Search Results (304)

Bifidobacterium animalis subsp. lactis is a widely used probiotic, yet its efficacy is highly strain-specific, and growing antibiotic resistance necessitates rigorous safety evaluations. We used whole-genome sequencing and in vitro assays to characterize the safety and probiotic traits of infant feces-sourced strain BD1, which shows preliminary mood-modulating and anti-inflammatory potential. The BD1 genome showed a favorable safety profile. VFDB analysis identified 139 low-similarity homologs, with no major toxins detected. Only four chromosomally encoded antibiotic resistance genes were found; phenotypic testing confirmed resistance solely to tetracycline and mupirocin. Although the tetracycline resistance gene tet(W) was identified in genomic island GI01, the absence of associated mobile genetic elements results in a negligible risk of its mobilization. Functional annotation highlighted a dominant metabolic capacity for carbohydrate and amino acid metabolism. BD1 is rich in CAZymes, enabling superior utilization of diverse substrates (starch, sucrose, galactose). Enrichment in lipid metabolism pathways (glycerolipid, sphingolipid) further suggests potential for enhancing fermented product flavor. In vitro assessment demonstrated moderate gastrointestinal tolerance and strong bile salt tolerance. Surface properties showed pronounced cell surface hydrophobicity and confirmed biofilm-forming potential. In conclusion, BD1 exhibits robust safety, metabolic versatility, and strong probiotic characteristics, supporting its development as a functional probiotic strain. Full article

Lactic acid bacteria (LAB) are increasingly recognized for their role in food biopreservation due to their ability to synthesize antimicrobial compounds. Milk naturally harbors a wide variety of LAB, offering a promising source for identifying strains with biopreservative potential. This study investigated the antagonistic effects, safety characteristics, and technological properties of LAB strains isolated from traditionally fermented milk. Thirty-two dairy samples were analyzed, and the resulting LAB isolates were screened for inhibitory activity against Listeria monocytogenes CECT 4032 and Staphylococcus aureus CECT 976 using agar spot and well diffusion assays. All tested strains exhibited strong antimicrobial effects, with particularly notable inhibition of L. monocytogenes. After phenotypic screening, five representative isolates were selected for molecular identification and further assessment of safety-related attributes, functional capabilities, auto- and co-aggregation properties. 16S rRNA gene sequencing revealed that four strains belonged to the genus Enterococcus, specifically, one E. faecium and three E. durans, while one was classified as a Lactococcus species. Moreover, none of the strains showed proteolytic or lipolytic activities which highlights their potential use in dairy fermentation processes. Full article

Astaxanthin, one of the most commercially valuable carotenoids, is renowned for its potent antioxidant and anti-inflammatory properties and is experiencing growing demand across diverse industries. To enhance astaxanthin production in Paracoccus marcusii, compound mutagenesis was performed using ethyl methanesulfonate (EMS), ultraviolet (UV) radiation, and atmospheric room temperature plasma (ARTP) treatment. Subsequently, a high-throughput microbial microdroplet culture (MMC) system was employed to select fast-growing microdroplet, followed by screening for high astaxanthin-producing mutants on dual-inhibitor plates. The mutant M21 was isolated and exhibited a significant increase of 16.86% in astaxanthin content (1.53 mg/g) and a 19.81% increase in astaxanthin production (11.71 mg/L) compared with the wild type (WT) (p < 0.05). Moreover, the enhanced phenotype of M21 was genetically stable. Response surface methodology (RSM)-based optimization of fermentation conditions further increased astaxanthin content and production to 1.72 mg/g and 12.92 mg/L, respectively, corresponding to improvements of 16.44% and 23.02% over the WT, while simultaneously reducing culture time, total nitrogen requirements, and sodium lactate consumption, thereby lowering production costs. This study achieved significant enhancement of astaxanthin production through novel mutant breeding and fermentation optimization, underscoring the effectiveness of this integrated strategy for application in industrial biotechnology. Full article

