Microorganisms

9 pages, 596 KiB

Open AccessArticle

Microbial Contamination on High-Touch Surfaces in Outpatient Clinics: Identification of Bacterial Strains from Areas of Patient and Medical Staff Occupancy

by Karolina Prasek, Iwona Kiersnowska, Jadwiga Wójkowska-Mach, Anna Różańska, Dorota Romaniszyn, Ewelina Foryciarz, Lucyna Barbara Kwiećkowska and Edyta Krzych-Fałta

Microorganisms 2025, 13(3), 698; https://doi.org/10.3390/microorganisms13030698 - 20 Mar 2025

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Abstract

Clinics and hospitals inherently increase the risk of adverse events, including hospital-acquired infections (HAIs) transmitted between healthcare personnel and patients. This study aimed to identify bacterial strains present on frequently touched surfaces in outpatient clinics used by patients as well as medical and [...] Read more.

Clinics and hospitals inherently increase the risk of adverse events, including hospital-acquired infections (HAIs) transmitted between healthcare personnel and patients. This study aimed to identify bacterial strains present on frequently touched surfaces in outpatient clinics used by patients as well as medical and non-medical personnel. This study was conducted in four outpatient care centers located in two major cities in Poland. A total of 85 samples were collected from frequently touched surfaces, including 53 samples from areas accessed by patients and 32 samples from surfaces used by medical staff. A statistically significant increase in moderate-to-heavy growth was observed in samples containing microbiota compared to those containing other microorganisms (p = 0.003). Similarly, a higher prevalence of spore-forming bacteria was noted compared to non-spore-forming bacteria (p = 0.001). A significant difference was also observed between samples with no or scant growth versus those with moderate-to-heavy growth in both the microbiota and other microorganism groups (p = 0.003), as well as between the spore-forming and non-spore-forming groups (p = 0.001). The findings of this study prompted revisions in cleaning procedures. The frequency of training for medical staff was increased, and systematic quality control of the cleaning company’s performance was implemented. Full article

(This article belongs to the Special Issue Environmental Microorganisms as a Risk Factor of Healthcare-Associated Infections—Prevention Measures and Epidemiology)

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18 pages, 5386 KiB

Open AccessArticle

Composition, Distribution and Mobility Potential of the Antibiotic Resistome in Sediments from the East China Sea Revealed by Metagenomic Analysis

by Xiaozhong Chen, Long Gao, Yanxue Kou, Xiaoxuan Wang, Xintong Li, Hui He and Min Wang

Microorganisms 2025, 13(3), 697; https://doi.org/10.3390/microorganisms13030697 - 20 Mar 2025

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Abstract

Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the [...] Read more.

Marine sediments are recognized as crucial reservoirs of antibiotic resistance genes (ARGs). However, the antibiotic resistome in sediments of the East China Sea, an area heavily impacted by human activities, has not been thoroughly studied. Here, we conducted a systematic investigation into the antibiotic resistome in these sediments using metagenomic analysis. Overall, we detected eighty ARG subtypes and nineteen ARG types. Beta-lactams were the dominant ARG type, and Gammaproteobacteria was the main ARG host in this study. Mobile genetic elements (MGEs) were not major drivers of ARG profiles. Although the ARG host communities significantly differed between the spring and autumn (p < 0.05), the antibiotic resistome remained stable across the two seasons. The assembly of ARGs and their hosts was governed by stochastic processes, and a high ratio of stochastic processes implied its crucial role in the assembly and stabilization of the antibiotic resistome. Co-occurrence network analysis revealed an important role of Deltaproteobacteria in the stabilization of ARG profiles across seasons. Environmental parameters (e.g., temperature and density) played certain roles in the stabilization of the antibiotic resistome between spring and autumn. Moreover, nine human pathogen bacteria (HPB) were detected in this study. We also found that the health risks caused by ARGs were relatively higher in the spring. Our results will provide a strong foundation for the development of targeted management strategies to mitigate the further dissemination and spread of ARGs in marine sediments. Full article

(This article belongs to the Section Microbiomes)

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18 pages, 4543 KiB

Open AccessArticle

Integrating Cover Crops and Manure to Boost Goji Berry Yield: Responses of Soil Physicochemical Properties and Microbial Communities

by Haonan Chen, Fang Wang, Yamiao Gao, Yaran Ma, Lizhen Zhu and Xiongxiong Nan

Microorganisms 2025, 13(3), 696; https://doi.org/10.3390/microorganisms13030696 - 20 Mar 2025

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Abstract

A sustainable Goji berry (Lycium barbarum L.) planting system that integrates forage radish cover crops (Raphanus sativus L.) and animal manure has been established in northwestern China. This study investigated the effects of different cropping systems and manure application levels on [...] Read more.

A sustainable Goji berry (Lycium barbarum L.) planting system that integrates forage radish cover crops (Raphanus sativus L.) and animal manure has been established in northwestern China. This study investigated the effects of different cropping systems and manure application levels on soil physicochemical properties, microbial community structure, and L. barbarum yield under field conditions. A split-plot design was used, with the main-plot treatments consisting of two cropping systems and the sub-plot treatments involving three manure application levels. The results showed that compared to L. barbarum monocropping, cover cropping with R. sativus led to a decrease in soil bulk density (1.90%) and increase in soil electrical conductivity (11.5%), nutrient contents (total N and available N, P, and K: 30.3–138%), and microbial biomass (C: 79.0%; N: 184%). Cover cropping additionally enhanced the community diversity and richness of soil bacteria. Beta-diversity analysis revealed significant differences in bacterial rather than fungal community composition among various treatments. The bacterial network showed a lower ratio of positive to negative correlations and reduced complexity in response to cover cropping, which contrasted with fungal network patterns. Integration of cover cropping and medium manure application increased fruit yield by 8.71%. Cover crops and manure influenced soil microbial diversity mainly through their positive effects on soil total and available N contents. Full article

(This article belongs to the Special Issue Feature Paper in Plant–Microbe Interactions in Asia)

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22 pages, 14596 KiB

Open AccessArticle

The Minute Virus of Canines (MVC) Activates the RhoA/ROCK1/MLC2 Signal Transduction Pathway Resulting in the Dissociation of Tight Junctions and Facilitating Occludin-Mediated Viral Infection

by Xiang Ren, Zhiping Hei, Kai Ji, Yan Yan, Chuchu Tian, Yin Wei and Yuning Sun

Microorganisms 2025, 13(3), 695; https://doi.org/10.3390/microorganisms13030695 - 20 Mar 2025

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Abstract

The Minute Virus of Canines (MVC), belonging to the genus Bocaparvovirus within the family Parvoviridae, is associated with enteritis and embryonic infection in neonatal canines. Viral attachment to host cells is a critical step in infection, and viral protein 2 (VP2) as [...] Read more.

The Minute Virus of Canines (MVC), belonging to the genus Bocaparvovirus within the family Parvoviridae, is associated with enteritis and embryonic infection in neonatal canines. Viral attachment to host cells is a critical step in infection, and viral protein 2 (VP2) as an important structural protein of MVC influences host selection and infection severity. Nevertheless, little is known about the interaction between VP2 protein and host cells. In this study, we identified that VP2 directly interacts with the kinase domain of RhoA-associated protein kinase 1 (ROCK1) by using mass spectrometry and immunoprecipitation approach and demonstrated that the RhoA/ROCK1/myosin light chain 2 (MLC2) signaling pathway was activated during the early stage of MVC infection in Walter Reed canine cell/3873D (WRD) cells. Further studies indicated that RhoA/ROCK1-mediated phosphorylation of MLC2 triggers the contraction of the actomyosin ring, disrupts tight junctions, and exposes the tight junction protein Occludin, which facilitates the interaction between VP2 and Occludin. Specific inhibitors of RhoA and ROCK1 restored the MVC-induced intracellular translocation of Occludin and the increase in cell membrane permeability. Moreover, the two inhibitors significantly reduced viral protein expression and genomic copy number. Collectively, our study provides the first evidence that there is a direct interaction between the structural protein VP2 of MVC and ROCK1, and that the tight junction protein Occludin can serve as a potential co-receptor for MVC infection, which may offer new targets for anti-MVC strategies. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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23 pages, 6419 KiB

Open AccessArticle

The Genomic Characteristics of Potential Probiotics: Two Streptococcus salivarius Isolates from a Healthy Individual in China

by Mingyue Sun, Qian Li, Feiran Zhang, Ding Yao, Wenhua Huang, Qingyu Lv, Hua Jiang, Decong Kong, Yuhao Ren, Shaolong Chen, Yongqiang Jiang and Peng Liu

Microorganisms 2025, 13(3), 694; https://doi.org/10.3390/microorganisms13030694 - 20 Mar 2025

Viewed by 541

Abstract

The isolation and characterization of novel probiotics from dairy products, fermented foods, and the gut have gained significant attention. In particular, Streptococcus salivarius shows promise for use in oral probiotic preparations. In this study, we isolated two strains of S. salivarius—S.82.15 and [...] Read more.

