Pub Date : 2025-01-01DOI: 10.1016/j.crmicr.2025.100497
Christopher J. Ne Ville , Paul M. Orwin
Approximately 10% of all bacterial genomes sequenced thus far contain a secondary replicon. This property of bacterial populations vastly increases genomic diversity within phylogenetically narrow groups. Members of the genus Variovorax have extensive heterogeneity in genome architecture, including sequenced isolates containing plasmids, megaplasmids, and chromids. Many of the Variovorax genomes in the NCBI database were generated using short-read data exclusively and were assembled to the permanent draft stage. We acquired a set of these isolates and used the Oxford Nanopore MinION to generate additional data to allow for hybrid assembly of these genomes. Here we present the finished assemblies of 15 Variovorax isolates from diverse ecosystems that were previously only available as permanent drafts. When added to the previously published Variovorax assemblies for EPS, CSUSB, and VAI-C and those published by other groups, we found significant diversity in genome architecture. We found that there are plasmids, megaplasmids, and chromids that are distinguishable using Guanine-Cytosine (G+C content) content as a signal. We identified a plasmid integration event in NFACC27 and suggest potential evolutionary relationships in the secondary replicons based on ParB homology as well as ANI. The evidence suggests that Variovorax, like its sister taxon Burkholderia, is highly capable of acquiring and maintaining stable secondary replicons. The plasticity of these architectures and the mechanisms for maintenance remain a topic for future research.
{"title":"Completed genomes from Variovorax provide insight into genome diversification through horizontal gene transfer","authors":"Christopher J. Ne Ville , Paul M. Orwin","doi":"10.1016/j.crmicr.2025.100497","DOIUrl":"10.1016/j.crmicr.2025.100497","url":null,"abstract":"<div><div>Approximately 10% of all bacterial genomes sequenced thus far contain a secondary replicon. This property of bacterial populations vastly increases genomic diversity within phylogenetically narrow groups. Members of the genus <em>Variovorax</em> have extensive heterogeneity in genome architecture, including sequenced isolates containing plasmids, megaplasmids, and chromids. Many of the <em>Variovorax</em> genomes in the NCBI database were generated using short-read data exclusively and were assembled to the permanent draft stage. We acquired a set of these isolates and used the Oxford Nanopore MinION to generate additional data to allow for hybrid assembly of these genomes. Here we present the finished assemblies of 15 <em>Variovorax</em> isolates from diverse ecosystems that were previously only available as permanent drafts. When added to the previously published <em>Variovorax</em> assemblies for EPS, CSUSB, and VAI-C and those published by other groups, we found significant diversity in genome architecture. We found that there are plasmids, megaplasmids, and chromids that are distinguishable using Guanine-Cytosine (G+C content) content as a signal. We identified a plasmid integration event in NFACC27 and suggest potential evolutionary relationships in the secondary replicons based on ParB homology as well as ANI. The evidence suggests that <em>Variovorax,</em> like its sister taxon <em>Burkholderia,</em> is highly capable of acquiring and maintaining stable secondary replicons. The plasticity of these architectures and the mechanisms for maintenance remain a topic for future research.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100497"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145415380","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}
Pyrazinamide (PZA) plays a crucial role in the treatment of both active and latent tuberculosis, particularly in regimens designed to treat drug-resistant TB. However, diagnosing resistance to PZA poses challenges for managing TB, highlighting the need for accurate detection methods. This study aims to address the challenges in detecting PZA resistance by modifying the standard MGIT960 PZA drug susceptibility testing method by optimizing the inoculum dilution. Briefly, three MGIT DST versions were evaluated: the standard method, the reduced inoculum (RI) method employing a 1:20 inoculum dilution and the sparse dilution (SD) method using a 1:50 dilution of the inoculum for growth control tube, while the undiluted MGIT positive culture was used for the PZA test tube. The SD MGIT DST approach minimized the number of false-resistant PZA results to (31/401) 7.7 % against 27 % by standard MGIT DST and 11.7 % by RI MGIT DST approach, thereby reducing the false-positivity rate by 19.3 %. Targeted sequencing of pncA gene identified mutations in only 14/401 isolates (3.5 %). Whole genome sequencing (WGS) of the 31 phenotypically resistant isolates identified resistance -associated mutations in pncA gene (45 %), panD (9.6 %), mas (12.9 %), glpK (3.2 %), and lprG (3.2 %), and others efflux associated genes like Rv1258c (3.2 %), Rv0191c (3.2 %), and Rv3008 (6.45 %), except for 4 isolates, for which no mutations were detected in the target genes. These genes are involved in various resistance mechanisms including cell wall synthesis, metabolic pathways, and drug tolerance, which are essential for PZA efficacy. Notably, new mutations in glpK and mas were detected in isolates with wild-type pncA and were absent in the sensitive isolates. Our study substantiates the improvement of phenotypic testing methods and enhances the detection of PZA resistance even in resource-limited settings and direct research towards improving the diagnostic accuracy in TB drug resistance management.
