Microorganisms

19 pages, 1583 KB

Open AccessArticle

Population Dynamics of Plasmodium vivax in Mexico Determined by CSP, Pvs25, and SSU 18S rRNA S-Type Polymorphism Analyses

by Lilia González-Cerón, Delfino de Jesús Gómez-Pérez, Frida Santillán-Valenzuela, Marbella Ovilla-Muñoz, Carmen Guzmán-Bracho, Angélica Pech-May, Gerardo R. Amores, Alberto Montoya-Pérez and Cuauhtémoc Villarreal-Treviño

Microorganisms 2025, 13(9), 2221; https://doi.org/10.3390/microorganisms13092221 - 22 Sep 2025

Abstract

In Mexico, Plasmodium vivax transmission has been confined to the northwestern and southern regions since 2000. Parasites from five malaria foci were analyzed using three genetic markers. The circumsporozoite gene was examined by PCR-RFLP and sequencing, and pvs25 mutations and variants of ribosomal [...] Read more.

In Mexico, Plasmodium vivax transmission has been confined to the northwestern and southern regions since 2000. Parasites from five malaria foci were analyzed using three genetic markers. The circumsporozoite gene was examined by PCR-RFLP and sequencing, and pvs25 mutations and variants of ribosomal 18S SSU rRNA S-type were also determined. Previous data from the southernmost Pacific in Chiapas were included in the analysis. Both the VK210 and VK247 types of pvcsp were detected, and VK210 had greater haplotype diversity (0.860) than VK247 parasites (0.198). Two pvs25 mutations (Q87K and I130T) yielded three haplotypes, and two ribosomal variants were detected. Gene and multilocus haplotype frequencies varied among malarious foci (p < 0.001). An AMOVA test, F_ST values, and Spearman’s correlation suggested a structured P. vivax population among the malaria foci. Each malaria focus across the northwestern and southern regions retained a portion of the past countrywide P. vivax population, which seems unique in Latin America. In the Lacandon region (LR), a linkage equilibrium between pvs25 haplotypes and the ribosomal variants within the VK247 or VK210 populations was observed. This region harbored the broadest reservoir of P. vivax haplotypes, and the high adaptation of parasites in the northwestern region represents a challenge for malaria elimination. These finding are relevant for monitoring and epidemiological surveillance. Full article

(This article belongs to the Special Issue Research on Mosquito-Borne Pathogens)

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18 pages, 1759 KB

Open AccessArticle

Prevalence and Genetic Characteristics of Avian Chlamydia in Birds in Guangxi, Southwestern China

by Jian-Ming Long, Hai-Tao Zhong, Ya-Yu Deng, Jun-Wei Yang, Mei-Chi Chen, Yan-Jiao Liang, Ke-Wei Chen, Jing-Ting Yang, Tian-Chao Wei, Ping Wei and Jian-Ni Huang

Microorganisms 2025, 13(9), 2220; https://doi.org/10.3390/microorganisms13092220 - 22 Sep 2025

Abstract

Avian chlamydiosis, primarily caused by Chlamydia psittaci (C. psittaci), poses significant threats to poultry and avian trade. Emerging species such as Chlamydia gallinacea (C. gallinacea), Chlamydia avium (C. avium), and Chlamydia ibidis (C. ibidis) have [...] Read more.

Avian chlamydiosis, primarily caused by Chlamydia psittaci (C. psittaci), poses significant threats to poultry and avian trade. Emerging species such as Chlamydia gallinacea (C. gallinacea), Chlamydia avium (C. avium), and Chlamydia ibidis (C. ibidis) have recently been detected in birds. However, the prevalence and genetic diversity of avian chlamydia in birds within Guangxi remain unknown. In this study, 1744 samples collected from apparently healthy birds were screened, revealing an overall positivity rate of 28.20% (95% CI, 27.58–28.90%, 492/1744) for avian chlamydia. Among poultry, pigeons had the highest positivity rate at 62.30% (95% CI, 55.37–68.69%, 152/244), followed by chickens at 25.05% (95% CI, 21.25–29.23%, 128/511), geese at 18.12% (95% CI, 12.93–24.82%, 29/160), and ducks at 14.14% (95% CI, 11.57–17.26%, 82/580). Additionally, pet and wild birds exhibited positivity rates of 40.35% (95% CI, 34.20–46.83%, 92/228) and 42.86% (95% CI, 24.52–61.83%, 9/21), respectively. Phylogenetic analysis based on the outer-membrane protein A gene indicated that chicken samples belonged to genotypes B of C. psittaci and C. gallinacea. In ducks, genotypes A and B of C. psittaci and C. gallinacea were identified, representing the first documented occurrence of C. psittaci genotypes B and C. gallinacea in ducks in China. The nucleotide sequences from goose samples were initially clustered into genotype A group, while those from pigeons were clustered within genotype B. Furthermore, positive samples from pet birds were classified into genotypes A and B, as well as the C. gallinacea group. Similarly, samples from wild birds were classified into genotypes A and B. These findings suggest that diverse avian chlamydia genotypes are circulating among bird populations in Guangxi, with an expanding host range indicating potential cross-species transmission. Moreover, certain strains derived from waterfowl were found to cluster with those linked to recent psittacosis outbreaks, highlighting the zoonotic potential of avian chlamydia. Therefore, sustained surveillance for avian chlamydia in bird populations and monitoring its genetic evolutionary characteristics are essential to decrease public health risks. Full article

(This article belongs to the Special Issue Epidemiology of Zoonotic Pathogens)

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19 pages, 3913 KB

Open AccessArticle

The CRISPR-Cas9 System in Entamoeba histolytica Trophozoites: ehcp112 Gene Knockout and Effects on Other Genes in the V1 Virulence Locus

by Luz Virginia Reyes, Guillermina García-Rivera, Rosario Javier-Reyna, Edgar Morales-Rios, Sergio Tinajero, Cecilia Bañuelos, Daniel Talamás-Lara and Esther Orozco

Microorganisms 2025, 13(9), 2219; https://doi.org/10.3390/microorganisms13092219 - 22 Sep 2025

Abstract

Gene editing enables a better understanding of protein functions. The genome of the protozoan parasite Entamoeba histolytica contains a 4500 bp DNA fragment comprising the ehcp112, ehadh, and ehrabb genes, which together form the V1 virulence locus. Studying these genes has [...] Read more.

Gene editing enables a better understanding of protein functions. The genome of the protozoan parasite Entamoeba histolytica contains a 4500 bp DNA fragment comprising the ehcp112, ehadh, and ehrabb genes, which together form the V1 virulence locus. Studying these genes has been challenging due to the lack of suitable methodologies. Here, we report the first in vitro and in vivo knockout in E. histolytica (ehcp112 gene) using a modified CRISPR-Cas9 strategy and explore its effects on the other V1 locus genes. Confocal and transmission electron microscopy were used to detect the RNP pathway formed by the Cas9 enzyme and the crRNA–tracrRNA complex, from their entry into the trophozoites until their arrival at the nucleus and heterochromatin. Scanning electron microscopy revealed that the mutant cells (EhCP112-KO) were smaller, with fewer pseudopodia and plasma membrane depressions. DNA sequencing and RT-qPCR assays identified a four-base deletion in the ehcp112 gene in the mutant trophozoites. Western blot assays of EhCP112-KO extracts revealed the absence of the EhCP112 protein. While the EhCP112-KO lysates digested gelatin more efficiently than the HM1:IMSS extracts, their secreted products showed poor enzymatic activity. The ehcp112 knockout also affected the transcription of the ehadh and ehrabb genes, probably due to their genomic position. In conclusion, the implementation of the CRISPR-Cas9 strategy in E. histolytica evidenced the coordinated expression of the ehcp112 gene and the other members of the V1 locus. Full article

(This article belongs to the Special Issue Advances in Molecular Biology of Entamoeba histolytica)

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15 pages, 3999 KB

Open AccessArticle

Effects of Waxy Maize Starch and Malate-Debranched Waxy Maize Starch on Gut Microbiota of Humans In Vitro and Mice In Vivo

by Zhonglin Zhao, Wei Liu, Lulu Wu, Guoyu Yang, Yizhe Yan and Xiaolong Ji

Microorganisms 2025, 13(9), 2218; https://doi.org/10.3390/microorganisms13092218 - 22 Sep 2025

Abstract

The gut microbiota plays a pivotal role in host health. Dietary components such as waxy maize starch (WMS) and malate-debranched WMS (MADBS) may serve as modulators of microbial composition and function. In this study, the effects of WMS and MADBS on murine gut [...] Read more.

