Microorganisms

19 pages, 3082 KiB

Open AccessArticle

Pharmacologic Inhibition of Erythrocyte Ferroportin Expression Exacerbates Plasmodium Infection

by Sareh Zeydabadinejad, Benjamin Frederick Theis, Jun Sung Park, Amira F. Gohara, Matam Vijay-Kumar, Beng San Yeoh and Piu Saha

Microorganisms 2025, 13(8), 1859; https://doi.org/10.3390/microorganisms13081859 - 8 Aug 2025

Abstract

Plasmodium parasites rely on host iron for survival and replication, making host iron availability a critical determinant of malaria pathogenesis. Central to iron homeostasis is the hepcidin–ferroportin regulatory axis, where hepcidin suppresses iron export by inducing ferroportin degradation, thus modulating systemic and cellular [...] Read more.

Plasmodium parasites rely on host iron for survival and replication, making host iron availability a critical determinant of malaria pathogenesis. Central to iron homeostasis is the hepcidin–ferroportin regulatory axis, where hepcidin suppresses iron export by inducing ferroportin degradation, thus modulating systemic and cellular iron availability. In the Plasmodium infection model (P. yoelii), we observed a significant downregulation of hepatic hepcidin expression, accompanied by an increase in hepatic ferroportin expression. On the contrary, RBC-ferroportin protein level was notably suppressed upon P. yoelii infection. Given these findings, we aim to investigate the role of a ferroportin inhibitor in Plasmodium infection. In a P. yoelii mouse model, treatment with an oral ferroportin inhibitor, VIT-2763 (Vamifeport) increased parasitemia, accompanied by increased levels of pro-inflammatory cytokines, erythropoietin, and liver injury markers. In P. yoelii infected mice, VIT-2763 treatment suppressed hepcidin expression and increased ferroportin expression in hepatocytes, while reducing ferroportin protein levels in RBCs. VIT-2763 mediated exacerbation of P. yoelii infection reveals the tissue-specific regulation of ferroportin in hepatocytes and RBCs, underscoring the therapeutic potential of modulating the hepcidin–ferroportin axis as an intervention strategy in malaria. Full article

(This article belongs to the Special Issue Latest Research in Parasitology: Unlocking Mechanisms, Developing Solutions)

16 pages, 944 KiB

Open AccessArticle

Efficacy of Lactobacillus rhamnosus and Its Metabolites to Mitigate the Risk of Foodborne Pathogens in Hydroponic Nutrient Solution

by Esther Oginni, Robin Choudhury and Veerachandra Yemmireddy

Microorganisms 2025, 13(8), 1858; https://doi.org/10.3390/microorganisms13081858 - 8 Aug 2025

Abstract

Hydroponic nutrient solution (HNS) has been established as an ideal conduit for pathogen contamination and proliferation. This study evaluated the efficacy of lactic acid bacteria and their metabolites in mitigating the risk of foodborne pathogens in HNS when compared to conventional chemical treatments. [...] Read more.

Hydroponic nutrient solution (HNS) has been established as an ideal conduit for pathogen contamination and proliferation. This study evaluated the efficacy of lactic acid bacteria and their metabolites in mitigating the risk of foodborne pathogens in HNS when compared to conventional chemical treatments. Hoagland’s HNS were prepared according to the manufacturer’s instructions and inoculated with Salmonella Typhimurium, Escherichia coli 0157:H7, and Listeria innocua at 10⁵ CFU/mL cell concentration. These nutrient solutions were subjected to treatment with various concentrations of Lactobacillus rhamnosus live cells, a cell-free extract (CFE) of L. rhamnosus metabolites, sodium hypochlorite and peroxyacetic acid at 22 ± 1 °C for up to 96 h using appropriate controls. The survived cells were enumerated on respective selective media at regular intervals. Additionally, the impact of these treatments on lettuce growth and the physico-chemical properties of HNS, such as pH, electrical conductivity, salinity, total dissolved solids, and % lactic acid content, were determined over 21 days using standard procedures. Both S. Typhimurium and E. coli O157: H7, when in combination with L. rhamnosus, remained stable in HNS over a 96 h period, while L. innocua showed a 3-log reduction. Whereas CFE treatment of HNS showed a significant reduction in Salmonella and E. coli O157: H7 (both undetectable after 96 h; LOD: <1 log CFU/mL). Interestingly, L. innocua levels remained stable after CFE treatment. PAA treatments at 12 mg/L notably reduced Salmonella and L. innocua growth, but not E. coli O157:H7. Lettuce plants in untreated control were significantly taller and heavier compared to those treated with CFE. These findings highlight the potential of biological interventions while emphasizing their limitations in hydroponic systems for pathogen control. Full article

(This article belongs to the Special Issue Feature Papers in Food Microbiology)

31 pages, 9922 KiB

Open AccessArticle

Integrated Microbiome–Metabolome Analysis and Functional Strain Validation Reveal Key Biochemical Transformations During Pu-erh Tea Pile Fermentation

by Mengkai Hu, Huimin Zhang, Leisa Han, Wenfang Zhang, Xinhui Xing, Yi Wang, Shujian Ou, Yan Liu, Xiangfei Li and Zhenglian Xue

Microorganisms 2025, 13(8), 1857; https://doi.org/10.3390/microorganisms13081857 - 8 Aug 2025

Abstract

Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria [...] Read more.

