Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study.

AIM: Periodontitis is a potential risk factor for preterm birth (PTB) in women; however, the causal relationship or the exact mechanism remain unknown. This study aimed to compare the oral microbiome features of mothers with full-term birth (FTB) with those who had preterm delivery. METHODS: This study prospectively enrolled 60 women (30 mothers with PTB and 30 mothers with FTB), and subgingival plaque samples were collected and analysed by metagenomic 16S rDNA sequencing. Clinical measurements, including periodontal probing depth, clinical attachment level, modified gingival index (mGI) and plaque index, were performed to determine the periodontal state of the participants. Medical and obstetric data were collected as well. RESULTS: Among the periodontal measurements, mGI score, reflecting the level of gingival inflammation, exhibited a statistically significant association with PTB (adjusted odds ratio 2.705, 95% confidence interval 1.074-6.811, p = .035). When subgroup analysis was conducted based on mean mGI scores (mGI ≥ 2, high inflammation [HI] versus mGI < 2, low inflammation [LI]), microbiome analysis revealed clear distinctions in microbial compositions between PTB and FTB mothers in both the HI and LI groups. Especially in the HI group, alpha diversity exhibited a decreasing trend in PTB mothers compared to FTB mothers. Beta diversity also revealed significant differences between the two groups. In Linear Discriminant Analysis Effect Size analysis, certain anaerobic taxa, including the genera Spirochaetes, Treponema and Porphyromonas, were relatively abundant in the FTB/HI group, whereas the PTB/HI group showed a high abundance of the order Actinomycetales. Network analysis showed that the FTB/HI had relatively stronger connectivity in microbial composition than the PTB/HI group. Dysbiosis ratio of plaque microbiome, in terms of periodontitis, was significantly lower in PTB/HI group compared to FTB/HI group. CONCLUSION: The compositions of maternal subgingival microbiomes differed between PTB and FTB mothers in both the high and low levels of gingival inflammation groups. In the presence of high level of gingival inflammation, dysbiosis in plaque microbiome, in terms of periodontitis, was decreased in PTB mothers compared to FTB mothers.

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 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.

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.

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.

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 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.

Long-term population dynamics of viable microbes in a closed ecosystem of fermented vegetables.

This study was performed to investigate the succession of various microorganisms naturally present in raw ingredients and the changes in metabolites following long-term fermentation of kimchi. Kimchi was stored at 4 °C for 500 days, and the composition of the microbial community and the nature of metabolites were analyzed using metataxonomics and metabolomics. We confirmed that the taxa belonging to Leuconostoc and Weissella were dominant in the early stages of fermentation, while Latilactobacillus and Levilactobacillus were dominant in the middle and late fermentation stages, respectively. In the eukaryotic community, Cladosporium was dominant in the early stages, while Pichia and Hanseniaspora tended to increase in the middle and late fermentation stages. The longitudinal metabolite profile demonstrated that about half (55.7%) of the metabolites present in kimchi after 500 days of fermentation were produced within 15 days of fermentation due to rapid fermentation in the initial stage. These results revealed that even in a closed environment, the viable microbiota in fermented vegetables are not static but dynamic, and the composition of metabolites evolves accordingly during long-term fermentation.

The transcription factor ORA59 exhibits dual DNA binding specificity that differentially regulates ethylene- and jasmonic acid-induced genes in plant immunity.