The isolation and characterization of novel probiotics from dairy products, fermented foods, and the gut have gained significant attention. In particular, Streptococcus salivarius shows promise for use in oral probiotic preparations. In this study, we isolated two strains of S. salivarius—S.82.15 and S.82.20—from the oral cavity of a healthy individual. These strains exhibited distinct antimicrobial profiles. We thoroughly assessed the morphology and growth patterns of both strains and confirmed auto-aggregation and hemolytic activity. Through comprehensive genomic analysis, we found notable strain differences within the same bacterial species isolated from the same individual. Notably, the presence or absence of plasmids varied between the two strains. The genome of S.82.15 spans 2,175,688 bps and contains 1994 coding DNA sequences (CDSs), while S.82.20 has a genome size of 2,414,610 bps, a GC content of 40.62%, and 2276 annotated CDSs. Both strains demonstrated antibacterial activity against Group A Streptococcus (GAS), Micrococcus. luteus, and Porphyromonas gingivalis. To investigate the antibacterial properties further, we identified a gene cluster of salivaricin 9 on the plasmid of S.82.20 and a blp gene family on the chromosomes of both S.82.15 and S.82.20. Moreover, the gene expression of the blp family was upregulated when the isolated strains were co-cultured with GAS. Full article

(This article belongs to the Special Issue Probiotics: Identification and Applications)

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11 pages, 2282 KiB

Open AccessArticle

Reporting of Salmonellosis Markedly Declined in Finland During 28 Years of Surveillance, 1995–2022

by Kristiina Suominen, Jukka Ollgren, Elina Leinonen and Ruska Rimhanen-Finne

Microorganisms 2025, 13(3), 693; https://doi.org/10.3390/microorganisms13030693 - 20 Mar 2025

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Abstract

Salmonellosis is the second most common foodborne bacterial gastroenteritis in humans in Finland and worldwide. In Finland, a national salmonella control program covering cattle, pigs, and poultry, as well as the meat and eggs obtained from them, has been in place since the [...] Read more.

Salmonellosis is the second most common foodborne bacterial gastroenteritis in humans in Finland and worldwide. In Finland, a national salmonella control program covering cattle, pigs, and poultry, as well as the meat and eggs obtained from them, has been in place since the country joined the EU in 1995. To identify trends in the incidence of salmonellosis and to reflect on their causes, we analyzed Salmonella case data from the Finnish Infectious Disease Register (FIDR) from 1995 to 2022 and outbreak data from the national food and waterborne outbreak register (the FWO register) in the period 2010–2022. From 1995–1999 to 2015–2019, the incidence of salmonellosis decreased by 66% and 63% for domestic and travel-related cases, respectively. Most salmonellosis cases (72%) were travel-related, and, of them, 27% were infected in Southeast Asia. The most common serovars were S. Typhimurium and S. Enteritidis (38% and 19% of domestic cases, and 7% and 39% of travel-related cases). During 2010–2022, Salmonella sp. was reported as a cause in 31 foodborne outbreaks. In 14 of them, the source was identified at foodstuff level, and 12 sources were of foreign origin. The results of this study indicate that the national salmonella control program may have prevented domestic human infections in Finland. Full article

(This article belongs to the Special Issue Salmonella Infections: Trends and Updates)

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17 pages, 3166 KiB

Open AccessArticle

Exploring the Antimicrobial, Antioxidant and Extracellular Enzymatic Activities of Culturable Endophytic Fungi Isolated from the Leaves of Kirkia acuminata Oliv

by Sagwadi Kubayi, Raymond Tshepiso Makola and Khumiso Dithebe

Microorganisms 2025, 13(3), 692; https://doi.org/10.3390/microorganisms13030692 - 19 Mar 2025

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Abstract

Fungal endophytes of medicinal plants produce diverse secondary metabolites and extracellular enzymes with therapeutic and biotechnological potential. However, the biological and biotechnological potential of fungal endophytes from South African medicinal plants remain relatively underexplored. In this study, the antimicrobial, antioxidant, anti-inflammatory and extracellular [...] Read more.

Fungal endophytes of medicinal plants produce diverse secondary metabolites and extracellular enzymes with therapeutic and biotechnological potential. However, the biological and biotechnological potential of fungal endophytes from South African medicinal plants remain relatively underexplored. In this study, the antimicrobial, antioxidant, anti-inflammatory and extracellular enzymatic capabilities of five fungal endophytes previously isolated from the leaves of Kirkia acuminata Oliv. were investigated. Sequencing of the internal transcribed spacer (ITS) regions revealed that the isolates belonged to the genera Setosphaeria, Diaporthe and Corynespora. The broth micro-dilution assay and the Folin–Ciocalteau reagent method were used to assess the antibacterial activity and the total phenolic content (TPC) of the fungal endophytes’ ethyl acetate crude extracts (CEs), respectively. The antioxidant activity was assessed using the ferric reducing antioxidant power (FRAP) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging assays. The influence of the CE of the Setosphaeria rostrata KaL-4 on the viability and LPS-induced interleukin-6 (IL-6) production in Raw 264.7 macrophages was assessed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and an ELISA, respectively. The ability of the isolates to produce extracellular proteases, laccases and peroxidases was also determined. The CEs displayed antimicrobial activity with MICs ranging from 0.63 to 1.25 mg/mL and reducing power and scavenging activity ranging from 40% to 18% and from 60% to 48%, respectively. The S. rostrata KaL-4 CE possessed the highest TPC and demonstrated dose-dependent cytotoxicity. The CE further demonstrated a significant reduction in IL-6 production at a concentration of 0.75 µg/mL. Only one isolate demonstrated the ability to produce proteases with an enzymatic index (EI) of 0.66, while laccases (EI range of 0.14 to 1.15) and peroxidases were produced by all of the isolates. These findings suggest that fungal endophytes from South African medicinal plants are promising sources of bioactive compounds and industry-significant extracellular enzymes. Full article

(This article belongs to the Special Issue Endophytic Fungus as Producers of New and/or Bioactive Substances)

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17 pages, 2129 KiB

Open AccessArticle

In Infants with Neuroblastoma Standard Therapy Only Partially Reverts the Fecal Microbiome Dysbiosis Present at Diagnosis

by Maria Valeria Corrias, Eddi Di Marco, Carola Bonaretti, Margherita Squillario, Loredana Amoroso, Massimo Conte, Mirco Ponzoni and Roberto Biassoni

Microorganisms 2025, 13(3), 691; https://doi.org/10.3390/microorganisms13030691 - 19 Mar 2025

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Abstract

The fecal microbiomes of 15 infants with neuroblastoma (NB) at the onset of the disease and after standard-of-care therapy have been prospectively analyzed compared to those of age-matched healthy infants. By applying several algorithms to 16S sequencing, we found that the fecal microbiomes [...] Read more.

The fecal microbiomes of 15 infants with neuroblastoma (NB) at the onset of the disease and after standard-of-care therapy have been prospectively analyzed compared to those of age-matched healthy infants. By applying several algorithms to 16S sequencing, we found that the fecal microbiomes of infants with NB at onset were abundant in Pseudomonadota, including different descendants of Gammaproteobacteria. After completing therapy, their abundance decreased to a level like that observed in healthy infants. In contrast, the Bacillota that showed at the onset an abundance like that of healthy infants doubled their amount after treatment. In infants with NB, the beta diversity of the fecal microbiomes was significantly reduced compared to healthy infants and patients at the end of treatment. The Random Forest algorithm and the Reingold–Tilford heat tree showed that Enterobacteriaceae had a higher abundance at the onset, which declined after therapy. Picrust2 inferred pathway analysis indicated that the drug treatment was associated with a reduction in the polyamine pathway, highly represented in samples of NB at the onset. In conclusion, the dysbiosis observed in infants with NB at onset changed following standard-of-care treatment. Still, the composition at the end of treatment did not completely resemble that of healthy infants. Full article

(This article belongs to the Section Gut Microbiota)

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18 pages, 4030 KiB

Open AccessArticle

Red Mud Potentially Alleviates Ammonia Nitrogen Inhibition in Swine Manure Anaerobic Digestion by Enhancing Phage-Mediated Ammonia Assimilation

by Yulong Peng, Luhua Jiang, Junzhao Wu, Jiejie Yang, Ziwen Guo, Manjun Miao, Zhiyuan Peng, Meng Chang, Bo Miao, Hongwei Liu, Yili Liang, Huaqun Yin, Qiang He and Xueduan Liu

Microorganisms 2025, 13(3), 690; https://doi.org/10.3390/microorganisms13030690 - 19 Mar 2025

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Abstract

Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria–phages interactions in this process remains poorly understood. Thus, this study [...] Read more.