Fermentation plays a pivotal role in shaping the flavor and overall quality of Pu-erh tea, a microbially fermented dark tea. Here, we monitored physicochemical properties, chemical constituents, and microbial succession at 15 fermentation time points. Amplicon sequencing identified Staphylococcus, Bacillus, Kocuria, Aspergillus, Blastobotrys, Thermomyces, and Rasamsonia as dominant genera, with prokaryotic communities showing greater richness and diversity than eukaryotic ones. Beta diversity and clustering analyses revealed stable microbial structures during late fermentation stages. Non-targeted metabolomics detected 347 metabolites, including 56 significantly differential compounds enriched in caffeine metabolism and unsaturated fatty acid biosynthesis. Fermentation phases exhibited distinct metabolic patterns, with volatile aroma compounds (2-acetyl-1-pyrroline, 2,5-dimethylpyrazine) and health-beneficial fatty acids (linoleic acid, arachidonic acid) accumulating in later stages. OPLS-DA and KEGG PATHWAY analyses confirmed significant shifts in metabolite profiles relevant to flavor and biofunctionality. RDA revealed strong correlations between microbial taxa, environmental parameters, and representative metabolites. To functionally verify microbial contributions, 17 bacterial and 10 fungal strains were isolated. Six representative strains, mainly Bacillus and Aspergillus, exhibited high enzymatic activity on macromolecules, confirming their roles in polysaccharide and protein degradation. This integrative multi-omics investigation provides mechanistic insights into Pu-erh tea fermentation and offers a scientific basis for microbial community optimization in tea processing. Full article

(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)

19 pages, 2244 KiB

Open AccessArticle

Swift Realisation of Wastewater-Based SARS-CoV-2 Surveillance for Aircraft and Airports: Challenges from Sampling to Variant Detection

by Cristina J. Saravia, Kira Zachmann, Natalie Marquar, Ulrike Braun, Claus Gerhard Bannick, Timo Greiner, Peter Pütz, Susanne Lackner and Shelesh Agrawal

Microorganisms 2025, 13(8), 1856; https://doi.org/10.3390/microorganisms13081856 - 8 Aug 2025

Abstract

International air traffic has contributed to the global spread of SARS-CoV-2 and its variants. In early 2023, wastewater-based epidemiology (WBE) has been implemented at airports as a surveillance tool to detect emerging variants at short notice. This study investigates the feasibility and challenges [...] Read more.

International air traffic has contributed to the global spread of SARS-CoV-2 and its variants. In early 2023, wastewater-based epidemiology (WBE) has been implemented at airports as a surveillance tool to detect emerging variants at short notice. This study investigates the feasibility and challenges of applying WBE at Berlin Brandenburg (BER) Airport, including a rapid implementation of wastewater sampling and analysis under unprecedented circumstances. For this purpose, aircraft and airport wastewater was sampled over 13 weeks. Established sampling and analysis protocols for municipal wastewater treatment plants (WWTPs) had to be adapted to the specific conditions of the airport environment. SARS-CoV-2 RNA was quantified and sequenced, revealing SARS-CoV-2 mutations not previously observed in clinical surveillance data in Germany. Despite the logistical and methodological challenges, the study demonstrates that WBE can serve as an early warning system for pathogen introduction. However, our study also underscores the need for realistic timelines for the establishment and validation of WBE monitoring strategies in new contexts. Investments in the establishment of WBE systems, e.g., infrastructure, protocols, trained personnel, and a network of stakeholders at strategic nodes including airports, can act as an effective tool for pandemic preparedness and global health security. Full article

(This article belongs to the Special Issue Surveillance of SARS-CoV-2 Employing Wastewater)

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8 pages, 518 KiB

Open AccessCase Report

Cervical Actinomycosis Diagnosed via Metagenomic Next-Generation Sequencing of Formalin-Fixed Paraffin-Embedded Tissue: A Case Report and Literature Review

by Teresa K. F. Wang, Hin-Fung Tsang, Sze Chuen Cesar Wong and Stanley W. M. Leung

Microorganisms 2025, 13(8), 1855; https://doi.org/10.3390/microorganisms13081855 - 8 Aug 2025

Abstract

Actinomycosis is an uncommon but significant chronic bacterial infection affecting various parts of the body caused by Actinomyces species. Because of the nonspecific symptoms and rarity of the condition, the diagnosis of head-and-neck or cervicofacial actinomycosis is usually challenging and delayed. A 39-year-old [...] Read more.

Actinomycosis is an uncommon but significant chronic bacterial infection affecting various parts of the body caused by Actinomyces species. Because of the nonspecific symptoms and rarity of the condition, the diagnosis of head-and-neck or cervicofacial actinomycosis is usually challenging and delayed. A 39-year-old woman presented with an enlarging right neck mass and dysphagia after steroid exposure for treatment of De Quervain thyroiditis. MRI showed a large irregular infiltration mass over the right side of her neck, with a multi-loculated rim-enhancing area over the right retropharyngeal space. Excisional biopsy of the lesion only showed evidence of acute on chronic inflammation, and the results of all microbiological testing (including bacterial culture, Gram-staining, and molecular detection) were negative. Metagenomic next-generation sequencing (mNGS) of the formalin-fixed paraffin-embedded (FFPE) tissue from the patient was performed. DNA of Actinomyces israelii and Methylobacterium was detected. The patient was confirmed to have cervical actinomycosis and completely recovered after 6 months of oral amoxicillin. Our patient is the first case utilizing mNGS on FFPE tissue to diagnose cervical actinomycosis. This case shows that mNGS is a promising, unbiased tool for detecting Actinomyces species in FFPE tissues and diagnosing cervical actinomycosis. It also highlights the diagnostic difficulties of cervical actinomycosis. Full article

