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Microbiology Research
Volume 16
Issue 5
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Microbiol. Res., Volume 16, Issue 5 (May 2025) – 20 articles

Cover Story (view full-size image): Vitreoscilla sp. C1 carries a functional Krebs cycle and the genes for a branched aerobic respiratory chain, minus the genes for complexes III and IV, and our results show that Vitreoscilla sp. C1 sugar metabolism is carried out through a unique pathway that shunts intermediaries from glycolysis, bypassing phosphofructokinase-I, into the non-oxidative section of the pentose phosphate pathway, reducing its oxygen dependency, which appears as an adaptation to the microaerophilic environment that this organism inhabits. Although Vitreoscilla sp. C1 features a simplified respiratory chain, experimental data demonstrate that all predicted branches are functional, with two main dehydrogenases and two terminal oxidases. View this paper
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20 pages, 3633 KiB  
Article
Identification and Evaluation of the Salt and Acid—Alkaline Resistance of Rhizobium Species of Desmodium
by Yunchi Zhu, An Hu, Xinyong Li, Lijuan Luo and Rongshu Dong
Microbiol. Res. 2025, 16(5), 106; https://doi.org/10.3390/microbiolres16050106 - 21 May 2025
Viewed by 98
Abstract
Inoculation with Rhizobium can improve not only host yield and quality but also host adaptability to stress. The match between inoculated strains and hosts and resistance to stress are the key factors determining the inoculation effect. Four types of Desmodium, Pleurolobus gangeticus [...] Read more.
Inoculation with Rhizobium can improve not only host yield and quality but also host adaptability to stress. The match between inoculated strains and hosts and resistance to stress are the key factors determining the inoculation effect. Four types of Desmodium, Pleurolobus gangeticus, Puhuaea sequax, Grona heterocarpos, and Polhillides velutina, were used to capture Rhizobium strains in soil, and the phylogenetic classification and salt and acid—alkaline resistances of the strains were determined through isolation, identification, and different salt and pH treatments. The phylogenetic classification of the 62 rhizobial strains was determined by 16S rDNA analysis. After comparison, the strains were grouped into 10 groups with known strains of rhizobia, including 14 strains of fast-growing rhizobia grouped with Rhizobium tropici and Rhizobium oryzicola and 48 strains of slow-growing rhizobia. The salt tolerance and acid—base adaptability of 52 strains were qualitatively and quantitatively determined in this study, and salt stress was found to have varying effects on the growth of different strains. Some strains grew normally on media with NaCl concentrations of 0.4 and 0.35 mol/L and had strong salt tolerance. The plants grew normally on media with pH 5–9. This study provides theoretical support for the classification of Desmodium and provides efficient Rhizobium strains for the cultivation and application of Desmodium. Full article
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24 pages, 767 KiB  
Review
The Potential of Beneficial Microbes for Sustainable Alternative Approaches to Control Phytopathogenic Diseases
by Ramadan Bakr, Ali Abdelmoteleb, Vianey Mendez-Trujillo, Daniel Gonzalez-Mendoza and Omar Hewedy
Microbiol. Res. 2025, 16(5), 105; https://doi.org/10.3390/microbiolres16050105 - 20 May 2025
Viewed by 199
Abstract
Sustainable agricultural practices are essential for eradicating global hunger, especially in light of the growing world population. Utilizing natural antagonists, such as fungi and bacteria, to combat plant diseases, rather than relying solely on synthetic chemical pesticides, which pose significant risks to the [...] Read more.
Sustainable agricultural practices are essential for eradicating global hunger, especially in light of the growing world population. Utilizing natural antagonists, such as fungi and bacteria, to combat plant diseases, rather than relying solely on synthetic chemical pesticides, which pose significant risks to the environment and human health, is known as biocontrol. Microbial biological control agents (MBCAs) have proven effective against phytopathogens and are increasingly embraced in agricultural practices. MBCAs possess several beneficial traits, including antagonistic potential, rhizosphere competence, and the ability to produce lytic enzymes, antibiotics, and toxins. These biocontrol mechanisms directly target soil-borne pathogens or indirectly stimulate a plant-mediated resistance response. The effectiveness of MBCAs in managing plant diseases depends on various mechanisms, such as hyperparasitism, antibiosis, competition for nutrients or space, disruption of quorum-sensing signals, production of siderophores, generation of cell wall-degrading enzymes, and the induction and priming of plant resistance. Formulating effective biopesticides requires optimal conditions, including selecting effective strains, considering biosafety, appropriate storage methods, and ensuring a prolonged shelf life. Therefore, formulation is crucial in developing pesticide products, particularly concerning efficacy and production costs. However, several challenges must be addressed to ensure the successful application of biological control, including the shelf life of biopesticides, slower efficacy in pest management, inadequate awareness and understanding of biocontrol methods, regulatory registration for commercialization, and suitable agricultural applications. This review clarifies the principles of plant disease biocontrol, highlighting the mechanisms of action and functionality of MBCAs in biocontrol activities, the formulation of biopesticides derived from microorganisms, and the challenges and barriers associated with the development, registration, commercialization, and application of biopesticides. Full article
(This article belongs to the Collection Microorganisms and Their Incredible Potential to Face Societal Challenges)
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18 pages, 1935 KiB  
Review
Progress in CRISPR Technology for Antiviral Treatments: Genome Editing as a Potential Cure for Chronic Viral Infections
by Fatemeh Nouri, Farnaz Alibabaei, Behina Forouzanmehr, Hamed Tahmasebi, Valentyn Oksenych and Majid Eslami
Microbiol. Res. 2025, 16(5), 104; https://doi.org/10.3390/microbiolres16050104 - 20 May 2025
Viewed by 251
Abstract
The CRISPR–Cas system has transformed molecular biology by providing precise tools for genome editing and pathogen detection. Originating from bacterial adaptive immunity, CRISPR technology identifies and cleaves genetic material from pathogens, thereby preventing infections. CRISPR–Cas9, the most widely utilized variant, creates double-stranded breaks [...] Read more.