Red mud has been demonstrated to improve the methane production performance of anaerobic digestion (AD). However, the influence of red mud on ammonia nitrogen inhibition during AD through the mediating role of bacteria–phages interactions in this process remains poorly understood. Thus, this study investigated the impact of red mud on nitrogen metabolism in AD and characterized the phage and prokaryotic communities through a metagenomic analysis. The results showed that red mud significantly increased methane production by 23.1% and promoted the conversion of ammonia nitrogen into organic nitrogen, resulting in a 4.8% increase in total nitrogen. Simultaneously, it enriched the key microbial genera Methanothrix, Proteinophilum, and Petrimonas by 0.5%, 0.8%, and 2.7%, respectively, suggesting an enhancement in syntrophic acetate oxidation with greater ammonia tolerance. A viral metagenomic analysis identified seven nitrogen-metabolism-related auxiliary metabolic genes (AMGs), with glnA (encoding glutamine synthetase) being the most abundant. Compared to the control treatments, the red mud treatments led to a higher abundance of temperate phages and an increased number of AMGs. Furthermore, two new hosts carrying glnA (Mycolicibacteria smegmatis and Kitasatopola aureofaciens) were predicted, indicating that red mud expanded the host range of phages and promoted the spread of AMGs. Overall, our findings highlight the importance of phages in alleviating ammonia nitrogen inhibition and provide a novel understanding of the role of red mud in the AD of swine manure. Full article

(This article belongs to the Section Microbial Biotechnology)

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26 pages, 307 KiB

Open AccessArticle

Effects of Butyric Acid Supplementation on the Gut Microbiome and Growth Performance of Weanling Pigs Fed a Low-Crude Protein, Propionic Acid-Preserved Grain Diet

by Kathryn Ruth Connolly, Torres Sweeney, Marion T. Ryan, Stafford Vigors and John V. O’Doherty

Microorganisms 2025, 13(3), 689; https://doi.org/10.3390/microorganisms13030689 - 19 Mar 2025

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Abstract

Reducing crude protein (CP) in weaner pig diets lowers post-weaning diarrhoea risk but may impair growth performance. This study aimed to identify the beneficial effects of organic acid (OA)-preserved grain and butyric acid supplementation on gut health and growth in low-CP diets. At [...] Read more.

Reducing crude protein (CP) in weaner pig diets lowers post-weaning diarrhoea risk but may impair growth performance. This study aimed to identify the beneficial effects of organic acid (OA)-preserved grain and butyric acid supplementation on gut health and growth in low-CP diets. At harvest, grain was divided into two batches: one dried at 65 °C, the other treated with a propionic acid. Ninety-six piglets (28 days old) were assigned to four treatments: (1) dried grain, (2) OA-preserved grain, (3) dried grain + 3% butyric acid, and (4) OA-preserved grain + 3% butyric acid. On day 8, microbial composition, inflammatory markers, volatile fatty acids, and intestinal morphology were assessed. The OA-preserved grain improved feed conversion ratio (p < 0.05) increased beneficial gut bacteria (p < 0.01), elevated caecal butyrate (p < 0.05), reduced jejunal CXCL8 expression (p < 0.05), and enhanced nutrient digestibility (p < 0.01). Butyric acid reduced feed intake (p < 0.05), improved nutrient digestibility (p < 0.01), decreased colonic Proteobacteria (p < 0.05), and increased colonic propionate and butyrate (p < 0.01). Combining OA-preserved grain with butyric acid elevated ileal Proteobacteria and Pasteurellaceae (p < 0.05). In conclusion, while OA-preserved grain improves feed efficiency, nutrient digestibility, and gut microbiota, supplementing butyric acid enhances nutrient digestibility but reduces feed intake, and their combination may disrupt the microbial balance. Full article

(This article belongs to the Special Issue Gut Microbiota and Nutrients, 2nd Edition)

18 pages, 1445 KiB

Open AccessArticle

Antibiotic Resistance and Virulence Determinants of Pseudomonas aeruginosa Isolates Cultured from Hydrocarbon-Contaminated Environmental Samples

by Chioma Lilian Ozoaduche, Balázs Libisch, Daniel Itoro, Iyore Blessing Idemudia, Katalin Posta and Ferenc Olasz

Microorganisms 2025, 13(3), 688; https://doi.org/10.3390/microorganisms13030688 - 19 Mar 2025

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Abstract

Crude oil and its derivates are among the most important environmental pollutants, where P. aeruginosa strains producing AlkB1 and AlkB2 alkane hydroxylases are often involved in their biodegradation. The aim of this study was to analyze antibiotic resistance and virulence determinants of a [...] Read more.

Crude oil and its derivates are among the most important environmental pollutants, where P. aeruginosa strains producing AlkB1 and AlkB2 alkane hydroxylases are often involved in their biodegradation. The aim of this study was to analyze antibiotic resistance and virulence determinants of a P. aeruginosa isolate cultured from a hydrocarbon-contaminated soil sample from Ogoniland, Nigeria, and to compare its characteristics with P. aeruginosa isolates cultured worldwide from hydrocarbon-contaminated environments or from clinical samples. Using the ResFinder reference database, a catB7 chloramphenicol acetyltransferase gene, an ampC-type PDC β-lactamase gene, and an OXA-50 type β-lactamase gene were identified in all P. aeruginosa strains analyzed in this study. In some of these P. aeruginosa strains, loss-of-function mutations were detected in the regulatory genes mexR, nalC, or nalD, predicting an efflux-mediated acquired antibiotic-resistance mechanism. Several P. aeruginosa sequence types that were associated with oil-contaminated environments have also been cultured from human clinical samples worldwide, including sequence types ST532, ST267, ST244, and ST1503. Our findings also indicate that environmental P. aeruginosa may serve as the source of human infections, warranting further studies from a One Health perspective about the application of P. aeruginosa for the in situ bioremediation of hydrocarbon-contaminated sites. Full article

(This article belongs to the Special Issue Bacterial Antibiotic Resistance, Second Edition)

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14 pages, 4792 KiB

Open AccessArticle

Characteristics and Mechanisms of Simultaneous Quinoline and Ammonium Nitrogen Removal by a Robust Bacterium Pseudomonas stutzeri H3

by Jie Hu, Bing Xu, Jiabao Yan and Guozhi Fan

Microorganisms 2025, 13(3), 687; https://doi.org/10.3390/microorganisms13030687 - 19 Mar 2025

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Abstract

The discharge of organic and inorganic nitrogenous pollutants in wastewater leads to eutrophication and disrupts the ecological balance. Therefore, the pressing need for an effective treatment method has become increasingly evident. A robust bacterium Pseudomonas stutzeri H3 capable of simultaneous organic and inorganic [...] Read more.