Lactiplantibacillus plantarum is widely used in fermented foods and as a probiotic, yet the genomic basis underlying its γ-aminobutyric acid (GABA) production capacity and strain-level functional diversity remains incompletely resolved. We analyzed 1240 publicly available genomes to map species-wide genome architecture, the distribution of GABA-related genes, and accessory drivers of phenotypes. Pangenome analysis identified 45,201 gene families, including 622 strict core genes (1.38%) and 444 soft-core genes (2.36%). The accessory genome dominated (3138 shell and 40,997 cloud genes; 97.64%), indicating a strongly open pangenome. In contrast, the GABA (gad) operon was universally conserved: gadB (glutamate decarboxylase) and gadC (glutamate/GABA antiporter) were present in all genomes regardless of isolates source. Accessory-genome clustering revealed ecological and geographic structure without loss of the operon, suggesting that phenotypes variability relevant to fermentation and probiotic performance is primarily shaped by accessory modules. Accessory features included carbohydrate uptake and processing islands, bacteriocins and immunity systems, stress- and membrane-associated functions, and plasmid-encoded traits. Analysis of complete genomes confirmed substantial variation in plasmid load (median = 2; range = 0–17), highlighting the role of mobile elements in niche-specific adaptation. Carbohydrate-Active Enzymes database (CAZy) and biosynthetic gene cluster (BGC) profiling revealed a conserved enzymatic and metabolic backbone complemented by rare lineage-specific functions. Collectively, these results position L. plantarum as a genetically stable GABA producer with extensive accessory-encoded flexibility and provide a framework for rational strain selection. Full article

Background/Objectives: Recent reports on the co-occurrence of allergies and endometriosis have provided grounds for expanding research in this area, suggesting that diagnostics should be extended to women with endometriosis. However, numerous studies on nutrients and antioxidants do not specify the type of diet that supports the treatment process. In our review, we focus on the types of food elimination and dietary approaches that have been used. Methods: This systematic review was conducted according to the PRISMA guidelines. We searched the EMBASE, PUBMED and SCOPUS databases, as well as the bibliographies of research papers and reviews, including the latest reports from June 2025. The search keywords were “endometriosis” and “type of diet”, “nutrition”, “food products”, “nutrients”, “elimination diet”, and “allergies”. Results: Excluding coexisting allergies and introducing an anti-inflammatory diet low in animal products, limiting butter and margarine, and eliminating fried foods and refined simple sugars may be the best solution to help treat endometriosis. Conclusions: Personalised nutritional counselling for patients with endometriosis is particularly helpful and necessary, as there is no single elimination diet that can be recommended for all patients with endometriosis. The first step should be an anti-inflammatory diet, such as the Mediterranean diet or the MIND diet (Mediterranean-DASH diet intervention for neurological delay), followed by more in-depth allergy screening. The phenotypic diversity of this group of patients may require the use of a low-FODMAP (fermentable oligo-, di-, monosaccharides and polyols), low-nickel, gluten-free or other elimination diet. Full article

Wheat (Triticum aestivum L.), a key global cereal for food and feed, is being improved through gamma irradiation to enhance its nutritional and functional value for forage use. This study examined the forage potential and functional traits of gamma-irradiated colored wheat mutants through integrated analyses of agronomic performance, chemical composition, silage quality, and antioxidant capacity. Nine mutant lines (S1–S9), original colored wheat, and two control cultivars, ‘Cheongwoo’ (forage type) and ‘Keumkang’ (bread type), were evaluated under field conditions. Gamma irradiation (200 Gy) broadened phenotypic and biochemical diversity within the colored wheat background, generating genotypes with distinct biomass and compositional profiles. Several lines, particularly S6 and S8, produced high dry matter yields with balanced crude protein and fiber contents comparable to ‘Cheongwoo’ while maintaining optimal fiber levels for ruminant feeding. Most mutants showed stable fermentation and buffering properties, indicating that radiation-induced variation did not impair silage quality. Antioxidant analyses revealed clear genotypic variation, with the S3 and S1 lines exhibiting elevated phenolic and anthocyanin contents associated with strong radical scavenging activity. Overall, gamma irradiation proved to be an effective approach for generating colored wheat lines with enhanced agronomic performance and functional value, highlighting S3 as a promising dual-purpose whole-crop forage candidate. Full article