The CRISPR–Cas system has transformed molecular biology by providing precise tools for genome editing and pathogen detection. Originating from bacterial adaptive immunity, CRISPR technology identifies and cleaves genetic material from pathogens, thereby preventing infections. CRISPR–Cas9, the most widely utilized variant, creates double-stranded breaks in the target DNA, enabling genetic disruptions or edits. This approach has shown significant potential in antiviral therapies, addressing chronic infections, such as HIV, SARS-CoV-2, and hepatitis viruses. In HIV, CRISPR–Cas9 edits the essential viral genes and disrupts latent reservoirs, while CCR5 gene modifications render the T cells resistant to viral entry. Similarly, SARS-CoV-2 is targeted using CRISPR–Cas13d to inhibit the conserved viral genes, significantly reducing viral loads. Hepatitis B and C treatments leverage CRISPR technologies to target conserved genomic regions, limiting replication and expression. Emerging innovations, such as the PAC-MAN approach for influenza and base-editing systems to reduce off-target effects, further highlight the therapeutic versatility of CRISPR. Additionally, advances in Cas12a and Cas13 have driven the development of diagnostic platforms like DETECTR and SHERLOCK, which provide rapid and cost-effective viral detection. Innovative tools like AIOD-CRISPR enable accessible point-of-care diagnostics for early viral detection. Experimental approaches, such as targeting latent HSV-1 reservoirs, highlight the transformative potential of CRISPR in combating persistent infections. Full article
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11 pages, 1233 KiB  
Case Report
Atopobium vaginae: An Overview of the Bacteria Through Clinical Cases
by Anna Vaseruk, Stepan Nedzelskyi, Roksolana Konechna, Halyna Lavryk, Alicja Sękowska and Yulian Konechnyi
Microbiol. Res. 2025, 16(5), 103; https://doi.org/10.3390/microbiolres16050103 - 20 May 2025
Viewed by 166
Abstract
Atopobium vaginae (nowadays Fannyhessea vaginae) is an anaerobic bacterium increasingly implicated not only in bacterial vaginosis (BV) but also in a broader range of infections. Despite growing recognition of its clinical relevance, comprehensive data on the characteristics of A. vaginae remain limited. [...] Read more.
Atopobium vaginae (nowadays Fannyhessea vaginae) is an anaerobic bacterium increasingly implicated not only in bacterial vaginosis (BV) but also in a broader range of infections. Despite growing recognition of its clinical relevance, comprehensive data on the characteristics of A. vaginae remain limited. This study aimed to isolate and thoroughly characterize the clinical strains of A. vaginae from both vaginal and oral cavity samples. A multifaceted methodological approach was employed, including antibiotic susceptibility testing to assess resistance and sensitivity profiles, PCR for genetic identification, and biochemical profiling using the VITEK-2 Compact system. Additionally, the morphological traits and growth dynamics of the isolates were examined. Given the established role of A. vaginae as a significant contributor to BV, the results of this study aim to support the development of evidence-based antimicrobial strategies for effective management of A. vaginae-associated infections. Full article
(This article belongs to the Topic Microbiota Diversity and Its Broader Biological Implications Across Human and Animal Health)
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10 pages, 610 KiB  
Article
Polysaccharides from Marine Bacteria and Their Anti-SARS-CoV-2 Activity
by Tatyana A. Kuznetsova, Natalia V. Krylova, Maksim S. Kokoulin, Elena V. Persiyanova, Olga S. Maistrovskaya, Pavel. G. Milovankin, Yurii A. Belov and Mikhail Yu. Shchelkanov
Microbiol. Res. 2025, 16(5), 102; https://doi.org/10.3390/microbiolres16050102 - 19 May 2025
Viewed by 229
Abstract
This study investigated the anti-SARS-CoV-2 activity of Polysaccharides (PSs) from three species of marine bacteria (Alteromonas nigrifaciens KMM 156, Cobetia amphilecti KMM 3890, and Idiomarina abyssalis KMM 227T). The chemical structure of PSs from marine bacteria is characterized using 1 [...] Read more.
