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.

Effects of Donepezil Treatment on Brain Metabolites, Gut Microbiota, and Gut Metabolites in an Amyloid Beta-Induced Cognitive Impairment Mouse Pilot Model.

Accumulated clinical and biomedical evidence indicates that the gut microbiota and their metabolites affect brain function and behavior in various central nervous system disorders. This study was performed to investigate the changes in brain metabolites and composition of the fecal microbial community following injection of amyloid ß (Aß) and donepezil treatment of Aß-injected mice using metataxonomics and metabolomics. Aß treatment caused cognitive dysfunction, while donepezil resulted in the successful recovery of memory impairment. The Aß + donepezil group showed a significantly higher relative abundance of Verrucomicrobia than the Aß group. The relative abundance of 12 taxa, including Blautia and Akkermansia, differed significantly between the groups. The Aß + donepezil group had higher levels of oxalate, glycerol, xylose, and palmitoleate in feces and oxalate, pyroglutamic acid, hypoxanthine, and inosine in brain tissues than the Aß group. The levels of pyroglutamic acid, glutamic acid, and phenylalanine showed similar changes in vivo and in vitro using HT-22 cells. The major metabolic pathways in the brain tissues and gut microbiota affected by Aß or donepezil treatment of Aß-injected mice were related to amino acid pathways and sugar metabolism, respectively. These findings suggest that alterations in the gut microbiota might influence the induction and amelioration of Aß-induced cognitive dysfunction via the gut-brain axis. This study could provide basic data on the effects of Aß and donepezil on gut microbiota and metabolites in an Aß-induced cognitive impairment mouse model.

Aminipila terrae sp. nov., a strictly anaerobic bacterium isolated from river sediment.

In this study, aimed at investigating and characterizing river sediment bacteria, we isolated a Gram-stain-positive, rod-shaped, obligate anaerobic bacterium, strain CBA3637T, from the sediment of the Geum River. This strain grew at 10-40 °C (optimum, 30 °C), 0-1% NaCl (optimum, 0%), and pH 7-8 (optimum, pH 7). The 16S rRNA gene sequence comparison revealed Aminipila butyrica DSM 103574T to be the closest relative of strain CBA3637T (96.6-96.7% similarity); and both strains clustered together in phylogenetic analysis. The genome of strain CBA3637T was found to consist of a single chromosome (3.51 Mbp; 36.98% G + C content). Comparative genomic analysis of the strain CBA3637T with A. butyrica DSM 103574T revealed that strain CBA3637T possessed five unique pathways related to polyamine biosynthesis, lipopolysaccharide metabolism, pyrimidine metabolism, and cofactor and vitamin metabolism. Strain CBA3637T contained C14:0, C16:0, and C18:1 ω9c as the major fatty acids, and diphosphatidylglycerol as the major polar lipid. No respiratory quinone was observed. Biochemical, chemotaxonomic, and genotypic data revealed that the strain CBA3637T is a representative of a novel species within the genus Aminipila, for which the name Aminipila terrae is proposed. The type strain is CBA3637T (= KACC 21651T = DSM 110662T).

Anaerocolumna sedimenticola sp. nov., isolated from fresh water sediment.

Strain CBA3638T was isolated from the Geum River sediment, Republic of Korea. The cells of strain CBA3638T were Gram-stain-positive, strictly anaerobic, rod-shaped, and 0.5-1.0 µm wide, and 4.0-4.5 µm long. Optimal growth occurred at 37 °C, pH 7.0, and 1.0% (w/v) NaCl. Based on the 16S rRNA gene sequence, the phylogenetic analysis showed that strain CBA3638T belongs to the genus Anaerocolumna in the family Lachnospiraceae, and is most closely related to Anaerocolumna cellulosilytica (94.6-95.0%). The DDH value with A. cellulosilytica SN021T showed 15.0% relatedness. The genome of strain CBA3638T consisted of one circular chromosome that is 5,500,435 bp long with a 36.7 mol% G + C content. The genome contained seven 16S-5S-23S rRNA operons and one antibiotic resistance-related transporter gene (mefA). Quinones were not detected. The predominant cellular fatty acids were C16:0 and C14:0 and the polar lipids were diphosphatidylglycerol, phosphatidylcholine, and uncharacterised polar lipids. Based on the polyphasic taxonomic analysis, we propose strain CBA3638T as a novel species in the genus Anaerocolumna, with the name Anaerocolumna sedimenticola sp. nov. The type strain is CBA3638T (= KACC 21652T = DSM 110663T).

Metabolomics Reveals the Alteration of Metabolic Pathway by Alpha-Melanocyte-Stimulating Hormone in B16F10 Melanoma Cells.

