Microbiology Research

18 pages, 7277 KiB

Open AccessArticle

Comprehensive Analysis of the Molecular Epidemiological Characteristics of Duck-Derived Salmonella in Certain Regions of China

by Jiawen Chen, Xiangdi Li, Yanling Liu, Wenjia Rong, Laiyu Fu, Shuhua Wang, Yan Li, Xiaoxiao Duan, Yongda Zhao and Lili Guo

Microbiol. Res. 2025, 16(8), 184; https://doi.org/10.3390/microbiolres16080184 - 7 Aug 2025

Abstract

Salmonella is a major foodborne pathogen, yet real-time data on duck-derived strains in China remain scarce. This study investigated the epidemiology, antimicrobial resistance (AMR), gene profiles, and PFGE patterns of 114 Salmonella isolates recovered from 397 deceased ducks (2021–2024) across nine provinces (isolation [...] Read more.

Salmonella is a major foodborne pathogen, yet real-time data on duck-derived strains in China remain scarce. This study investigated the epidemiology, antimicrobial resistance (AMR), gene profiles, and PFGE patterns of 114 Salmonella isolates recovered from 397 deceased ducks (2021–2024) across nine provinces (isolation rate: 28.72%). Fourteen serotypes were identified, with S. Typhimurium (23.68%), S. Indiana (21.93%), S. Kentucky (18.42%), and S. Enteritidis (12.28%) being predominant. Most isolates showed high resistance to β-lactams, tetracyclines, quinolones, and sulfonamides, with extensive multidrug resistance (MDR) observed—especially in S. Indiana, S. Typhimurium, and S. Kentucky. Among the 23 detected resistance genes, tet(B) had the highest prevalence (75.44%), particularly in S. Indiana. Biofilm formation was observed in 99.12% of isolates, with 84.21% demonstrating moderate to strong capacity. Eighteen virulence genes were detected; S. Enteritidis carried more spvB/C, sipB, and sodC1, while S. Indiana had higher cdtB carriage. PFGE revealed substantial genetic diversity among strains. This comprehensive analysis highlights the high AMR and biofilm potential of duck-derived Salmonella in China, emphasizing the urgent need for enhanced surveillance and control measures to mitigate public health risks. Full article

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24 pages, 957 KiB

Open AccessReview

Biofilm and Antimicrobial Resistance: Mechanisms, Implications, and Emerging Solutions

by Bharmjeet Singh, Manju Dahiya, Vikram Kumar, Archana Ayyagari, Deepti N. Chaudhari and Jayesh J. Ahire

Microbiol. Res. 2025, 16(8), 183; https://doi.org/10.3390/microbiolres16080183 - 6 Aug 2025

Abstract

Biofilms are a spontaneously formed slimy matrix of extracellular polymeric substances (EPS) enveloping miniature bacterial colonies, which aid in pathogen colonization, shielding the bacteria from antibiotics, as well as imparting them resistance towards the same. Biofilms employ a robust communication mechanism called quorum [...] Read more.

Biofilms are a spontaneously formed slimy matrix of extracellular polymeric substances (EPS) enveloping miniature bacterial colonies, which aid in pathogen colonization, shielding the bacteria from antibiotics, as well as imparting them resistance towards the same. Biofilms employ a robust communication mechanism called quorum sensing that serves to keep their population density constant. What is most significant about biofilms is that they contribute to the development of bacterial virulence by providing protection to pathogenic species, allowing them to colonize the host, and also inhibiting the activities of antimicrobials on them. They grow on animate surfaces (such as on teeth and intestinal mucosa, etc.) and inanimate objects (like catheters, contact lenses, pacemakers, endotracheal devices, intrauterine devices, and stents, etc.) alike. It has been reported that as much as 80% of human infections involve biofilms. Serious implications of biofilms include the necessity of greater concentrations of antibiotics to treat common human infections, even contributing to antimicrobial resistance (AMR), since bacteria embedded within biofilms are protected from the action of potential antibiotics. This review explores various contemporary strategies for controlling biofilms, focusing on their modes of action, mechanisms of drug resistance, and innovative approaches to find a solution in this regard. This review interestingly targets the extracellular polymeric matrix as a highly effective strategy to counteract the potential harm of biofilms since it plays a critical role in biofilm formation and significantly contributes to antimicrobial resistance. Full article

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20 pages, 3465 KiB

Open AccessArticle

Inhibitory Effects of Selected Chemical Substances on the Growth of Filamentous Fungi Occurring in Cellar Management

by Karolina Kostelnikova, Romana Heralecka, Anna Krpatova, Filip Matousek, Jiri Sochor and Mojmir Baron

Microbiol. Res. 2025, 16(8), 182; https://doi.org/10.3390/microbiolres16080182 - 4 Aug 2025

Abstract

This study evaluated the inhibitory efficacy of sulphur dioxide, hydrogen peroxide, copper sulphate pentahydrate, chlorine-based formulations, a chlorine-free formulation, ethanol, and acetic acid against Cladosporium cladosporioides, Aspergillus niger, and Penicillium expansum. An in vitro inhibition test was employed to investigate [...] Read more.

