The human breast milk microbiota plays a key role in newborn microbial colonisation. Its composition varies throughout the postpartum period and is modulated by maternal and perinatal factors. This scoping review aimed to systematically map current knowledge of the breast milk bacterial microbiota in healthy lactating women and describe its compositional dynamics in relation to identified modulating factors. A systematic search was conducted across five databases (PubMed, ScienceDirect, Scopus, Google Scholar, and Web of Science) following the PRISMA-ScR guidelines targeting studies that used 16S rRNA sequencing. Twenty-three studies from America (6), Europe (5), Asia (11) and Oceania (1) published between 2019 and 2025 were selected, with sample sizes ranging from five to 334 breast milk samples per study. The most consistently reported genera were Streptococcus, Staphylococcus, Lactobacillus, Pseudomonas, and Acinetobacter. The most frequently reported and analysed associated factors across the 23 studies were lactation stage, maternal body mass index (BMI), and mode of delivery. However, the methodological heterogeneity across studies, particularly regarding the hypervariable region analysed, represents the main source of variability in the results. These findings enhance our understanding of breast milk microbiota dynamics and highlight how maternal and perinatal factors influence its composition.

Olfactory impairment is a common early non-motor feature of Parkinson's disease (PD), often preceding motor symptoms by several years. However, the biological mechanisms underlying PD-associated olfactory dysfunction remain poorly understood. This study investigated the relationship between nasal microbiota, metabolites, and olfactory function in PD and explored potential therapeutic targets. A total of 66 participants, including PD patients and healthy controls, were enrolled. Nasal samples were analyzed using 16S rRNA sequencing and metabolomic profiling by GC-MS. An MPTP-induced PD mouse model was used to evaluate the effects of cholic acid supplementation. PD patients exhibited distinct alterations in nasal microbial composition and metabolic profiles, which were associated with olfactory dysfunction severity. Cholic acid showed potential as a candidate biomarker for PD-associated olfactory impairment (AUC > 0.97). In MPTP mice, cholic acid improved olfactory performance and increased TH expression in the olfactory bulb and substantia nigra, but did not significantly improve motor deficits or striatal dopaminergic neuron loss. These findings suggest a potential association between nasal microbiota-associated metabolic alterations and olfactory dysfunction in PD.

The xerophilic fungal genus Wallemia is an important cause of fungal contamination in bread manufacturing environments, but its detection by conventional culture-based methods is often difficult because of slow growth and competitive overgrowth by other fungi. Here, we report the development of a genus-specific TaqMan real-time PCR assay targeting the internal transcribed spacer (ITS) region for rapid detection of Wallemia. Primer and probe sequences were designed based on comparative ITS analysis of all nine recognized Wallemia species and non-target fungi commonly encountered in bakery environments. The probe-binding region was fully conserved among all Wallemia ITS reference sequences evaluated. Analytical specificity was confirmed using synthetic DNA fragments representing predicted amplicon groups, with amplification observed exclusively in Wallemia. The assay demonstrated excellent linear over 10[2]-10[6] copies per reaction (R[2] = 0.9988), with an amplification efficiency of 102.7%. Analytical sensitivity evaluation yielded an estimated LOD95 of 9.46 copies per reaction. Application to environmental swab samples from an operational bakery production line enabled culture-independent detection of Wallemia, including in samples in which culture-based identification was obscured by fungal overgrowth. This assay provides a rapid and specific molecular tool for culture-independent monitoring of Wallemia contamination and may support improved hygienic control in bakery manufacturing environments.

This study aimed to identify kefir-derived microorganisms, evaluate their probiotic potential to select the most promising strain, and assess the selected strain's antibacterial and antibiofilm activities against foodborne isolates, Escherichia coli, and Klebsiella pneumoniae. Kefir grains were cultivated in selective media, and isolates were identified using MALDI-TOF mass spectrometry. Their acid and NaCl tolerance, auto- and co-aggregation, and antimicrobial activity were assessed to identify the most effective probiotic strain. Subsequently, the selected strain was subjected to spot overlay tests, broth microdilution assays, and biofilm inhibition experiments against E. coli and K. pneumoniae isolates. Enterococcus durans, Leuconostoc pseudomesenteroides, Lacticaseibacillus paracasei, and Kluyveromyces marxianus were identified. Among these, L. paracasei (Lpk 01) demonstrated the best probiotic characteristics, with 50% survival at pH 5, tolerance to 2% NaCl, and high co-aggregation with K. pneumoniae (40%). It inhibited pathogens (inhibition zones >14 mm), and its cell-free supernatant (Lpk-cf) reduced biofilm biomass by approximately 50%, with effects minimized upon neutralization, suggesting the involvement of organic acids. These findings affirm the antimicrobial potential of L. paracasei, highlighting its application as a natural alternative against bacterial pathogens.