(This article belongs to the Special Issue Recent Advances of Microbiome Researches in One Health and Their Potential Applications)

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24 pages, 1320 KiB

Open AccessArticle

Genomic Epidemiology of ESBL- and Carbapenemase-Producing Enterobacterales in a Spanish Hospital: Exploring the Clinical–Environmental Interface

by Sandra A. Martínez-Álvarez, María Ángeles Asencio-Egea, María Huertas-Vaquero, Teresa Cardona-Cabrera, Myriam Zarazaga, Ursula Höfle and Carmen Torres

Microorganisms 2025, 13(8), 1854; https://doi.org/10.3390/microorganisms13081854 - 8 Aug 2025

Abstract

Antimicrobial resistance (AMR), particularly due to extended-spectrum β-lactamases (ESBLs) and carbapenemases (CPs), poses a critical threat to global health. This study aimed to characterize the molecular epidemiology, resistance profiles, and genomic features of ESBL- and CP-producing Escherichia coli and Klebsiella pneumonaie (ESBL/CP-Ec/Kp) isolates [...] Read more.

Antimicrobial resistance (AMR), particularly due to extended-spectrum β-lactamases (ESBLs) and carbapenemases (CPs), poses a critical threat to global health. This study aimed to characterize the molecular epidemiology, resistance profiles, and genomic features of ESBL- and CP-producing Escherichia coli and Klebsiella pneumonaie (ESBL/CP-Ec/Kp) isolates from a Spanish hospital (2020–2024) and explore links to environmental reservoirs like white storks foraging at a nearby landfill. A total of 121 clinical Ec/Kp isolates (55 ESBL-Ec, 1 CP-Ec, 35 ESBL-Kp, 17 CP-Kp, 13 ESBL+CP-Kp) underwent phenotypic testing, PCR, and whole-genome sequencing (WGS). Analyses included phylogenomics (cgMLST), detection of AMR genes, plasmid typing, and comparative genomics. Among ESBL-Ec, bla_CTX-M-15 was the most prevalent (60.0%), and one CP-Ec carrying bla_NDM-5 was identified. WGS of 44 selected ESBL/CP-Ec isolates revealed a variety of AMR genes, and 56.8% of isolates carried class one integrons (56.8%). IncF-type plasmids predominated, and 84.1% of isolates were assigned as ExPEC/UPEC. The lineage ST131 dominated (75%), with IncF-bla_CTX-M-15-carrying plasmids. Among the 18 ESBL/CP-Kp isolates sequenced, the lineage ST307 was the most frequent (44.4%), followed by ST15 and ST11, carrying a diversity of AMR determinants and plasmids (IncFIB(K), IncL, ColpVC). Virulence included ybt loci in ICEKp; hypervirulence genes were absent. Genomic analysis of 62 clinical isolates (44 Ec, 18 Kp) showed close phylogenetic links to stork-derived strains, with ST131-Ec and ST307-Kp from humans and birds differing just by ≤22 and ≤10 ADs, respectively, with a conserved plasmid content (i.e., IncL-bla_OXA-48, IncFIB(K)-bla_CTX-M-15). High-risk ESBL/CP-Ec/Kp clones persist across clinical and environmental contexts. WGS-based surveillance is key for understanding AMR spread and guiding interventions. Results support a One Health approach to combat AMR through cross-sector collaboration. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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17 pages, 3914 KiB

Open AccessArticle

The Community Structure and Diversity of Heterotrophic Microorganisms in the Soils of Taiga Forests, China

by Siyuan Liu, Zhichao Cheng, Mingliang Gao, Libin Yang and Yongzhi Liu

Microorganisms 2025, 13(8), 1853; https://doi.org/10.3390/microorganisms13081853 - 8 Aug 2025

Abstract

Heterotrophic microorganisms derive energy by decomposing organic matter. Their composition and community structure are influenced by environmental factors and interactions. Soil heterotrophic respiration was assessed by establishing vegetation removal plots (Hr) and control plots (Sr). Soil physicochemical properties were analyzed, and the composition [...] Read more.

Heterotrophic microorganisms derive energy by decomposing organic matter. Their composition and community structure are influenced by environmental factors and interactions. Soil heterotrophic respiration was assessed by establishing vegetation removal plots (Hr) and control plots (Sr). Soil physicochemical properties were analyzed, and the composition and biomass were evaluated using Illumina HiSeq sequencing and PLFA. The pH of Hr exhibited a significant increase (p < 0.05), whereas MC, MBC, SOC, DOC, TN, and AN all showed significant decreases (p < 0.05). PLFA analysis revealed that the biomass of bacteria, fungi, and total microorganisms in Hr was significantly lower than in Sr (p < 0.05). The predominant bacterial phyla were Acidobacteria, Verrucomycota, and Proteobacteria, with Verrucomycota significantly more abundant in Hr. The dominant fungal phyla were Ascomycota and Basidiomycota, both significantly more abundant in Hr. Community assembly was governed primarily by homogeneous selection in both Hr and Sr. The Hr co-occurrence network showed higher complexity, with >60% positive associations. Mantel tests confirmed significant links between soil properties (MC, pH, MBC, SOC, DOC, TN, and AN) and microbial composition. Vegetation removal induced soil heterogeneity and reduced microbial biomass with specific taxa shifts (Verrucomicrobia, Ascomycota, and Basidiomycota). Altered soil conditions and carbon resources reorganize microbial structure and function. Full article

(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 2nd Edition)

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15 pages, 689 KiB

Open AccessArticle

Antioxidant, Anti-Inflammatory, Antagonistic, and Probiotic Properties of Lactic Acid Bacteria Isolated from Traditional Algerian Fermented Wheat

by Rachida Benguiar, Rachida Benaraba, Chayma Farhat, Habib Chouchane, Djilali Boughaddou, Fethi Belalem and Ameur Cherif

Microorganisms 2025, 13(8), 1852; https://doi.org/10.3390/microorganisms13081852 - 8 Aug 2025

Abstract

This study focuses on the identification of three lactic acid bacteria isolates obtained from traditional Algerian fermented wheat as well as the evaluation of their biological activities, mainly their probiotic, antimicrobial, anti-inflammatory, and antioxidant properties. These isolates were identified through phenotypic and genotypic [...] Read more.