This study evaluated the inhibitory efficacy of sulphur dioxide, hydrogen peroxide, copper sulphate pentahydrate, chlorine-based formulations, a chlorine-free formulation, ethanol, and acetic acid against Cladosporium cladosporioides, Aspergillus niger, and Penicillium expansum. An in vitro inhibition test was employed to investigate the inhibitory properties. The results demonstrated different sensitivities of filamentous fungi to the inhibitors. All tested substances displayed fungicidal properties. Sulphur dioxide (40% NH₄HSO₃ solution) inhibited growth at a 4% v/v concentration. No minimum effective concentration was established for H₂O₂; only a 30% w/v solution inhibited P. expansum. CuSO₄·5H₂O completely inhibited fungal growth at 5% w/v solution, with 2.5% w/v also proving effective. For the chlorine-based product, 40% w/v solution (48 g∙L⁻¹ active chlorine) had the most substantial effect, though it only slowed growth, and NaClO solution completely inhibited growth at 2.35 g NaClO per 100 g of product (50% w/v solution). FungiSAN demonstrated fungicidal effects; however, the recommended dose was insufficient for complete inhibition. Ethanol exhibited the lowest efficacy, while the inhibitory threshold for CH₃COOH was found to be a 5% v/v solution. The findings of this study may serve as a basis for informed decision-making when selecting the most suitable product, depending on specific application conditions. Full article

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11 pages, 593 KiB

Open AccessArticle

Burden of Streptococcus pyogenes and emm12 Type in Severe Otitis Media Among Children

by Alexandra S. Alexandrova, Adile A. Muhtarova, Vasil S. Boyanov and Raina T. Gergova

Microbiol. Res. 2025, 16(8), 181; https://doi.org/10.3390/microbiolres16080181 - 3 Aug 2025

Abstract

Streptococcus pyogenes (GAS) is a leading cause of acute otitis media (AOM) and its complications. This study aimed to evaluate the antimicrobial resistance of all isolated bacterial agents recovered from children with AOM and to perform the emm typing of GAS isolates. Antibiotic [...] Read more.

Streptococcus pyogenes (GAS) is a leading cause of acute otitis media (AOM) and its complications. This study aimed to evaluate the antimicrobial resistance of all isolated bacterial agents recovered from children with AOM and to perform the emm typing of GAS isolates. Antibiotic susceptibility testing was evaluated according to EUCAST criteria. Phenotyping and genotyping were performed for the macrolide-resistant GAS isolates. All GAS isolates were subjected to emm typing. Among the 103 AOM cases considered, we identified GAS isolates (39.4%), Staphylococcus aureus (26.6%), Haemophilus influenzae (13.8%), Streptococcus pneumoniae (11.7%), Moraxella catarrhalis (7.4%), and Serratia marcescens (1.1%). GAS exhibited 32.4% macrolide resistance and 10.8% clindamycin resistance. The M phenotype and mefE gene (18.9%) were the most common, followed by cMLSB (10.8% with ermB), a combination of mefA and ermB (8.1%), and iMLSB (2.7% with ermA). The most prevalent emm types were emm12 (27.0%), emm1 (21.6%), and emm3 (16.2%). The most common GAS emm types identified among AOM patients in this study are found worldwide and are associated with invasive infections in various countries. This may influence the virulence and invasive potential of these strains. Full article

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16 pages, 1226 KiB

Open AccessArticle

Occurrence and Transfer by Conjugation of Linezolid-Resistance Among Non-Enterococcus faecalis and Enterococcus faecium in Intensive Pig Farms

by Giorgia Piccioni, Andrea Di Cesare, Raffaella Sabatino, Gianluca Corno, Gianmarco Mangiaterra, Daniela Marchis and Barbara Citterio

Microbiol. Res. 2025, 16(8), 180; https://doi.org/10.3390/microbiolres16080180 - 2 Aug 2025

Abstract

Enterococcus spp. are opportunistic and nosocomial pathogens. Intensive pig farms have been recently described as important hotspots for antibiotic resistance and reservoirs of potentially pathogenic enterococci, including other species than the most known E. faecalis and E. faecium. Here, we identified Linezolid-resistant [...] Read more.

Enterococcus spp. are opportunistic and nosocomial pathogens. Intensive pig farms have been recently described as important hotspots for antibiotic resistance and reservoirs of potentially pathogenic enterococci, including other species than the most known E. faecalis and E. faecium. Here, we identified Linezolid-resistant non-E. faecalis and E. faecium (NFF) Enterococcus strains isolated from different production stages (suckling piglets, weaning pigs, and fatteners) across six intensive pig farms. The transferability of the linezolid-resistance determinants was assessed by bacterial conjugation and strains were also characterized for biofilm production, hemolytic and gelatinase activity. Among 64 identified NFF Enterococcus strains, 27 were resistant to at least three different antibiotic classes and 8/27 specifically to Linezolid. E. gallinarum and E. casseliflavus both transferred their Linezolid resistance determinants to the main pathogenic species E. faecium. Remarkably, this is the first report of the optrA gene transfer from E. casseliflavus to E. faecium by conjugation, which can greatly contribute to the spread of antibiotic resistance genes among pathogenic enterococcal species. The “weaning pigs” stage exhibited a significantly higher number of antibiotic-resistant enterococci than the “fatteners”. These findings highlight the importance of monitoring pig farms as hotspots for the spread of antibiotic-resistant enterococci, especially in the early stages of production. Furthermore, they underscore the significant role of NFF Enterococcus species as carriers of antibiotic resistance genes, even to last-resort antibiotics, which may be transferable to the major enterococcal species. Full article