Jasmonic acid (JA) and ethylene (ET) signaling modulate plant defense against necrotrophic pathogens in a synergistic and interdependent manner, while JA and ET also have independent roles in certain processes, e.g. in responses to wounding and flooding, respectively. These hormone pathways lead to transcriptional reprogramming, which is a major part of plant immunity and requires the roles of transcription factors. ET response factors are responsible for the transcriptional regulation of JA/ET-responsive defense genes, of which ORA59 functions as a key regulator of this process and has been implicated in the JA-ET crosstalk. We previously demonstrated that Arabidopsis (Arabidopsis thaliana) GDSL LIPASE 1 (GLIP1) depends on ET for gene expression and pathogen resistance. Here, promoter analysis of GLIP1 revealed ERELEE4 as the critical cis-element for ET-responsive GLIP1 expression. In a yeast one-hybrid screening, ORA59 was isolated as a specific transcription factor that binds to the ERELEE4 element, in addition to the well-characterized GCC box. We found that ORA59 regulates JA/ET-responsive genes through direct binding to these elements in gene promoters. Notably, ORA59 exhibited a differential preference for GCC box and ERELEE4, depending on whether ORA59 activation is achieved by JA and ET, respectively. JA and ET induced ORA59 phosphorylation, which was required for both activity and specificity of ORA59. Furthermore, RNA-seq and virus-induced gene silencing analyses led to the identification of ORA59 target genes of distinct functional categories in JA and ET pathways. Our results provide insights into how ORA59 can generate specific patterns of gene expression dynamics through JA and ET hormone pathways.

Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice.

Obesity can be caused by microbes producing metabolites; it is thus important to determine the correlation between gut microbes and metabolites. This study aimed to identify gut microbiota-metabolomic signatures that change with a high-fat diet and understand the underlying mechanisms. To investigate the profiles of the gut microbiota and metabolites that changed after a 60% fat diet for 8 weeks, 16S rRNA gene amplicon sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomic analyses were performed. Mice belonging to the HFD group showed a significant decrease in the relative abundance of Bacteroidetes but an increase in the relative abundance of Firmicutes compared to the control group. The relative abundance of Firmicutes, such as Lactococcus, Blautia, Lachnoclostridium, Oscillibacter, Ruminiclostridium, Harryflintia, Lactobacillus, Oscillospira, and Erysipelatoclostridium, was significantly higher in the HFD group than in the control group. The increased relative abundance of Firmicutes in the HFD group was positively correlated with fecal ribose, hypoxanthine, fructose, glycolic acid, ornithine, serum inositol, tyrosine, and glycine. Metabolic pathways affected by a high fat diet on serum were involved in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, cysteine and methionine metabolism, glyoxylate and dicarboxylate metabolism, and phenylalanine, tyrosine, and trypto-phan biosynthesis. This study provides insight into the dysbiosis of gut microbiota and metabolites altered by HFD and may help to understand the mechanisms underlying obesity mediated by gut microbiota.

Identification of Salivary Microorganisms and Metabolites Associated with Halitosis.

Halitosis is mainly caused by the action of oral microbes. The purpose of this study was to investigate the differences in salivary microbes and metabolites between subjects with and without halitosis. Of the 52 participants, 22 were classified into the halitosis group by the volatile sulfur compound analysis on breath samples. The 16S rRNA gene amplicon sequencing and metabolomics approaches were used to investigate the difference in microbes and metabolites in saliva of the control and halitosis groups. The profiles of microbiota and metabolites were relatively different between the halitosis and control groups. The relative abundances of Prevotella, Alloprevotella, and Megasphaera were significantly higher in the halitosis group. In contrast, the relative abundances of Streptococcus, Rothia, and Haemophilus were considerably higher in the control group. The levels of 5-aminovaleric acid and n-acetylornithine were significantly higher in the halitosis group. The correlation between identified metabolites and microbiota reveals that Alloprevotella and Prevotella might be related to the cadaverine and putrescine pathways that cause halitosis. This study could provide insight into the mechanisms of halitosis.

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.

Intervention with kimchi microbial community ameliorates obesity by regulating gut microbiota.

