Pub Date : 2024-05-23DOI: 10.3389/fmicb.2024.1385724
Likhona Dingiswayo, O. Adelabu, Emmanuel Arko-Cobbah, Carolina Pohl, Nthabiseng Mokoena, Morne Du Plessis, Jolly Musoke
A distinct strain of Klebsiella pneumoniae (K. pneumoniae) referred to as hypervirulent (hvKp) is associated with invasive infections such as pyogenic liver abscess in young and healthy individuals. In South Africa, limited information about the prevalence and virulence of this hvKp strain is available. The aim of this study was to determine the prevalence of hvKp and virulence-associated factors in K. pneumoniae isolates from one of the largest tertiary hospitals in a South African province.A total of 74 K. pneumoniae isolates were received from Pelonomi Tertiary Hospital National Health Laboratory Service (NHLS), Bloemfontein. Virulence-associated genes (rmpA, capsule serotype K1/K2, iroB and irp2) were screened using Polymerase Chain Reaction (PCR). The iutA (aerobactin transporter) gene was used as a primary biomarker of hvKp. The extracted DNAs were sequenced using the next-generation sequencing pipeline and the curated sequences were used for phylogeny analyses using appropriate bioinformatic tools. The virulence of hvKp vs. classical Klebsiella pneumoniae (cKp) was investigated using the Caenorhabditis elegans nematode model.Nine (12.2%) isolates were identified as hvKp. Moreover, hvKp was significantly (p < 0.05) more virulent in vivo in Caenorhabditis elegans relative to cKp. The virulence-associated genes [rmpA, iroB, hypermucoviscous phenotype (hmv) phenotype and capsule K1/K2] were significantly (p < 0.05) associated with hvKp. A homology search of the curated sequences revealed a high percentage of identity between 99.8 and 100% with other homologous iutA gene sequences of other hvKp in the GenBank.Findings from this study confirm the presence of hvKp in a large tertiary hospital in central South Africa. However, the low prevalence and mild to moderate clinical presentation of infected patients suggest a marginal threat to public health. Further studies in different settings are required to establish the true potential impact of hvKp in developing countries.
{"title":"Hypervirulent Klebsiella pneumoniae in a South African tertiary hospital—Clinical profile, genetic determinants, and virulence in Caenorhabditis elegans","authors":"Likhona Dingiswayo, O. Adelabu, Emmanuel Arko-Cobbah, Carolina Pohl, Nthabiseng Mokoena, Morne Du Plessis, Jolly Musoke","doi":"10.3389/fmicb.2024.1385724","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1385724","url":null,"abstract":"A distinct strain of Klebsiella pneumoniae (K. pneumoniae) referred to as hypervirulent (hvKp) is associated with invasive infections such as pyogenic liver abscess in young and healthy individuals. In South Africa, limited information about the prevalence and virulence of this hvKp strain is available. The aim of this study was to determine the prevalence of hvKp and virulence-associated factors in K. pneumoniae isolates from one of the largest tertiary hospitals in a South African province.A total of 74 K. pneumoniae isolates were received from Pelonomi Tertiary Hospital National Health Laboratory Service (NHLS), Bloemfontein. Virulence-associated genes (rmpA, capsule serotype K1/K2, iroB and irp2) were screened using Polymerase Chain Reaction (PCR). The iutA (aerobactin transporter) gene was used as a primary biomarker of hvKp. The extracted DNAs were sequenced using the next-generation sequencing pipeline and the curated sequences were used for phylogeny analyses using appropriate bioinformatic tools. The virulence of hvKp vs. classical Klebsiella pneumoniae (cKp) was investigated using the Caenorhabditis elegans nematode model.Nine (12.2%) isolates were identified as hvKp. Moreover, hvKp was significantly (p < 0.05) more virulent in vivo in Caenorhabditis elegans relative to cKp. The virulence-associated genes [rmpA, iroB, hypermucoviscous phenotype (hmv) phenotype and capsule K1/K2] were significantly (p < 0.05) associated with hvKp. A homology search of the curated sequences revealed a high percentage of identity between 99.8 and 100% with other homologous iutA gene sequences of other hvKp in the GenBank.Findings from this study confirm the presence of hvKp in a large tertiary hospital in central South Africa. However, the low prevalence and mild to moderate clinical presentation of infected patients suggest a marginal threat to public health. Further studies in different settings are required to establish the true potential impact of hvKp in developing countries.","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141106789","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 : 2024-05-23DOI: 10.3389/fmicb.2024.1409677