The gut microbiota plays a pivotal role in host health. Dietary components such as waxy maize starch (WMS) and malate-debranched WMS (MADBS) may serve as modulators of microbial composition and function. In this study, the effects of WMS and MADBS on murine gut microbiota in vivo and human fecal in vitro fermentation were investigated. The results of gut microbiota in mice revealed that WMS increased the abundance of Muribaculaceae and Bifidobacterium, while MADBS enriched Ileibacterium, Muribaculaceae, and Dubosiella. The in vitro fermentation model demonstrated that WMS increased the abundance of Bifidobacterium, Lactobacillus, Megamonas, and Megasphaera, whereas MADBS enhanced Weissella, Lactobacillus, and Prevotella. Both compounds decreased the levels of Escherichia-Shigella. Metabolically, compared to the control group, WMS improved the production of acetic, propionic, butyric, and valproic acids, while MADBS decreased the concentrations of all short-chain fatty acids (SCFAs). Compared to the control group, WMS reduced the production of CH₄, NH₃, and H₂S while increasing CO₂ yield. MADBS reduced the generation of CH₄, NH₃, H₂S, and CO₂. These findings suggest that WMS and MADBS can modulate the gut ecosystem by selectively promoting probiotics, inhibiting pathogens, and altering metabolic profiles. Full article

(This article belongs to the Section Gut Microbiota)

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34 pages, 4308 KB

Open AccessReview

Harnessing Microbial Power for a Sustainable Future Food System

by Andreea Loredana Birgovan (Rhazzali), Elena Simina Lakatos, Lucian Ionel Cioca, Natalia Lorela Paul, Sorin Daniel Vatca, Erzsebeth Kis and Roxana Lavinia Pacurariu

Microorganisms 2025, 13(9), 2217; https://doi.org/10.3390/microorganisms13092217 - 22 Sep 2025

Abstract

Microorganisms are transforming the way we address sustainability across agriculture, food production, waste remediation, bioenergy, and industrial bioprocessing, offering novel solutions for the food systems of tomorrow. This systematic review examines literature from the last twenty years in order to identify key advances, [...] Read more.

Microorganisms are transforming the way we address sustainability across agriculture, food production, waste remediation, bioenergy, and industrial bioprocessing, offering novel solutions for the food systems of tomorrow. This systematic review examines literature from the last twenty years in order to identify key advances, challenges, and future directions in harnessing microbial systems for sustainable applications, especially those underpinning a resilient future food system. The selected documents allowed a mapping of the most important trends: innovations based on metabolic engineering and omics, the use of integrated biorefineries, and digital monitoring platforms are emerging as catalysts for the transition, while high scaling costs, regulatory challenges, and low public acceptance continue to limit large-scale implementation. The analysis highlights both the major advantages (reducing ecological impact, valorizing waste, diversifying food sources) and the current limits of these technologies, proposing a multi-stakeholder roadmap to accelerate the transition to a circular bioeconomy and a low-carbon and climate-resilient food system. Full article

(This article belongs to the Special Issue Harnessing Microbial Power for a Sustainable Future)

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13 pages, 656 KB

Open AccessArticle

In Vitro Antimicrobial Activity of Contezolid Against Mycobacterium tuberculosis and Absence of Cross-Resistance with Linezolid

by Li Wang, Jianxia Chen, Yifan He, Ruijuan Zheng, Jie Wang, Xiaochen Huang, Wei Sha and Lianhua Qin

Microorganisms 2025, 13(9), 2216; https://doi.org/10.3390/microorganisms13092216 - 22 Sep 2025

Abstract

Tuberculosis (TB) persists as a formidable global health threat, especially with the rising incidence of multidrug-resistant strains. This study aimed to evaluate the in vitro activity of contezolid, a novel oxazolidinone antibiotic, against Mycobacterium tuberculosis (Mtb) and assess potential cross-resistance with [...] Read more.

Tuberculosis (TB) persists as a formidable global health threat, especially with the rising incidence of multidrug-resistant strains. This study aimed to evaluate the in vitro activity of contezolid, a novel oxazolidinone antibiotic, against Mycobacterium tuberculosis (Mtb) and assess potential cross-resistance with linezolid. Thirty-one Mtb clinical isolates (5 susceptible, 8 multidrug-resistant [MDR], 18 pre-extensively drug-resistant [pre-XDR]) were tested. Minimum inhibitory concentrations (MICs) of contezolid and linezolid were determined, along with mutation resistance frequencies. Intracellular replication inhibition in macrophages and whole-genome sequencing of resistant colonies were assessed. Cytotoxicity was evaluated via luciferase-coupled ATP assay. The MIC50 and MIC90 values of contezolid were comparable to those of linezolid. Contezolid induced higher mutation frequencies in 7 isolates. At 12 mg/L, both drugs similarly inhibited intracellular Mtb replication. Whole-genome sequencing revealed that the mce3R gene was linked to contezolid resistance, with no cross-resistance observed between two drugs. No significant cytotoxicity was observed in contezolid-treated mouse peritoneal macrophages (p > 0.05). Contezolid exhibits anti-Mtb activity, with mce3R potentially associated with resistance. No cross-resistance with linezolid was found. Full article

(This article belongs to the Special Issue Prevention, Treatment and Diagnosis of Tuberculosis, Third Edition)

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19 pages, 3460 KB

Open AccessArticle

The Reorganization of Rice Rhizosphere Microbial Communities Driven by Nitrogen Utilization Efficiency and the Regulatory Mechanism of Soil Nitrogen Cycling

by Zhuang Xiong, Qiang Li, Rongtao Fu, Jian Wang, Daihua Lu and Cheng Chen

Microorganisms 2025, 13(9), 2215; https://doi.org/10.3390/microorganisms13092215 - 22 Sep 2025

Abstract

Nitrogen use efficiency (NUE) in rice cultivation is a key determinant of sustainable agriculture, yet the interaction between NUE and the dynamics of rhizosphere soil microbial communities remain poorly understood. In this study, the changes in rhizosphere soil microbial community composition and function [...] Read more.

Nitrogen use efficiency (NUE) in rice cultivation is a key determinant of sustainable agriculture, yet the interaction between NUE and the dynamics of rhizosphere soil microbial communities remain poorly understood. In this study, the changes in rhizosphere soil microbial community composition and function due to NUE were analyzed in six rice genotypes across six treatments. Through 16S rRNA/ITS amplicon sequencing, it was found that rice with different NUEs reshaped the rhizosphere soil microbial community structure, but did not significantly alter the α-diversity of the bacterial community. There was a notable difference in the average abundance of the fungus Arnium in the rhizosphere soil of high-NUE rice compared to low-NUE rice, with a 222.2% increase in the former. Correlation analysis indicated that in high-NUE rice, soil nitrate and nitrite contents drove changes in the fungal community, while in low-NUE rice, soil water-soluble nitrogen and total potassium contents were the key influencing factors for changes in the fungal and nitrogen-fixing bacterial communities, respectively. The findings of this study demonstrate a link between NUE-induced changes in the rhizosphere soil microbiome and nitrogen cycling in rice, providing a basis for targeted nitrogen fertilizer management approaches guided by microbial control. Full article

(This article belongs to the Section Plant Microbe Interactions)

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12 pages, 716 KB

Open AccessArticle

Development of a Chemiluminescence Immunoassay for the Serological Diagnosis of Sheep and Bovine Brucellosis

by Xin Yan, Mingze Chen, Yuning Liu, Mingjun Sun, Mengkun Huang, Jihui Jin, Jiaqi Li, Xiangxiang Sun, Mengda Liu, Haobo Zhang, Weixing Shao, Shufang Sun, Xiaoxu Fan and Wenlong Nan

Microorganisms 2025, 13(9), 2214; https://doi.org/10.3390/microorganisms13092214 - 22 Sep 2025

Abstract

Brucellosis, a zoonotic infection caused by the intracellular pathogen Brucella, leads to chronic multi-organ damage. Currently, rapid, accurate, and sensitive diagnostic technologies are crucial for the prevention and control of brucellosis. This study describes the development of a chemiluminescent immunoassay (Bru-CLIA) for [...] Read more.

