{"title":"A genus-specific TaqMan real-time polymerase chain reaction assay for the rapid detection of Wallemia in bakery production environments.","authors":"Akira Aoki, Megumi Watanabe, Asuka Maruo, Machiko Kuchiji, Yoshinori Okamoto","doi":"10.1093/lambio/ovag072","DOIUrl":"10.1093/lambio/ovag072","url":null,"abstract":"<p><p>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 polymerase chain reaction 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 linearity over 10²-10⁶ copies per reaction (R² = 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.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Loisa R Hancco-Vera, Ana M Ahuate-Toribio, Kevin W Lévano-Olín, Rodrigo A Suarez-Silva, Yndalú K Huillca-Pari, Luis C Lizarraga-Vargas, Sandra Condori-Catachura, Cinthya J Lovon-Luque
{"title":"Breast milk microbiota in healthy women: a scoping review of modulating factors and the dynamics of bacterial composition during lactation.","authors":"Loisa R Hancco-Vera, Ana M Ahuate-Toribio, Kevin W Lévano-Olín, Rodrigo A Suarez-Silva, Yndalú K Huillca-Pari, Luis C Lizarraga-Vargas, Sandra Condori-Catachura, Cinthya J Lovon-Luque","doi":"10.1093/lambio/ovag070","DOIUrl":"10.1093/lambio/ovag070","url":null,"abstract":"<p><p>The human breast milk microbiota plays a key role in newborn microbial colonization. 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 analyzed 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 analyzed, 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.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"From clean to colonized: microbial dynamics of bed linen over time.","authors":"Caroline Cayrou, Marina Abu-Aita, Katie Laird","doi":"10.1093/lambio/ovag078","DOIUrl":"10.1093/lambio/ovag078","url":null,"abstract":"<p><p>Bed linen can act as a reservoir for microorganisms transferred from skin, dust, and the environment. Despite the importance of linen hygiene in healthcare and hospitality, evidence on bed-changing frequency is limited, with studies reporting only cross-sectional microbiological data. This study investigated longitudinal bacterial and fungal colonization of bed linen over 4 weeks in a domestic environment. Nine participants used polycotton bed linen for 1 day to 4 weeks. Swatches were collected from the pillow, hip, and foot regions, analyzed using viable counts and amplicon-based sequencing. After use, bacterial and fungal loads increased, respectively, from 3.61 log₁₀CFU/25 cm² and 3.25 log₁₀CFU/25 cm² at day one to 3.96 log₁₀CFU/25 cm² and 3.63 log₁₀CFU/25 cm² after one week. Loads remained stable over four weeks (bacteria > 3.9 log₁₀; fungi > 3.5 log₁₀CFU/25 cm²). Amplicon-based sequencing showed that 65% of samples were dominated by Staphylococcus spp. (50%-99% relative abundance), with S. capitis, S. hominis, and S. epidermidis most frequent. Fungal communities varied but commonly included Naganishia spp., Candida spp., and Penicillium spp. These findings demonstrate rapid microbial accumulation on bed linen, which remains stable over a month. Although based on a small domestic cohort, the microbial burden suggests a potential role for bed linen in exposure risk, supporting the need to consider bed-changing practices.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148977140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Victor Alves Carneiro, Maria Leilah Monte Coelho Lourenço, Edrine Vasconcelos Farias Magalhães, Paulo Adenes Teixeira Coelho, Benise Ferreira Silva, Rafaela Mesquita Bastos Cavalcante, Renata Albuquerque Costa
{"title":"Kefir-derived Lacticaseibacillus paracasei as a promising candidate against planktonic and biofilm cells of foodborne Escherichia coli and Klebsiella pneumoniae.","authors":"Victor Alves Carneiro, Maria Leilah Monte Coelho Lourenço, Edrine Vasconcelos Farias Magalhães, Paulo Adenes Teixeira Coelho, Benise Ferreira Silva, Rafaela Mesquita Bastos Cavalcante, Renata Albuquerque Costa","doi":"10.1093/lambio/ovag069","DOIUrl":"10.1093/lambio/ovag069","url":null,"abstract":"<p><p>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 ∼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.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148726558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alethea Vlen M Lopez, Kenshi Watanabe, Mark Kevin P Devanadera, Ray Angelo G Santos, Reuel M Bennett, Tsunehiro Aki, Gina R Dedeles
{"title":"Cocultivation and pH shape the metabolite profile of Chaetomium globosum SCF-24: insights from gas chromatography-mass spectrometry analysis.","authors":"Alethea Vlen M Lopez, Kenshi Watanabe, Mark Kevin P Devanadera, Ray Angelo G Santos, Reuel M Bennett, Tsunehiro Aki, Gina R Dedeles","doi":"10.1093/lambio/ovag075","DOIUrl":"10.1093/lambio/ovag075","url":null,"abstract":"<p><p>This study investigated the effects of cocultivation and pH on the metabolite profile of Chaetomium globosum SCF-24. Axenic and coculture fermentation systems were established at pH 5-8, and resulting extracts were analyzed by gas chromatography-mass spectrometry (GC-MS). A hierarchical clustered heatmap was used to compare metabolite profiles based on presence-absence data. GC-MS detected 51 putatively identified primary and secondary metabolites, some of which were detected across all treatments, whereas others were condition-specific. Metabolite profiles also differed between axenic cultures and cocultures, even at identical pH, with numerous metabolites detected exclusively in cocultures, demonstrating that microbial interactions influenced metabolite profiles beyond the effects of pH. Antibacterial assays showed that only extracts from axenic cultures and cocultures at pH 6 inhibited both Gram-positive and Gram-negative test bacteria. Notably, treatments with similar metabolite profiles did not exhibit comparable antibacterial activity, and the treatment with the highest number of detected metabolites was not the most bioactive, suggesting that bioactivity depends more on metabolite composition than on the number of detected metabolites. Overall, these findings demonstrate the combined influence of biotic and abiotic cultivation factors on metabolite composition and associated antibacterial activity.