Effects of gnotobiotic fermentation on global gene expression of germ-free vegetables.

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.

Survival of O157 and non-O157 shiga toxin-producing Escherichia coli in Korean style kimchi.

Korean style kimchi contaminated with Shiga toxin-producing Escherichia coli (STEC) O157:H7 was the cause of an outbreak in Canada from December 2021 to January 2022. To determine if this STEC O157:H7 has greater potential for survival in kimchi than other STEC, the outbreak strain and six other STEC strains (O26:H11, O91:H21, O103:H2, O121:H19, and two O157:H7) were inoculated individually at 6 to 6.5 log CFU/g into commercially sourced kimchi and incubation at 4 °C. At intervals of seven days inoculated and control kimchi was plated onto MacConkey agar to enumerate lactose utilising bacteria. The colony counts were interpreted as enumerating the inoculated STEC, since no colonies were observed on MacConkey agar plated with uninoculated kimchi. Over eight weeks of incubation the pH was stable at 4.10 to 4.05 and the STEC strains declined by 0.7-1.0 log, with a median reduction of 0.9 log. The linear rate of reduction of kimchi outbreak STEC O157:H7 was -0.4 log per 30 days (Slope Uncertainty 0.05), which was not significantly different from the other O157 and nonO157 STEC strains (P = 0.091). These results indicate that the outbreak was not due to the presence of strain better adapted to survival in kimchi than other STEC, and that STEC can persist in refrigerated Korean style kimchi with a minimal decline over the shelf-life of the product.

Does kimchi deserve the status of a probiotic food?

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.

A comprehensive assessment of the antimicrobial and immunomodulatory effects of frequently consumed fermented foods: insights in the management of COVID-19.

COVID-19, which is caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), is the deadliest outbreak of this millennium. Despite adopting several precautionary strategies and guidelines, COVID-19 has spread rapidly, and the number of cases is still in escalation across the world. The various immune-boosting drugs with severe side effects and the vaccines approved after negotiated clinical trials have been struggling to cope with the emergence of new variants of the virus. Nevertheless, given a large number of asymptomatic cases, a high magnitude of recovery rate, and a relatively higher prevalence of morbidity and mortality among immunologically compromised individuals, those affected by an illness, and the elderly, it appears that a healthy microbiome and the associated immune responses are the key factors for survival. Incidentally, the consumption of traditionally popular and nutritious fermented foods, which are composed of biologically functional ingredients and several health-promoting probiotics, offers promising health benefits through the improvement of the immune system in general. Given the progress in functional food research, it has become crucial to understand the impact of a healthy microbiome and the immunomodulatory roles of fermented foods on the battles to combat infectious diseases. Based on the evidence of the impact of probiotics-based fermented foods, the beneficial roles of a few frequently consumed fermented foods in the management of various infections have been resolutely discussed in the present study, with a focus on their antagonistic and immune-modulating effects in the context of the current COVID-19 pandemic.

Effect of the addition of maltodextrin on metabolites and microbial population during kimchi fermentation.

Gelatinized starch sauce, one of the sub-ingredients have been widely used in kimchi for their roles in increasing viscosity of kimchi seasoning, and fermentation. Gelatinized glutinous rice (GGR), which is one of the most used starch sources in kimchi preparation. However, GGR is accelerated to the fermentation process but lead to a reduction in the shelf life of the kimchi. Therefore, in this study, we demonstrate the effectiveness of using maltodextrin (MD) as a novel starch source instead of GGR to slow down the rate of kimchi fermentation. The properties of the kimchi with MD and GGR fermentation (free sugar content, organic acid content, pH, and acidity) as well as their microbial growth rates after 12 days of fermentation were compared. After fermentation of 12 days, the free sugar of GGR-kimchi (GGRK) increased more rapidly than those of MD-kimchi (MDK), while higher sugar alcohol (mannitol) and organic acid contents were observed for GGRK than for MDK. Furthermore, initial aerobic and lactic acid bacteria counts were higher for GGRK than for MDK. These results indicate that fermentation proceeds at a slower rate in MDK than in GGRK, and they will provide a basis for further research into storage of kimchi. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-023-05742-y.

Effect of headspace gas composition in kimchi packaging on the quality characteristics of kimchi.