Jichun Jia, Linjie Nan, Zehao Song, Xu Chen, Jinsheng Xia, Lihong Cheng, Baojun Zhang, Fan Mu
Mycoviruses have been found in various fungal species across different taxonomic groups, while no viruses have been reported yet in the fungus Exserohilum rostratum. In this study, a novel orfanplasmovirus, namely Exserohilum rostratum orfanplasmovirus 1 (ErOrfV1), was identified in the Exserohilum rostratum strain JZ1 from maize leaf. The complete genome of ErOrfV1 consists of two positive single-stranded RNA segments, encoding an RNA-dependent RNA polymerase and a hypothetical protein with unknown function, respectively. Phylogenetic analysis revealed that ErOrfV1 clusters with other orfanplasmoviruses, forming a distinct phyletic clade. A new family, Orfanplasmoviridae, is proposed to encompass this newly discovered ErOrfV1 and its associated orfanplasmoviruses. ErOrfV1 exhibits effective vertical transmission through conidia, as evidenced by its 100% presence in over 200 single conidium isolates. Moreover, it can be horizontally transmitted to Exserohilum turcicum. Additionally, the infection of ErOrfV1 is cryptic in E. turcicum because there were no significant differences in mycelial growth rate and colony morphology between ErOrfV1-infected and ErOrfV1-free strains. This study represents the inaugural report of a mycovirus in E. rostratum, as well as the first documentation of the biological and transmission characteristics of orfanplasmovirus. These discoveries significantly contribute to our understanding of orfanplasmovirus.
{"title":"Cross-species transmission of a novel bisegmented orfanplasmovirus in the phytopathogenic fungus Exserohilum rostratum","authors":"Jichun Jia, Linjie Nan, Zehao Song, Xu Chen, Jinsheng Xia, Lihong Cheng, Baojun Zhang, Fan Mu","doi":"10.3389/fmicb.2024.1409677","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1409677","url":null,"abstract":"Mycoviruses have been found in various fungal species across different taxonomic groups, while no viruses have been reported yet in the fungus Exserohilum rostratum. In this study, a novel orfanplasmovirus, namely Exserohilum rostratum orfanplasmovirus 1 (ErOrfV1), was identified in the Exserohilum rostratum strain JZ1 from maize leaf. The complete genome of ErOrfV1 consists of two positive single-stranded RNA segments, encoding an RNA-dependent RNA polymerase and a hypothetical protein with unknown function, respectively. Phylogenetic analysis revealed that ErOrfV1 clusters with other orfanplasmoviruses, forming a distinct phyletic clade. A new family, Orfanplasmoviridae, is proposed to encompass this newly discovered ErOrfV1 and its associated orfanplasmoviruses. ErOrfV1 exhibits effective vertical transmission through conidia, as evidenced by its 100% presence in over 200 single conidium isolates. Moreover, it can be horizontally transmitted to Exserohilum turcicum. Additionally, the infection of ErOrfV1 is cryptic in E. turcicum because there were no significant differences in mycelial growth rate and colony morphology between ErOrfV1-infected and ErOrfV1-free strains. This study represents the inaugural report of a mycovirus in E. rostratum, as well as the first documentation of the biological and transmission characteristics of orfanplasmovirus. These discoveries significantly contribute to our understanding of orfanplasmovirus.","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141104024","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 : 2024-05-23DOI: 10.3389/fmicb.2024.1373077
Meina Yang, Hongxia Deng, Siyu Zhou, Danhua Lu, Xiaoyang Shen, Lu Huang, Yan Chen, Liangzhi Xu
Folliculogenesis and oligo/anovulation are common pathophysiological characteristics in polycystic ovary syndrome (PCOS) patients, and it is also accompanied by gut microbiota dysbiosis. It is known that physical activity has beneficial effects on improving metabolism and promoting ovulation and menstrual cycle disorder in PCOS patients, and it can also modulate the gastrointestinal microbiota in human beings. However, the mechanism remains vague. Irisin, a novel myokine, plays a positive role in the mediating effects of physical activity.Mice were randomly divided into the control group, PCOS group and PCOS+irisin group. PCOS model was induced by dehydroepiandrosterone (DHEA) and high-fat diet (HFD). The PCOS+irisin group was given irisin 400μg/kg intraperitoneal injection every other day for 21 days. The serum sex hormones were measured by radioimmunoassay. Hematoxylin and Eosin (H&E) Staining and immunohistochemistry (IHC) were conducted on ovarian tissue. The feces microbiota and metabolomic characteristics were collected by 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC–MS).In