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Microorganisms
Volume 13
Issue 6
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Microorganisms, Volume 13, Issue 6 (June 2025) – 262 articles

Cover Story (view full-size image): Postbiotics have gained recognition as promising modulators of gut health and disease, offering advantages over probiotics in terms of safety, stability, and formulation. This systematic review investigates the therapeutic potential of postbiotics derived from functional foods in the context of colorectal cancer (CRC), a leading cause of cancer-related mortality worldwide, uniquely categorizing research according to the experimental models employed, i.e., in vitro, in silico, in vivo, and ex vivo, and advanced models such as organoids and organ-on-chip platforms. These models help demonstrate how postbiotics may influence tumorigenesis through mechanisms involving inflammation, apoptosis, epigenetic regulation, and the maintenance of gut barrier integrity. View this paper
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18 pages, 2683 KiB  
Article
FpFumB Is Required for Basic Biological Processes and Virulence in Fusarium proliferatum by Modulating DNA Repair Through Interaction with FpSae2
by Yizhou Gao, Haibo Li, Yong Liu, Yuqing Wang, Jingwen Xue, Yitong Wang and Zhihong Wu
Microorganisms 2025, 13(6), 1433; https://doi.org/10.3390/microorganisms13061433 - 19 Jun 2025
Viewed by 341
Abstract
Fumarase plays a pivotal role in the tricarboxylic acid cycle, but its functions in plant pathogenic fungi are not well understood. We identified two fumarase genes in Fusarium proliferatum and generated individual deletion mutants. Loss of FpFumB led to defects in growth, sporulation, [...] Read more.
Fumarase plays a pivotal role in the tricarboxylic acid cycle, but its functions in plant pathogenic fungi are not well understood. We identified two fumarase genes in Fusarium proliferatum and generated individual deletion mutants. Loss of FpFumB led to defects in growth, sporulation, stress tolerance, and virulence. Exogenous malate supplementation restored growth defects. Site-directed mutagenesis of residues G452 and A463 reduced FpFumB enzyme activity. Transcriptomic analysis identified significant changes in gene expression related to different metabolic pathways. Protein interaction assays showed that FpFumB interacts with the DNA repair protein FpSae2. Both ΔFpFumB and ΔFpSae2 mutants displayed altered sensitivity to DNA-damaging agents and reduced virulence, indicating that FpFumB modulates DNA repair and pathogenicity through its interaction with FpSae2. Together, these findings highlight FpFumB as a key regulator of basic biological processes, DNA damage repair, and virulence in Fusarium proliferatum. Full article
(This article belongs to the Section Plant Microbe Interactions)
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17 pages, 11703 KiB  
Article
Host-Determined Diversity and Environment-Shaped Community Assembly of Phyllosphere Microbiomes in Alpine Steppes Ecosystems
by Kaifu Zheng, Xin Jin, Jingjing Li and Guangxin Lu
Microorganisms 2025, 13(6), 1432; https://doi.org/10.3390/microorganisms13061432 - 19 Jun 2025
Viewed by 286
Abstract
The Qinghai–Tibet Plateau is a key region for biodiversity conservation, where alpine grasslands are ecologically important. While previous studies have mainly addressed vegetation, ecosystem processes, and soil microbes, phyllosphere microorganisms are essential for nutrient cycling, plant health, and stress tolerance. However, their communities [...] Read more.
The Qinghai–Tibet Plateau is a key region for biodiversity conservation, where alpine grasslands are ecologically important. While previous studies have mainly addressed vegetation, ecosystem processes, and soil microbes, phyllosphere microorganisms are essential for nutrient cycling, plant health, and stress tolerance. However, their communities remain poorly understood compared to those in soil. The relative influence of host identity and environmental conditions on shaping phyllosphere microbial diversity and community assembly remains uncertain. In this study, we characterized phyllosphere bacterial and fungal communities of the phyllosphere at two alpine steppe sites with similar vegetation but climatic conditions: the Qilian Mountains (QLM) and the Qinghai Lake region (LQS). At both sites, Cyanobacteriota and Ascomycota were the predominant bacterial and fungal taxa, respectively. Microbial α-diversity did not differ significantly between the two regions, implying that host-associated mechanisms may stabilize within-site diversity. In contrast, β-diversity exhibited clear spatial differentiation. In QLM, bacterial β-diversity was significantly correlated with mean annual precipitation, while fungal α- and β-diversity were associated with soil nutrient levels (including nitrate, ammonium, available potassium, and phosphorus) and vegetation coverage. At LQS, the β-diversity of both bacterial and fungal communities was strongly influenced by soil electrical conductivity, and fungal communities were further shaped by vegetation cover. Community assembly processes were predominantly stochastic at both sites, although deterministic patterns were more pronounced in QLM. Variability in moisture availability contributed to random bacterial assembly at LQS, while increased environmental heterogeneity promoted deterministic assembly in fungal communities. The elevated diversity of microbes and plants in QLM also reinforced deterministic processes. Overall, our findings support a host–environment interaction hypothesis, indicating that host factors primarily govern α-diversity, while climatic and soil-related variables have stronger effects on β-diversity and microbial assembly dynamics. These insights advance our understanding of how phyllosphere microbial communities may respond to environmental change in alpine ecosystems. Full article
(This article belongs to the Section Environmental Microbiology)
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16 pages, 8686 KiB  
Article
Potential Natural Inhibitors of MRSA ABC Transporters and MecA Identified Through In Silico Approaches
by Benson Otarigho, Paul M. Duffin and Mofolusho O. Falade
Microorganisms 2025, 13(6), 1431; https://doi.org/10.3390/microorganisms13061431 - 19 Jun 2025
Viewed by 401
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant clinical challenge due to its resistance to multiple antibiotics. The urgent need for new therapeutic approaches has led to the exploration of natural compounds as potential treatments, particularly those targeting the key bacterial proteins involved in [...] Read more.
Methicillin-resistant Staphylococcus aureus (MRSA) poses a significant clinical challenge due to its resistance to multiple antibiotics. The urgent need for new therapeutic approaches has led to the exploration of natural compounds as potential treatments, particularly those targeting the key bacterial proteins involved in antibiotic resistance. This study focused on the multidrug ABC transporter and MecA proteins, which play crucial roles in MRSA′s pathogenicity and resistance mechanisms. Using computational techniques and molecular docking methods, we assessed the interactions of 80 natural compounds with S. aureus multidrug ABC transporter SAV1866 (SAV1866) and MecA proteins. Our analysis revealed 14 compounds with robust binding to SAV1866 and one compound with a strong affinity for MecA. Notably, these compounds showed weaker affinities for the MgrA, MepR, and arlR proteins, suggesting specificity in their interactions. Among the 15 promising compounds identified, 1′,2-Binaphthalen-4-one-2′,3-dimethyl-1,8′-epoxy-1,4′,5,5′,8,8′-hexahydroxy-8-O-β-glucopyranosyl-5′-O-β-xylopyranosyl(1→6)-β-glucopyranoside; Cis-3,4-dihydrohamacanthin b; and Mamegakinone exhibited the highest binding affinities to S. aureus SAV1866. These compounds represent diverse chemical classes, including alkaloids, indole derivatives, naphthalenes, and naphthoquinones, offering a range of structural scaffolds for further drug development. Our findings provide valuable insights into potential new antibacterial agents targeting S. aureus SAV1866 and MecA proteins. These results lay the groundwork for future in vitro and in vivo studies to validate these compounds′ efficacy for combating MRSA infections, potentially leading to the development of novel therapeutic strategies against antibiotic-resistant bacteria. Full article
(This article belongs to the Special Issue Research on Antimicrobial Activity of Natural Products, Second Edition)
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15 pages, 1465 KiB  
Article
Propagule-Type Specificity in Arbuscular Mycorrhizal Fungal Communities in Early Growth of Allium tuberosum
by Irem Arslan, Kohei Takahashi, Naoki Harada and Kazuki Suzuki
Microorganisms 2025, 13(6), 1430; https://doi.org/10.3390/microorganisms13061430 - 19 Jun 2025
Viewed by 485
Abstract
Arbuscular mycorrhizal fungi (AMF) exhibit diverse strategies for colonization and survival, yet the extent to which different propagule types—roots, extraradical hyphae, and spores—contribute to these processes remains unclear. In a pot experiment using Allium tuberosum and soils from three field sites, we characterized [...] Read more.
