Kimchi fermentation is governed by complex interactions among lactic acid bacteria (LAB), complicating the rational design of multi-strain starters. In this study, an integrated multi-omics approach was applied to evaluate LAB co-culture interactions and identify optimal strain combinations. Four flavor-related strains (FLs) and four function-related strains (FUs) were arranged in a 4×4 matrix and analyzed using quantitative microbial community profiling and GC–MS-based metabolomics. Co-cultures exhibited diverse, predominantly asymmetric interaction types that were strongly strain-dependent. Co-cultivation reshaped metabolic pathway selection rather than simply increasing total metabolite production, leading to distinct differences in mannitol, γ-aminobutyric acid (GABA), and biogenic amine accumulation. Stepwise screening identified FL3–FU3 as the optimal combination, demonstrating stable coexistence and enhanced production of desirable metabolites, with no increase in biogenic amines. These results highlight the importance of integrating microbial interactions and metabolic analyses for rational starter design in fermented foods.

Nanoplastics (NPs) are increasingly prevalent in ecosystems and human food chains and pose potential health risks, necessitating effective removal strategies applicable to both environmental and intestinal conditions. However, bacteria capable of functioning in both contexts remain poorly explored. Here, the food-derived bacterium Leuconostoc mesenteroides CBA3656 exhibited high NP biosorption efficiency across a wide range of NP concentrations (10-200 ppm), pH values (3-9), and temperatures (4-55°C), along with rapid adsorption at short contact times. Biosorption behavior followed pseudo-first-order kinetics and the Langmuir isotherm model, indicating predominantly physical adsorption. Fourier-transform infrared spectroscopy revealed that functional groups such as PO, CO, and COC in cell wall and membrane components contribute to NP interactions. Under simulated intestinal fluid, strain CBA3656 outperformed other Leuconostoc mesenteroides strains, and in vivo experiments demonstrated significantly enhanced fecal excretion of NPs. These results identify strain CBA3656 as a promising microbial biosorbent for NP mitigation.

Sugar supplementation enhances kimchi palatability and lactic acid bacteria metabolism, yet its effects on fermentation remain underexplored. Using a defined consortium of nine kimchi-derived lactic acid bacteria, we examined fermentation following glucose, fructose, xylose, or raffinose supplementation. Sugar supplementation was associated with delayed increases of compounds, including γ-aminobutyric acid (GABA) and amino acids. Dynamic time warping estimated significant delays of approximately 15-16 days to reach control-comparable levels. Machine learning identified five metabolites (GABA, β-alanine, pyroglutamic acid, serine, and nicotinic acid) that distinguish sugar-treated from control samples (mean PRAUC >0.86 for all five). Sugar type was associated with distinct profiles, with raffinose showing prolonged sucrose abundance (mean PRAUC = 0.97) and xylose showing extensive group-specific increases, including xylitol (mean PRAUC = 1.00). Transcriptomics linked Lactobacillus strains to delayed metabolite increases and Weissella hellenica to sugar type-specific traits. These associative multi-omic findings connect sugar composition to metabolite-accumulation patterns in a defined-consortium kimchi fermentation model.

Alcohol consumption disrupts the gut–liver axis by impairing intestinal barrier integrity, altering gut microbiota, and inducing hepatic inflammation. This study investigated whether gut-derived lactic acid bacteria, Lacticaseibacillus paracasei WiKim0110, could attenuate alcohol-induced injury in mice. Alcohol feeding reduced body weight, increased liver weight, and elevated serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, whereas WiKim0110 supplementation significantly ameliorated these alterations. In the large intestine, WiKim0110 supplementation significantly increased the expression of the mucin-related genes Muc2, Muc3a, and the goblet-cell differentiation factor Atoh1, while reducing the LPS-sensing markers Tlr4 and Cd14, suggesting enhancement of mucus barrier-associated responses and attenuation of LPS-associated innate immune signaling. Notably, Lb. paracasei WiKim0110 markedly induced Reg3g expression, suggesting enhanced epithelial antimicrobial defense. Microbiome analysis revealed alcohol-induced dysbiosis characterized by decreased α-diversity and expansion of Escherichia–Shigella, whereas taxa, including Bacteroides, Akkermansia, and Romboutsia, were enriched in the ADW group, suggesting partial restoration of alcohol-induced gut dysbiosis. In the liver, WiKim0110 suppressed inflammatory and lipogenic genes (Il1b, Fasn, and Acaca) and enhanced antioxidant-related genes (Sod1 and Nfe2l2). Collectively, these findings suggest that Lb. paracasei WiKim0110 attenuates alcohol-induced gut–liver axis dysfunction and enhances intestinal barrier-related responses.