{"title":"Enhancing diagnostic efficiency of pyrazinamide resistance in Mycobacterium tuberculosis via modified MGIT assay and genotypic correlation","authors":"Ananthi Rajendran , Ahmed Kabir Refaya , Balaji Subramanyam , Ramesh Karunaianantham , Dhandapani RaviKumar , Hemalatha Haribabu , Radha Gopalaswamy , Radhika Golla , Vadivel Senthildevi , Narayanan Sivaramakrishnan Gomathi , Sivakumar Shanmugam , Kannan Palaniyandi","doi":"10.1016/j.crmicr.2025.100462","DOIUrl":"10.1016/j.crmicr.2025.100462","url":null,"abstract":"<div><div>Pyrazinamide (PZA) plays a crucial role in the treatment of both active and latent tuberculosis, particularly in regimens designed to treat drug-resistant TB. However, diagnosing resistance to PZA poses challenges for managing TB, highlighting the need for accurate detection methods. This study aims to address the challenges in detecting PZA resistance by modifying the standard MGIT960 PZA drug susceptibility testing method by optimizing the inoculum dilution. Briefly, three MGIT DST versions were evaluated: the standard method, the reduced inoculum (RI) method employing a 1:20 inoculum dilution and the sparse dilution (SD) method using a 1:50 dilution of the inoculum for growth control tube, while the undiluted MGIT positive culture was used for the PZA test tube. The SD MGIT DST approach minimized the number of false-resistant PZA results to (31/401) 7.7 % against 27 % by standard MGIT DST and 11.7 % by RI MGIT DST approach, thereby reducing the false-positivity rate by 19.3 %. Targeted sequencing of <em>pncA</em> gene identified mutations in only 14/401 isolates (3.5 %). Whole genome sequencing (WGS) of the 31 phenotypically resistant isolates identified resistance -associated mutations in <em>pncA</em> gene (45 %), <em>panD</em> (9.6 %), <em>mas</em> (12.9 %), <em>glpK</em> (3.2 %), and <em>lprG</em> (3.2 %), and others efflux associated genes like <em>Rv1258c</em> (3.2 %)<em>, Rv0191c</em> (3.2 %), and <em>Rv3008</em> (6.45 %), except for 4 isolates, for which no mutations were detected in the target genes. These genes are involved in various resistance mechanisms including cell wall synthesis, metabolic pathways, and drug tolerance, which are essential for PZA efficacy. Notably, new mutations in <em>glpK</em> and <em>mas</em> were detected in isolates with wild-type <em>pncA</em> and were absent in the sensitive isolates. Our study substantiates the improvement of phenotypic testing methods and enhances the detection of PZA resistance even in resource-limited settings and direct research towards improving the diagnostic accuracy in TB drug resistance management.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100462"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911820","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 : 2025-01-01DOI: 10.1016/j.crmicr.2025.100369
Erin Bredeweg, Galya Orr, Dehong Hu
In this report, we present coordinated observations of protein and mRNA transcript counts at the single-cell level in the oleaginous yeast model Yarrowia lipolytica. The transcription factor Xbp1p regulates entry into a quiescent state, representing a shift of resources to sequestration of nutrients rather than cell division. We observed the responses of wild-type and Δxbp1 cells to protein (by fluorescence) and transcript quantification and localization at both single-cell and population-averaged levels. Data were collected via single-molecule fluorescence in situ hybridization (smFISH) and qPCR under nitrogen depletion, a condition that drives lipid accumulation. These techniques reveal a complex and heterogeneous population of Xbp1p dynamics and downstream regulation. Our findings highlight the need for single-cell resolution analyses to describe cellular dynamics and regulatory processes.
