The human microbiota and epigenetic processes have both been shown to play a crucial role in health and disease. However, there is extremely scarce information on epigenetic modulation of microbiota members except for a few pathogens. Mainly DNA adenine methylation has been described extensively in modulating the virulence of pathogenic bacteria in particular. It would thus appear likely that such mechanisms are widespread for most bacterial members of the microbiota. This review will present briefly the current knowledge on epigenetic processes in bacteria, give examples of known methylation processes in microbial members of the human microbiota and summarize the knowledge on regulation of host epigenetic processes by the human microbiota.
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.
Microbial communities during grape wine fermentations are diverse and dynamic.High-throughput sequencing (molecular methods enabling precise identification of microbial communities), was used to identify fungal diversity during fermentation of grape juice with different sulfite levels and yeast inoculations. Fermentation (0, 14, and 21 days) was evaluated on two grape varieties, Noble (Vitis rotundifolia) and Vignoles (Vitis hybrid) fermented at three sulfite levels (0, 10, and 20 mg/L) and three yeast inoculations (Uninoculated, Saccharomyces cerevisiae, and Torulaspora delbrueckii). Fungal taxonomy of both varieties included 6-7 phyla and 115-129 genera. Indigenous microbiota was impacted by sulfite levels and yeast inoculations but varied by grape variety. Sulfite levels had minimal impact on fungal communities but affected fermentation
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