Microbiota profiles and dynamics in fermented plant‐based products and preliminary assessment of their in vitro gut microbiota modulation

Abstract

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.

Microorganisms in Whole Botanical Fermented Foods Survive Processing and Simulated Digestion to Affect Gut Microbiota Composition

“…Lactobacillus and Bifidobacterium relative abundance was lower than the control but were two times and 10 times higher, respectively, than the sauerkraut samples. During the early stages of sauerkraut fermentation, Enterobacteriaceae levels in the food matrix have been shown to remain high ( Lavefve et al, 2021 ). Our study, concurrent with others, observed increasing LAB counts during fermentation, with a peak at around 13days.…”

“…Few studies explore how being part of a whole fermented food matrix affects microbial viability during fermentation, storage, and gastrointestinal (GI) transit ( Buriti et al, 2010 ; Fiorda et al, 2016 ; Valero-Cases et al, 2017 ; Yang et al, 2020 ). Even fewer investigate the effect of whole fermented food consumption on the gut microbiota ( Lavefve et al, 2021 ). The human gut microbiota is an important dietary target, with its central regulatory role in immune function and energy metabolism ( Gille et al, 2018 ).…”

“…Lactis ; (formerly Lactobacillus lactis ), yeasts (most notably Saccharomyces spp. ), and bioactive components ( Marsh et al, 2013 ; Laureys and De Vuyst, 2014 ; Lavefve et al, 2021 ). In vitro tests of Saccharomyces cerevisiae strain C41 and Lacticaseibacillus paracasei CT12 (formerly Lactobacillus paracasei ) isolated from tibicos showed similar probiotic activity to established comparable probiotic strains, with good resistance to gastric pH, bile salts, and in vitro digestive fluids ( Romero-Luna et al, 2017 , 2019 , 2020 ).…”

To Other Planets With Upgraded Millennial Kombucha in Rhythms of Sustainability and Health Support

“…Lactic acid bacteria are involved in the fermentation process in some KMC ecotypes (Chakravorty et al, 2016;Coton et al, 2017). The most beneficial genera detected in KMC samples were Bacteroides and Prevotella, which are known as dominant human gut microbiota members (Lavefve et al, 2021). Metagenomics studies also predicted opportunistic bacteria like Bacillus, Pseudomonas, etc.…”

“…Cellulose is useful for digestion because it stimulates the work of intestines that increases stool bulk and water absorption, and, thereby, decreases the gastrointestinal transit time. Earlier, we proposed KMC as a source of prebiotic for astronauts (Kozyrovska et al, 2012), and most recently, kombucha fermentation was reported to produce SCFAs (Utoiu et al, 2018;Annunziata et al, 2020) or support a significant potential prebiotic effect (Lavefve et al, 2021). The AAB, producing cellulose, are food-grade (Alexandraki et al, 2013) or GRAS bacteria (Gorgieva and Trček, 2019), which gives Komagataeibacter species potential for pro/pre/postbiotic use.…”