Arbuscular mycorrhizal fungi (AMF) exhibit diverse strategies for colonization and survival, yet the extent to which different propagule types—roots, extraradical hyphae, and spores—contribute to these processes remains unclear. In a pot experiment using Allium tuberosum and soils from three field sites, we characterized AMF communities in root, hyphal, and spore fractions through 18S rRNA gene sequencing. A total of 427 OTUs were identified, with Glomus and Paraglomus dominating. Root fractions contained significantly more OTUs than hyphal fractions, suggesting strong specialization for intraradical colonization. Only a small subset of taxa occurred across all propagule types. Indicator species analysis revealed 21 OTUs with significant associations, mainly in root and hyphal fractions, while spore-specific taxa were rare. PERMANOVA revealed that both propagule type and soil type shaped the community structure, with propagule identity being the stronger factor. These results highlight propagule-type specialization as a key ecological trait in AMF and underscore the importance of examining multiple fungal compartments to fully capture AMF diversity and function. Full article
(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)
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25 pages, 24039 KiB  
Article
Response of Endophytic Microbial Communities and Quality of Salvia miltiorrhiza to Fertilization Treatments
by Wenjing Chen, Wanyun Li, Yangyang Pan, Xin Zheng, Xinxin Fu, Menghui Wang, Wenyi Shi, Zhenzhou Wang, Xueli He, Chao He and Xianen Li
Microorganisms 2025, 13(6), 1429; https://doi.org/10.3390/microorganisms13061429 - 19 Jun 2025
Viewed by 385
Abstract
Salvia miltiorrhiza is a traditional herbal remedy for cardiovascular diseases and is in high demand in the market. Excessive chemical fertilizer application, resulting from unscientific fertilization practices, reduced the tanshinone content in S. miltiorrhiza roots. This study investigated how different fertilization types alter [...] Read more.
Salvia miltiorrhiza is a traditional herbal remedy for cardiovascular diseases and is in high demand in the market. Excessive chemical fertilizer application, resulting from unscientific fertilization practices, reduced the tanshinone content in S. miltiorrhiza roots. This study investigated how different fertilization types alter the endophytic microbial community composition of S. miltiorrhiza through field experiments, aiming to understand how fertilization affects its medicinal quality. The results showed that root fertilizers (F1) significantly increased root biomass and tanshinone I content, whereas foliar fertilizers (F2) increased tanshinone IIA content. High-throughput sequencing further revealed that F2 treatment significantly decreased the Shannon index of endophytic bacteria while significantly increasing the Shannon index of endophytic fungi. Co-occurrence network analysis revealed that fertilization significantly altered fungal community complexity and modularity, with F1 increasing network nodes and edges. Variance partitioning analysis indicated fungal diversity more strongly influenced medicinal compound levels under F2 and a combination of both (F3) than bacterial diversity. Septoria and Gibberella were positively correlated with tanshinone I and cryptotanshinone content under F2 treatment, respectively. Notably, the unique strains were isolated from different fertilization treatments for subsequent bacterial fertilizer development. These findings elucidate microbial responses to fertilization, guiding optimized cultivation for improved S. miltiorrhiza quality. Full article
(This article belongs to the Section Plant Microbe Interactions)
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16 pages, 2740 KiB  
Article
Limosilactobacillus reuteri M4-100 Mitigates the Pathogenicity of Escherichia coli Strain HMLN-1 in an Intestinal Epithelial Model and Modulates Host Cell Gene Expression
by Behnoush Asgari, Georgia Bradford, Eva Hatje, Anna Kuballa and Mohammad Katouli
Microorganisms 2025, 13(6), 1428; https://doi.org/10.3390/microorganisms13061428 - 19 Jun 2025
Viewed by 353
Abstract
Probiotics have been widely adopted due to their beneficial health properties. Here, we investigated the interactions of a probiotic Limosilactobacillus (Lactobacillus) reuteri M4-100, with a translocating Escherichia coli strain HMLN-1, in a co-culture of cells, representing the intestinal epithelium, and identified molecular mechanisms [...] Read more.
Probiotics have been widely adopted due to their beneficial health properties. Here, we investigated the interactions of a probiotic Limosilactobacillus (Lactobacillus) reuteri M4-100, with a translocating Escherichia coli strain HMLN-1, in a co-culture of cells, representing the intestinal epithelium, and identified molecular mechanisms associated with the host response. A co-culture of Caco-2:HT29-MTX cells was exposed to the HMLN-1 strain and the route of translocation was studied. Scanning and transmission electron microscopy revealed the adhesion of the strain to the microvilli, the establishment of close contact with the co-culture prior to being taken up by membrane-bound vesicles, and translocation via the intracellular pathway. When the HMLN-1 strain was challenged with L. reuteri M4-100 in co- and pre-inoculation experiments, its adhesion to the co-culture of cells was significantly reduced (p < 0.0001). A significant reduction in the invasion of the HMLN-1 strain was also observed upon the inoculation of L. reuteri M4-100 with the co-culture 60 min prior to HMLN-1 exposure (p < 0.0001). The L. reuteri M4-100 strain also significantly (p < 0.0001) reduced the translocation of the HMLN-1 strain in both co- and pre-inoculation experiments. Differential gene expression studies identified key cellular responses to the interaction with these bacteria, both alone. These data demonstrate the efficacy of L. reuteri M4-100 to reduce or inhibit the interaction of E. coli HMLN-1 with the intestinal epithelium. A prophylactic role of this probiotic strain is postulated as these effects were more pronounced in pre-inoculation experiments. Full article
(This article belongs to the Section Medical Microbiology)
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15 pages, 2623 KiB  
Article
Preliminary Insights into the Gut Microbiota of Captive Tigers in Republic of Korea: Influence of Geographic and Individual Variation
by Beoul Kim, Saebom Lee, You-Jeong Lee, Yong-Myung Kang, Man Hee Rhee, Dongmi Kwak, Yong-Gu Yeo, Ju Won Kang, Taehwan Kim and Min-Goo Seo
Microorganisms 2025, 13(6), 1427; https://doi.org/10.3390/microorganisms13061427 - 19 Jun 2025
Viewed by 309
Abstract
The gut microbiome plays a crucial role in the health and physiology of tigers (Panthera tigris), influencing digestion, immune function, and overall well-being. While numerous studies have characterized the gut microbiota of domestic carnivores and some wild felids, comparative analyses across [...] Read more.
The gut microbiome plays a crucial role in the health and physiology of tigers (Panthera tigris), influencing digestion, immune function, and overall well-being. While numerous studies have characterized the gut microbiota of domestic carnivores and some wild felids, comparative analyses across different tiger subspecies under varying environmental contexts remain limited. In this exploratory study, we investigated the gut microbiome diversity and composition of 15 captive tigers, including both Siberian (P. tigris altaica) and Bengal (P. tigris tigris) subspecies, housed in two different regions in Korea. Using 16S rRNA gene sequencing of fecal samples, we analyzed microbial diversity across multiple taxonomic levels. Preliminary analyses revealed significant differences in microbial composition between geographic locations, whereas sex-based differences appeared minimal. Alpha and beta diversity metrics demonstrated substantial inter-individual variability, likely influenced by regional and environmental factors. Given the small sample size and the confounding between subspecies and housing location, the findings should be regarded as preliminary and not generalized beyond this specific cohort. Nevertheless, these insights highlight the potential utility of gut microbiome profiling for health monitoring and management in captive-tiger populations. Future research incorporating larger, more diverse cohorts will be essential to validate these trends and clarify the roles of diet, health status, and enrichment in shaping the gut microbiota. Full article
(This article belongs to the Section Gut Microbiota)
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16 pages, 3362 KiB  
Article
The Clinically Significant Changes in the Composition and Functional Diversity of the Vaginal Microbiome in Women with Type 2 Diabetes Mellitus
by Min Jeong Kim, Jaeeun Yoo, Soonjib Yoo, Mi Yeon Kwon, Seungok Lee and Myungshin Kim
Microorganisms 2025, 13(6), 1426; https://doi.org/10.3390/microorganisms13061426 - 19 Jun 2025
Viewed by 364
Abstract
Type 2 diabetes mellitus (T2DM) significantly influences the composition and diversity of the vaginal microbiome, with implications for mucosal immunity, infection risk, and genitourinary health. This study aimed to investigate the vaginal microbiome profiles in women with T2DM, with a focus on differences [...] Read more.