Background: This study investigated the phenotypic and genotypic antibiotic resistance profiles of 50 Lactic Acid Bacteria (LAB) strains—25 Lactiplantibacillus plantarum and 25 Lacticaseibacillus paracasei—isolated from traditional Sardinian fermented foods of animal origin. Methods: The sensitivity of the isolates to antibiotics such as β-lactams, tetracyclines, aminoglycosides, macrolides, phenicols, and glycopeptides was initially assessed using disc diffusion and minimum inhibitory concentration (MIC) tests. Subsequently, PCR analyses were performed on both genomic DNA and plasmid DNA to detect blaZ, tet(W), strA, aac(6′)-Ie–aph(2″)-Ia, and vanX genes associated with resistance to ampicillin, tetracycline, streptomycin, gentamicin, and vancomycin. Results: The analysis revealed that L. plantarum strains frequently carried the tet(W) gene on the chromosome and strA on plasmids, while vanX was detected in most strains as a chromosomal determinant. By contrast, L. paracasei strains exhibited a predominantly plasmid-mediated distribution of resistance genes. For example, strA, aac(6′)-Ie–aph(2″)-Ia and blaZ were often found on plasmids, whereas vanX remained chromosomally encoded. Phenotypic assays confirmed high intrinsic resistance to vancomycin in both species, with L. plantarum showing a higher overall frequency and diversity of resistant phenotypes compared to L. paracasei. Conclusions: The co-occurrence of multiple resistance determinants, including plasmid-encoded ones, in most strains suggests that even autochthonous isolates from artisanal products may represent potential reservoirs for transmissible resistance genes. Full article

This study presents the phenotypic characterization and genomic mining of uric acid catabolism genes in Lactiplantibacillus plantarum YC, a novel food-grade lactic acid bacterium isolated from traditional fermented vegetables with potent uric acid-lowering activity. YC is non-hemolytic, catalase- and gelatinase-negative, exhibits strong adhesion and broad antibacterial activity, and degrades 29.22% of uric acid in vitro, along with complete (100%) degradation of inosine and guanosine. Whole-genome sequencing revealed a 3,214,448 bp chromosome encoding 3026 protein-coding genes. Comparative genomics-based functional annotation highlighted abundant CAZy-related genes and antimicrobial factors, including lysozyme and monooxygenase. Crucially, genomic mining identified a complete uric acid degradation gene cluster, comprising pucK (uric acid permease), hpxO (uric acid hydroxylase), eight copies of hiuH (5-hydroxyisourate hydrolase), allB (allantoinase), and purine nucleoside transport/metabolism genes (rihA, rihB, rihC, pbuG). This work provides the first comparative genomic insight into the genetic architecture and distribution of uric acid metabolism in L. plantarum, elucidating YC’s dual urate-lowering mechanism and delivering key molecular markers for developing enzyme-based functional foods and microbial therapeutics against hyperuricemia. Full article

The functional landscape of the skin microbiome is largely defined by dominant genera such as Cutibacterium and Staphylococcus, whereas rare commensals remain poorly understood. In this study, we identified Rothia kristinae BF00107, a skin-resident strain with a complete pantothenate biosynthesis pathway, as a novel postbiotic candidate with distinct dermatological benefits. BF00107 fermentation filtrate suppressed pro-inflammatory cytokines (IL-1β and TNF-α) in keratinocytes and restored extracellular matrix homeostasis in UVB-irradiated fibroblasts by upregulating COL1A1 expression and reducing MMP-1 levels. Consistent with the observed phenotypes, transcriptomic profiling revealed a strain-specific signature characterized by downregulation and upregulation of the expression of inflammatory mediators and barrier- and ECM-associated genes, respectively. Comparative genomics and metabolite profiling confirmed BF00107 as a unique high-pantothenate producer. Supplementation with pantothenic acid reproduced the anti-inflammatory and barrier-supporting effects of the strain, confirming its role as a key effector metabolite. Furthermore, BF00107 passed standard safety assessments, including the Human Repeat Insult Patch Test (HRIPT), Ames, and irritation tests, supporting its suitability for human applications. These findings establish the pantothenate-producing R. kristinae BF00107 as the first functionally validated Rothia strain with anti-inflammatory and photoaging-protective properties. This study expands the functional scope of the skin microbiome and highlights rare commensals as valuable reservoirs for safe, strain-specific postbiotic development. Full article