The purpose of this study was to understand the changes of metabolic pathway induced by alpha-melanocyte-stimulating hormone (α-MSH) in B16F10 melanoma cells in an untargeted metabolomics approach. Cells were treated with 100 nM of α-MSH and then incubated for 48 h. α-MSH increased tyrosinase activity and melanin content by 56.5 and 61.7%, respectively, compared to untreated cells after 48 h of cultivation. The clear separation between groups was observed in the principal component analysis score plot, indicating that the levels of metabolites of melanoma cells were altered by treatment with α-MSH. Metabolic pathways affected by α-MSH were involved in some amino acid metabolisms. The increased levels of fumaric acid, malic acid, oxaloacetic acid and citric acid related to the citric acid cycle pathway after α-MSH treatment suggested enhanced energy metabolism. Metabolic pathways altered by α-MSH treatment can provide useful information to develop new skin pigmentation inhibitors or anti-obesity drugs.

Effect of Fungi on Metabolite Changes in Kimchi During Fermentation.

The purpose of this study is to investigate the effect of fungi on kimchi metabolites during fermentation. A gas chromatography-mass spectrometry (GC-MS) based metabolite profiling approach in combination with principal component analysis (PCA) is performed to differentiate metabolites produced by fungi or bacteria. To avoid bacterial growth, kimchi is treated with 100 µg/mL of ampicillin every three days from 30 to 50 days of fermentation. The relative content of the major fungi at 50 days of fermentation, between the control group and the ampicillin treatment group, was not significantly different. The administration of ampicillin changed the metabolites in kimchi by affecting the growth of kimchi bacteria. Based on the pattern of change of each metabolite, the changed metabolites are grouped into four categories: (1) metabolites produced or consumed by fungi, (2) metabolites involving both fungi and bacteria, (3) metabolites produced or consumed by bacteria, and (4) metabolites of undetermined origin. Alanine, thymine, galacturonic acid, and malonic acid can be regarded as the metabolites produced by fungi between 30 and 50 days of fermentation. In contrast, malic acid, oxaloacetic acid, galactitol, glucose, and mannitol are presumed to be the metabolites mainly consumed by fungi. This study is meaningful as the first study conducted by inhibiting growth of bacteria to identify the metabolites contributed by fungi or bacteria in the kimchi fermentation process. These results could be used to make customized kimchi that controls the production of desired metabolites by selectively controlling the formation of microbial communities in the kimchi industry.

Metabolomic Approach for Discrimination of Cultivation Age and Ripening Stage in Ginseng Berry Using Gas Chromatography-Mass Spectrometry.

The purpose of this study was to analyze metabolic differences of ginseng berries according to cultivation age and ripening stage using gas chromatography-mass spectrometry (GC-MS)-based metabolomics method. Ginseng berries were harvested every week during five different ripening stages of three-year-old and four-year-old ginseng. Using identified metabolites, a random forest machine learning approach was applied to obtain predictive models for the classification of cultivation age or ripening stage. Principal component analysis (PCA) score plot showed a clear separation by ripening stage, indicating that continuous metabolic changes occurred until the fifth ripening stage. Three-year-old ginseng berries had higher levels of valine, glutamic acid, and tryptophan, but lower levels of lactic acid and galactose than four-year-old ginseng berries at fully ripened stage. Metabolic pathways affected by different cultivation age were involved in amino acid metabolism pathways. A random forest machine learning approach extracted some important metabolites for predicting cultivation age or ripening stage with low error rate. This study demonstrates that different cultivation ages or ripening stages of ginseng berry can be successfully discriminated using a GC-MS-based metabolomic approach together with random forest analysis.

Effects of Harvest Time on Phytochemical Constituents and Biological Activities of Panax ginseng Berry Extracts.

Ginseng (Panax ginseng) has long been used as a traditional medicine for the prevention and treatment of various diseases. Generally, the harvest time and age of ginseng have been regarded as important factors determining the efficacy of ginseng. However, most studies have mainly focused on the root of ginseng, while studies on other parts of ginseng such as its berry have been relatively limited. Thus, the aim of this study iss to determine effects of harvest time on yields, phenolics/ginsenosides contents, and the antioxidant/anti-elastase activities of ethanol extracts of three- and four-year-old ginseng berry. In both three- and fourfour-year-old ginseng berry extracts, antioxidant and anti-elastase activities tended to increase as berries ripen from the first week to the last week of July. Liquid chromatography-tandem mass spectrometry analysis has revealed that contents of ginsenosides except Rg1 tend to be the highest in fourfour-year-old ginseng berries harvested in early July. These results indicate that biological activities and ginsenoside profiles of ginseng berry extracts depend on their age and harvest time in July, suggesting the importance of harvest time in the development of functional foods and medicinal products containing ginseng berry extracts. To the best of our knowledge, this is the first report on the influence of harvest time on the biological activity and ginsenoside contents of ginseng berry extracts.