This study investigated the anti-SARS-CoV-2 activity of Polysaccharides (PSs) from three species of marine bacteria (Alteromonas nigrifaciens KMM 156, Cobetia amphilecti KMM 3890, and Idiomarina abyssalis KMM 227T). The chemical structure of PSs from marine bacteria is characterized using 1H and 13C NMR spectroscopy, including 2D NMR experiments. PS from A. nigrifaciens KMM 156 consists of tetrasaccharide repeating units containing two L-rhamnose residues and one residue each of 2-acetamido-2-deoxy-D-glucose and an ether of D-glucose with (R)-lactic acid, 3-O-[(R)-1-carboxyethyl]-D-glucose. PS from C. amphilecti KMM 3890 is constructed from branched trisaccharide repeating units consisting of D-glucose, D-mannose, and sulfated 3-deoxy-D-manno-oct-2-ulosonic acid. A unique PS from deep-sea marine bacterium I. abyssalis KMM 227T consists of branched pentasaccharide repeating units and is characterized by the presence of a rare bacterial polysaccharide component 2-O-sulfate-3-N-(4-hydroxybutanoyl)-3,6-dideoxy-D-glucose. The activity of PSs against SARS-CoV-2 was assessed by inhibition of the virus cytopathogenic effect (CI) in the methylthiazolyl tetrazolium (MTT) test and using a real-time reverse transcription polymerase chain reaction (RT-PCR-RV). Results of the study demonstrate that PSs, which differ in chemical structure, exhibited anti-SARS-CoV-2 activity differences. This is confirmed both in the test of inhibition of the virus CI and in the reduction in the SARS-CoV-2 virus RNA level. PSs from A. nigrifaciens KMM 156 exhibited the strongest anti-SARS-CoV-2 effect, effectively inhibiting the stages of attachment and penetration of SARS-CoV-2 into the cells. Full article
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12 pages, 748 KiB  
Article
Evaluation of Antimicrobial Activity of Different Essential Oil Gutta–Percha Solvents Against Enterococcus faecalis and Candida albicans
by Media Saeed
Microbiol. Res. 2025, 16(5), 101; https://doi.org/10.3390/microbiolres16050101 - 19 May 2025
Viewed by 195
Abstract
Essential oils are a common alternative to chloroform for dissolving gutta–percha. This study evaluated the antimicrobial effects of chloroform and six essential oil gutta–percha solvents: eucalyptus oil, orange oil, clove oil, rosemary oil, grapefruit oil, and castor oil, against Enterococcus faecalis and Candida [...] Read more.
Essential oils are a common alternative to chloroform for dissolving gutta–percha. This study evaluated the antimicrobial effects of chloroform and six essential oil gutta–percha solvents: eucalyptus oil, orange oil, clove oil, rosemary oil, grapefruit oil, and castor oil, against Enterococcus faecalis and Candida albicans by using disk diffusion techniques. The impregnated sterile disk with 10 μL of pure, tested solvents was inoculated on agar plates at three time contacts: 3 min, 10 min, and 24 h. The mean diameter of the zone of inhibition (ZOI) of each solvent was measured after 24 h of incubation. Against Enterococcus faecalis, in both 3 min and 10 min contact, rosemary oil had the largest ZOI (11.40 ± 0.90 and 11.55 ± 0.68 mm), and orange oil showed the smallest ZOI (7.90 ± 0.31 and 9.05 ± 0.68 mm), respectively. Eucalyptus oil exhibited ZOI with persistence, while grapefruit oil and castor oil showed no ZOI. After 24 h of contact, the largest ZOI was recorded for orange oil. Against Candida albicans, at all three time points, clove oil produced the largest ZOI (20.25 ± 0.82, 23.10 ± 0.93, 30.59 ± 0.74 mm) and chloroform the smallest (10.4 ± 0.77, 9.85 ± 0.62, 11.6 ± 0.65 mm), for 3 min, 10 min, and 24 h, respectively. Conclusively, clove oil, orange oil, and rosemary oil exhibit significant antimicrobial activity like chloroform. Full article
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26 pages, 3678 KiB  
Review
Azo Dyes and the Microbial World: Synthesis, Breakdown, and Bioactivity
by Valery M. Dembitsky and Alexander O. Terent’ev
Microbiol. Res. 2025, 16(5), 100; https://doi.org/10.3390/microbiolres16050100 - 16 May 2025
Viewed by 166
Abstract
This review discusses natural and synthetic azo compounds found in bacteria, fungal endophytes, fungi, plants, and invertebrates. More than 100 of these compounds have demonstrated significant pharmacological activity, including antitumor, antimicrobial, and antibacterial effects. Using mathematical algorithms and the PASS program, researchers predict [...] Read more.
This review discusses natural and synthetic azo compounds found in bacteria, fungal endophytes, fungi, plants, and invertebrates. More than 100 of these compounds have demonstrated significant pharmacological activity, including antitumor, antimicrobial, and antibacterial effects. Using mathematical algorithms and the PASS program, researchers predict new potential applications based on their structure–activity relationships. This review emphasizes the importance of natural azo compounds as promising drug prototypes and key players in drug discovery. It also explores the synthesis and degradation of azo dyes and their potential uses in medicine, food, cosmetics, and related fields. Additionally, the role of microorganisms in producing natural azo compounds and their synthetic counterparts is examined, showcasing their potential in drug development and human health advancements. Full article
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17 pages, 484 KiB  
Article
Microbiological and Molecular Characterization of Bacterial Communities in Domestic Water Sources in Nabuti Village, Mukono District, Central Uganda
by Catherine A. Najjembe, Oluwatoyin M. Aladejana, Jessica N. Uwanibe, Christian T. Happi and Onikepe A. Folarin
Microbiol. Res. 2025, 16(5), 99; https://doi.org/10.3390/microbiolres16050099 - 15 May 2025
Viewed by 193
Abstract
Access to clean and safe water is crucial for community well-being. Water samples from storage tank water (STW) and municipal tap water (MTW) were aseptically collected, and total bacterial and coliform counts were determined. Isolates were Gram-stained, and conventional biochemical tests were conducted. [...] Read more.