Background/Objectives: The growing demand for functional foods and alternative therapeutic strategies has intensified the search for novel probiotic strains from underexplored ecosystems. This study aimed to isolate and phenotypically characterize lactic acid bacteria (LAB) from spontaneously fermented fruits found in the Legal Amazon (Ananas comosus, Humiria balsamifera, Manilkara zapota, and Platonia insignis) and to perform genome-based analysis of the most promising isolate to evaluate its probiotic potential. Methods: The isolates were identified by MALDI-TOF-MS and screened for tolerance to low pH, bile salts, lysozyme, growth at 39 °C, and antimicrobial activity against five enteric pathogens. The most promising isolate was evaluated by coaggregation and biofilm assays, in silico proteome and CAZyme analysis, bacteriocin cluster mining, and in vivo efficacy testing using Tenebrio molitor larvae. Results: Three isolates from H. balsamifera were identified as Lactiplantibacillus plantarum (M1, M2, M4) by MALDI-TOF-MS. These isolates exhibited high resilience to all tested physiological stressors. Antimicrobial activity was contact-dependent, with no inhibition by cell-free supernatants. M2 showed the strongest pathogen exclusion, moderate biofilm formation, and high coaggregation with S. enterica and E. faecalis. Genome analysis of M2 revealed a 3.40 Mb chromosome, absence of acquired resistance or virulence genes, two plantaricin gene clusters, and 93 CAZymes, including GT families linked to exopolysaccharides biosynthesis. SignalP predicted secretion signals in 10 CAZymes. M2 significantly improved larval survival against E. coli and S. enterica, especially under prophylactic treatment. Conclusions: L. plantarum M2 combines safety, stress tolerance, genomic features, and in vivo efficacy, positioning it as a promising probiotic candidate adapted to tropical niches. These findings highlight H. balsamifera as a reservoir of novel probiotic strains. Full article

Donkey milk is an underexplored biological niche with distinctive nutritional and microbiological properties, potentially harboring lactic acid bacteria (LAB) with technological or probiotic value. In this study, raw milk from the endangered Zamorano-Leonesa donkey breed was stored at 4 °C for 24 h to simulate realistic cold-chain conditions and favor the recovery of cold-tolerant microorganisms. Fourteen isolates were obtained, eight of which belonged to LAB or species with potential technological interest and were selected for functional evaluation. Phenotypic screening showed that most isolates tolerated acidic conditions (pH 2.5) and that four also resisted 0.3% bile salts. Acidification assays in pasteurized donkey milk revealed variable fermentation performance, with L. mesenteroides subsp. mesenteroides B8 and Lacticaseibacillus paracasei subsp. tolerans B19 displaying the most favorable profiles. These two strains were selected for genome sequencing. Genomic analysis revealed genes associated with acid and bile resistance, adhesion, cold and environmental stress responses, and carbohydrate metabolism. Both genomes also encoded biosynthetic gene clusters linked to secondary metabolites, including β-lactones, lincosamides, and RiPP-like compounds. No acquired antimicrobial resistance genes were detected. To our knowledge, this is the first study combining isolation, phenotypic screening, and genome-based characterization of cold-tolerant LAB from Zamorano-Leonesa donkey milk. Our findings highlight this milk as a valuable reservoir of safe, cold-adapted microorganisms with promising applications in functional dairy products and food biotechnology. Full article

Brettanomyces bruxellensis is a yeast that causes spoilage in red wines due to its ability to produce volatile phenols, compounds associated with major sensory defects. Specific monitoring of low populations of this species in complex ecosystems such as wine during fermentation or aging often relies on plating onto selective media supplemented with cycloheximide. However, the variability of B. bruxellensis sensitivity to this antibiotic needs to be better characterized. A collection of 175 B. bruxellensis strains was, thus, grown on YPD medium supplemented with increasing concentrations of cycloheximide (0 to 0.5 g.L⁻¹), and yeast development was monitored for 20 days by image analysis. This study revealed significant inter-strain variability, with some strains showing very late or even no growth at high cycloheximide concentrations. The cycloheximide inhibitory effect was also dose- and population-dependent. In addition, colony size was frequently reduced at high doses. Additional tests were conducted on a subset of strains grown in wines with either low pH or high alcohol content or containing sulfur dioxide and then plated in the presence of increasing concentrations of cycloheximide. This revealed a cumulative effect of wine and cycloheximide stresses that resulted in an even higher delay in yeast detection. The results confirm the huge phenotypic diversity of the species and highlight the need to adapt the plates’ incubation time, particularly when the selectivity and the doses of cycloheximide needed are high (samples taken in pre-fermentation phases or during fermentation) or in case of stressful wine analysis, to minimize the risk of false negatives. Full article