this study, we demonstrated that irisin supplementation alleviated reproductive endocrine disorders of PCOS mice, including estrous cycle disturbance, ovarian polycystic degeneration, and hyperandrogenemia. Irisin also improved the PCOS follicles dysplasia and ovulation disorders, while it had no significant effect on the quality of oocytes. Moreover, irisin could mitigate the decreased bacteria of Odoribacter and the increased bacteria of Eisenbergiella and Dubosiella in PCOS mice model. Moreover, irisin could alleviate the increased fecal metabolites: Methallenestril and PS (22:5(4Z,7Z,10Z,13Z,16Z)/ LTE4).These results suggest that irisin may alleviate the status of PCOS mice model by modulating androgen-induced gut microbiota dysbiosis and fecal metabolites. Hence, our study provided evidence that irisin may be considered as a promising strategy for the treatment of PCOS.
{"title":"Irisin alleviated the reproductive endocrinal disorders of PCOS mice accompanied by changes in gut microbiota and metabolomic characteristics","authors":"Meina Yang, Hongxia Deng, Siyu Zhou, Danhua Lu, Xiaoyang Shen, Lu Huang, Yan Chen, Liangzhi Xu","doi":"10.3389/fmicb.2024.1373077","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1373077","url":null,"abstract":"Folliculogenesis and oligo/anovulation are common pathophysiological characteristics in polycystic ovary syndrome (PCOS) patients, and it is also accompanied by gut microbiota dysbiosis. It is known that physical activity has beneficial effects on improving metabolism and promoting ovulation and menstrual cycle disorder in PCOS patients, and it can also modulate the gastrointestinal microbiota in human beings. However, the mechanism remains vague. Irisin, a novel myokine, plays a positive role in the mediating effects of physical activity.Mice were randomly divided into the control group, PCOS group and PCOS+irisin group. PCOS model was induced by dehydroepiandrosterone (DHEA) and high-fat diet (HFD). The PCOS+irisin group was given irisin 400μg/kg intraperitoneal injection every other day for 21 days. The serum sex hormones were measured by radioimmunoassay. Hematoxylin and Eosin (H&E) Staining and immunohistochemistry (IHC) were conducted on ovarian tissue. The feces microbiota and metabolomic characteristics were collected by 16S rRNA gene sequencing and liquid chromatography-mass spectrometry (LC–MS).In this study, we demonstrated that irisin supplementation alleviated reproductive endocrine disorders of PCOS mice, including estrous cycle disturbance, ovarian polycystic degeneration, and hyperandrogenemia. Irisin also improved the PCOS follicles dysplasia and ovulation disorders, while it had no significant effect on the quality of oocytes. Moreover, irisin could mitigate the decreased bacteria of Odoribacter and the increased bacteria of Eisenbergiella and Dubosiella in PCOS mice model. Moreover, irisin could alleviate the increased fecal metabolites: Methallenestril and PS (22:5(4Z,7Z,10Z,13Z,16Z)/ LTE4).These results suggest that irisin may alleviate the status of PCOS mice model by modulating androgen-induced gut microbiota dysbiosis and fecal metabolites. Hence, our study provided evidence that irisin may be considered as a promising strategy for the treatment of PCOS.","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141103791","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 : 2024-05-23DOI: 10.3389/fmicb.2024.1398527
Shiqin Tang, Yanyan Xu, Xiaojing Li
Candida albicans (C. albicans), an opportunistic pathogen, is implicated in the carcinogenesis of various cancers, thereby significantly impacting human health. This study conducts an in-depth analysis of the prevailing research dynamics concerning the relationship between C. albicans and cancer over the past decade, offering a comprehensive overview of the knowledge structure and emerging focal points in this field through bibliometric scrutiny.A methodical quantitative and visual scrutiny of pertinent literature from the Web of Science Core Collection (WoSCC) spanning the previous decade was carried out employing VOS Viewer and CiteSpace software.From January 1, 2014, to January 1, 2024, a comprehensive corpus of 1,259 articles was delineated. Prominent research institutions included the Egyptian Knowledge Bank, Cairo University, and King Saud University. The top three prolific countries were the United States, China, and India. Among the authors, Mohamed, Gehad G., Mahmoud, Walaa H., and Netea, Mihai G., emerged as the most prolific, with Pfaller, Ma being distinguished as the most frequently cited author. The journal Molecules published the highest number of articles, while PLoS One had the highest citation