The discharge of organic and inorganic nitrogenous pollutants in wastewater leads to eutrophication and disrupts the ecological balance. Therefore, the pressing need for an effective treatment method has become increasingly evident. A robust bacterium Pseudomonas stutzeri H3 capable of simultaneous organic and inorganic nitrogen removal was isolated from the activated sludge in the coking wastewater treatment system. The optimal conditions for the simultaneous removal of ammonium nitrogen and quinoline were as follows: C/N ratio of 15–20, initial pH of 7–8, culture temperature of 30 °C, and shaking speed of 150–300 rpm. At 200 mg/L ammonium nitrogen and 100 mg/L quinoline, strain H3 achieved above 90% of removal efficiency, exhibiting excellent simultaneous nitrogen removal capabilities. The outstanding nitrogen removal efficiencies in the presence of quinoline and different inorganic nitrogen sources further confirmed the simultaneous organic and inorganic nitrogen removal capability of strain H3. The whole genome sequencing and nitrogen metabolic intermediates determination of strain H3 were performed to elucidate the gene function annotations, nitrogen removal function genes, and nitrogen metabolic pathways. The findings provide a promising pathway to treat the organic and inorganic nitrogenous pollutants in wastewater. Full article

(This article belongs to the Section Environmental Microbiology)

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10 pages, 1330 KiB

Open AccessCase Report

Case Report: Long-Term Follow-Up of Visceral Leishmaniasis and HIV Coinfected Patients Without Relapse: Lymphoproliferative Response After Stimulation with Soluble Leishmania Antigen

by Begoña Monge-Maillo, Daniel Roger-Zapata, Fernando Dronda, Eugenia Carrillo, Javier Moreno, María Dolores Corbacho-Loarte, Diego Gayoso Cantero, Oihane Martín, Sandra Chamorro-Tojeiro, Jose A. Perez-Molina, Francesca Norman, Marta González-Sanz and Rogelio López-Vélez

Microorganisms 2025, 13(3), 686; https://doi.org/10.3390/microorganisms13030686 - 19 Mar 2025

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Abstract

Highly active antiretroviral therapy (HAART) has reduced the incidence of VL/HIV dramatically. However, HAART only partially prevents relapses, with one-year relapse rates ranging from 30 to 60%. Consequently, secondary prophylaxis is recommended for patients with <200 CD4+ cells/μL. In clinical practice, characterizing cellular [...] Read more.

Highly active antiretroviral therapy (HAART) has reduced the incidence of VL/HIV dramatically. However, HAART only partially prevents relapses, with one-year relapse rates ranging from 30 to 60%. Consequently, secondary prophylaxis is recommended for patients with <200 CD4+ cells/μL. In clinical practice, characterizing cellular immune response could help estimate the risk of relapse in VL/HIV coinfected patients. In this study, the lymphoproliferative response after stimulation with soluble Leishmania antigen was assessed in 2022 and 2023 in three cases of VL/HIV coinfection with long-term follow-up (17, 8 and 19 years). PCR and rK-39 results for Leishmania, HIV viral load, CD4 cell count, proliferation index, IFN-γ, IL-2, IP-10, IL-10 and TNF-α were determined. Heterogeneous results were obtained, with only one patient having developed specific cellular immunity against Leishmania. No cases of relapse were observed. The heterogeneity of lymphoproliferative test results in the three cases described highlights the need to identify surrogate markers of cure to guide maintenance or withdrawal of prophylaxis. Full article

(This article belongs to the Special Issue New Advancements in the Field of Leishmaniasis)

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20 pages, 4070 KiB

Open AccessArticle

Insights into a Novel and Efficient Microbial Nest System for Treating Pig Farm Wastewater

by Lifei Chen, Lusheng Li, Guiying Wang, Meng Xu, Yizhen Xin, Hanhan Song, Jiale Liu, Jiani Fu, Qi Yang, Qile Tian, Yuxi Wang, Haoyang Sun, Jianqun Lin, Linxu Chen, Jiang Zhang and Jianqiang Lin

Microorganisms 2025, 13(3), 685; https://doi.org/10.3390/microorganisms13030685 - 19 Mar 2025

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Abstract

A microbial nest system (MNS) represents a novel and efficient approach to treating solid–liquid mixtures from pig farming instead of the conventional method, which separates the solid and liquid at first using centrifugation before treating the solid and liquid. However, the key environmental [...] Read more.

A microbial nest system (MNS) represents a novel and efficient approach to treating solid–liquid mixtures from pig farming instead of the conventional method, which separates the solid and liquid at first using centrifugation before treating the solid and liquid. However, the key environmental factors influencing the efficiency of this system and the microbial structure are still not clear. This study aimed to elucidate the changes in an MNS considering physicochemical properties, spectral analysis, and correlations between microbial community structures and environmental factors during the treatment. The results showed that the MNS underwent three temperature stages during the treatment process of piggery slurry: a warming period, a high-temperature period, and a cooling period. In the high-temperature period, the most abundant bacterium was Bacillus, with a relative abundance of 22.16%, and Chaetomium dominated the fungal community with a relative abundance of 11.40%. Moreover, the moisture content, pH value, and electrical conductivity (EC) exhibited an increasing trend, whereas the carbon-to-nitrogen (C/N) ratio and the ratio of ammonia nitrogen to nitrate nitrogen (NH₄⁺-N/NO₃⁻-N) showed a decreasing trend. The accumulation of humic acid and fulvic acid suggested that the humification process of organic matter was occurring. The moisture content and C/N ratio were identified as crucial factors influencing the bacterial and fungal community structures, respectively. This study provides a theoretical basis for enhancing the efficiency of piggery slurry treatment using an MNS and rational optimisation of the associated processes. Full article

(This article belongs to the Section Environmental Microbiology)

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24 pages, 2248 KiB

Open AccessArticle

Whole-Genome Sequencing of Linezolid-Resistant and Linezolid-Intermediate-Susceptibility Enterococcus faecalis Clinical Isolates in a Mexican Tertiary Care University Hospital

by Pedro Martínez-Ayala, Leonardo Perales-Guerrero, Adolfo Gómez-Quiroz, Brenda Berenice Avila-Cardenas, Karen Gómez-Portilla, Edson Alberto Rea-Márquez, Violeta Cassandra Vera-Cuevas, Crisoforo Alejandro Gómez-Quiroz, Jaime Briseno-Ramírez and Judith Carolina De Arcos-Jiménez

Microorganisms 2025, 13(3), 684; https://doi.org/10.3390/microorganisms13030684 - 19 Mar 2025

Viewed by 575

Abstract

Linezolid-non-susceptible Enterococcus faecalis (LNSEf) has emerged as a critical clinical concern worldwide, yet data from Latin American settings remain scarce. This study aimed to investigate the molecular epidemiology and mechanisms underlying LNSEf in a Mexican tertiary care university hospital, focusing on clinical correlates [...] Read more.

Linezolid-non-susceptible Enterococcus faecalis (LNSEf) has emerged as a critical clinical concern worldwide, yet data from Latin American settings remain scarce. This study aimed to investigate the molecular epidemiology and mechanisms underlying LNSEf in a Mexican tertiary care university hospital, focusing on clinical correlates and clonal relationships. A total of 392 non-duplicated E. faecalis isolates were collected over 12 months, of which 24 with minimum inhibitory concentrations ≥4 µg/mL underwent whole-genome sequencing to identify specific resistance determinants (optrA, cfrA, 23S rRNA mutations) and to perform multilocus sequence typing (MLST) and phylogenetic analyses. Of the 392 isolates, 6.12% showed linezolid non-susceptibility, predominantly linked to plasmid- or chromosomally encoded optrA; only two isolates carried cfrA. No mutations were detected in 23S rRNA domain V or ribosomal proteins L3/L4. Clinically, LNSEf strains were associated with immunosuppression, previous surgical interventions, and prolonged hospital stays. Although most LNSEf isolates retained susceptibility to ampicillin, vancomycin, and daptomycin, they exhibited high rates of resistance to other antibiotic classes, particularly aminoglycosides and fluoroquinolones. These findings underscore the emergence of LNSEf in this region, highlighting the need for robust genomic surveillance, strict infection control, and judicious antimicrobial stewardship to curb further dissemination. Full article

(This article belongs to the Special Issue Next-Generation Sequencing in Antimicrobial Resistance)

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23 pages, 7248 KiB

Open AccessArticle

Cas5 Regulates the Exposure of β-Glucan, the Cell Surface Hydrophobicity, and the Expression of Cell Wall Proteins to Remodel the Candida albicans Cell Wall and Participates in the Recruitment of Neutrophils

by Qiyue Zhang, Guanglin Li, Yanmei Wang, Chen Yang, Wenhui Bai, Qingqing Li, Jiye Zhang and Peipei Zhang

Microorganisms 2025, 13(3), 683; https://doi.org/10.3390/microorganisms13030683 - 19 Mar 2025

Viewed by 327

Abstract

Candida albicans (C. albicans) is a major opportunistic fungal pathogen that causes life-threatening infections, particularly in immunocompromised individuals, underscoring the critical need to understand its pathogenic mechanisms. This study investigates the role of Cas5, a key transcription factor, in regulating C. [...] Read more.

