Microorganisms

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Open AccessArticle

Distribution and Potential Metabolic Functions of Soil Actinobacteria in Degraded Alpine Grassland on the Northern Tibetan Plateau

by Junze Zhang, Sicen Luo, Yanying Wang, Yebing Yin, Yu Li, Wenxiang Zhao, Shirui Zheng, Guoqi Xu, Hongmei Ma, Pengxi Cao and Yixuan Liu

Microorganisms 2025, 13(10), 2230; https://doi.org/10.3390/microorganisms13102230 - 23 Sep 2025

Abstract

Actinobacteria play major roles in human health and soil nutrient biogeochemical cycles, which are important for environmental protection. On the northern Qinghai–Tibet Plateau, the Qiangtang Alpine Grasslands have recently become degraded to varying degrees due to global climate changes and human disturbances. Here, [...] Read more.

Actinobacteria play major roles in human health and soil nutrient biogeochemical cycles, which are important for environmental protection. On the northern Qinghai–Tibet Plateau, the Qiangtang Alpine Grasslands have recently become degraded to varying degrees due to global climate changes and human disturbances. Here, we compared the community diversity, composition, and potential metabolic functions of Actinobacteria in soil from different degradation conditions through Illumina MiSeq sequencing. The soil Actinobacteria community structure in the Qiangtang Alpine Grasslands of northern Tibet was dominated by Nocardioides, Gaiella, Solirubrobacter, and Pseudonocardia, with evidence of previously unidentified taxa. Compared with non-degraded and severely degraded grasslands, the moderately degraded grassland had the highest soil Actinobacteria alpha-diversity, and the community composition showed significant differences between degraded grasslands with different degrees of degradation. The interactions between Actinobacteria and KO functions predominantly show negative correlations, but significant positive correlations outnumber significant negative ones. This study showed that Actinobacteria diversity and potential ecological functions in the alpine grasslands of northern Tibet decreased with grassland degradation due to the loss of vegetation cover. Therefore, it is necessary to effectively manage and protect the Qiangtang Alpine Grasslands on the northern Tibetan Plateau. Full article

(This article belongs to the Section Environmental Microbiology)

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Open AccessArticle

Isolation of Endophytic Phosphate-Solubilizing Bacteria from Chinese Cymbidium (Cymbidium spp.) Orchid Roots

by Yanmei Sun, Jianpeng Jin, Xiting Wang, Wei Zhu, Jie Gao, Jie Li, Qi Xie, Yonglu Wei, Chuqiao Lu, Genfa Zhu and Fengxi Yang

Microorganisms 2025, 13(10), 2229; https://doi.org/10.3390/microorganisms13102229 - 23 Sep 2025

Abstract

This study aims to identify and evaluate the phosphate-solubilizing ability of endophytic bacteria isolated from roots of Chinese Cymbidium and to assess their impact on phosphorus uptake and plant growth. Thirty strains of endophytic bacteria were isolated from six orchid varieties. Molecular identification [...] Read more.

