Pub Date : 2026-01-01Epub Date: 2026-02-11DOI: 10.1016/j.crmicr.2026.100568
Tim Kamara , Geoffrey Martinez , Nicolas Eugénie , Murielle Dutertre , Fabrice Confalonieri , Esma Bentchikou , Pascale Servant
The bacterial cell wall is composed of peptidoglycan (PG), a sugar polymer cross-linked by short peptide stems. PG determines cell morphology and protects it from environmental stresses. Cell growth and division require a balance between synthesis and hydrolysis of the PG. One class of PG hydrolase is the NlpC/P60 superfamily which is broadly distributed in bacteria, archaea, eukaryotes and viruses. Deinococcus radiodurans, characterized by its extreme radioresistance, is a diderm bacterium with a thick layer of PG located between the inner and outer membrane. D. radiodurans exhibits three NlpC/P60 endopeptidases, their role in morphogenesis and cell cycle remains unexplored. In this work, we investigated the role of each endopeptidase in cell division to assess their specific role. Here, we showed that the CwlB protein is involved in cell division and that cwlA gene is essential for cell viability. The CwlC protein is not required for cell shape maintenance or cell division. We showed that CwlA protein is homogeneously localized around the cell except on septal region. CwlA-depleted cells lost viability, displayed morphological changes, and produced numerous membrane vesicles, similarly to cells exposed to sublethal mitomycin C (a DNA-damaging agent) or to DdrO depletion, the transcriptional repressor of the main genotoxic stress response in Deinococcus. We showed that cwlA expression is highly repressed under DdrO depletion. These data suggested a link between response pathway to genotoxic conditions and cell wall remodeling.
{"title":"Specific role of two NlpC/P60 endopeptidases in cell division and membrane vesicle formation in Deinococcus radiodurans","authors":"Tim Kamara , Geoffrey Martinez , Nicolas Eugénie , Murielle Dutertre , Fabrice Confalonieri , Esma Bentchikou , Pascale Servant","doi":"10.1016/j.crmicr.2026.100568","DOIUrl":"10.1016/j.crmicr.2026.100568","url":null,"abstract":"<div><div>The bacterial cell wall is composed of peptidoglycan (PG), a sugar polymer cross-linked by short peptide stems. PG determines cell morphology and protects it from environmental stresses. Cell growth and division require a balance between synthesis and hydrolysis of the PG. One class of PG hydrolase is the NlpC/P60 superfamily which is broadly distributed in bacteria, archaea, eukaryotes and viruses. <em>Deinococcus radiodurans</em>, characterized by its extreme radioresistance, is a diderm bacterium with a thick layer of PG located between the inner and outer membrane. <em>D. radiodurans</em> exhibits three NlpC/P60 endopeptidases, their role in morphogenesis and cell cycle remains unexplored. In this work, we investigated the role of each endopeptidase in cell division to assess their specific role. Here, we showed that the CwlB protein is involved in cell division and that <em>cwlA</em> gene is essential for cell viability. The CwlC protein is not required for cell shape maintenance or cell division. We showed that CwlA protein is homogeneously localized around the cell except on septal region. CwlA-depleted cells lost viability, displayed morphological changes, and produced numerous membrane vesicles, similarly to cells exposed to sublethal mitomycin C (a DNA-damaging agent) or to DdrO depletion, the transcriptional repressor of the main genotoxic stress response in <em>Deinococcus</em>. We showed that <em>cwlA</em> expression is highly repressed under DdrO depletion. These data suggested a link between response pathway to genotoxic conditions and cell wall remodeling.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100568"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147310745","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 : 2026-01-01Epub Date: 2026-01-27DOI: 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 : 2026-01-01Epub Date: 2025-12-13DOI: 10.1016/j.crmicr.2025.100533
Hui Zhang , Xueru Song , Qi Zhou , Yuming Yin , Ying Yang , Jilai Zhang , Yonghe Cui , Lingduo Bu , Yulong Su , Youbo Su
Arbuscular mycorrhizal fungi (AMF) are key species in plant-microbe interactions, and this study is the first to suggest their dynamic survival in the fermentation system of cigar tobacco. To explore the functional significance of AMF in cigar tobacco fermentation, this study focused on the Yunxue variety of cigar tobacco. We combined multi-time point sampling over a 35-day fermentation process and used Internal Transcribed Spacer (ITS) gene high-throughput sequencing to analyze the AMF community structure in the fermenting material. Diversity indices, species correlation networks, and Mantel tests were employed to explore the relationship between AMF and chemical components. The results showed a significant dynamic succession in AMF OTUs within the fermenting material throughout the fermentation process, identifying 22 species (comprising 524 OTUs), with Paraglomus being the predominant species. Core functional flora included OTU217 and OTU88, whose abundance variations aligned with the generation of volatile flavor compounds. AMF diversity peaked during the mid-fermentation stage and exhibited a negative correlation with total nitrogen, total sulfur, and reducing sugars, indicating that sugar and nitrogen metabolism were driving factors in the reorganization of the AMF community. The observations suggest that us to propose that Glomus-group-B-Glomus-lamellosu-VTX00193 may have a marked increase in abundance towards the end of fermentation, suggesting its crucial role in the degradation of complex organic compounds. Analysis specific to different tobacco varieties revealed a significant increase in the number of OTUs unique to Yunxue 6, with fluctuations in total acidity content significantly associated with changes in AMF abundance. The findings suggest a the regulatory role of AMF in modulating the chemical composition of cigar tobacco leaves through carbon and nitrogen metabolism, with Paraglomus and Glomus identified as core functional funga. These results suggests the importance of further research on confirmation of AMF, if any, in the tobacco fermenting process.