Type 2 diabetes mellitus (T2DM) significantly influences the composition and diversity of the vaginal microbiome, with implications for mucosal immunity, infection risk, and genitourinary health. This study aimed to investigate the vaginal microbiome profiles in women with T2DM, with a focus on differences according to menopausal status and associations with Candida colonization and the use of sodium–glucose cotransporter 2 (SGLT2) inhibitors. Compared to healthy controls, women with T2DM exhibited a decreased abundance of Lactobacillus species and increased microbial diversity. Community state of type (CST) IV, characterized by low Lactobacillus abundance and dominance of anaerobic taxa, was prevalent in the T2DM group. Among Candida-positive patients, Lactobacillus iners-dominant CST III was frequently observed, along with elevated levels of total and L-lactic acid. SGLT2 inhibitor users exhibited a different CST distribution pattern and slightly lower microbial richness and diversity, although these differences were not statistically significant. These findings underscore the impact of T2DM and its treatment on vaginal microbial composition and highlight the importance of considering vaginal health as part of comprehensive diabetes management in women. Full article
(This article belongs to the Special Issue Microbiome and Genitourinary Diseases)
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23 pages, 3735 KiB  
Article
Taxonomic Diversity and Antimicrobial Potential of Thermophilic Bacteria from Two Extreme Algerian Hot Springs
by Marwa Aireche, Mohamed Merzoug, Amaria Ilhem Hammadi, Zohra Yasmine Zater, Keltoum Bendida, Chaimaa Naila Brakna, Meryem Berrazeg, Ahmed Yassine Aireche, Yasmine Saidi, Svetoslav Dimitrov Todorov, Dallel Arabet and Djamal Saidi
Microorganisms 2025, 13(6), 1425; https://doi.org/10.3390/microorganisms13061425 - 19 Jun 2025
Viewed by 437
Abstract
This study investigated thermophilic bacterial communities from two Algerian hot springs: Hammam Debagh (94–98 °C), recognized as the second hottest spring in the world, and Hammam Bouhadjar (61–72 °C), one of the hottest in northwest Algeria. Thirty isolates were obtained, able to grow [...] Read more.
This study investigated thermophilic bacterial communities from two Algerian hot springs: Hammam Debagh (94–98 °C), recognized as the second hottest spring in the world, and Hammam Bouhadjar (61–72 °C), one of the hottest in northwest Algeria. Thirty isolates were obtained, able to grow between 45 °C and 80 °C, tolerating pH 5.0–12.0 and NaCl concentrations up to 3%. Colonies displayed diverse morphologies, from circular and smooth to star-shaped and Saturn-like forms. All isolates were characterized as Gram-positive, catalase-positive rods or filamentous bacteria. Identification by MALDI-TOF, rep-PCR and 16S rRNA sequencing classified them mainly within Bacillus, Brevibacillus, Aneurinibacillus, Geobacillus, and Aeribacillus, with Geobacillus predominating. Rep-PCR provided higher resolution, revealing intra-species diversity overlooked by MALDI-TOF MS and 16S rRNA. A subset of six isolates, mainly Geobacillus spp., was selected based on phenotypic and genotypic diversity and tested for antimicrobial activity against thermophilic target isolates from the same hot spring environments. Strong inhibition zones (~24 mm) were observed, with Geobacillus thermoleovorans B8 displaying the highest activity. Optimization on Modified Nutrient Agar medium with Gelrite enhanced antimicrobial production and inhibition clarity. These findings highlight the ecological and biotechnological significance of thermophilic bacteria from Algerian geothermal ecosystems. While this study focused on microbial interactions within thermophilic communities, the promising inhibitory profiles reported here provide a foundation for future research targeting foodborne and antibiotic-resistant pathogens, as part of broader efforts in biopreservation and sustainable antimicrobial development. Full article
(This article belongs to the Special Issue Microbial Life and Ecology in Extreme Environments)
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12 pages, 937 KiB  
Article
Antiviral Activity of Brazilian Propolis from Stingless Bees Against Rotavirus
by Guadalupe González-Ochoa, Ana Paola Balderrama-Carmona, Jesús Antonio Erro-Carvajal, José Guadalupe Soñanez-Organis, Luis Alberto Zamora-Álvarez and Marcelo Andrés Umsza Guez
Microorganisms 2025, 13(6), 1424; https://doi.org/10.3390/microorganisms13061424 - 19 Jun 2025
Viewed by 323
Abstract
Group A rotavirus (RV) causes gastrointestinal disease in infants worldwide, and there is currently no specific treatment to eliminate the virus. Due to its chemical properties, propolis is a promising compound for improving gastrointestinal infections. This study aimed to evaluate the action of [...] Read more.
Group A rotavirus (RV) causes gastrointestinal disease in infants worldwide, and there is currently no specific treatment to eliminate the virus. Due to its chemical properties, propolis is a promising compound for improving gastrointestinal infections. This study aimed to evaluate the action of stingless bee propolis against RV. The method involved determining the concentrations of the extracts that do not exhibit cytotoxicity in colon adenocarcinoma cells using the MTT assay and measuring the reduction in infectivity through a focus forming assay. The results showed that stingless bee propolis was non-cytotoxic up to 200 µg/mL. The reduction in RV infectivity exceeded 99% when using propolis from Plebeia droryana and Melipona quadrifasciata. Brazilian stingless bee propolis, whose active components are known for their activity against various viruses, was experimentally tested and demonstrated effective antiviral activity against RV, supporting its potential application as an antiviral agent. Full article
(This article belongs to the Section Microbial Biotechnology)
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20 pages, 1953 KiB  
Article
Cepharanthine Inhibits Fusarium solani via Oxidative Stress and CFEM Domain-Containing Protein Targeting
by Yuqing Wang, Zenghui Yang, Jingwen Xue, Yitong Wang, Haibo Li, Zhihong Wu and Yizhou Gao
Microorganisms 2025, 13(6), 1423; https://doi.org/10.3390/microorganisms13061423 - 18 Jun 2025
Viewed by 435
Abstract
Cepharanthine (CEP) is a natural bisbenzylisoquinoline alkaloid known for its antibacterial, antiviral, and anti-inflammatory activities. Its antifungal effect, however, has not been well studied. In this work, we used machine learning-based virtual screening with Random Forest, Neural Network, and Support Vector Machine models [...] Read more.
Cepharanthine (CEP) is a natural bisbenzylisoquinoline alkaloid known for its antibacterial, antiviral, and anti-inflammatory activities. Its antifungal effect, however, has not been well studied. In this work, we used machine learning-based virtual screening with Random Forest, Neural Network, and Support Vector Machine models to identify potential inhibitors of Fusarium solani. CEP was selected as a candidate and tested experimentally. The results showed that it inhibited the growth of Fusarium solani, Fusarium proliferatum, Fusarium oxysporum, Alternaria alternata, and Botrytis cinerea. It also reduced the sporulation and spore germination of Fusarium solani and disrupted its redox balance. Transcriptome analysis showed changes in gene expression related to basic metabolic pathways. Molecular docking suggested that CEP binds to the FsCFEM1 protein, and molecular dynamics simulations confirmed stable binding, with key roles for residues THR748 and LEU950. These results suggest that CEP is a potential bio-based antifungal agent and provide novel insights into its mechanism against Fusarium solani. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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30 pages, 1493 KiB  
Review
Improving the Properties of Laccase Through Heterologous Expression and Protein Engineering
by Guoqiang Guan, Beidian Li, Ling Xu, Jingya Qian, Bin Zou, Shuhao Huo, Zhongyang Ding, Kai Cui and Feng Wang
Microorganisms 2025, 13(6), 1422; https://doi.org/10.3390/microorganisms13061422 - 18 Jun 2025
Viewed by 429
Abstract
Laccase, a member of the blue multicopper oxidase family, is widely distributed across diverse taxonomic groups, including fungi, bacteria, plants, and insects. This enzyme drives biocatalytic processes through the oxidation of phenolic compounds, aromatic amines, and lignin derivatives, underpinning its significant potential in [...] Read more.