This study aims to identify and evaluate the phosphate-solubilizing ability of endophytic bacteria isolated from roots of Chinese Cymbidium and to assess their impact on phosphorus uptake and plant growth. Thirty strains of endophytic bacteria were isolated from six orchid varieties. Molecular identification based on 16S rRNA gene sequencing revealed that the most frequently isolated strains belonged to the genera Pseudomonas and Burkholderia. Among them, 10 bacterial strains exhibited the capacity to solubilize inorganic and organic phosphorus. Two strains, designated X1 (Paraburkholderia sp. Beta-32) and X13 (Rhizobium freirei PRF81 (X13), were identified as the most effective phosphate-solubilizing bacteria (PSB). Gluconic acid was the dominant organic acid secreted, driving inorganic phosphorus solubilization, while alkaline phosphatase activities facilitated organic phosphorus mineralization. Inoculation with phosphate-solubilizing bacteria (PSB) resulted in increased plant growth and phosphorus content in both leaves and roots as compared to the control plants. PSB treatments also increased available phosphorus content in soil, reduced total phosphorus content, and increased exopolysaccharide and alkaline phosphatase activities. Real-time q-PCR analysis showed that PSB inoculation significantly upregulated the expression of phosphorus transport-related genes, including PDR2, PHF1, PHR1, PHT1;9, and PHT4;4, thereby enhancing phosphorus absorption. Moreover, strains X1 and X13 not only exhibited strong phosphate-solubilizing capacity but also demonstrated stable colonization in both roots and root rhizosphere soil of orchids over extended periods. In conclusion, the endophytic PSB identified with phosphate-solubilizing abilities increased phosphorus availability and its uptake in Chinese Cymbidium, thereby promoting plant growth and development. This is the first attempt to characterize endophytic PSB from roots of Chinese Cymbidium orchids. These findings provide a basis for selection of PSB that are efficient in P uptake for application in microbial fertilizers for orchid cultivation. Full article

(This article belongs to the Section Plant Microbe Interactions)

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Open AccessArticle

Improving the Quality of Ensiling High-Moisture Alfalfa with Peanut Vine in Different Additives: Fermentation, Nutritional Quality, and Microbial Communities

by Haikuo Jia, Chunhui Wu, Zhenling Liu, Yu Sun, Ying He, Huan Chen, Xiaowei Zu, Lixin Wang, Yanxia Gao, Mingya Wang and Qiufeng Li

Microorganisms 2025, 13(10), 2228; https://doi.org/10.3390/microorganisms13102228 (registering DOI) - 23 Sep 2025

Abstract

Ensiling high-moisture alfalfa with peanut vine not only avoids alfalfa nutrient loss during the wilting stage but also maximizes the use of agricultural waste peanut vine. The appropriate mixed ratio of high-moisture alfalfa and peanut vine has been studied in our previous study. [...] Read more.

Ensiling high-moisture alfalfa with peanut vine not only avoids alfalfa nutrient loss during the wilting stage but also maximizes the use of agricultural waste peanut vine. The appropriate mixed ratio of high-moisture alfalfa and peanut vine has been studied in our previous study. However, the effect of additives on improving the nutrition and fermentation quality of the mixed silage of alfalfa and peanut vine has not been investigated. This study aimed to assess the adaptation and association of Lactiplantibacillus plantarum, cellulase and tannin in the mixed silage of alfalfa and peanut vine alone or in combination on fermentation quality, chemical composition, and microbial communities. The harvested fresh alfalfa and dry peanut vine were cut into 2 cm lengths by a crop chopper and they were thoroughly mixed at a ratio of 7:3. The mixtures were treated with no addition (CK), L. plantarum (Lp, 1 × 10⁶ CFU/g fresh weight), cellulase (Ce, 5 g/kg fresh weight), tannin (Ta, 40 g/kg dry matter), and their combinations (LpCe, LpTa, CeTa, LpCeTa). After 45 days of fermentation, silage treated with Lp, Ce, and Ta had lower pH and ammonia-N (NH₃-N) content and higher concentrations of lactic acid compared with the CK group. LpCeTa-treated silage inhibited protein degradation by reducing pH value and ammonia-N concentrations during ensiling processes. The LpCeTa group increased (p < 0.05) water-soluble carbohydrate (WSC) content and reduced (p < 0.05) acid detergent fiber and neutral detergent fiber contents in mixed silage. Furthermore, the LpCeTa group increased the relative abundance of Lactobacillus and decreased the relative abundance of Enterococcus and Weissella as compared with the CK group. Results of the current study indicated that the combined use of L. plantarum, cellulase, and tannin could serve as a promising strategy for the preservation of ensiling fresh alfalfa mixed with peanut vine and provide a reference for the re-utilization of by-product. Full article

(This article belongs to the Special Issue Microorganisms in Silage)