{"title":"Discoveries in non-symbiotic environments: Dynamic changes and potential contributions of arbuscular mycorrhizal fungi in cigar tobacco fermentation","authors":"Hui Zhang , Xueru Song , Qi Zhou , Yuming Yin , Ying Yang , Jilai Zhang , Yonghe Cui , Lingduo Bu , Yulong Su , Youbo Su","doi":"10.1016/j.crmicr.2025.100533","DOIUrl":"10.1016/j.crmicr.2025.100533","url":null,"abstract":"<div><div>Arbuscular mycorrhizal fungi (AMF) are key species in plant-microbe interactions, and this study is the first to suggest their dynamic survival in the fermentation system of cigar tobacco. To explore the functional significance of AMF in cigar tobacco fermentation, this study focused on the Yunxue variety of cigar tobacco. We combined multi-time point sampling over a 35-day fermentation process and used Internal Transcribed Spacer (ITS) gene high-throughput sequencing to analyze the AMF community structure in the fermenting material. Diversity indices, species correlation networks, and Mantel tests were employed to explore the relationship between AMF and chemical components. The results showed a significant dynamic succession in AMF OTUs within the fermenting material throughout the fermentation process, identifying 22 species (comprising 524 OTUs), with <em>Paraglomus</em> being the predominant species. Core functional flora included OTU217 and OTU88, whose abundance variations aligned with the generation of volatile flavor compounds. AMF diversity peaked during the mid-fermentation stage and exhibited a negative correlation with total nitrogen, total sulfur, and reducing sugars, indicating that sugar and nitrogen metabolism were driving factors in the reorganization of the AMF community. The observations suggest that us to propose that <em>Glomus</em>-group-B-<em>Glomus-lamellosu</em>-VTX00193 may have a marked increase in abundance towards the end of fermentation, suggesting its crucial role in the degradation of complex organic compounds. Analysis specific to different tobacco varieties revealed a significant increase in the number of OTUs unique to Yunxue 6, with fluctuations in total acidity content significantly associated with changes in AMF abundance. The findings suggest a the regulatory role of AMF in modulating the chemical composition of cigar tobacco leaves through carbon and nitrogen metabolism, with <em>Paraglomu</em>s and <em>Glomus</em> identified as core functional funga. These results suggests the importance of further research on confirmation of AMF, if any, in the tobacco fermenting process.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100533"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145790539","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 : 2026-01-01Epub Date: 2026-03-11DOI: 10.1016/j.crmicr.2026.100580
Gabriele Rigano , Joerg Doellinger , Peter Lasch , Giorgia Di Stefano , Beatriz Gallego Fernandez , Loredana Santo , Daniela Billi
Space exploration demands sustainable technologies to minimize reliance on Earth-based resources. The extreme-tolerant cyanobacterium Chroococcidiopsis sp. CCMEE 029 exhibits remarkable resistance to perchlorate salts ubiquitously found on Martian soil, holding promise for in situ resource utilization. Exploring the proteomic responses to this chaotropic agent is fundamental for understanding the mechanisms of salt-stress response in cyanobacteria and to develop biotechnologies based on local resources to support human outposts. Hence, using liquid chromatography–tandem mass spectrometry, we analyzed the protein expression after 21 days of cultivation in the presence of increasing perchlorate concentrations with triplicates per experimental condition (|log2FC| ≥ 0.5; FDR ≤ 0.05). This study shows that this cyanobacterium displays a broad suite of enzymatic and non-enzymatic mechanisms for mitigating reactive oxygen species, as well as formaldehyde assimilation capacity from the RuMP pathway. The upregulation of polyhydroxybutyrate and siderophore biosynthesis further supports its suitability for putative bioplastic production, nutrient mobilization, and plant protection in extraterrestrial environments. Overall, Chroococcidiopsis sp. CCMEE 029 modulates its metabolism to maintain energy balance, support growth, and synthesize biotechnologically relevant compounds. This versatility underscores its suitability as a candidate for Martian bioprocessing, where robustness, low resource requirements and multifunctionality are paramount. By providing molecular insights into cyanobacterial stress responses, this research advances our understanding of microbial adaptation to environmental constraints occurring on Mars and lays the groundwork for optimizing microbial biotechnologies to support astronauts in long-term missions on the red planet.