Selective influence of garlic as a key ingredient in kimchi on lactic acid bacteria in a fermentation model system.

Garlic is an essential ingredient added to kimchi, a fermented vegetable, in small amounts owing to its sensory and antibacterial properties. This study aimed to elucidate the complex relationship between garlic and specific lactic acid bacteria (LAB) and the resulting metabolite changes in a controlled kimchi model system using nine strains as mixed and individual starters. The group without garlic using mixed starters showed the highest LAB growth activity, which influenced lactic acid production, pH, and titratable acidity. The group without garlic also showed differences in the composition of bacteria, such as Latilactobacillus sakei, Levilactobacillus brevis, unclassified Leuconostoc, and Weissella koreensis, during the fermentation period. In addition, the altering patterns of metabolites in the group without garlic during fermentation differed from those in the group with garlic. In addition, the metabolic profile of L. brevis group was mostly different from that of the other strains in the controlled model kimchi system using individual starters, suggesting that changes in LAB composition by garlic could subsequently affect metabolites during fermentation. This study provides valuable insights into the complex interactions among food ingredients, LAB succession, and metabolite production during fermentation.

Impact of essential and optional ingredients on microbial and metabolic profiles of kimchi.

This study aimed to examine the impacts of essential and optional ingredients on the microbial and metabolic profiles of kimchi during 100 days of fermentation, using a mix-omics approach. Kimchi manufactured without essential ingredients (e.g., red pepper, garlic, ginger, green onion, and radish) had lower lactic acid content. The absence of garlic was associated with a higher proportion of Latilactobacillus and Lactococcus, while the absence of red pepper was associated with a greater proportion of Leuconostoc than the control group. In addition, red pepper and garlic served as primary determinants of the levels of organic acids and biogenic amines. Sugar was positively correlated with the levels of melibiose, and anchovy sauce was positively correlated with the levels of amino acids such as methionine, leucine, and glycine. These findings contribute to a fundamental understanding of how ingredients influence kimchi fermentation, offering valuable insights for optimizing kimchi production to meet various preferences.

Effects of seasonal harvest of kimchi cabbage on microbial and metabolic profiles of kimchi.

Kimchi cabbage, the key ingredient in kimchi, is cultivated year-round to meet high production demands. This study aimed to examine the effects of seasonal harvesting (spring, summer, fall, and winter) on the microbial and metabolic profiles of kimchi during 30 days of fermentation. Lactic acid bacteria distribution is notably influenced by seasonal variations, with Latilactobacillus dominant in fall-harvested kimchi group and Weissella prevailing in spring, summer, and winter. The microbial communities of spring and fall group exhibited similar profiles before fermentation, whereas the microbial communities and metabolic profiles of spring and summer group were similar after 30 days of fermentation. Seasonal disparities in metabolite concentrations, including glutamic acid, serine, and cytosine, persist throughout fermentation. This study provides a comprehensive understanding of the substantial impact of seasonal harvesting of kimchi cabbage on the microbial and metabolic characteristics of kimchi, providing valuable insights into producing kimchi with diverse qualities.

Investigation of lactic acid bacterial profiles in commercial rice wine and their effect on metabolites during low-temperature storage.

Makgeolli, the traditional Korean rice wine, is generally considered to contain lactic acid bacteria (LAB) despite its bacterial inoculation-free brewing process. The existence of LAB in makgeolli often presents inconsistent trends in microbial profiles and cell numbers. Therefore, to establish LAB-related insights, 94 commercial non-pasteurized products were collected and microbial communities and metabolites were analyzed using 16S rRNA amplicon sequencing and GC-MS, respectively. All samples contained various LAB genera and species, with an average viable cell number of 5.61 log CFU/mL. Overall, 10 LAB genera and 25 LAB species were detected; the most abundant and frequent LAB genus was Lactobacillus. There was no significant change in the LAB composition profile or lactic acid content during low-temperature storage, indicating the presence of LAB did not significantly affect the quality of makgeolli under low-temperature storage conditions. Overall, this study contributes to understand the microbial profile and role of LAB in makgeolli.

Effects of saccharification agents on the microbial and metabolic profiles of Korean rice wine (makgeolli).

