Antibacterial efficacy and possible mechanism of action of 2-hydroxyisocaproic acid (HICA)

Pathway and Production Differences in Branched-Chain Hydroxy Acids as Bioactive Metabolites in Limosilactobacillus fermentum, Ligilactobacillus salivarius, and Latilactobacillus sakei

Branched-chain hydroxy acids (BCHAs) as bioactive metabolites of Lactobacillaceae include 2-hydroxy isovaleric acid (HIVA), 2-hydroxy isocaproic acid (HICA), and 2-hydroxy-3-methyl isovaleric acid (HMVA). Combining targeted and untargeted metabolomics, this study elucidates differences in extracellular BCHA production in Limosilactobacillus fermentum, Ligilactobacillus salivarius, and Latilactobacillus sakei alongside comparing comprehensive metabolic changes. Through targeted metabolomics, BCHA production among 38 strains exhibited strain specificity, except for L. sakei, which showed significantly lower BCHA production. Explaining the lower production in L. sakei, which lacks the branched-chain amino acid (BCAA)-utilizing pathway, comparison of BCHA production by precursor reaction revealed that the pathway utilizing BCAAs is more dominant than the pathway utilizing pyruvate. Expanding upon the targeted approach, untargeted metabolomics revealed the effects of the reaction compound on other metabolic pathways besides BCHAs. Metabolism alterations induced by BCAA reactions varied among species. Significant differences were observed in glycine, serine, and threonine metabolism, pyruvate metabolism, butanoate metabolism, and galactose metabolism (p < 0.05). These results emphasize the importance of the synergy between fermentation strains and substrates in influencing nutritional components of fermented foods. By uncovering novel aspects of BCAA metabolism pathways, this study could inform the selection of fermentation strains and support the targeted production of BCHAs.

Fermentation of Polygonati Rhizoma aqueous extract using Lactiplantibacillus plantarum under the condition of eutrophication

In this experiment, the eutrophication system was established by adding sucrose and yeast powder, and the pH and dissolved oxygen were measured in a bioreactor in real time to study the effect of aerobic environment on the fermentation process of Polygonati Rhizoma extract by Lactiplantibacillus plantarum. To further analyze metabolic changes, UPLC-Q-Exactive MS was used for metabolomic analysis and metabolic profiling. Multivariate analysis was performed using principal component analysis and Orthogonal projections to latent structures discriminant analysis. Finally, 313 differential metabolites were selected, 196 of which were annotated through database matching. After fermentation, the content of short-chain fatty acids, lactic acid, and their derivatives increased significantly, and there were 13 kinds and 4 kinds, respectively. Both compounds and their derivatives are beneficial to the intestinal flora. Consequently, incorporating L. plantarum into the aerobic fermentation process of Polygonati Rhizoma extract within the eutrophic system is potentially advantageous in enhancing the impact of its fermentation solution on the gut microbiota and its effects on human health. Our findings for this kind of edible and medicinal material research and development offer useful insights.

Implication of Molecular Constraints Facilitating the Functional Evolution of Pseudomonas aeruginosa KPR2 into a Versatile α-Keto-Acid Reductase

Theoretical concepts linking the structure, function, and evolution of a protein, while often intuitive, necessitate validation through investigations in real-world systems. Our study empirically explores the evolutionary implications of multiple gene copies in an organism by shedding light on the structure-function modulations observed in Pseudomonas aeruginosa's second copy of ketopantoate reductase (PaKPR2). We demonstrated with two apo structures that the typical active site cleft of the protein transforms into a two-sided pocket where a molecular gate made up of two residues controls the substrate entry site, resulting in its inactivity toward the natural substrate ketopantoate. Strikingly, this structural modification made the protein active against several important α-keto-acid substrates with varied efficiency. Structural constraints at the binding site for this altered functional trait were analyzed with two binary complexes that show the conserved residue microenvironment faces restricted movements due to domain closure. Finally, its mechanistic highlights gathered from a ternary complex structure help in delineating the molecular perspectives behind its kinetic cooperativity toward these broad range of substrates. Detailed structural characteristics of the protein presented here also identified four key amino acid residues responsible for its versatile α-keto-acid reductase activity, which can be further modified to improve its functional properties through protein engineering.