Candida albicans (C. albicans) is a major opportunistic fungal pathogen that causes life-threatening infections, particularly in immunocompromised individuals, underscoring the critical need to understand its pathogenic mechanisms. This study investigates the role of Cas5, a key transcription factor, in regulating C. albicans cell wall remodeling, virulence, and host interactions. Genetic manipulation and biochemical assays were used to examine the effects of Cas5 depletion on C. albicans cell wall structure, adhesion to host cells, morphology transition, innate immune cells recruitment, and pathogenicity in a BALB/C mouse model of oropharyngeal candidiasis (OPC). The results showed that the Cas5 depletion mediated β-glucan exposure and enhanced C. albicans’s ability to recruit neutrophils in vivo. Additionally, Cas5-mediated changes in cell surface hydrophobicity (CSH), CWP expressions, and morphological transition promoted C. albicans adhesion to biologically active surfaces (host cells) and increased fungal burden in the mouse model of OPC. In conclusion, Cas5 modulates C. albicans cell wall remodeling by masking cell wall β-glucan, altering CSH, and regulating the expression of cell wall proteins (CWPs). Additionally, Cas5 participates in inhibiting neutrophil recruitment and enhancing the C. albicans adhesion to host cells, as well as facilitating morphological transitions. These actions promote the colonization and invasion of C. albicans in OPC pathogenesis. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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13 pages, 662 KiB

Open AccessArticle

Comparative Analysis of Metagenomic Next-Generation Sequencing, Sanger Sequencing, and Conventional Culture for Detecting Common Pathogens Causing Lower Respiratory Tract Infections in Clinical Samples

by Qiaolian Yi, Ge Zhang, Tong Wang, Jin Li, Wei Kang, Jingjia Zhang, Yali Liu and Yingchun Xu

Microorganisms 2025, 13(3), 682; https://doi.org/10.3390/microorganisms13030682 - 18 Mar 2025

Viewed by 356

Abstract

Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 [...] Read more.

Metagenomic next-generation sequencing (mNGS) has emerged as a revolutionary tool for infectious disease diagnostics. The necessity of mNGS in real-world clinical practice for common Lower Respiratory Tract Infections (LRTI) needs further evaluation. A total of 184 bronchoalveolar lavage fluid (BALF) samples and 322 sputa associated with LRTI were fully examined. The detection performance was compared between mNGS and standard microbiology culture, using Sanger sequencing as the reference method. 52.05% (165/317) of sputa showed identical results for all three methods. Compared to Sanger sequencing, the same results obtained by mNGS were 88.20% (284/322). In 2.80% (9/322) of cases, Sanger sequencing detected more microorganisms, while mNGS detected more in 9% (29/322) of cases. For BALF, 49.41% (85/172) of cases showed identical results for all three methods. In 91.30% (168/184) of cases, identical results were produced by both mNGS and Sanger sequencing. mNGS detected more species in 7.61% (14/184) of cases, whereas in 2.80% (2/184) instances, the Sanger sequencing detected more microorganisms than mNGS. In the 184 BALF samples, 66 samples were identified as having co-infections by mNGS, Sanger sequencing identified 64 samples, and cultures identified 22 samples. Our study demonstrates that mNGS offers a significant advantage over conventional culture methods in detecting co-infections. For common bacterial pathogens, conventional culture methods are sufficient for detection. However, mNGS provides comprehensive pathogen detection and is particularly useful for identifying rare and difficult-to-culture pathogens. Full article

(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)

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13 pages, 717 KiB

Open AccessArticle

The Prevalence of Polyketide Synthase-Positive E. coli in Cystic Fibrosis

by Christopher Chan, Michael Coffey, Caitlin Murphy, Isabelle McKay, Jumaana Abdu, Keerti Paida, Rachel Y. Tam, Hannah Wrigley-Carr, Bernadette Prentice, Louisa Owens, Yvonne Belessis, Sandra Chuang, Adam Jaffe, Josie van Dorst and Chee Y. Ooi

Microorganisms 2025, 13(3), 681; https://doi.org/10.3390/microorganisms13030681 - 18 Mar 2025

Viewed by 428

Abstract

Cystic fibrosis (CF) patients experience higher risks of colorectal cancer but the pathogenesis is unclear. In the general population, polyketide synthase-positive (pks⁺) E. coli is implicated in intestinal carcinogenesis via the production of colibactin; however, the relevance in CF is unknown. In [...] Read more.

Cystic fibrosis (CF) patients experience higher risks of colorectal cancer but the pathogenesis is unclear. In the general population, polyketide synthase-positive (pks⁺) E. coli is implicated in intestinal carcinogenesis via the production of colibactin; however, the relevance in CF is unknown. In this study, we investigate pks⁺E. coli prevalence in CF and potential associations between pks⁺E. coli, gastrointestinal inflammation, and microbiome dynamics with fecal calprotectin and 16SrRNA gene taxonomic data. Cross-sectional analysis demonstrated no difference in pks⁺E. coli carriage between CF patients and healthy controls, 21/55 (38%) vs. 26/55 (47%), p = 0.32. Pks⁺E. coli was not associated with significant differences in mean (SD) calprotectin concentration (124 (154) vs. 158 (268) mg/kg; p = 0.60), microbial richness (159 (76.5) vs. 147 (70.4); p = 0.50) or Shannon diversity index (2.78 (0.77) vs. 2.65 (0.74); p = 0.50) in CF. Additionally, there was no association with exocrine pancreatic status (p = 0.2) or overall antibiotic use (p = 0.6). Longitudinally, CF subjects demonstrated intra-individual variation in pks⁺E. coli presence but no significant difference in overall prevalence. Future investigation into the effects of repeat exposure on risk profile and analysis of older CF cohorts is necessary to identify if associations with colorectal cancer exist. Full article

(This article belongs to the Special Issue Effects of Gut Microbiota on Human Health and Disease, 2nd Edition)

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23 pages, 3499 KiB

Open AccessArticle

Gut Microbiome Alterations, Mental Health, and Alcohol Consumption: Investigating the Gut–Brain Axis in Firefighters

by Ji Youn Yoo, Anujit Sarkar, Hyo-Sook Song, Sunghwan Bang, Gyusik Shim, Cary Springer, Morgan E. O’Brien, Yoonhwa Shin, Songhyun Ju, Sunhee Han, Sung Soo Kim, Usha Menon, Tae Gyu Choi and Maureen E. Groer

Microorganisms 2025, 13(3), 680; https://doi.org/10.3390/microorganisms13030680 - 18 Mar 2025

Viewed by 771

Abstract

Firefighters across the world face higher risks of occupational hazards, such as exposure to chemicals, extreme heat, traumatic stressors, and intense physical demands, which can increase their vulnerability to a range of psychological and physiological difficulties. These challenges include the risk of developing [...] Read more.

Firefighters across the world face higher risks of occupational hazards, such as exposure to chemicals, extreme heat, traumatic stressors, and intense physical demands, which can increase their vulnerability to a range of psychological and physiological difficulties. These challenges include the risk of developing chronic stress, depression, and post-traumatic stress disorder (PTSD), potentially leading to detrimental negative coping patterns such as alcohol abuse. The consequent health implications impact both short-term and long-term health and well-being. This study aimed to explore the relationship between mental health status, alcohol consumption patterns, and gut microbiome alterations in firefighters from two different regions—America and Korea. By investigating these relationships, we hope to gain insights into how repeated exposure to severe stressors impacts gut health. Healthy male firefighters (ages 21–50) and controls (matched sex, geography, and age) were recruited via flyers and snowball sampling in the United States and South Korea, resulting in 203 participants (102 firefighters and 101 controls). Firefighters reported significantly higher PTSD symptoms and depression and drank 2.3 times more alcohol than the control group. American firefighters reported more drinking than Koreans. There was a significant correlation between higher alcohol consumption and the likelihood of witnessing deaths by suicide. However, there were no correlations between alcohol consumption and PTSD symptom severity. There were associations between alcohol consumption patterns and aspects of the gut microbiome. This study highlights the mental health challenges faced by firefighters, including elevated rates of PTSD, depression, and alcohol consumption, with specific microbial imbalances linked to PTSD and alcohol use, emphasizing the role of the gut–brain axis. Full article

(This article belongs to the Special Issue The Role of Microbiota in Upper and Lower Gastrointestinal Functional Disorders)

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16 pages, 3350 KiB

Open AccessArticle

Bacterial Distribution in the Glacier Borehole Meltwater on the Eastern Broknes Peninsula of the Larsemann Hills and Adjacent Lake Water, East Antarctica

by Hongpeng Cui, Jibin Han, Bing Li, Youhong Sun, Da Gong, Xiaopeng Fan, Talalay Pavel, Dayi Zhang, Liang Gao and Hongchen Jiang

Microorganisms 2025, 13(3), 679; https://doi.org/10.3390/microorganisms13030679 - 18 Mar 2025

Viewed by 327

Abstract

The distribution and assembly mechanisms of microorganisms in Antarctic lakes and glaciers remain poorly understood, despite their ecological significance. This study investigates the bacterial diversity and community composition in glacier borehole meltwater samples from the eastern Broknes Peninsula of the Larsemann Hills and [...] Read more.

