Lytic bacteriophages (phages) are promising clinically viable therapeutic options against carbapenem-resistant Klebsiella pneumoniae (CRKP). In China, the predominant strains are those assigned to sequence type 11 and capsular type 64 (ST11-KL64). The emergence of phage resistance is a major bottleneck hindering effective phage therapy, requiring more new phages to provide the flexibility for creating different phage cocktails. However, the majority of phages against ST11-KL64 CRKP belong to the genus Przondovirus of the family Autographiviridae, which limits the options for constructing cocktails. We recovered a novel lytic phage of the genus Taipeivirus within the family Ackermannviridae against ST11-KL64 CRKP from a river in China. We phenotypically characterized this phage and obtained its genome sequence for analysis. This phage can inhibit the growth of ST11-KL64 CRKP for 6.5 h at a 0.1 multiplicity of infection and exhibits a narrow host range, being unable to attack CRKP strains of the other 30 capsular types. This phage carries no genes encoding antimicrobial resistance, virulence, or lysogeny. It is stable across a wide range of temperatures and pH values, making it suitable for phage therapy. Unlike other Taipeivirus phages, P01 has two tail spike proteins and a unique tail fiber protein. The distinct tail composition of this phage contributes to its activity against ST11-KL64 CRKP and its narrow host range. Taken together, we recovered a phage of a novel viral species with the potential for therapy, which expands the phage biobank against CRKP.
{"title":"<i>Ackermannviridae</i> bacteriophage against carbapenem-resistant <i>Klebsiella pneumoniae</i> of capsular type 64.","authors":"Juan Li, Yu Feng, Huan Luo, Qingqing Fang, Yongqiang Yang, Zhiyong Zong","doi":"10.3389/fmicb.2024.1462459","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1462459","url":null,"abstract":"<p><p>Lytic bacteriophages (phages) are promising clinically viable therapeutic options against carbapenem-resistant <i>Klebsiella pneumoniae</i> (CRKP). In China, the predominant strains are those assigned to sequence type 11 and capsular type 64 (ST11-KL64). The emergence of phage resistance is a major bottleneck hindering effective phage therapy, requiring more new phages to provide the flexibility for creating different phage cocktails. However, the majority of phages against ST11-KL64 CRKP belong to the genus <i>Przondovirus</i> of the family <i>Autographiviridae</i>, which limits the options for constructing cocktails. We recovered a novel lytic phage of the genus <i>Taipeivirus</i> within the family <i>Ackermannviridae</i> against ST11-KL64 CRKP from a river in China. We phenotypically characterized this phage and obtained its genome sequence for analysis. This phage can inhibit the growth of ST11-KL64 CRKP for 6.5 h at a 0.1 multiplicity of infection and exhibits a narrow host range, being unable to attack CRKP strains of the other 30 capsular types. This phage carries no genes encoding antimicrobial resistance, virulence, or lysogeny. It is stable across a wide range of temperatures and pH values, making it suitable for phage therapy. Unlike other <i>Taipeivirus</i> phages, P01 has two tail spike proteins and a unique tail fiber protein. The distinct tail composition of this phage contributes to its activity against ST11-KL64 CRKP and its narrow host range. Taken together, we recovered a phage of a novel viral species with the potential for therapy, which expands the phage biobank against CRKP.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11456439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Introduction: The rhizosphere is the zone of soil surrounding plant roots that is directly influenced by root exudates released by the plant, which select soil microorganisms. The resulting rhizosphere microbiota plays a key role in plant health and development by enhancing its nutrition or immune response and protecting it from biotic or abiotic stresses. In particular, plant growth-promoting rhizobacteria (PGPR) are beneficial members of this microbiota that represent a great hope for agroecology, since they could be used as bioinoculants for sustainable crop production. Therefore, it is necessary to decipher the molecular dialog between roots and PGPR in order to promote the establishment of bioinoculants in the rhizosphere, which is required for their beneficial functions.
Methods: Here, the ability of root exudates from rapeseed (Brassica napus), pea (Pisum sativum), and ryegrass (Lolium perenne) to attract and feed three PGPR (Bacillus subtilis, Pseudomonas fluorescens, and Azospirillum brasilense) was measured and compared, as these responses are directly involved in the establishment of the rhizosphere microbiota.
Results: Our results showed that root exudates differentially attracted and fed the three PGPR. For all beneficial bacteria, rapeseed exudates were the most attractive and induced the fastest growth, while pea exudates allowed the highest biomass production. The performance of ryegrass exudates was generally lower, and variable responses were observed between bacteria. In addition, P. fluorescens and A. brasilense appeared to respond more efficiently to root exudates than B. subtilis. Finally, we proposed to evaluate the compatibility of each plant-PGPR couple by assigning them a "love match" score, which reflects the ability of root exudates to enhance bacterial rhizocompetence.
Discussion: Taken together, our results provide new insights into the specific selection of PGPR by the plant through their root exudates and may help to select the most effective exudates to promote bioinoculant establishment in the rhizosphere.