Access to clean and safe water is crucial for community well-being. Water samples from storage tank water (STW) and municipal tap water (MTW) were aseptically collected, and total bacterial and coliform counts were determined. Isolates were Gram-stained, and conventional biochemical tests were conducted. Antibiotic susceptibility testing was performed using Kirby–Bauer’s disk diffusion technique. Selected isolates were confirmed through Sanger sequencing of amplified 16S rRNA genes. Polymerase chain reaction and gel electrophoresis techniques were used to determine the presence of quinolone and beta-lactam resistance genes. A total of 50 water samples were analyzed. The mean total coliform counts (TCCs) were 5.75 for STW and 5.5 for MTW. In total, 43 and 13 bacterial isolates were recovered from STW and MTW, respectively, with Gram-negative bacteria being more prevalent 58.14% (25/43) in STW and 81.82% (9/11) in MTW. The isolates appeared to belong to seven different presumptive bacterial genera on biochemical tests. The 16S rRNA gene amplicon Sanger sequencing of 38 isolates revealed 15 different species. A total of 38 isolates tested for resistance genes revealed that 47.37%, 31.58%, 21.05%, 10.53%, 28.95%, and 13.16% harbored gyrB, parC, gyrA, parE, blaSHV, and blaTEM genes, respectively. Antibiotic susceptibility profiling revealed a predominance of multidrug-resistant (MDR) strains among the bacterial isolates from both water sources. Regular monitoring and enhanced water treatment are critical to protect the public health and reduce the spread of potential pathogenic and antibiotic-resistant bacterial strains in household water systems. Full article
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10 pages, 2632 KiB  
Communication
Nematophagous Fungi Occurrence: Prediction Using Bioclimatic Variables
by Ana Martha Cruz-Avalos, Montserrat Chagoya-Sánchez, César Andres Ángel-Sahagún, Ana Isabel Mireles-Arriaga, Griselda Maki-Díaz, René Loredo-Portales and Jesús Hernández-Ruíz
Microbiol. Res. 2025, 16(5), 98; https://doi.org/10.3390/microbiolres16050098 - 14 May 2025
Viewed by 180
Abstract
This study aimed to identify bioclimatic variables that favour the occurrence of three fungal species of the genus Arthrobotrys. For this purpose, 122 samples were collected from agricultural soils, 41 of which were positive for nematophagous fungi. In total, 13 pure Arthrobotrys [...] Read more.
This study aimed to identify bioclimatic variables that favour the occurrence of three fungal species of the genus Arthrobotrys. For this purpose, 122 samples were collected from agricultural soils, 41 of which were positive for nematophagous fungi. In total, 13 pure Arthrobotrys spp. cultures tested positive for pathogenicity to entomopathogenic nematodes and were identified at the species level based on their morphology and morphometry. The environmental and bioclimatic characteristics of positive sampling sites were evaluated using the maximum entropy algorithm, with 22 bioclimatic variables as predictors; among them, the main variables that promoted the occurrence of Arthrobotrys spp. were moisture regime (35.1%), precipitation of warmest quarter (21.3%), and altitude (20.5%). The total surface area with these conditions was 109,568 ha. In Guanajuato, Mexico, conditions favour the occurrence of nematophagous fungi. The bioclimatic variables that increased the incidence of the genus Arthrobotrys were moisture regime, precipitation of the warmest quarter, and altitude. The municipalities in Guanajuato of Abasolo (001), Irapuato (017), Jaral del progreso (018), León (020), Pueblo Nuevo (024), Salamanca (027), and Valle de Santiago (042) encompass regions conducive to finding nematophagous fungi. Full article
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17 pages, 2511 KiB  
Article
Serratia marcescens Strain VIRS2 Isolated from Saline Soil Enhances Rice Growth and Salt Tolerance
by Tuong M. Ho, Manh V. Le, Ha H. T. Nguyen, Quyen Phan, Thao P. Bui, Linh K. Ly, Van B. Lam, Michiel Vandecasteele, Sofie Goormachtig, Ha H. Chu and Phat T. Do
Microbiol. Res. 2025, 16(5), 97; https://doi.org/10.3390/microbiolres16050097 - 9 May 2025
Viewed by 296
Abstract
Soil salinization, a major challenge caused by climate change over the past century, critically affects cultivated land and consequently reduces agricultural production worldwide. Recently, plant growth-promoting rhizobacteria have been collected and utilized to enhance plant growth and mitigate the effects of salt stress [...] Read more.
Soil salinization, a major challenge caused by climate change over the past century, critically affects cultivated land and consequently reduces agricultural production worldwide. Recently, plant growth-promoting rhizobacteria have been collected and utilized to enhance plant growth and mitigate the effects of salt stress in different plant species including rice. In our current study, the Serratia marcescens strain VIRS2 with remarkable salt tolerance was successfully isolated from the saline soil in the Mekong River Delta of Vietnam. This isolate exhibited diverse plant growth-promoting properties, especially the production of a high indole acetic acid level. Treatments under both in vitro and greenhouse conditions indicated that VIRS2 could enhance growth and salt tolerance in rice. The VIRS2-inoculated rice plants exhibited biochemical profile alterations including proline, malondialdehyde, and relative water contents. In addition, the expression of genes involved in the plant stress response pathways was upregulated in the VIRS2-inoculated rice under salt treatments. Importantly, the whole genome sequencing data of VIRS2 also showed the presence of different genes associated with plant growth-promotion and stress-tolerance mechanisms. These results indicated the potential of the VIRS2 isolate for enhancing growth and salt tolerance in rice as well as other important crops. Full article
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10 pages, 1710 KiB  
Article
First Insights into the Biological Activity and Molecular Docking of Citral (3,7-Dimethyl-2, 6-Octadienal) Against Trichomonas vaginalis
by Alexia Brauner de Mello, Juliana Montelli Fenalti, Bruna Baccega, Yan Wahast Islabão, Filipe Obelar Martins, Paloma Taborda Birmann, Angela Maria Casaril, Tallyson Nogueira Barbosa, Angela Sena-Lopes, Francieli Liz Monteiro, Lucielli Savegnago, Sibele Borsuk, Silvia de Oliveira Hubner, Nara de Amélia da Rosa Farias, Alexandra Ibáñez-Escribano and Camila Belmonte Oliveira
Microbiol. Res. 2025, 16(5), 96; https://doi.org/10.3390/microbiolres16050096 - 9 May 2025
Viewed by 205
Abstract
The increasing resistance of Trichomonas vaginalis to the only approved chemical family of drugs for treatment, the 5-nitroimidazoles, has prompted the exploration of new therapeutic agents against this prevalent non-viral sexually transmitted infection. Natural products have emerged as a significant source of novel [...] Read more.