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Open AccessArticle

Antimicrobial Resistance in Chicken Meat: Comparing Salmonella, Escherichia coli, and Enterococcus from Conventional and Antibiotic-Free Productions

by Camila Koutsodontis Cerqueira-Cézar, Aryele Nunes da Cruz Encide Sampaio, Evelyn Fernanda Flores Caron, Thaisy Tino Dellaqua, Lucas Franco Miranda Ribeiro, Leonardo Ereno Tadielo, José Carlos de Figueiredo Pantoja, Gustavo Guimarães Fernandes Viana, Gabriel Augusto Marques Rossi, Carlo Spanu, Fábio Sossai Possebon and Juliano Gonçalves Pereira

Microorganisms 2025, 13(10), 2227; https://doi.org/10.3390/microorganisms13102227 - 23 Sep 2025

Abstract

Chicken meat production is a critical component of the global protein supply, significantly influenced by rearing advancements, including the use of antimicrobial agents. However, the pervasive use of antibiotics has raised concerns regarding the occurrence of antimicrobial resistance (AMR). This study examined the [...] Read more.

Chicken meat production is a critical component of the global protein supply, significantly influenced by rearing advancements, including the use of antimicrobial agents. However, the pervasive use of antibiotics has raised concerns regarding the occurrence of antimicrobial resistance (AMR). This study examined the prevalence and AMR profiles of Salmonella spp., Escherichia coli, and Enterococcus spp. in chicken meat from conventional and antibiotic-free (ABF) production chains. A total of 284 samples were analyzed for Salmonella spp. and E. coli, while 164 samples were tested for Enterococcus spp. From that, 143 were from conventional production chains and 141 were from ABF chains. The results indicated a 10.9% prevalence of Salmonella spp., 22.1% for E. coli, and 93.9% for Enterococcus spp. Regarding production chains, the conventional chain had 18.2% of the isolates for Salmonella spp., 20.3% for E. coli, and 91.6% for Enterococcus spp., while the ABF chain had 3.5% of the isolates for Salmonella spp., 24.1% for E. coli, and 96.3% for Enterococcus spp. In terms of AMR, 86.1% of the Salmonella spp. isolates that underwent the disk diffusion test were resistant to at least one antibiotic tested, 95.1% of E. coli, and 88.4% of Enterococcus spp. Notably, carbapenem resistance was detected in Salmonella spp., with 2.3% of isolates being resistant to imipenem, while resistance to vancomycin and linezolid was detected in Enterococcus spp., all of which are critically important antimicrobials. Comparisons between these production chains revealed significant differences in antibiotic resistance patterns in Salmonella spp. for two antibiotics, amoxicillin/clavulanic acid and nitrofurantoin, while no differences were observed in E. coli. For Enterococcus spp., resistance varied for three antibiotics: streptomycin, penicillin, and tetracycline. For all other antibiotics tested, the resistance profiles were consistent across both conventional and ABF production chains. Multidrug resistance (MDR) was observed in 90.7% of Salmonella spp. isolates, 42.9% of E. coli isolates, and 12.0% of Enterococcus spp. isolates. Statistically significant differences were noted in MDR prevalence between production chains, with conventional production systems exhibiting higher levels of MDR isolates compared to ABF systems. These findings underscore the need for targeted AMR control strategies that consider the complexity of resistance dynamics across production systems. Full article

(This article belongs to the Special Issue Epidemiology, Prevention and Control of Foodborne Microbial Pathogens, Second Edition)

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Open AccessArticle

RNA Sequencing of Immune Response-Related Gene Expression Characteristics in Bovine Mammary Glands Infected with Escherichia coli

by Kai Zhang, Yuanyuan Zhang, Hong Su, Min Zhang, Feifei Zhao, Daqing Wang, Guifang Cao, Yong Zhang and Caiyun Wang

Microorganisms 2025, 13(10), 2226; https://doi.org/10.3390/microorganisms13102226 - 23 Sep 2025

Abstract

Bovine mastitis is one of the most prevalent and economically significant diseases affecting dairy cows worldwide, with Escherichia coli (E. coli) recognized as one of the principal pathogens causing acute mastitis. The innate immune system plays a crucial role in the [...] Read more.