Bacterial Growth Modulatory Effects of Two Branched-Chain Hydroxy Acids and Their Production Level by Gut Microbiota

Branched-chain hydroxy acids (BCHAs), produced by lactic acid bacteria, have recently been suggested as bioactive compounds contributing to the systemic metabolism and modulation of the gut microbiome. However, the relationship between BCHAs and gut microbiome remains unclear. In this study, we investigated the effects of BCHAs on the growth of seven different families in the gut microbiota. Based on in vitro screening, both 2-hydroxyisovaleric acid (HIVA) and 2-hydroxyisocaproic acid (HICA) stimulated the growth of Lactobacillaceae and Bifidobacteriaceae, with HIVA showing a significant growth promotion. Additionally, we observed not only the growth promotion of probiotic Lactobacillaceae strains but also growth inhibition of pathogenic B. fragilis in a dosedependent manner. The production of HIVA and HICA varied depending on the family of the gut microbiota and was relatively high in case of Lactobacillaceae and Lachnosporaceae. Furthermore, HIVA and HICA production by each strain positively correlated with their growth variation. These results demonstrated gut microbiota-derived BCHAs as active metabolites that have bacterial growth modulatory effects. We suggest that BCHAs can be utilized as active metabolites, potentially contributing to the treatment of diseases associated with gut dysbiosis.

Facemask acne attenuation through modulation of indirect microbiome interactions

During the COVID-19 pandemic, facemasks played a pivotal role in preventing person-person droplet transmission of viral particles. However, prolonged facemask wearing causes skin irritations colloquially referred to as 'maskne' (mask + acne), which manifests as acne and contact dermatitis and is mostly caused by pathogenic skin microbes. Previous studies revealed that the putative causal microbes were anaerobic bacteria, but the pathogenesis of facemask-associated skin conditions remains poorly defined. We therefore characterized the role of the facemask-associated skin microbiota in the development of maskne using culture-dependent and -independent methodologies. Metagenomic analysis revealed that the majority of the facemask microbiota were anaerobic bacteria that originated from the skin rather than saliva. Previous work demonstrated direct interaction between pathogenic bacteria and antagonistic strains in the microbiome. We expanded this analysis to include indirect interaction between pathogenic bacteria and other indigenous bacteria classified as either 'pathogen helper (PH)' or 'pathogen inhibitor (PIn)' strains. In vitro screening of bacteria isolated from facemasks identified both strains that antagonized and promoted pathogen growth. These data were validated using a mouse skin infection model, where we observed attenuation of symptoms following pathogen infection. Moreover, the inhibitor of pathogen helper (IPH) strain, which did not directly attenuate pathogen growth in vitro and in vivo, functioned to suppress symptom development and pathogen growth indirectly through PH inhibitory antibacterial products such as phenyl lactic acid. Taken together, our study is the first to define a mechanism by which indirect microbiota interactions under facemasks can control symptoms of maskne by suppressing a skin pathogen.

A Potential Intracanal Medicament, 2-Hydroxyisocaproic Acid (HICA): Cytotoxicity, Genotoxicity, and Its Effect on SCAP Differentiation

Intracanal medicaments with maximal antimicrobial efficacy and minimal damage to resident stem cells are essential for successful regenerative endodontic procedures. 2-Hydroxyisocaproic acid (HICA) could have the attributes of a potential intracanal medicament. This study evaluates its cytotoxicity, genotoxicity, and effects on the odontogenic and osteogenic differentiation of the stem cells of the apical papilla (SCAP). Cytotoxicity and cell viability assays were performed on cells treated for 24, 48, and 72 h with varying concentrations of HICA and compared to the standard intracanal medicament, calcium hydroxide. The genotoxicity was assessed via immunofluorescence for two markers of DNA double-strand breaks: phosphorylated γH2AX and 53BP1. The SCAP differentiation was evaluated based on the alkaline phosphatase activity, Alizarin Red staining, and expression of odontogenic and osteogenic genes (DSPP1, BSP1, OCN, RUNX2) in the presence of selected HICA concentrations. HICA was not cytotoxic at concentrations up to 10 mg/mL, regardless of the exposure time, although it was cytostatic at all tested concentrations. HICA was not genotoxic at concentrations below 5 mg/mL. No difference in cytotoxicity or genotoxicity was found between HICA and calcium hydroxide at 1 mg/mL. HICA retained about 70% of the osteogenic differentiation potential at 1 mg/mL. Within the limitations of this in vitro study, we show that HICA at 1 mg/mL could be a potential intracanal medicament for REPs.