This study focuses on the identification of three lactic acid bacteria isolates obtained from traditional Algerian fermented wheat as well as the evaluation of their biological activities, mainly their probiotic, antimicrobial, anti-inflammatory, and antioxidant properties. These isolates were identified through phenotypic and genotypic characterizations. It was found that isolate LB3 was Lactiplantibacillus plantarum, while isolates LB1 and LB2 were identified as Weissella confusa. It was observed that the strains LB1, LB2, and LB3 are capable of maintaining their growth at pH 3.0 and in bile salts after 4 h, with individual survival rates ranging from 41% to 90% depending on the strain. Furthermore, their co-aggregation capacity with Staphylococcus aureus ATCC6528 indicated a percentage higher than 50%. The three strains displayed powerful inhibitory effects against pathogenic bacteria, showing inhibition rates of 5% to 40%. They also exhibited significant anti-inflammatory activity ranging from 20% to 39%. All three lactic acid bacteria (LAB) isolates exhibited significant antioxidant activity. Their intact cells demonstrated a high ability to scavenge DPPH radicals and possessed substantial ferric reducing power, while their intracellular extracts showed high levels of glutathione (GSH). Additionally, they exerted a protective effect against plasma lipid peroxidation, with inhibition rates ranging from 20% to 39%. These findings suggest that these strains possess promising probiotic potential as future therapeutic agents to be used in the development of novel functional fermented foods. Full article

(This article belongs to the Section Food Microbiology)

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14 pages, 311 KiB

Open AccessArticle

Virulence Genes and Antimicrobial Resistance Profiles in Aeromonas hydrophila and Aeromonas dhakensis Isolated from the Brazilian Food Chain

by Emily Moraes Roges, Veronica Dias Gonçalves, Marcelle da Silva Rodrigues, Marcia Lima Festivo, Paulo Henrique Ott, André Luiz Araujo, Salvatore Siciliano, Lucia Helena Berto, Maria Helena Cosendey de Aquino and Dalia dos Prazeres Rodrigues

Microorganisms 2025, 13(8), 1851; https://doi.org/10.3390/microorganisms13081851 - 8 Aug 2025

Abstract

Aeromonas hydrophila and A. dhakensis are ubiquitous microorganisms, widespread in aquatic environments, and can cause severe infections in humans and animals. This study aimed to determine the diversity of virulence genes aerA, hlyA, act, and alt through polymerase chain reaction [...] Read more.

Aeromonas hydrophila and A. dhakensis are ubiquitous microorganisms, widespread in aquatic environments, and can cause severe infections in humans and animals. This study aimed to determine the diversity of virulence genes aerA, hlyA, act, and alt through polymerase chain reaction and the antimicrobial resistance through disk diffusion test of 101 A. hydrophila and 34 A. dhakensis strains from environmental, animal, and human sources gathered between 2016 and 2019 at the National Reference Laboratory for Enteric Diseases. Overall, the virulence gene distribution was act in 35.5% of the samples, alt in 40.7%, aerA in 42.2%, and hlyA in 44.5%. Our results revealed that 76.3% of the 135 isolated Aeromonas exhibited at least one of the genes above. 76.3% of A. hydrophila and 76.5% of A. dhakensis exhibited virulence genes distributed among 15 and 12 virulence profiles, respectively. Antimicrobial resistance was observed in 86% of the strains (87.1% in A. hydrophila and 82.4% in A. dhakensis), with higher rates of resistance to Nalidixic acid (69.3%), Imipenem (31.1%), and Sulfamethoxazole-trimethoprim (15.5%). The occurrence of virulence genes and antimicrobial resistance in A. hydrophila and A. dhakensis from different sources indicates their diversity and pathogenicity, reinforcing that they can be a potential health risk source. Full article

(This article belongs to the Special Issue An Update on Aeromonas 2.0)

17 pages, 854 KiB

Open AccessReview

Mycoplasma Biofilms: Characteristics and Control Strategies

by Jingyi Liang, Baoyi Deng, Weihuo Li, Jingjing Qi, Yangshuo Li, Xueyan Wang, Ming Li, Hong Yang and Nan Zhang

Microorganisms 2025, 13(8), 1850; https://doi.org/10.3390/microorganisms13081850 - 7 Aug 2025

Abstract

The Mycoplasmataceae are a family of bacteria that typically cause respiratory, arthritic, and genitourinary disease in humans. Mycoplasma spp. of animal origin are also the causative agents of porcine wheezing disease, chronic respiratory disease and arthritis in chickens and other conditions. These diseases [...] Read more.