Brucellosis, a zoonotic infection caused by the intracellular pathogen Brucella, leads to chronic multi-organ damage. Currently, rapid, accurate, and sensitive diagnostic technologies are crucial for the prevention and control of brucellosis. This study describes the development of a chemiluminescent immunoassay (Bru-CLIA) for sheep and bovine brucellosis antibody detection, utilizing Brucella abortus strain A19 lipopolysaccharide-coated magnetic particles (LPS-MPs) as the serum antigen and acridinium ester-labeled recombinant streptococcal protein G (AE-SPG) for signal generation. After optimizing the assay’s parameters, the Bru-CLIA demonstrated a sensitivity of approximately 1 IU/mL and 2 IU/mL for detecting sheep and bovine brucellosis, respectively. No cross-reactivity was observed with sera from animals immunized with Escherichia coli O157:H7, Mycobacterium tuberculosis, Vibrio cholerae, Legionella, Salmonella, Foot and Mouth Disease virus types O and A, Bovine viral diarrhea virus, Sheep contagious pleuropneumonia, Goat pox virus, or Peste des Petits Ruminants virus, indicating strong specificity. The testing of 81 sheep serum samples and 96 bovine serum samples revealed that Bru-CLIA showed 87.65% and 93.75% concordance with the ID-VET commercial kits for sheep and bovine brucellosis detection, respectively. These results demonstrate that Bru-CLIA offers high specificity, sensitivity, repeatability, and reliability, making it a viable rapid diagnostic tool for the epidemiological surveillance of brucellosis. Full article

(This article belongs to the Section Veterinary Microbiology)

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30 pages, 1124 KB

Open AccessReview

Gut Microbiota and Neurodevelopment in Preterm Infants: Mechanistic Insights and Prospects for Clinical Translation

by Kun Dai, Lingli Ding, Xiaomeng Yang, Suqing Wang and Zhihui Rong

Microorganisms 2025, 13(9), 2213; https://doi.org/10.3390/microorganisms13092213 - 22 Sep 2025

Abstract

Preterm birth remains a significant global health challenge and is strongly associated with heightened risks of long-term neurodevelopmental impairments, including cognitive delays, behavioural disorders, and emotional dysregulation. In recent years, accumulating evidence has underscored the critical role of the gut microbiota in early [...] Read more.

Preterm birth remains a significant global health challenge and is strongly associated with heightened risks of long-term neurodevelopmental impairments, including cognitive delays, behavioural disorders, and emotional dysregulation. In recent years, accumulating evidence has underscored the critical role of the gut microbiota in early brain development through the gut–brain axis. In preterm infants, microbial colonisation is frequently delayed or disrupted due to caesarean delivery, perinatal antibiotic exposure, formula feeding, and prolonged stays in neonatal intensive care units (NICUs), all of which contribute to gut dysbiosis during critical periods of neurodevelopment. This review synthesises current knowledge on the sources, temporal patterns, and determinants of gut microbiota colonisation in preterm infants. This review focuses on the gut bacteriome and uses faecal-sample bacteriome sequencing as its primary method of characterisation. We detail five mechanistic pathways that link microbial disturbances to adverse neurodevelopmental outcomes: immune activation and white matter injury, short-chain fatty acids (SCFAs)-mediated neuroprotection, tryptophan–serotonin metabolic signalling, hypothalamic–pituitary–adrenal (HPA) axis modulation, and the integrity of intestinal and blood–brain barriers (BBB). We also critically examine emerging microbiota-targeted interventions—including probiotics, prebiotics, human milk oligosaccharides (HMOs), antibiotic stewardship strategies, skin-to-skin contact (SSC), and faecal microbiota transplantation (FMT)—focusing on their mechanisms of action, translational potential, and associated ethical concerns. Finally, we identify key research gaps, including the scarcity of longitudinal studies, limited functional modelling, and the absence of standardised protocols across clinical settings. A comprehensive understanding of microbial–neurodevelopmental interactions may provide a foundation for the development of targeted, timing-sensitive, and ethically sound interventions aimed at improving neurodevelopmental outcomes in this vulnerable population. Full article

(This article belongs to the Section Gut Microbiota)

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21 pages, 2608 KB

Open AccessArticle

Molecular Insights into Ammonium Sulfate-Induced Secretome Reprogramming of Bacillus subtilis Czk1 for Enhanced Biocontrol Against Rubber Tree Root Rot

by Yanqiong Liang, Shibei Tan, Ying Lu, Helong Chen, Xing Huang, Kexian Yi, Chunping He and Weihuai Wu

Microorganisms 2025, 13(9), 2212; https://doi.org/10.3390/microorganisms13092212 - 21 Sep 2025

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Abstract

Root rot diseases caused by Ganoderma pseudoferreum and Pyrrhoderma noxium inflict substantial economic losses in rubber tree (Hevea brasiliensis) cultivation, while conventional control methods face environmental and resistance challenges. This study aimed to specifically investigate the molecular mechanisms by which ammonium [...] Read more.

Root rot diseases caused by Ganoderma pseudoferreum and Pyrrhoderma noxium inflict substantial economic losses in rubber tree (Hevea brasiliensis) cultivation, while conventional control methods face environmental and resistance challenges. This study aimed to specifically investigate the molecular mechanisms by which ammonium sulfate enhances the biocontrol efficacy of Bacillus subtilis Czk1. Using label-free quantitative proteomics (LC-MS/MS), we characterized ammonium sulfate-induced alterations in the secretory proteome of Czk1. A total of 351 differentially expressed proteins (DEPs) were identified, with 329 significantly up-regulated and 22 down-regulated. GO functional enrichment analysis indicated that up-regulated DEPs were associated with metabolic pathways (glyoxylate/dicarboxylate, arginine/proline, cofactor biosynthesis) and extracellular localization (13 proteins), while down-regulated DEPs were linked to small molecule catabolism. KEGG pathway annotation identified DEP involvement in 124 pathways, including secondary metabolite biosynthesis and membrane transport. These findings demonstrate that ammonium sulfate remodels the Czk1 secretome to enhance the expression of key antagonistic proteins, thereby providing crucial molecular targets and a scientific foundation for developing effective biofungicides against rubber root rot, with clear practical implications for sustainable disease management. Full article

(This article belongs to the Section Plant Microbe Interactions)

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18 pages, 1700 KB

Open AccessArticle

When Precision Matters: Bone Marrow Cytology Meets qPCR in a Pilot Study Quantifying Leishmania infantum Load in Dogs

by Juliana Costa, Ana Rita Silva, Filipe Sampaio, Ana Patrícia Alves, Hugo Silva, Hugo Lima de Carvalho, Carlos Sousa, Manuel Simões, Cátia Fernandes, Ana Patrícia Lopes, Andreia Garcês, Elsa Leclerc Duarte, Ana Cláudia Coelho, Luís Cardoso and Ricardo Lopes

Microorganisms 2025, 13(9), 2211; https://doi.org/10.3390/microorganisms13092211 - 21 Sep 2025

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Abstract

Leishmania infantum is the causative agent of canine leishmaniosis (CanL), a zoonotic disease of considerable clinical and epidemiological concern. Quantification of parasite load is valuable for clinical management, particularly in low-parasite-load cases. This pilot study evaluated the correlation between cytological and molecular techniques [...] Read more.