{"title":"A \"love match\" score to compare root exudate attraction and feeding of the plant growth-promoting rhizobacteria <i>Bacillus subtilis</i>, <i>Pseudomonas fluorescens</i>, and <i>Azospirillum brasilense</i>.","authors":"Eulalie Fourneau, Mélissa Pannier, Wassila Riah, Emmanuelle Personeni, Annette Morvan-Bertrand, Josselin Bodilis, Barbara Pawlak","doi":"10.3389/fmicb.2024.1473099","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1473099","url":null,"abstract":"<p><strong>Introduction: </strong>The rhizosphere is the zone of soil surrounding plant roots that is directly influenced by root exudates released by the plant, which select soil microorganisms. The resulting rhizosphere microbiota plays a key role in plant health and development by enhancing its nutrition or immune response and protecting it from biotic or abiotic stresses. In particular, plant growth-promoting rhizobacteria (PGPR) are beneficial members of this microbiota that represent a great hope for agroecology, since they could be used as bioinoculants for sustainable crop production. Therefore, it is necessary to decipher the molecular dialog between roots and PGPR in order to promote the establishment of bioinoculants in the rhizosphere, which is required for their beneficial functions.</p><p><strong>Methods: </strong>Here, the ability of root exudates from rapeseed (<i>Brassica napus</i>), pea (<i>Pisum sativum</i>), and ryegrass (<i>Lolium perenne</i>) to attract and feed three PGPR (<i>Bacillus subtilis</i>, <i>Pseudomonas fluorescens</i>, and <i>Azospirillum brasilense</i>) was measured and compared, as these responses are directly involved in the establishment of the rhizosphere microbiota.</p><p><strong>Results: </strong>Our results showed that root exudates differentially attracted and fed the three PGPR. For all beneficial bacteria, rapeseed exudates were the most attractive and induced the fastest growth, while pea exudates allowed the highest biomass production. The performance of ryegrass exudates was generally lower, and variable responses were observed between bacteria. In addition, <i>P. fluorescens</i> and <i>A. brasilense</i> appeared to respond more efficiently to root exudates than <i>B. subtilis</i>. Finally, we proposed to evaluate the compatibility of each plant-PGPR couple by assigning them a \"love match\" score, which reflects the ability of root exudates to enhance bacterial rhizocompetence.</p><p><strong>Discussion: </strong>Taken together, our results provide new insights into the specific selection of PGPR by the plant through their root exudates and may help to select the most effective exudates to promote bioinoculant establishment in the rhizosphere.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11456545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389361","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-23eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1464720
Juan F Villacís, Andrea López-Rosero, Juan José Bustillos, Matías Cadena, César A Yumiseva, Mario J Grijalva, Anita G Villacís
Introduction: Chagas disease is a neglected tropical disease caused by the parasite Trypanosoma cruzi that is transmitted mainly by the feces of infected Triatomines. In Ecuador the main vector is Rhodnius ecuadoriensis which is distributed in several provinces of the country. More than 40% of these insects in the wild have T. cruzi as part of their intestinal microbiota. For this reason, the objective of this research was to characterize the intestinal bacterial microbiota of R. ecuadoriensis.
Methods: The methodology used was based on the DNA extraction of the intestinal contents from the wild collected insects (adults and nymphs V), as well as the insects maintained at the insectary of the CISeAL. Finally, the samples were analyzed by metagenomics extensions based on the different selected criteria.
Results: The intestinal microbiota of R. ecuadoriensis presented a marked divergence between laboratory-raised and wild collected insects. This difference was observed in all stages and was similar between insects from Loja and Manabí. A large loss of microbial symbionts was observed in laboratory-raised insects.
Discussion: This study is a crucial first step in investigating microbiota interactions and advancing new methodologies.
{"title":"Bacterial microbiota from the gut of <i>Rhodnius ecuadoriensis</i>, a vector of Chagas disease in Ecuador's Central Coast and Southern Andes.","authors":"Juan F Villacís, Andrea López-Rosero, Juan José Bustillos, Matías Cadena, César A Yumiseva, Mario J Grijalva, Anita G Villacís","doi":"10.3389/fmicb.2024.1464720","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1464720","url":null,"abstract":"<p><strong>Introduction: </strong>Chagas disease is a neglected tropical disease caused by the parasite <i>Trypanosoma cruzi</i> that is transmitted mainly by the feces of infected Triatomines. In Ecuador the main vector is <i>Rhodnius ecuadoriensis</i> which is distributed in several provinces of the country. More than 40% of these insects in the wild have <i>T. cruzi</i> as part of their intestinal microbiota. For this reason, the objective of this research was to characterize the intestinal bacterial microbiota of <i>R. ecuadoriensis</i>.</p><p><strong>Methods: </strong>The methodology used was based on the DNA extraction of the intestinal contents from the wild collected insects (adults and nymphs V), as well as the insects maintained at the insectary of the CISeAL. Finally, the samples were analyzed by metagenomics extensions based on the different selected criteria.</p><p><strong>Results: </strong>The intestinal microbiota of <i>R. ecuadoriensis</i> presented a marked divergence between laboratory-raised and wild collected insects. This difference was observed in all stages and was similar between insects from Loja and Manabí. A large loss of microbial symbionts was observed in laboratory-raised insects.</p><p><strong>Discussion: </strong>This study is a crucial first step in investigating microbiota interactions and advancing new methodologies.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11456480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Introduction: This study aimed to assess the diagnostic values of bronchoalveolar lavage fluid (BALF) real-time polymerase chain reaction (PCR) and BALF metagenomic next-generation sequencing (mNGS) for Pneumocystis jirovecii pneumonia (PJP) in patients infected with human immunodeficiency virus (HIV).
