Introduction

The human gastrointestinal tract harbors a large and dynamic community of microorganisms collectively referred to as the gut microbiota [1]. This complex ecosystem plays a crucial role in preserving host health through its involvement in various physiological processes such as nutrient metabolism, immune modulation, preservation of gut barrier integrity, and protection against pathogens [1,2,3,4]. Disruptions in the composition or function of the gut microbiota, commonly known as dysbiosis, are associated with various chronic diseases such as obesity, type 2 diabetes (T2D), inflammatory bowel disease (IBD), and colorectal cancer [5, 6].

Among the environmental factors that shape the gut microbiome, diet has the most profound and modifiable influence [3, 7]. Short-term dietary changes can rapidly alter microbial composition, whereas long-term dietary patterns help determine the stability and diversity of the gut ecosystem [8, 9]. A high consumption of fiber- and polyphenol-rich diets increases gut microbial diversity and enriches beneficial taxa within Ruminococcaceae and Lachnospiraceae [10]. Conversely, a high intake of Western-style diets that are abundant in fats, sugars, and ultra-processed ingredients can reduce gut microbial richness and increase the abundance of pro-inflammatory species [11].

Plant-based diets are rich in fiber, polyphenols, antioxidants, and unsaturated fats [12, 13], which can contribute to long-term weight maintenance and reduce insulin resistance, dyslipidemia, high blood pressure, and inflammation [14,15,16,17,18]. Several studies have uncovered the association between the consumption of plant-based foods and human health. According to a meta-analysis of 55 prospective cohort studies, higher adherence to a plant-based dietary pattern, including whole grains, vegetables, fruits, and legumes, was associated with a lower risk T2D, cardiovascular diseases, and cancer [19]. Moreover, plant-based diets may alter the composition and metabolic pathways of gut microbiota, influencing gut health [20]. For instance, the consumption of fruits and vegetables was inversely associated with the development of IBDs, such as ulcerative colitis and Crohn’s disease [21].

The Asian population, particularly in South Korea, consumes more plant-based foods than Western populations, with approximately 78% of the Korean diet consisting of plant-based foods—though this proportion has slightly decreased over the past decade [22,23,24,25]. Furthermore, many Asians have traditionally stored and consumed plant foods through fermentation. In South Korea, fermented plant foods, such as fermented soybeans and cabbages, have been consumed for over 2000 years, rooted in the country’s long-standing farming culture [26, 27]. This long history of fermentation has relied on naturally occurring microbial communities and the addition of specific starter cultures [28]. Lactic acid bacteria (LAB), including species belonging to Lactobacillus, Lactococcus, Streptococcus, and Leuconostoc, as well as fungi, including yeasts, contribute to the complex microbial ecosystems involved in plant-based fermentation [29].

Fermented foods are produced through controlled microbial growth and the enzymatic conversion of various food components [30]. Fermentation enhances digestibility and nutritional value, resulting in a rich source of functional microbes and microbial metabolites. Recent advances in high-throughput sequencing and metabolomics have enabled the detailed characterization of microbial communities and functional compounds present in fermented plant foods, shedding light on their potential roles in host health and physiology. For instance, a large longitudinal cohort study in the USA investigated the gut microbiome and metabolic markers associated with the consumption of fermented plants [31]. The consumption of fermented plant foods was associated with a higher abundance of several gut microbial taxa, such as Bacteroides spp., Pseudomonas spp., and Dorea spp., as well as elevated levels of conjugated linoleic acid, a metabolite with health-promoting properties [31]. It was hypothesized that the production of conjugated linoleic acid may be attributed to microbial taxa associated with fermented plant intake, highlighting the interplay between diet, microbes, and bioactive metabolites.

Building on these insights, this review summarizes recent preclinical, clinical, and mechanistic research findings on the effects of fermented plant foods on gut microbial communities and their contributions to intestinal and systemic health.

Microbial composition and functional metabolites in fermented plant foods

Fermented soybean foods

Fermented soybean foods are widely consumed in East and Southeast Asia and are typically produced through the microbial fermentation of soybeans.

Cheonggukjang

Cheonggukjang is a traditional Korean short-term fermented soybean paste, produced by fermenting steamed soybeans for 2 to 3 days, traditionally using rice straw as a source of Bacillus species [32]. A recent study identified strains responsible for the production of tyramine, a biogenic amine (BA) [33]. Shotgun metagenomic sequencing revealed that Bacillus species, particularly Bacillus piscis, dominated the microbial community and correlated with tyrosine metabolism, suggesting its involvement in tyramine production. These results are consistent with those of previous studies finding Bacillus thermoamylovorans as dominant [34], reinforcing that Bacillus species form a conserved core microbiota in cheonggukjang. Glycine, glutamic acid, histidine, and tyrosine were the most abundant free amino acids, reflecting active microbial amino acid biosynthesis during fermentation [34]. Recent studies have suggested that the overall community structure can vary depending on the manufacturing methods and regional microbiota. For instance, some traditional cheonggukjang samples were enriched with Lactobacillus species, such as Lactobacillus sakei (L. sakei), while others were dominated by Bacillus licheniformis [35]. Although Firmicutes and Bacilli were the dominant phyla and classes across all samples, the relative abundance of taxa at lower taxonomic levels, including Lactobacillaceae, Bacillaceae, and Enterococcus faecium, varied depending on their origins (Table 1).