(This article belongs to the Special Issue Zoonotic Bacteria: Infection, Pathogenesis and Drugs—Second Edition)

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Graphical abstract

20 pages, 1876 KiB

Open AccessArticle

Evaluation of Clean-Label Additives to Inhibit Molds and Extend the Shelf Life of Preservative-Free Bread

by Ricardo H. Hernández-Figueroa, Aurelio López-Malo, Beatriz Mejía-Garibay, Nelly Ramírez-Corona and Emma Mani-López

Microbiol. Res. 2025, 16(8), 179; https://doi.org/10.3390/microbiolres16080179 - 1 Aug 2025

Abstract

This study evaluates the efficacy of commercial clean-label additives, specifically fermentates, in inhibiting mold growth in vitro and extending the shelf life of preservative-free bread. The mold growth on selected bread was modeled using the time-to-growth approach. The pH, a_w, and [...] Read more.

This study evaluates the efficacy of commercial clean-label additives, specifically fermentates, in inhibiting mold growth in vitro and extending the shelf life of preservative-free bread. The mold growth on selected bread was modeled using the time-to-growth approach. The pH, a_w, and moisture content of fresh bread were determined. In addition, selected fermentates were characterized physicochemically. Fermentates, defined as liquid or powdered preparations containing microorganisms, their metabolites, and culture supernatants, were tested at varying concentrations (1% to 12%) to assess their antimicrobial performance and impact on bread quality parameters, including moisture content, water activity, and pH. The results showed significant differences in fermentate efficacy, with Product A as the best mold growth inhibitor in vitro and a clear dose-dependent response. For Penicillium corylophilum, inhibition increased from 51.90% at 1% to 62.60% at 4%, while P. chrysogenum had an inhibition ranging from 32.26% to 34.49%. Product F exhibited moderate activity on both molds at 4%, inhibiting between 28.48% and 46.27%. The two molds exhibited differing sensitivities to the fermentates, with P. corylophilum consistently more susceptible to inhibition. Product A displayed a low pH (2.61) and high levels of lactic acid (1053.6 mmol/L) and acetic acid (1061.3 mmol/L). Product F presented a similar pH but lower levels of lactic and acetic acid. A time-to-growth model, validated by significant coefficients (p < 0.05) and high predictive accuracy (R² > 0.95), was employed to predict the appearance of mold on bread loaves. The model revealed that higher concentrations of fermentates A and F delayed mold growth, with fermentate A demonstrating superior efficacy. At 2% concentration, fermentate A delayed mold growth for 8 days, compared to 6 days for fermentate F. At 8% concentration, fermentate A prevented mold growth for over 25 days, significantly outperforming the control (4 days). Additionally, fermentates influenced bread quality parameters, with fermentate A improving crust moisture retention and reducing water activity at higher concentrations. These findings highlight the potential of fermentates as sustainable, consumer-friendly alternatives to synthetic preservatives, offering a viable solution to the challenge of bread spoilage while maintaining product quality. Full article

(This article belongs to the Collection Microbiology and Technology of Fermented Foods)

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18 pages, 2714 KiB

Open AccessArticle

Assessing the Efficacy of Chemical and Green-Synthesized CuO Nanoparticles in Combatting Clinical Candida Species: A Comparative Study

by Hiba Younis Khalaf, Ferid Ben Nasr, Bashar Sadeq Noomi, Sami Mnif and Sami Aifa

Microbiol. Res. 2025, 16(8), 178; https://doi.org/10.3390/microbiolres16080178 - 1 Aug 2025

Abstract

The most prevalent growth of Candida cells is based on biofilm development, which causes the intensification of antifungal resistance against a large range of chemicals. Nanoparticles can be synthesized using green methods via various biological extracts and reducing agents to control Candida biofilms. [...] Read more.

The most prevalent growth of Candida cells is based on biofilm development, which causes the intensification of antifungal resistance against a large range of chemicals. Nanoparticles can be synthesized using green methods via various biological extracts and reducing agents to control Candida biofilms. This study aims to compare copper oxide nanoparticles (CuONPs) synthesized through chemical methods and those synthesized using Cinnamomum verum-based green methods against Candida infections and their biofilms isolated from Iraqi patients, with the potential to improve treatment outcomes. The physical and chemical properties of these nanoparticles were characterized using Fourier-transform infrared spectroscopy (FT-IR,) scanning electron microscopy (SEM), transmission electron microscopy (TEM), atomic force microscopy (AFM) and X-ray diffraction (XRD). Four strains of Candida were isolated and characterized from Iraqi patients in Tikrit Hospital and selected based on their ability to form biofilm on polystyrene microplates. The activity of green-synthesized CuONPs using cinnamon extract was compared with both undoped and doped (Fe, Sn) chemically synthesized CuONPs. Four pathogenic Candida strains (Candida glabrata, Candida lusitaniae, Candida albicans, and Candida tropicalis) were isolated from Iraqi patients, demonstrating high biofilm formation capabilities. Chemically and green-synthesized CuONPs from Cinnamomum verum showed comparable significant antiplanktonic and antibiofilm activities against all strains. Doped CuONPs with iron or tin demonstrated lower minimum inhibitory concentration (MIC) values, indicating stronger antibacterial activity, but exhibited weaker anti-adhesive properties compared to other nanoparticles. The antiadhesive activity revealed that C. albicans strain seems to produce the most resistant biofilms while C. glabrata strain seems to be more resistant towards the doped CuONPs. Moreover, C. tropicalis was the most sensitive to all the CuONPs. Remarkably, at a concentration of 100 µg/mL, all CuONPs were effective in eradicating preformed biofilms by 47–66%. The findings suggest that CuONPs could be effective in controlling biofilm formation by Candida species resistant to treatment in healthcare settings. Full article