To brew rice wine, a saccharification agent is critical to provide sugars necessary for yeast to ferment alcohol. Nuruk, a traditional Korean saccharification agent, contains saccharification enzymes and various microorganisms, including fungi and lactic acid bacteria (LAB). To investigate the effect of saccharification agents on Korean rice wine (makgeolli), we analyzed makgeolli brewed with different saccharification agents, such as koji and nuruk. In contrast to koji makgeolli, nuruk makgeolli had a distinct microbial profile with higher proportion of LAB. Comparing the microbial profiles of the saccharification agents and makgeolli revealed that the dominant microorganisms in the makgeolli were possibly derived from the saccharification agents. Several metabolites also exhibited distinct profiles depending on the saccharification agent generating the total metabolic profile difference of makgeolli samples. Collectively, the saccharification agent could provide dominant microorganisms in the makgeolli microbiota, leading to a distinct microbial and metabolic profile of makgeolli depending on its type.

Effects of sediment and temperature on the long-term aging process of rice wine: Microbial and metabolic insights.

Rice wine is low in alcohol content (6 %), rich in nutrients, and contains live microorganisms; therefore, it is generally produced without an aging process during manufacturing. In this study, we investigated the microbial and metabolic changes that occur during the long-term aging of undiluted rice wine with different amount of sediment and aging temperatures. Rice wine samples with higher amounts of sediment had higher yeast counts and alcohol content, indicating a crucial role of sediment in providing nutrients for yeast survival during aging. Furthermore, the rice wine samples that were aged at 12 °C exhibited a notable increase in the relative abundance of Lactobacillus after 100 days of aging. Metabolic profiling revealed that the production of metabolites during rice wine aging was greatly influenced by the amount of sediment and aging temperature, with most metabolites showing a strong correlation with these factors. This study provides valuable insights into the impact of sediment and temperature on the microbial and metabolic changes that occur during the long-term aging of rice wine.

Effects of ingredient size on microbial communities and metabolites of radish kimchi.

In this study, changes in physicochemical characteristics, microbial communities, and metabolites were investigated to identify the fermentation characteristics of radish kimchi according to the size of radish cubes used. The small-sized radish kimchi group showed the highest hardness value and glucose content in the early stages of fermentation. The relative abundance of major lactic acid bacteria, including Leuconostoc, Weissella, and Lactobacillus, was the highest in the small-sized radish kimchi group on day 5 of fermentation, which resulted in rapid production of lactic acid, thereby causing a decrease in pH and an increase in titratable acidity. The size of the radish in kimchi plays a pivotal role in determining various factors, most notably during the first 5 days of fermentation, leading to marked metabolic changes. A total of 17 metabolites, including glucose, sucrose, lactic acid, malic acid, citric acid, and GABA, exhibited significant differences in the small-size radish kimchi group. Interestingly, the sucrose content was higher in the large-sized radish group at the beginning of fermentation. This study revealed that ingredient size can selectively affect the growth of specific microorganisms in an environment where several microorganisms coexist, which could change the quality of radish kimchi.

In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract.

The urogenital microbiota is the potential principal factor in the pathophysiology of urinary tract infection and the protection of urinary tract health. Little is known about the urogenital archaeome although several reports have indicated that the archaeomes of various regions of the human body are associated with health. Accordingly, we aimed to determine the presence and diversity of archaeomes in the human urogenital tract. To explore the urogenital archaeome, voided urine specimens from 373 asymptomatic Korean individuals were used. No difference was observed in body mass index, age, or gender, according to presence of archaea. Analysis of archaeal 16S rRNA gene amplicons of archaea positive samples consisted of simple community structures, including diverse archaea, such as the phyla Methanobacteriota, Thermoproteota, and Halobacteriota. Asymptomatic individuals showed high participant-dependent intervariability in their urogenital archaeomes. The mean relative archaeal abundance was estimated to be 0.89%, and fluorescence in situ hybridisation micrographs provided evidence of archaeal cells in the human urogenital tract. In addition, the urogenital archaeome shared partial taxonomic compositional characteristics with those of the other body sites. In this study, Methanobacteriota, Thermoproteota, and Halobacteriota were suggested as inhabitants of the human urogenital tract, and a distinct human urogenital archaeome was characterised. These findings expand our knowledge of archaea-host associations in the human urogenital tract and may lead to novel insights into the role of archaea in urinary tract health.

Association between Mild Cognitive Impairment and Gut Microbiota in Elderly Korean Patients.