{"title":"Proteomics of long-term acclimation of the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 in perchlorate-rich medium and its implications for in situ resource utilization on Mars","authors":"Gabriele Rigano , Joerg Doellinger , Peter Lasch , Giorgia Di Stefano , Beatriz Gallego Fernandez , Loredana Santo , Daniela Billi","doi":"10.1016/j.crmicr.2026.100580","DOIUrl":"10.1016/j.crmicr.2026.100580","url":null,"abstract":"<div><div>Space exploration demands sustainable technologies to minimize reliance on Earth-based resources. The extreme-tolerant cyanobacterium <em>Chroococcidiopsis</em> sp. CCMEE 029 exhibits remarkable resistance to perchlorate salts ubiquitously found on Martian soil, holding promise for in situ resource utilization. Exploring the proteomic responses to this chaotropic agent is fundamental for understanding the mechanisms of salt-stress response in cyanobacteria and to develop biotechnologies based on local resources to support human outposts. Hence, using liquid chromatography–tandem mass spectrometry, we analyzed the protein expression after 21 days of cultivation in the presence of increasing perchlorate concentrations with triplicates per experimental condition (|log<sub>2</sub>FC| ≥ 0.5; FDR ≤ 0.05). This study shows that this cyanobacterium displays a broad suite of enzymatic and non-enzymatic mechanisms for mitigating reactive oxygen species, as well as formaldehyde assimilation capacity from the RuMP pathway. The upregulation of polyhydroxybutyrate and siderophore biosynthesis further supports its suitability for putative bioplastic production, nutrient mobilization, and plant protection in extraterrestrial environments. Overall, <em>Chroococcidiopsis</em> sp. CCMEE 029 modulates its metabolism to maintain energy balance, support growth, and synthesize biotechnologically relevant compounds. This versatility underscores its suitability as a candidate for Martian bioprocessing, where robustness, low resource requirements and multifunctionality are paramount. By providing molecular insights into cyanobacterial stress responses, this research advances our understanding of microbial adaptation to environmental constraints occurring on Mars and lays the groundwork for optimizing microbial biotechnologies to support astronauts in long-term missions on the red planet.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100580"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147448635","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 : 2026-01-01Epub Date: 2025-12-05DOI: 10.1016/j.crmicr.2025.100529
Hongying Zhou , Lixu Li , Yuhua Gong , Hualin Liu , Hongli Wu , Alejandra Bravo , Mario Soberón , Jinshui Zheng , Donghai Peng , Bo Sun , Ming Sun
The domesticated silkworm, Bombyx mori, is critically impacted by bacterial pathogens, yet the environmental and ecological drivers of their spatiotemporal dynamics remain poorly defined. In this study, 514 bacterial strains were isolated from diseased and healthy silkworm larvae across major sericultural regions in China. Through 16S rRNA gene sequencing and multi-tier pathogenicity assays, 51 isolates were identified as potential novel insect pathogens. Fulfilling Koch’s postulates via oral infection tests, the pathogenicity of nine strains belonging to the genera Raoultella, Stenotrophomonas, and Citrobacter were confirmed, while the remaining isolates are considered putative pathogens. All isolates were classified into 33 genera within the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, with Enterobacter, Bacillus, and Serratia being the most prevalent. Multivariate analysis indicated that geographic and climatic factors—specifically distance from the coastline and key thermal and radiative variables—collectively explained a significant though modest portion of the variance in bacterial community composition. Bacterial diversity correlated positively with cocoon yield. Guangxi presented the highest potential pathogen diversity and co-infection frequency, aligning with its intensive sericulture practices. Seasonal analyses indicated higher bacterial abundance and virulence in spring–summer compared to summer–autumn. Many isolates are taxonomically affiliated with genera containing insect gut microbiota, plant-associated bacteria, and human (opportunistic) pathogens, suggesting diverse environmental and anthropogenic origin. The detection of bacteria related to mulberry phyllosphere microbes underscore the role of host plant ecology in shaping the silkworm microbiome. These findings illuminate the ecological drivers of silkworm-associated bacterial communities and highlight the complex microbial connections within sericulture ecosystems, suggesting potential pathways relevant to a One Health perspective. Furthermore, the repository of 514 identified bacterial isolates from the model lepidopteran B. mori here provides a valuable resources for exploring novel biocontrol agents against other lepidopteran pests.