Meju-based fermented soybean products: Doenjang and Ganjang

Unlike the short-term fermentation of cheonggukjang, doenjang (paste) and ganjang (soy sauce) are produced via a long-term, two-stage fermentation involving a solid-state fermented soybean brick, meju. It is subsequently fermented in brine and then separated into solid (doenjang) and liquid (ganjang) fractions for further aging [36, 37]. Microbial succession during meju fermentation is critically influenced by temperature. Bacillus dominates at high temperatures, whereas LAB such as Weissella and Latilactobacillus prevail at low temperatures [38]. In doenjang ferments, genera such as Leuconostoc, Logilactobacillus, and Tetragenococcus are predominant, regardless of the fermentation conditions. In the fungal community, Mucor was dominant in meju, whereas Debaryomyces was dominant in doenjang, with fungal succession largely unaffected by temperature.

In addition to temperature, variations in fermentation characteristics among different manufacturers lead to distinct the microbial and metabolic profiles. A comparative analysis of doenjang-meju revealed two distinct fermentation types—Bacillus dominated and LAB dominated—and fermentation was performed primarily by Enterococcus [39]. These microbial profiles were associated with distinct metabolic signatures, including differences in the concentrations of sugars, organic acids, BAs, and volatile compounds. The LAB-dominated samples contained fewer volatile compounds, and Bacillus and LAB exhibited a strong negative relationship. Bacterial species produce specific metabolites, including lactate (Enterococcus), flavonoid aglycones (LAB), and putrescine (Bacillus). Another comparative study identified doenjang was enriched with functional compounds, such as isoflavones, soyasaponins, and amino acids, as well as the bacterial genera Debaryomyces and Staphylococcus [40]. In contrast, ganjang contained elevated levels of BAs, phenylpropanoids, and the taxa Meyerozyma and Tetragenococcus [40].

In ganjang, the fermentation shifts the microbial community from meju-derived microbes to halophilic or halotolerant microbes from solar salts, such as Debaryomyces, Tetragenococcus, and Staphylococcus [41]. Salinity and meju proportion are key factors; Tetragenococcus was linked to lactate in low-salt batches, whereas Staphylococcus was enriched in high-salt batches. Debaryomyces remained abundant across all salt levels. Metabolite profiling revealed that carbohydrate and amino acid levels were largely influenced by the proportion of meju, while salt concentration played a lesser role. These findings suggest that amino acid production in ganjang is primarily driven by endogenous proteases present in meju rather than by microbial proteolytic activity during fermentation. While Bacilli were dominant at the class level, substantial variation exists at lower taxonomic levels (e.g., Lactobacillales vs. Bacillales) depending on fermentation conditions, influencing the final bioactive compounds [42, 43]. The above description is summarized in Table 1.

Gochujang

Gochujang is a long-term (≥ 6 months) fermented paste made from powdered meju, red pepper, a malted rice mixture, and salt [36, 37]. This process develops a diverse microbial community, dominated by the phylum Firmicutes [44]. B. subtilis and Bacillus licheniformis are the predominant species, and several region-specific bacterial species were identified, including Bacillus sonorensis, Bacillus pumilus, and Weissella salipiscis [44]. To support this regional variation, the analysis of 73 traditionally made gochujang samples from five provinces in South Korea identified significant geographic differences in bacterial composition and functional attributes [45]. Although Bacillus spp. remained the predominant genus across regions, samples from Kyungsang Province showed a marked reduction in the abundance of Bacillus species, along with an increase in the abundance of Enterococcus and Staphylococcus species [45]. Despite these microbial shifts, the levels of histamine and tyramine were not significantly different across regions [45] (Table 1).

