Pub Date : 2026-01-01DOI: 10.1016/j.crmicr.2025.100545
Janina Rahlff , Pierre Amato
Clouds are aqueous atmospheric systems hosting diverse and active microorganisms. Viruses may also persist despite harsh conditions, support active viral infections, and contribute to microbial dynamics during aerial transport. However, assessing viruses, and even more, virus-bacteria interactions in the atmospheric environment is highly challenging, and knowledge remains very limited. Here, based on current knowledge in cloud microbiology, we estimate the cloud virome at ∼1021 virus particles globally. One out of a million of cloud droplets is susceptible to host virus-bacteria interactions, which represents considerable volume at global scale, and we discuss potential implications for microbial ecology. We finally propose future research directions to explore further the cloud virosphere and its ecological roles.
{"title":"A look into the virosphere of clouds: A world yet to be explored","authors":"Janina Rahlff , Pierre Amato","doi":"10.1016/j.crmicr.2025.100545","DOIUrl":"10.1016/j.crmicr.2025.100545","url":null,"abstract":"<div><div>Clouds are aqueous atmospheric systems hosting diverse and active microorganisms. Viruses may also persist despite harsh conditions, support active viral infections, and contribute to microbial dynamics during aerial transport. However, assessing viruses, and even more, virus-bacteria interactions in the atmospheric environment is highly challenging, and knowledge remains very limited. Here, based on current knowledge in cloud microbiology, we estimate the cloud virome at ∼10<sup>21</sup> virus particles globally. One out of a million of cloud droplets is susceptible to host virus-bacteria interactions, which represents considerable volume at global scale, and we discuss potential implications for microbial ecology. We finally propose future research directions to explore further the cloud virosphere and its ecological roles.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100545"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.crmicr.2026.100550
Liang Liu , Shiqi Zhang , Faxian Wu, Linjing Zhao, Huajie Zhao, Duan Li, Fan Yang, Liang Liu
Vaccination is a promising strategy for preventing Klebsiella pneumoniae infection, yet strain heterogeneity poses a limitation. The optimal antigen target for an anti-Klebsiella pneumoniae vaccine should be expressed by all or most strains. This study identified the TamA protein as highly conserved across Klebsiella pneumoniae strains, irrelevant of serotype. A recombinant TamA protein vaccine was developed and evaluated for protective efficacy against lethal challenge in a murine model. The recombinant TamA was cloned in Escherichia coli and used to immunize mice, resulting in significantly higher total serum IgG concentrations compared to adjuvant-only controls, indicating robust antibody induction. In vitro experiments showed that TamA-induced specific antibodies blocked bacterial adherence to epithelial cells. Following a lethal dose challenge, 80% of TamA-vaccinated mice survived over 10 days, compared to less than 48 h for controls. The TamA recombinant protein vaccine provided protection, with significantly reduced bacterial loads and pathological changes in vaccinated mice. This study suggests TamA as a promising candidate vaccine for preventing Klebsiella pneumoniae infections.