{"title":"Geographic and seasonal variation of culturable bacteria associated with the diseased silkworm (Bombyx mori)","authors":"Hongying Zhou , Lixu Li , Yuhua Gong , Hualin Liu , Hongli Wu , Alejandra Bravo , Mario Soberón , Jinshui Zheng , Donghai Peng , Bo Sun , Ming Sun","doi":"10.1016/j.crmicr.2025.100529","DOIUrl":"10.1016/j.crmicr.2025.100529","url":null,"abstract":"<div><div>The domesticated silkworm, <em>Bombyx mori</em>, is critically impacted by bacterial pathogens, yet the environmental and ecological drivers of their spatiotemporal dynamics remain poorly defined. In this study, 514 bacterial strains were isolated from diseased and healthy silkworm larvae across major sericultural regions in China. Through 16S rRNA gene sequencing and multi-tier pathogenicity assays, 51 isolates were identified as potential novel insect pathogens. Fulfilling Koch’s postulates via oral infection tests, the pathogenicity of nine strains belonging to the genera <em>Raoultella, Stenotrophomonas</em>, and <em>Citrobacter</em> were confirmed, while the remaining isolates are considered putative pathogens. All isolates were classified into 33 genera within the phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes, with <em>Enterobacter, Bacillus</em>, and <em>Serratia</em> being the most prevalent. Multivariate analysis indicated that geographic and climatic factors—specifically distance from the coastline and key thermal and radiative variables—collectively explained a significant though modest portion of the variance in bacterial community composition. Bacterial diversity correlated positively with cocoon yield. Guangxi presented the highest potential pathogen diversity and co-infection frequency, aligning with its intensive sericulture practices. Seasonal analyses indicated higher bacterial abundance and virulence in spring–summer compared to summer–autumn. Many isolates are taxonomically affiliated with genera containing insect gut microbiota, plant-associated bacteria, and human (opportunistic) pathogens, suggesting diverse environmental and anthropogenic origin. The detection of bacteria related to mulberry phyllosphere microbes underscore the role of host plant ecology in shaping the silkworm microbiome. These findings illuminate the ecological drivers of silkworm-associated bacterial communities and highlight the complex microbial connections within sericulture ecosystems, suggesting potential pathways relevant to a One Health perspective. Furthermore, the repository of 514 identified bacterial isolates from the model lepidopteran <em>B. mori</em> here provides a valuable resources for exploring novel biocontrol agents against other lepidopteran pests.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100529"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145976920","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 : 2026-01-01Epub Date: 2026-01-03DOI: 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}
Pub Date : 2026-01-01Epub Date: 2025-12-07DOI: 10.1016/j.crmicr.2025.100531
Ning Li , Zheng Dong , Shuping Zhang , Juan Ma , Sijin Liu
Growing research has highlighted the participation of lung microbiota in various pathological processes. Despite its low bacterial biomass compared with other organs, the resident flora of the healthy lung is essential for immune system development, immune tolerance fostering, and defense against foreign substance incursion. The host-microbial crosstalk, typically mediated by microbial metabolites, pattern recognition receptors, and immune cells, exerts bidirectional regulatory effects on the pulmonary immune microenvironment. Specifically, the lung microbiota modulates the activation status or tolerance of mucosal immune cell populations to maintain immune balance; conversely, perturbations to the lung's homeostatic microbiome, arising from dysbiosis, immune dysfunction, or pathogenic invasion, drive lung disease by inciting chronic inflammation and tissue remodeling via direct and immune mediated damage. Although the importance of host-microbial interactions in lung health is well recognized, the mechanisms of the relationship between changes in microbiota composition and immune dysregulation in different diseases have not been fully elucidated. Therefore, we summarize the latest research progress on the involvement of the lung microbiota in pulmonary disease development, focusing on the interaction mechanisms among microorganisms, immune homeostasis, and lung diseases. The aim of this review is to expand our mechanistic understanding of the lung microbiota-mediated regulation of immune cell function. Insights from various disciplines into lung microbiota could pave the way for innovative ideas and technologies aimed at preventing and treating respiratory illnesses.