Benzalkonium chloride (BAC) is a widely used disinfectant, but its improper application can induce Salmonella Typhimurium (S. Typhimurium) to develop tolerance to subsequent stressors. In this study, we demonstrated that adaptation of S. Typhimurium to BAC conferred both direct protection and cross-protection against cold stress, resulting in significantly enhanced survival at -20°C compared with non-adapted cells. BAC-adapted S. Typhimurium also exhibited a survival advantage on chicken meat during frozen storage at -20°C. Membrane fatty acid analysis indicated that adaptation of S. Typhimurium to BAC led to a 2.2-fold increase in the levels of cyclopropane fatty acids. Moreover, BAC-adapted S. Typhimurium showed a significant 8.0% increase in cell surface hydrophobicity. RT-qPCR analysis demonstrated upregulation of efflux pump genes tolC, acrB, and mdfA (3.6-, 3.4-, and 3.0-fold, respectively) and cold shock-related genes cspA, cspE, and rpoS (2.4-, 4.0-, and 2.6-fold, respectively). These findings suggest that upregulation of cold shock genes in BAC-adapted cells was associated with the observed cross-protection. Taken together, adaptation of S. Typhimurium to BAC promoted the development of direct and cross-protective phenotypes, which may increase the risk of cross-contamination and salmonellosis in the food industry, posing a serious threat to food safety and public health.

The combination of sophorolipids and copaiba essential oil in a multifunctional facial formulation aimed at the treatment of conditions such as acne and herpetic folliculitis was evaluated. Sophorolipids produced by Starmerella bombicola reached 38.37 g/l, predominantly in the lactonic form. Their antimicrobial activity, alone and combined with copaiba oil, was evaluated against Cutibacterium acnes, Staphylococcus aureus, and Staphylococcus epidermidis. The combination reduced the minimum inhibitory concentration against C. acnes from 62.50 to 31.25 μg/ml, demonstrating an additive effect. Antiviral assays showed strong anti-HSV-1 activity, with 95.58% inhibition in the virucidal test and 63.99% in the antiviral assay. Three dermocosmetic formulations were developed, and the optimized formulation achieved 91.45% inhibition of C. acnes and 26.17% antioxidant activity, confirming its multifunctional potential. The application of a formulation combining sophorolipids and copaiba oil shows promising potential for the treatment of skin conditions, demonstrating significant antimicrobial activity against C. acnes as well as adequate physicochemical stability.

The increasing prevalence of multidrug-resistant (MDR) Pseudomonas aeruginosa highlights the need for alternative therapeutic strategies. This study evaluated the potential of a commercial bacteriophage cocktail combined with antimicrobial agents and compared two practical methods for screening phage-antimicrobial synergy. A lytic bacteriophage isolated from thepyophage (PYO) phage cocktail was characterized by host range, size, pH, and thermal stability, and lytic activity against the reference strain PAO1. Synergy was assessed with nine antimicrobial agents, including conventional antibiotics, efflux pump inhibitors (EPIs), and essential oil compounds, using agar-based plaque assays and broth microdilution checkerboard assays. Plaque diameter and plaque number were evaluated at sub-MIC concentrations, whereas synergistic interactions were determined by the fractional inhibitory concentration index (FICI). Statistical significance was analyzed using one-way ANOVA followed by Dunnett's multiple comparison test, and the association between plaque parameters and FICI values was explored using Spearman's rank correlation. The isolated phage exhibited a burst size of approximately 259 PFU per infected cell and remained stable over a broad pH and temperature range, with significant reductions under highly acidic, highly alkaline, and high-temperature conditions. In agar-based assays, colistin, meropenem, and cinnamaldehyde significantly increased plaque diameter and/or plaque number (P <0.05-0.001), depending on the bacterial strain tested. Checkerboard analysis identified the same four combinations as synergistic (FICI ≤0.5). Spearman's rank correlation indicated a relationship between plaque parameters and FICI values. Overall, both methods identified the same synergistic combinations, suggesting that agar-based plaque assays may serve as a practical preliminary screening tool for phage-antimicrobial combinations, although further validation is required.

Traditional and industrial soybean fermentations harbor distinct microbial communities that influence product quality and safety. In this study, long-read rRNA operon sequencing was applied to investigate the bacterial communities of traditional and commercial doenjang and cheonggukjang. The 16S-23S rRNA operon (∼4.2 kb) was amplified and sequenced using the Oxford Nanopore MinION platform to obtain high-resolution taxonomic profiles. Traditional doenjang and cheonggukjang exhibited greater microbial diversity than commercial products, as revealed by alpha and beta diversity analyses. Bacillus species, particularly Bacillus velezensis and Bacillus subtilis, were dominant across all samples, while Loigolactobacillus coryniformis, Caldifermentibacillus hisashii, and Tetragenococcus halophilus were more abundant in traditionally fermented samples. These genera are associated with proteolysis, amino acid metabolism, and flavor compound formation during fermentation. Overall, these findings provide insights into the microbial ecology of fermented soybean foods and suggest that non-starter lactic acid bacteria and thermophilic species may contribute to the unique sensory characteristics of traditionally fermented doenjang.