{"title":"The TamA protein as a subunit vaccine improves immune protection against highly virulent Klebsiella pneumoniae infection in mice","authors":"Liang Liu , Shiqi Zhang , Faxian Wu, Linjing Zhao, Huajie Zhao, Duan Li, Fan Yang, Liang Liu","doi":"10.1016/j.crmicr.2026.100550","DOIUrl":"10.1016/j.crmicr.2026.100550","url":null,"abstract":"<div><div>Vaccination is a promising strategy for preventing <em>Klebsiella pneumoniae</em> infection, yet strain heterogeneity poses a limitation. The optimal antigen target for an anti-<em>Klebsiella pneumoniae</em> vaccine should be expressed by all or most strains. This study identified the TamA protein as highly conserved across <em>Klebsiella pneumoniae</em> strains, irrelevant of serotype. A recombinant TamA protein vaccine was developed and evaluated for protective efficacy against lethal challenge in a murine model. The recombinant TamA was cloned in <em>Escherichia coli</em> and used to immunize mice, resulting in significantly higher total serum IgG concentrations compared to adjuvant-only controls, indicating robust antibody induction. In vitro experiments showed that TamA-induced specific antibodies blocked bacterial adherence to epithelial cells. Following a lethal dose challenge, 80% of TamA-vaccinated mice survived over 10 days, compared to less than 48 h for controls. The TamA recombinant protein vaccine provided protection, with significantly reduced bacterial loads and pathological changes in vaccinated mice. This study suggests TamA as a promising candidate vaccine for preventing <em>Klebsiella pneumoniae</em> infections.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100550"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.crmicr.2026.100553
Tong Ma , Yeteng Xu , Xinyue Wang , Zhiyuan Chen , Pengfei Chen , Junming Guo , Shichang Kang , Shanjia Li , Wei Zhang , Tuo Chen , Guangxiu Liu , Binglin Zhang
Glacier retreat driven by global warming is releasing previously sequestered microbial communities, including potential human pathogens, into downstream environments. However, the diversity, ecological assembly mechanisms, and dispersal processes of these bacteria remain largely unknown in high-altitude glacier systems. In this study, we characterized potential pathogenic bacterial communities along a 1200 m elevation gradient (5293–6476 m) on the East Rongbuk Glacier, northern slope of Mount Everest, using high-throughput 16S rRNA gene sequencing for snow, ice, cryoconite, and moraine samples. A total of 833 pathogenic bacterial species were identified, with Proteobacteria and Cyanobacteria dominating the communities. Distinct altitude-dependent variations were observed, with taxa such as Paracoccus_yeei and Sphingomonas_paucimobilis enriched at high elevations. Canonical correspondence analysis indicated that geographic (e.g., altitude, latitude) and environmental variables (e.g., total carbon, organic carbon) significantly influenced community structure. β-nearest taxon index (βNTI) and generalized additive models (GAMs) revealed that both deterministic and stochastic processes governed community assembly. Network analysis suggested that non-pathogenic taxa with high modularity and centrality may suppress potential pathogens through ecological interactions. Source Tracker analysis demonstrated frequent microbial exchange among glacier habitats, with moraine and cryoconite acting as dominant sources. Certain pathogenic taxa showed clear signatures of downstream migration, highlighting the potential risk of glacier-derived pathogen dissemination via meltwater and aeolian processes. This study provides a comprehensive assessment of the diversity, drivers, and dispersal of potential pathogenic bacteria in a high-altitude glacier ecosystem, offering new insights into their ecological dynamics and informing future risk assessments under climate change scenarios.
{"title":"Diversity and transmission processes of potentially pathogenic bacterial communities in the East Rongbuk Glaciers, Mt. Everest","authors":"Tong Ma , Yeteng Xu , Xinyue Wang , Zhiyuan Chen , Pengfei Chen , Junming Guo , Shichang Kang , Shanjia Li , Wei Zhang , Tuo Chen , Guangxiu Liu , Binglin Zhang","doi":"10.1016/j.crmicr.2026.100553","DOIUrl":"10.1016/j.crmicr.2026.100553","url":null,"abstract":"<div><div>Glacier retreat driven by global warming is releasing previously sequestered microbial communities, including potential human pathogens, into downstream environments. However, the diversity, ecological assembly mechanisms, and dispersal processes of these bacteria remain largely unknown in high-altitude glacier systems. In this study, we characterized potential pathogenic bacterial communities along a 1200 m elevation gradient (5293–6476 m) on the East Rongbuk Glacier, northern slope of Mount Everest, using high-throughput 16S rRNA gene sequencing for snow, ice, cryoconite, and moraine samples. A total of 833 pathogenic bacterial species were identified, with Proteobacteria