Laccase, a member of the blue multicopper oxidase family, is widely distributed across diverse taxonomic groups, including fungi, bacteria, plants, and insects. This enzyme drives biocatalytic processes through the oxidation of phenolic compounds, aromatic amines, and lignin derivatives, underpinning its significant potential in the food industry, cosmetics, and environmental remediation. However, wild-type laccases face critical limitations, such as low catalytic efficiency, insufficient expression yields, and poor stability. To address these bottlenecks, this review systematically examines optimization strategies for heterologous laccase expression by fungal and bacterial systems. Additionally, we discuss protein engineering for laccase modification, with a focus on the structural basis and active-site redesign. The comprehensive analysis presented herein provides strategic suggestions for advancing laccase engineering, ultimately establishing a theoretical framework for developing high-efficiency, low-cost engineered variants for large-scale biomanufacturing and green chemistry applications. Full article
(This article belongs to the Section Microbial Biotechnology)
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15 pages, 421 KiB  
Article
Fermentation of Sainfoin Seed Flour with Saccharomyces boulardii: Effects on Total Dietary Fiber, Anti-Nutrients, Antimicrobial Activity, and Bioaccessibility of Bioactive Compounds
by Havva Polat Kaya, Burcu Kaya, Necati Barış Tuncel, Gulay Ozkan, Esra Capanoglu, Seedhabadee Ganeshan and Mehmet Caglar Tulbek
Microorganisms 2025, 13(6), 1421; https://doi.org/10.3390/microorganisms13061421 - 18 Jun 2025
Viewed by 307
Abstract
This study investigates the effects of fermentation on sainfoin seed flour using Saccharomyces boulardii for total dietary fiber (TDF) content, anti-nutritional profiles (including phytates, tannins, saponins, and trypsin inhibitors), and bioactive compounds. It also focused on assessing the in vitro availability of phenolic [...] Read more.
This study investigates the effects of fermentation on sainfoin seed flour using Saccharomyces boulardii for total dietary fiber (TDF) content, anti-nutritional profiles (including phytates, tannins, saponins, and trypsin inhibitors), and bioactive compounds. It also focused on assessing the in vitro availability of phenolic compounds, antioxidant potential, and anti-nutrient compounds after gastrointestinal digestion. Four treatment groups were designed: a non-fermented control group, and flour samples fermented with S. boulardii CNCM I-745 for 24, 48, and 72 h. All fermentations were carried out at 30 °C. The effects of fermentation and the analysis results were statistically evaluated at the significance level of p < 0.05, and significant differences were detected. Fermentation significantly increased soluble dietary fiber (from 3.32% to 4.43%) and reduced anti-nutritional factors, including phytates (by 18%), tannin (by 19%), and trypsin inhibitor activity (TIA) (by 79%). However, saponin content increased by 21% after 72 h of fermentation. Tannin levels of non-fermented and fermented sainfoin flour decreased dramatically after in vitro digestion. Moreover, it was concluded that the bioaccessibility of phytic acid significantly increased through fermentation, while that of tannins declined. Antimicrobial activity against Escherichia coli ATCC 25922 improved after fermentation, while the antioxidant capacity was enhanced post-digestion. In addition, the highest phenolic content (612 mg GAE/100 g) and antioxidant capacity (1745 mg TE/100 g by CUPRAC assay and 1127 mg TE/100 g by DPPH assay) were determined in fermented sainfoin seed flour at 72 h after gastrointestinal digestion. Full article
(This article belongs to the Section Food Microbiology)
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17 pages, 1602 KiB  
Article
Genome Analysis of the Multidrug-Resistant Campylobacter coli BCT3 of the Sequence Type (ST) 872 Isolated from a Pediatric Diarrhea Case
by Konstantinos Papadimitriou, Anastasios Ioannidis, Aleksandra Slavko, Genovefa Chronopoulou, Nektarios Marmaras, Anastasia Pangalis, Elisavet Olntasi, Niki Vassilaki, Efthymia Ioanna Koufogeorgou, Iris Kolida, Dimitrios Theodoridis and Stylianos Chatzipanagiotou
Microorganisms 2025, 13(6), 1420; https://doi.org/10.3390/microorganisms13061420 - 18 Jun 2025
Viewed by 360
Abstract
Campylobacter jejuni and Campylobacter coli are the two main campylobacter species that cause foodborne campylobacteriosis. Recent studies have reported that Campylobacter spp. are prone to developing resistance to antibiotics commonly used for their treatment, with many C. coli strains identified as multidrug-resistant. This [...] Read more.
Campylobacter jejuni and Campylobacter coli are the two main campylobacter species that cause foodborne campylobacteriosis. Recent studies have reported that Campylobacter spp. are prone to developing resistance to antibiotics commonly used for their treatment, with many C. coli strains identified as multidrug-resistant. This study presents the results of the whole-genome sequencing analysis of the multidrug-resistant C. coli strain BCT3 isolated in Greece from a stool specimen of a pediatric patient presenting with diarrhea. The strain was isolated using selective culture media and, based on antimicrobial susceptibility tests, was found to be resistant to ciprofloxacin, tetracycline, erythromycin, azithromycin, clarithromycin, and doxycycline. To further characterize it, we performed whole-genome sequencing, which identified strain BCT3 as C. coli. Moreover, multilocus sequence typing assigned the BCT3 to the sequence type (ST) 872, belonging to clonal complex ST-828. The presence of multiple virulence genes revealed its pathogenic potential. The detection of antimicrobial resistance genes and mutated alleles was indicative of its resistance to fluoroquinolones, macrolides, and tetracyclines, supporting the observed phenotype. To our knowledge, this is the first reported clinical case of such a multidrug-resistant C. coli strain in Greece. Full article
(This article belongs to the Special Issue Human Gut Microbiome, Diets and Health)
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15 pages, 1840 KiB  
Review
A Review of the Epidemiology of Lassa Fever in Nigeria
by Danny Asogun, Bosede Arogundade, Faith Unuabonah, Olorunkemi Olugbenro, Joyce Asogun, Fatelyn Aluede and Deborah Ehichioya
Microorganisms 2025, 13(6), 1419; https://doi.org/10.3390/microorganisms13061419 - 18 Jun 2025
Viewed by 395
Abstract
Lassa fever, a viral hemorrhagic illness that first came into the limelight as a clinical entity in 1969 when it was discovered in Northern Nigeria, is now found in other West African countries such as Sierra Leone, Liberia, Guinea, Togo, and the Benin [...] Read more.
Lassa fever, a viral hemorrhagic illness that first came into the limelight as a clinical entity in 1969 when it was discovered in Northern Nigeria, is now found in other West African countries such as Sierra Leone, Liberia, Guinea, Togo, and the Benin Republic. Over the years, the disease, which is primarily transmitted from contact with infected mastomys rodents to humans, has the capability of secondary human-to-human transmission with significant morbidity and mortality, especially in healthcare settings. The disease is typically characterized by seasonal outbreaks, which peak during the dry season months of December to March. Lassa fever significantly impacts public health and the socioeconomic life of people in affected communities. In Nigeria, the Integrated Disease Surveillance and Response Strategy (IDSR), along with other medical countermeasures, have been employed to curtail the impact of the disease in endemic regions of Nigeria and other West Africa countries. The one-health approach to combat the disease is a promising strategy. This, along with the hope of a safe and effective vaccine, is a ray of hope on the horizon for public health authorities in Nigeria and other West African countries that the battle against Lassa fever might indeed end sooner than later. Full article
(This article belongs to the Special Issue Epidemiology of Hemorrhagic Fever Viruses)
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17 pages, 1400 KiB  
Article
Evaluation of Aspergillus flavus Growth on Weathered HDPE Plastics Contaminated with Diesel Fuel
by Juan Valenzuela, César Sáez-Navarrete, Xavier Baraza, Fernando Martínez and Bastián Márquez
Microorganisms 2025, 13(6), 1418; https://doi.org/10.3390/microorganisms13061418 - 18 Jun 2025
Viewed by 288
Abstract
Plastic containers used for diesel storage represent an underexplored but significant environmental challenge due to hydrocarbon retention and prolonged weathering. This study evaluates the capacity of Aspergillus flavus to colonize and grow on high-density polyethylene (HDPE) surfaces contaminated with weathered and fresh diesel [...] Read more.