Slow-transit constipation (STC) is characterized by reduced colonic motility, impaired smooth muscle function, and altered mucosal signaling. Among these pathways, mucosal serotonin (5-HT), mainly produced by enterochromaffin cells, contributes to intestinal motility regulation. In a loperamide-induced constipation model in male C57BL/6 J mice, we evaluated the effects of Lactiplantibacillus plantarum NCHBL-004 on bowel function and associated molecular changes. Compared with loperamide-treated mice, live NCHBL-004 at 1 × 10[9] CFU improved fecal output and gastrointestinal transit and partially preserved fecal water content, whereas the lower live dose and heat-killed preparation showed no significant effects. These functional changes were accompanied by preservation of colonic muscularis thickness and increased expression of smooth muscle-associated markers, including Acta2 and Myh11. NCHBL-004 also modulated mucosal serotonergic gene expression, as indicated by increased Tph1, which encodes a key enzyme for 5-HT synthesis, and decreased Slc6a4, which encodes the serotonin transporter involved in 5-HT reuptake. Overall, these findings suggest that live NCHBL-004 improves intestinal motility in loperamide-induced constipation, with associated changes in colonic smooth muscle phenotype and mucosal serotonergic regulation.

Streptococcus agalactiae is a significant opportunistic pathogen causing severe infections, including urinary tract infections and pyelonephritis in diabetic individuals. To explore the molecular mechanisms behind this susceptibility, we used a streptozotocin-induced diabetic murine model to evaluate S. agalactiae renal infection and performed the first comparative proteomic analysis of S. agalactiae COH1 isolates recovered from the kidneys of diabetic and non-diabetic mice. Diabetic mice exhibited significantly higher bacterial loads and more severe renal histopathological damage. Comparative proteomic profiling identified 2751 proteins, with 82 significantly upregulated and 91 downregulated proteins in S. agalactiae COH1 isolate recovered from the kidneys of diabetic animals. Upregulated virulence factors included serine-rich repeat 2, type VII secretion, BibA, C5a peptidase, and PI-1. Functional analysis revealed a metabolic shift toward increased glycolysis, PTS system activity, and translation machinery, suggesting that the hyperglycemia promoted bacterial proliferation and energy production. Conversely, proteins related to proteolysis were downregulated. Our findings demonstrated that hyperglycemia induced a metabolic reprogramming and enhanced the expression of virulence-associated proteins in S. agalactiae. These adaptations contributed to increased colonization and tissue damage in diabetic kidney, providing potential molecular targets for future therapeutic interventions.

Quinolone-resistant Escherichia coli are increasing in humans and livestock; however, their distribution and underlying mechanisms in shared environments remain incompletely characterized. We analyzed quinolone resistance in E. coli isolates from swine (n = 100) and humans (n = 65) associated with an agroecological farm in Morelos, Mexico. Antimicrobial susceptibility testing was performed for quinolones [nalidixic acid (NAL) and ciprofloxacin (CIP)], and the minimum inhibitory concentrations were determined. Phylogenetic grouping and genotypic analyses targeting gyrA mutations and plasmid-mediated quinolone resistance (PMQR) genes were conducted. High frequencies of NAL and moderate CIP resistance were observed in both swine (NAL, 79%; CIP, 23%) and human (NAL, 65%; CIP, 15%) isolates. The predominant phenotype was NAL-resistant/CIP-susceptible, particularly among commensals of phylogroups A and B1. High-level resistance to both antimicrobials was associated with double mutations in gyrA (S83L + D87N), whereas PMQR determinants, including qnr variants and aac(6')-Ib-cr, were widely distributed and linked to lower-level resistance. These findings indicate that quinolone resistance is shaped by the combined contribution of chromosomal mutations and plasmid-mediated mechanisms. The presence of PMQR determinants in isolates with reduced susceptibility highlights their potential role in the early stages of resistance development, emphasizing the urgent need for integrated surveillance of antimicrobial resistance in agricultural and community settings.