and Cyanobacteria dominating the communities. Distinct altitude-dependent variations were observed, with taxa such as <em>Paracoccus_yeei</em> and <em>Sphingomonas_paucimobilis</em> enriched at high elevations. Canonical correspondence analysis indicated that geographic (e.g., altitude, latitude) and environmental variables (e.g., total carbon, organic carbon) significantly influenced community structure. β-nearest taxon index (βNTI) and generalized additive models (GAMs) revealed that both deterministic and stochastic processes governed community assembly. Network analysis suggested that non-pathogenic taxa with high modularity and centrality may suppress potential pathogens through ecological interactions. Source Tracker analysis demonstrated frequent microbial exchange among glacier habitats, with moraine and cryoconite acting as dominant sources. Certain pathogenic taxa showed clear signatures of downstream migration, highlighting the potential risk of glacier-derived pathogen dissemination via meltwater and aeolian processes. This study provides a comprehensive assessment of the diversity, drivers, and dispersal of potential pathogenic bacteria in a high-altitude glacier ecosystem, offering new insights into their ecological dynamics and informing future risk assessments under climate change scenarios.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100553"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146038052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.crmicr.2025.100539
Kangqiao Dong , Peilin Cai , Liping Lyu , Juan Yang , Yi Wu , Letizia Modeo , Xiao Chen , Jing Xu , Xinpeng Fan
Extrusive organelles (extrusomes) represent a specialized class of dense-core granules in protists that exhibit remarkably complex morphology and secretory mechanisms compared to their metazoan counterparts, reflecting key adaptations in single-celled eukaryote evolution. Protrichocysts, which are among the most intricate projectile extrusomes in ciliates, have thus far been understood primarily in terms of their general morphology. In this study, we employed a comprehensive approach to investigate the protrichocysts of Pseudourostyla cristata, thereby expanding our understanding of these organelles. Through predator-prey interaction experiments and electron microscopy, we demonstrated the ejection of protrichocysts in response to a predator’s attack and revealed that their ejection process consists of three main stages: (i) cap dissolution, (ii) dual-phase body expansion, and (iii) controlled shaft exposure. Histochemical analysis indicated that extruded protrichocysts contain acid mucopolysaccharides and microtubules. SDS-PAGE and HPLC-MS/MS analyses identified the major protein bands and the presence of glycoproteins, phosphoproteins, and potential defense-related proteins. Single-cell transcriptome analysis suggested the involvement of conserved carboxypeptidase-mediated extrusome biogenesis. These findings establish protrichocysts as multifunctional organelles that employ a unique hybrid defense strategy combining mechanical projection with chemical secretion. Their distinctive microtubular cap architecture and specialized matrix composition further suggest potential roles in intercellular communication. Additionally, this research improves our understanding of protist extrusome biology and provides new insights into the evolution of eukaryotic secretory systems.
{"title":"Protrichocysts: a hybrid defense extrusive organelle bridging mechanical projection and chemical secretion in ciliates","authors":"Kangqiao Dong , Peilin Cai , Liping Lyu , Juan Yang , Yi Wu , Letizia Modeo , Xiao Chen , Jing Xu , Xinpeng Fan","doi":"10.1016/j.crmicr.2025.100539","DOIUrl":"10.1016/j.crmicr.2025.100539","url":null,"abstract":"<div><div>Extrusive organelles (extrusomes) represent a specialized class of dense-core granules in protists that exhibit remarkably complex morphology and secretory mechanisms compared to their metazoan counterparts, reflecting key adaptations in single-celled eukaryote evolution. Protrichocysts, which are among the most intricate projectile extrusomes in ciliates, have thus far been understood primarily in terms of their general morphology. In this study, we employed a comprehensive approach to investigate the protrichocysts of <em>Pseudourostyla cristata</em>, thereby expanding our understanding of these organelles. Through predator-prey interaction experiments and electron microscopy, we demonstrated the ejection of protrichocysts in response to a predator’s attack and revealed that their ejection process consists of three main stages: (i) cap dissolution, (ii) dual-phase body expansion, and (iii) controlled shaft exposure. Histochemical analysis indicated that extruded protrichocysts contain acid mucopolysaccharides and microtubules. SDS-PAGE and HPLC-MS/MS analyses identified the major protein bands and the presence of glycoproteins, phosphoproteins, and potential defense-related proteins. Single-cell transcriptome analysis suggested the involvement of conserved carboxypeptidase-mediated extrusome biogenesis. These findings establish protrichocysts as multifunctional organelles that employ a unique hybrid defense strategy combining mechanical projection with chemical secretion. Their distinctive microtubular cap architecture and specialized matrix composition further suggest potential roles in intercellular communication. Additionally, this research improves our understanding of protist extrusome biology and provides new insights into the evolution of eukaryotic secretory systems.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100539"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.crmicr.2026.100551