Plastic containers used for diesel storage represent an underexplored but significant environmental challenge due to hydrocarbon retention and prolonged weathering. This study evaluates the capacity of Aspergillus flavus to colonize and grow on high-density polyethylene (HDPE) surfaces contaminated with weathered and fresh diesel residues. Circular plastic samples from HDPE tanks exposed to environmental conditions for over two years (weathered) and for less than two months (non-weathered) were inoculated with A. flavus and incubated at 20 °C, 25 °C, and 30 °C. Growth kinetics were assessed through radial expansion and halo formation, quantified via digital imaging and ImageJ analysis. Results showed the most robust fungal growth occurred on weathered diesel-contaminated gray plastics at 30 °C, with colony areas exceeding 350 mm2 and halos over 3000 mm2. Conversely, white HDPE with fresh diesel showed limited and inconsistent growth, likely due to the presence of volatile hydrocarbons and polymer additives. These findings underscore the critical role of diesel aging and polymer characteristics in shaping fungal adaptability, providing a foundation for the development of environmentally sustainable bioremediation strategies targeting diesel-contaminated HDPE plastics. Full article
(This article belongs to the Section Environmental Microbiology)
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15 pages, 1687 KiB  
Article
Detection and Prevalence of Rabies in Bats from Oaxaca
by María Isabel Medina Matías, Margarita García-Luis, Oscar Ezequiel Blanco Esquivel, Israel Nicolás Reyes, Miguel Ángel Domínguez Martínez and Gisela Fuentes-Mascorro
Microorganisms 2025, 13(6), 1417; https://doi.org/10.3390/microorganisms13061417 - 18 Jun 2025
Viewed by 658
Abstract
The rabies virus (genus Lyssavirus), is a deadly zoonotic agent affecting humans and animals. Although Mexico has been declared free of canine rabies (V1), sylvatic rabies persists. This study aimed to determine the prevalence of the virus in Desmodus rotundus and other non-hematophagous [...] Read more.
The rabies virus (genus Lyssavirus), is a deadly zoonotic agent affecting humans and animals. Although Mexico has been declared free of canine rabies (V1), sylvatic rabies persists. This study aimed to determine the prevalence of the virus in Desmodus rotundus and other non-hematophagous bat species in Oaxaca. The methodology comprised four stages: a literature review, data requests to the Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria (SENASICA), fieldwork using mist nets across 15 municipalities in Oaxaca, and diagnosis via direct immunofluorescence at the Centro Nacional de Servicios de Diagnóstico en Salud Animal (CENASA). SENASICA reported 89 positive rabies cases (2014–2023) across six laboratories, with the majority (67.02%) attributed to the Oaxaca State Public Health Laboratory. Among the 194 bats analyzed (129 D. rotundus), only three tested positive for the virus, yielding a prevalence of 1.54%. Positive cases were exclusively identified in D. rotundus from San Lucas Ojitlán and The Heroic City of Tlaxiaco. This prevalence aligns with that of national studies, which ranges from 0.05% to 3%. These findings underscore the need to maintain epidemiological surveillance in wild and domestic fauna, alongside public awareness campaigns highlighting bats’ ecological importance for ecosystem conservation and the risks associated with their decline. Full article
(This article belongs to the Special Issue Rabies Virus: Infections, Reservoirs and Vectors)
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15 pages, 2577 KiB  
Article
Adaptive Laboratory Evolution of a Microbial Consortium Enhancing Non-Protein Nitrogen Assimilation for Feed Protein Production
by Yi He, Shilei Wang, Yifan Mi, Mengyu Liu, Huimin Ren, Zhengxiang Guo, Zhen Chen, Yafan Cai, Jingliang Xu, Dong Liu, Chenjie Zhu, Zhi Wang and Hanjie Ying
Microorganisms 2025, 13(6), 1416; https://doi.org/10.3390/microorganisms13061416 - 18 Jun 2025
Viewed by 393
Abstract
The increasing global demand for protein underscores the necessity for sustainable alternatives to soybean-based animal feed, which poses a challenge to human food security. Thus, the search for sustainable, alternative protein sources is transforming the feed industry in its effort to sustainable operations. [...] Read more.
The increasing global demand for protein underscores the necessity for sustainable alternatives to soybean-based animal feed, which poses a challenge to human food security. Thus, the search for sustainable, alternative protein sources is transforming the feed industry in its effort to sustainable operations. In this study, a microbial consortium was subjected to adaptive laboratory evolution using non-protein nitrogen (NPN) and wheat straw as the sole carbon source. The evolved microbial consortium was subsequently utilized to perform solid-state fermentation on wheat straw and NPN to produce feed protein. After 20 generations, the microbial consortium demonstrated tolerance to 5 g/L NPN, including ammonium sulfate, ammonium chloride, and urea, which represents a fivefold increase compared to the original microbial consortium. Among the three NPNs tested, the evolved microbial consortium exhibited optimal growth performance with ammonium sulfate. Subsequently, the evolved microbial consortium was employed for the solid-state fermentation (SSF) of wheat straw, and the fermentation conditions were optimized. It was found that the true protein content of wheat straw could be increased from 2.74% to 10.42% under specific conditions: ammoniated wheat straw (15% w/w), non-sterilization of the substrate, an inoculation amount of 15% (v/w), nitrogen addition amount of 0.5% (w/w), an initial moisture content of 70%, a fermentation temperature of 30 °C, and a fermentation duration of 10 days. Finally, the SSF process for wheat straw was successfully scaled up from 0.04 to 2.5 kg, resulting in an increased true protein content of 9.84%. This study provides a promising approach for the production of feed protein from straw and NPN through microbial fermentation, addressing protein resource shortages in animal feed and improving the value of waste straw. Full article
(This article belongs to the Special Issue Microbial-Sourced Nutritional Supplements for Human and Animal)
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12 pages, 820 KiB  
Article
Prevalence, Antimicrobial Resistance Profile, and Genetic Characteristics of Methicillin-Resistant Staphylococcus aureus Isolated from Retail Raw Fish in South Korea
by Haiseong Kang, Jonghoon Lee, Ji Min Han, Yong hoon Kim, Insun Joo and Hyochin Kim
Microorganisms 2025, 13(6), 1415; https://doi.org/10.3390/microorganisms13061415 - 17 Jun 2025
Viewed by 387
Abstract
Given the limited genetic characterization of methicillin-resistant Staphylococcus aureus (MRSA) in South Korea, we performed whole-genome sequencing (WGS) on eight MRSA strains isolated from raw fish products, including 327 sliced raw flatfish, 111 flatfish stew products, 85 sliced raw rockfish, and 11 rockfish [...] Read more.
Given the limited genetic characterization of methicillin-resistant Staphylococcus aureus (MRSA) in South Korea, we performed whole-genome sequencing (WGS) on eight MRSA strains isolated from raw fish products, including 327 sliced raw flatfish, 111 flatfish stew products, 85 sliced raw rockfish, and 11 rockfish stew products. Phylogenetic analysis revealed two distinct clusters—comprising five ST72-t324-SCCmecIVc strains and two novel sequence types—as well as a singleton strain (ST630-t4549-SCCmecV). A total of five antimicrobial resistance genes (ARGs), four plasmid replicon genes, three mobile genetic element genes, and seventy-three virulence factor genes were identified, with distinct genetic profiles observed between the clusters. Notably, several MRSA strains were isolated from samples obtained at the same retail market, indicating potential local clustering. Four ST72-t324-SCCmecIVc strains, collected from the same market, shared identical profiles in terms of four ARGs, two plasmid replicons, two mobile genetic elements, and several virulence factor genes. These findings provide valuable insights into the genomic characteristics of MRSA in raw fish products and highlight the need for ongoing surveillance and monitoring efforts in South Korea. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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15 pages, 3010 KiB  
Article
Effects of Years of Operation of Photovoltaic Panels on the Composition and Diversity of Soil Bacterial Communities in Rocky Desertification Areas
by Wenjiao Gao, Yungen Liu, Jun Hu, Zhifeng Luo, Jiaxu Zhang and Yan Wang
Microorganisms 2025, 13(6), 1414; https://doi.org/10.3390/microorganisms13061414 - 17 Jun 2025
Viewed by 353
Abstract
Soil bacterial community composition and diversity can be an important bioindicator for assessing ecosystem stability, and photovoltaic (PV) shading is a key factor influencing soil bacterial communities in rocky desertification areas; however, how the composition and diversity of soil bacterial communities change with [...] Read more.