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22 pages, 7580 KiB

Open AccessArticle

Bacterial and Physicochemical Dynamics During the Vermicomposting of Bovine Manure: A Comparative Analysis of the Eisenia fetida Gut and Compost Matrix

by Tania Elizabeth Velásquez-Chávez, Jorge Sáenz-Mata, Jesús Josafath Quezada-Rivera, Rubén Palacio-Rodríguez, Gisela Muro-Pérez, Alan Joel Servín-Prieto, Mónica Hernández-López, Pablo Preciado-Rangel, María Teresa Salazar-Ramírez, Juan Carlos Ontiveros-Chacón and Cristina García-De la Peña

Microbiol. Res. 2025, 16(8), 177; https://doi.org/10.3390/microbiolres16080177 - 1 Aug 2025

Abstract

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition [...] Read more.

Vermicomposting is a sustainable biotechnological process that transforms organic waste through the synergistic activity of earthworms, such as Eisenia fetida, and their associated microbiota. This study evaluated bacterial and physicochemical dynamics during the vermicomposting of bovine manure by analyzing the microbial composition of the substrate and the gut of E. fetida at three time points (weeks 0, 6, and 12). The V3–V4 region of the 16S rRNA gene was sequenced, and microbial diversity was characterized using QIIME2. Significant differences in alpha diversity (observed features, Shannon index, and phylogenetic diversity) and beta diversity indicated active microbial succession. Proteobacteria, Bacteroidota, and Actinobacteriota were the dominant phyla, with abundances varying across habitats and over time. A significant enrichment of Proteobacteria, Bacteroidota, and the genera Chryseolinea, Flavobacterium, and Sphingomonas was observed in the manure treatments. In contrast, Actinobacteriota, Firmicutes, and the genera Methylobacter, Brevibacillus, Enhygromyxa, and Bacillus, among others, were distinctive of the gut samples and contributed to their dissimilarity from the manure treatments. Simultaneously, the physicochemical parameters indicated progressive substrate stabilization and nutrient enrichment. Notably, the organic matter and total organic carbon contents decreased (from 79.47% to 47.80% and from 46.10% to 27.73%, respectively), whereas the total nitrogen content increased (from 1.70% to 2.23%); these effects reduced the C/N ratio, which is a recognized indicator of maturity, from 27.13 to 12.40. The macronutrient contents also increased, with final values of 1.41% for phosphorus, 1.50% for potassium, 0.89% for magnesium, and 2.81% for calcium. These results demonstrate that vermicomposting modifies microbial communities and enhances substrate quality, supporting its use as a biofertilizer for sustainable agriculture, soil restoration, and agrochemical reduction. Full article

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13 pages, 1123 KiB

Open AccessArticle

Protective Effects of Grape Seed Extract on Lipopolysaccharide Exposure and Radiation-Induced Intestinal Mucosal Damage: Insights from an In Vitro Study

by Annamaria Altomare, Michele Fiore, Elena Imperia, Gabriele D’Ercole, Ludovica Spagnuolo, Laura De Gara, Gabriella Pasqua, Michele Cicala, Sara Ramella and Michele Pier Luca Guarino

Microbiol. Res. 2025, 16(8), 176; https://doi.org/10.3390/microbiolres16080176 - 1 Aug 2025

Abstract

Backgrounds and aim: Protective effects of natural compounds have been suggested in the prevention and treatment of radiation-induced mucositis or bacterial infections. In this study, the protective effects of proanthocyanidin-rich grape seed extract (GSE) on bacterial Lipopolysaccharide (LPS) and radiation-induced epithelial barrier damage [...] Read more.

Backgrounds and aim: Protective effects of natural compounds have been suggested in the prevention and treatment of radiation-induced mucositis or bacterial infections. In this study, the protective effects of proanthocyanidin-rich grape seed extract (GSE) on bacterial Lipopolysaccharide (LPS) and radiation-induced epithelial barrier damage and Reactive Oxygen Species (ROS) production were investigated in an in vitro model. Methods: Human intestinal epithelial cells Caco-2, previously treated with LPS, GSE, or LPS + GSE, were irradiated with 10 Gy divided into five daily treatments. Epithelial barrier integrity and ROS production were measured before and after each treatment. Results: Irradiation, at different doses, significantly increased intestinal permeability and ROS production; pretreatment with GSE was able to significantly prevent the increased intestinal permeability (4.63 ± 0.76 vs. 15.04 ± 1.5; p < 0.05) and ROS production (12.9 ± 1.08 vs. 1048 ± 0.5; p < 0.0001) induced by irradiation treatment. When the cells were pretreated with LPS, the same results were observed: GSE cotreatment was responsible for preventing permeability alterations (5.36 ± 0.16 vs. 49.26 ± 0.82; p < 0.05) and ROS production (349 ± 1 vs. 7897.67 ± 1.53; p < 0.0001) induced by LPS exposure when added to the irradiation treatment. Conclusions: The results of the present investigation demonstrated, in an in vitro model, that GSE prevents the damage to intestinal permeability and the production of ROS that are induced by LPS and ionizing radiation, suggesting a potential protective effect of this extract on the intestinal mucosa during irradiation treatment. Full article