This study evaluated the effects of gas composition in kimchi packaging on kimchi quality. Completely sealed packaging without gas inflow/outflow during fermentation (S1), packaging allowing gas outflow (S2), and packaging allowing gas inflow and outflow (S3) were used. Microbial composition analysis, volatile compound content analysis, and sensory evaluation were performed to determine the differences in kimchi quality among samples. Metabolites were examined using principal component analysis. Gas composition analysis showed that the ratio of CO2 increased during the storage period in S1, the ratio of nitrogen and CO2 contents was constant in S2, and the ratio of oxygen was significantly higher in S3. No significant differences in the lactic acid bacteria number were observed. However, coliforms were only detected in S3, and yeast and mold proliferated faster in S3 than in S2 or S1. The main compounds detected in S1 and S2 were alcohols, whereas those in S3 were esters such as ß-phenethyl acetate produced by yeast. Sensory evaluation showed that S3 had the lowest odor, taste, and overall scores, whereas S2 had the highest. In conclusion, the gas composition inside the kimchi package greatly affects the quality of kimchi. Our findings provide important data that can be useful in the manufacture of commercial kimchi. Supplementary Information: The online version contains supplementary material available at 10.1007/s13197-023-05795-z.

Screening of gamma-aminobutyric acid-producing lactic acid bacteria and the characteristic of glutamate decarboxylase from Levilactobacillus brevis F109-MD3 isolated from kimchi.

AIMS: This study aimed to screen the γ-aminobutyric acid (GABA)-producing lactic acid bacteria (LAB) from kimchi, and investigate the glutamate decarboxylase (GAD) activity of the highest GABA-producing strain. METHODS AND RESULTS: Seven strains of LAB were screened from kimchi with GABA-producing activity. Strain Levilactobacillus brevis F109-MD3 showed the highest GABA-producing ability. It produced GABA at a concentration of 520 mmol l-1 with a 97.4% GABA conversion rate in MRS broth containing 10% monosodium glutamate for 72 h. The addition of pyridoxal 5'-phosphate had no significant effect on the GAD activity of L. brevis F109-MD3. The optimal pH range of GAD was 3.0-5.0 and the optimal temperature was 65°C. The D value of GAD at 50, 60 and 70°C was 7143, 971 and 124 min respectively and Z value was 11.36°C. CONCLUSIONS: Seven strains isolated from kimchi, especially F109-MD3, showed high GABA-production ability even in the high concentrations of MSG at 7.5% and 10%. The GAD activity showed an effective broad pH range and higher optimal temperature. SIGNIFICANCE AND IMPACT OF THE STUDY: These seven strains could be potentially useful for food-grade GABA production and the development of healthy foods.

Distribution and characterization of prophages in Lactobacillus plantarum derived from kimchi.

Prophage distribution and phage characteristics based on the genome of Lactobacillus plantarum derived from kimchi were investigated. Prophage genomes retrieved from a database were analyzed in silico with prophage inducibility. Twenty-one kimchi-derived L. plantarum had at least one intact prophage, including a putative cryptic state on the chromosome. They were all confirmed to belong to the Siphoviridae family. Intact prophages can be classified into three different groups: PM411-like, Sha1-like, and unclassified phage groups. Some prophage regions were encoded with superinfection exclusion proteins and orphan methylases, suggesting that the phages co-evolved with their hosts. Interestingly, prophage inducibility showed that only DNA damage could induce prophages and that pH stresses by organic acids could not. Therefore, the prophage of L. plantarum did not affect the host unless DNA was damaged, and it would hardly affect the viability of the host through phage induction during kimchi fermentation. Our results might provide insights into the distribution and non-inducibility of prophages, existence of phage-immunity genes, and role of plant-derived L. plantarum prophages in host survival during late acidic kimchi fermentation.

Safety assessment of white colony-forming yeasts in kimchi.

White colony-forming yeasts (WCFYs) have been reported to form a white colony on the surface of kimchi, resulting in the deterioration of kimchi sensory quality. However, toxicity of WCFY has rarely been studied. Thus, to evaluate the safety of WCFY (i.e., Kazachstania servazzii, Candia sake, and Pichia kudriavzevii), we conducted cell and animal experiments as well as genomic analysis. In vitro studies indicated that WCFY did not induce cytotoxic responses such as lactate dehydrogenase release, excessive oxidative stress, and mitochondrial damage at concentrations of up to 2.5 × 105 CFU/mL in human intestinal and liver cells. In animal studies using rats (single-dose and 14-day repeated-dose oral toxicity studies), WCFY did not induce death, clinical signs of toxicity, histological alterations of the liver, or increases in the expression of pro-inflammatory cytokines nor cytochrome P450-2E1 in liver tissue at concentrations of up to 5 × 108 CFU/head/day. Genomic analysis revealed that P. kudriavzevii did not harbor genes related to toxicity and antimicrobial resistance. Taken together, our data suggest that exposure to WCFY through kimchi intake did not induce toxic response in the Caco-2, HepG2, and Sprague-Dawley rats. The current work provides evidence for the safety of accidental major WCFY ingestion via kimchi.