Sugar supplementation in kimchi enhances palatability and promotes carbohydrate metabolism in lactic acid bacteria, yet its effects on fermentation remain largely unexplored. We investigated how glucose, fructose, xylose, or raffinose supplementation affects kimchi fermentation and found that sugar addition delayed production of multiple compounds, including γ-aminobutyric acid (GABA) and amino acids. Dynamic time warping quantified delays exceeding 14 days for metabolites to reach control-comparable levels. Machine learning identified five metabolites (GABA, β-alanine, pyroglutamic acid, lactic acid, and nicotinic acid) that consistently distinguished sugar-treated from control samples (PRAUC>0.94). Sugar type distinctly influenced metabolite profiles: raffinose prolonged sucrose availability (PRAUC=0.97–1.00), while xylose induced extensive group-specific production, including putrescine and xylitol (PRAUC=1.00). Transcriptomic analysis linked Lactobacillus species to delayed metabolite production, while Weissella koreensis and Leuconostoc gelidum mediated sugar type-specific metabolic traits. This study provides mechanistic insights for modulating sugar composition to influence fermented product profiles.

Alcohol consumption disrupts the gut-liver axis by impairing intestinal barrier integrity, altering gut microbiota, and inducing hepatic inflammation. This study investigated whether gut-derived lactic acid bacteria (LAB), Lacticaseibacillus paracasei WiKim0110, could attenuate alcohol-induced injury in mice. Alcohol feeding reduced body weight, increased liver weight, shortened colon length, and elevated serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, whereas WiKim0110 supplementation significantly ameliorated these alterations. In the large intestine, alcohol suppressed mucin-related and goblet-cell differentiation genes (Muc2, Muc3a, Muc4, and Atoh1) and increased LPS-sensing markers (Tlr4 and Cd14). WiKim0110 reversed these changes by restoring mucin gene expression and significantly reducing Tlr4 and Cd14, thereby attenuating LPS-mediated innate immune activation and suppressing downstream NF-κB-mediated inflammatory signaling. Notably, Lb. paracasei WiKim0110 markedly induced Reg3g expression, suggesting enhanced epithelial antimicrobial defense. Microbiome analysis revealed alcohol-induced dysbiosis characterized by decreased α-diversity and expansion of Escherichia–Shigella, whereas WiKim0110 supplementation enriched beneficial taxa including Bacteroides, Akkermansia, and Romboutsia, indicating patial restoration of alcohol-induced dysbiosis was recovered. In the liver, WiKim0110 suppressed inflammatory and lipogenic genes (Il1b, Fasn, and Acaca) and enhanced antioxidant-related genes (Sod1 and Nfe2l2). Collectively, Lb. paracasei WiKim0110 protects against alcohol-induced gut-liver axis dysfunction by reinforcing mucosal barrier integrity and limiting inflammatory signaling.