The impact of probiotic cell-free metabolites in MDR Pseudomonas aeruginosa: antibacterial properties and effect on antibiotic resistance genes expression

There is a significant demand for novel antibacterial agents against multidrug-resistant (MDR) gram-negative bacteria. Recently, probiotics have been noted for their antibacterial properties against various pathogens. This study aimed to investigate the effects of probiotic cell-free supernatants on MDR Pseudomonas aeruginosa. Clinical isolates demonstrating the highest degree of antibiotic resistance were chosen, and the antibacterial effect of probiotic metabolites was evaluated using an agar-well diffusion assay. In addition, the effect of probiotics on the expression of resistance genes was evaluated using real-time PCR. The CFS was assessed using GC-MS to determine the antibacterial compounds. The supernatants inhibited the growth of the isolates (P < 0.0001); however, there was no noticeable difference in the effectiveness of the probiotics. In addition, the supernatants decreased the expression levels of mexD, mexB, mexF, and ampC, and an increase in oprD was observed in some groups. After the assessment of Lactobacillus acidophilus by GC-MS, antibacterial compounds, such as acetamide, nonadecane, 9-methyl, and tetradecane, were determined. Our findings showed that probiotic metabolites can effectively inhibit the growth of MDR P. aeruginosa. Gene expression analysis also revealed that the mechanism of antibacterial action was most likely related to the regulation of efflux pumps.

Biochemical, functional and genomic characterization of a new probiotic Ligilactobacillus salivarius F14 from the gut of tribes of Odisha

Characterization of new potential probiotics is desirable in the field of research on probiotics for their extensive use in health and disease. Tribes could be an unusual source of probiotics due to their unique food habits and least dependence on medications and consumption of antibiotics. The aim of the present study is to isolate lactic acid bacteria from tribal fecal samples of Odisha, India, and characterize their genetic and probiotic attributes. In this context one of the catalase-negative and Gram-positive isolates, identified using 16S rRNA sequencing as Ligilactobacillus salivarius, was characterized in vitro for its acid and bile tolerance, cell adhesion and antimicrobial properties. The whole genome sequence was obtained and analyzed for strain level identification, presence of genomic determinants for probiotic-specific features, and safety. Genes responsible for its antimicrobial and immunomodulatory functions were detected. The secreted metabolites were analyzed using high resolution mass spectroscopy; the results indicated that the antimicrobial potential could be due to the presence of pyroglutamic acid, propionic acid, lactic acid, 2-hydroxyisocaproic acid, homoserine, and glutathione, and the immuno-modulating activity, contributed by the presence of short chain fatty acids such as acetate, propionate, and butyrate. So, to conclude we have successfully characterized a Ligilactobacillus salivarius species with potential antimicrobial and immunomodulatory ability. The health-promoting effects of this probiotic strain and/or its derivatives will be investigated in future.

Commensal Lactobacilli Metabolically Contribute to Cervical Epithelial Homeostasis in a Species-Specific Manner

In reproductive-age women, the vaginal microbiome is typically dominated by one or a few Lactobacillus species, including Lactobacillus crispatus, Lactobacillus iners, Lactobacillus paragasseri, Lactobacillus mulieris, and Lactobaccillus crispatus, has been associated with optimal cervicovaginal health; however, much is still unknown about how other lactobacilli metabolically contribute to cervicovaginal health. We hypothesized that metabolites of each Lactobacillus species differ and uniquely contribute to health and homeostasis. To address this hypothesis, we utilized a human three-dimensional (3D) cervical epithelial cell model in conjunction with genomics analyses and untargeted metabolomics to determine the metabolic contributions of less-studied vaginal lactobacilli-L. iners, L. paragasseri, and L. mulieris. Our study validated that vaginal lactobacilli exhibit a close phylogenetic relationship. Genomic findings from publicly available strains and those used in our study indicated that L. iners is metabolically distinct from other species of lactobacilli, likely due to a reduced genome size. Lactobacilli and mock controls were distinguishable based on global metabolic profiles. We identified 95 significantly altered metabolites (P < 0.05) between individual lactobacilli and mock controls. Metabolites related to amino acid metabolism were shared among the lactobacilli. N-Acetylated amino acids with potential antimicrobial properties were significantly elevated in a species-specific manner. L. paragasseri and L. iners shared aromatic, but not carbohydrate-derived, lactic acid metabolites with potential antimicrobial properties that may contribute to homeostasis of the cervicovaginal environment. Additionally, L. iners uniquely altered lipid metabolism, which may be a sign of adaptation to the cervicovaginal niche. Overall, these findings further elucidate the metabolic contributions of three key vaginal Lactobacillus species in gynecological health. IMPORTANCE Lactobacillus species contribute to cervicovaginal health by their production of lactic acid and other antimicrobial compounds. Yet, much is still unknown regarding the metabolic potential of lesser-studied but common vaginal lactobacilli. Here, we used untargeted metabolomics coupled with our 3D cervical epithelial cell model to identify metabolic differences among vaginal Lactobacillus species (Lactobacillus iners, Lactobacillus paragasseri, and Lactobacillus mulieris) and how those differences related to maintaining homeostasis of the cervical epithelium. Human 3D cell models are essential tools for studying host-bacteria interactions and reducing confounding factors inherent in clinical studies. Therefore, these unique models allowed us to decipher the putative lactobacilli mechanisms that contribute to their roles in health or disease. Metabolic analyses revealed distinct profiles of each Lactobacillus species but also shared metabolic contributions associated with antimicrobial activity: amino acid metabolism, N-acetylated amino acids, and aromatic lactic acids. These patterns provided validation of metabolites associated with health in clinical studies and provided novel targets, including immunomodulatory and antimicrobial metabolites, for postbiotic therapies.