Xiyan Luo , Pengjie He , Jiajia Zhang , Ping Wang , Wenjia Wang , Xiaoqin Chen , Xiaorui Cheng , Wenyan Cui
Honeysuckle leaf spot disease, caused by Alternaria alternata, severely affects the yield and quality of honeysuckle crops. Biological control using native antagonist microorganisms offers a promising alternative to chemical fungicides. In this study, strain HC-9, previously isolated from honeysuckle leaves, was molecularly identified as Bacillus sp. This strain exhibited broad-spectrum antifungal activity, effectively inhibiting eight phytopathogenic fungi, including A. alternata, with an in vitro inhibition rate of 70.91 %. The cell-free supernatant of HC-9 fermentation broth demonstrated strong antifungal activity (72.79 % inhibition after 48 h of fermentation), which was concentration-dependent and stable under high temperature (100°C), UV exposure (1 h), and acidic conditions, though it was sensitive to alkaline environments. The supernatant also markedly suppressed A. alternata conidial germination by 82.02 % and induced significant hyphal morphological abnormalities. Enzymatic profiling showed that HC-9 produced extracellular enzymes such as protease, cellulase, chitinase, and β-1, 3-glucanase, which are likely contributors to fungal cell wall degradation. Moreover, treatments with HC-9 induced the accumulation of reactive oxygen species and malondialdehyde in honeysuckle leaves and enhanced the activity of defense-related and antioxidant enzymes, suggesting the activation of systemic resistance. Both pot and field trials showed that HC-9 significantly reduced disease severity, achieving biocontrol efficiencies of 66.52 %–71.28 % under greenhouse conditions and up to 80.52 % in the field. These findings highlight the potential of Bacillus sp. HC-9 as a promising biocontrol agent for the sustainable management of honeysuckle leaf spot disease.
{"title":"Biocontrol efficiency of native Bacillus sp. HC-9 on honeysuckle leaf spot caused by Alternaria alternata","authors":"Xiyan Luo , Pengjie He , Jiajia Zhang , Ping Wang , Wenjia Wang , Xiaoqin Chen , Xiaorui Cheng , Wenyan Cui","doi":"10.1016/j.crmicr.2026.100551","DOIUrl":"10.1016/j.crmicr.2026.100551","url":null,"abstract":"<div><div>Honeysuckle leaf spot disease, caused by <em>Alternaria alternata</em>, severely affects the yield and quality of honeysuckle crops. Biological control using native antagonist microorganisms offers a promising alternative to chemical fungicides. In this study, strain HC-9, previously isolated from honeysuckle leaves, was molecularly identified as <em>Bacillus</em> sp. This strain exhibited broad-spectrum antifungal activity, effectively inhibiting eight phytopathogenic fungi, including <em>A. alternata</em>, with an <em>in vitro</em> inhibition rate of 70.91 %<em>.</em> The cell-free supernatant of HC-9 fermentation broth demonstrated strong antifungal activity (72.79 % inhibition after 48 h of fermentation), which was concentration-dependent and stable under high temperature (100°C), UV exposure (1 h), and acidic conditions, though it was sensitive to alkaline environments. The supernatant also markedly suppressed <em>A. alternata</em> conidial germination by 82.02 % and induced significant hyphal morphological abnormalities<em>.</em> Enzymatic profiling showed that HC-9 produced extracellular enzymes such as protease, cellulase, chitinase, and β-1, 3-glucanase, which are likely contributors to fungal cell wall degradation. Moreover, treatments with HC-9 induced the accumulation of reactive oxygen species and malondialdehyde in honeysuckle leaves and enhanced the activity of defense-related and antioxidant enzymes, suggesting the activation of systemic resistance. Both pot and field trials showed that HC-9 significantly reduced disease severity, achieving biocontrol efficiencies of 66.52 %–71.28 % under greenhouse conditions and up to 80.52 % in the field. These findings highlight the potential of <em>Bacillus</em> sp. HC-9 as a promising biocontrol agent for the sustainable management of honeysuckle leaf spot disease.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100551"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3–14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.