The increasing resistance of Trichomonas vaginalis to the only approved chemical family of drugs for treatment, the 5-nitroimidazoles, has prompted the exploration of new therapeutic agents against this prevalent non-viral sexually transmitted infection. Natural products have emerged as a significant source of novel treatments for trichomoniasis. The aim of this study was to evaluate the anti-T. vaginalis activity of citral (3,7-dimethyl-2,6-octadienal), the main constituent of the essential oil of Cymbopogon species, commonly known as lemongrass. Our findings indicate that citral exhibits a minimum inhibitory concentration (MIC) of 100 μM, effectively inhibiting the growth of T. vaginalis trophozoites within 12 h of exposure, and a 50% inhibitory concentration (IC50) of approximately 40 μM after 24 h. Furthermore, the evaluation of nitric oxide (NO) levels suggests that citral possesses antioxidant properties. Molecular docking studies reveal a weak interaction with three parasite proteins: thioredoxin reductase (TvTrxR), purine nucleoside phosphorylase (TvPNP), and methionine gamma lyase (TvMGL). The present study highlights the potential of citral as a candidate for the development of no-nitroimidazole drugs, offering new avenues for trichomoniasis treatment and underscoring the importance of further investigation into citral’s mechanism of action. Full article
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19 pages, 2564 KiB  
Article
Genomic Insights into Plant Growth-Promoting Traits of Lysinibacillus fusiformis and Bacillus cereus from Rice Fields in Panama
by Celestino Aguilar, Rito Herrera, José L. Causadías, Betzaida Bernal, Oris Chavarria, Claudia González, Jessica Gondola, Ambar Moreno and Alexander A. Martínez
Microbiol. Res. 2025, 16(5), 95; https://doi.org/10.3390/microbiolres16050095 - 7 May 2025
Viewed by 236
Abstract
Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice ( [...] Read more.
Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice (Oryza sativa L.) were identified. In this study, we sequenced, assembled, and annotated the genomes of Lysinibacillus fusiformis C6 and 24, and Bacillus cereus D23 and 59. The C6 genome was 4,754,472 bp long with 10 contigs, 37.62% guanine-cytosine (GC) content, and 4657 coding sequences (CDS). The 24 genome was 4,683,219 bp with five contigs, 37.65% GC content, and 4550 CDS. The D23 genome was 6,199,908 bp long with 18 contigs, 34.84% GC content, and 6141 CDS. The 59 genome was 6,194,462 bp with 21 contigs, 34.87% GC content, and 6122 CDS. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) confirmed that C6 and 24 belong to Lysinibacillus fusiformis, whereas D23 and 59 belong to the Bacillus cereus species. Further results revealed that these bacteria contained genes characteristic of plant growth-promoting bacteria, such as siderophore, phytohormone auxin (IAA) production, and nitrogen-fixing abilities that promote plant growth. Moreover, the antiSMASH database identified gene clusters involved in secondary metabolite production (biosynthetic gene clusters), such as betalactone, NRPS-like, NRP-siderophore, terpene, and RiPP-like clusters. Moreover, diverse and novel biosynthetic clusters (BCGs) have included non-ribosomal peptides (NRPs), polyketides (PKs), bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). This work offers new insights into the genomic basis of the studied strains’ plant growth-promoting capabilities. Full article
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10 pages, 1298 KiB  
Article
Energy Metabolism and Aerobic Respiratory Chain of Vitreoscilla sp. C1: Comparison with β-Proteobacteria
by Paul T. Nguyen, Yuyao Hu, Anne Caroline Mascarenhas dos Santos, Pingdong Liang, Benjamin C. Stark, Karina Tuz and Oscar Juárez
Microbiol. Res. 2025, 16(5), 94; https://doi.org/10.3390/microbiolres16050094 - 4 May 2025
Viewed by 283
Abstract
As the source of the first reported class of non-mammalian hemoglobin, Vitreoscilla sp. C1 is a historically important microorganism that has offered important clues to understanding how bacteria can thrive at low oxygen tension, with potential applications to wastewater and sludge bioengineering. However, [...] Read more.