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148912742","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Correction to: Integrating metagenomics and high-throughput screening for bioprospecting marine producers of polyhydroxyalkanoates.","authors":"","doi":"10.1093/lambio/ovag076","DOIUrl":"https://doi.org/10.1093/lambio/ovag076","url":null,"abstract":"","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":"79 9","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149039685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"An assessment of the microbiological quality and safety of cheese on sale in England and Northern Ireland during 2024-2025.","authors":"Caroline Willis, Frieda Jørgensen, Michelle Kesby, Claire Jenkins, Heather Aird, Sandra Lai, Lorraine Sadler-Reeves","doi":"10.1093/lambio/ovag073","DOIUrl":"10.1093/lambio/ovag073","url":null,"abstract":"<p><p>Foodborne outbreaks have been associated with both pasteurized and unpasteurized milk cheeses in the UK in recent years. This study aimed to assess and compare the microbiological quality of cheese made from pasteurized and unpasteurized milk on sale in England and Northern Ireland. Overall, 2032 cheese samples were collected from retailers and producers throughout England and Northern Ireland. Samples originated from 27 countries, with the UK (53%) and France (15%) being the most common. When compared to UK legislation and guidance, 96% were considered to be of satisfactory microbiological quality, with a greater proportion of unsatisfactory results in unpasteurized (6%) than pasteurized milk cheeses (2%). Five samples (0.2%), all made from unpasteurized milk, were potentially injurious to health due to the detection of shiga toxin-producing Escherichia coli (STEC) in two, >104 CFU/g of coagulase positive staphylococci in two and > 100 CFU/g of Listeria monocytogenes in one. Neither the L. monocytogenes nor the STEC isolates were genetically closely related to those from recent cases of human illness. While the majority of samples were of satisfactory microbiological quality, a small number of results of public health concern were highlighted, particularly where cheeses were made with unpasteurized milk.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148874428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Conserved residues in the CHASE3 domain of BmsA are involved in motility and biofilm formation in Pseudomonas alkylphenolica KL28.","authors":"Gangsu Ha, Meriem Harrache, Kyoung Lee","doi":"10.1093/lambio/ovag079","DOIUrl":"10.1093/lambio/ovag079","url":null,"abstract":"<p><p>The bmsA gene of Pseudomonas alkylphenolica KL28T encodes a conserved protein involved in motility and multicellular biofilm formation. Sequence analysis revealed that BmsA contains an extracellular CHASE3 sensory domain, suggesting a role in environmental signal perception. To investigate its function, a CHASE3 domain deletion mutant and six alanine substitution mutants targeting conserved residues, including Arg73 and Phe75 within the RG(Y/F) motif, were constructed and introduced into a bmsA mutant background. SDS-PAGE confirmed the production of BmsA and its variants, although most proteins migrated at ~145 kDa, above the predicted 130.3 kDa. Phenotypic and motility analyses showed that deletion of the CHASE3 domain and substitution of Arg73 resulted in smooth colony morphology and reduced pellicle and aerial structure formation, similar to the phenotypes observed in the bmsA mutant. In addition, the Arg73 substitution exhibited increased swimming motility in soft agar, resembling the bmsA mutant phenotype. The other alanine substitutions showed no substantial phenotypic differences compared with the control strain. These results indicate that the conserved Arg73 residue within the RG(Y/F) motif of the CHASE3 domain contributes to the modulation of BmsA-dependent phenotypes in strain KL28.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148956115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fang Liu, Qitong Wang, Xinyu Wang, Yuzhao Ye, Tao Chen, Benchi Cai
{"title":"Exploring the nasal microbiome-metabolite axis as a potential therapeutic target in Parkinson's disease-associated olfactory dysfunction.","authors":"Fang Liu, Qitong Wang, Xinyu Wang, Yuzhao Ye, Tao Chen, Benchi Cai","doi":"10.1093/lambio/ovag071","DOIUrl":"10.1093/lambio/ovag071","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148795035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fermentation technology of Ganoderma lucidum and Cordyceps militaris: advances in process optimization, bioactive compound transformation, and functional food development.","authors":"Junfei Zhu, Yuliang Wang, Hongrui Lv","doi":"10.1093/lambio/ovag077","DOIUrl":"10.1093/lambio/ovag077","url":null,"abstract":"<p><p>The growing global demand for functional foods has intensified interest in the biotechnological exploitation of medicinal mushrooms. Ganoderma lucidum and Cordyceps militaris are the two most widely recognized medicinal mushrooms in China, each possessing a well-characterized repertoire of bioactive compounds including polysaccharides, triterpenoids, and cordycepin. This review adopts a substrate-process-product framework to systematically evaluate how submerged fermentation, solid-state fermentation, and co-fermentation strategies influence the yield, structural diversity, and bioactivity of these compounds. Key process innovations are critically assessed, including two-stage temperature control, fed-batch operation, exogenous elicitor supplementation, and bidirectional solid-state fermentation on medicinal herb matrices. The translation of fermentation outputs into functional food formats is surveyed, and the persistent gap between in vitro bioactivity data and clinical validation is highlighted. Future progress will require multi-omics-guided strain engineering, artificial-intelligence-driven process control, and rigorous human intervention trials to substantiate functional efficacy claims.</p>","PeriodicalId":17962,"journal":{"name":"Letters in Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148920166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}