Natto

Natto is a traditional Japanese fermented soybean food produced by fermenting steamed soybeans with a starter culture of B. subtilis var. natto (commonly known as Bacillus natto) for 18–20 h at 40–45 °C [46, 47]. This bacterium contributes to the proteolysis and transformation of soy components, enhancing their digestibility and bioactivity. Among key functional products secreted during fermentation, nattokinase is a fibrinolytic enzyme with potential cardiovascular benefits [48, 49]. Fermentation leads to the degradation of anti-nutritional factors, such as trypsin inhibitors, and the formation of extracellular polymers composed of glutamic acid, amino acids, and fructans, which contribute to the slimy and sticky texture of natto [47]. In addition to these macroscopic changes, a recent untargeted metabolomics study found significant chemical differences between soybeans and natto, identifying 160 differentially abundant metabolites, including amino acids, flavonoids, alkaloids, and nucleotides [50]. Another metabolomic analysis of the production of poly-γ-glutamic acid (γ-PGA), which is responsible for the slimy texture of natto, identified 257 key metabolites that were differentially abundant between high- and low-γ-PGA-producing natto and soybean substrates [51]. Enrichment analysis revealed that the metabolites involved in the synthesis of purines, nucleotides, fructose/mannose, and isoflavonoids were significantly altered, providing a biochemical basis for optimizing natto fermentation and diversifying its characteristics.

Building on this metabolomic insight into the biochemical complexity of natto, recent advances in microbial co-fermentation strategies aim to enhance its functionality. The co-fermentation strategies with Lactobacillus, Bifidobacterium, or Mucor strains can significantly increase nattokinase and protease activities, as well as free amino nitrogen content, compared to single-strain fermentation [52, 53]. This approach also reduced the levels of BAs, particularly tyramine and cadaverine, while improving sensory acceptance. The above description is summarized in Table 1.

Tempeh

Tempeh is a traditional Indonesian food made from the solid-state fermentation of boiled soybeans inoculated with the fungus Rhizopus spp. The production process involves sequential steps such as soaking, dehulling, boiling, inoculation, and incubation [54], which create favorable conditions for microbial growth and enzymatic activity. Soaking initiates natural acidification, which suppresses the growth of pathogenic microorganisms. A metagenomic analysis of soaking water during tempeh production identified ten major bacterial genera, including Prevotella, Bacillus, Paenibacillus, Staphylococcus, and Lactobacillus [55]. The soaking process can be optimized by co-inoculation with Lactiplantibacillus plantarum [56]. A targeted metabolomic study revealed that soaking soybeans with L. plantarum or Pichia burtonii led to significant changes in the metabolite profile of tempeh [57]. This process increased the levels of amino acids and bioactive compounds and decreased the levels of sugars, indicating potential advantages for enhancing tempeh quality through microbial intervention.

After soaking and inoculation, the fermentation stage begins, during which fungal activity by Rhizopus mycelium becomes dominant and binds soybeans into a cohesive matrix [58]. Fermentation enhances the nutritional profile through the enzymatic hydrolysis of proteins, lipids, and isoflavone glycosides and improves the bioaccessibility of minerals, such as iron [59, 60]. Shotgun metagenomic analysis of tempeh samples revealed a high prevalence of genes related to iron acquisition, such as the iron complex outer membrane receptor protein [61]. The predominant bacterial phyla were Proteobacteria, Firmicutes, and Bacteroidetes, with representative species including Lactobacillus fermentum, Enterococcus cecorum, and Klebsiella pneumoniae. During over-fermentation, the community shifts toward yeasts belonging to the order Mucorales (Kluyveromyces marxianus, Candida spp., and Trichosporon spp.) and LAB (Lactobacillus agilis and Lactococcus spp.), accompanied by changes in metabolite composition [62]. Sugars and sugar alcohols such as gentiobiose and galactinol accumulated during early fermentation and declined over time. In contrast, amino acids such as glutamine and bioactive compounds such as the isoflavones daidzein and genistein increased progressively up to 72 h [63] (Table 1).

Fermented vegetable food: Kimchi

Kimchi is a traditional Korean dish, widely consumed as fermented cabbage in Northeast Asian countries. Recently, kimchi has drawn global attention for its symbiotic properties, as it contains non-digestible fibers, probiotics, and prebiotics [64]. Moreover, various health-promoting metabolites are produced during kimchi fermentation, which are not easily obtained from any single food source [64].

Kimchi is commonly fermented through lactic acid fermentation. Kimchi is made by salting various vegetables with condiments. There are more than two hundred varieties of kimchi depending on the major ingredients and preparation methods [65]. It can be produced with several vegetables (cabbage, radishes, cucumbers, mustard leaves, and green onions), spices (red pepper powder, garlic, and ginger), sugar, and fish sauce [66, 67]. Cabbage is the main ingredient [68] and is usually fermented with microorganisms that naturally exist in raw ingredients at temperatures below 10 °C [69].