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32 pages, 4311 KiB

Open AccessArticle

Proteomics-Based Prediction of Candidate Effectors in the Interaction Secretome of Trichoderma harzianum and Pseudocercospora fijiensis

by Jewel Nicole Anna Todd, Karla Gisel Carreón-Anguiano, Gabriel Iturriaga, Roberto Vázquez-Euán, Ignacio Islas-Flores, Miguel Tzec-Simá, Miguel Ángel Canseco-Pérez, César De Los Santos-Briones and Blondy Canto-Canché

Microbiol. Res. 2025, 16(8), 175; https://doi.org/10.3390/microbiolres16080175 - 1 Aug 2025

Abstract

Microbe–microbe interactions have been explored at the molecular level to a lesser degree than plant–pathogen interactions, primarily due to the economic impact of crop losses caused by pathogenic microorganisms. Effector proteins are well known for their role in disease development in many plant–pathogen [...] Read more.

Microbe–microbe interactions have been explored at the molecular level to a lesser degree than plant–pathogen interactions, primarily due to the economic impact of crop losses caused by pathogenic microorganisms. Effector proteins are well known for their role in disease development in many plant–pathogen pleinteractions, but there is increasing evidence showing their involvement in other types of interaction, including microbe–microbe interactions. Through the use of LC-MS/MS sequencing, effector candidates were identified in the in vitro interaction between a banana pathogen, Pseudocercospora fijiensis and a biological control agent, Trichoderma harzianum. The diverse interaction secretome revealed various glycoside hydrolase families, proteases and oxidoreductases. T. harzianum secreted more proteins in the microbial interaction compared to P. fijiensis, but its presence induced the secretion of more P. fijiensis proteins that were exclusive to the interaction secretome. The interaction secretome, containing 256 proteins, was screened for effector candidates using the algorithms EffHunter and WideEffHunter. Candidates with common fungal effector motifs and domains such as LysM, Cerato-platanin, NPP1 and CFEM, among others, were identified. Homologs of true effectors and virulence factors were found in the interaction secretome of T. harzianum and P. fijiensis. Further characterization revealed a potential novel effector of T. harzianum. Full article

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13 pages, 1801 KiB

Open AccessReview

Lactobacillus acidophilus in Aquaculture: A Review

by Lu Zhang, Jian Zhou, Zhipeng Huang, Han Zhao, Zhongmeng Zhao, Chengyan Mou, Yang Feng, Huadong Li, Qiang Li and Yuanliang Duan

Microbiol. Res. 2025, 16(8), 174; https://doi.org/10.3390/microbiolres16080174 - 1 Aug 2025

Abstract

Microbial feed additives can effectively promote the healthy development of aquaculture, and Lactobacillus acidophilus can be utilized to mitigate disease risks and enhance productivity while minimizing antibiotic use. This article summarizes research on the application of L. acidophilus in aquaculture, focusing on growth [...] Read more.

Microbial feed additives can effectively promote the healthy development of aquaculture, and Lactobacillus acidophilus can be utilized to mitigate disease risks and enhance productivity while minimizing antibiotic use. This article summarizes research on the application of L. acidophilus in aquaculture, focusing on growth and nutrient utilization, intestinal structure and microbial communities, disease prevention and control in aquatic organisms, and the regulation of water quality. This review holds significant implications for the development of compound feed additives and environmental regulators involving L. acidophilus, as well as for future aquatic food safety. Full article

(This article belongs to the Topic The Role of Microorganisms in Waste Treatment)

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15 pages, 1894 KiB

Open AccessArticle

Microbial Communities’ Composition of Supralittoral and Intertidal Sediments in Two East African Beaches (Djibouti Republic)

by Sonia Renzi, Alessandro Russo, Aldo D’Alessandro, Samuele Ciattini, Saida Chideh Soliman, Annamaria Nistri, Carlo Pretti, Duccio Cavalieri and Alberto Ugolini

Microbiol. Res. 2025, 16(8), 173; https://doi.org/10.3390/microbiolres16080173 - 1 Aug 2025

Abstract

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial [...] Read more.

Tropical sandy beaches are dynamic ecosystems where microbial communities play crucial roles in biogeochemical processes and tracking human impact. Despite their importance, these habitats remain underexplored. Here, using amplicon-based sequencing of bacterial (V3-V4 16S rRNA) and fungal (ITS2) markers, we first describe microbial communities inhabiting supralittoral–intertidal sediments of two contrasting sandy beaches in the Tadjoura Gulf (Djibouti Republic): Sagallou-Kalaf (SK, rural, siliceous sand) and Siesta Plage (SP, urban, calcareous sand). Sand samples were collected at low tide along 10 m transects perpendicular to the shoreline. Bacterial communities differed significantly between sites and along the sea-to-land gradient, suggesting an influence from both anthropogenic activity and sediment granulometry. SK was dominated by Escherichia-Shigella, Staphylococcus, and Bifidobacterium, associated with human and agricultural sources. SP showed higher richness, with enriched marine-associated genera such as Hoeflea, Xanthomarina, and Marinobacter, also linked to hydrocarbon degradation. Fungal diversity was less variable, but showed significant shifts along transects. SK communities were dominated by Kluyveromyces and Candida, while SP hosted a broader fungal assemblage, including Pichia, Rhodotorula, and Aureobasidium. The higher richness at SP suggests that calcium-rich sands, possibly due to their buffering capacity and greater moisture retention, offer more favorable conditions for microbial colonization. Full article