The Mycoplasmataceae are a family of bacteria that typically cause respiratory, arthritic, and genitourinary disease in humans. Mycoplasma spp. of animal origin are also the causative agents of porcine wheezing disease, chronic respiratory disease and arthritis in chickens and other conditions. These diseases have a significant impact on public health and the economic development of livestock breeding. Clinical prevention and treatment of mycoplasma infections is primarily dependent on the use of antibiotics. However, inappropriate and excessive use of antimicrobials has enabled resistance development that has become a significant clinical concern. Mycoplasma are also robust biofilm producers, and this process is a major factor for the persistence of these infections, especially in conjunction with common antibiotic resistance mechanisms, including target gene mutations and the action of efflux pumps. A mycoplasma biofilm refers to a structured and stable microbial community formed by Mycoplasma spp. adhering to biological or non-biological surfaces under suitable conditions and secreting extracellular polymers (EPS) such as polysaccharides. This process allows the microorganisms to adapt to their surrounding environment and survive during the growth process. These biofilms render bacteria more resistant to antimicrobials than planktonic bacteria, resulting in biofilm-associated infections that are more challenging to eradicate and more likely to recur. The current study reviews progress from the fields of biofilm formation, structure and identification, correlations between biofilms and drug resistance and virulence as well as methods of biofilm prevention and control. Our aim was to provide a reference basis for the subsequent in-depth understanding of the research of mycoplasma biofilms. Full article

(This article belongs to the Special Issue Advanced Research on Microbial Biofilms—a Themed Issue in Honor of Professor Gianfranco Donelli)

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24 pages, 4458 KiB

Open AccessReview

Selenium-Enriched Microorganisms: Metabolism, Production, and Applications

by Lin Luo, Xue Hou, Dandan Yi, Guangai Deng, Zhiyong Wang and Mu Peng

Microorganisms 2025, 13(8), 1849; https://doi.org/10.3390/microorganisms13081849 - 7 Aug 2025

Abstract

Microorganisms, as abundant biological resources, offer significant potential in the development of selenium-enrichment technologies. Selenium-enriched microorganisms not only absorb, reduce, and accumulate selenium efficiently but also produce various selenium compounds without relying on synthetic chemical processes. In particular, nano-selenium produced by these microorganisms [...] Read more.

Microorganisms, as abundant biological resources, offer significant potential in the development of selenium-enrichment technologies. Selenium-enriched microorganisms not only absorb, reduce, and accumulate selenium efficiently but also produce various selenium compounds without relying on synthetic chemical processes. In particular, nano-selenium produced by these microorganisms during cultivation has garnered attention due to its unique physicochemical properties and biological activity, making it a promising raw material for functional foods and pharmaceutical products. This paper reviews selenium-enriched microorganisms, focusing on their classification, selenium metabolism, and transformation mechanisms. It explores how selenium is absorbed, reduced, and transformed within microbial cells, analyzing the biochemical processes by which inorganic selenium is converted into organic and nano-selenium forms. Finally, the broad applications of selenium-enriched microbial products in food, medicine, and agriculture are explored, including their roles in selenium-rich foods, nano-selenium materials, and disease prevention and treatment. Full article

(This article belongs to the Special Issue Exploring the Diversity of Microbial Applications)

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16 pages, 580 KiB

Open AccessArticle

Effects of Dietary Tannic Acid and Tea Polyphenol Supplementation on Rumen Fermentation, Methane Emissions, Milk Protein Synthesis and Microbiota in Cows

by Rong Zhao, Jiajin Sun, Yitong Lin, Haichao Yan, Shiyue Zhang, Wenjie Huo, Lei Chen, Qiang Liu, Cong Wang and Gang Guo

Microorganisms 2025, 13(8), 1848; https://doi.org/10.3390/microorganisms13081848 - 7 Aug 2025

Abstract

To develop sustainable strategies for mitigating ruminal methanogenesis and improving nitrogen efficiency in dairy systems, this study investigated how low-dose tannic acid (T), tea polyphenols (TP), and their combination (T+TP; 50:50) modulate rumen microbiota and function. A sample of Holstein cows were given [...] Read more.

To develop sustainable strategies for mitigating ruminal methanogenesis and improving nitrogen efficiency in dairy systems, this study investigated how low-dose tannic acid (T), tea polyphenols (TP), and their combination (T+TP; 50:50) modulate rumen microbiota and function. A sample of Holstein cows were given four dietary treatments: (1) control (basal diet); (2) T (basal diet + 0.4% DM tannic acid); (3) TP (basal diet + 0.4% DM tea polyphenols); and (4) T+TP (basal diet + 0.2% DM tannic acid + 0.2% DM tea polyphenols). We comprehensively analyzed rumen fermentation, methane production, nutrient digestibility, milk parameters, and microbiota dynamics. Compared with the control group, all diets supplemented with additives significantly reduced enteric methane production (13.68% for T, 11.40% for TP, and 10.89% for T+TP) and significantly increased milk protein yield. The crude protein digestibility significantly increased in the T group versus control. The results did not impair rumen health or fiber digestion. Critically, microbiota analysis revealed treatment-specific modulation: the T group showed decreased Ruminococcus flavefaciens abundance, while all tannin treatments reduced abundances of Ruminococcus albus and total methanogens. These microbial shifts corresponded with functional outcomes—most notably, the T+TP synergy drove the largest reductions in rumen ammonia-N (34.5%) and milk urea nitrogen (21.1%). Supplementation at 0.4% DM, particularly the T+TP combination, effectively enhances nitrogen efficiency and milk protein synthesis while reducing methane emissions through targeted modulation of key rumen microbiota populations, suggesting potential sustainability benefits linked to altered rumen fermentation. Full article

(This article belongs to the Section Veterinary Microbiology)