Food-to-gut microbial transmission is well-established through the detection of fermented food-associated microbes in the human gut. However, the transcriptional reconfiguration that enables these bacteria to adapt during this ecological transition remains poorly understood. In this study, we established a unified gnotobiotic platform—pairing germ-free kimchi with a gnotobiotic mouse model—to dissect the strain-resolved transcriptional responses of lactic acid bacteria (LAB) to these two environments. Using three phylogenetically distant LAB genera originally isolated from the human gut and capable of driving kimchi fermentation, we performed comparative transcriptomic profiling to identify environment-specific transcriptional signatures. In the kimchi environment, LAB exhibited a survival-oriented transcriptional profile characterized by the upregulation of glutamine metabolism, sulfur-containing amino acid biosynthesis, and molecular chaperones, reflecting adaptation to the acidic and oxidatively stressful fermentation matrix. Conversely, transition to the mouse gut triggered a transcriptional shift toward substrate exploitation, which was marked by the induction of sugar phosphotransferase systems, mixed-acid fermentation pathways, and cell surface remodeling genes associated with host adhesion. Notably, while comparative genomic analysis revealed certain habitat-associated structural variations in metabolic clusters, these genomic features did not predict real-time mRNA expression levels, demonstrating a decoupling of the genotype and transcriptional phenotype. Our findings show that phylogenetically diverse LAB converge on similar transcriptional programs in response to specific ecological cues, suggesting that transcriptional plasticity, rather than genomic inventory alone, drives cross-habitat adaptation. This study provides a mechanistic framework for evaluating the adaptive capacity of probiotic candidates through the lens of transcriptional responsiveness.

Fermentation is driven by dynamic interactions between substrates and microbial communities. However, the complexity of natural consortia limits their predictive control. To address this problem, we developed a gnotobiotic kimchi model via inoculation with defined lactic acid bacterial (LAB) consortia and individual strains under controlled temperatures. Consortium fermentations exhibited temperature-dependent growth and acidification, with stable proliferation under 6 °C and 10 °C, whereas 15 °C induced a rapid shift in community structure. Phase normalisation revealed convergence of microbial and metabolite profiles along a shared successional pattern. Machine learning identified a nine-metabolite signature (lactate, sucrose, fructose, glycine, glucose, succinate, threonine, choline, and glutamate) that accurately classified the fermentation phases with robust performance across internal and external datasets. Network analyses highlighted Leuconostoc mesenteroides and Lactococcus lactis as keystone metabolic species, whereas mono-association fermentation uncovered strain-specific metabolic endpoints and strategies. These findings established a predictive framework for LAB-driven kimchi fermentation.

The global rise in obesity and its associated metabolic complications underscores the urgent need for safe and effective interventions. This study investigated the anti-obesity efficacy of a probiotic mixture containing Bifidobacterium breve BR3 and Lactiplantibacillus plantarum LP3 in C57BL/6 mice with high-fat diet (HFD)-induced obesity. After obesity was established by feeding a 60% kcal HFD, the probiotic mixture was administered orally for 4 weeks. Compared with the control group, mice receiving the L. plantarum LP3 and B. breve BR3 mixture exhibited significant reductions in body weight and total fat mass, as assessed by Dual-energy X-ray Absorptiometry (DXA) and Echo Magnetic Resonance Imaging (EchoMRI). The probiotic treatment also lowered serum Aspartate Aminotransferase (AST), Alanine Aminotransferase (ALT), and glucose levels, and attenuated lipid accumulation in both hepatic and epididymal adipose tissues. Transcriptomic profiling revealed upregulation of lipolytic genes (Sirt1, Pparα) and downregulation of lipogenic genes (Srebp1c, Fas), suggesting that the probiotic mixture promotes lipid catabolism while suppressing lipid synthesis. Additionally, serum adipokine levels were favorably modulated, indicating improved metabolic homeostasis. Gut microbiota analysis demonstrated an increased relative abundance of beneficial genera, including Akkermansia and Bacteroides, highlighting a microbiome-mediated contribution to the observed metabolic benefits. Overall, our findings indicate that the combined administration of Lactiplantibacillus plantarum LP3 and Bifidobacterium breve BR3 exerts multi-faceted anti-obesity effects by enhancing lipolysis, regulating lipid metabolism, and restoring a healthy gut microbial balance. This probiotic mixture represents a promising therapeutic approach for managing obesity and related metabolic disorders.