{"title":"Quantitative multiplexed analysis of gene and protein expression patterns in Yarrowia lipolytica","authors":"Erin Bredeweg, Galya Orr, Dehong Hu","doi":"10.1016/j.crmicr.2025.100369","DOIUrl":"10.1016/j.crmicr.2025.100369","url":null,"abstract":"<div><div>In this report, we present coordinated observations of protein and mRNA transcript counts at the single-cell level in the oleaginous yeast model <em>Yarrowia lipolytica</em>. The transcription factor Xbp1p regulates entry into a quiescent state, representing a shift of resources to sequestration of nutrients rather than cell division. We observed the responses of wild-type and Δ<em>xbp1</em> cells to protein (by fluorescence) and transcript quantification and localization at both single-cell and population-averaged levels. Data were collected via single-molecule fluorescence <em>in situ</em> hybridization (smFISH) and qPCR under nitrogen depletion, a condition that drives lipid accumulation. These techniques reveal a complex and heterogeneous population of Xbp1p dynamics and downstream regulation. Our findings highlight the need for single-cell resolution analyses to describe cellular dynamics and regulatory processes.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100369"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144202455","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 : 2025-01-01DOI: 10.1016/j.crmicr.2025.100451
Jiayan Li , Yuheng Luo , Bing Yu, Jun He, Huifen Wang, Quyuan Wang, Daiwen Chen
Carbohydrates are essential energy sources in the diets of humans and animals, yet the mechanisms underlying their utilization by gut fungi remain poorly understood. To address this gap, we employed Candida albicans—a prevalent gut fungal species in humans and pigs—as a model to investigate fungal carbohydrate utilization strategies. Using a multi-omics approach integrating transcriptomic and metabolomic analyses, we examined fungal growth dynamics, carbohydrate degradation patterns, and enzyme activity during in vitro fermentation. Our results revealed that C. albicans preferentially utilizes soluble polysaccharides, such as inulin and mannan-oligosaccharides (MOS), while exhibiting lower efficiency in degrading starch. Integrated transcriptomic and metabolomic analyses identified distinct metabolites and differentially expressed genes associated with carbohydrate metabolism, with strong correlations observed between carbohydrate-active enzymes (CAZymes) and specific metabolic intermediates. Notably, CAZyme expression was substrate-dependent: inulin specifically induced glycoside hydrolase family 15 (GH15, EC 3.2.1.3), which targets α-1,2-glycosidic linkages, whereas MOS upregulated a broader set of enzymes—including GH13_40 (EC 3.2.1.10), GH15, GH16_2 (EC 3.2.1-/2.4.1-) and GH17 (EC 3.2.1.58/2.4.1-) — that act on β-1,4-, α-1,6-, α-1,2-, and α-1,3-glycosidic bonds, mediating efficient extracellular hydrolysis of complex carbohydrates into absorbable monosaccharides. This study highlights the critical role of gut fungi in dietary carbohydrate utilization and provides novel insights into the mechanisms by which CAZymes mediate fungal carbohydrate metabolism.
{"title":"Multi-omics analysis provides insights into mechanisms of intestinal fungi adaptation to dietary carbohydrates","authors":"Jiayan Li , Yuheng Luo , Bing Yu, Jun He, Huifen Wang, Quyuan Wang, Daiwen Chen","doi":"10.1016/j.crmicr.2025.100451","DOIUrl":"10.1016/j.crmicr.2025.100451","url":null,"abstract":"<div><div>Carbohydrates are essential energy sources in the diets of humans and animals, yet the mechanisms underlying their utilization by gut fungi remain poorly understood. To address this gap, we employed <em>Candida albicans</em>—a prevalent gut fungal species in humans and pigs—as a model to investigate fungal carbohydrate utilization strategies. Using a multi-omics approach integrating transcriptomic and metabolomic analyses, we examined fungal growth dynamics, carbohydrate degradation patterns, and enzyme activity during in vitro fermentation. Our results revealed that <em>C. albicans</em> preferentially utilizes soluble polysaccharides, such as inulin and mannan-oligosaccharides (MOS), while exhibiting lower efficiency in degrading starch. Integrated transcriptomic and metabolomic analyses identified distinct metabolites and differentially expressed genes associated with carbohydrate metabolism, with strong correlations observed between carbohydrate-active enzymes (CAZymes) and specific metabolic intermediates. Notably, CAZyme expression was substrate-dependent: inulin specifically induced glycoside hydrolase family 15 (GH15, EC 3.2.1.3), which targets α-1,2-glycosidic linkages, whereas MOS upregulated a broader set of enzymes—including GH13_40 (EC 3.2.1.10), GH15, GH16_2 (EC 3.2.1-/2.4.1-) and GH17 (EC 3.2.1.58/2.4.1-) — that act on β-1,4-, α-1,6-, α-1,2-, and α-1,3-glycosidic bonds, mediating efficient extracellular hydrolysis of complex carbohydrates into absorbable monosaccharides. This study highlights the critical role of gut fungi in dietary carbohydrate utilization and provides novel insights into the mechanisms by which CAZymes mediate fungal carbohydrate metabolism.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100451"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144764042","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 : 2025-01-01DOI: 10.1016/j.crmicr.2025.100459