The growing complexity of food-safety systems and the increasing emergence of multidrug-resistant (MDR) foodborne pathogens demonstrate the importance of enhanced genomic surveillance. This study employed whole genome sequencing (WGS) to characterise the genomes of Bacillus safensis NWU MK_WT, Enterococcus lactis ENT7_CNKT_NWU, and ENT3_CNKT_NWU, isolated from food sources. Phenotypic antibiotic susceptibility testing revealed that all strains displayed MDR phenotypes, with resistance to erythromycin, ampicillin, and meropenem. Genome assemblies ranged from 2.6 to 3.7 Mb, exhibiting high completeness (100%) and diverse functional gene profiles. Furthermore, antibiotic resistance genes (ARGs), including vanT and aac(6'), mediating antibiotic inactivation, efflux, and target modification, were identified. Virulence factors, including adhesion, invasion, and biofilm formation, were detected across genomes, indicating pathogenic potential. Mobile genetic element profiling revealed the presence of insertion sequences, plasmids, and an intact prophage in B. safensis NWU MK_WT, demonstrating genomic plasticity and the potential for horizontal gene transfer (HGT). Phylogenomic comparison showed close relatedness between the isolates and strains from Asia, suggesting possible transboundary movement of genetic material. These findings highlight the growing relevance of WGS for monitoring opportunistic foodborne bacteria that harbour and disseminate resistance and virulence determinants, provide foundational data for improving food safety surveillance, and support antimicrobial resistance (AMR) mitigation strategies.

Rising levels of antimicrobial resistance (AMR) among foodborne pathogens is an increasing threat to food safety and product quality, driving the search for effective natural alternatives to conventional preservatives. Antimicrobial peptides (AMPs) have emerged as promising candidates for food preservation because of their broad-spectrum activity, diverse mechanisms of action and lower propensity for resistance development. Within this group, the macin family represents a promising yet underexplored class of cysteine-rich AMPs characterised by eight conserved cysteine residues that form four disulfide bonds. Macins have been identified across diverse taxa, including leeches, bivalves, gastropods, and hydrozoans and exhibit diverse antimicrobial mechanisms ranging from bacterial aggrelgation mediated by hydrophobic and electrostatic interactions and membrane permeabilization. This review provides a comprehensive synthesis of current knowledge of the macin family within the broader landscape of AMPs, highlighting their structural diversity, mechanisms of action and potential applications. Collectively, these characteristics suggest that macins may represent promising candidates for controlling resistant foodborne pathogens while maintaining product quality.

This study aimed to elucidate transcriptional adaptation mechanisms in Zygosaccharomyces mellis under high-glucose (50%) conditions and to identify cellular processes involved in osmotic stress tolerance. Transcriptomic analysis was performed to characterize global gene expression changes in cells cultured in yeast extract-malt medium containing 50% glucose (G50). Genes involved in glycolysis, including GAL7 and FBP1, were downregulated, whereas PYC2, associated with the tricarboxylic acid cycle (TCA), was upregulated, suggesting suppression of fermentative metabolism and maintenance of respiratory activity. Genes involved in membrane phospholipid synthesis (AGPAT and PLPP) were downregulated, while an acid sphingomyelinase-like gene (ASM) was upregulated, suggesting altered membrane lipid metabolism under osmotic stress. In addition, the cytokinesis-related gene MYO1 was upregulated, suggesting structural reinforcement under osmotic stress. Furthermore, the growth of Δmmr1 and Δhxt4 mutants in Saccharomyces cerevisiae was significantly impaired under G50 conditions, highlighting the importance of mitochondrial inheritance and regulated glucose uptake. These findings suggest that Z. mellis adapts to high-glucose stress by coordinating changes in gene expression associated with respiratory activity, lipid metabolism, and cell division processes.

Glucosamine and its derivatives have been extensively used in the nutraceutical, cosmetic, food and pharmaceutical industries. Commercial glucosamine production traditionally relies on the acid or enzymatic hydrolysis of crustacean shells, particularly those of shrimp and crabs. However, these processes are often associated with high production costs, environmental concerns, extensive chemical usage, and the generation of hazardous waste. In recent years, microbial production of glucosamine has emerged as a sustainable and environmentally friendly alternative, offering advantages such as milder processing conditions, reduced chemical inputs, and improved process scalability. Microbial approaches include direct glucosamine biosynthesis by native microorganisms, bioconversion of chitin-rich substrates by chitinolytic microbes, and metabolic engineering of recombinant strains for enhanced production. This review explores microbial approaches for glucosamine production, including direct biosynthesis, chitin bioconversion, and recombinant microbial systems. Key challenges related to substrate utilization, process scalability, strain stability, and product recovery are critically evaluated, along with emerging solutions involving metabolic engineering and process optimisation. Additionally, strategies to overcome such challenges such as CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats)-based gene editing, optimization of culture and fermentation conditions etc. have been discussed. This review emphasizes the fact that while microbial production of glucosamine offers clear environmental and economic advantages, their large-scale feasibility depends on addressing these challenges through integrated approaches.