{"title":"A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity","authors":"Chandni Sachdeva , Seetharam Shiva Prasad , Kallya Rajgopal Shenoy , Annappa Kudva , Lakshminarayana Badareesh , Bharath S Veerabhadrappa , Sunil M Krishna , Thokur Sreepathy Murali","doi":"10.1016/j.crmicr.2025.100544","DOIUrl":"10.1016/j.crmicr.2025.100544","url":null,"abstract":"<div><div>Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified <em>Pseudomonas</em> to be consistently present across all cohorts, higher abundance of <em>Escherichia</em> and <em>Prevotella</em> in DFU samples across visits while <em>Acinetobacter</em> and <em>Morganella</em> were predominant in non-DFU wounds. Healed DFUs were enriched in <em>Alcaligenes</em> and <em>Corynebacterium</em> while worsened DFUs showed increased abundance of <em>Enterococcus</em> and <em>Serratia</em>. In amputated individuals, <em>Escherichia</em> was found in high abundance, while <em>Staphylococcus</em> was reduced. DFU subjects with high HbA1c levels (7.3–14.9%) had higher abundance of <em>Pseudomonas</em> and <em>Acinetobacter</em>, while <em>Prevotella</em> and <em>Escherichia</em> were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100544"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.crmicr.2025.100543
Margarida Ruivo, Anna-Margarita Schötta, Theresa Stelzer, Michael Reiter, Michiel Wijnveld
Borrelia, a highly prevalent tick-borne pathogen, has a genome with a linear chromosome and numerous linear and circular plasmids. There are three groups of Borrelia: Lyme borreliosis, relapsing fever, and Echidna-reptile. In Europe, Borrelia afzelii and Borrelia garinii are the main causative agents of Lyme borreliosis.
The primary defence mechanism of bacteria against bacteriophages and other invading DNA elements is the restriction-modification system (RMS), which discriminates between native and foreign DNA based on their distinct methylation patterns.
This present study compares the RMS of all the Borrelia species available in the REBASE database. Additionally, it investigates the effect of the RMS on the transformation efficiency of low-passage B. afzelii and B. garinii isolates.
Upon comparing the RMS of 18 Borrelia species, differences in the number, location and characteristics of genes were observed between groups. Given that Lyme borreliosis species exhibit higher genomic plasticity, we hypothesise that they possess a greater number of RMS genes to ensure functionality of the RMS even if some plasmids are lost.
In this study, we demonstrate a large increase in transformation efficiency of low-passage strains by using an in vitro methylated shuttle vector, confirming our hypothesis that the RMS of Borrelia recognises pre-methylated vectors as native DNA.
The knowledge gained in this study contributes to the understanding of Borrelia defence mechanisms and provides possible explanations for the relatively low transformation efficiency observed in previous studies. Consequently, in vitro methylation can serve as a valuable tool for facilitating studies involving genetic manipulation of Borrelia.