Hengkang Xu , Yuchuan Shi , Siyi Wang , Chao Chen , Zhuo Pang , Guofang Zhang , Weiwei Zhang , Haiming Kan
The response of snow microbial communities to environmental variations represents a critical topic in ecological research, particularly given that winter snowfall constitutes the main form of precipitation in northern China. In this study, snow samples were collected from city and suburb areas within the same region across seven provinces in northern China. The physical and chemical properties, metal ion content, and microbial community diversity and network stability were analyzed. Results indicated that the concentrations of Cu²⁺ and Na⁺ in city snow were significantly higher than those in suburb snow. While no significant differences were observed in the richness and diversity of bacterial and fungal communities between city and suburb areas, microbial network stability was higher in suburb samples. Latitude significantly influenced bacterial richness and Shannon diversity in city areas but not in suburb areas; however, fungal Shannon diversity in suburb snow showed a significant correlation with latitude. Mental analyses revealed that NO₃⁻ and chemical oxygen demand (COD) exerted distinct effects on bacterial communities in city and suburb areas, while TN, TC, and COD influenced fungal communities. Environmental factors were found to have significant impacts on microbial community structure, with geographical distance playing a key role in shaping snow microbial community composition. These findings highlight the influence of geographical location and environmental conditions on microbial diversity and community composition, offering valuable insights into the ecological impacts of urbanization and environmental changes on snow microbiomes.
{"title":"Geographical and environmental factors influence snow microbial communities in city and suburban areas of Northern China","authors":"Hengkang Xu , Yuchuan Shi , Siyi Wang , Chao Chen , Zhuo Pang , Guofang Zhang , Weiwei Zhang , Haiming Kan","doi":"10.1016/j.crmicr.2025.100459","DOIUrl":"10.1016/j.crmicr.2025.100459","url":null,"abstract":"<div><div>The response of snow microbial communities to environmental variations represents a critical topic in ecological research, particularly given that winter snowfall constitutes the main form of precipitation in northern China. In this study, snow samples were collected from city and suburb areas within the same region across seven provinces in northern China. The physical and chemical properties, metal ion content, and microbial community diversity and network stability were analyzed. Results indicated that the concentrations of Cu²⁺ and Na⁺ in city snow were significantly higher than those in suburb snow. While no significant differences were observed in the richness and diversity of bacterial and fungal communities between city and suburb areas, microbial network stability was higher in suburb samples. Latitude significantly influenced bacterial richness and Shannon diversity in city areas but not in suburb areas; however, fungal Shannon diversity in suburb snow showed a significant correlation with latitude. Mental analyses revealed that NO₃⁻ and chemical oxygen demand (COD) exerted distinct effects on bacterial communities in city and suburb areas, while TN, TC, and COD influenced fungal communities. Environmental factors were found to have significant impacts on microbial community structure, with geographical distance playing a key role in shaping snow microbial community composition. These findings highlight the influence of geographical location and environmental conditions on microbial diversity and community composition, offering valuable insights into the ecological impacts of urbanization and environmental changes on snow microbiomes.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100459"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144886113","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 : 2025-01-01DOI: 10.1016/j.crmicr.2025.100460
Carlos Farkas , Matías Guerra , Adan Andreu Heredia , Jean Franco Castro
Fragaria chiloensis ssp. chiloensis, endemic to Chile, includes a wild form (f. patagonica) and a cultivated “white strawberry” (f. chiloensis) historically grown in central-south Chile. In this study high throughput metagenomic sequencing was employed to examine the rhizosphere microbial communities of wild and cultivated plants were examined to explore how domestication has shaped microbial structure and function. This enabled binning and functional annotations indicating that wild rhizospheres were dominated by Frankia and Bradyrhizobium, whereas cultivated samples exhibited broader genus‐level diversity yet preserving a core ecological function through functional redundancy. Metabolic reconstructions further spotlight high‐biomass taxa, with Frankia in wild plants and Nocardia in cultivated plants, that harbored extensive biosynthetic gene clusters, linking robust growth to specialized metabolite production and putative osmoprotection. Collectively, these findings illustrated how domestication reshapes the rhizosphere microbiome and contributes to One Health-aligned strategies for sustainable agriculture.