Cabbage and fermented vegetables: From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID-19.

Large differences in COVID-19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS-CoV-2 binds to its receptor, the angiotensin-converting enzyme 2 (ACE2). As a result of SARS-CoV-2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT1 R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID-19. The nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT1 R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof-of-concept of dietary manipulations that may enhance Nrf2-associated antioxidant effects, helpful in mitigating COVID-19 severity.

Lactic acid bacteria starter in combination with sodium chloride controls pathogenic Escherichia coli (EPEC, ETEC, and EHEC) in kimchi.

Kimchi is one of the primary sources of high sodium content in the Korean diet. Low-sodium kimchi is commercially manufactured to minimize the health effects of high salt. We investigated the influence of lactic acid bacteria (LAB) as starter culture in combination with 1% or 2.5% salt on the survival of pathogenic Escherichia coli and physicochemical properties of kimchi during fermentation at 10 °C and 25 °C. Among ten strains of LAB isolated from kimchi, Leuconostoc mesenteroides (KCTC 13374) and Lactobacillus plantarum (KCTC 33133) exhibited antimicrobial activities against pathogenic E. coli (EPEC, ETEC, and E. coli O157:H7) and strong tolerance to low pH (2 and 3) and 0.3% bile salts. Thus, L. mesenteroides and L. plantarum were used as starter cultures for kimchi that contained 1% and 2.5% salt. All pathogenic E. coli strains survived in kimchi regardless of starter cultures or salt concentration for over 15 days at 10 °C, but they died off within 4 days at 25 °C. Survival of pathogenic E. coli was better in naturally fermented kimchi (titratable acidity:0.65%) than kimchi fermented with starter cultures (titratable acidity:1.0%). At 10 °C, the average delta value of E. coli O157:H7 (16.15 d) was smaller than those of EPEC (20.76 d) and ETEC (20.20 d) in naturally fermented kimchi. Overall, survival ability of E. coli O157:H7 was lower than EPEC and ETEC, although differences were not significant. Reduced salt concentration from 2.5% to 1% in kimchi did not affect the growth of LAB and the fermentation period. Pathogenic E. coli died at a faster rate in kimchi fermented with starter cultures and 1% salt than in naturally fermented kimchi with 2.5% salt.

Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing.

Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.

Fecal microbiota changes with fermented kimchi intake regulated either formation or advancement of colon adenoma.

Gut bacteria might contribute in early stage of colorectal cancer through the development and advancement of colon adenoma, by which exploring either beneficial bacteria, which are decreased in formation or advancement of colon adenoma and harmful bacteria, which are increased in advancement of colon adenoma may result in implementation of dietary interventions or probiotic therapies to functional means for prevention. Korean fermented kimchi is one of representative probiotic food providing beneficiary microbiota and exerting significant inhibitory outcomes in both APC/Min+ polyposis model and colitis-associated cancer. Based on these backgrounds, we performed clinical trial to document the changes of fecal microbiota in 32 volunteers with normal colon, simple adenoma, and advanced colon adenoma with 10 weeks of fermented kimchi intake. Each amplicon is sequenced on MiSeq of Illumina and the sequence reads were clustered into Operational Taxonomic Units using VSEARCH and the Chao Indices, an estimator of richness of taxa per individual, were estimated to measure the diversity of each sample. Though significant difference in α or ß diversity was not seen between three groups, kimchi intake significantly led to significant diversity of fecal microbiome. After genus analysis, Acinobacteria, Cyanobacteria, Clostridium sensu, Turicibacter, Gastronaeophillales, H. pittma were proven to be increased in patients with advanced colon adenoma, whereas Enterococcua Roseburia, Coryobacteriaceau, Bifidobacterium spp., and Akkermansia were proven to be significantly decreased in feces from patients with advanced colon adenoma after kimchi intake. Conclusively, fermented kimchi plentiful of beneficiary microbiota can afford significant inhibition of either formation or advancement of colon adenoma.

Transcriptome profiling implicated in beneficiary actions of kimchi extracts against Helicobacter pylori infection.