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13 pages, 7865 KiB

Open AccessArticle

FlbD: A Regulator of Hyphal Growth, Stress Resistance, Pathogenicity, and Chlamydospore Production in the Nematode-Trapping Fungus Arthrobotrys flagrans

by Yu Zhang, Shun-Qiao Peng, Wang-Ting He, Fei-Fei Gao, Qian-Fei Shi and Guo-Hong Li

Microorganisms 2025, 13(8), 1847; https://doi.org/10.3390/microorganisms13081847 - 7 Aug 2025

Abstract

Arthrobotrys flagrans is a typical nematode-trapping fungus that captures nematodes by producing three-dimensional networks. FlbD is a DNA-binding protein containing a Myb domain, which plays a significant role in fungal development. However, the biological function of FlbD in nematode-trapping fungi remains unknown. In [...] Read more.

Arthrobotrys flagrans is a typical nematode-trapping fungus that captures nematodes by producing three-dimensional networks. FlbD is a DNA-binding protein containing a Myb domain, which plays a significant role in fungal development. However, the biological function of FlbD in nematode-trapping fungi remains unknown. In this study, we analyzed the physicochemical properties and conserved domains of AfFlbD and constructed the AfFlbD knockout strains (ΔAfFlbD) using homologous recombination. Our functional analysis revealed that the mutants produced more cottony aerial mycelia at the colony center. Additionally, the cell length of the mutants was reduced, indicating that AfFlbD regulates cell morphology in A. flagrans. Chemical stress tolerance assays of the mutants demonstrated reduced sensitivity to NaCl and sorbitol stresses but increased sensitivity to SDS and H₂O₂ stresses compared to the WT strain. Interestingly, the mutants spontaneously produced traps, and its pathogenicity to nematodes was significantly enhanced, suggesting that AfFlbD negatively regulates the pathogenicity of A. flagrans. Furthermore, the number of chlamydospores produced by the mutants was markedly reduced, though their morphology remained unchanged. Fluorescence localization analysis showed that AfFlbD localizes to the nuclei of chlamydospores, thereby regulating chlamydospore formation. This study provides important theoretical insights into the biological function of the FlbD transcription factor and offers new perspectives for the application of nematode-trapping fungi as a method of controlling plant-parasitic nematodes. Full article

(This article belongs to the Special Issue Microorganisms as Biocontrol Agents in Plant Pathology, 2nd Edition)

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21 pages, 1539 KiB

Open AccessArticle

Context-Dependent Fitness Trade-Offs in Penicillium expansum Isolates Resistant to Multiple Postharvest Fungicides

by Jonathan T. Puglisi and Achour Amiri

Microorganisms 2025, 13(8), 1846; https://doi.org/10.3390/microorganisms13081846 - 7 Aug 2025

Abstract

Blue mold of pome fruit, caused by Penicillium expansum, is controlled through postharvest applications of thiabendazole (TBZ), pyrimethanil (PYR), and fludioxonil (FDL). However, multi-fungicide-resistant isolates have emerged in the U.S. Pacific Northwest and their impact on decay control in long-term storage is [...] Read more.

Blue mold of pome fruit, caused by Penicillium expansum, is controlled through postharvest applications of thiabendazole (TBZ), pyrimethanil (PYR), and fludioxonil (FDL). However, multi-fungicide-resistant isolates have emerged in the U.S. Pacific Northwest and their impact on decay control in long-term storage is unknown. This study evaluated the fitness of P. expansum isolates sensitive to all three postharvest fungicides (wild-types) and those resistant to TBZ (single-resistant), TBZ and PYR, or PYR and FDL (dual-resistant), and triple-resistant to the three fungicides. On nutrient-poor media, resistant isolates showed reduced conidial germination, whereas no significant differences were observed in germination, mycelial growth, or sporulation between phenotypes on nutrient-rich media at 1.5 and 20 °C. Regardless of their sensitivity phenotype, FDL-resistant isolates showed increased sensitivity to osmotic and oxidative stresses. Pathogenicity and virulence were not affected by the sensitivity phenotype on apples after six months of storage at 1.5 °C. Analysis of cumulative fitness changes indicated fitness loss under low-temperature in vitro and increased fitness under fungicide selection pressure on fruit in most resistant phenotypes. Gene expression analysis showed differential regulation of fitness-related genes, with most being up-regulated by TBZ. Overall, the results suggest that resistance in P. expansum may carry context-dependent fitness penalties, especially under high-stress conditions. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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15 pages, 1544 KiB

Open AccessArticle

Optimizing Scaled up Production and Purification of Recombinant Hydrophobin HFBI in Pichia pastoris

by Mason A. Kinkeade, Aurora L. Pagan and Bryan W. Berger

Microorganisms 2025, 13(8), 1845; https://doi.org/10.3390/microorganisms13081845 - 7 Aug 2025

Abstract

Hydrophobins are small, surface-active protein biosurfactants secreted by filamentous fungi with potential applications in industries such as pharmaceuticals, sanitation, and biomaterials. Additionally, hydrophobins are known to stabilize enzymatic processing of biomass for improved catalytic efficiency. In this study, Pichia pastoris was used to [...] Read more.