{"title":"Comparative metagenomics of wild and cultivated Fragaria chiloensis reveals major rhizosphere microbiome shifts linked to stress adaptation","authors":"Carlos Farkas , Matías Guerra , Adan Andreu Heredia , Jean Franco Castro","doi":"10.1016/j.crmicr.2025.100460","DOIUrl":"10.1016/j.crmicr.2025.100460","url":null,"abstract":"<div><div><em>Fragaria chiloensis</em> ssp. <em>chiloensis</em>, endemic to Chile, includes a wild form (f. <em>patagonica</em>) and a cultivated “white strawberry” (f. <em>chiloensis</em>) historically grown in central-south Chile. In this study high throughput metagenomic sequencing was employed to examine the rhizosphere microbial communities of wild and cultivated plants were examined to explore how domestication has shaped microbial structure and function. This enabled binning and functional annotations indicating that wild rhizospheres were dominated by <em>Frankia</em> and <em>Bradyrhizobium</em>, whereas cultivated samples exhibited broader genus‐level diversity yet preserving a core ecological function through functional redundancy. Metabolic reconstructions further spotlight high‐biomass taxa, with <em>Frankia</em> in wild plants and <em>Nocardia</em> in cultivated plants, that harbored extensive biosynthetic gene clusters, linking robust growth to specialized metabolite production and putative osmoprotection. Collectively, these findings illustrated how domestication reshapes the rhizosphere microbiome and contributes to One Health-aligned strategies for sustainable agriculture.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"9 ","pages":"Article 100460"},"PeriodicalIF":5.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144888781","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 : 2025-01-01DOI: 10.1016/j.crmicr.2025.100385
Christina Papazlatani , Annabell Wagner , Zhijun Chen , Hans Zweers , Wietse de Boer , Paolina Garbeva
Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating Burkholderia AD24 and Paenibacillus AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi Fusarium culmorum PV and Rhizoctonia solani AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only Burkholderia AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by Burkholderia AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When Burkholderia AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of F. culmorum, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of R. solani. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.
{"title":"Enhancement of production of pathogen-suppressing volatiles using amino acids","authors":"Christina Papazlatani , Annabell Wagner , Zhijun Chen , Hans Zweers , Wietse de Boer , Paolina Garbeva","doi":"10.1016/j.crmicr.2025.100385","DOIUrl":"10.1016/j.crmicr.2025.100385","url":null,"abstract":"<div><div>Bacterial volatile organic compounds can play a significant role in antagonistic interactions. Enhancing the production of bacterial volatiles that suppress the growth of soil-borne phytopathogenic fungi, has perspective as a sustainable disease control strategy. In the present study, we explored the potential of stimulating <em>Burkholderia</em> AD24 and <em>Paenibacillus</em> AD87 to produce volatiles that suppress the growth of the plant pathogenic fungi <em>Fusarium culmorum</em> PV and <em>Rhizoctonia solani</em> AG2.2IIIb. We provided the bacterial strains with a mixture of amino acids that can serve as precursor molecules in metabolic routes leading to emission of suppressive bacterial volatiles. Only <em>Burkholderia</em> AD24 was stimulated to produce a volatile blend that led to higher suppression of both pathogens. Subsequent analysis of the volatile composition emitted by <em>Burkholderia</em> AD24 in the presence of amino acids, showed higher abundance of antifungal compounds, including sulfur compounds (DMDS), pyrazines (2,5-dimethyl pyrazine) and carbohydrates (3-methyl-1-butanol). Follow-up trials with single amino acids revealed a pathogen specific response effect. When <em>Burkholderia</em> AD24 was cultivated in the presence of glutamine and asparagine, the emitted volatile blend suppressed the growth of <em>F. culmorum</em>, whereas when cultivated in the presence of glycine, glutamine, arginine and lysine the volatile blend suppressed the growth of <em>R. solani</em>. Analysis of the volatile blend composition showed differences between the amino acid treatments. Our findings show that amino acid precursor molecules can stimulate the production of fungistatic volatiles but the sensitivity of the fungal pathogens to these bacterial volatiles varies. This should be considered in future application strategies.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100385"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143821498","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}