Recent studies aim to prevent kimchi spoilage and enhance the sensory and nutritional qualities using lactic acid bacteria, particularly Leuconostoc species, as kimchi starters. However, the factors enabling the successful adaptation and predominance of Leuconostoc species remain unclear. This study investigates the factors that contribute to the successful adaptation of Leuconostoc starter strains WiKim32, WiKim33, WiKim0121 and CBA3628 during kimchi fermentation using a comprehensive multi-omics approach. Our findings reveal that ATP-dependent molecular chaperones, which respond to cold and acidic kimchi environments, play crucial roles in successfully adapting Leuconostoc starter strains. Moreover, genes involved in carbohydrate metabolic pathways enhance ATP production, thereby supporting chaperone activity and bacterial growth. This study highlights the practical use of Leuconostoc starter strains WiKim32, WiKim33 and WiKim0121 and identifies essential factors for their successful adaptation and predominance during kimchi fermentation.

A novel Gram-stain-positive, non-spore-forming, non-motile and rod-shaped bacterium, designated strain CBA3109 T , was isolated from jogae-jeotgal (fermented clam), a traditional Korean fermented seafood. Strain CBA3109 T showed growth at 10–30 °C (optimum, 25 °C) and pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 0–15% (w/v) NaCl (optimum, 5%). Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain CBA3109 T belonged to the genus Brevibacterium , with the highest similarities to Brevibacterium aurantiacum NCDO 739 T (98.26%) and B. antiquum VKM Ac-2118 T (98.14%). Strain CBA3109 T contained MK-8(H 2 ) as the major menaquinone. The cell wall peptidoglycan contained meso -diaminopimelic acid. The major fatty acids (>10%) were anteiso-C 15 : 0 and anteiso-C 17 : 0 . The main polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The average nucleotide identity and digital DNA–DNA hybridization values between strain CBA3109 T and the closest species were 86.2–87.0% and 31.1–33.0 %, respectively. The DNA G+C content of strain CBA3109 T was 62.7%. Based on the morphological, phylogenetic, chemotaxonomic and genotypic data, strain CBA3109 T represents a novel species of the genus Brevibacterium , for which the name Brevibacterium koreense sp. nov. is proposed. The type strain is CBA3109 T (= KACC 23387 T = DSM 117564 T ).

Fermentation has been a long-established method for preserving food, enhancing their nutritional value, and improving their sensory properties. While lactic acid bacteria (LAB) have been extensively studied, the role of bacteriophages in microbial dynamics during fermentation remains underexplored. In this study, we employed metagenomic analysis to investigate bacterial and viral communities in traditional Korean fermented products, kimchi and rice beer. LAB such as Weissella, Latilactobacillus, Lactiplantibacillus, and Pediococcus became predominant during fermentation, with phages influencing microbial succession by targeting specific bacterial strains. Additionally, phages containing host-beneficial viral genes were particularly abundant in rice beer, potentially enhancing bacterial fitness and survival under fermentation-related stress conditions. These findings indicate a crucial role of phages in shaping microbial communities by lysing specific strains and helping bacterial dominance through viral genes. This study provides valuable insights into microbial ecology and highlights avenues for optimizing fermentation processes.