The distribution and assembly mechanisms of microorganisms in Antarctic lakes and glaciers remain poorly understood, despite their ecological significance. This study investigates the bacterial diversity and community composition in glacier borehole meltwater samples from the eastern Broknes Peninsula of the Larsemann Hills and adjacent lake water samples in East Antarctica using high—throughput 16S rRNA gene sequencing. The results show that bacterial diversity in glacier borehole meltwater increased with depth, but remained lower than in lake water. Significant compositional differences were observed between lake and glacier borehole bacterial communities, with higher relative abundances of Actinobacteria, Bacteroidia, Cyanobacteriia, and Verrucomicrobiae in glacier borehole water samples, while Alphaproteobacteria, Gammaproteobacteria, OLB14 (phylum Chloroflexi), Acidimicrobiia, and Thermoleophilia were more abundant in lake samples. These differences were attributed to distinct community assembly mechanisms: stochastic processes (ecological drift and dispersal limitation) dominated in lakes, while both stochastic (ecological drift and homogeneous dispersal) and deterministic (homogeneous selection) processes played key roles in glacier boreholes. This study enhances our understanding of bacterial community assembly and distribution patterns in Antarctic glacier ecosystems, providing insights into microbial biodiversity and biogeochemical cycling in these extreme environments. Full article

(This article belongs to the Section Environmental Microbiology)

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18 pages, 1350 KiB

Open AccessArticle

Impact of Zika and Chikungunya Viruses on Spontaneous Abortions: Insights from a Reference Maternity Hospital

by Anne Kerollen Pinheiro de Carvalho, Ana Cecília Ribeiro Cruz, Juarez Antônio Simões Quaresma, Arnaldo Jorge Martins Filho, Darlene de Brito Simith Durans, Orlando Pereira Amador Neto, Ligia do Socorro Oliveira de Lima, Norma Suely de Carvalho Fonseca Assunçao, Edna Cristina Santos Franco, Patrícia Brazão Cohen and Eliana Vieira Pinto da Silva

Microorganisms 2025, 13(3), 678; https://doi.org/10.3390/microorganisms13030678 - 18 Mar 2025

Viewed by 359

Abstract

To investigate the association between miscarriage and ZIKV and CHIKV infection. The study population consisted of pregnant women who had miscarriages between 2015, 2016 and 2017, comprising a total of 30 women who were treated at the Santa Casa de Misericórdia do Pará [...] Read more.

To investigate the association between miscarriage and ZIKV and CHIKV infection. The study population consisted of pregnant women who had miscarriages between 2015, 2016 and 2017, comprising a total of 30 women who were treated at the Santa Casa de Misericórdia do Pará Foundation (FSCMPA). The processed samples came from already paraffinized material containing placental and fetal remains, where they were tested with hematoxylin–eosin and immunohistochemistry for ZIKV and CHIKV. Regarding the sociodemographic, clinical and obstetric characteristics of the patients, they correspond to the age group between 20 and 29 years of age; of brown color; women who had abortions for the first time; miscarriages occurring in the first trimester of pregnancy; women belonging to the metropolitan region of Belém; diagnosed with incomplete abortion and who had undergone uterine curettage procedure. Regarding the histopathologic and immunohistochemical findings, an inflammatory infiltrate rich in neutrophils and lymphocytes, among others, was found in the endometrial fragments and chorionic membranes. In addition, placental areas consisting of edema, necrosis and hemorrhage were found. The study identified ZIKV and CHIKV in 40% (n = 12) of samples from spontaneous abortion specimens, and CHIKV was the most prevalent virus in the study, representing 36.11% of the total specimens, with reddish granular material in the cytoplasm of decidua cells and placental villi suggesting that the viruses may be present in these regions of the placenta. Full article

(This article belongs to the Special Issue Detection and Identification of Pathogenic Bacteria and Viruses)

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21 pages, 5438 KiB

Open AccessArticle

Enhancing Lignocellulose Degradation and Mycotoxin Reduction in Co-Composting with Bacterial Inoculation

by Cheng Chen, Xiaolong Tang, Chaosheng Liao, Xiaokang Huang, Mingjie Zhang, Yubo Zhang, Pan Wang, Siqi Yang, Ping Li and Chao Chen

Microorganisms 2025, 13(3), 677; https://doi.org/10.3390/microorganisms13030677 - 18 Mar 2025

Viewed by 363

Abstract

The burgeoning global silage industry has precipitated challenges related to the sustainable utilization of mycotoxin-contaminated silage. To understand the effect of bio-enhancement on lignocellulose degradation and mycotoxin reduction, mycotoxin-contaminated silage and rape straw were co-composted without (CK) or with different bacterial agents and [...] Read more.

The burgeoning global silage industry has precipitated challenges related to the sustainable utilization of mycotoxin-contaminated silage. To understand the effect of bio-enhancement on lignocellulose degradation and mycotoxin reduction, mycotoxin-contaminated silage and rape straw were co-composted without (CK) or with different bacterial agents and their combinations. Compared to CK, the inoculation of Weissella paramesenteroides and Bacillus subtilis could increase the degradation rate of cellulose by 39.24% and lignin by 22.31% after composting. Inoculation of W. paramesenteroides and Paenibacillus sp. significantly enhanced cellulose and lignin degradation rates by 26.75% and 15.48%, respectively. Furthermore, this treatment significantly reduced mycotoxin levels (p < 0.05), including Aflatoxin B1 (AFB1, 64.48% reduction), T-2 toxin (65.02%), Ochratoxin A (OTA, 61.30%), Zearalenone (ZEN, 67.67%), and Vomitoxin (DON, 48.33%). Inoculation with Paenibacillus sp. and other bacteria increased total nitrogen by 48.34–65.52% through enhancing microbiological activity. Therefore, Paenibacillus sp. in combination with other bacteria could increase compost efficiency and reduce mycotoxin presence for better and safer utilization of agricultural waste by-products, enabling faster conversion of contaminated silage into safe soil amendments, which could reduce agricultural waste management costs. Full article

(This article belongs to the Section Veterinary Microbiology)

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13 pages, 708 KiB

Open AccessArticle

Baseline Characteristics of Bronchial Secretions and Bronchoalveolar Lavage Fluid in Patients with Ventilator-Associated Pneumonia

by Rodopi Stamatiou, Efrosyni Gerovasileiou, Maria Angeli, Konstantina Deskata, Vasiliki Tsolaki, Konstantinos Mantzarlis, Epameinondas Zakynthinos and Demosthenes Makris

Microorganisms 2025, 13(3), 676; https://doi.org/10.3390/microorganisms13030676 - 18 Mar 2025

Viewed by 332

Abstract

Mechanically ventilated (MV) patients often develop ventilator-associated pneumonia (VAP) with increased mortality risk, especially in VAP caused by multidrug-resistant (MDR) microorganisms. We evaluated MV patients and monitored VAP presentation, microbiologically confirmed. The patients underwent bronchoalveolar lavage (BAL) and blind bronchial aspiration (AC) at [...] Read more.