Leishmania infantum is the causative agent of canine leishmaniosis (CanL), a zoonotic disease of considerable clinical and epidemiological concern. Quantification of parasite load is valuable for clinical management, particularly in low-parasite-load cases. This pilot study evaluated the correlation between cytological and molecular techniques in bone marrow samples from dogs clinically affected with leishmaniosis. Amastigotes were quantified by two independent observers using light microscopy, and the same samples were analysed by real-time polymerase chain reaction (qPCR) employing Leishmania spp. specific commercial primers. Inter-observer agreement was moderate according to Cohen’s kappa (κ = 0.47) and substantial according to the intraclass correlation coefficient (ICC = 0.63), respectively, confirming measurement reproducibility. A very strong inverse correlation was found between parasite counts and qPCR cycle threshold (Ct) values (Spearman’s ρ = −0.89; p < 0.001). Furthermore, a robust logarithmic relationship (amastigotes/μL = 10^{(−0.158 × Ct + 7.61)}; R² = 0.99994) was established allowing direct estimation of in vivo parasite concentration from molecular data. These preliminary findings suggest that qPCR can serve as a reliable, semi-quantitative tool, offering higher sensitivity in subclinical infections. The integration of molecular quantification with cytological methods enhances diagnostic accuracy and supports personalised therapeutic decision-making, advancing clinical management of CanL in a One Health context. Full article

(This article belongs to the Special Issue Microorganisms in Neglected Tropical Diseases)

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17 pages, 3173 KB

Open AccessArticle

MicroAIbiome: Decoding Cancer Types from Microbial Profiles Using Explainable Machine Learning

by Md Motiur Rahman, Shiva Shokouhmand, Saeka Rahman, Nafisa Nawar Tamzi, Smriti Bhatt and Miad Faezipour

Microorganisms 2025, 13(9), 2210; https://doi.org/10.3390/microorganisms13092210 - 21 Sep 2025

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Abstract

Microbial communities within human tissues are increasingly recognized as promising biomarkers for cancer detection. However, leveraging microbiome data for multiclass cancer classification remains challenging due to its compositional structure, high dimensionality, and lack of model interpretability. In this study, we address these challenges [...] Read more.

Microbial communities within human tissues are increasingly recognized as promising biomarkers for cancer detection. However, leveraging microbiome data for multiclass cancer classification remains challenging due to its compositional structure, high dimensionality, and lack of model interpretability. In this study, we address these challenges by introducing MicroAIbiome, a machine learning-based artificial intelligence (AI) pipeline designed to classify five cancer types such as esophageal carcinoma (ESCA), head and neck squamous cell carcinoma (HNSC), stomach adenocarcinoma (STAD), colon adenocarcinoma (COAD), and rectum adenocarcinoma (READ), using genus-level microbial relative abundances. Our pipeline incorporates zero-replacement, centered log-ratio (CLR) transformation, correlation filtering, and recursive feature elimination (RFE) to enable robust learning from compositional data. Among five evaluated classifiers, XGBoost achieved the highest accuracy of 78.23%, outperforming prior work. We further enhance interpretability using SHapley Additive exPlanations (SHAP)-based feature attribution to uncover class-specific microbial signatures, such as Corynebacterium in ESCA and Bacteroides in COAD. Our results highlight the importance of compositional preprocessing and explainable AI in advancing microbiome-based cancer diagnostics. Full article

(This article belongs to the Special Issue Host–Microbiome Cross-Talk in Cancer Development and Progression)

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10 pages, 781 KB

Open AccessCase Report

Diagnostic Challenges of Cyclosporiasis in Chronic Diarrhea: A Case Study

by Estera Banasik, Agnieszka Dobrowolska, Lucyna Woźnicka-Leśkiewicz and Piotr Eder

Microorganisms 2025, 13(9), 2209; https://doi.org/10.3390/microorganisms13092209 - 21 Sep 2025

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Abstract

Cyclosporiasis, caused by Cyclospora cayetanensis, is a rare opportunistic infection, particularly in immunosuppressed patients with inflammatory bowel disease (IBD). Its clinical presentation may mimic IBD, with chronic diarrhea and anemia resistant to standard therapy. We report the case of a 24-year-old woman [...] Read more.

Cyclosporiasis, caused by Cyclospora cayetanensis, is a rare opportunistic infection, particularly in immunosuppressed patients with inflammatory bowel disease (IBD). Its clinical presentation may mimic IBD, with chronic diarrhea and anemia resistant to standard therapy. We report the case of a 24-year-old woman with ulcerative colitis (UC) and a history of liver transplantation, treated with vedolizumab and immunosuppressants. Despite endoscopic remission, she experienced persistent abdominal pain, diarrhea, and iron deficiency anemia. Escalation of biologic therapy was ineffective. After exclusion of bacterial and viral causes, stool testing identified Cyclospora cayetanensis. Treatment with nitazoxanide led to rapid clinical and laboratory improvement. Biologic therapy was temporarily discontinued and later resumed without recurrence of symptoms. This case shows that chronic diarrhea in IBD patients may not always result from the underlying disease. Immunosuppression increases the risk of opportunistic infections. Early diagnosis and specific treatment can improve outcomes and allow safe continuation of IBD therapy. Full article

(This article belongs to the Section Medical Microbiology)

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11 pages, 980 KB

Open AccessCase Report

Periorbital and Central Nervous System Infection Due to Arcanobacterium haemolyticum: Case Report and Review of the Literature

by Pierangelo Chinello, Alessandro Capone, Samir Al Moghazi, Paolo Cirillo, Carla Fontana and Stefania Cicalini

Microorganisms 2025, 13(9), 2208; https://doi.org/10.3390/microorganisms13092208 - 20 Sep 2025

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Abstract

Arcanobacterium haemolyticum is a facultative anaerobe, catalase-negative, Gram-positive pleomorphic rod, most commonly responsible for pharyngeal infections. Invasive A. haemolyticum infections are rare and typically involve immunocompromised patients; however, severe and invasive infections in immunocompetent patients have also been reported. Here we describe a [...] Read more.

Arcanobacterium haemolyticum is a facultative anaerobe, catalase-negative, Gram-positive pleomorphic rod, most commonly responsible for pharyngeal infections. Invasive A. haemolyticum infections are rare and typically involve immunocompromised patients; however, severe and invasive infections in immunocompetent patients have also been reported. Here we describe a case of sinusitis complicated by periorbital cellulitis, subdural empyema and cerebritis due to A. haemolyticum in an immunocompetent patient. The patient was initially treated with daptomycin + piperacillin/tazobactam and subsequently with linezolid + meropenem and required multiple surgical interventions to attain source control. Although uncommon, A. haemolyticum should be considered as a causative agent of severe infections complicating pharyngitis or sinusitis that may result from local extension or haematogenous spread, even in an immunocompetent host. We also present a literature review on central nervous system involvement by A. haemolyticum infection. Full article

(This article belongs to the Section Medical Microbiology)

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15 pages, 3176 KB

Open AccessArticle

Postbiotic Effects of Pediococcus acidophilus LS for Anti-Melanogenesis, Photoprotection, and Wound Repair

by Chiung-Hung Chang, Jai-Sing Yang, Yen-Ju Lai, Bi Yu and Yuan-Man Hsu

Microorganisms 2025, 13(9), 2207; https://doi.org/10.3390/microorganisms13092207 - 20 Sep 2025

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Abstract

Skin health is significantly impacted by factors such as melanin production, UV-induced photodamage, and wound healing. Excessive melanin leads to hyperpigmentation, while UVA radiation accelerates skin aging and oxidative stress. This study investigated the multi-functional dermatological potential of S strain LS-derived cell-free supernatant [...] Read more.

Skin health is significantly impacted by factors such as melanin production, UV-induced photodamage, and wound healing. Excessive melanin leads to hyperpigmentation, while UVA radiation accelerates skin aging and oxidative stress. This study investigated the multi-functional dermatological potential of S strain LS-derived cell-free supernatant (CFS-LS) to address these concerns. Our findings demonstrate that CFS-LS effectively inhibits melanogenesis in B16F10 cells. It significantly reduced α-MSH-induced melanin synthesis, comparable to arbutin, by downregulating key melanogenic enzymes (tyrosinase, TRP-1, and TRP-2) and regulatory proteins (p-CREB, MITF, SOX9, and SOX10). Mechanistically, CFS-LS suppressed the phosphorylation of MEK, ERK, p38, and JNK, indicating a dual inhibitory effect on both PKA/CREB and MAPK pathways. Furthermore, CFS-LS mitigated UVA-induced photodamage in HaCaT cells by significantly reducing intracellular reactive oxygen species and suppressing the downstream phosphorylation of p53 and α-MSH levels. It also restored UVA-suppressed Nrf-2 and HO-1 expression, enhancing cellular antioxidant defenses. Lastly, CFS-LS promoted skin wound healing by significantly enhancing HaCaT cell migration in a scratch assay, associated with increased p-MEK1/2 and p-ERK1/2 levels, and notably elevated collagen type I synthesis. Collectively, these results highlight CFS-LS as a potent multi-functional agent for skin protection and repair, with significant potential for cosmetic and therapeutic applications. The active components of CFS-LS warrant further investigation. Full article

(This article belongs to the Section Food Microbiology)

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21 pages, 8325 KB

Open AccessArticle

Comparative Transcriptomics Reveals Distinct Adaptation Mechanisms for Degradation of n-Alkane and Branched Alkane in the Salt-Tolerant Bacterium Dietzia sp. CN-3

by Weiwei Chen, Jiawei Sun, Xin Zhang, Jiawen Zhang, Yuan Wang and Shiwei Cheng

Microorganisms 2025, 13(9), 2206; https://doi.org/10.3390/microorganisms13092206 - 20 Sep 2025

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Abstract

Although hydrocarbon-degrading bacteria utilize a wide range of alkanes, the global metabolic features and regulatory mechanisms governing their growth on alkanes with different chain lengths remain incompletely elucidated. In this study, we analyzed the comparative transcriptomics of a salt-tolerant bacterium, Dietzia sp. CN-3, [...] Read more.