Methods: A total of 99 HIV-infected PJP patients and 61 HIV-infected patients diagnosed with non-PJP pneumonia between March 2019 and December 2022 were enrolled. P. jirovecii and multiple other co-pathogens detected in BALF by mNGS were analyzed. The clinical final diagnosis was employed as a benchmark. We compared the diagnostic performance of mNGS in PJP with serum BDG and BALF real-time PCR. The mixed infections detected by mNGS and modifications of antimicrobial treatment were also analyzed.
Results: The sensitivity of mNGS test of BALF samples reached 85.86%, which was significantly higher than serum BDG (39.39%, P < 0.001). The sensitivity of BALF P. jirovecii PCR (84.85%) was similar with mNGS (P > 0.05). The specificity of mNGS (100%) was also same as PCR (100.0%), and superior to serum BDG (88.52%, P < 0.001). Besides, mNGS performs remarkably well in identifying co-pathogens of PJP patients infected with HIV. In addition to P. jirovecii, 82 cases (82.83%) of other co-pathogens were identified based on mNGS. Moreover, thirty-four patients (34.34%) increased therapeutic dose of trimethoprim-sulfamethoxazole (TMP-SMZ) based on BALF P. jirovecii PCR. Based on the mNGS results, initial antimicrobial treatment was modified in 86.87% (86/99) of PJP patients.
Conclusion: BALF mNGS and real-time PCR are two powerful techniques for rapid diagnosis of PJP with high specificity and sensitivity. Moreover, the benefit of mNGS is that it may identify other organisms besides PJP and it may benefit proper and prompt treatment.
{"title":"Diagnostic values of BALF metagenomic next-generation sequencing, BALF real-time PCR and serum BDG for <i>Pneumocystis jirovecii</i> pneumonia in HIV-infected patients.","authors":"Qianhui Chen, Xiaoping Chen, Pingzheng Mo, Liangjun Chen, Qian Du, Wenjia Hu, Qunqun Jiang, Zhongwei Zhang, Yongxi Zhang, Qinglian Guo, Yong Xiong, Liping Deng","doi":"10.3389/fmicb.2024.1421660","DOIUrl":"10.3389/fmicb.2024.1421660","url":null,"abstract":"<p><strong>Introduction: </strong>This study aimed to assess the diagnostic values of bronchoalveolar lavage fluid (BALF) real-time polymerase chain reaction (PCR) and BALF metagenomic next-generation sequencing (mNGS) for Pneumocystis jirovecii pneumonia (PJP) in patients infected with human immunodeficiency virus (HIV).</p><p><strong>Methods: </strong>A total of 99 HIV-infected PJP patients and 61 HIV-infected patients diagnosed with non-PJP pneumonia between March 2019 and December 2022 were enrolled. <i>P. jirovecii</i> and multiple other co-pathogens detected in BALF by mNGS were analyzed. The clinical final diagnosis was employed as a benchmark. We compared the diagnostic performance of mNGS in PJP with serum BDG and BALF real-time PCR. The mixed infections detected by mNGS and modifications of antimicrobial treatment were also analyzed.</p><p><strong>Results: </strong>The sensitivity of mNGS test of BALF samples reached 85.86%, which was significantly higher than serum BDG (39.39%, <i>P</i> < 0.001). The sensitivity of BALF <i>P. jirovecii</i> PCR (84.85%) was similar with mNGS (<i>P</i> > 0.05). The specificity of mNGS (100%) was also same as PCR (100.0%), and superior to serum BDG (88.52%, <i>P</i> < 0.001). Besides, mNGS performs remarkably well in identifying co-pathogens of PJP patients infected with HIV. In addition to <i>P. jirovecii</i>, 82 cases (82.83%) of other co-pathogens were identified based on mNGS. Moreover, thirty-four patients (34.34%) increased therapeutic dose of trimethoprim-sulfamethoxazole (TMP-SMZ) based on BALF <i>P. jirovecii</i> PCR. Based on the mNGS results, initial antimicrobial treatment was modified in 86.87% (86/99) of PJP patients.</p><p><strong>Conclusion: </strong>BALF mNGS and real-time PCR are two powerful techniques for rapid diagnosis of PJP with high specificity and sensitivity. Moreover, the benefit of mNGS is that it may identify other organisms besides PJP and it may benefit proper and prompt treatment.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11449763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-20eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1454683
Min Hu, Lulu Wang, Dapeng Su, Qingsong Yuan, Chenghong Xiao, Lanping Guo, Meidan Wang, Chuanzhi Kang, Jinqiang Zhang, Tao Zhou