Recent studies have confirmed that gut microbiota differs according to race or country in many diseases, including mild cognitive impairment (MCI) and Alzheimer's disease. However, no study has analyzed the characteristics of Korean MCI patients. This study was performed to observe the association between gut microbiota and MCI in the Korean elderly and to identify potential markers for Korean MCI patients. For this purpose, we collected fecal samples from Korean subjects who were divided into an MCI group (n = 40) and control group (n = 40) for 16S rRNA gene amplicon sequencing. Although no significant difference was observed in the overall microbial community profile, the relative abundance of several genera, including Bacteroides, Prevotella, and Akkermansia, showed significant differences between the two groups. In addition, the relative abundance of Prevotella was negatively correlated with that of Bacteroides (r = 0.733). This study may provide Korean-specific basic data for comparing the characteristics of the gut microbiota between Korean and non-Korean MCI patients.

Analgesic effects and metabolome analyses of laser- and electro-acupuncture combined therapies in paclitaxel-induced neuropathic pain model.

Introduction: Allodynia, which can be induced by paclitaxel administration, is the presence of pain as a result of a stimulus that does not usually provoke pain. Many studies have investigated the analgesic efficacy of acupuncture, including laser acupuncture (LA) and electroacupuncture (EA). Although pain-related diseases are relatively common, few studies have analyzed the analgesic effects and mechanisms of LA combined with EA. The purpose of this study was to investigate the therapeutic effect and mechanism of manual acupuncture (MA), EA, LA, and combined therapy (LA + EA) in a paclitaxel-induced allodynia rat model. Methods: A total of 56 rats were classified into eight groups: a normal (Nor, n = 7), a control (Con, n = 7), an MA (n = 7), an EA (n = 7), a 650-nm LA (650LA, n = 7), an 830-nm LA (830LA, n = 7), a 650-nm LA combined with EA (650LA + EA, n = 7), and an 830-nm LA combined with EA group (830LA + EA, n = 7). Allodynia was induced by intraperitoneal injection of 2 mg/kg of paclitaxel every other day for a total of four times except the Nor group. Acupuncture treatments were conducted at the points of Jungwan (CV12) and Joksamni (ST36) once every other day for 6 min, for a total of nine times. Withdrawal response reaction times and force intensity of the foot were measured before the start of the experiment, after the 4th paclitaxel administration (day 8), and after the 9th and last treatment (day 15). On the 16th day, mRNA and protein expression in the spinal nerves was assessed, and a metabolome analysis of the animals' feces was performed. Results and discussion: Our analyses show that 650LA + EA treatment resulted in an upregulation of protein expression related to pain relief and nerve regeneration, whereas 830LA + EA treatment led to significant changes in metabolomes. This study demonstrates that a combination treatment of EA and LA can suppress allodynia and promote upregulation of protein expression related to nerve regeneration and is effective in changing the intestinal microbiome. Further large-scale research is required to assess the exact mechanism underlying the therapeutic effect of this combination treatment in pain-related diseases.

Machine learning model for predicting age in healthy individuals using age-related gut microbes and urine metabolites.

Age-related gut microbes and urine metabolites were investigated in 568 healthy individuals using metataxonomics and metabolomics. The richness and evenness of the fecal microbiota significantly increased with age, and the abundance of 16 genera differed between the young and old groups. Additionally, 17 urine metabolites contributed to the differences between the young and old groups. Among the microbes that differed by age, Bacteroides and Prevotella 9 were confirmed to be correlated with some urine metabolites. The machine learning algorithm eXtreme gradient boosting (XGBoost) was shown to produce the best performing age predictors, with a mean absolute error of 5.48 years. The accuracy of the model improved to 4.93 years with the inclusion of urine metabolite data. This study shows that the gut microbiota and urine metabolic profiles can be used to predict the age of healthy individuals with relatively good accuracy.

Comprehensive elucidation of the terroir of Korean kimchi through the study of recipes, metabolites, microbiota, and sensory characteristics.

The aim of this study was to investigate the differences in characteristics of the fermented food kimchi based on the regions where it is produced. A total of 108 kimchi samples were collected from five different provinces in Korea to analyze the recipes, metabolites, microbes, and sensory characteristics. Overall, 18 ingredients (including salted anchovy and seaweed), 7 quality indicators (such as salinity and moisture content), 14 genera of microorganisms (mainly Tetragenococcus and Weissella belonging to LAB), and 38 metabolites contributed to the characteristics of kimchi by region. Kimchi from the southern and northern regions showed distinct metabolite profile (collected 108 kimchi) and flavor profile differences (kimchi manufactured using the standard regional recipes). This is the first study to investigate the terroir effect of kimchi by identifying differences in ingredients, metabolites, microbes, and sensory characteristics based on the region of production, and the correlations between these factors.