count. Nature had the highest impact factor. The research focal points in this field encompassed the interactions between C. albicans and cancer, the correlation with oral cancer, the underlying mechanisms of C. albicans carcinogenic potential, as well as antifungal and anticancer therapies.This investigation constitutes a pioneering bibliometric analysis elucidating the trends and advancements in research regarding the correlation between C. albicans and cancer. Said analyses uncover the prevailing research focal points and trends, offering insightful guidance for subsequent inquiry in this domain.https://www.webofscience.com/wos/woscc/summary/df33afba-f843-41e8-b932-cb3678eb8243-e92e7316/relevance/1
白念珠菌（C. albicans）是一种机会性病原体，与多种癌症的致癌过程有关，从而对人类健康产生重大影响。本研究深入分析了近十年来有关白念珠菌与癌症关系的研究动态，通过文献计量学的仔细研究，全面概述了该领域的知识结构和新出现的焦点问题。该研究采用 VOS Viewer 和 CiteSpace 软件，对过去十年间科学网核心文献集（WoSCC）中的相关文献进行了定量和可视化审查。主要研究机构包括埃及知识银行、开罗大学和沙特国王大学。文章最多的前三个国家分别是美国、中国和印度。在作者中，Mohamed, Gehad G.、Mahmoud, Walaa H.和Netea, Mihai G.是最多产的作者，而Pfaller, Ma则是被引用次数最多的作者。分子》杂志发表的文章数量最多，而《PLoS One》的引用次数最多。自然》的影响因子最高。该领域的研究重点包括白僵菌与癌症之间的相互作用、与口腔癌的相关性、白僵菌致癌潜能的潜在机制以及抗真菌和抗癌疗法。上述分析揭示了当前的研究重点和趋势，为这一领域的后续研究提供了深刻的指导。https://www.webofscience.com/wos/woscc/summary/df33afba-f843-41e8-b932-cb3678eb8243-e92e7316/relevance/1
{"title":"Worldwide trend in research on Candida albicans and cancer correlations: a comprehensive bibliometric analysis","authors":"Shiqin Tang, Yanyan Xu, Xiaojing Li","doi":"10.3389/fmicb.2024.1398527","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1398527","url":null,"abstract":"Candida albicans (C. albicans), an opportunistic pathogen, is implicated in the carcinogenesis of various cancers, thereby significantly impacting human health. This study conducts an in-depth analysis of the prevailing research dynamics concerning the relationship between C. albicans and cancer over the past decade, offering a comprehensive overview of the knowledge structure and emerging focal points in this field through bibliometric scrutiny.A methodical quantitative and visual scrutiny of pertinent literature from the Web of Science Core Collection (WoSCC) spanning the previous decade was carried out employing VOS Viewer and CiteSpace software.From January 1, 2014, to January 1, 2024, a comprehensive corpus of 1,259 articles was delineated. Prominent research institutions included the Egyptian Knowledge Bank, Cairo University, and King Saud University. The top three prolific countries were the United States, China, and India. Among the authors, Mohamed, Gehad G., Mahmoud, Walaa H., and Netea, Mihai G., emerged as the most prolific, with Pfaller, Ma being distinguished as the most frequently cited author. The journal Molecules published the highest number of articles, while PLoS One had the highest citation count. Nature had the highest impact factor. The research focal points in this field encompassed the interactions between C. albicans and cancer, the correlation with oral cancer, the underlying mechanisms of C. albicans carcinogenic potential, as well as antifungal and anticancer therapies.This investigation constitutes a pioneering bibliometric analysis elucidating the trends and advancements in research regarding the correlation between C. albicans and cancer. Said analyses uncover the prevailing research focal points and trends, offering insightful guidance for subsequent inquiry in this domain.https://www.webofscience.com/wos/woscc/summary/df33afba-f843-41e8-b932-cb3678eb8243-e92e7316/relevance/1","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141106045","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}
Soil salinization poses a significant environmental challenge affecting plant growth and agricultural sustainability. This study explores the potential of salt-tolerant endophytes to mitigate the adverse effects of soil salinization, emphasizing their impact on the development and resistance of Arachis hypogaea L. (peanuts).The diversity of culturable plant endophytic bacteria associated with Miscanthus lutarioriparius was investigated. The study focused on the effects of Bacillus tequilensis, Staphylococcus epidermidis, and Bacillus siamensis on the development and germination of A. hypogaea seeds in pots subjected to high NaCl concentrations (200 mM L−1).Under elevated NaCl concentrations, the inoculation of endophytes significantly (p < 0.05) enhanced seedling germination and increased the activities of enzymes such as Superoxide dismutase, catalase, and polyphenol oxidase, while reducing malondialdehyde and peroxidase levels. Additionally, endophyte inoculation resulted in increased root surface area, plant height, biomass contents, and leaf surface area of peanuts under NaCl