Soil bacterial community composition and diversity can be an important bioindicator for assessing ecosystem stability, and photovoltaic (PV) shading is a key factor influencing soil bacterial communities in rocky desertification areas; however, how the composition and diversity of soil bacterial communities change with PV operation duration remains unclear. Focusing on the experimental demonstration site of Shilin ecological photovoltaic (PV) power plant in Yunnan Province, we compared soil properties under PV arrays and non-PV control areas with different operation durations (7 and 13 years). The results showed that long-term PV operation significantly increased soil TN and TK content compared to CK, while increasing Ure and ALP activities, but inhibiting CAT activity and decreasing soil moisture, pH, SOC, and TP. High-throughput sequencing revealed stable dominant bacterial phyla (e.g., Aspergillus, Acidobacteriota) and beneficial genera (e.g., RB41, Sphingomonas), with an increase in relative abundance of Bacillota-like phyla but a decrease in Acidobacterium. The α-diversity (ACE, Chao1 index) and β-diversity of soil bacteria greatly increased with years of PV operation, reaching a maximum in the 13-year PV operation area. Correlation analyses showed that differences in soil bacterial communities in regions with different years of PV operation were mainly influenced by differences in PH and enzyme activities. Full article
(This article belongs to the Section Environmental Microbiology)
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17 pages, 5545 KiB  
Article
A Comprehensive Investigation of Potential Bacterial Pathogens in Largemouth Bass (Micropterus salmoides)
by Yun-Yao Tu, Qun Lu, Na Zhang, Jie Leng, Qin Yang, Jie Yu, Cheng-Ke Zhu, Tao He, Jian-Yong Hu, Ming-Ji Lv and Song Zhu
Microorganisms 2025, 13(6), 1413; https://doi.org/10.3390/microorganisms13061413 - 17 Jun 2025
Viewed by 397
Abstract
In the study, a comprehensive investigation on potential bacterial pathogens affecting largemouth bass (Micropterus salmoides) was performed. Monthly surveys were conducted from April to October 2024. Diseased largemouth bass exhibited diverse clinical symptoms, such as rot of gill and fin, ulcers [...] Read more.
In the study, a comprehensive investigation on potential bacterial pathogens affecting largemouth bass (Micropterus salmoides) was performed. Monthly surveys were conducted from April to October 2024. Diseased largemouth bass exhibited diverse clinical symptoms, such as rot of gill and fin, ulcers on body surface, and petechial hemorrhages in liver. Following isolation and identification, a total of 21 potential bacterial pathogens (numbered strain 1 to 21, respectively) were identified. The genus Aeromonas had the highest proportion (67.14%), among which the frequency of Aeromonas veronii was 24.60%. TEM analysis revealed that the bacterial strains exhibited three predominant shapes (rod-shaped, spherical, and curved) with length ranging from 0.5 to 3 μm. Flagellar structures were observed in strains 1–4, 6–8, 11–17, and 19–21, with variations in number and growth sites. Three isolates (strains 9, 10, 18) demonstrated Gram-positive characteristic, and strains 5, 11, and 18 have capsule structures. Strains 5, 9, 10, and 18 were non-motile, and strains 1–4, 6, 7, 9–11, 16–18, and 21 exhibited β-hemolysis. Physiological and biochemical characteristics of the 21 bacterial isolates were comprehensively analyzed. Antibiotic sensitivity testing revealed that florfenicol and enrofloxacin exhibited excellent antibacterial effects. These data will enrich the potential bacterial diseases information and promote the healthy development of the largemouth bass industry. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)
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20 pages, 3756 KiB  
Article
Reducing Cd Uptake by Wheat Through Rhizosphere Soil N-C Cycling and Bacterial Community Modulation by Urease-Producing Bacteria and Organo-Fe Hydroxide Coprecipitates
by Junqing Zhang, Shuangjiao Tang, Hao Wei, Lunguang Yao, Zhaojin Chen, Hui Han, Mingfei Ji and Jianjun Yang
Microorganisms 2025, 13(6), 1412; https://doi.org/10.3390/microorganisms13061412 - 17 Jun 2025
Viewed by 370
Abstract
The bioavailability of heavy metals is profoundly influenced by their interactions with active soil components (microorganisms, organic matter, and iron minerals). However, the effects of urease-producing bacteria combined with organo-Fe hydroxide coprecipitates (OFCs) on Cd accumulation in wheat, as well as the mechanisms [...] Read more.
The bioavailability of heavy metals is profoundly influenced by their interactions with active soil components (microorganisms, organic matter, and iron minerals). However, the effects of urease-producing bacteria combined with organo-Fe hydroxide coprecipitates (OFCs) on Cd accumulation in wheat, as well as the mechanisms underlying these effects, remain unclear. In this study, pot experiments integrated with high-throughput sequencing were employed to investigate the impacts of the urease-producing bacterial strain TJ6, ferrihydrite (Fh), and OFCs on Cd enrichment in wheat grains, alongside the underlying soil–microbial mechanisms. The results demonstrate that the strain TJ6-Fh/OFC consortium significantly (p < 0.05) reduced (50.1–66.7%) the bioavailable Cd content in rhizosphere soil while increasing residual Cd fractions, thereby decreasing (77.4%) Cd accumulation in grains. The combined amendments elevated rhizosphere pH (7.35), iron oxide content, and electrical conductivity while reducing (14.5–21.1%) dissolved organic carbon levels. These changes enhanced soil-colloid-mediated Cd immobilization and reduced Cd mobility. Notably, the NH4+ content and NH4+/NO3− ratio were significantly (p < 0.05) increased, attributed to the ureolytic activity of TJ6, which concurrently alkalinized the soil and inhibited Cd uptake via competitive ion channel interactions. Furthermore, the relative abundance of functional bacterial taxa (Proteobacteria, Gemmatimonadota, Enterobacter, Rhodanobacter, Massilia, Nocardioides, and Arthrobacter) was markedly increased in the rhizosphere soil. These microbes exhibited enhanced abilities to produce extracellular polymeric substances, induce phosphate precipitation, facilitate biosorption, and promote nutrient (C/N) cycling, synergizing with the amendments to immobilize Cd. This study for the first time analyzed the effect and soil science mechanism of urease-producing bacteria combined with OFCs in blocking wheat’s absorption of Cd. Moreover, this study provides foundational insights and a practical framework for the remediation of Cd-contaminated wheat fields through microbial–organic–mineral collaborative strategies. Full article
(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture, Second Edition)
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24 pages, 393 KiB  
Review
New Trends in Sexually Transmitted Infections Among Adolescents and Young People: Epidemiology, Clinical and Diagnostic Management
by Nunzia Zanotta, Nicole West, Carolina Cason, Stefania degli Ivanissevich, Alessia Meneghel, Francesco Righi, Laura Brunelli, Alessandra Casuccio, Silvia Gazzetta, Daniele Gianfrilli, Teresa Maria Assunta Fasciana, Maria Cristina Salfa, Franz Sesti, Barbara Suligoi, Francesca Valent, ESPRIT Study Collaboration Group and Manola Comar
Microorganisms 2025, 13(6), 1411; https://doi.org/10.3390/microorganisms13061411 - 17 Jun 2025
Viewed by 541
Abstract
Sexually transmitted infections (STIs) are a significant public health issue, especially among adolescents and young adults. Despite improvements in diagnostic tools and treatments, over 1 million new STIs occur daily worldwide, many of which are asymptomatic. These infections can severely affect quality of [...] Read more.