Medicinal herbs have been increasingly used for therapeutic purposes against a diverse range of human diseases worldwide. However, inevitable contaminants, including mycotoxins, in medicinal herbs can cause serious problems for humans despite their health benefits. The increasing consumption of medicinal plants has made their use a public health problem due to the lack of effective surveillance of the use, efficacy, toxicity, and quality of these natural products. Radix Dipsaci is commonly utilized in traditional Chinese medicine and is susceptible to contamination with mycotoxins. Here, we evaluated the mycotoxins, mycobiota and toxigenic fungi in the traditional medicine Radix Dipsaci. A total of 28 out of 63 Radix Dipsaci sample batches (44.4%) were found to contain mycotoxins. Among the positive samples, the contamination levels of AFB1, AFG1, AFG2, and OTA in the positive samples ranged from 0.52 to 32.13 μg/kg, 5.14 to 20.05 μg/kg, 1.52 to 2.33 μg/kg, and 1.81 to 19.43 μg/kg respectively, while the concentrations of ZEN and T-2 were found to range from 2.85 to 6.33 μg/kg and from 2.03 to 2.53 μg/kg, respectively. More than 60% of the contaminated samples were combined with multiple mycotoxins. Fungal diversity and community were altered in the Radix Dipsaci contaminated with various mycotoxins. The abundance of Aspergillus and Fusarium increased in the Radix Dipsaci contaminated with aflatoxins (AFs) and ZEN. A total of 95 strains of potentially toxigenic fungi were isolated from the Radix Dipsaci samples contaminated with mycotoxins, predominantly comprising Aspergillus (73.7%), Fusarium (20.0%), and Penicillium (6.3%). Through morphological identification, molecular identification, mycotoxin synthase gene identification and toxin production verification, we confirmed that AFB1 and AFG1 primarily derive from Aspergillus flavus, OTA primarily derives from Aspergillus westerdijkiae, ZEN primarily derives from Fusarium oxysporum, and T-2 primarily derives from Fusarium graminearum in Radix Dipsaci. These data can facilitate our comprehension of prevalent toxigenic fungal species and contamination levels in Chinese herbal medicine, thereby aiding the establishment of effective strategies for prevention, control, and degradation to mitigate the presence of fungi and mycotoxins in Chinese herbal medicine.
{"title":"Evaluation of mycotoxins, mycobiota and toxigenic fungi in the traditional medicine <i>Radix Dipsaci</i>.","authors":"Min Hu, Lulu Wang, Dapeng Su, Qingsong Yuan, Chenghong Xiao, Lanping Guo, Meidan Wang, Chuanzhi Kang, Jinqiang Zhang, Tao Zhou","doi":"10.3389/fmicb.2024.1454683","DOIUrl":"10.3389/fmicb.2024.1454683","url":null,"abstract":"<p><p>Medicinal herbs have been increasingly used for therapeutic purposes against a diverse range of human diseases worldwide. However, inevitable contaminants, including mycotoxins, in medicinal herbs can cause serious problems for humans despite their health benefits. The increasing consumption of medicinal plants has made their use a public health problem due to the lack of effective surveillance of the use, efficacy, toxicity, and quality of these natural products. <i>Radix Dipsaci</i> is commonly utilized in traditional Chinese medicine and is susceptible to contamination with mycotoxins. Here, we evaluated the mycotoxins, mycobiota and toxigenic fungi in the traditional medicine <i>Radix Dipsaci</i>. A total of 28 out of 63 <i>Radix Dipsaci</i> sample batches (44.4%) were found to contain mycotoxins. Among the positive samples, the contamination levels of AFB<sub>1</sub>, AFG<sub>1</sub>, AFG<sub>2</sub>, and OTA in the positive samples ranged from 0.52 to 32.13 μg/kg, 5.14 to 20.05 μg/kg, 1.52 to 2.33 μg/kg, and 1.81 to 19.43 μg/kg respectively, while the concentrations of ZEN and T-2 were found to range from 2.85 to 6.33 μg/kg and from 2.03 to 2.53 μg/kg, respectively. More than 60% of the contaminated samples were combined with multiple mycotoxins. Fungal diversity and community were altered in the <i>Radix Dipsaci</i> contaminated with various mycotoxins. The abundance of <i>Aspergillus</i> and <i>Fusarium</i> increased in the <i>Radix Dipsaci</i> contaminated with aflatoxins (AFs) and ZEN. A total of 95 strains of potentially toxigenic fungi were isolated from the <i>Radix Dipsaci</i> samples contaminated with mycotoxins, predominantly comprising <i>Aspergillus</i> (73.7%), <i>Fusarium</i> (20.0%), and <i>Penicillium</i> (6.3%). Through morphological identification, molecular identification, mycotoxin synthase gene identification and toxin production verification, we confirmed that AFB<sub>1</sub> and AFG<sub>1</sub> primarily derive from <i>Aspergillus flavus</i>, OTA primarily derives from <i>Aspergillus westerdijkiae</i>, ZEN primarily derives from <i>Fusarium oxysporum</i>, and T-2 primarily derives from <i>Fusarium graminearum</i> in <i>Radix Dipsaci</i>. These data can facilitate our comprehension of prevalent toxigenic fungal species and contamination levels in Chinese herbal medicine, thereby aiding the establishment of effective strategies for prevention, control, and degradation to mitigate the presence of fungi and mycotoxins in Chinese herbal medicine.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-20eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1491295