Diet influences brain health through many connected metabolic and molecular pathways, and these effects are stronger in obesity. This review links diet quality with cognitive decline and dementia risk. Ultra-processed, high-fat, high-sugar diets drive weight gain, insulin resistance, and chronic inflammation. These changes trigger brain oxidative stress, reduce DNA repair, deplete NAD⁺, disturb sirtuin/PARP balance, and alter epigenetic marks. Gut dysbiosis and leaky gut add inflammatory signals, weaken the blood–brain barrier, and disrupt microglia. Mediterranean and MIND diets, rich in plants, fiber, polyphenols, and omega-3 fats, slow cognitive decline and lower dementia risk. Trials show extra benefit when diet improves alongside exercise and vascular risk control. Specific nutrients can help in certain settings. DHA and EPA support brain health in people with low omega-3 status or early disease. B-vitamins slow brain shrinkage in mild cognitive impairment when homocysteine is high. Vitamin D correction is beneficial when levels are low. A practical plan emphasizes healthy eating and good metabolic control. It includes screening for deficiencies and supporting the microbiome with fiber and fermented foods. Mechanism-based add-ons, such as NAD⁺ boosters, deserve testing in lifestyle-focused trials. Together, these measures may reduce diet-related brain risk across the life span. At the same time, artificial intelligence can integrate diet exposures, adiposity, metabolic markers, multi-omics, neuroimaging, and digital phenotyping. This can identify high-risk phenotypes, refine causal links along the diet–obesity–brain axis, and personalize nutrition-plus-lifestyle interventions. It can also highlight safety, equity, and privacy considerations. Translationally, a pattern-first strategy can support early screening and personalized risk reduction by integrating diet quality, adiposity, vascular risk, micronutrient status, and microbiome-responsive behaviors. AI can aid measurement and risk stratification when developed with privacy, equity, and interpretability safeguards, but clinical decisions should remain mechanism-aligned and trial-anchored. Full article

The high level of acetaldehyde produced by yeast is a significant concern for all enterprises of beer production. To obtain industrial beer yeast strains with low ability to produce acetaldehyde, a multi-step screening strategy was established, using Co⁶⁰γ mutagenesis, high-throughput screening, and adaptive evolution. A mutant strain (Lager-C) with low production of acetaldehyde was obtained, which had 54% less activity of alcohol dehydrogenase and 64% more activity of acetaldehyde dehydrogenase. Consequently, the formation of acetaldehyde by the Lager-C strain was 63% lower than that of wild-type Lager yeast. In addition, the Lager-C strain maintained phenotypic stability and a consistently lower content of acetaldehyde when continuously fermented for five generations. Furthermore, this mutant strain has similar fermentation performance to that of the wild-type strain. Thus, this novel applied screening strategy and the Lager-C strain will lay a solid foundation for the subsequent development of improved yeast strains for the beer industry. Full article

Gut-derived uremic toxins may play a key role in neurodevelopmental conditions such as autism spectrum disorder (ASD) via host-microbe metabolic interactions. We evaluated five uremic toxins—p-cresyl sulfate (PCS), indoxyl sulfate (IS), trimethylamine N-oxide (TMAO), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA)—in urine samples of 97 children with ASD and 71 neurotypical controls, stratified by Bristol Stool Chart (BSC) consistency types. Four of these toxins (PCS, IS, TMAO, ADMA) were integrated into a novel composite biomarker called the Metabolic Index of Gut Dysfunction (MIGD), while SDMA was measured as a complementary renal function marker. While individual metabolite levels showed no statistically significant differences, group-wise analysis by stool phenotype revealed distinct trends. ASD children with hard stools (BSC 1–2) showed elevated PCS levels and the MIGD score (median 555.3), reflecting phenolic fermentation dominance with reduced indolic detoxification. In contrast, children with loose stools (BSC 6–7) had the lowest MIGD values (median 109.8), driven by higher IS and lower ADMA concentrations, suggestive of enhanced indole metabolism. These findings indicate that MIGD may serve as a novel biomarker to stratify metabolic phenotypes in ASD, linking urinary metabolite patterns to gut function. Further validation in larger and longitudinal cohorts is warranted to confirm its potential utility in precision microbiota-targeted interventions. Full article