{"title":"Comparative analysis of Borrelia’s Defence mechanisms and their impact on genetic manipulation of low-passage isolates of Borrelia afzelii and Borrelia garinii","authors":"Margarida Ruivo, Anna-Margarita Schötta, Theresa Stelzer, Michael Reiter, Michiel Wijnveld","doi":"10.1016/j.crmicr.2025.100543","DOIUrl":"10.1016/j.crmicr.2025.100543","url":null,"abstract":"<div><div><em>Borrelia,</em> a highly prevalent tick-borne pathogen, has a genome with a linear chromosome and numerous linear and circular plasmids. There are three groups of <em>Borrelia</em>: Lyme borreliosis, relapsing fever, and Echidna-reptile. In Europe, <em>Borrelia afzelii</em> and <em>Borrelia garinii</em> are the main causative agents of Lyme borreliosis.</div><div>The primary defence mechanism of bacteria against bacteriophages and other invading DNA elements is the restriction-modification system (RMS), which discriminates between native and foreign DNA based on their distinct methylation patterns.</div><div>This present study compares the RMS of all the <em>Borrelia</em> species available in the REBASE database. Additionally, it investigates the effect of the RMS on the transformation efficiency of low-passage <em>B. afzelii</em> and <em>B. garinii</em> isolates.</div><div>Upon comparing the RMS of 18 <em>Borrelia</em> species, differences in the number, location and characteristics of genes were observed between groups. Given that Lyme borreliosis species exhibit higher genomic plasticity, we hypothesise that they possess a greater number of RMS genes to ensure functionality of the RMS even if some plasmids are lost.</div><div>In this study, we demonstrate a large increase in transformation efficiency of low-passage strains by using an in vitro methylated shuttle vector, confirming our hypothesis that the RMS of <em>Borrelia</em> recognises pre-methylated vectors as native DNA.</div><div>The knowledge gained in this study contributes to the understanding of <em>Borrelia</em> defence mechanisms and provides possible explanations for the relatively low transformation efficiency observed in previous studies. Consequently, in vitro methylation can serve as a valuable tool for facilitating studies involving genetic manipulation of <em>Borrelia.</em></div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100543"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Estuarine wetlands are critical biogeochemical hotspots where vegetation and soil properties jointly regulate microbial processes such as denitrification. This study investigated soil physicochemical properties and denitrifying bacterial communities (harboring nirS and nirK genes) across different vegetation types (Reed, Zhongshanshan, and Reed-Willow Mix) and soil depths (0–20 cm, 20–40 cm, and 40–60 cm) in the mudflat of the Paihe River estuary, Chaohu Lake. Soil nutrient availability and pH varied significantly with vegetation, with mixed vegetation supporting higher organic matter, nitrate, and total phosphorus levels. Proteobacteria dominated both nirS and nirK-type communities, but nirS assemblages exhibited greater compositional richness and stronger depth-related shifts. Environmental drivers differed between groups, nirS communities correlated mainly with pH, total nitrogen, and C/N, whereas nirK communities were more responsive to pH, total phosphorus, and nitrate. Co-occurrence network analysis revealed vegetation and depth-dependent structural complexity, with mixed vegetation showing increased network complexity with depth. Denitrification rates declined with depth and ranked Reed-Willow Mix > Reed > Zhongshanshan. nirK taxa explained more rate variation than nirS, with Bradyrhizobium, Sinorhizobium, and Mesorhizobium most influential; regression implicated Brucella and Achromobacter positively and Bosea negatively. Mixed vegetation thus enhances denitrification by improving soil conditions and selecting nirK-dominated guilds in the active layer. The findings provide novel evidence that vegetation composition shapes both the structure and function of denitrifying microbial communities, with Reed-Willow Mix enhancing microbial diversity, interaction complexity, and denitrification efficiency. These results underscore the importance of vegetation management in sustaining nitrogen removal capacity and ecosystem functioning in estuarine wetlands.