stress. Transcriptome data revealed an augmented defense and resistance response induced by the applied endophyte (B. tequilensis, S. epidermidis, and B. siamensis) strain, including upregulation of abiotic stress related mechanisms such as fat metabolism, hormones, and glycosyl inositol phosphorylceramide (Na+ receptor). Na+ receptor under salt stress gate Ca2+ influx channels in plants. Notably, the synthesis of secondary metabolites, especially genes related to terpene and phenylpropanoid pathways, was highly regulated.The inoculated endophytes played a possible role in enhancing salt tolerance in peanuts. Future investigations should explore protein–protein interactions between plants and endophytes to unravel the mechanisms underlying endophyte-mediated salt resistance in plants.
{"title":"Endophyte-mediated enhancement of salt resistance in Arachis hypogaea L. by regulation of osmotic stress and plant defense-related genes","authors":"Qihua Liang, Dedong Tan, Haohai Chen, Xiaoli Guo, Muhammad Afzal, Xiaolin Wang, Zhiyuan Tan, Guixiang Peng","doi":"10.3389/fmicb.2024.1383545","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1383545","url":null,"abstract":"Soil salinization poses a significant environmental challenge affecting plant growth and agricultural sustainability. This study explores the potential of salt-tolerant endophytes to mitigate the adverse effects of soil salinization, emphasizing their impact on the development and resistance of Arachis hypogaea L. (peanuts).The diversity of culturable plant endophytic bacteria associated with Miscanthus lutarioriparius was investigated. The study focused on the effects of Bacillus tequilensis, Staphylococcus epidermidis, and Bacillus siamensis on the development and germination of A. hypogaea seeds in pots subjected to high NaCl concentrations (200 mM L−1).Under elevated NaCl concentrations, the inoculation of endophytes significantly (p < 0.05) enhanced seedling germination and increased the activities of enzymes such as Superoxide dismutase, catalase, and polyphenol oxidase, while reducing malondialdehyde and peroxidase levels. Additionally, endophyte inoculation resulted in increased root surface area, plant height, biomass contents, and leaf surface area of peanuts under NaCl stress. Transcriptome data revealed an augmented defense and resistance response induced by the applied endophyte (B. tequilensis, S. epidermidis, and B. siamensis) strain, including upregulation of abiotic stress related mechanisms such as fat metabolism, hormones, and glycosyl inositol phosphorylceramide (Na+ receptor). Na+ receptor under salt stress gate Ca2+ influx channels in plants. Notably, the synthesis of secondary metabolites, especially genes related to terpene and phenylpropanoid pathways, was highly regulated.The inoculated endophytes played a possible role in enhancing salt tolerance in peanuts. Future investigations should explore protein–protein interactions between plants and endophytes to unravel the mechanisms underlying endophyte-mediated salt resistance in plants.","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141107958","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 : 2024-05-23DOI: 10.3389/fmicb.2024.1366272
Zinuo Yang, Lei Wang, Xiangrui Zhang, Bin Zeng, Zhen Zhang, Xin Liu
Numerous studies show that microbes in the human body are very closely linked to the human host and can affect the human host by modulating the efficacy and toxicity of drugs. However, discovering potential microbe-drug associations through traditional wet labs is expensive and time-consuming, hence, it is important and necessary to develop effective computational models to detect possible microbe-drug associations.In this manuscript, we proposed a new prediction model named LCASPMDA by combining the learnable graph convolutional attention network and the self-paced iterative sampling ensemble strategy to infer latent microbe-drug associations. In LCASPMDA, we first constructed a heterogeneous network based on newly downloaded known microbe-drug associations. Then, we adopted the learnable graph convolutional attention network to learn the hidden features of nodes in the heterogeneous network. After that, we utilized the self-paced iterative sampling ensemble strategy to select the most informative negative samples to train the Multi-Layer Perceptron classifier and put the newly-extracted hidden features into the trained MLP classifier to infer possible microbe-drug associations.Intensive experimental results on two different public databases including the MDAD and the aBiofilm showed that LCASPMDA could achieve better performance than state-of-the-art baseline methods in microbe-drug association prediction.