Bacillus amyloliquefaciens is a soil-associated and plant growth-promoting bacterium. It is the focus of numerous studies due to its ability to sporulate, form biofilms, produce antimicrobial peptides and commercial enzymes. The ability of B. amyloliquefaciensl-17 to form floating biofilm at the air-liquid interface “pellicle” was previously demonstrated. This pellicle exhibits a highly structured architecture which is provided by loosely and tightly matrix bound polysaccharides and proteins. In this study, a first large scale proteomic investigation of both the pellicle and the cell-free liquid phase of l-17 strain was performed. An approach based on physical and chemical extraction of the pellicular matrix combined with protein analysis by mass spectrometry identified 87 weakly matrix-bound proteins and 62 tightly bound proteins. A total of 131 pellicle-associated proteins were identified, including (i) the conserved proteins TasA and TapA, involved in biofilm formation and cohesion (ii) BslA, important for biofilm hydrophobicity (iii) several enzymes that make nutrients available and protect the biofilm from competitors (iv) flagellin and (v) proteins involved in the sporulation process. Proteomic characterization of the cell-free liquid phase underlying the analyzed pellicle allowed the identification of 423 proteins including 118 proteins yet identified in the matrix of the pellicle. The proteins identified specifically in the liquid phase include enzymes involved in the biosynthesis process of non-ribosomal peptides and a variety of commercial enzymes such as proteases, lipases, aminotransferases, peroxidases and phytases. This provides valuable clues to promote the industrial and agricultural application of the cell-free liquid phase of B. amyloliquefaciensl-17.
{"title":"Large scale identification of pellicle and cell-free liquid phase associated proteins in Bacillus amyloliquefaciens L-17","authors":"Tassadit Ouidir , Julie Hardouin , Claire-Emmanuelle Marcato-Romain , Elisabeth Girbal-Neuhauser , Yassine Nait Chabane","doi":"10.1016/j.crmicr.2025.100387","DOIUrl":"10.1016/j.crmicr.2025.100387","url":null,"abstract":"<div><div><em>Bacillus amyloliquefaciens</em> is a soil-associated and plant growth-promoting bacterium. It is the focus of numerous studies due to its ability to sporulate, form biofilms, produce antimicrobial peptides and commercial enzymes. The ability of <em>B. amyloliquefaciens</em> <span>l</span>-17 to form floating biofilm at the air-liquid interface “pellicle” was previously demonstrated. This pellicle exhibits a highly structured architecture which is provided by loosely and tightly matrix bound polysaccharides and proteins. In this study, a first large scale proteomic investigation of both the pellicle and the cell-free liquid phase of <span>l</span>-17 strain was performed. An approach based on physical and chemical extraction of the pellicular matrix combined with protein analysis by mass spectrometry identified 87 weakly matrix-bound proteins and 62 tightly bound proteins. A total of 131 pellicle-associated proteins were identified, including (i) the conserved proteins TasA and TapA, involved in biofilm formation and cohesion (ii) BslA, important for biofilm hydrophobicity (iii) several enzymes that make nutrients available and protect the biofilm from competitors (iv) flagellin and (v) proteins involved in the sporulation process. Proteomic characterization of the cell-free liquid phase underlying the analyzed pellicle allowed the identification of 423 proteins including 118 proteins yet identified in the matrix of the pellicle. The proteins identified specifically in the liquid phase include enzymes involved in the biosynthesis process of non-ribosomal peptides and a variety of commercial enzymes such as proteases, lipases, aminotransferases, peroxidases and phytases. This provides valuable clues to promote the industrial and agricultural application of the cell-free liquid phase of <em>B. amyloliquefaciens</em> <span>l</span>-17.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100387"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143833814","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 : 2025-01-01DOI: 10.1016/j.crmicr.2025.100392
George Michael Nicolas
The discovery of antibiotics is a significant medical breakthrough, saving millions of lives. However, the widespread misuse and overuse of antibiotics led to the development of antimicrobial resistance. Spore-forming probiotics from Bacillus spp. show great interest as antimicrobial agents through the production of strain-specific bioactive secondary metabolites. This review summarizes the broad-spectrum antimicrobial activities of Bacillus spp. secondary metabolite groups and their reported mechanisms of action, underscoring the urgency in developing novel antimicrobial drugs.