Although hydrocarbon-degrading bacteria utilize a wide range of alkanes, the global metabolic features and regulatory mechanisms governing their growth on alkanes with different chain lengths remain incompletely elucidated. In this study, we analyzed the comparative transcriptomics of a salt-tolerant bacterium, Dietzia sp. CN-3, to investigate molecular adaptations and metabolic processes when grown on n-hexadecane (C₁₆), branched alkane (pristane), and glucose. A total of 1766 differentially expressed genes (DEGs) were identified in the C₁₆ group compared to the glucose control, with 1024 (58.0%) being upregulated and 742 (42.0%) being downregulated. Notably, the pristane group exhibited 1542 DEGs, of which 488 (31.6%) were upregulated and 1054 (68.4%) were downregulated. Our results demonstrate that C₁₆ and pristane induced common genes of alkane hydroxylation in the core alkane degradation pathway, while eliciting distinct transcriptional patterns of genes involved in lipid metabolism, energy metabolism, metal ion transportation, cell surface composition biosynthesis, and transcription regulation. The findings reveal that CN-3 employs diverse metabolic strategies to adapt to alkanes with different chain lengths, displaying considerable metabolic plasticity. This study significantly enhances our understanding of molecular adaptation of bacteria to hydrocarbon-containing environments and may provide valuable information for further studies of petroleum hydrocarbon bioremediation. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 987 KB

Open AccessArticle

Synergistic Potential of Contamination Remediation and Carbon Fixation: Functional Resilience of Carbon Fixation in Petroleum Hydrocarbon-Degrading Microbial Communities Under Enhanced Natural Attenuation

by Pingping Cai, Shuang Gan, Zhuo Ning and Min Zhang

Microorganisms 2025, 13(9), 2205; https://doi.org/10.3390/microorganisms13092205 - 20 Sep 2025

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Abstract

Enhanced Natural Attenuation (ENA) can accelerate pollutant degradation by adding electron acceptors or nutrients. However, its impact on carbon-fixing microorganisms, which are widely found in the natural attenuation process, remains unclear. In this study, four types of ENA materials were added in batch [...] Read more.

Enhanced Natural Attenuation (ENA) can accelerate pollutant degradation by adding electron acceptors or nutrients. However, its impact on carbon-fixing microorganisms, which are widely found in the natural attenuation process, remains unclear. In this study, four types of ENA materials were added in batch experiments. Chemical analysis and metagenomic sequencing were employed to analyze the degradation kinetics of petroleum hydrocarbons, the consumption pattern of nitrate, as well as the functional genes and population evolution characteristics of carbon-fixing microorganisms. Results showed that nitrate-based enhancement materials significantly improved the petroleum hydrocarbon degradation rate but suppressed the expression of some carbon fixation genes, such as those involved in the Calvin–Benson–Bassham cycle. Nevertheless, the overall abundance of carbon fixation genes did not show a notable decline. Dominant bacterial genera such as Pseudomonas and Achromobacter possessed both hydrocarbon degradation and carbon fixation capabilities. Although the calcium peroxide treatment group only achieved a 40% petroleum hydrocarbon degradation rate, it significantly promoted the abundance of carbon fixation genes involved in the reductive tricarboxylic acid cycle pathway. Therefore, ENA alters carbon fixation pathways but does not diminish carbon fixation potential, indicating its potential for synergistically achieving pollution remediation and carbon fixation. Full article

(This article belongs to the Section Environmental Microbiology)

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10 pages, 3265 KB

Open AccessCommunication

Human Herpesvirus 6 Activates NF-κB Signalling and CD163-Positive Macrophage Recruitment in Alcohol-Induced Hepatic Injury

by Anda Upane, Simons Svirskis, Valerija Groma and Sandra Skuja

Microorganisms 2025, 13(9), 2204; https://doi.org/10.3390/microorganisms13092204 - 20 Sep 2025

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Abstract

Human herpesvirus 6 (HHV-6) establishes lifelong latency in immune cells and may contribute to the progression of ethanol-induced liver injury. To elucidate the contribution of HHV-6 to alcohol-induced hepatic injury, this study evaluated HHV-6 protein expression, NF-κB signalling, and CD163-positive macrophage recruitment in [...] Read more.

Human herpesvirus 6 (HHV-6) establishes lifelong latency in immune cells and may contribute to the progression of ethanol-induced liver injury. To elucidate the contribution of HHV-6 to alcohol-induced hepatic injury, this study evaluated HHV-6 protein expression, NF-κB signalling, and CD163-positive macrophage recruitment in liver samples from control subjects, young individuals with recent alcohol exposure, and individuals with long-term chronic alcohol use. Liver lobules displaying HHV-6 positivity were more frequent in alcohol users (64% in young and 72% in chronic users) compared to controls (48%). CD163-positive macrophage counts were higher in both young and chronic alcohol users compared to controls, with the greatest increase in HHV-6-positive chronic users. NF-κB expression intensity was elevated in alcohol users (p < 0.005), and further increased in HHV-6-positive samples (p = 0.02). These findings indicate an association between HHV-6 persistence, NF-κB pathway activation, and CD163-positive macrophage-driven inflammatory responses in liver tissue under conditions of chronic alcohol use. Further research is warranted to uncover the mechanisms underlying the interaction between HHV-6 and ethanol in liver injury. Full article

(This article belongs to the Special Issue Selected Papers from the 3rd International Electronic Conference on Microbiology (ECM 2025))

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12 pages, 1339 KB

Open AccessArticle

Development of an RPA-CRISPR/LbaCas12a-Lateral Flow Assay for the Visual Detection of Chrysotila dentata (Haptophyta)

by Jiating Yu, Yun Shen, Qinfei Zhang, Xuxu Luo, Yujie Zong, Chengxu Zhou, Hailong Huang and Haibo Jiang

Microorganisms 2025, 13(9), 2203; https://doi.org/10.3390/microorganisms13092203 - 20 Sep 2025

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Abstract

Chrysotila dentata (Haptophyta), a harmful algal bloom (HAB) species frequently occurring in coastal waters of China, is one with strong environmental adaptability that poses a serious threat to marine ecosystems and fisheries. Current molecular detection techniques and early warning systems for this species [...] Read more.

Chrysotila dentata (Haptophyta), a harmful algal bloom (HAB) species frequently occurring in coastal waters of China, is one with strong environmental adaptability that poses a serious threat to marine ecosystems and fisheries. Current molecular detection techniques and early warning systems for this species remain limited. To address this, we developed a rapid and highly sensitive detection method for C. dentata. This method integrates recombinase polymerase amplification (RPA) with CRISPR-LbaCas12a and lateral flow dipstick (LFD) technologies, enabling visual readout of results. Key parameters, including the single-stranded DNA (ssDNA) reporter concentration, reaction time, and temperature, were systematically optimized. Field water sample testing demonstrated high specificity and sensitivity, achieving a detection limit of 5 × 10⁻⁶ pg μL⁻¹ for genomic DNA under laboratory conditions and 2.82 × 10¹ cells mL⁻¹ in simulated environmental samples. The entire detection process takes only 1 h (at a constant 39 °C), and results can be directly interpreted via LFD strips. For early warning and prevention of C. dentata outbreaks, this assay provides a powerful, reliable, and field-ready monitoring tool. Full article

(This article belongs to the Section Microbial Biotechnology)

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28 pages, 3573 KB

Open AccessArticle

Pathogen Identification, Antagonistic Microbe Screening, and Biocontrol Strategies for Aconitum carmichaelii Root Rot

by Xingxun Dai, Yuqin He, Yu Su, Huishu Mo, Weichun Li, Wanting Li, Shuhui Zi, Lufeng Liu and Yining Di

Microorganisms 2025, 13(9), 2202; https://doi.org/10.3390/microorganisms13092202 - 19 Sep 2025

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Abstract

The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile [...] Read more.