Bovine mastitis is one of the most prevalent and economically significant diseases affecting dairy cows worldwide, with Escherichia coli (E. coli) recognized as one of the principal pathogens causing acute mastitis. The innate immune system plays a crucial role in the defense of the bovine mammary gland, serving as the first line of defense against pathogen invasion. This study elucidated the pathological mechanisms and immune response-related molecular regulatory networks involved in E. coli-induced bovine mastitis. Histopathological and apoptosis analyses of mammary tissues were performed using hematoxylin-eosin (HE) staining and TUNEL staining, respectively, while RNA sequencing (RNA-seq) was conducted to identify differentially expressed genes (DEGs) and their associated signaling pathways. HE staining revealed typical inflammatory lesions in the mammary glands of mastitis cows. TUNEL staining further confirmed that the level of apoptosis in the mastitis group was significantly higher than in the healthy control group (p < 0.0001). RNA-seq analysis identified 2717 DEGs, with 2238 upregulated and 479 downregulated genes. The top 20 significantly upregulated genes (e.g., S100A12, IL1RN, IL1R2, CXCL8, SAA3, S100A8, S100A9, TREML2, TREM1, M-SAA3.2, PTX3, MMP9) were predominantly involved in inflammatory immune regulation, acute phase responses (e.g., HP, SAA3), and cellular signal transduction (e.g., PLEK, LPAR3). Gene Ontology (GO) enrichment analysis revealed that these DEGs were mainly associated with biological processes, such as signal transduction, immune response, inflammatory response, and transcriptional regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DEGs were significantly enriched in key inflammatory and immune regulatory pathways, including the TNF signaling pathway, C-type lectin receptor signaling pathway, Chemokine signaling pathway, NOD-like receptor signaling pathway, NF-κ B signaling pathway, and IL-17 signaling pathway, suggesting that these pathways play central roles in the mammary immune defense against E. coli infection. In conclusion, this study demonstrated at the histopathological, cellular apoptosis, and transcriptomic levels that E. coli infection induces mammary tissue damage and apoptosis by activating immune and inflammation-related genes (S100A12, IL1RN, IL1R2, CXCL8, SAA3, S100A8, S100A9, TREML2, TREM1, M-SAA3.2, PTX3, MMP9) and key signaling pathways (TNF signaling pathway, C-type lectin receptor signaling pathway, Chemokine signaling pathway, NOD-like receptor signaling pathway, NF-κ B signaling pathway, IL-17 signaling pathway). The findings of this study provide a theoretical basis for probing into the pathogenesis of bovine mastitis and the development of targeted interventions. Full article

(This article belongs to the Special Issue Microbial Infections in Ruminants)

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Open AccessArticle

Prevalence, Serotypes, and Antimicrobial Resistance of Salmonella Species in Ready-to-Eat Foods in Erbil, Iraq

by Dhary Alewy Almashhadany, Abdulwahed Ahmed Hassan and Izhar U. H. Khan

Microorganisms 2025, 13(10), 2225; https://doi.org/10.3390/microorganisms13102225 - 23 Sep 2025

Abstract

Ready-to-eat (RTE) foods including sandwiches, pastries, shawarma, and burgers are widely consumed and may potentially increase the risk of foodborne infections. This study investigated the prevalence, serovar diversity, and antimicrobial resistance (AMR) of Salmonella spp. in RTE foods collected between January and June [...] Read more.