Mechanically ventilated (MV) patients often develop ventilator-associated pneumonia (VAP) with increased mortality risk, especially in VAP caused by multidrug-resistant (MDR) microorganisms. We evaluated MV patients and monitored VAP presentation, microbiologically confirmed. The patients underwent bronchoalveolar lavage (BAL) and blind bronchial aspiration (AC) at baseline. Systematic bronchial secretion and radiologic assessments were performed daily. The patients were classified as MDR-VAP, non-MDR-VAP, or non-VAP. The APACHE II and SOFA scores, microbiology, inflammatory markers, respiratory system characteristics, and ventilator settings were evaluated. BAL and AC were assessed for total protein levels, cellular number and profile, and IL-1β and TNF-α levels. Of the VAP patients, 46.1% presented with MDR-VAP due to Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, or Stenotrophomonas maltophilia, and 53.8%—with non-MDR-VAP. The VAP patients had higher APACHE II scores and airway pressure but a lower baseline PO₂/FIO₂ compared to the non-VAP patients, while PO₂/FIO₂ was increased in MDR-VAP compared to non-MDR-VAP. BAL protein, IL-1β, and cellular levels were increased in VAP vs. non-VAP and in non-MDR-VAP compared to MDR-VAP. Macrophages and polymorphonuclears were 34.36% and 23.76% in VAP, statistically significant increased compared to non-VAP. Their percentages were also increased in non-MDR-VAP compared to MDR-VAP. These differences imply a different immunological profile in non-MDR-VAP patients. In conclusion, MDR-VAP patients may present significant differences in baseline clinical characteristics and molecular biomarkers, which may help in prompt diagnosis and an improved therapeutic approach. Full article

(This article belongs to the Section Medical Microbiology)

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21 pages, 3563 KiB

Open AccessArticle

Faecalibacterium prausnitzii Is Associated with Disease Severity in MASLD but Its Supplementation Does Not Improve Diet-Induced Steatohepatitis in Mice

by Eliane Münte, Greta Viebahn, Amit Khurana, Jumpei Fujiki, Tomohiro Nakamura, Sonja Lang, Münevver Demir, Bernd Schnabl and Phillipp Hartmann

Microorganisms 2025, 13(3), 675; https://doi.org/10.3390/microorganisms13030675 - 18 Mar 2025

Viewed by 531

Abstract

The gut microbiota plays an important role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). In this study, we aimed to evaluate the role of the butyrate-producing bacterium Faecalibacterium prausnitzii in MASLD and whether supplementation with butyrate-producing bacteria, in particular Faecalibacterium [...] Read more.

The gut microbiota plays an important role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). In this study, we aimed to evaluate the role of the butyrate-producing bacterium Faecalibacterium prausnitzii in MASLD and whether supplementation with butyrate-producing bacteria, in particular Faecalibacterium prausnitzii, can ameliorate diet-induced steatohepatitis in mice. The relative abundance of the genus Faecalibacterium and its most abundant strain Faecalibacterium prausnitzii was determined by 16S rRNA sequencing and quantitative polymerase chain reaction (qPCR), respectively, in 95 participants with MASLD and 19 healthy control subjects. Butyrate and butyrate-producing bacteria (Faecalibacterium prausnitzii and Coprococcus comes) were gavaged to C57BL/6 mice fed a steatohepatitis-inducing diet. The fecal relative abundance of Faecalibacterium and Faecalibacterium prausnitzii was decreased in subjects with MASLD versus healthy controls and lower in individuals with MASLD and stage 3–4 fibrosis versus those with stage 0–2 fibrosis. Sodium-butyrate supplementation improved hepatic steatosis in mice on high-fat diet (HFD). Gavage of various butyrate-producing bacteria including Faecalibacterium prausnitzii and Coprococcus comes isolated from humans did not improve HFD-induced liver disease in mice. Although the abundance of Faecalibacterium prausnitzii is associated with MASLD severity in humans, its gavage to mice does not improve experimental diet-induced liver disease. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 2nd Edition)

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10 pages, 472 KiB

Open AccessArticle

The Role of the OLM CandID Real-Time PCR in the Invasive Candidiasis Diagnostic Surveillance in Intensive Care Unit Patients

by Laura Trovato, Maddalena Calvo, Concetta Ilenia Palermo, Maria Rita Valenti and Guido Scalia

Microorganisms 2025, 13(3), 674; https://doi.org/10.3390/microorganisms13030674 - 18 Mar 2025

Viewed by 448

Abstract

Molecular techniques recently integrated the candidiasis diagnostic workflow, avoiding the culture-based prolonged turn-around time and lack of sensitivity. The present retrospective study evaluated the OLM CandID Real-Time PCR on serum samples in the early and rapid candidaemia diagnosis among ICU patients. The final [...] Read more.

Molecular techniques recently integrated the candidiasis diagnostic workflow, avoiding the culture-based prolonged turn-around time and lack of sensitivity. The present retrospective study evaluated the OLM CandID Real-Time PCR on serum samples in the early and rapid candidaemia diagnosis among ICU patients. The final purpose of the protocol was to demonstrate the effectiveness of a PCR assay in the invasive candidiasis diagnostic workflow due to the high sensitivity rates and species identification possibility. The evaluation screened 60 suitable patients, accounting for 10 probable and 7 proven candidiasis cases. Patients with at least a positive (1→3)-β-D-glucan (BDG) value underwent molecular procedures. A sensitivity of 83.3%, a specificity of 94.3%, a positive predictive value of 87.5%, and a negative predictive value of 91.7% emerged for the PCR assay. As a conclusion, Candida PCR assays may represent useful diagnostic assistance tools when applied together with serological markers and culture-based assays. Full article

(This article belongs to the Special Issue State-of-the-Art Medical Microbiology in Italy (2023, 2024))

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23 pages, 6857 KiB

Open AccessArticle

Research Status and Trends of Gut Microbiota and Intestinal Diseases Based on Bibliometrics

by Xiao Sun and Jiancheng Zhai

Microorganisms 2025, 13(3), 673; https://doi.org/10.3390/microorganisms13030673 - 17 Mar 2025

Viewed by 594

Abstract

Gut microbiota plays an important role in gut health, and its dysbiosis is closely related to the pathogenesis of various intestinal diseases. The field of gut microbiota and intestinal diseases has not yet been systematically quantified through bibliometric methods. This study conducted bibliometric [...] Read more.

Gut microbiota plays an important role in gut health, and its dysbiosis is closely related to the pathogenesis of various intestinal diseases. The field of gut microbiota and intestinal diseases has not yet been systematically quantified through bibliometric methods. This study conducted bibliometric analysis to delineate the evolution of research on gut microbiota and intestinal diseases. Data were sourced from the Web of Science Core Collection database from 2009 to 2023 and were scientometrically analyzed using CiteSpace. We have found that the number of annual publications has been steadily increasing and showing an upward trend. China and the Chinese Academy of Sciences are the country and institution with the most contributions, respectively. Frontiers in Microbiology and Nutrients are the journals with the most publications, while Plos One and Nature are the journals with the most citations. The field has shifted from focusing on traditional descriptive analysis of gut microbiota composition to exploring the causal relationship between gut microbiota and intestinal diseases. The research hotspots and trends mainly include the correlation between specific intestinal diseases and gut microbiota diversity, the mechanism of gut microbiota involvement in intestinal diseases, the exploration of important gut microbiota related to intestinal diseases, and the relationship between gut microbiota and human gut health. This study provides a comprehensive knowledge map of gut microbiota and intestinal diseases, highlights key research areas, and outlines potential future directions. Full article

(This article belongs to the Section Gut Microbiota)

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16 pages, 5104 KiB

Open AccessArticle

A Succession of Microbiome Communities in the Early Establishing Process of an Epilithic Algal Matrix in a Fringing Reef

by Beiye Zhang, Simin Hu, Chen Zhang, Tiancheng Zhou, Tao Li, Hui Huang and Sheng Liu

Microorganisms 2025, 13(3), 672; https://doi.org/10.3390/microorganisms13030672 - 17 Mar 2025

Viewed by 308

Abstract

An epilithic algal matrix (EAM) exhibits rapid expansion, recovery capacity, and high adaptability, leading to widespread distribution in degraded coral reef habitats. However, limited research on the dynamic processes of succession hinders a comprehensive understanding of EAM formation. To examine the influence of [...] Read more.