{"title":"Pathogenesis of various pulmonary diseases by tuning immune response: insight from host-microbial crosstalk","authors":"Ning Li , Zheng Dong , Shuping Zhang , Juan Ma , Sijin Liu","doi":"10.1016/j.crmicr.2025.100531","DOIUrl":"10.1016/j.crmicr.2025.100531","url":null,"abstract":"<div><div>Growing research has highlighted the participation of lung microbiota in various pathological processes. Despite its low bacterial biomass compared with other organs, the resident flora of the healthy lung is essential for immune system development, immune tolerance fostering, and defense against foreign substance incursion. The host-microbial crosstalk, typically mediated by microbial metabolites, pattern recognition receptors, and immune cells, exerts bidirectional regulatory effects on the pulmonary immune microenvironment. Specifically, the lung microbiota modulates the activation status or tolerance of mucosal immune cell populations to maintain immune balance; conversely, perturbations to the lung's homeostatic microbiome, arising from dysbiosis, immune dysfunction, or pathogenic invasion, drive lung disease by inciting chronic inflammation and tissue remodeling via direct and immune mediated damage. Although the importance of host-microbial interactions in lung health is well recognized, the mechanisms of the relationship between changes in microbiota composition and immune dysregulation in different diseases have not been fully elucidated. Therefore, we summarize the latest research progress on the involvement of the lung microbiota in pulmonary disease development, focusing on the interaction mechanisms among microorganisms, immune homeostasis, and lung diseases. The aim of this review is to expand our mechanistic understanding of the lung microbiota-mediated regulation of immune cell function. Insights from various disciplines into lung microbiota could pave the way for innovative ideas and technologies aimed at preventing and treating respiratory illnesses.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"10 ","pages":"Article 100531"},"PeriodicalIF":5.8,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145737806","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 : 2025-07-24eCollection Date: 2025-01-01DOI: 10.1016/j.crmicr.2025.100449
Charlotte Mejlstrup Hymøller, Trine S Jensen, Pernille Vigsø Rasmussen, Ditte Bech, Gunna Christiansen, Svend Birkelund
Klebsiella pneumoniae is an opportunistic, gram-negative pathogen causing life-threatening sepsis in patients with co-morbidity. In contrast, in healthy persons, K. pneumoniae rarely causes sepsis. To elucidate how K. pneumoniae is eliminated from normal human blood, eleven K. pneumoniae sepsis isolates were analysed. Most of the isolates were serum-resistant. They solely activated the alternative pathway (AP), and only iC3b was present on their surface due to a rapid cleavage of C3b. Despite serum resistance, all isolates were killed in normal blood. To analyse the mechanism of uptake, two isolates (serum-resistant HA391 and partially resistant HA569) were transfected with a plasmid encoding red fluorescent protein, added to whole blood, analysed by flow cytometry and uptake in neutrophil granulocytes. HA391 was not phagocytosed in 50% heat-inactivated serum (HIHS), but in normal human serum (NHS), it was phagocytosed and subsequently killed. The iC3b deposited on the bacterial surface, colocalised with complement receptor 3 (CR3) and myeloperoxidase (MPO), confirming opsonophagocytosis. HA569 was rapidly phagocytosed by granulocytes in NHS but more slowly in HIHS. Thus, the complement system is essential for the elimination of serum-resistant K. pneumoniae isolates, as neutrophil granulocytes phagocytose HA391 through opsonophagocytosis, while HA569 is also phagocytosed independently of complement. AP lacks specific pattern recognition; however, it plays an essential role in the elimination of serum-resistant K. pneumoniae, as AP is activated by these bacteria, which, nonetheless, escape complement lysis by cleaving C3b to iC3b. Hereby, the bacteria are susceptible to opsonophagocytosis, an ancient function of AP that is crucial for eliminating bacteria.