Rapid Quantitative Analysis of Metabolites in Kimchi Using LC-Q-Orbitrap MS

Kimchi is a traditional Korean salted spontaneous lactic acid bacteria (LAB)-fermented food made using various vegetables. Organic acids, free sugars, and amino acids are key metabolites produced during LAB fermentation that determine the taste and quality of kimchi. However, each metabolite is typically analyzed using an independent analytical method, which is time-consuming and expensive. Therefore, in this study, we developed a method based on LC-Q-Orbitrap MS using which 20 types of representative fermented kimchi metabolites were selected and simultaneously analyzed within 10 min. The established method was validated, and its detection and quantification limits, linearity, precision, and accuracy were found to satisfy the Association of Official Agricultural Chemists (AOAC) validation guidelines. The 20 metabolites were simultaneously extracted from kimchi with different degrees of fermentation and quantitatively analyzed using LC-Q-Orbitrap MS. These results were analyzed using linear discriminant analysis and heat mapping, and the metabolites were grouped into early, middle, and late stages of fermentation. Malic acid (6.518-7.701 mMol) was only present in the initial stage of fermentation, and l-phenylalanine rapidly increased from the middle stage (2.180 mMol) to late stage (4.770 mMol). Lactic acid, which is representative of the sour taste of kimchi, was detected in the middle stage and increased rapidly up to 74.452 mMol in the late stage. In summary, in this study, 20 major kimchi metabolites were accurately analyzed within 10 min and grouped based on the degree of fermentation. Therefore, the method established in this study accurately and rapidly provides information on kimchi consumption and fermentation that could be highly valuable to the kimchi industry and kimchi consumers.

Comprehensive analysis of metabolites produced by co-cultivation of Bifidobacterium breve MCC1274 with human iPS-derived intestinal epithelial cells

Examining how host cells affect metabolic behaviors of probiotics is pivotal to better understand the mechanisms underlying the probiotic efficacy in vivo. However, studies to elucidate the interaction between probiotics and host cells, such as intestinal epithelial cells, remain limited. Therefore, in this study, we performed a comprehensive metabolome analysis of a co-culture containing Bifidobacterium breve MCC1274 and induced pluripotent stem cells (iPS)-derived small intestinal-like cells. In the co-culture, we observed a significant increase in several amino acid metabolites, including indole-3-lactic acid (ILA) and phenyllactic acid (PLA). In accordance with the metabolic shift, the expression of genes involved in ILA synthesis, such as transaminase and tryptophan synthesis-related genes, was also elevated in B. breve MCC1274 cells. ILA production was enhanced in the presence of purines, which were possibly produced by intestinal epithelial cells (IECs). These findings suggest a synergistic action of probiotics and IECs, which may represent a molecular basis of host-probiotic interaction in vivo.

Valorization of Spent Sugarcane Fermentation Broth as a Source of Phenolic Compounds

A methodology based on a solid phase extraction (SPE) was optimized for the recovery of phenolic compounds from the spent fermentation broth generated from Biofene® (trans-β-farnesene) production. For this purpose, two resins (XAD-2 and HP-20) and three desorption solutions (water, 50/50 ethanol/water, and ethanol) were tested. The most efficient resin revealed to be the HP-20, using ethanol as desorption solution, reaching an overall total phenolic compound recovery of ca. 80% when 6 BV (bed volume) of both feed and ethanol were applied. The optimization of the resin’s process cycle pointed to 15 BV feed to be treated per cycle and using the same volume of ethanol in the desorption step, with no need for an extra resin regeneration step, stably yielding 48% total phenolic compound recovery from the spent broth for at least 4 cycles, translating into 60 BV of feed being treated per BV of resin, and with the resin being still perfectly active. The extract was characterized using LC−ESI−UHR−QqTOF−MS, and a total of 82 and 15 compounds were identified, in negative and positive ionization modes, respectively. Organic acids were the main class of compounds identified in the phenolic-rich extract, followed by phenolic compounds, saccharides, peptides or amino acids and vitamins. Additionally, the extract revealed a significant antioxidant capacity (914.1 ± 51.6 and 2764.5 ± 142.8 µmol Trolox equivalents/g-dw, respectively, with ABTS and ORAC methodologies), which might be interesting for a wide variety of applications.