The undefined microbial ecology of Aconitum carmichaelii root rot in western Yunnan constrains the advancement of eco-friendly control strategies. The identification of potential pathogenic determinants affecting A. carmichaelii growth is imperative for sustainable cultivation and ecosystem integrity. High-throughput sequencing was employed to profile microbial communities across four critical niches, namely rhizosphere soil, tuberous root epidermis, root endosphere, and fibrous roots of healthy and diseased A. carmichaelii. The physicochemical properties of corresponding rhizosphere soils were concurrently analyzed. Putative pathogens were isolated from diseased rhizospheres and tubers through culturing with Koch’s postulates validation, while beneficial microorganisms exhibiting antagonism against pathogens and plant growth-promoting (PGP) traits were isolated from healthy rhizospheres. Highly virulent strains (2F14, FZ1, L23) and their consortia were targeted for suppression. Strain DX3, demonstrating optimal PGP and antagonistic capacity in vitro, was selected for pot trials evaluating growth enhancement and disease control efficacy. Significant disparities in rhizosphere soil properties and bacterial/fungal community structures were evident between healthy and diseased cohorts. Fifteen putative pathogens spanning eight species across four genera were isolated: Fusarium solani, F. avenaceum, Clonostachys rosea, Mucor racemosus, M. irregularis, M. hiemalis, Serratia liquefaciens, and S. marcescens. Concurrently, eight PGP biocontrol strains were identified: Bacillus amyloliquefaciens, B. velezensis, B. subtilis, B. pumilus, and Paenibacillus polymyxa. Pot trials revealed that Bacillus spp. enhanced soil physiochemical properties through nitrogen fixation, phosphate solubilization, potassium mobilization, siderophore production, and cellulose degradation, significantly promoting plant growth. Critically, DX3 inoculation elevated defense-related enzyme activities in A. carmichaelii, enhanced host resistance to root rot, and achieved >50% disease suppression efficacy. This work delineates key pathogenic determinants of Yunnan A. carmichaelii root rot and identifies promising multifunctional microbial resources with dual PGP and biocontrol attributes. Our findings provide novel insights into rhizosphere microbiome-mediated plant health and establish a paradigm for sustainable disease management. Full article

(This article belongs to the Section Plant Microbe Interactions)

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21 pages, 3200 KB

Open AccessArticle

Probiotic Potential of Lactic Acid Bacteria Isolated from Moroccan Traditional Food Products

by Ange Olivier Parfait Yao, Majid Mounir, Hary Razafindralambo and Philippe Jacques

Microorganisms 2025, 13(9), 2201; https://doi.org/10.3390/microorganisms13092201 - 19 Sep 2025

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Abstract

This study assessed the performance and potential use of lactic acid bacteria (LAB) from Moroccan traditional foods as probiotics in animal feed. Five LAB strains Lactiplantibacillus plantarum from whey sourdough, Leuconostoc pseudomesenteroides and Leuconostoc mesenteroides from goat cheese, Enterococcus durans and Lacticaseibacillus casei [...] Read more.

This study assessed the performance and potential use of lactic acid bacteria (LAB) from Moroccan traditional foods as probiotics in animal feed. Five LAB strains Lactiplantibacillus plantarum from whey sourdough, Leuconostoc pseudomesenteroides and Leuconostoc mesenteroides from goat cheese, Enterococcus durans and Lacticaseibacillus casei from fermented milk were isolated and identified by 16S rRNA gene sequencing and MALDI-TOF mass spectrometry. Probiotic traits were evaluated by measuring acid/bile tolerance, cell surface hydrophobicity, emulsifying properties, antimicrobial activity and organic acid production, and safety checked through hemolysis and antibiotic sensitivity tests. L. plantarum, L. casei, and E. durans showed high survival rates after 24 h of culture under acid/bile stress conditions. The surface hydrophobicity of all strains ranged from 14.4 to 39.2%. L. plantarum showed the highest emulsifying capacity (81.4%) and stability (20%) after 24 h. Most strains inhibited pathogenic Staphylococcus epidermidis, Bacillus cereus, and Escherichia coli. Metabolite profiling revealed L. pseudomesenteroides as an interesting butyric acid-producing bacterium and L. plantarum as a remarkable strain releasing high content of organic acids. Their antibiotic susceptibility and non-hemolytic nature support their safety and potential use as feed additives. Full article

(This article belongs to the Section Microbial Biotechnology)

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22 pages, 1640 KB

Open AccessArticle

Proteomic Research of the Stress Response of Saccharomyces cerevisiae W303 Yeast to Metal Ions Eluted from Orthodontic Appliances

by Lara Dežulović, Božena Ćurko-Cofek and Gordana Čanadi Jurešić

Microorganisms 2025, 13(9), 2200; https://doi.org/10.3390/microorganisms13092200 - 19 Sep 2025

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Abstract

Although orthodontic appliances are widely used in daily practice, they also have their downsides due to the large amount of metal ions released from their surface. In this study, the influence of such released metal ions on the yeast Saccharomyces cerevisiae W303 as [...] Read more.

Although orthodontic appliances are widely used in daily practice, they also have their downsides due to the large amount of metal ions released from their surface. In this study, the influence of such released metal ions on the yeast Saccharomyces cerevisiae W303 as a model organism was investigated. Experimental yeast media in which metal ions (iron, aluminum, nickel, chromium, copper, and manganese) were eluted for 3, 7, 14, and 28 days were prepared and then used for yeast cultivation (up to the early stationary growth phase). The growth, increase, and viability of the cells were tested. The mitochondria were isolated from the spheroplasts, and the mitochondrial proteins were obtained and analyzed by liquid chromatography/mass spectrometry. Fortythree significantly altered proteins were identified. They showed significantly reduced expression in all metal-treated groups compared to the control. The metabolic processes for energy supply (glycolysis, gluconeogenesis, tricarboxylic acid cycle, and adenosine triphosphate synthesis) dominated with 50% of the total amount of significantly altered proteins in all samples, but their proportions changed at different time points. The downregulation of mitochondrial proteins such as Atp1, Atp2, and Pet9 under conditions of metal overload suggests a broader impairment of mitochondrial function. Three levels of response to stress can be observed—at relatively low metal ion concentrations in the medium (3 days of elution, approx. 3 mg/L), at medium concentrations (7 days of elution, approx. 5.5 mg/L), and at high concentrations (>8 mg/L, 14 and 28 days of elution), each affecting a specific group of proteins. The results show that mixtures of metal ions in experimental media led to a specific response (in terms of the amount and type of proteins) in each sample type to combat the provoked stress. Full article

(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research, 2nd Edition)

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25 pages, 1882 KB

Open AccessReview

Neutralizing Antibodies vs. Viruses: Interacting Mechanisms and Escape Tactics

by Hao Lu, Yichen Liu, Yue Song, Longxin Chen, Limeng Zhang, Runting Li, Xiaoning Nie, Guoqiang Zhu, Xueyan Ding and Linqing Wang

Microorganisms 2025, 13(9), 2199; https://doi.org/10.3390/microorganisms13092199 - 19 Sep 2025

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Abstract

Virus-neutralizing antibodies (VNAs) serve as critical components of host immune defense, countering viral infections by specifically recognizing epitopes on viral surface antigens to block viral entry and replication. This review elucidates the functional mechanisms of VNAs, with a focus on the dynamic interactions [...] Read more.