Armin Tarrah, Lu Meng, Taurai Tasara, Tanushree B Gupta
{"title":"Editorial: Impact of dairy farming on the safety of raw milk and milk products.","authors":"Armin Tarrah, Lu Meng, Taurai Tasara, Tanushree B Gupta","doi":"10.3389/fmicb.2024.1491295","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1491295","url":null,"abstract":"","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11449836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Since 2011, the emergence of Pseudorabies virus (PRV) variants has led to significant vaccine failures, resulting in severe economic losses in China's swine industry. Conventional PRV vaccines have shown limited efficacy against these emergent variants, underscoring the urgent need for novel immunization strategies. This study aimed to develop and evaluate a novel recombinant PRV vaccine candidate with improved safety and immunogenicity profiles. Utilizing the homology-directed repair (HDR)-CRISPR/Cas9 system, we generated a recombinant PRV strain, designated PRV SX-10ΔgI/gE/TK/UL24, with deletions in the gI, gE, TK, and UL24 genes. In vitro analyses demonstrated that the recombinant virus exhibited similar replication kinetics and growth curves comparable to the parental strain. The immunological properties of the recombinant PRV were assessed in murine and porcine models. All animals inoculated with PRV SX-10ΔgI/gE/TK/UL24 survived without exhibiting significant clinical signs or pathological alterations. Immunological assays revealed that PRV SX-10ΔgI/gE/TK/UL24 elicited significantly higher levels of gB-specific antibodies, neutralizing antibodies, and cytokines (including IFN-γ, IL-2, and IL-4) compared to both the Bartha-K61 and PRV SX-10ΔgI/gE/TK strains. Notably, both murine and porcine subjects immunized with PRV SX-10ΔgI/gE/TK/UL24 demonstrated enhanced protection against challenges with the variant PRV SX-10 strain, compared to other vaccine strains. These findings suggest that PRV SX-10ΔgI/gE/TK/UL24 represents a promising PRV vaccine candidate strain, offering valuable insights for the prevention and control of PRV in clinical applications.
{"title":"Development and immunogenicity evaluation of a quadruple-gene-deleted pseudorabies virus strain.","authors":"Hui Li, Riteng Zhang, Jiahao Qu, Yahao Kang, Jingnan Zhang, Ruhai Guo, JunDa Li, Xiao Zhang, Likang Han, Honglin Xie, Xinglong Wang","doi":"10.3389/fmicb.2024.1479794","DOIUrl":"10.3389/fmicb.2024.1479794","url":null,"abstract":"<p><p>Since 2011, the emergence of Pseudorabies virus (PRV) variants has led to significant vaccine failures, resulting in severe economic losses in China's swine industry. Conventional PRV vaccines have shown limited efficacy against these emergent variants, underscoring the urgent need for novel immunization strategies. This study aimed to develop and evaluate a novel recombinant PRV vaccine candidate with improved safety and immunogenicity profiles. Utilizing the homology-directed repair (HDR)-CRISPR/Cas9 system, we generated a recombinant PRV strain, designated PRV SX-10ΔgI/gE/TK/UL24, with deletions in the gI, gE, TK, and UL24 genes. <i>In vitro</i> analyses demonstrated that the recombinant virus exhibited similar replication kinetics and growth curves comparable to the parental strain. The immunological properties of the recombinant PRV were assessed in murine and porcine models. All animals inoculated with PRV SX-10ΔgI/gE/TK/UL24 survived without exhibiting significant clinical signs or pathological alterations. Immunological assays revealed that PRV SX-10ΔgI/gE/TK/UL24 elicited significantly higher levels of gB-specific antibodies, neutralizing antibodies, and cytokines (including IFN-<i>γ</i>, IL-2, and IL-4) compared to both the Bartha-K61 and PRV SX-10ΔgI/gE/TK strains. Notably, both murine and porcine subjects immunized with PRV SX-10ΔgI/gE/TK/UL24 demonstrated enhanced protection against challenges with the variant PRV SX-10 strain, compared to other vaccine strains. These findings suggest that PRV SX-10ΔgI/gE/TK/UL24 represents a promising PRV vaccine candidate strain, offering valuable insights for the prevention and control of PRV in clinical applications.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11449858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-20eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1448629
XuWen Zheng, MaoBing Chen, Yi Zhuang, Liang Zhao, YongJun Qian, ChengCheng Shi
Background: Multiple studies suggest a potential connection between the gut microbiome and asthma. Our objective is to use advanced genetic and metagenomic techniques to elucidate the causal relationships and underlying mechanisms between gut microbiota and asthma.