{"title":"Secondary Metabolites from Bacillus spp. probiotics as potential treatments for multidrug-resistant pathogens: A comprehensive review","authors":"George Michael Nicolas","doi":"10.1016/j.crmicr.2025.100392","DOIUrl":"10.1016/j.crmicr.2025.100392","url":null,"abstract":"<div><div>The discovery of antibiotics is a significant medical breakthrough, saving millions of lives. However, the widespread misuse and overuse of antibiotics led to the development of antimicrobial resistance. Spore-forming probiotics from <em>Bacillus</em> spp. show great interest as antimicrobial agents through the production of strain-specific bioactive secondary metabolites. This review summarizes the broad-spectrum antimicrobial activities of <em>Bacillus</em> spp. secondary metabolite groups and their reported mechanisms of action, underscoring the urgency in developing novel antimicrobial drugs.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100392"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143869016","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}
Burkholderia pseudomallei (B. pseudomallei) is the causative agent of the high-mortality disease called melioidosis. It is a severe infection that can be misdiagnosed due to variable presentation and low awareness among clinicians of the disease. It is endemic in India and well-described in southern and eastern coastal states. In the last decade, sporadic cases of melioidosis have been diagnosed in North Indian states, predominantly Rajasthan and Gujarat. The reported cases highlight the many risk factors for infection in this region that was not previously recognised as being endemic for melioidosis, including high prevalence of diabetes mellitus, alcoholism, and large rural population engaged in paddy cultivation. Climate change results in frequent flooding and waterlogging in urban areas, leading to exposure of soil harbouring B. pseudomallei, thus a contributing factor to the rise in cases in cities. As North India has not previously been considered an endemic region for melioidosis, wider awareness amongst clinicians and laboratorians is essential for early identification of symptoms, testing for B. pseudomallei in microbiology laboratories, and timely management of the disease to save lives lost to misdiagnosis. The present article describes various aspects of melioidosis in North India including diverse clinical manifestations, risk factors, and possible reasons for misdiagnosis and underreporting.
{"title":"Unearthing the burden of melioidosis in North India – an emerging threat in a non-endemic region","authors":"Shweta Raina , Disha Gautam , Rohit Kumar , Kavita Sisodia , Chiranjay Mukhopadhyay , Harpreet Kaur , Mohammed Ashiq , Rushika Saksena","doi":"10.1016/j.crmicr.2025.100344","DOIUrl":"10.1016/j.crmicr.2025.100344","url":null,"abstract":"<div><div><em>Burkholderia pseudomallei (B. pseudomallei)</em> is the causative agent of the high-mortality disease called melioidosis. It is a severe infection that can be misdiagnosed due to variable presentation and low awareness among clinicians of the disease. It is endemic in India and well-described in southern and eastern coastal states. In the last decade, sporadic cases of melioidosis have been diagnosed in North Indian states, predominantly Rajasthan and Gujarat. The reported cases highlight the many risk factors for infection in this region that was not previously recognised as being endemic for melioidosis, including high prevalence of diabetes mellitus, alcoholism, and large rural population engaged in paddy cultivation. Climate change results in frequent flooding and waterlogging in urban areas, leading to exposure of soil harbouring <em>B. pseudomallei,</em> thus a contributing factor to the rise in cases in cities. As North India has not previously been considered an endemic region for melioidosis, wider awareness amongst clinicians and laboratorians is essential for early identification of symptoms, testing for <em>B. pseudomallei</em> in microbiology laboratories, and timely management of the disease to save lives lost to misdiagnosis. The present article describes various aspects of melioidosis in North India including diverse clinical manifestations, risk factors, and possible reasons for misdiagnosis and underreporting.</div></div>","PeriodicalId":34305,"journal":{"name":"Current Research in Microbial Sciences","volume":"8 ","pages":"Article 100344"},"PeriodicalIF":4.8,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143104684","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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