Dietary intervention to prevent Helicobacter pylori (H. pylori)-gastric cancer might be ideal because of no risk of bacterial resistance, safety, and rejuvenating action of atrophic gastritis. We have published data about the potential of fermented kimchi as nutritional approach for H. pylori. Hence recent advances in RNAseq analysis lead us to investigate the transcriptome analysis to explain these beneficiary actions of kimchi. gastric cells were infected with either H. pylori or H. pylori plus kimchi. 943 genes were identified as significantly increased or decreased genes according to H. pylori infection and 68 genes as significantly changed between H. pylori infection and H. pylori plus kimchi (p<0.05). Gene classification and Medline database showed DLL4, FGF18, PTPRN, SLC7A11, CHAC1, FGF21, ASAN, CTH, and CREBRF were identified as significantly increased after H. pylori, but significantly decreased with kimchi and NEO1, CLDN8, KLRG1, and IGFBP1 were identified as significantly decreased after H. pylori, but increased with kimchi. After KEGG and STRING-GO analysis, oxidative stress, ER stress, cell adhesion, and apoptosis genes were up-regulated with H. pylori infection but down-regulated with kimchi, whereas tissue regeneration, cellular anti-oxidative response, and anti-inflammation genes were reversely regulated with kimchi (p<0.01). Conclusively, transcriptomes of H. pylori plus kimchi showed significant biological actions.

Microbiota changes with fermented kimchi contributed to either the amelioration or rejuvenation of Helicobacter pylori-associated chronic atrophic gastritis.

Korean fermented kimchi is probiotic food preventing Helicobacter pylori (H. pylori)-associated atrophic gastritis in both animal and human trial. In order to reveal the effect of fermented kimchi against H. pylori infection, we performed clinical trial to document the changes of fecal microbiota in 32 volunteers (H. pylori (-) chronic superficial gastritis (CSG), H. pylori (+) CSG, and H. pylori (+) chronic atrophic gastritis (CAG) with 10 weeks kimchi. Each amplicon is sequenced on MiSeq of Illumina and the sequence reads were clustered into operational taxonomic units using VSEARCH and the Chao, Simpson, and Shannon Indices. Though significant difference in α- or ß-diversity was not seen in three groups, kimchi intake led to significant diversity of fecal microbiome. As results, Klebsiella, Enterococcus, Ruminococcaceae, Streptococcus, Roseburia, and Clostirdiumsensu were significantly increased in H. pylori (+) CAG, while Akkermansia, Citrobacter, and Lactobacillus were significantly decreased in H. pylori (+) CAG. With 10 weeks of kimchi administration, Bifidobacterium, Lactobacillus, and Ruminococcus were significantly increased in H. pylori (+) CAG, whereas Bacteroides, Subdoligranulum, and Eubacterium coprostanolines were significantly decreased in H. pylori (-) CAG. 10 weeks of kimchi intake significantly improved pepsinogen I/II ratio (p<0.01) with significant decreases in interleukin-1ß. Conclusively, fermented kimchi significantly changed fecal microbiota to mitigate H. pylori-associated atrophic gastritis.

Proteomic evaluation of kimchi, a traditional Korean fermented vegetable, and comparison of kimchi manufactured in China and Korea.

Kimchi is a traditional Korean fermented vegetable, which is also widely consumed in Japan and China. However, little is known about the kimchi proteome. In this study, Korean and Chinese kimchi proteomes were evaluated by shotgun proteomics. A total of 250 proteins were annotated, and 29 of these were expressed at > 1% of the average relative abundance. Discrimination of the geographical origins of Korean and Chinese kimchi samples was possible using multivariate analysis of the proteomic data, and 23 proteins were expressed differently between the two types (p < 0.001), and represent possible markers to discriminate between Chinese and Korean kimchi. This study provides important insights into the kimchi proteome and illustrates the proteomic differences caused by geographical origin.

Characterization of a potential probiotic bacterium Lactococcus raffinolactis WiKim0068 isolated from fermented vegetable using genomic and in vitro analyses.

BACKGROUND: Lactococcus members belonging to lactic acid bacteria are widely used as starter bacteria in the production of fermented dairy products. From kimchi, a Korean food made of fermented vegetables, Lactococcus raffinolactis WiKim0068 was isolated and its genome was analyzed. RESULTS: The complete genome of the strain WiKim0068 consists of one chromosome and two plasmids that comprises 2,292,235 bp, with a G + C content of 39.7 mol%. Analysis of orthoANI values among Lactococcus genome sequences showed that the strain WiKim0068 has > 67% sequence similarity to other species and subspecies. In addition, it displayed no antibiotic resistance and can metabolize nicotinate and nicotinamide (vitamin B3). CONCLUSION: These results augments our understanding of the genus Lactococcus and suggest that this new strain has potential industrial applications.