An epilithic algal matrix (EAM) exhibits rapid expansion, recovery capacity, and high adaptability, leading to widespread distribution in degraded coral reef habitats. However, limited research on the dynamic processes of succession hinders a comprehensive understanding of EAM formation. To examine the influence of succession processes and environmental factors on the composition of EAM microbial communities, a three-factor (time × depth × attached substrate type) crossover experiment was conducted in the Luhuitou Reef Area, Sanya, China. Microbial community compositions were analyzed through 16S rRNA gene amplicon sequencing. The community was predominantly composed of proteobacteria (61.10–92.75%), cyanobacteria (2.47–23.54%), bacteroidetes (0.86–8.49%), and firmicutes (0.14–7.76%). Successional processes were found to significantly shape the EAM-associated microbial communities in the Luhuitou Reef Area. Proteobacteria played a crucial role in biofilm formation during this process, while cyanobacteria contributed to the structural complexity of microhabitats within the EAM. A chaotic aggregation stage of approximately one month was observed before transitioning into an expansion stage, eventually stabilizing into a low-diversity community. Although the relatively smooth substrate supported high biodiversity, microorganisms displayed no preference for the three different substrates. While no significant differences in community composition were observed at small-scale depths, cyanobacteria and bacteroidetes showed positive correlations with light and temperature, respectively. The EAM-associated microbial community exhibited higher complexity in the shallower regions under increased light intensity and temperature. Given the characteristics of the microbial community succession process, continuous monitoring of changes in microbial community structure and key taxa (such as proteobacteria and cyanobacteria) during EAM formation is recommended. Full article

(This article belongs to the Section Environmental Microbiology)

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12 pages, 2789 KiB

Open AccessCase Report

Primary Axillary Actinomycosis: A Case Report on the Integration of Culture and Molecular Diagnostics for Accurate Diagnosis of Polymicrobial Infections

by Junko Tezuka, Noriyuki Abe and Hiroshi Tanabe

Microorganisms 2025, 13(3), 671; https://doi.org/10.3390/microorganisms13030671 - 17 Mar 2025

Viewed by 317

Abstract

Actinomycosis is a chronic suppurative granulomatous disease caused by Actinomyces spp. Although cutaneous actinomycosis is rare, dermatologists must consider it due to its potential coexistence with other pathogens, often as part of polymicrobial infections. We present a rare case of primary axillary cutaneous [...] Read more.

Actinomycosis is a chronic suppurative granulomatous disease caused by Actinomyces spp. Although cutaneous actinomycosis is rare, dermatologists must consider it due to its potential coexistence with other pathogens, often as part of polymicrobial infections. We present a rare case of primary axillary cutaneous actinomycosis in a young woman, likely triggered by cosmetic axillary hair removal and home shaving practices. Histological examination revealed characteristics of actinomycosis, including sulfur granules and Gram-positive filamentous structures. Bacterial cultures failed to isolate Actinomyces, but identified Staphylococcus epidermidis, S. aureus (MRSA), and Corynebacterium simulans, suggesting a polymicrobial infection contributing to the inflammatory response. Molecular analysis of DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue yielded a 675 bp PCR product using Actinomyces-specific primers. BLAST analysis confirmed the species as A. gerencseriae, establishing the diagnosis of actinomycosis. However, a 1000 bp PCR product obtained using universal 16S rDNA primers could not be sequenced successfully, likely due to the presence of multiple bacterial species. Notably, Actinomyces was detected only through molecular methods, while bacterial cultures identified the aforementioned bacteria. This discrepancy between FFPE-PCR results and bacterial culture findings demonstrates a key challenge in the microbiological diagnosis of polymicrobial infections. This case highlights the importance of integrating histopathological, microbiological, and molecular techniques for accurate pathogen identification in polymicrobial infections. The failure to detect Actinomyces in bacterial cultures, despite its presence in FFPE-PCR, suggests that conventional culture methods alone may be insufficient for diagnosing such infections. Extended culture durations, selective anaerobic culture techniques, and molecular diagnostic methods are essential for a comprehensive evaluation. Recognizing Actinomyces as more than a contaminant is important for timely diagnosis and effective treatment. Increased awareness of its potential involvement in polymicrobial infection should improve clinical outcomes. Full article

(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)

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13 pages, 1798 KiB

Open AccessArticle

Epidemiological and Antimicrobial Resistance Trends in Bacterial Keratitis: A Hospital-Based 10-Year Study (2014–2024)

by Qingquan Shi, Deshuo Mao, Zijun Zhang, Ahyan Ilman Qudsi, Mingda Wei, Zhen Cheng, Yang Zhang, Zhiqun Wang, Kexin Chen, Xizhan Xu, Xinxin Lu and Qingfeng Liang

Microorganisms 2025, 13(3), 670; https://doi.org/10.3390/microorganisms13030670 - 17 Mar 2025

Viewed by 399

Abstract

Bacterial keratitis (BK) is a severe ocular infection that can lead to vision loss, with antimicrobial resistance (AMR) posing a growing challenge. This study retrospectively analyzed 1071 bacterial isolates from corneal infections over a 10-year period (2014–2024) at a tertiary ophthalmic center in [...] Read more.

Bacterial keratitis (BK) is a severe ocular infection that can lead to vision loss, with antimicrobial resistance (AMR) posing a growing challenge. This study retrospectively analyzed 1071 bacterial isolates from corneal infections over a 10-year period (2014–2024) at a tertiary ophthalmic center in Beijing, categorizing them into three distinct phases: pre-COVID-19, during COVID-19, and post-COVID-19. The results indicated significant changes in pathogen distribution, including a marked decrease in Gram-positive cocci (from 69.8% pre-COVID-19 to 49.3% in post-COVID-19, p < 0.001), particularly in Staphylococcus epidermidis. In contrast, Gram-positive bacilli, particularly Corynebacterium spp., increased from 4.2% to 16.1% (p < 0.001). The susceptibility to gatifloxacin, moxifloxacin, and ciprofloxacin significantly declined in both Gram-positive cocci and bacilli during the COVID-19 period (all p < 0.01). Gatifloxacin resistance in Staphylococcus rose from pre-COVID-19 (15.2%) to COVID-19 (32.7%), remaining high post-COVID-19 (29.7%). A similar trend was observed in Streptococcus and Corynebacterium, where resistance rose sharply from 12.0% and 22.2% pre-COVID-19 to 42.9% during COVID-19, and remained elevated at 40.0% and 46.4% post-COVID-19, respectively (p < 0.01). These findings emphasize the rapid rise of fluoroquinolone resistance in several bacterial groups, underscoring the urgent need for continuous surveillance and improved antimicrobial stewardship to enhance treatment outcomes. Full article

(This article belongs to the Special Issue Ocular Microorganisms)

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Open AccessArticle

Efficacy of Molnupiravir in Reducing the Risk of Severe Outcomes in Patients with SARS-CoV-2 Infection: A Real-Life Full-Matched Case–Control Study (SAVALO Study)

by Ivan Gentile, Riccardo Scotto, Maria Michela Scirocco, Francesco Di Brizzi, Federica Cuccurullo, Maria Silvitelli, Luigi Ametrano, Francesco Antimo Alfè, Daria Pietroluongo, Irene Irace, Mariarosaria Chiariello, Noemi De Felice, Simone Severino, Giulio Viceconte, Nicola Schiano Moriello, Alberto Enrico Maraolo, Antonio Riccardo Buonomo, Agnese Giaccone and on behalf of Federico II COVID Team

Microorganisms 2025, 13(3), 669; https://doi.org/10.3390/microorganisms13030669 - 15 Mar 2025

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Abstract

We conducted a real-life case–control study among outpatients with Omicron SARS-CoV-2 infection to assess the effectiveness of molnupiravir (MNP) in reducing hospital admission, admission to the intensive care unit, and death at day 28. Cases were SARS-CoV-2-positive patients seeking medical care within five [...] Read more.

We conducted a real-life case–control study among outpatients with Omicron SARS-CoV-2 infection to assess the effectiveness of molnupiravir (MNP) in reducing hospital admission, admission to the intensive care unit, and death at day 28. Cases were SARS-CoV-2-positive patients seeking medical care within five days of symptom onset from 1 January to 31 December 2022, who received MNP. Controls were selected from a regional database among positive subjects who did not receive antiviral treatment for SARS-CoV-2. A total of 1382 patients were included (146 cases, 1236 controls). Vaccinated patients had a lower risk of mortality and of the composite outcome (hospital admission, ICU admission, or all-cause death) than unvaccinated ones (0.6% vs. 7.8%, p < 0.001 and 2% vs. 7.8%, p = 0.001, respectively). After full-matching propensity score analysis, MNP-treated subjects had a lower incidence of the composite outcome, although no effect was observed on individual outcomes. In subgroup analyses by vaccination status, MNP was effective in preventing all outcomes among unvaccinated patients and reduced the risk of ICU admission in both vaccinated and unvaccinated patients. Molnupiravir treatment effectively reduced the composite outcome risk in outpatients with SARS-CoV-2 infection, with a more pronounced benefit in unvaccinated patients. These findings highlight MNP’s potential to help prevent disease progression in high-risk patients, thereby supporting its role as an outpatient therapeutic option for COVID-19. Full article

(This article belongs to the Special Issue New Obstacles in Bacterial, Fungal and Viral Infections: Antimicrobial Resistance and Emerging Pathogens)

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Microorganisms, Volume 13, Issue 3 (March 2025) – 230 articles

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