The objective of this study was to evaluate anti-obesity effects of kimchi microbial community (KMC) on obesity and gut microbiota using a high fat diet-induced mouse model compared to effects of a single strain. Administration of KMC decreased body weight, adipose tissue, and liver weight gains. Relative content of Muribaculaceae in the gut of the KMC-treated group was higher than that in the high-fat diet (HFD) group whereas relative contents of Akkermansiaceae, Coriobacteriaceae, and Erysipelotrichaceae were lower in KMC-treated group. Metabolic profile of blood was found to change differently according to the administration of KMC and a single strain of Lactobacillus plantarum. Serum metabolites significantly increased in the HFD group but decreased in the KMC-treated group included arachidic acid, stearic acid, fumaric acid, and glucose, suggesting that the administration of KMC could influence energy metabolism. The main genus in KMC was not detected in guts of mice in KMC-treated group. Since the use of KMC has advantages in terms of safety, it has potential to improve gut microbial community for obese people.

The Arabidopsis Cysteine-Rich Receptor-Like Kinase CRK36 Regulates Immunity through Interaction with the Cytoplasmic Kinase BIK1.

Receptor-like kinases are important signaling components that regulate a variety of cellular processes. In this study, an Arabidopsis cDNA microarray analysis led to the identification of the cysteine-rich receptor-like kinase CRK36 responsive to the necrotrophic fungal pathogen, Alternaria brassicicola. To determine the function of CRK36 in plant immunity, T-DNA-insertion knockdown (crk36) and overexpressing (CRK36OE) plants were prepared. CRK36OE plants exhibited increased hypersensitive cell death and ROS burst in response to avirulent pathogens. Treatment with a typical pathogen-associated molecular pattern, flg22, markedly induced pattern-triggered immune responses, notably stomatal defense, in CRK36OE plants. The immune responses were weakened in crk36 plants. Protein-protein interaction assays revealed the in vivo association of CRK36, FLS2, and BIK1. CRK36 enhanced flg22-triggered BIK1 phosphorylation, which showed defects with Cys mutations in the DUF26 motifs of CRK36. Disruption of BIK1 and RbohD/RbohF genes further impaired CRK36-mediated stomatal defense. We propose that CRK36, together with BIK1 and NADPH oxidases, may form a positive activation loop that enhances ROS burst and leads to the promotion of stomatal immunity.

GDSL lipase 1 regulates ethylene signaling and ethylene-associated systemic immunity in Arabidopsis.

Arabidopsis GDSL lipase 1 (GLIP1) has been shown to modulate systemic immunity through the regulation of ethylene signaling components. Here we demonstrate that the constitutive triple response mutant ctr1-1 requires GLIP1 for the ethylene response, gene expression, and pathogen resistance. The glip1-1 mutant was defective in induced resistance following primary inoculation of necrotrophic pathogens, whereas GLIP1-overexpressing plants showed resistance to multiple pathogens. Necrotrophic infection triggered the downregulation of EIN3 and the activation of ERF1 and SID2 in a GLIP1-dependent manner. These results suggest that GLIP1 positively and negatively regulates ethylene signaling, resulting in an ethylene-associated, necrotroph-induced immune response.

GDSL LIPASE1 modulates plant immunity through feedback regulation of ethylene signaling.

Ethylene is a key signal in the regulation of plant defense responses. It is required for the expression and function of GDSL LIPASE1 (GLIP1) in Arabidopsis (Arabidopsis thaliana), which plays an important role in plant immunity. Here, we explore molecular mechanisms underlying the relationship between GLIP1 and ethylene signaling by an epistatic analysis of ethylene response mutants and GLIP1-overexpressing (35S:GLIP1) plants. We show that GLIP1 expression is regulated by ethylene signaling components and, further, that GLIP1 expression or application of petiole exudates from 35S:GLIP1 plants affects ethylene signaling both positively and negatively, leading to ETHYLENE RESPONSE FACTOR1 activation and ETHYLENE INSENSITIVE3 (EIN3) down-regulation, respectively. Additionally, 35S:GLIP1 plants or their exudates increase the expression of the salicylic acid biosynthesis gene SALICYLIC ACID INDUCTION-DEFICIENT2, known to be inhibited by EIN3 and EIN3-LIKE1. These results suggest that GLIP1 regulates plant immunity through positive and negative feedback regulation of ethylene signaling, and this is mediated by its activity to accumulate a systemic signal(s) in the phloem. We propose a model explaining how GLIP1 regulates the fine-tuning of ethylene signaling and ethylene-salicylic acid cross talk.