Ready-to-eat (RTE) foods including sandwiches, pastries, shawarma, and burgers are widely consumed and may potentially increase the risk of foodborne infections. This study investigated the prevalence, serovar diversity, and antimicrobial resistance (AMR) of Salmonella spp. in RTE foods collected between January and June 2024 from street vendors and restaurants across Erbil, Iraq. A total of 350, including 85 sandwiches, 75 pastries, 95 shawarma, and 95 burgers obtained from 115 cafeteria, 120 street vendors, and 115 restaurants were analyzed. Salmonella was detected in 7.1% (n = 25) of samples, with a high contamination in shawarma (8.4%; n = 95), followed by sandwiches (7.1%; n = 85), pastries (6.7%; n = 75), and burgers (6.3%; n = 95). Street vendors exhibited a higher (9.2%; n = 120) contamination rate compared to the cafeteria (6.9%; n = 115) and restaurants (5.2%; n = 115). Among 25 Salmonella isolates, 10 serotypes were identified, with S. Anatum (20%) and S. Typhimurium (16%) being the most prevalent. All isolates were susceptible to colistin, cefadroxil, and gentamicin, while showing high resistance to streptomycin (52%) and levofloxacin (48%). Contamination peaked during the warmer months, particularly in June (15.4%) and May (11.5%), when compared to the other sampling months. These findings highlight significant food safety concerns related to Salmonella contamination and AMR in RTE foods, emphasizing the urgent need for enhanced hygiene practices and regulatory oversight especially among street vendors. Full article

(This article belongs to the Special Issue Salmonella and Food Safety)

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Open AccessArticle

Comparative Analysis of Bacterial Diversity and Functional Potential in Two Athalassohaline Lagoons in the Monegros Desert (NE Spain)

by Mercedes Berlanga, Arnau Blasco, Ricardo Guerrero, Andrea Butturini and Jordi Urmeneta

Microorganisms 2025, 13(10), 2224; https://doi.org/10.3390/microorganisms13102224 - 23 Sep 2025

Abstract

This study compared bacterial diversity and putative functionality between two saline lagoons, La Muerte and Salineta, in the Monegros desert ecosystem. Amplicon sequencing analysis revealed distinct taxonomic and functional patterns between the lagoons. Pseudomonadota dominated both systems, averaging 31.0% in La Muerte and [...] Read more.

This study compared bacterial diversity and putative functionality between two saline lagoons, La Muerte and Salineta, in the Monegros desert ecosystem. Amplicon sequencing analysis revealed distinct taxonomic and functional patterns between the lagoons. Pseudomonadota dominated both systems, averaging 31.0% in La Muerte and 47.4% in Salineta, reflecting their well-documented osmotic stress tolerance. However, significant compositional differences were observed: Cyanobacteriota comprised 18.4% of La Muerte communities but remained below 1% in Salineta, while Bacteroidota showed higher abundance in La Muerte (16.6%) compared to Salineta (6.7%). Principal coordinate analysis demonstrated strong community differentiation between lagoons (Bray–Curtis dissimilarity p < 0.05). Functional profiling revealed contrasting metabolic capabilities: La Muerte communities showed enhanced autotrophic carbon fixation pathways (especially the Calvin–Benson cycle) and nitrogen cycling processes, while Salineta exhibited stronger denitrification signatures indicative of anoxic conditions. Carbohydrate indices suggested different organic matter quality and polymer composition between lagoons. La Muerte demonstrated significantly elevated stress response mechanisms compared to Salineta, which can be attributed to its ephemeral, shallow, and high evaporation rates that collectively generate more severe osmotic, thermal, and oxidative stress conditions for the sediment microbiota. These findings demonstrate that site-specific environmental factors, including hydroperiod variability and salinity dynamics, strongly influence microbial community structure and metabolic potential in saline wetland ecosystems. Full article

(This article belongs to the Special Issue Interaction Between Microorganisms and Environment)

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Open AccessReview

Probiotics as Adjuvants to Standard Helicobacter pylori Treatment: Evidence for the Use of Lacidofil^®, an Established Blend of Thoroughly Characterized Strains

by Noémie Auclair-Ouellet, Annie Tremblay, Ola Kassem, Sara E. Caballero-Calero, Stéphane Bronner and Sylvie Binda

Microorganisms 2025, 13(10), 2223; https://doi.org/10.3390/microorganisms13102223 - 23 Sep 2025

Abstract

Helicobacter pylori (H. pylori) is a bacterial pathogen that infects half of the world population. While standard treatment was initially effective, eradication rates have declined over the last 20 to 30 years, and the use of adjuvants, such as probiotic supplements, [...] Read more.