Methods: The study utilized comprehensive Linkage Disequilibrium Score Regression (LDSC) and Mendelian randomization (MR) analyses to examine the relationship between 119 gut microbiota genera and asthma, using publicly accessible genome-wide association studies (GWAS). The meta-analysis synthesized summary effect estimates obtained from LDSC, forward MR, and reverse MR. The MiBioGen collaboration, involving 18,340 individuals, identified genetic variations associated with gut bacteria. Asthma data were collected from the UK Biobank, FinnGen, and GERA, encompassing a total of 82,060 cases and 641,049 controls.
Results: LDSC analysis revealed significant negative genetic correlations between asthma and RuminococcaceaeUCG004 (Rg = -0.55, p = 7.66 × 10-5) and Subdoligranulum (Rg = -0.35, p = 3.61 × 10-4). Forward MR analysis suggested associations between Butyricicoccus (OR = 0.92, p = 0.01), Turicibacter (OR = 0.95, p = 0.025), Butyrivibrio (OR = 0.98, p = 0.047), and reduced asthma risk. Conversely, Coprococcus2 (OR = 1.10, p = 0.035) and Roseburia (OR = 1.07, p = 0.039) were associated with increased risk. Reverse MR analysis indicated significant associations between genetically predicted asthma and Eubacteriumxylanophilumgroup (Beta = -0.08, p = 9.25 × 10-7), LachnospiraceaeNK4A136group (Beta = -0.05, p = 1.26 × 10-4), and Eisenbergiella (Beta = 0.06, p = 0.015, Rg_P = 0.043).
Conclusion: The findings underscore significant genetic correlations and causal relationships between specific gut microbiota and asthma. These insights highlight the potential of gut microbiota as both markers and modulators of asthma risk, offering new avenues for targeted therapeutic strategies.
{"title":"Unveiling genetic links between gut microbiota and asthma: a Mendelian randomization.","authors":"XuWen Zheng, MaoBing Chen, Yi Zhuang, Liang Zhao, YongJun Qian, ChengCheng Shi","doi":"10.3389/fmicb.2024.1448629","DOIUrl":"10.3389/fmicb.2024.1448629","url":null,"abstract":"<p><strong>Background: </strong>Multiple studies suggest a potential connection between the gut microbiome and asthma. Our objective is to use advanced genetic and metagenomic techniques to elucidate the causal relationships and underlying mechanisms between gut microbiota and asthma.</p><p><strong>Methods: </strong>The study utilized comprehensive Linkage Disequilibrium Score Regression (LDSC) and Mendelian randomization (MR) analyses to examine the relationship between 119 gut microbiota genera and asthma, using publicly accessible genome-wide association studies (GWAS). The meta-analysis synthesized summary effect estimates obtained from LDSC, forward MR, and reverse MR. The MiBioGen collaboration, involving 18,340 individuals, identified genetic variations associated with gut bacteria. Asthma data were collected from the UK Biobank, FinnGen, and GERA, encompassing a total of 82,060 cases and 641,049 controls.</p><p><strong>Results: </strong>LDSC analysis revealed significant negative genetic correlations between asthma and <i>RuminococcaceaeUCG004</i> (Rg = -0.55, <i>p</i> = 7.66 × 10<sup>-5</sup>) and <i>Subdoligranulum</i> (Rg = -0.35, <i>p</i> = 3.61 × 10<sup>-4</sup>). Forward MR analysis suggested associations between <i>Butyricicoccus</i> (OR = 0.92, <i>p</i> = 0.01), <i>Turicibacter</i> (OR = 0.95, <i>p</i> = 0.025), <i>Butyrivibrio</i> (OR = 0.98, <i>p</i> = 0.047), and reduced asthma risk. Conversely, <i>Coprococcus2</i> (OR = 1.10, <i>p</i> = 0.035) and <i>Roseburia</i> (OR = 1.07, <i>p</i> = 0.039) were associated with increased risk. Reverse MR analysis indicated significant associations between genetically predicted asthma and <i>Eubacteriumxylanophilumgroup</i> (Beta = -0.08, <i>p</i> = 9.25 × 10<sup>-7</sup>), <i>LachnospiraceaeNK4A136group</i> (Beta = -0.05, <i>p</i> = 1.26 × 10<sup>-4</sup>), and <i>Eisenbergiella</i> (Beta = 0.06, <i>p</i> = 0.015, Rg_<i>P</i> = 0.043).</p><p><strong>Conclusion: </strong>The findings underscore significant genetic correlations and causal relationships between specific gut microbiota and asthma. These insights highlight the potential of gut microbiota as both markers and modulators of asthma risk, offering new avenues for targeted therapeutic strategies.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11449699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-20eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1465346
Pupu Yan, Jiali Liu, Yongxi Huang, Tilin Yi, Heng Zhang, Gang Dai, Xiong Wang, Zhenzhen Gao, Bin He, Weili Guo, Yingbing Su, Liwei Guo
Introduction: The aim of this research was to clarify the mechanism through which baicalin exerts its inhibitory effects on Aeromonas hydrophila infection.
