archaea were not only viable but actively growing. The plant‐associated bacterial microbiota of cabbage and jalapeno were dominated by Proteobacteria, specifically Pseudomonas (51% and 39% respectively), while the okra harbored roughly equal numbers of firmicutes and proteobacteria. In cabbage and jalapeno fermentations, lactic acid bacteria (LAB), which were detected in extremely low levels in raw products, became dominant with expected succession of heterofermentative and homofermentative species. These two stages were not detected in the fermentation of okra, and Lactobacillus remained the most abundant genera. The kombucha fermentation was dominated by Gluconacetobacter as reported previously, but also characterized by high abundance of Bacteroides. Intriguingly, the microbiota composition and dynamics were very different between the two kombucha batches tested, suggesting redundancy in microorganisms’ fermentative roles. Finally, a preliminary in vitro fermentation study was indicative of a potential bifidogenic effect of microbial metabolites from kombucha. Collectively, these data indicate that fermented plant products harbor a highly diverse microbiota, bacteria, and archaea, even after the end of the fermentation.