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12 pages, 1161 KiB

Open AccessArticle

Power Ultrasound and Organic Acid-Based Hurdle Technology to Reduce Listeria monocytogenes and Salmonella enterica on Fresh Produce

by Megan L. Fay, Priya Biswas, Xinyi Zhou, Bashayer A. Khouja, Diana S. Stewart, Catherine W. Y. Wong, Wei Zhang and Joelle K. Salazar

Microbiol. Res. 2025, 16(8), 172; https://doi.org/10.3390/microbiolres16080172 - 1 Aug 2025

Abstract

The increasing demand for fresh fruits and vegetables has been accompanied by a rise in foodborne illness outbreaks linked to fresh produce. Traditional antimicrobial washing treatments, such as chlorine and peroxyacetic acid, have limitations in efficacy and pose environmental and worker health concerns. [...] Read more.

The increasing demand for fresh fruits and vegetables has been accompanied by a rise in foodborne illness outbreaks linked to fresh produce. Traditional antimicrobial washing treatments, such as chlorine and peroxyacetic acid, have limitations in efficacy and pose environmental and worker health concerns. This study evaluated the effectiveness of organic acids (citric, malic, and lactic acid) and power ultrasound, individually and in combination, for the reduction in Salmonella enterica and Listeria monocytogenes on four fresh produce types: romaine lettuce, cucumber, tomato, and strawberry. Produce samples were inoculated with bacterial cocktails at 8–9 log CFU/unit and treated with organic acids at 2 or 5% for 2 or 5 min, with or without power ultrasound (40 kHz). Results showed that pathogen reductions varied based on the produce matrix with smoother surfaces such as tomato, exhibiting greater reductions than rougher surfaces (e.g., romaine lettuce and strawberry). Lactic and malic acids were the most effective treatments, with 5% lactic acid achieving a reduction of >5 log CFU/unit for S. enterica and 4.53 ± 0.71 log CFU/unit for L. monocytogenes on tomatoes. The combination of organic acids and power ultrasound demonstrated synergistic effects, further enhancing pathogen reduction by <1.87 log CFU/unit. For example, S. enterica on cucumbers was reduced by an additional 1.87 log CFU/unit when treated with 2% malic acid and power ultrasound for 2 min compared to malic acid alone. Similarly, L. monocytogenes on strawberries was further reduced by 1.84 log CFU/unit when treated with 5% malic acid and power ultrasound for 2 min. These findings suggest that organic acids, particularly malic and lactic acids, combined with power ultrasound, may serve as an effective hurdle technology for enhancing the microbial safety of fresh produce. Future research can include validating these treatments in an industrial processing environment. Full article

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8 pages, 890 KiB

Open AccessCommunication

Single-Cell Protein Using an Indigenously Isolated Methanotroph Methylomagnum ishizawai, Using Biogas

by Jyoti A. Mohite, Kajal Pardhi and Monali C. Rahalkar

Microbiol. Res. 2025, 16(8), 171; https://doi.org/10.3390/microbiolres16080171 - 1 Aug 2025

Abstract

The use of methane as a carbon source for producing bacterial single-cell protein (SCP) has been one of the most interesting developments in recent years. Most of these upcoming industries are using a methanotroph, Methylococcus capsulatus Bath, for SCP production using natural gas [...] Read more.

The use of methane as a carbon source for producing bacterial single-cell protein (SCP) has been one of the most interesting developments in recent years. Most of these upcoming industries are using a methanotroph, Methylococcus capsulatus Bath, for SCP production using natural gas as the substrate. In the present study, we have explored the possibility of using an indigenously isolated methanotroph from a rice field in India, Methylomagnum ishizawai strain KRF4, for producing SCP from biogas [derived from cow dung]. The process was eco-friendly, required minimal instruments and chemicals, and was carried out under semi-sterile conditions in a tabletop fish tank. As the name suggests, Methylomagnum is a genus of large methanotrophs, and the strain KRF4 had elliptical to rectangular size and dimensions of ~4–5 µm × 1–2 µm. In static cultures, when biogas and air were supplied in the upper part of the growing tank, the culture grew as a thick pellicle/biofilm that could be easily scooped. The grown culture was mostly pure, from the microscopic observations where the large size of the cells, with rectangular-shaped cells and dark granules, could easily help identify any smaller contaminants. Additionally, the large cell size could be advantageous for separating biomass during downstream processing. The amino acid composition of the lyophilized biomass was analyzed using HPLC, and it was seen that the amino acid composition was comparable to commercial fish meal, soymeal, Pruteen, and the methanotroph-derived SCP-UniProtein^®. The only difference was that a slightly lower percentage of lysine, tryptophan, and methionine was observed in Methylomagnum-derived SCP. Methylomagnum ishizawai could be looked at as an alternative for SCP derived from methane or biogas due to the comparable SCP produced, on the qualitative level. Further intensive research is needed to develop a continuous, sustainable, and economical process to maximize biomass production and downstream processing. Full article