Hydrophobins are small, surface-active protein biosurfactants secreted by filamentous fungi with potential applications in industries such as pharmaceuticals, sanitation, and biomaterials. Additionally, hydrophobins are known to stabilize enzymatic processing of biomass for improved catalytic efficiency. In this study, Pichia pastoris was used to recombinantly express hydrophobin HFBI from Trichoderma reesei, a well-characterized fungal system used industrially for bioethanol production. Iterative optimization was performed on both the induction and purification of HFBI, ultimately producing yields of 86.6 mg/L HFBI and elution concentrations of 48 μM HFBI determined pure by SDS-PAGE, over a five-day methanol-fed batch shake flask induction regiment followed by a single unit operation multimodal cation exchange purification. This final purified material represents an improvement over prior approaches to enable a wider range of potential applications for biosurfactants. Full article

(This article belongs to the Special Issue Advances in Microbial Surfactants: Production and Applications (2nd Edition))

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14 pages, 6774 KiB

Open AccessArticle

Antimicrobial Activities of Propolis Nanoparticles in Combination with Ampicillin Sodium Against Methicillin-Resistant Staphylococcus aureus

by Kaiyue Feng, He Sang, Han Jin, Peng Song, Wei Xu, Hongzhuan Xuan and Fei Wang

Microorganisms 2025, 13(8), 1844; https://doi.org/10.3390/microorganisms13081844 - 7 Aug 2025

Abstract

Combining antibiotics with propolis is an effective method to combat bacterial drug resistance. Nanoparticles are of interest in the antimicrobial field because of their higher drug stability, solubility, penetration power, and treatment efficacy. In this study, propolis nanoparticles (PNPs) were synthesized, and their [...] Read more.

Combining antibiotics with propolis is an effective method to combat bacterial drug resistance. Nanoparticles are of interest in the antimicrobial field because of their higher drug stability, solubility, penetration power, and treatment efficacy. In this study, propolis nanoparticles (PNPs) were synthesized, and their antibacterial and anti-biofilm activities against methicillin-resistant Staphylococcus aureus (MRSA) in combination with ampicillin sodium (AS) were analyzed. The PNPs had an average particle diameter of 118.0 nm, a polydispersity index of 0.129, and a zeta potential of −28.2 mV. The fractional inhibitory concentration indices of PNPs and AS against tested MRSA strains highlighted this synergy, ranging between 0.375 and 0.5. Crystal violet staining showed that combined PNPs and AS significantly inhibited biofilm formation and reduced existing biofilm biomass. We then discovered that PNPs inhibited bacterial adhesion, extracellular polysaccharide synthesis, and mecR1, mecA, blaZ, and icaADBC gene expression. These results indicated that PNPs exerted a synergistic antibacterial effect with AS by inhibiting mecR1, mecA, and blaZ gene expressions to reduce the drug resistance of MRSA. Meanwhile, PNPs weakened bacterial adhesion and aggregation by suppressing icaADBC gene expression, allowing antibiotics to penetrate the biofilm, and exhibiting significant synergistic anti-biofilm activity. In summary, PNPs are promising candidates for combating MRSA-related diseases. Full article

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

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20 pages, 3576 KiB

Open AccessArticle

Urban Wetland Sediments in Yangzhou: Physicochemical Properties, Microbial Communities, and Functional Associations

by Dongmei He, Liwen Li, Runyang Zhou, Sumei Qiu, Wei Xing and Yingdan Yuan

Microorganisms 2025, 13(8), 1843; https://doi.org/10.3390/microorganisms13081843 - 7 Aug 2025

Abstract

Urban wetlands play a crucial role in maintaining ecological balance, carbon sequestration, and water purification. Sediments are key carriers for wetlands to store elements such as carbon, nitrogen, and phosphorus in the aquatic environment. This study analyzed different sediment layers of seven wetlands [...] Read more.

Urban wetlands play a crucial role in maintaining ecological balance, carbon sequestration, and water purification. Sediments are key carriers for wetlands to store elements such as carbon, nitrogen, and phosphorus in the aquatic environment. This study analyzed different sediment layers of seven wetlands in Yangzhou, aiming to explore the relationship between physicochemical factors and microbial communities in wetland sediments, as well as to predict the functions of microbial communities. Functional prediction of microbial communities was conducted based on amplicon sequencing analysis, and the neutral community model was used to determine the formation and evolution process of microbial communities. The results showed that in three wetlands, namely Zhuyu Bay (ZYW), Luyang Lake (LYH), and Runyang Wetland (RYSD), the contents of carbon components (total carbon, total soluble carbon, microbial biomass carbon) in the 0–20 cm sediment layer were higher, while the carbon component contents in Baoying Lake (BYH) showed the opposite trend. Among them, the contents of total nitrogen, alkali-hydrolyzable nitrogen, total phosphorus, available phosphorus, total potassium, and available potassium in the 0–20 cm sediment layer of Runyang Wetland (RYSD) were significantly the highest. This indicates that in Runyang Wetland (RYSD), the 0–20 cm layer has more abundant carbon components and mineral nutrients compared to the 20–40 cm layer. Among the seven wetlands, it was found that the content of total potassium was all greater than 10 g/kg, which was much higher than the contents of total phosphorus and total nitrogen. Analysis of microbial communities revealed that the dominant archaeal phyla were Thaumarchaeota and Euryarchaeota, and the dominant bacterial phyla were Proteobacteria and Acidobacteria. The distribution of functional genes was mainly concentrated in Zhuyu Bay (ZYW) and Luyang Lake (LYH). Zhuyu Bay Wetland (ZYW) had potential advantages in light utilization function, and Luyang Lake (LYH) had potential advantages in carbon and nitrogen cycle functions. The assembly process of the archaeal community was mainly affected by stochastic processes, while the bacterial community was mainly affected by deterministic processes. However, water content, total phosphorus, and available potassium all had strong correlations with both archaeal and bacterial communities. The research results preliminarily reveal the connections between the physicochemical properties of sediments, microbial communities, and their potential functions in Yangzhou urban wetlands, providing an important scientific basis for the protection and management of wetland ecosystems. Full article