Methods: The antibacterial efficacy of baicalin was assessed by determining its minimum inhibitory concentration (MIC) against A. hydrophila. Various parameters, including the growth curve, cell wall integrity, biofilm formation, AKP content, and morphological alterations of A. hydrophila, were analyzed. In vivo experiments involved the administration of A. hydrophila 4 h postintraperitoneal injection of varying doses of baicalin to induce infection, with subsequent monitoring of mortality rates. After a 3 d period, liver, spleen, and intestinal tissues were harvested to evaluate organ indices, antioxidant and immune parameters, as well as intestinal microbial composition.
Results: The findings indicated that baicalin treatment resulted in the disruption of the cell wall of A. hydrophila, leading to the loss of its normal structural integrity. Furthermore, baicalin significantly inhibited biofilm formation and facilitated the release of intracellular proteins (P < 0.05). In vivo, baicalin enhanced the survival rates of yellow catfish infected with A. hydrophila. Compared to the control group, the liver index of yellow catfish was elevated, while the spleen and intestinal indices were reduced in the baicalin-treated group (P < 0.05). Additionally, baicalin at an appropriate dosage was found to increase levels of SOD, GSH, CAT, ACP, and AKP in yellow catfish (P < 0.05), while simultaneously decreasing MDA accumulation and the mRNA expression of inflammatory markers such as Keap1, IL1, IFN-γ, and TNF-α, (P < 0.05). Moreover, baicalin significantly enhanced the operational taxonomic unit (OTU) count in A. hydrophila-infected yellow catfish (P < 0.05), restoring the abundance of Barnesiellaceae, Enterobacteriaceae, Plesiomonas, and UBA1819 (P < 0.05).
Discussion: In summary, baicalin demonstrates the potential to improve the survival rate of yellow catfish subjected to A. hydrophila infection, augment antioxidant and immune responses, mitigate inflammation, and enhance intestinal microbial diversity.
{"title":"Baicalin enhances antioxidant, inflammatory defense, and microbial diversity of yellow catfish (<i>Pelteobagrus fulvidraco</i>) infected with <i>Aeromonas hydrophila</i>.","authors":"Pupu Yan, Jiali Liu, Yongxi Huang, Tilin Yi, Heng Zhang, Gang Dai, Xiong Wang, Zhenzhen Gao, Bin He, Weili Guo, Yingbing Su, Liwei Guo","doi":"10.3389/fmicb.2024.1465346","DOIUrl":"10.3389/fmicb.2024.1465346","url":null,"abstract":"<p><strong>Introduction: </strong>The aim of this research was to clarify the mechanism through which baicalin exerts its inhibitory effects on <i>Aeromonas hydrophila</i> infection.</p><p><strong>Methods: </strong>The antibacterial efficacy of baicalin was assessed by determining its minimum inhibitory concentration (MIC) against <i>A. hydrophila</i>. Various parameters, including the growth curve, cell wall integrity, biofilm formation, AKP content, and morphological alterations of <i>A. hydrophila</i>, were analyzed. In vivo experiments involved the administration of <i>A. hydrophila</i> 4 h postintraperitoneal injection of varying doses of baicalin to induce infection, with subsequent monitoring of mortality rates. After a 3 d period, liver, spleen, and intestinal tissues were harvested to evaluate organ indices, antioxidant and immune parameters, as well as intestinal microbial composition.</p><p><strong>Results: </strong>The findings indicated that baicalin treatment resulted in the disruption of the cell wall of <i>A. hydrophila</i>, leading to the loss of its normal structural integrity. Furthermore, baicalin significantly inhibited biofilm formation and facilitated the release of intracellular proteins (<i>P</i> < 0.05). In vivo, baicalin enhanced the survival rates of yellow catfish infected with <i>A. hydrophila</i>. Compared to the control group, the liver index of yellow catfish was elevated, while the spleen and intestinal indices were reduced in the baicalin-treated group (<i>P</i> < 0.05). Additionally, baicalin at an appropriate dosage was found to increase levels of SOD, GSH, CAT, ACP, and AKP in yellow catfish (<i>P</i> < 0.05), while simultaneously decreasing MDA accumulation and the mRNA expression of inflammatory markers such as Keap1, IL1, IFN-γ, and TNF-α, (<i>P</i> < 0.05). Moreover, baicalin significantly enhanced the operational taxonomic unit (OTU) count in <i>A. hydrophila</i>-infected yellow catfish (<i>P</i> < 0.05), restoring the abundance of Barnesiellaceae, Enterobacteriaceae, Plesiomonas, and <i>UBA1819</i> (<i>P</i> < 0.05).</p><p><strong>Discussion: </strong>In summary, baicalin demonstrates the potential to improve the survival rate of yellow catfish subjected to <i>A. hydrophila</i> infection, augment antioxidant and immune responses, mitigate inflammation, and enhance intestinal microbial diversity.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11449889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-20eCollection Date: 2024-01-01DOI: 10.3389/fmicb.2024.1457624