Sexually transmitted infections (STIs) are a significant public health issue, especially among adolescents and young adults. Despite improvements in diagnostic tools and treatments, over 1 million new STIs occur daily worldwide, many of which are asymptomatic. These infections can severely affect quality of life and reproductive health, particularly when contracted at a young age. This review provides an overview of STIs’ recent epidemiology data, clinical trends, and diagnostic challenges in Italian adolescents and young adults, focusing on the Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, Thricomonas vaginalis, and Mycoplasma/Ureaplasma species. Worrying new evidence indicates that young women are at a higher risk of contracting STIs than men and multidrug-resistant strains have increased in young heterosexuals. This evidence shows a general change in lifestyle, where a lack of awareness about the risks of STI reflects a significant educational gap. To address the rising STI rates, targeted school educational interventions and innovative multidisciplinary healthcare models, such as the hub-and-spoke approach, are needed. Full article
(This article belongs to the Section Medical Microbiology)
20 pages, 1053 KiB  
Review
The Interplay Between the Gut Microbiota and Colorectal Cancer: A Review of the Literature
by Marco Cintoni, Marta Palombaro, Eleonora Zoli, Giuseppe D’Agostino, Gabriele Pulcini, Elena Leonardi, Pauline Raoul, Emanuele Rinninella, Flavio De Maio, Esmeralda Capristo, Antonio Gasbarrini and Maria Cristina Mele
Microorganisms 2025, 13(6), 1410; https://doi.org/10.3390/microorganisms13061410 - 17 Jun 2025
Viewed by 594
Abstract
Lifestyle, diet, and genetics are established risk factors for developing colorectal cancer (CRC). In recent years, the role of the gut microbiota (GM) has been increasingly highlighted in several studies, suggesting an effect on both the disease’s pathogenesis and the efficacy and tolerability [...] Read more.
Lifestyle, diet, and genetics are established risk factors for developing colorectal cancer (CRC). In recent years, the role of the gut microbiota (GM) has been increasingly highlighted in several studies, suggesting an effect on both the disease’s pathogenesis and the efficacy and tolerability of treatments. We conducted a search on Medline, aiming to identify published studies exploring the role of the GM in the development and treatment of CRC. Dysbiosis, an imbalance in GM, is common in CRC patients and is associated with precancerous lesions, aggressive tumors, and varied therapy outcomes. Restoring GM balance can reduce treatment complications and may improve prognosis. The review details how GM influences CRC through metabolite production, inflammation modulation, and immune response alteration. Diet significantly impacts GM composition, with processed meats and high-fat diets increasing CRC risk, while fiber-rich diets are protective. The role of the GM in CRC treatments like surgery, chemotherapy, radiotherapy, and immunotherapy is also explored, noting its influence on complications, chemoresistance, and treatment efficacy. Future strategies involving GM modulation through diet, probiotics, and fecal microbiota transplantation (FMT) show promise for CRC prevention and treatment, warranting further research. Full article
(This article belongs to the Special Issue Gut Microbiota, Diet, and Gastrointestinal Cancer)
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18 pages, 2333 KiB  
Article
Molecular Structure and Biosynthesis of Pyoverdines Produced by Pseudomonas fulva
by Eri Ochiai, Takeru Kawabe, Masafumi Shionyu and Makoto Hasegawa
Microorganisms 2025, 13(6), 1409; https://doi.org/10.3390/microorganisms13061409 - 17 Jun 2025
Viewed by 324
Abstract
This study explored the biosynthetic mechanisms and structural diversity of pyoverdines (PVDs) produced by Pseudomonas fulva. Genomic analysis using antiSMASH identified the PVD biosynthetic gene cluster, although the C-terminal peptide sequence could not be predicted. Subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) [...] Read more.
This study explored the biosynthetic mechanisms and structural diversity of pyoverdines (PVDs) produced by Pseudomonas fulva. Genomic analysis using antiSMASH identified the PVD biosynthetic gene cluster, although the C-terminal peptide sequence could not be predicted. Subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis revealed the full peptide structure, including modified residues, such as N-acetylhydroxyornithine and cyclohydroxyornithine, and confirmed the presence of several PVD isoforms with different chromophore side chains. Comparative LC-MS analysis across Pseudomonas species demonstrated that P. fulva produces unique PVD molecular mass patterns. The bioinformatic and structural modeling of non-ribosomal peptide synthetase PvdL open reading frame 3 revealed that the A2 and A3 adenylation domains are lysine selective. Although their sequences differ from known lysine-specific signatures, AlphaFold3-based structural prediction revealed conserved substrate-binding configurations, suggesting that similar substrate-binding features may have arisen independently. Notably, Thr297, a unique residue in the non-ribosomal code, likely plays a key role in lysine recognition. The high degree of sequence similarity between the A2 and A3 domains may reflect domain duplication and could be involved in the diversification of the PVD structure. Further functional and ecological studies are required to assess the physiological significance of P. fulva PVDs in microbial iron acquisition. Full article
(This article belongs to the Section Environmental Microbiology)
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21 pages, 1894 KiB  
Article
Optimizing Cocoa Productivity Through Soil Health and Microbiome Enhancement: Insights from Organic Amendments and a Locally Derived Biofertilizer
by Jennifer E. Schmidt, Julia Flores, Luigy Barragan, Freddy Amores, Jr. and Sat Darshan S. Khalsa
Microorganisms 2025, 13(6), 1408; https://doi.org/10.3390/microorganisms13061408 - 17 Jun 2025
Viewed by 415
Abstract
Despite growing interest in improving soil health on cocoa farms, applied research on the impacts of specific amendments on soil and plant outcomes is lacking. An integrated assessment of the impacts of two different organic amendments (compost and vermicompost) and a microbial biofertilizer [...] Read more.
Despite growing interest in improving soil health on cocoa farms, applied research on the impacts of specific amendments on soil and plant outcomes is lacking. An integrated assessment of the impacts of two different organic amendments (compost and vermicompost) and a microbial biofertilizer on soil physical, chemical, and biological properties, as well as cocoa flowering, fruit set, and yield, was conducted in Guayaquil, Ecuador. Complementary culture-dependent and culture-independent methods were used to assess the impacts of amendments on microbial diversity, community composition, and specific taxa. Compost or vermicompost application affected soil chemical properties, including potassium, phosphorus, and sodium, and had small but significant effects on fungal beta diversity. Biofertilizer application slightly lowered soil pH and altered the total abundance of specific taxonomic groups including Azotobacter sp. and Trichoderma sp., with borderline significant effects on Azospirillum sp., Lactobacillus sp., Pseudomonas sp., calcium-solubilizing bacteria, and phosphorus-solubilizing bacteria. Amplicon sequencing (16S, ITS) identified 15 prokaryotic and 68 fungal taxa whose relative abundance was influenced by organic amendments or biofertilizer. Biofertilizer application increased cherelle formation by 19% and monthly harvestable pod counts by 11% despite no impact on flowering index or annual pod totals. This study highlights the tangible potential of microbiome optimization to simultaneously improve on-farm yield and achieve soil health goals on cocoa farms. Full article
(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture, Second Edition)
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22 pages, 1052 KiB  
Review
Antimicrobial Photodynamic Therapy for Superficial, Skin, and Mucosal Fungal Infections: An Update
by Laura Beatriz Borim da Silva, Ivana Giovannetti Castilho, Fabiana Alves de Souza Silva, Mahmoud Ghannoum, Maíra Terra Garcia and Paulo Henrique Fonseca do Carmo
Microorganisms 2025, 13(6), 1406; https://doi.org/10.3390/microorganisms13061406 - 17 Jun 2025
Viewed by 475
Abstract
The global burden of fungal infections is rising at an alarming rate, with superficial, cutaneous, and mucosal mycoses among the most prevalent. Conventional treatments rely on oral and topical antifungal agents; however, these therapies are often limited by adverse effects, toxicity, frequent recurrence, [...] Read more.
The global burden of fungal infections is rising at an alarming rate, with superficial, cutaneous, and mucosal mycoses among the most prevalent. Conventional treatments rely on oral and topical antifungal agents; however, these therapies are often limited by adverse effects, toxicity, frequent recurrence, and poor patient adherence due to prolonged treatment regimens. Moreover, the emergence of antifungal resistance and multidrug-resistant species such as Candidozyma auris and Trichophyton indotineae highlights the urgent need for alternative therapeutic strategies, such as antimicrobial photodynamic therapy (aPDT). aPDT is based on photophysical and photochemical processes involving a photosensitizer (PS), a light source, and molecular oxygen. When combined, these elements generate reactive oxygen species that selectively destroy microbial cells. In this review, we explore various PSs and their effectiveness in aPDT against infections caused by dermatophytes, Candida spp., and other pathogenic fungi. Promisingly, aPDT has demonstrated antifungal activity against both susceptible and resistant strains. In addition, aPDT has been successfully used in cases of mycoses unresponsive to conventional therapies, showing favorable clinical outcomes and overall safety. Current evidence supports aPDT as a valuable strategy for the management of cutaneous, mucosal, and superficial fungal infections and as a potential strategy to combat antifungal resistance. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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16 pages, 2408 KiB  
Article
Bacteriome Signature in SARS-CoV-2-Infected Patients Correlates with Increased Gut Permeability and Systemic Inflammatory Cytokines
by Larissa S. Souza, Alexandre S. Ferreira-Junior, Pedro C. Estella, Ricardo K. Noda, Lhorena F. Sousa, Miguel T. Y. Murata, Lucas A. L. Carvalho, João L. Brisotti, Daniel G. Pinheiro, Josias Rodrigues, Carlos M. C. B. Fortaleza and Gislane L. V. de Oliveira
Microorganisms 2025, 13(6), 1407; https://doi.org/10.3390/microorganisms13061407 - 16 Jun 2025
Viewed by 553
Abstract
The COVID-19 pandemic has highlighted the complex interplay between the gut microbiota and systemic immune responses, particularly through the gut–lung axis. Disruptions in gut microbial diversity and function—commonly referred to as dysbiosis—have been increasingly implicated in the pathogenesis of SARS-CoV-2 infection. In this [...] Read more.