Two Gram-stain-positive, facultatively anaerobic, rod-shaped, and non-motile lactic acid bacterial strains, designated as strains CBA3605T and CBA3606T, were isolated from kimchi, a traditional Korean fermented food. Both strains were oxidase- and catalase-negative, non-spore-forming, non-hemolytic, and non-gas-producing. Optimal growth conditions for the two strains were observed at 30°C, pH 5.0, and 0% NaCl. The two genomes were composed of a circular chromosome and three plasmids and the DNA G + C content of 43.0%, respectively. Strains CBA3605T and CBA3606T were most closely related to Lactiplantibacillus (Lp.) pingfangensis 382-1T with 16S rRNA sequence similarity of 99.4% and 99.1%, respectively. However, the orthologous average nucleotide identities between CBA3605T and CBA3606T were 91.7%, and those with strain 382-1T were 76.9% and 76.5%, respectively. Digital DNA–DNA hybridization values between CBA3605T and CBA3606T were 45.0%, and those with strain 382-1T were 21.4% and 21.0%, respectively. The major fatty acids detected in both strains included C16:0, C18:1 ω9c, and summed features 7 (C19:1 ω7c, C19:1 ω6c, C19:0 cyclo ω10c, and/or C19:0 ω6c). The peptidoglycan of both strains CBA3605T and CBA3606T contained meso-diaminopimelic acid and was classified as A4α type (L-Lys–D-Asp). In polar lipid analyses, only strain CBA3605T contained aminophosphoglycolipid, which was absent in CBA3606T, although both strains harbored same major polar lipids (diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine). Based on phenotypic, phylogenetic, genomic, biochemical, and chemotaxonomic analyses, strains CBA3605T and CBA3606T represent two novel species of the genus Lactiplantibacillus, for which the names Lactiplantibacillus koreensis sp. nov. and Lactiplantibacillus kimchii sp. nov. are proposed, with CBA3605T (= KACC 81073BPT = JCM 37965T), and CBA3606T (= KACC 81074BPT = JCM 37966T) as the type strains.

The novel strain CBA3628(T) was isolated from kimchi, a Korean fermented vegetable. CBA3628(T) is a cocci-shaped, Gram-stain-positive, catalase- and oxidase-negative and facultatively anaerobic bacterium. The results of phylogenetic analysis based on 16S rRNA gene sequencing indicated that CBA3628(T) represented a member of the genus Leuconostoc of the family Leuconostocaceae. CBA3628(T) has a circular chromosomal genome and three plasmids of 1 864 558 bp (37% DNA G+C content), containing 1,887 genes, 1,762 predicted protein-coding genes, 4 complete rRNA loci and 70 tRNA genes. The cells were non-haemolytic, non-motile and non-spore forming. The optimal growth of CBA3628(T) occurred at 30 degrees C, pH 6.0 and with 0-2% (w/v) NaCl. The major polar lipids of CBA3628(T) were diphosphatidylglycerol and phosphatidylglycerol. The major fatty acids (>10%) of CBA3628(T) were C-16:0, C-20:0 and C-19:0 cyclo omega 8c. CBA3628(T) contained A3 alpha-type peptidoglycans. CBA3628(T) was most closely related to Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293(T), L. mesenteroides subsp. dextranicum DSM 20484(T) and L. suionicum DSM 20241(T) with 99.52% 16S rRNA gene sequence similarity. However, the average nucleotide identities of 91.9%, 91.7% and 91.1% and the digital DNA-DNA hybridisation values of 45.6%, 45.4% and 45.4% indicated that the novel isolate represented a distinct species. Phylogenetic analyses of both the 16S rRNA gene and genome sequences revealed that CBA3628(T) formed a distinct phylogenetic lineage within the genus Leuconostoc and was most closely related to Leuconostoc litchii MB7(T). The ANI and dDDH values between CBA3628(T) and L. litchii MB7(T) were 84.9 and 22.8%, respectively. Functional genes belonging to COG categories E, J and K were enriched in the genome of CBA3628(T) (>7.9%). On the basis of its physiological, chemotaxonomic, phylogenetic and genomic properties, strain CBA3628(T) represents a novel species from the genus Leuconostoc, for which we propose the name Leuconostoc koreense sp. nov., with the type strain CBA3628(T) (= KACC 23049(T) = DSM 116836(T)).

The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and affected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably different, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome influences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fiber diets, for example, present beneficial effects through the production of short-chain fatty acids. Additionally, genetically modified probiotics to secrete some beneficial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.