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12 pages, 773 KiB

Open AccessCommunication

Bat Species Identification and Alphacoronavirus, Beta- and Gammaherpesvirus Findings in Bat Colonies in Tuscany and Latium Regions During Lyssavirus Surveillance

by Silvia Tofani, Ida Ricci, Cersini Antonella, Giuseppe Manna, Raffaella Conti, Andrea Lombardo, Davide La Rocca, Marco Scalisi, Roberta Giordani, Massimiliano Simula, Gabriele Pietrella, Roberto Nardini, Erica Tilesi and Maria Teresa Scicluna

Microbiol. Res. 2025, 16(8), 170; https://doi.org/10.3390/microbiolres16080170 - 1 Aug 2025

Abstract

Chiroptera includes over 1400 bat species, with at least 35 of these present in Italy. Due to their role as Lyssavirus reservoirs, bats found dead, with and without signs suggestive of this infection, are routinely submitted to the laboratory network of the Istituti [...] Read more.

Chiroptera includes over 1400 bat species, with at least 35 of these present in Italy. Due to their role as Lyssavirus reservoirs, bats found dead, with and without signs suggestive of this infection, are routinely submitted to the laboratory network of the Istituti Zooprofilattici Sperimentali in the framework of the rabies national passive and active surveillance program. Carcasses and biological samples collected from January to December 2021 in Latium and Tuscany, regions of our jurisdiction, were further screened for the presence of Coronaviruses (CoVs) and Herpesviruses using pan-family virus PCR tests, and relative PCR products were Sanger sequenced. Genetic characterization through sequencing detected AlphaCoVs in Miniopterus schreibersii and Beta- and Gammaherpesviruses in Tadarida teniotis. Samples were also submitted to bat genetic species identification. Full article

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12 pages, 788 KiB

Open AccessArticle

Gut Microbial Composition on Dienogest Therapy in Patients with Endometriosis

by Veronika Pronina, Pavel Denisov, Vera Muravieva, Alexey Skorobogatiy, Ksenia Zhigalova, Galina Chernukha, Gennady Sukhikh and Tatiana Priputnevich

Microbiol. Res. 2025, 16(8), 169; https://doi.org/10.3390/microbiolres16080169 - 1 Aug 2025

Abstract

Endometriosis is a chronic inflammatory condition affecting approximately 10% of women of reproductive age, characterized by pelvic pain, dysmenorrhea, and infertility. Emerging evidence suggests a potential link between gut microbiota dysbiosis and endometriosis pathogenesis, mediated through hormonal regulation, immune modulation, and systemic inflammation. [...] Read more.

Endometriosis is a chronic inflammatory condition affecting approximately 10% of women of reproductive age, characterized by pelvic pain, dysmenorrhea, and infertility. Emerging evidence suggests a potential link between gut microbiota dysbiosis and endometriosis pathogenesis, mediated through hormonal regulation, immune modulation, and systemic inflammation. Dienogest (DNG) is widely used for endometriosis management, but its effects on gut microbiota remain underexplored. This study investigates the impact of DNG on gut microbial composition in endometriosis patients, aiming to elucidate its therapeutic mechanisms beyond hormonal modulation. DNG therapy led to a significant reduction in the Bacillota/Bacteroidota ratio (p = 0.0421), driven by decreased Staphylococcus spp. (p = 0.0244) and increased commensal bacteria such as Lactobacillus spp. and Collinsella aerofaciens (p = 0.049). Species richness and alpha diversity indices showed a non-significant upward trend. Notably, C. aerofaciens, a butyrate producer linked to gut barrier integrity, was detected twice as frequently during therapy. The study also observed reductions in facultative anaerobes like Enterococcus spp. and a trend toward higher titers of beneficial Bacteroidota. This study provides the first evidence that DNG therapy modulates gut microbiota in endometriosis patients, favoring a composition associated with anti-inflammatory and barrier-protective effects. The observed shifts—reduced opportunistic pathogens and increased symbionts—suggest a novel mechanism for DNG’s efficacy, potentially involving the microbial regulation of estrogen metabolism and immune responses. Full article

(This article belongs to the Topic Microbiota Diversity and Its Broader Biological Implications Across Human and Animal Health)

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15 pages, 1487 KiB

Open AccessArticle

Protective Effects of a Bifidobacterium-Based Probiotic Mixture on Gut Inflammation and Barrier Function

by Yeji You, Tae-Rahk Kim, Minn Sohn, Dongmin Yoo and Jeseong Park

Microbiol. Res. 2025, 16(8), 168; https://doi.org/10.3390/microbiolres16080168 - 1 Aug 2025

Abstract

Disruption of the intestinal epithelial barrier is a key driver of gut-derived inflammation in various disorders, yet strategies to preserve or restore barrier integrity remain limited. To address this, we evaluated a four-strain Bifidobacterium mixture—selected for complementary anti-inflammatory potency and industrial scalability—in lipopolysaccharide [...] Read more.