Lactococcus kimchii sp. nov., a new lactic acid bacterium isolated from kimchi.

A coccus strain designated S-13T was isolated from commercial baechu-kimchi in Korea. Comparison of the 16S rRNA gene sequence indicated that strain S-13T had the highest similarity to Lactococcus taiwanensis 0905C15T (97.9 %), Lactococcus lactis subsp. tructae L105T (97.6 %), Lactococcus lactis subsp. cremoris NCDO 607T (97.5 %), Lactococcus lactis subsp. hordniae NBRC 100931T (97.2 %), and Lactococcus lactis subsp. lactis JCM 5805T (97.2 %). The detailed phylogenetic analyses based on the 16S rRNA, rpoB and recA genes indicated that S-13T was separated from the other species and subspecies in the genus Lactococcus. The DNA-DNA relatedness between S-13T and closely related type strains, such as L. taiwanensis 0905C15T, L. lactis subsp. tructae L105T, L. lactis subsp. cremoris NCDO 607T, L. lactis subsp. hordniae NBRC 100931T, and L. lactis subsp. lactis JCM 5805T was 25.6, 20.4, 25.1, 20.2 and 21.7 %, respectively. The major fatty acids were C16 : 0, cyclo-C19 : 0ω8c and C 14 : 0. The DNA G+C content of S-13T was 39.4 mol%. From the results of the phenotypic characteristics and chemotaxonomic analysis, it was concluded that strain S-13T represents a novel species in the genus Lactococcus for which the name Lactococcus kimchii sp. nov. (=KCTC 21096T=NBRC 113348T) is proposed.

Unraveling microbial fermentation features in kimchi: from classical to meta-omics approaches.

Kimchi is a traditional Korean fermented food prepared via spontaneous fermentation by various microorganisms originating from vegetables such as kimchi cabbage, radishes, and garlic. Recent advances in meta-omics approaches that integrate metataxonomics, metagenomics, metatranscriptomics, and metabolomics have contributed to explaining and understanding food fermentation processes. Kimchi microbial communities are composed of majorly lactic acid bacteria such as Leuconostoc, Lactobacillus, and Weissella and fewer eukaryotic microorganisms and kimchi fermentation are accomplished by complex microbial metabolisms to produce diverse metabolites such as lactate, acetate, CO2, ethanol, mannitol, amino acids, formate, malate, diacetyl, acetoin, and 2, 3-butanediol, which determine taste, quality, health benefit, and safety of fermented kimchi products. Therefore, in the future, kimchi researches should be systematically performed using the meta-omics approaches to understand complex microbial metabolisms during kimchi fermentation. KEY POINTS: • Spontaneous fermentation by raw material microbes gives kimchi its unique flavor. • The kimchi microbiome is altered by environmental factors and raw materials. • Through the multi-omics approaches, it is possible to accurately analyze the diversity and metabolic characteristics of kimchi microbiome and discover potential functionalities.

Genomic and metabolic features of Lactobacillus sakei as revealed by its pan-genome and the metatranscriptome of kimchi fermentation.

The genomic and metabolic features of Lactobacillus sakei were investigated using its pan-genome and by analyzing the metatranscriptome of kimchi fermentation. In the genome-based relatedness analysis, the strains were divided into the Lb. sakei ssp. sakei and Lb. sakei ssp. carnosus lineage groups. Genomic and metabolic pathway analysis revealed that all Lb. sakei strains have the capability of producing d/l-lactate, ethanol, acetate, CO2, formate, l-malate, diacetyl, acetoin, and 2,3-butanediol from d-glucose, d-fructose, d-galactose, sucrose, d-lactose, l-arabinose, cellobiose, d-mannose, d-gluconate, and d-ribose through homolactic and heterolactic fermentation, whereas their capability of d-maltose, d-xylose, l-xylulose, d-galacturonate, and d-glucuronate metabolism is strain-specific. All strains carry genes for the biosynthesis of folate and thiamine, whereas genes for biogenic amine and toxin production, hemolysis, and antibiotic resistance were not identified. The metatranscriptomic analysis showed that the expression of Lb. sakei transcripts involved in carbohydrate metabolism increased as kimchi fermentation progressed, suggesting that Lb. sakei is more competitive during late fermentation stage. Homolactic fermentation pathway was highly expressed and generally constant during kimchi fermentation, whereas expression of heterolactic fermentation pathway increased gradually as fermentation progressed. l-Lactate dehydrogenase was more highly expressed than d-lactate dehydrogenase, suggesting that l-lactate is the major lactate metabolized by Lb. sakei.