The COVID-19 pandemic has highlighted the complex interplay between the gut microbiota and systemic immune responses, particularly through the gut–lung axis. Disruptions in gut microbial diversity and function—commonly referred to as dysbiosis—have been increasingly implicated in the pathogenesis of SARS-CoV-2 infection. In this study, we assessed the gut bacteriome and permeability in SARS-CoV-2-infected patients using 16S sequencing and ELISA assays, respectively. We also measured blood inflammatory cytokines and fecal secretory IgA to evaluate systemic and mucosal immune responses. Significant alterations in both alpha and beta diversity metrics were observed in patients with COVID-19 (n = 79) and those with post-COVID-19 condition (n = 141) compared to the controls (n = 97). Differential abundance and taxonomic analyses revealed distinct microbial profiles in the infected groups. Increased plasma levels of IL-2, IL-6, IL-17A, IFN-γ, and zonulin were detected in patient samples. Some genera were elevated during acute infection, which was positively correlated with C-reactive protein, while Enterobacteriaceae and Escherichia-Shigella were associated with increased zonulin levels, indicating compromised intestinal barrier function. These findings suggest that gut dysbiosis may contribute to bacterial translocation and systemic inflammation. Overall, our results highlight the importance of the gut–lung axis and suggest that modulating the gut microbiota could support immune regulation in SARS-CoV-2 infection. Full article
(This article belongs to the Special Issue Correlations Between the Gastrointestinal Microbiome and Diseases)
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15 pages, 1043 KiB  
Article
Clinical Characteristics and Outcomes in Multisystemic Inflammatory Syndrome in Children (MIS-C) Associated with COVID-19: A 12-Month Prospective Study
by Viorela Gabriela Nitescu, Diana-Andreea Usurelu, Teodora Olsavszky, Ana-Maria Mihalcea, Andra Postelnicu, Ruxandra Florea, Simona Stanca, Iolanda Cristina Vivisenco, Madalina Elena Petran, Maria-Dorina Craciun, Carmen-Daniela Chivu, Alexandru Ulici and Coriolan Emil Ulmeanu
Microorganisms 2025, 13(6), 1405; https://doi.org/10.3390/microorganisms13061405 - 16 Jun 2025
Viewed by 400
Abstract
Multisystemic inflammatory syndrome in children (MIS-C) is a rare but potentially severe condition that affects multiple organ systems. This study aimed to assess the clinical characteristics and outcomes of patients diagnosed with multisystemic inflammatory syndrome in children (MIS-C) associated with COVID-19. A 12-month [...] Read more.
Multisystemic inflammatory syndrome in children (MIS-C) is a rare but potentially severe condition that affects multiple organ systems. This study aimed to assess the clinical characteristics and outcomes of patients diagnosed with multisystemic inflammatory syndrome in children (MIS-C) associated with COVID-19. A 12-month prospective study was conducted at the “Grigore Alexandrescu” Clinical Emergency Hospital for Children, Bucharest. This study included children aged 0–18 years who were diagnosed with MIS-C, as defined by the World Health Organization (WHO), the Royal College of Paediatrics and Child Health (RCPCH), and the Centers for Disease Control and Prevention (CDC) criteria. Data on age, gender, clinical and laboratory findings, treatment, and outcomes were analyzed. Follow-up evaluations occurred at one, three, six, nine, and twelve months post-discharge. Among 36 patients (47.3% female, 52.7% male; mean age, 9.9 years), fever and inflammatory syndrome were present in all patients. Other common symptoms included mucocutaneous (63.8%), gastrointestinal (52.7%), cardiac (47.2%), pulmonary (38.8%), and neurological (11.1%) manifestations. At admission, 14/36 were IgM-positive, while 34/36 were IgG-positive. Follow-up revealed sequelae in two patients, including coronary aneurysms and ground-glass pulmonary opacities. Although MIS-C can be severe, most patients had favorable outcomes with proper treatment. Few long-term, organ-specific complications were observed, highlighting the importance of systematic monitoring to ensure full recovery. Full article
(This article belongs to the Special Issue Infectious Disease Surveillance in Romania)
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18 pages, 2791 KiB  
Article
Assessment of Biodegradation Mechanisms of Ceftiofur Sodium by Escherichia sp. CS-1 and Insights from Transcriptomic Analysis
by Meng-Yang Yan, Cai-Hong Zhao, Jie Wu, Adil Mohammad, Yi-Tao Li, Liang-Bo Liu, Yi-Bo Cao, Xing-Mei Deng, Jia Guo, Hui Zhang, Hong-Su He and Zhi-Hua Sun
Microorganisms 2025, 13(6), 1404; https://doi.org/10.3390/microorganisms13061404 - 16 Jun 2025
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Abstract
Ceftiofur sodium (CFS) is a clinically significant cephalosporin widely used in the livestock and poultry industries. However, CFS that is not absorbed by animals is excreted in feces, entering the environment and contributing to the emergence of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes [...] Read more.
Ceftiofur sodium (CFS) is a clinically significant cephalosporin widely used in the livestock and poultry industries. However, CFS that is not absorbed by animals is excreted in feces, entering the environment and contributing to the emergence of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs). This situation poses substantial challenges to both environmental integrity and public health. Currently, research on the biodegradation of CFS is limited. In this study, we isolated a strain of Escherichia coli, designated E. coli CS-1, a Gram-negative, rod-shaped bacterium capable of utilizing CFS as its sole carbon source, from fecal samples collected from hog farms. We investigated the effects of initial CFS concentration, pH, temperature, and inoculum size on the degradation of CFS by E. coli CS-1 through a series of single-factor experiments conducted under aerobic conditions. The results indicated that E. coli CS-1 achieved the highest CFS degradation rate under the following optimal conditions: an initial CFS concentration of 50 mg/L, a pH of 7.0, a temperature of 37 °C, and an inoculum size of 6% (volume fraction). Under these conditions, E. coli CS-1 was able to completely degrade CFS within 60 h. Additionally, E. coli CS-1 exhibited significant capabilities for CFS degradation. In this study, six major degradation products of (CFS) were identified by UPLC–MS/MS: desfuroyl ceftiofur, 5-hydroxymethyl-2-furaldehyde, 7-aminodesacetoxycephalosporanic acid, 5-hydroxy-2-furoic acid, 2-furoic acid, and CEF-aldehyde. Based on these findings, two degradation pathways are proposed. Pathway I: CFS is hydrolyzed to break the sulfur–carbon (S–C) bond, generating two products. These products undergo subsequent hydrolysis and redox reactions for gradual transformation. Pathway II: The β-lactam bond of CFS is enzymatically cleaved, forming CEF-aldehyde as the primary degradation product, which is consistent with the biodegradation mechanism of most β-lactam antibiotics via β-lactam ring cleavage. Transcriptome sequencing revealed that 758 genes essential for degradation were upregulated in response to the hydrolysis and redox processes associated with CFS. Furthermore, the differentially expressed genes (DEGs) of E. coli CS-1 were functionally annotated using a combination of genomics and bioinformatics approaches. This study highlights the potential of E. coli CS-1 to degrade CFS in the environment and proposes hypotheses regarding the possible biodegradation mechanisms of CFS for future research. Full article
(This article belongs to the Special Issue Antibiotic and Resistance Gene Pollution in the Environment)
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