As the source of the first reported class of non-mammalian hemoglobin, Vitreoscilla sp. C1 is a historically important microorganism that has offered important clues to understanding how bacteria can thrive at low oxygen tension, with potential applications to wastewater and sludge bioengineering. However, the processes that enable this bacterium to thrive in such environments remain unclear. In this study, we analyzed the published Vitreoscilla sp. C1 genome to predict the core metabolic pathways used by this microorganism to support cell growth under hypoxic conditions, compared them with the predicted metabolism of other important β-proteobacteria, and tested Vitreoscilla’s respiratory activity in vitro in the presence of various substrates and inhibitors. Vitreoscilla sp. C1 carries a functional Krebs cycle and the genes for a branched aerobic respiratory chain, minus the genes for complexes III and IV, and our results show that Vitreoscilla sp. C1 sugar metabolism is carried out through a unique pathway that shunts intermediaries from glycolysis, bypassing phosphofructokinase-I, into the non-oxidative section of the pentose phosphate pathway, reducing its oxygen dependency, which appears as an adaptation to the microaerophilic environment that this organism inhabits. Although Vitreoscilla sp. C1 features a simplified respiratory chain, experimental data demonstrate that all predicted branches are functional, with two main dehydrogenases and two terminal oxidases. Full article
(This article belongs to the Topic Redox in Microorganisms, 2nd Edition)
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11 pages, 1349 KiB  
Article
Detoxification of Ustiloxin A by Hydroxylation of Endophytic Fungus Petriella setifera Nitaf10
by Peng Li, Xuwen Hou, Gan Gu, Daowan Lai and Ligang Zhou
Microbiol. Res. 2025, 16(5), 93; https://doi.org/10.3390/microbiolres16050093 - 29 Apr 2025
Viewed by 175
Abstract
Ustiloxins are a kind of cyclopeptide mycotoxins produced by rice false smut pathogen Villosiclava virens, which seriously threatens the safe production of rice and health of humans and animals. Hydroxylation, a biotransformation reaction that regio- and stereoselectively introduces a hydroxyl group into [...] Read more.
Ustiloxins are a kind of cyclopeptide mycotoxins produced by rice false smut pathogen Villosiclava virens, which seriously threatens the safe production of rice and health of humans and animals. Hydroxylation, a biotransformation reaction that regio- and stereoselectively introduces a hydroxyl group into the molecule catalyzed by the hydroxylase produced by organisms, has been considered an efficient way to detoxify mycotoxins. In this study, the endophytic fungus Petriella setifera Nitaf10 was found to be able to detoxify ustiloxin A, the main toxic component in V. virens. In addition to the two main transformed products previously identified, ustiloxins A1 and A2, an additional transformed product was obtained by using cell-free extract (CFE) of P. setifera Nitaf10 prepared with 5 mmol/L of pH 9.0 carbonate-buffered solution (CBS). It was structurally characterized as a novel ustiloxin analog named 13-hydroxy ustiloxin A (1) by analysis of the 1D and 2D NMR and HRESIMS spectra as well as by comparison with known ustiloxins. Biotransformation reaction of ustiloxin A was found to proceed via hydroxylation, and was possibly catalyzed by the intracellular hydroxylase in the CFE. The cytotoxic and phytotoxic activities of 13-hydroxy ustiloxin A (1) were much weaker than those of ustiloxin A. Detoxification of ustiloxin A by hydroxylation of P. setifera will be an efficient strategy. Full article
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22 pages, 2721 KiB  
Review
Gut Bacteria-Based Cancer Therapy and Anti-Solid Tumor Mechanisms
by Tianzhu Zhang, Xiao-Mei Yu, Shang-Tian Yang and Wen-Wen Zhou
Microbiol. Res. 2025, 16(5), 92; https://doi.org/10.3390/microbiolres16050092 - 26 Apr 2025
Viewed by 415
Abstract
Cancer constitutes a significant global health challenge, ranking among the leading contributors to worldwide mortality. The inherent limitations of conventional oncologic interventions, particularly their frequent inability to induce durable remissions in advanced malignancies, continue to drive transformative explorations into novel therapeutic paradigms. In [...] Read more.
Cancer constitutes a significant global health challenge, ranking among the leading contributors to worldwide mortality. The inherent limitations of conventional oncologic interventions, particularly their frequent inability to induce durable remissions in advanced malignancies, continue to drive transformative explorations into novel therapeutic paradigms. In recent years, bacteria-based therapies have gained recognition in the management of solid tumors. Compared to traditional therapeutic modalities, extensive research has demonstrated that bacteria possess remarkable anticancer properties. Gut bacteria, which naturally coexist within the human body, represent a unique category of living cells with inherent advantages for solid tumor treatment. These microorganisms are characterized by their relative safety, ease of cultivation, and potential for use in precision medicine through genetic modifications. Furthermore, gut bacteria exhibit diverse mechanisms of action against tumor cells, with different bacterial species potentially exerting synergistic effects. However, the precise anticancer mechanisms of these bacteria, particularly those of gut microbiota, require further detailed investigation. This review categorizes anticancer gut bacteria according to their effects on cancer cells and elucidates their anticancer mechanisms across five domains: modification of the tumor microenvironment, competitive inhibition, activation of immune cells, vectors for gene therapy, and production of bacterial anticancer biomolecules. Additionally, we discuss the potential challenges of utilizing different gut bacteria for cancer treatment, highlight their anticancer advantages, and suggest promising directions for future research. Ultimately, this review serves as a comprehensive guide for utilizing both natural and engineered gut bacteria as therapeutic agents against solid tumors in cancer treatment. Full article
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14 pages, 3517 KiB  
Article
In Utero Exposure to 2,3,7,8-Tetrachlorodibenzo-p-dioxin Impairs the Ability of Mice to Clear a Pseudomonas aeruginosa Infection in Adulthood
by Victoria R. Stephens, Julia K. Bohannon, Kaylon L. Bruner-Tran, Xenia D. Davis, Mary A. Oliver, Margaret A. McBride, Sharareh Ameli, Jelonia T. Rumph, Jennifer A. Gaddy, Edward R. Sherwood and Kevin G. Osteen
Microbiol. Res. 2025, 16(5), 91; https://doi.org/10.3390/microbiolres16050091 - 26 Apr 2025
Viewed by 214
Abstract
Exposure to endocrine-disrupting chemicals (EDCs) has been linked to several pathologies in human health, especially those involving the immune system. The vast majority of studies have focused on cells and functions of the adaptive immune system with little investigation of the impact of [...] Read more.