{"title":"The role of opsonophagocytosis in killing of <i>Klebsiella pneumoniae</i> in human blood.","authors":"Charlotte Mejlstrup Hymøller, Trine S Jensen, Pernille Vigsø Rasmussen, Ditte Bech, Gunna Christiansen, Svend Birkelund","doi":"10.1016/j.crmicr.2025.100449","DOIUrl":"10.1016/j.crmicr.2025.100449","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> is an opportunistic, gram-negative pathogen causing life-threatening sepsis in patients with co-morbidity. In contrast, in healthy persons, <i>K. pneumoniae</i> rarely causes sepsis. To elucidate how <i>K. pneumoniae</i> is eliminated from normal human blood, eleven <i>K. pneumoniae</i> sepsis isolates were analysed. Most of the isolates were serum-resistant. They solely activated the alternative pathway (AP), and only iC3b was present on their surface due to a rapid cleavage of C3b. Despite serum resistance, all isolates were killed in normal blood. To analyse the mechanism of uptake, two isolates (serum-resistant HA391 and partially resistant HA569) were transfected with a plasmid encoding red fluorescent protein, added to whole blood, analysed by flow cytometry and uptake in neutrophil granulocytes. HA391 was not phagocytosed in 50% heat-inactivated serum (HIHS), but in normal human serum (NHS), it was phagocytosed and subsequently killed. The iC3b deposited on the bacterial surface, colocalised with complement receptor 3 (CR3) and myeloperoxidase (MPO), confirming opsonophagocytosis. HA569 was rapidly phagocytosed by granulocytes in NHS but more slowly in HIHS. Thus, the complement system is essential for the elimination of serum-resistant <i>K. pneumoniae</i> isolates, as neutrophil granulocytes phagocytose HA391 through opsonophagocytosis, while HA569 is also phagocytosed independently of complement. AP lacks specific pattern recognition; however, it plays an essential role in the elimination of serum-resistant <i>K. pneumoniae</i>, as AP is activated by these bacteria, which, nonetheless, escape complement lysis by cleaving C3b to iC3b. Hereby, the bacteria are susceptible to opsonophagocytosis, an ancient function of AP that is crucial for eliminating bacteria.</p>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"100449"},"PeriodicalIF":5.8,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12356408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144875579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-01Epub Date: 2025-02-18DOI: 10.1016/j.crmicr.2025.100362
Heng Ke, Hongbing Yao, Ping Wei
Epidemiological studies indicate a rising prevalence of allergic diseases, now recognized as a major global public health concern. In children, the progression of these diseases often follows the "atopic march," beginning with eczema, followed by food allergies, allergic rhinitis, and asthma. Recent research has linked gut microbiota dysbiosis to the development of allergic diseases in children. The gut microbiota, a crucial component of human health, plays a vital role in maintaining overall well-being, highlighting its potential in preventing and modifying the course of allergic diseases. This review examines the relationship between childhood allergic diseases and gut microbiota, drawing on the latest evidence. We first elaborated the concepts of allergic diseases and gut microbiota, followed by a discussion of the developmental trajectory of the gut microbiota in healthy children. This review further explored the richness, diversity, and composition of the gut microbiota, as well as specific microbial taxa associated with allergic disease. Lastly, we discussed the current status and future potential of probiotic interventions in managing pediatric allergic diseases.
{"title":"Advances in research on gut microbiota and allergic diseases in children","authors":"Heng Ke, Hongbing Yao, Ping Wei","doi":"10.1016/j.crmicr.2025.100362","DOIUrl":"10.1016/j.crmicr.2025.100362","url":null,"abstract":"<div><div>Epidemiological studies indicate a rising prevalence of allergic diseases, now recognized as a major global public health concern. In children, the progression of these diseases often follows the \"atopic march,\" beginning with eczema, followed by food allergies, allergic rhinitis, and asthma. Recent research has linked gut microbiota dysbiosis to the development of allergic diseases in children. The gut microbiota, a crucial component of human health, plays a vital role in maintaining overall well-being, highlighting its potential in preventing and modifying the course of allergic diseases. This review examines the relationship between childhood allergic diseases and gut microbiota, drawing on the latest evidence. We first elaborated the concepts of allergic diseases and gut microbiota, followed by a discussion of the developmental trajectory of the gut microbiota in healthy children. This review further explored the richness, diversity, and composition of the gut microbiota, as well as specific microbial taxa associated with allergic disease. Lastly, we discussed the current status and future potential of probiotic interventions in managing pediatric allergic diseases.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100362"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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