Disruption of the intestinal epithelial barrier is a key driver of gut-derived inflammation in various disorders, yet strategies to preserve or restore barrier integrity remain limited. To address this, we evaluated a four-strain Bifidobacterium mixture—selected for complementary anti-inflammatory potency and industrial scalability—in lipopolysaccharide (LPS)-challenged RAW 264.7 macrophages and a Caco-2/THP-1 transwell co-culture model. Pretreatment with the probiotic blend reduced nitric oxide (NO) release in a dose-dependent manner by 25.9–48.3% and significantly down-regulated the pro-inflammatory markers in macrophages. In the co-culture system, the formulation decreased these markers, increased transepithelial electrical resistance (TEER) by up to 31% at 10⁵ colony-forming unit (CFU)/mL after 48 h, and preserved the membrane localization of tight junction (TJ) proteins. Adhesion to Caco-2 cells (≈ 6%) matched that of the benchmark probiotic Lacticaseibacillus rhamnosus GG, suggesting direct epithelial engagement. These in vitro findings demonstrate that this probiotic mixture can attenuate LPS-driven inflammation and reinforce epithelial architecture, providing a mechanistic basis for its further evaluation in animal models and clinical studies of intestinal inflammatory disorders. Full article

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13 pages, 1191 KiB

Open AccessArticle

Gut Microbiome Structural Dynamics in Japanese Quail Across Developmental Stages

by Daniela da Silva Gomes, Alexandre Lemos de Barros Moreira Filho, Wydemberg José de Araújo, Gustavo Felipe Correia Sales, Hemilly Marques da Silva, Thalis José de Oliveira, Antonio Venício de Sousa, Celso José Bruno de Oliveira and Patrícia Emília Naves Givisiez

Microbiol. Res. 2025, 16(8), 167; https://doi.org/10.3390/microbiolres16080167 - 1 Aug 2025

Abstract

The cecal microbiota is essential for intestinal health and performance. This study describes the succession patterns of the cecal microbiota in Japanese quail (Coturnix japonica) until 42 days of age. Sixty quails were raised using standard conditions and fed corn–soybean meal [...] Read more.

The cecal microbiota is essential for intestinal health and performance. This study describes the succession patterns of the cecal microbiota in Japanese quail (Coturnix japonica) until 42 days of age. Sixty quails were raised using standard conditions and fed corn–soybean meal diets. Cecal contents were sampled from five birds weekly from 7 to 42 days of age and submitted to Illumina 16S rRNA sequencing for metabarcoding analysis. Diversity and functional prediction were carried out with QIIME2, PICRUSt2, STAMP and MicrobiomeAnalyst 2.0. Firmicutes increased from 50% at 7 days to more than 80% at 42 days, whereas Bacteroidota decreased from 45% to 12% in the same period. Alpha diversity progressively increased with age, indicating a richer and more balanced microbiota at later ages. Genera such as Bacteroides were predominant in the beginning and later were replaced by Lachnospiraceae, Ruminococcus and Faecalibacterium. These developmental taxonomic features aligned with significant shifts in ten metabolic pathways identified by prediction, revealing a transition from biosynthetic functions to complex carbohydrate metabolism and cell wall biosynthesis. The first seven days are considered a critical window for probiotics intervention, which may favor the establishment of a microbiota that is more stable and beneficial to quail performance. Full article

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16 pages, 2790 KiB

Open AccessArticle

AiiA Lactonase Suppresses ETEC Pathogenicity Through 3OC12-HSL Quenching in a Murine Model

by Yang Yang, Ji Shao, Zixin Han, Junpeng Li, Qiaoqiao Fang and Guoqiang Zhu

Microbiol. Res. 2025, 16(8), 166; https://doi.org/10.3390/microbiolres16080166 - 31 Jul 2025

Abstract

This study elucidates how the quorum-sensing (QS) signal 3OC12-HSL exacerbates enterotoxigenic E. coli (ETEC) pathogenicity and intestinal barrier dysfunction. In vitro, 3OC12-HSL enhanced ETEC C83902 growth (66.7% CFU increase at 8 h) and dysregulated stress/growth genes (e.g., eight-fold rmf upregulation under static conditions). [...] Read more.

This study elucidates how the quorum-sensing (QS) signal 3OC12-HSL exacerbates enterotoxigenic E. coli (ETEC) pathogenicity and intestinal barrier dysfunction. In vitro, 3OC12-HSL enhanced ETEC C83902 growth (66.7% CFU increase at 8 h) and dysregulated stress/growth genes (e.g., eight-fold rmf upregulation under static conditions). In synthetic gut microbiota, 3OC12-HSL selectively augmented E. coli colonization (37.6% 16S rDNA increase at 12 h). Murine studies revealed 3OC12-HSL reduced jejunal villus height (381.5 μm vs. 543.2 μm in controls), elevated serum LPS, D-lactate, and DAO, and altered microbial composition (Firmicutes/Bacteroidetes imbalance). The lactonase AiiA reversed these effects by degrading 3OC12-HSL. It abrogated bacterial growth stimulation (in vitro CFU restored to baseline), normalized microbiota diversity (Shannon index recovered to control levels), suppressed pro-inflammatory cytokines (IL-6/TNF-α reduction), and restored intestinal integrity (villus length: 472.5 μm, 20.5% increase vs. ETEC-infected mice). Our findings establish AiiA as a potent quorum-quenching agent that counteracts ETEC virulence via targeted signal inactivation, highlighting its translational value. Full article

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