Virus-neutralizing antibodies (VNAs) serve as critical components of host immune defense, countering viral infections by specifically recognizing epitopes on viral surface antigens to block viral entry and replication. This review elucidates the functional mechanisms of VNAs, with a focus on the dynamic interactions between the Fab region and viral epitopes, including steric hindrance and conformational locking, as well as the effector functions mediated by the Fc segment. Furthermore, we dissect diverse viral evasion strategies against neutralization that have emerged in recent studies, encompassing antigenic drift/shift, glycan shielding, epitope occlusion, antibody-dependent enhancement, and mutation accumulation under population immune pressure. Integrating structural biology insights with clinical evidence, we analyze challenges in developing broadly neutralizing antibodies and highlight innovative technological approaches. Our synthesis aims to establish a theoretical framework for the rational design and clinical translation of next-generation VNAs, thereby advancing novel strategies for antiviral therapeutics development. Full article

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

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20 pages, 2671 KB

Open AccessArticle

Role of NaCl and Glutamine on Biofilm Production from Pseudomonas aeruginosa

by Laura Maria De Plano, Antonella Iaconis, Salvatore Papasergi, Francesco Mediati, Daniele Caruso, Salvatore Pietro Paolo Guglielmino and Domenico Franco

Microorganisms 2025, 13(9), 2198; https://doi.org/10.3390/microorganisms13092198 - 19 Sep 2025

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Abstract

Pseudomonas aeruginosa is an opportunistic pathogen capable of forming antibiotic-resistant biofilms, contributing to persistent infections and treatment failure. Environmental factors such as osmolarity and nutrient availability are known to influence biofilm formation and virulence. In this study, we investigated the effects of NaCl [...] Read more.

Pseudomonas aeruginosa is an opportunistic pathogen capable of forming antibiotic-resistant biofilms, contributing to persistent infections and treatment failure. Environmental factors such as osmolarity and nutrient availability are known to influence biofilm formation and virulence. In this study, we investigated the effects of NaCl depletion and glutamine supplementation on biofilm production in three P. aeruginosa strains: the laboratory strain ATCC 27853 and two clinical isolates with distinct antibiotic resistance profiles and phenazine production patterns (P. aeruginosa Pr, pyorubrin-producing, and P. aeruginosa Pc, pyocyanin-producing). Bacteria were cultured in standard Luria–Bertani (LB) medium, LB without NaCl, and LB in which yeast extract was replaced by glutamine. For each strain and condition, we assessed growth kinetics, phenazine production, and biofilm formation. Biofilm development was quantified via XTT assays and compared to secondary metabolite profiles. NaCl removal did not substantially affect growth, whereas glutamine supplementation reduced growth, especially in the laboratory strain. Both conditions modulated secondary metabolite production and biofilm formation in a strain-specific manner. In P. aeruginosa ATCC 27853, NaCl depletion significantly increased pyoverdine, pyocyanin, and QS gene expression, while biofilm formation showed significant differences only at 72 h; in contrast, glutamine supplementation affected only pyoverdine. A similar trend was observed in the clinical strain P. aeruginosa Pc, although NaCl depletion did not significantly impact pyoverdine production but already enhanced biofilm formation at 48 h. In P. aeruginosa Pr, only glutamine appeared to alter the considered parameters, increasing pyoverdine production while reducing pyocyanin and biofilm levels, although the absence of NaCl also negatively impacted biofilm formation. These findings highlight the impact of osmotic and nutritional signals on P. aeruginosa virulence traits. Full article

(This article belongs to the Special Issue Pathogenic Biofilms: Physiology, Molecular Mechanisms and Counter Strategies)

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15 pages, 401 KB

Open AccessArticle

Targeted Screening with the Use of Clinical Risk Factors for Detecting Congenital Cytomegalovirus Infection in Newborns: A Prospective Multicenter Cohort Study

by Soromon Kataoka, Masatoki Kaneko, Li Yang, Hajime Ota, Moeka Seki, Aya Kobamatsu, Daiki Nakayama, Yu Furuta, Fumie Tanuma, Yoshiyuki Fukushi, Shinichiro Wada, Keiji Haseyama and Hideto Yamada

Microorganisms 2025, 13(9), 2197; https://doi.org/10.3390/microorganisms13092197 - 19 Sep 2025

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Abstract

Congenital cytomegalovirus infection (cCMV) is one of the most common congenital infections. This study aimed to evaluate the diagnostic performance of targeted screening with the use of clinical risk factors for cCMV. A total of 3063 pregnant women and their 3139 newborns were [...] Read more.

Congenital cytomegalovirus infection (cCMV) is one of the most common congenital infections. This study aimed to evaluate the diagnostic performance of targeted screening with the use of clinical risk factors for cCMV. A total of 3063 pregnant women and their 3139 newborns were enrolled. Six clinical findings consisting of maternal fever or flu-like symptoms during pregnancy (fever/flu-like symptoms), hospitalization for threatened miscarriage or preterm labor before 34 weeks of gestation, preterm delivery before 34 weeks of gestation, fetal ultrasound abnormalities, small for gestational age (SGA), and refer results of automated auditory brainstem response screening (AABR refer) were defined as cCMV risk factors before participant registration. All newborns underwent urine cytomegalovirus polymerase chain reaction tests within one week of birth. The predictive accuracy of these six risk factors was analyzed. Nine (0.29%) of the three thousand one hundred and thirty-nine newborns were diagnosed with cCMV, having at least one of the six risk factors. Logistic regression analysis identified fever/flu-like symptoms (odds ratio (OR), 7.5; 95% CI, 1.9–30.3), fetal ultrasound abnormalities (OR, 17.9; 95% CI, 4.4–72.8), SGA (OR, 6.8; 95% CI, 1.8–25.6), and AABR refer (OR, 75.5; 95% CI, 19.7–289) as significant risk factors. The predictive accuracy of the targeted screening for cCMV, when at least one of the six risk factors was present, yielded 100% sensitivity (95% CI, 55.5–100) and 70.7% specificity (95% CI, 69.1–72.3), with a Youden index of 0.707. When at least one of the four significant risk factors was present, 100% sensitivity (95% CI, 55.5–100) and 81.2% specificity (95% CI, 79.8–82.6) with the maximum Youden index of 0.812 were achieved. In conclusion, targeted screening with the use of clinical risk factors in mothers and their newborns could effectively identify cCMV. Full article

(This article belongs to the Special Issue Emerging and Re-Emerging Infections in the Immunocompromised Host)

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31 pages, 2380 KB

Open AccessArticle

Metabarcoding Unveils Seasonal Soil Microbiota Shifts and Their Influence on Boletus edulis and Boletus reticulatus Mycelium in Quercus robur Stands

by Serena Santolamazza-Carbone, Laura Iglesias-Bernabé, Elena Benito-Rueda, Esther Barreal and Pedro Pablo Gallego

Microorganisms 2025, 13(9), 2196; https://doi.org/10.3390/microorganisms13092196 - 19 Sep 2025

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Abstract

Forest ecosystems undergo seasonal shifts in bacterial and fungal communities, but little is known about the specific microbiota associated with Quercus robur–Boletus edulis systems. This study represents the first examination of seasonal changes in soil microbiota in pedunculate oak habitats in [...] Read more.

Forest ecosystems undergo seasonal shifts in bacterial and fungal communities, but little is known about the specific microbiota associated with Quercus robur–Boletus edulis systems. This study represents the first examination of seasonal changes in soil microbiota in pedunculate oak habitats in Galicia (NW Spain) and their relationship with Boletus edulis and Boletus reticulatus mycelium prevalence and concentration. Soil microbiota richness, diversity, and composition, as well as seasonal variation in Boletus mycelium, were assessed using DNA metabarcoding and qPCR, respectively. Sampling was conducted in autumn at two 30–40-year-old Q. robur stands. Bacterial communities were dominated by Acidobacteria (34%) and Proteobacteria (33%), with Acidobacterium (12%), Paludibaculum (9%), and Edaphobacter (7%) identified as most abundant. Fungal communities were primarily Basidiomycota (93%), led by Russula (46%). For both bacteria and fungi, the highest OTU richness was observed in September, followed by a significant decrease in October and a partial recovery in November. Boletus species were found to exhibit positive correlations with specific bacteria (e.g., Massilia, Rhizobium) and fungi (e.g., Amanita, Clavaria, Inocybe, Scleroderma, Suillus and Mortierella), suggesting a potential influence of these microbes on mycelium development. This study provides novel insights into the seasonal dynamics of soil microbiota and their potential role in Boletus ecology, thereby advancing understanding of host–microbe interactions in temperate forests. Full article

(This article belongs to the Special Issue Soil Fungi in Sustainable Agriculture, 2nd Edition)

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13 pages, 946 KB

Open AccessArticle

Acanthospermum australe Extract Inhibits the Chaperone Activity of Plasmodium falciparum Heat Shock Protein 70-1

by Ntombikhona Appear Koza, Ntokozo Nkosinathi Myeza, Heinrich Hoppe, Rebamang Anthony Mosa, Abidemi Paul Kappo, Mthokozisi Blessing Cedric Simelane and Andrew Rowland Opoku

Microorganisms 2025, 13(9), 2195; https://doi.org/10.3390/microorganisms13092195 - 19 Sep 2025

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Abstract

The resistance of malaria parasites towards the current antimalarial therapies continues to fuel the search for new antimalarial drugs, preferably from natural sources. This study aimed to investigate the potential of the dichloromethane extract of Acanthospermum australe to inhibit Plasmodium falciparum heat shock [...] Read more.