Arabidopsis GDSL lipase 2 plays a role in pathogen defense via negative regulation of auxin signaling.

GLIP1 was isolated previously from Arabidopsis, as a salicylic acid-responsive secreted GDSL lipase that functions in resistance to Alternaria brassicicola [I.S. Oh, A.R. Park, M.S. Bae, S.J. Kwon, Y.S. Kim, J.E. Lee, N.Y. Kang, S. Lee, H. Cheong, O.K. Park, Secretome analysis reveals an Arabidopsis lipase involved in defense against Alternaria brassicicola. Plant Cell 17 (2005) 2832-2847.]. To extend our knowledge of the roles played by GLIPs in Arabidopsis, we conducted functional studies of another family member, GLIP2. GLIP2 transcripts were expressed in young seedlings, as well as in the root and stem tissues of mature plants. GLIP2 transcript levels were elevated by treatment with salicylic acid, jasmonic acid and ethylene. Recombinant GLIP2 proteins possessed lipase and anti-microbial activities, inhibiting germination of fungal spores. In comparison to wild type plants, T-DNA insertion glip2 mutants exhibited enhanced auxin responses, including increased lateral root formation and elevated AUX/IAA gene expression. When challenged with the necrotropic bacteria Erwinia carotovora, glip2 mutants exhibited more susceptible phenotypes than wild type plants. These results suggest that GLIP2 plays a role in resistance to Erwinia carotovora via negative regulation of auxin signaling.

GDSL lipase-like 1 regulates systemic resistance associated with ethylene signaling in Arabidopsis.

Systemic resistance is induced by necrotizing pathogenic microbes and non-pathogenic rhizobacteria and confers protection against a broad range of pathogens. Here we show that Arabidopsis GDSL LIPASE-LIKE 1 (GLIP1) plays an important role in plant immunity, eliciting both local and systemic resistance in plants. GLIP1 functions independently of salicylic acid but requires ethylene signaling. Enhancement of GLIP1 expression in plants increases resistance to pathogens including Alternaria brassicicola, Erwinia carotovora and Pseudomonas syringae, and limits their growth at the infection site. Furthermore, local treatment with GLIP1 proteins is sufficient for the activation of systemic resistance, inducing both resistance gene expression and pathogen resistance in systemic leaves. The PDF1.2-inducing activity accumulates in petiole exudates in a GLIP1-dependent manner and is fractionated in the size range of less than 10 kDa as determined by size exclusion chromatography. Our results demonstrate that GLIP1-elicited systemic resistance is dependent on ethylene signaling and provide evidence that GLIP1 may mediate the production of a systemic signaling molecule(s).

Isolation of the Arabidopsis phosphoproteome using a biotin-tagging approach.

Protein phosphorylation plays a key role in signal transduction in cells. Since phosphoproteins are present in low abundance, enrichment methods are required for their purification and analysis. Chemical derivatization strategies have been devised for enriching phosphoproteins and phosphopeptides. In this report, we employed a strategy that replaces the phosphate moieties on serine and threonine residues with a biotin-containing tag via a series of chemical reactions. Ribulose 1,5-bis-phosphate carboxylase/oxygenase (RUBISCO)-depleted protein extracts prepared from Arabidopsis seedlings were chemically modified for 'biotin-tagging'. The biotinylated (previously phosphorylated) proteins were then selectively isolated by avidin-biotin affinity chromatography, followed by two-dimensional gel electrophoresis (2-DE) and matrix-assisted laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). This led to the identification of 31 protein spots, representing 18 different proteins, which are implicated in a variety of cellular processes. Despite its current technical limitations, with further improvements in tools and techniques this strategy may be developed into a useful approach.