Exposure to endocrine-disrupting chemicals (EDCs) has been linked to several pathologies in human health, especially those involving the immune system. The vast majority of studies have focused on cells and functions of the adaptive immune system with little investigation of the impact of EDCs on innate immunity. While EDC exposure remains a threat throughout the lifetime of an individual, the most detrimental effects on human health occur during critical stages of development, such as in utero. Fetal development is not only associated with growth and tissue remodeling but also with the establishment of key processes, including those of the immune system. Unfortunately, due to fetal plasticity, developmental exposure to certain EDCs, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), can affect mammalian health well into adulthood by altering fetal programming. Herein, we hypothesize that in utero exposure to TCDD induces developmental reprogramming of the innate immune system that subsequently impacts the adult response to infection. To interrogate our hypothesis, we challenged adult mice with and without a history of in utero TCDD exposure with 1 × 108 CFU Pseudomonas aeruginosa via intraperitoneal injection. Results revealed a significant decrease in the number of innate leukocytes at the site of infection six hours after inoculation in toxicant-exposed mice compared to unexposed mice. The reduction in the number of phagocytes correlated with a reduction in bacterial clearance in toxicant-exposed mice. We also noted a decreased ability of peritoneal immune cells from toxicant-exposed mice to produce chemokines necessary for immune cell recruitment. Taken together, our results indicate that in utero EDC exposure impairs the innate immune response to a bacterial infection in adult offspring, particularly in males. Full article
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19 pages, 9785 KiB  
Article
The Presence of an ESBL-Encoding Plasmid Reported During a Klebsiella pneumoniae Nosocomial Outbreak in the United Kingdom
by Stephen Mark Edward Fordham, Anna Mantzouratou and Elizabeth Sheridan
Microbiol. Res. 2025, 16(5), 90; https://doi.org/10.3390/microbiolres16050090 - 25 Apr 2025
Viewed by 271
Abstract
An EBSL-encoding plasmid, pESBL-PH, was identified during a nosocomial outbreak of Klebsiella pneumoniae ST628 at a United Kingdom general district hospital in 2018. The plasmid from the earliest 2018 K. pneumoniae strain discovered during the outbreak was assembled using both Oxford nanopore long [...] Read more.
An EBSL-encoding plasmid, pESBL-PH, was identified during a nosocomial outbreak of Klebsiella pneumoniae ST628 at a United Kingdom general district hospital in 2018. The plasmid from the earliest 2018 K. pneumoniae strain discovered during the outbreak was assembled using both Oxford nanopore long reads and illumina short reads, yielding a fully closed plasmid, pESBL-PH-2018. pESBL-PH-2018 was queried against the complete NCBI RefSeq Plasmid Database, comprising 93,823 plasmids, which was downloaded on 16 July 2024. To identify structurally similar plasmids, strict thresholds were applied, including a mash similarity ≥0.98. This returned 61 plasmids belonging to 13 unique sequence types (STs) hosts. The plasmids were detected from 13 unique countries, dating from 2012 to 2023. The AMR region of the plasmids varied. Interestingly IS26-mediated tandem amplification of resistance genes, including the ESBL gene blaCTX-M-15 was identified in two independent strains, raising their copy number to three. Furthermore, the genomic background of strains carrying a pESBL-PH-2018-like plasmid were analyzed, revealing truncation of the chromosomal ompK36 porin gene and carbapenem resistance gene carriage on accessory plasmids in 17.85% and 26.78% of strains with a complete chromosome available. This analysis reveals the widespread dissemination of an ESBL-encoding plasmid in a background of resistance-encoding strains, requiring active surveillance. Full article
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18 pages, 3457 KiB  
Essay
Diversity Analysis of Rhizosphere Microorganisms in Helichrysum arenarium (L.) Moench and Screening of Growth-Promoting Bacteria in Xinjiang, China
by Xiaoyan Xin, Wei He, Junhui Zhou, Yong Chen, Xin Huang, Jinyu Yang, Jianjun Xu and Suqin Song
Microbiol. Res. 2025, 16(5), 89; https://doi.org/10.3390/microbiolres16050089 - 25 Apr 2025
Viewed by 276
Abstract
Rhizosphere microorganisms effectively exploit nutrient resources within the rhizosphere, while growth-promoting bacteria in this environment play a vital role in regulating soil fertility and enhancing plant health. In this study, we utilized a comprehensive approach that included the isolation, purification, and identification of [...] Read more.