The dominant microorganisms in kimchi are Leuconostoc, Lactobacillus, and Weissella; however, the microbial composition depends on the raw ingredients and environmental factors [67, 69]. During fermentation at temperatures from 4 to 10 °C, Leuconostoc gelidum is found at 4 °C, whereas L. plantarum and L. spicheri are detected in late fermentation at a temperature of 10 °C. W. confusa is found independently of temperature throughout the entire fermentation process [70]. Salinity also affects microbial composition. L. sakei is identified at a high salinity (1.6–2.1%) after 2 weeks of fermentation, while Leuconostoc mesenteroides, Leuconostoc lactis, and Weissella soli are present independently of salinity [71]. As essential ingredients, red pepper powder increases the proportion of Weisella, while allicin in garlic stimulates the growth of LAB [72, 73]. Different types of microbiomes were found depending on the varieties of jeotgal, a traditional salted fish consumed in South Korea. L. sakei and Weissella koreensis were predominant in salted anchovy and salted shrimp, respectively [74].

South Korea has four seasons, and kimchi is traditionally prepared in the fall and winter. However, modern refrigeration technologies allow for year-round production of kimchi. Seasonal harvesting affects microbial composition and demonstrates seasonal variations after 30 days of fermentation [75]. Microbial profiles differed between spring and fall. Latilactobacillus was dominant in fall-harvested kimchi, while Weissella prevailed in spring, summer, and winter. Hence, the metabolite profiles were similar in spring and summer. Aspartic acid, putrescine, and cadaverine predominated in spring and summer, whereas glutamic acid, tryptamine, and serine persisted throughout the fermentation process.

Kimchi also contains bioactive compounds derived from its main ingredients: sulforaphane, 3,3’-diindolylmethane, indole-3-carbinol, benzyl isothiocyanate, phenyl isothiocyanate, and allyl isothiocyanate from cabbage; capsaicin from red pepper; organosulfur compounds from garlic; and shogaol and gingerol from ginger. These compounds have anti-obesity, anti-cardiovascular, anti-inflammatory, anti-cancer, and anti-COVID-19 effects [64]. The above description is summarized in Table 1.

Clinical evidence: effects on human gut microbiota and health

Overall alterations in gut microbiota composition

Fermented soybean foods have beneficial effects on gut microbiota and host health. A large cross-sectional study involving 222 Korean adults revealed that the habitual intake of fermented foods such as doenjang and cheonggukjang was positively associated with gut microbial diversity and the relative abundance of Firmicutes genera, including Lactobacillus, Ruminococcus, and Eubacterium [76]. These associations were not observed in individuals who consumed non-fermented foods, suggesting that fermentation helps to modulate the gut microbiome. The consumption of fermented legumes, vegetables, nuts, and seeds was also associated with high alpha diversity of bacteria, particularly Ruminococcus. These findings underscore the potential of fermented soybean foods as key modulators of a healthy gut microbiome.

Cheonggukjang also influences gut microbiota and host metabolism. An interventional study involving 48 healthy Korean men investigated the gut microbiome and metabolomic responses to a 7-day intake of cheonggukjang [77]. The intake induced inter-individual shifts in B-type (Bacteroides), P-type (Prevotella), and R-type (Ruminococcaceae) enterotypes, reflecting the dynamic nature of the gut microbiome in response to the intake of fermented foods. Individuals with the R-type enterotype exhibited the most pronounced microbial shifts following cheonggukjang intake, including a significant decrease in the Firmicutes to Bacteroidetes (F/B) ratio, along with a decreased abundance of families Ruminococcaceae, Lachnospiraceae, and Streptococcaceae. At the genus level, the R-type group showed a decrease in the abundance of Faecalibacterium, Gemmiger, Coprococcus, and Streptococcus, while showing a significant increase in the abundance of Prevotella. Half of the R-type individuals transitioned to the P-type after the intervention, highlighting the responsiveness of this enterotype to dietary modulation. Individuals with the P-type enterotype had higher levels of 5-hydroxy equol, an isoflavone metabolite produced by Prevotella. Metagenomic analysis identified clusters of reductase genes associated with equol biosynthesis in these individuals, suggesting that enterotype-specific microbial functions underlie individual differences in metabolite production.

In addition, natto can modulate the composition and metabolic activity of gut microbiota. In a clinical intervention study, eight healthy adults in Japan maintained their habitual free-choice diet for 7 days (run-in), then consumed miso soup containing natto once daily for 2 weeks, followed by 7 days of the habitual diet (washout) [78]. Fecal samples were collected at baseline (day 0), during the intervention (days 7 and 14), and after the intervention (day 21) to assess changes in fecal microbiota, short-chain fatty acids (SCFAs), and putrefactive metabolites. The intervention meal consisted of 50 g of commercially available natto—containing approximately 9.0 × 109 CFU/g of B. subtilis—added to 200 mL of miso soup and boiled for 1 min. Despite heat treatment, the viability of B. subtilis spores was presumed to be retained because of thermal resistance. The intervent