The resistance of malaria parasites towards the current antimalarial therapies continues to fuel the search for new antimalarial drugs, preferably from natural sources. This study aimed to investigate the potential of the dichloromethane extract of Acanthospermum australe to inhibit Plasmodium falciparum heat shock protein 70-1 (PfHsp70-1). The plasmodium lactate dehydrogenase (pLDH) assay was used to determine the antiplasmodial activity of the crude extract against the chloroquine-sensitive P. falciparum strain 3D7. The inhibitory effect of the plant extract on the chaperone activity of P. falciparum heat shock protein 70-1 (PfHsp70-1) was determined using the ATPase, thermally induced luciferase and malate dehydrogenase (MDH) assays. The extract showed a significantly high activity against P. falciparum strain 3D7 with an IC₅₀ value of 1.3 µg/mL. A decrease in thermally induced aggregation of MDH and luciferase was observed when each of the proteins was incubated with PfHsp70-1 only. However, an increased protein aggregation was observed when the proteins were incubated with PfHsp70-1 in the presence of the plant extract. The extract also exhibited inhibitory activity on the ATPase activity of PfHsp70-1. The results obtained from this study suggest that A. australe extract contains compounds that could target malaria parasite Hsp70 functions. Full article

(This article belongs to the Special Issue Research on Mosquito-Borne Pathogens)

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16 pages, 599 KB

Open AccessReview

An Overview of the Epidemiology of Multidrug Resistance and Bacterial Resistance Mechanisms: What Solutions Are Available? A Comprehensive Review

by Victoria Birlutiu and Rares-Mircea Birlutiu

Microorganisms 2025, 13(9), 2194; https://doi.org/10.3390/microorganisms13092194 - 19 Sep 2025

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Abstract

Antimicrobial resistance has emerged as one of the most critical public health challenges of the 21st century, threatening to undermine the foundations of modern medicine. In 2019, bacterial infections accounted for 13.6% of all global deaths, with more than 7.7 million fatalities directly [...] Read more.

Antimicrobial resistance has emerged as one of the most critical public health challenges of the 21st century, threatening to undermine the foundations of modern medicine. In 2019, bacterial infections accounted for 13.6% of all global deaths, with more than 7.7 million fatalities directly attributable to 33 bacterial pathogens, most prominently Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Resistance mechanisms are multifactorial, encompassing enzymatic degradation, target modification, efflux pump overexpression, reduced membrane permeability, and biofilm formation, often in combination, leading to multidrug-resistant, extensively drug-resistant, and pandrug-resistant phenotypes. Alarmingly, projections estimate that by 2050 AMR could result in over 10 million deaths annually. This comprehensive review synthesizes global epidemiological data, insights into bacterial resistance mechanisms, and emerging therapeutic solutions, including novel antibiotics such as lasso peptides and macrocyclic peptides (e.g., zosurabalpin), naturally derived compounds (e.g., corallopyronin, clovibactin, chlorotonil A), and targeted inhibitors (e.g., Debio 1453 for Neisseria gonorrhoeae). Addressing the AMR crisis requires coordinated international efforts, accelerated drug discovery, and the integration of innovative non-antibiotic approaches to preserve the efficacy of existing therapies and ensure preparedness against future bacterial threats. Full article

(This article belongs to the Special Issue The Epidemiology, Clinical Aspects, Treatment and Preventive Strategies for Infectious Diseases in the Era of Antimicrobial Resistance (AMR))

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20 pages, 1651 KB

Open AccessReview

Emerging Roles of the Gut Microbiome in Musculoskeletal Injury and Repair

by Joseph L. Roberts and Connor C. Park

Microorganisms 2025, 13(9), 2193; https://doi.org/10.3390/microorganisms13092193 - 19 Sep 2025

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Abstract

Over the past decade, significant attention has been directed toward understanding the role of the gut microbiome in health and disease. The gut microbiota, comprising a complex and diverse community of microorganisms, has been linked to numerous conditions, including metabolic disorders, gastrointestinal diseases, [...] Read more.

Over the past decade, significant attention has been directed toward understanding the role of the gut microbiome in health and disease. The gut microbiota, comprising a complex and diverse community of microorganisms, has been linked to numerous conditions, including metabolic disorders, gastrointestinal diseases, and inflammatory or autoimmune conditions. Recently, a growing body of evidence has revealed a compelling relationship between gut microbiota composition and musculoskeletal injury recovery, highlighting its potential as a novel therapeutic target. Musculoskeletal injuries, including fractures, post-traumatic osteoarthritis, and tendon or ligament injuries, commonly lead to changes in the community structure of the gut microbiota, intestinal permeability, and systemic inflammation, processes known to negatively influence tissue repair. Preclinical studies demonstrate that microbiota-targeted interventions, such as probiotics, prebiotics, and fecal microbiota transplantation, effectively restore gut barrier integrity, modulate inflammation, and normalize gut-derived metabolite profiles. Despite these promising findings, critical gaps remain in translating these effects into clinical practice, particularly regarding the mechanisms linking specific microbiota changes to improved musculoskeletal healing outcomes. Future research incorporating rigorous clinical trials, multi-omics analyses, and advanced predictive tools, including artificial intelligence and microbiome-informed digital twins, is urgently needed to fully harness the therapeutic potential of microbiome-based interventions in musculoskeletal injury recovery. This narrative review provides insights into our evolving understanding of the relationship between the gut microbiota and musculoskeletal injury and explores the potential of gut microbiota-targeted therapies for improved healing outcomes. Full article

(This article belongs to the Special Issue Intestine as a Hub for Host-Microbe Interactions and Its Impact on Local and Systemic Health)

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19 pages, 3409 KB

Open AccessArticle

Unveiling Bacterial Diversity in Portuguese Red Wine Effluents Through a Metagenomic Approach

by Ana Gabriela Gomes, Ana Cláudia Sousa, João S. Carreira, Alberto Oliveira, Marta C. Justino and Carla Amarelo Santos

Microorganisms 2025, 13(9), 2192; https://doi.org/10.3390/microorganisms13092192 - 19 Sep 2025

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Abstract

The sustainable reuse of agro-industrial effluents requires a detailed understanding of their microbial composition, especially in the context of integrated vineyard–winery ecosystems. This study investigated the bacterial communities present in winery effluents generated during the early stages of red wine production, using samples [...] Read more.

The sustainable reuse of agro-industrial effluents requires a detailed understanding of their microbial composition, especially in the context of integrated vineyard–winery ecosystems. This study investigated the bacterial communities present in winery effluents generated during the early stages of red wine production, using samples collected at a winery in the Setúbal Peninsula, Portugal. Metagenomic analysis targeting the 16S rRNA gene was used to characterise microbial diversity and identify taxa with potential relevance for biotechnology and environmental applications. The effluents exhibited a diverse microbiome, including Prevotella paludivivens, species from the Lactobacillus genus, and members of the Clostridiaceae family, the latter representing about 5% of the total community. Functional profiling of lactic acid bacteria revealed the predominance of Oenococcus and Lactobacillus genera, highlighting adaptive traits that may be beneficial under stress conditions. These results suggest that winery effluents, often considered waste, harbour microbial communities with functional potential that extends beyond fermentation, contributing to a broader grape–wine microbial system. The findings emphasise the value of studying winemaking byproducts as reservoirs of microbial diversity and as resources for developing innovative and sustainable applications in biotechnology and environmental management within the wine industry. Full article

(This article belongs to the Special Issue Microbiology of the Grape-Wine System)

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