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Volume 16, April
 
 

Microbiol. Res., Volume 16, Issue 5 (May 2025) – 9 articles

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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
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
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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 91
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 157
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 149
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 178
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 193
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 280
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 179
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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