(This article belongs to the Section Environmental Microbiology)

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20 pages, 5610 KiB

Open AccessArticle

The Gut Microbial Adaptation of Wild Goitered Gazelles Under Antibiotic Pressure in the Qaidam Basin

by Qing Zhao, Yiran Wang, Jingqing Ma and Wen Qin

Microorganisms 2025, 13(8), 1842; https://doi.org/10.3390/microorganisms13081842 - 7 Aug 2025

Abstract

Gut microbiota plays a vital role in host resilience but may be disrupted under environmental antibiotic pressure. The goitered gazelle (Gazella subgutturosa), a keystone ungulate in the Qaidam Basin, is crucial for ecosystem stability. We aimed to investigate how this species [...] Read more.

Gut microbiota plays a vital role in host resilience but may be disrupted under environmental antibiotic pressure. The goitered gazelle (Gazella subgutturosa), a keystone ungulate in the Qaidam Basin, is crucial for ecosystem stability. We aimed to investigate how this species responds to antibiotic pressure through gut microbial adaptation. Using 16S rRNA sequencing and weighted gene co-expression network analysis (WGCNA) on fecal and soil samples from six regions, we identified 18 microbial modules, of which three were strongly associated with antibiotics (|r| ≥ 0.75, p < 0.05). Gut microbial α-diversity was lowest in the antibiotic-rich, vegetation-poor TGL region and highest in XRH, where diverse vegetation appeared to buffer antibiotic impact. Antibiotic pressure can reshape gut microbial communities, exerting both adaptive benefits and adverse effects. High-quality habitats may alleviate the negative impacts of antibiotic pressure. Full article

(This article belongs to the Section Gut Microbiota)

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21 pages, 3405 KiB

Open AccessArticle

Allelic Variation of Helicobacter pylori vacA Gene and Its Association with Gastric Pathologies in Clinical Samples Collected in Jordan

by Mamoon M. Al-Hyassat, Hala I. Al-Daghistani, Lubna F. Abu-Niaaj, Sima Zein and Talal Al-Qaisi

Microorganisms 2025, 13(8), 1841; https://doi.org/10.3390/microorganisms13081841 - 7 Aug 2025

Abstract

Helicobacter pylori is a well-established causative agent of gastritis, peptic ulcers, gastric adenocarcinoma, and primary gastric lymphoma. It colonizes the human stomach and expresses numerous virulent factors that influence disease progression. Among these factors is the cytotoxin vacA gene, which encodes the vacuolating [...] Read more.

Helicobacter pylori is a well-established causative agent of gastritis, peptic ulcers, gastric adenocarcinoma, and primary gastric lymphoma. It colonizes the human stomach and expresses numerous virulent factors that influence disease progression. Among these factors is the cytotoxin vacA gene, which encodes the vacuolating capacity of the cytotoxin and plays a key role in the bacterium’s pathogenic potential. This study investigated the allelic diversity of the vacA among H. pylori strains infecting patients in Jordan with various gastric conditions and examined potential associations between vacA s-and m- genotypes, histopathological and endoscopic findings, and the development of gastric diseases. Gastric biopsies were collected from 106 patients at two hospitals in Jordan who underwent endoscopic examination. The collected biopsies for each patient were subjected to histopathological assessment, urease detection using the Rapid Urease Test (RUT), a diagnostic test for H. pylori, and molecular detection of the vacA gene and its s and m alleles. The histopathology reports indicated that 83 of 106 patients exhibited gastric disorders, of which 81 samples showed features associated with H. pylori infection. The RUT was positive in 76 of 106 with an accuracy of 93.8%. Real-time polymerase chain reaction (RT-PCR) targeting the 16S rRNA gene confirmed the presence of H. pylori in 79 of 81 histologically diagnosed cases as infected (97.5%), while the vacA gene was detected only in 75 samples (~95%). To explore genetic diversity, PCR-amplified fragments underwent sequence analysis of the vacA gene. The m-allele was detected in 58 samples (73%), the s-allele was detected in 45 (57%), while both alleles were not detected in 13% of samples. The predominant genotype combination among Jordanians was vacA s2/m2 (50%), significantly linked to mild chronic gastritis, followed by s1/m2 (35%) and s1/m1 (11.8%) which are linked to severe gastric conditions including malignancies. Age-and gender-related differences in vacA genotype were observed with less virulent s2m2 and s1m2 genotypes predominating in younger adults specially males, while the more virulent m1 genotypes were found exclusively in females and middle-aged patients. Genomic sequencing revealed extensive diversity within H. pylori, likely reflecting its long-standing co-evolution with human hosts in Jordan. This genetic variability plays a key role in modulating virulence and influencing clinical outcomes. Comprehensive characterization of vacA genotypic variations through whole-genome sequencing is essential to enhance diagnostic precision, strengthen epidemiological surveillance, and inform targeted therapeutic strategies. While this study highlights the significance of the vacA m and s alleles, future research is recommended in order to investigate the other vacA allelic variations, such as the i, d, and c alleles, to achieve a more comprehensive understanding of H. pylori pathogenicity and associated disease severity across different strains. These investigations will be crucial for improving diagnostic accuracy and guiding the development of targeted therapeutic strategies. Full article

(This article belongs to the Special Issue Helicobacter pylori Infection: Detection and Novel Treatment)

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