Chuandong Jiang, Fuyu Peng, Li Zhang, Yuqin Zhang, Jie Wang, Junmin Li, Binghui Cui, Changdai Cao, Chengqiang Wang, Yunlei Qin, Ran Wang, Zongpeng Zhao, Jiazhu Jiang, Mingfeng Yang, Mingming Sun, Long Yang, Qiang Zhang
Plant growth, crop yield, and pest and disease control are enhanced by PGPR (Plant growth promoting rhizobacteria), which are beneficial microorganisms found in a close symbiosis with plant roots. Phytohormones are secreted, nutrient uptake is improved, and soil properties along with the microbiological environment are regulated by these microorganisms, making them a significant focus in agricultural research. In this study, the efficient PGPR strain T1 was isolated and screened from tobacco inter-root soil, and identified and confirmed by ITS sequencing technology. Tobacco growth indicators and soil property changes were observed and recorded through potting experiments. The activities of key enzymes (e.g., sucrase, catalase, urease) in soil were further determined. High-throughput sequencing technology was utilized to sequence the soil microbial community, and combined with macro-genomics analysis, the effects of T1 strain on soil microbial diversity and metabolic pathways were explored. Following the application of T1, significant improvements were observed in the height, leaf length, and width of tobacco plants. Furthermore, the physical and chemical properties of the soil were notably enhanced, including a 26.26% increase in phosphorus availability. Additionally, the activities of key soil enzymes such as sucrase, catalase, and urease were significantly increased, indicating improved soil health and fertility. Comprehensive joint microbiomics and macrogenomics analyses revealed a substantial rise in the populations of beneficial soil microorganisms and an enhancement in metabolic pathways, including amino acid metabolism, synthesis, and production of secondary metabolites. These increase in beneficial microorganisms and the enhancement of their metabolic functions are crucial for plant growth and soil fertility. This study provides valuable references for the development of innovative microbial fertilizers and offers programs for the sustainable development of modern agriculture.
{"title":"Isolation, identification, and mechanism analysis of plant growth-promoting rhizobacteria in tobacco.","authors":"Chuandong Jiang, Fuyu Peng, Li Zhang, Yuqin Zhang, Jie Wang, Junmin Li, Binghui Cui, Changdai Cao, Chengqiang Wang, Yunlei Qin, Ran Wang, Zongpeng Zhao, Jiazhu Jiang, Mingfeng Yang, Mingming Sun, Long Yang, Qiang Zhang","doi":"10.3389/fmicb.2024.1457624","DOIUrl":"10.3389/fmicb.2024.1457624","url":null,"abstract":"<p><p>Plant growth, crop yield, and pest and disease control are enhanced by PGPR (Plant growth promoting rhizobacteria), which are beneficial microorganisms found in a close symbiosis with plant roots. Phytohormones are secreted, nutrient uptake is improved, and soil properties along with the microbiological environment are regulated by these microorganisms, making them a significant focus in agricultural research. In this study, the efficient PGPR strain T1 was isolated and screened from tobacco inter-root soil, and identified and confirmed by ITS sequencing technology. Tobacco growth indicators and soil property changes were observed and recorded through potting experiments. The activities of key enzymes (e.g., sucrase, catalase, urease) in soil were further determined. High-throughput sequencing technology was utilized to sequence the soil microbial community, and combined with macro-genomics analysis, the effects of T1 strain on soil microbial diversity and metabolic pathways were explored. Following the application of T1, significant improvements were observed in the height, leaf length, and width of tobacco plants. Furthermore, the physical and chemical properties of the soil were notably enhanced, including a 26.26% increase in phosphorus availability. Additionally, the activities of key soil enzymes such as sucrase, catalase, and urease were significantly increased, indicating improved soil health and fertility. Comprehensive joint microbiomics and macrogenomics analyses revealed a substantial rise in the populations of beneficial soil microorganisms and an enhancement in metabolic pathways, including amino acid metabolism, synthesis, and production of secondary metabolites. These increase in beneficial microorganisms and the enhancement of their metabolic functions are crucial for plant growth and soil fertility. This study provides valuable references for the development of innovative microbial fertilizers and offers programs for the sustainable development of modern agriculture.</p>","PeriodicalId":12466,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11449712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142380481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}