{"title":"LCASPMDA: a computational model for predicting potential microbe-drug associations based on learnable graph convolutional attention networks and self-paced iterative sampling ensemble","authors":"Zinuo Yang, Lei Wang, Xiangrui Zhang, Bin Zeng, Zhen Zhang, Xin Liu","doi":"10.3389/fmicb.2024.1366272","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1366272","url":null,"abstract":"Numerous studies show that microbes in the human body are very closely linked to the human host and can affect the human host by modulating the efficacy and toxicity of drugs. However, discovering potential microbe-drug associations through traditional wet labs is expensive and time-consuming, hence, it is important and necessary to develop effective computational models to detect possible microbe-drug associations.In this manuscript, we proposed a new prediction model named LCASPMDA by combining the learnable graph convolutional attention network and the self-paced iterative sampling ensemble strategy to infer latent microbe-drug associations. In LCASPMDA, we first constructed a heterogeneous network based on newly downloaded known microbe-drug associations. Then, we adopted the learnable graph convolutional attention network to learn the hidden features of nodes in the heterogeneous network. After that, we utilized the self-paced iterative sampling ensemble strategy to select the most informative negative samples to train the Multi-Layer Perceptron classifier and put the newly-extracted hidden features into the trained MLP classifier to infer possible microbe-drug associations.Intensive experimental results on two different public databases including the MDAD and the aBiofilm showed that LCASPMDA could achieve better performance than state-of-the-art baseline methods in microbe-drug association prediction.","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141106303","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 : 2024-05-23DOI: 10.3389/fmicb.2024.1383923
Taixiang Chen, Tian Wang, Mingxiang Du, Kamran Malik, Chunjie Li, Gensheng Bao
The Epichloë genus represents a significant group of above-ground endophytes extensively researched for their potential applications in agriculture and ecology. Additionally, Epichloë species synthesize bioactive alkaloids, which generally cause health problems in livestock and have detrimental effects on the performance of insect herbivores. Psathyrostachys lanuginosa serves as a valuable forage grass for livestock owing to its high nutritional value and resilience in adverse environmental conditions. Nevertheless, to date, no reports have documented Epichloë as endophytes of P. lanuginosa. In this study, four strains (PF5, PF9, QG2, and QG4) were isolated and identified through morphological, molecular, and phylogenetic analyses as endophytes of P. lanuginosa. Morphological analysis indicated colony characteristics and conidia features consistent with symbiotic Epichloë, with no significant differences observed in growth rates or conidia dimensions among the four strains. Phylogenetic analysis confirmed all strains as E. bromicola. Additionally, alkaloid biosynthetic genes were detected, revealing differences in the potential synthesis of peramine and indole diterpenoid alkaloids among strains from different geographic origins. However, all four E. bromicola strains exhibited similar potential for synthesizing ergot alkaloids, but not loline alkaloids. Overall, this study identified P. lanuginosa as a novel host for E. bromicola and provided insights into the alkaloid profiles of these strains, laying a solid foundation for the scientific and rational utilization of Epichloë resources.