A Gram-stain-positive, non-spore-forming, and obligate anaerobic bacteria designated strain CBA3647T was isolated from a horse faecal sample in Jeju, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA3647T formed a distinct phyletic lineage from closely related species within the genus Peptostreptococcus. Based on comparative analysis of 16S rRNA gene sequences, Peptostreptococcus anaerobius ATCC 27337T is most closely related to strain CBA3647T with a 16S rRNA gene similarity of 98.31 %, while similarity to other type strains is below 98.0 %. The genomic DNA G+C content of strain CBA3647T was 30.0 mol%. The digital DNA–DNA hybridization values between strain CBA3647T and the six Peptostreptococcus species were equal to or less than 24 %. Cells were non-motile and oval-shaped cocci with catalase-positive and oxidase-negative activities. Growth occurred at 20–40 °C (optimum, 35 °C), pH 6–8 (optimum, pH 7), and in the presence of 0–2 % (w/v) NaCl (optimum, 1 %). Strain CBA3647T contained C14 : 0 iso and C16 : 0 as major fatty acids. Phenotypic, chemotaxonomic, and molecular properties of strain CBA3647T suggest that it represents a novel species in the genus Peptostreptococcus, which has been named Peptostreptococcus equinus sp. nov. The type strain is CBA3647T (=KACC 22891T= JCM 35846T).

Two Gram-stain-positive, facultatively anaerobic, non-hemolytic, coccoid-shaped bacterial strains, designated MS01T and MS02, were isolated from cabbage watery kimchi in the Republic of Korea. Cellular growth occurred at 5–25 ℃ (optimum, 20 ℃), pH 5–8 (optimum, pH 7) and in the presence of 0–5

Existing research has underscored the vital interplay between host organisms and their associated microbiomes, which affects health and function. In both plants and animals, host factors critically shape microbial communities and influence growth, health, and immunity. Post-harvest plants, such as those used in kimchi, a traditional Korean dish, offer a unique avenue for exploring host-microbe dynamics during fermentation. Despite the emphasis on lactic acid bacteria (LAB) in fermentation studies, the roles of host factors remain unclear. This study aimed to investigate the influence of these factors on plant transcriptomes during kimchi fermentation. We individually inoculated nine LAB strains into germ-free kimchi to generate LAB-mono-associated gnotobiotic kimchi and performed RNA-sequencing analysis for the host vegetables during fermentation. The transcriptomes of post-harvest vegetables in kimchi change over time, and microbes affect the transcriptome profiles of vegetables. Differentially expressed gene analyses revealed that microbes affected the temporal expression profiles of several genes in the plant transcriptomes in unique directions depending on the introduced LAB strains. Cluster analysis with other publicly available transcriptomes of post-harvest vegetables and fruits further revealed that the plant transcriptome is more profoundly influenced by the environment harboring the host than by host phylogeny. Our results bridge the gap in understanding the bidirectional relationship between host vegetables and microbes during food fermentation, illuminating the complex interplay between vegetable transcriptomes, fermentative microbes, and the fermentation process in food production. The different transcriptomic responses elicited by specific LAB strains suggest the possibility of microbial manipulation to achieve the desired fermentation outcomes.

Kimchi is a traditional fermented vegetable side dish in Korea and has become a global health food. Kimchi undergoes spontaneous fermentation, mainly by lactic acid bacteria (LAB) originating from its raw ingredients. Numerous LAB, including the genera Leuconostoc, Weissella, and Lactobacillus, participate in kimchi fermentation, reaching approximately 9-10 log colony forming units per gram or milliliter of food. The several health benefits of LAB (e.g., antioxidant and anti-inflammatory properties) combined with their probiotic potential in complex diseases including obesity, cancer, atopic dermatitis, and immunomodulatory effect have generated an interest in the health effects of LAB present in kimchi. In order to estimate the potential of kimchi as a probiotic food, we comprehensively surveyed the health functionalities of kimchi and kimchi LAB, and their effects on human gut environment, highlighting the probiotics function.