{"title":"Vegetation composition shapes denitrifier community structure and enhances nitrogen removal in estuarine wetlands: evidence from Reed-Willow Mix promoting nirK-dominated guilds","authors":"Shengni Tian , Dan Huang , Guokai Yuan, Yupeng Chen, Penghui Zhang, Mingzhu Zhang","doi":"10.1016/j.crmicr.2026.100546","DOIUrl":"10.1016/j.crmicr.2026.100546","url":null,"abstract":"<div><div>Estuarine wetlands are critical biogeochemical hotspots where vegetation and soil properties jointly regulate microbial processes such as denitrification. This study investigated soil physicochemical properties and denitrifying bacterial communities (harboring <em>nirS</em> and <em>nirK</em> genes) across different vegetation types (Reed, Zhongshanshan, and Reed-Willow Mix) and soil depths (0–20 cm, 20–40 cm, and 40–60 cm) in the mudflat of the Paihe River estuary, Chaohu Lake. Soil nutrient availability and pH varied significantly with vegetation, with mixed vegetation supporting higher organic matter, nitrate, and total phosphorus levels. Proteobacteria dominated both <em>nirS</em> and <em>nirK</em>-type communities, but <em>nirS</em> assemblages exhibited greater compositional richness and stronger depth-related shifts. Environmental drivers differed between groups, <em>nirS</em> communities correlated mainly with pH, total nitrogen, and C/N, whereas <em>nirK</em> communities were more responsive to pH, total phosphorus, and nitrate. Co-occurrence network analysis revealed vegetation and depth-dependent structural complexity, with mixed vegetation showing increased network complexity with depth. Denitrification rates declined with depth and ranked Reed-Willow Mix > Reed > Zhongshanshan. <em>nirK</em> taxa explained more rate variation than <em>nirS</em>, with <em>Bradyrhizobium, Sinorhizobium</em>, and <em>Mesorhizobium</em> most influential; regression implicated <em>Brucella</em> and <em>Achromobacter</em> positively and <em>Bosea</em> negatively. Mixed vegetation thus enhances denitrification by improving soil conditions and selecting <em>nirK</em>-dominated guilds in the active layer. The findings provide novel evidence that vegetation composition shapes both the structure and function of denitrifying microbial communities, with Reed-Willow Mix enhancing microbial diversity, interaction complexity, and denitrification efficiency. These results underscore the importance of vegetation management in sustaining nitrogen removal capacity and ecosystem functioning in estuarine wetlands.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100546"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146037582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.crmicr.2026.100559
Xinni Zhou , Xiaojuan Chi , Benqun Peng , Ming Gao , Ning Li , Lu Liu , Jie Zeng , Yuxin Li , Yuzhang Chen , Song Wang
Long non-coding RNAs (lncRNAs) have been implicated in various cellular processes, including the regulation of gene expression and cellular response to viral infections. Herein, our RNA-seq analysis revealed a significant increase in the expression of an annotated lncRNA, GAS5, following influenza A virus (IAV) infection. Stimulation of cells with type I interferon, type III interferon or IL-6 can also result in upregulation of GAS5 expression. Additionally, overexpression of GAS5 promoted IAV replication, while knockdown of GAS5 decreased viral titers. Notably, we identified a novel 50-amino acid micropeptide encoded by GAS5, named GAS5-P50, through ribosome profiling and mass spectrometry analysis. It was found that overexpression of GAS5-P50 alone could facilitate the replication of IAV; conversely, frameshift mutation-mediated silencing of GAS5-P50 diminished the capacity of GAS5 to promote IAV replication, implying that GAS5-P50 is essential for GAS5-mediated enhancement of viral replication. Moreover, synthetic GAS5-P50 was demonstrated to boost IAV propagation both in vitro and in vivo. Mechanistically, GAS5-P50 interacted with NOTUM, a negative regulator of Wnt signaling, leading to enhanced Wnt/β-catenin pathway activation, which facilitated viral replication. These findings uncover a previously unrecognized function of GAS5 as a proviral lncRNA that encodes a functional micropeptide, which modulates host Wnt/β-catenin signaling to support IAV infection. Our study not only expands the understanding of lncRNA-encoded micropeptides in viral pathogenesis but also highlights GAS5-P50 as a potential target for antiviral intervention.