Rhizosphere microorganisms effectively exploit nutrient resources within the rhizosphere, while growth-promoting bacteria in this environment play a vital role in regulating soil fertility and enhancing plant health. In this study, we utilized a comprehensive approach that included the isolation, purification, and identification of dominant microorganisms, alongside high-throughput sequencing technology. This methodology was employed to analyze the primary microbial groups and their diversity within the rhizosphere soil of Helichrysum arenarium (L.) Moench in Altay, Xinjiang, China. By isolating bacterial strains from the rhizosphere soil using a dilution coating method, we successfully obtained 43 distinct strains. Subsequently, selective media were employed to screen for growth-promoting characteristics among these isolated strains derived from the rhizosphere soil of H. arenarium (L.) Moench. The results, obtained through high-throughput amplification sequencing, revealed diverse bacterial communities belonging to 35 phyla, 93 orders, 215 families, 324 genera, and 231 species associated with H. arenarium (L.) Moench, as well as fungal communities comprising 14 phyla, 47 orders, 96 families, 204 genera, and 571 species present in the rhizosphere soil. Among these identified communities, Actinobacteriota emerged as the predominant bacterial phylum while Ascomycetes and Mortieromycetes were recognized as the principal fungal phyla found in the rhizospheric soil of H. arenarium (L.) Moench. Analysis of culturable bacteria’s promotion activity within this rhizospheric environment indicated that three strains—S16, S31, and S29—exhibited the highest solubility index for inorganic phosphorus; additionally, the screened strains S7 and S10 demonstrated nitrogen-fixing capabilities. Furthermore, ten strains exhibiting excellent iron-bearing capacities were identified; notably, strain S16 displayed the highest D/d value indicating, its superior iron-bearing capacity. The growth-promoting bacteria were identified as Kocuria rosea, Priestia megaterium, Bacillus mobilis, Bacillus bataviensis, three variants of Bacillus mycoides, Bacillus paramobilis, Bacillus sonorensis, and Alcaligenes faecalis. This study provides a foundational understanding of how microorganisms in the rhizosphere of H. arenarium (L.) Moench influence soil nutrient release and offers valuable insights into enhancing yield and quality cultivation by isolating, screening, and identifying growth-promoting bacteria from rhizosphere soil. Full article
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14 pages, 995 KiB  
Article
Tick Dispersal and Borrelia Species in Ticks from Migratory Birds: Insights from the Asinara National Park, Sardinia, Italy
by Valentina Chisu, Laura Giua, Piera Bianco, Cipriano Foxi, Giovanna Chessa, Giovanna Masala and Ivana Piredda
Microbiol. Res. 2025, 16(5), 88; https://doi.org/10.3390/microbiolres16050088 - 23 Apr 2025
Viewed by 371
Abstract
Rapid environmental changes driven by human activities are contributing to a significant decline in global biodiversity, with avian species being particularly affected due to their migratory behavior. As highly mobile hosts, birds facilitate the geographic dispersal of ectoparasites, including ticks, which serve as [...] Read more.
Rapid environmental changes driven by human activities are contributing to a significant decline in global biodiversity, with avian species being particularly affected due to their migratory behavior. As highly mobile hosts, birds facilitate the geographic dispersal of ectoparasites, including ticks, which serve as vectors for numerous zoonotic pathogens. This study, conducted in collaboration with the Faunistic Observatory of the Asinara National Park between 2021 and 2023, aimed to investigate the potential role of migratory birds in tick dispersal and the presence of Borrelia spp. DNA. Birds were captured using mist nets during pre-breeding (April–May) and post-breeding (October–November) migration periods. Ticks were systematically collected and identified at the species level, and molecular analyses were performed using real-time and conventional PCR to detect the presence of Borrelia spp. DNA. Results showed a distinct seasonal variation in tick species composition. In autumn, Ixodes ricinus was predominant (99%), whereas Hyalomma species were more frequently observed in spring (78%). Molecular screening revealed Borrelia spp. DNA in 26.1% of the collected ticks, with Borrelia garinii being the most prevalent species. These findings underscore the ecological significance of migratory birds in the dissemination of ticks and tick-borne pathogens, highlighting their potential role in shaping disease transmission dynamics across different geographic regions. This study provides valuable insights into the seasonal fluctuations in tick populations associated with migratory avifauna and the epidemiological risks posed by these interactions. Continued surveillance of migratory birds as vectors of zoonotic pathogens is essential for informing public health strategies and mitigating the risks of emerging infectious diseases, but further investigation is needed to clarify the actual role of migratory birds in the transmission of Borrelia spp. Full article
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13 pages, 2818 KiB  
Article
Dual Detection of Pathogenic tdh and trh Genes of Vibrio parahaemolyticus in Oysters Using Multienzyme Isothermal Rapid Amplification (MIRA) Combined with Lateral-Flow Dipstick (LFD) Assay
by Seong Bin Park, Sam K. C. Chang, Lin Bi, Yunim Cha and Yan Zhang
Microbiol. Res. 2025, 16(5), 87; https://doi.org/10.3390/microbiolres16050087 - 22 Apr 2025
Viewed by 273
Abstract
Vibrio parahaemolyticus is a foodborne pathogen commonly associated with the consumption of contaminated seafood, particularly oysters. While PCR and real-time PCR are widely used to detect its pathogenicity through tdh and trh gene detection, these methods may not be practical in resource-limited settings [...] Read more.
Vibrio parahaemolyticus is a foodborne pathogen commonly associated with the consumption of contaminated seafood, particularly oysters. While PCR and real-time PCR are widely used to detect its pathogenicity through tdh and trh gene detection, these methods may not be practical in resource-limited settings such as field environments. To address this limitation, a rapid, sensitive, and specific duplex detection method was developed using the multienzyme isothermal rapid amplification (MIRA) assay in combination with lateral flow dipstick (LFD) technology. The assay utilized specific primer sets and probes to simultaneously amplify tdh and trh fragments tagged with 3′-FAM and 5′-Digoxigenin or Biotin during MIRA amplification, enabling the detection via respective antibody capture on the LFD strip. This duplex MIRA-LFD assay demonstrated a detection limit of 100 fg of DNA, 300 CFU/reaction for bacterial culture, and 3000 CFU/reaction for seeded oyster samples at 40 °C within 20 min. Notably, the assay exhibited no cross-reactivity with nine other Vibrio species or 18 foodborne pathogens, confirming its high specificity. Due to its simplicity, rapid turnaround time, and high sensitivity, this duplex MIRA-LFD assay offers a valuable tool for the surveillance of V. parahaemolyticus pathogenicity, aiding in public health protection and supporting the local seafood industry. Full article
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