Helicobacter pylori (H. pylori) is a bacterial pathogen that infects half of the world population. While standard treatment was initially effective, eradication rates have declined over the last 20 to 30 years, and the use of adjuvants, such as probiotic supplements, has been suggested to improve efficacy. This review presents evidence supporting the use of Lacidofil^®, an established blend of two thoroughly characterized probiotic strains, as an adjuvant to standard therapy for H. pylori eradication. The microbiology and epidemiology of H. pylori infection as well as current approaches to diagnosis and treatment are summarized, and the roles of probiotics to support standard H. pylori treatment are outlined. Lacidofil^® and its component strains are described, and evidence from eight clinical trials supporting its efficacy is presented. H. pylori eradication rates were increased in participants receiving Lacidofil^® (90–100%) compared to controls (70–86.7%), and the incidence of side effects was decreased (e.g., antibiotic-associated diarrhea—Lacidofil^®: 0–13.6%; controls: 20–40.9%). Published summaries, including systematic reviews with meta-analysis and an umbrella review, are discussed. To expand on the discussion of clinical studies, in vivo and in vitro studies are reviewed, including studies using state-of-the-art molecular methods. They characterize Lacidofil^®’s mechanism of action and further support its efficacy as an adjuvant strategy for H. pylori eradication, side effect reduction, and return to gut microbiota homeostasis. Full article

(This article belongs to the Special Issue Helicobacter pylori and Related Gastrointestinal Diseases: Infection, Treatment, Prevention, and Beyond)

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Open AccessArticle

The Role of Nitric Oxide in HSV-1 Infection: The Use of an Inducible Nitric Synthase Inhibitor Aminoguanidine to Treat Neuroinflammation

by Magdalena Patrycy, Martyna Janicka, Agnieszka Kauc, Aleksandra Osińska, Małgorzata Antos-Bielska, Klaudia Bylińska, Oliwia Obuch-Woszczatyńska, Paweł Szymański, Marcin Chodkowski and Małgorzata Krzyżowska

Microorganisms 2025, 13(10), 2222; https://doi.org/10.3390/microorganisms13102222 - 23 Sep 2025

Abstract

Herpes simplex virus-1 (HSV-1) is a neurotropic virus that can infect the brain, and an uncontrolled infection can lead to severe encephalitis. NO can exert both antiviral as well as cytotoxic effects in the central nervous system (CNS) depending on its concentration and [...] Read more.

Herpes simplex virus-1 (HSV-1) is a neurotropic virus that can infect the brain, and an uncontrolled infection can lead to severe encephalitis. NO can exert both antiviral as well as cytotoxic effects in the central nervous system (CNS) depending on its concentration and site of infection. In this study, we report that treatment of an intranasal murine HSV-1 infection with aminoguanidine (AMG) decreases both neuroinflammation and neurodegeneration markers, but its positive effect depends on the time of treatment. Specifically, early treatment with AMG impaired the activation of microglia/monocytes, leading to decreased virus-specific antiviral response and higher viral titers in the brain. However, AMG treatment during the peak of brain infection significantly improved antiviral response, reduced inflammation and improved general clinical score. We also found that treatment with AMG decreased beta amyloid levels during both primary and latent infections and protected from the accumulation of phosphorylated Tau protein during early infection. Our findings position inducible nitric oxide synthetase (iNOS) as a potential therapeutic target for mitigating virus-induced neuroinflammation and neurodegeneration. Full article

(This article belongs to the Special Issue Immunity and Viral Immune Evasion Strategies: Recent Insights)

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