{"title":"The lncRNA GAS5-encoded micropeptide facilitates influenza virus replication through modulation of the Wnt/β-catenin signaling pathway","authors":"Xinni Zhou , Xiaojuan Chi , Benqun Peng , Ming Gao , Ning Li , Lu Liu , Jie Zeng , Yuxin Li , Yuzhang Chen , Song Wang","doi":"10.1016/j.crmicr.2026.100559","DOIUrl":"10.1016/j.crmicr.2026.100559","url":null,"abstract":"<div><div>Long non-coding RNAs (lncRNAs) have been implicated in various cellular processes, including the regulation of gene expression and cellular response to viral infections. Herein, our RNA-seq analysis revealed a significant increase in the expression of an annotated lncRNA, GAS5, following influenza A virus (IAV) infection. Stimulation of cells with type I interferon, type III interferon or IL-6 can also result in upregulation of GAS5 expression. Additionally, overexpression of GAS5 promoted IAV replication, while knockdown of GAS5 decreased viral titers. Notably, we identified a novel 50-amino acid micropeptide encoded by GAS5, named GAS5-P50, through ribosome profiling and mass spectrometry analysis. It was found that overexpression of GAS5-P50 alone could facilitate the replication of IAV; conversely, frameshift mutation-mediated silencing of GAS5-P50 diminished the capacity of GAS5 to promote IAV replication, implying that GAS5-P50 is essential for GAS5-mediated enhancement of viral replication. Moreover, synthetic GAS5-P50 was demonstrated to boost IAV propagation both <em>in vitro</em> and <em>in vivo</em>. Mechanistically, GAS5-P50 interacted with NOTUM, a negative regulator of Wnt signaling, leading to enhanced Wnt/β-catenin pathway activation, which facilitated viral replication. These findings uncover a previously unrecognized function of GAS5 as a proviral lncRNA that encodes a functional micropeptide, which modulates host Wnt/β-catenin signaling to support IAV infection. Our study not only expands the understanding of lncRNA-encoded micropeptides in viral pathogenesis but also highlights GAS5-P50 as a potential target for antiviral intervention.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100559"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146077823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01DOI: 10.1016/j.crmicr.2026.100547
Merja Herzig , Malin Bomberg , Tuulia Hyötyläinen
The deep terrestrial subsurface (DTS) biosphere consists of a variety of distinct microbial taxa, mostly bacterial. The mechanisms by which microbes dynamically manage the uptake and concurrent utilization of nutrients within the DTS environments remain largely unexplored. Here, we examined the utilization patterns of amino acids and other polar metabolites in cultured DTS bacterial communities to investigate the adaptive responses and metabolic pathways employed under varying nutrient conditions to gain insight into how environmental shifts impact the metabolism of these communities. Previously, we found that changes in growth conditions affected the composition and size of the bacterial communities enriched from these oligotrophic, anoxic environments and induced changes in the production of primary and secondary metabolites. In the present study, metabolic fingerprinting was used to investigate the primary and secondary metabolite utilization and main metabolic pathways present in the enriched DTS bacterial consortium originating from the deep bedrock of the Fennoscandian Shield. We found that especially amino acids were predominantly degraded under different nutrient conditions. Notably, the degradation of phenylalanine and valine constituted a 'core' metabolic process that remained unaffected by variations in available nutrients within this community. Further, the most significant metabolic pathways employed were those connected to phenylalanine, cysteine and methionine.
{"title":"Microbial metabolism in deep terrestrial subsurface communities - amino acids as biosignatures","authors":"Merja Herzig , Malin Bomberg , Tuulia Hyötyläinen","doi":"10.1016/j.crmicr.2026.100547","DOIUrl":"10.1016/j.crmicr.2026.100547","url":null,"abstract":"<div><div>The deep terrestrial subsurface (DTS) biosphere consists of a variety of distinct microbial taxa, mostly bacterial. The mechanisms by which microbes dynamically manage the uptake and concurrent utilization of nutrients within the DTS environments remain largely unexplored. Here, we examined the utilization patterns of amino acids and other polar metabolites in cultured DTS bacterial communities to investigate the adaptive responses and metabolic pathways employed under varying nutrient conditions to gain insight into how environmental shifts impact the metabolism of these communities. Previously, we found that changes in growth conditions affected the composition and size of the bacterial communities enriched from these oligotrophic, anoxic environments and induced changes in the production of primary and secondary metabolites. In the present study, metabolic fingerprinting was used to investigate the primary and secondary metabolite utilization and main metabolic pathways present in the enriched DTS bacterial consortium originating from the deep bedrock of the Fennoscandian Shield. We found that especially amino acids were predominantly degraded under different nutrient conditions. Notably, the degradation of phenylalanine and valine constituted a 'core' metabolic process that remained unaffected by variations in available nutrients within this community. Further, the most significant metabolic pathways employed were those connected to phenylalanine, cysteine and methionine.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100547"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145925393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号