Epichloë 属是一个重要的地面内生菌群，因其在农业和生态学方面的潜在应用而受到广泛研究。此外，Epichloë 物种还能合成生物活性生物碱，这些生物碱通常会导致牲畜的健康问题，并对昆虫食草动物的表现产生不利影响。羊角芹营养价值高，对不利环境条件的适应能力强，是牲畜的重要饲料草。然而，迄今为止，还没有任何报告记载 Epichloë 是 P. lanuginosa 的内生菌。本研究分离了四株菌株（PF5、PF9、QG2 和 QG4），并通过形态学、分子和系统发育分析确定其为 P. lanuginosa 的内生菌。形态学分析表明，菌落特征和分生孢子特征与共生的 Epichloë 相符，四种菌株的生长速度和分生孢子大小没有明显差异。系统发育分析证实所有菌株都是 E. bromicola。此外，还检测到生物碱生物合成基因，揭示了来自不同地理起源的菌株在潜在合成过胺和吲哚二萜生物碱方面的差异。然而，所有四个 E. bromicola 菌株在合成麦角生物碱方面表现出相似的潜力，但不包括啉类生物碱。总之，这项研究确定了P. lanuginosa是E. bromicola的新宿主，并深入了解了这些菌株的生物碱特征，为科学合理地利用Epichloë资源奠定了坚实的基础。
{"title":"Discovery of Epichloë as novel endophytes of Psathyrostachys lanuginosa in China and their alkaloid profiling","authors":"Taixiang Chen, Tian Wang, Mingxiang Du, Kamran Malik, Chunjie Li, Gensheng Bao","doi":"10.3389/fmicb.2024.1383923","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1383923","url":null,"abstract":"The Epichloë genus represents a significant group of above-ground endophytes extensively researched for their potential applications in agriculture and ecology. Additionally, Epichloë species synthesize bioactive alkaloids, which generally cause health problems in livestock and have detrimental effects on the performance of insect herbivores. Psathyrostachys lanuginosa serves as a valuable forage grass for livestock owing to its high nutritional value and resilience in adverse environmental conditions. Nevertheless, to date, no reports have documented Epichloë as endophytes of P. lanuginosa. In this study, four strains (PF5, PF9, QG2, and QG4) were isolated and identified through morphological, molecular, and phylogenetic analyses as endophytes of P. lanuginosa. Morphological analysis indicated colony characteristics and conidia features consistent with symbiotic Epichloë, with no significant differences observed in growth rates or conidia dimensions among the four strains. Phylogenetic analysis confirmed all strains as E. bromicola. Additionally, alkaloid biosynthetic genes were detected, revealing differences in the potential synthesis of peramine and indole diterpenoid alkaloids among strains from different geographic origins. However, all four E. bromicola strains exhibited similar potential for synthesizing ergot alkaloids, but not loline alkaloids. Overall, this study identified P. lanuginosa as a novel host for E. bromicola and provided insights into the alkaloid profiles of these strains, laying a solid foundation for the scientific and rational utilization of Epichloë resources.","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141106418","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 : 2024-05-23DOI: 10.3389/fmicb.2024.1425952
Xuanxuan Ma, Rustam Aminov, Octavio Luiz Franco, César de la Fuente-Nunez, Guangshun Wang, Jianhua Wang
{"title":"Editorial: Antimicrobial peptides and their druggability, bio-safety, stability, and resistance","authors":"Xuanxuan Ma, Rustam Aminov, Octavio Luiz Franco, César de la Fuente-Nunez, Guangshun Wang, Jianhua Wang","doi":"10.3389/fmicb.2024.1425952","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1425952","url":null,"abstract":"","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141103522","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 : 2024-05-23DOI: 10.3389/fmicb.2024.1363158
N. Safaie, M. Salehi, Mona Felegari, S. Farhadi, Samira Karimzadeh, Sadegh Asadi, Jun-Li Yang, Mohammad-Reza Naghavi
A total of 1,348 endophytic fungal strains were isolated from Ferula ovina, F. galbaniflua, and F. persica. They included Eurotiales (16 species), Pleosporales (11 species), Botryosphaeriales (1 species), Cladosporiales (2 species), Helotiales (6 species), Hypocreales (31 species), Sordariales (7 species), Glomerellales (2 species), and Polyporales (1 species). F. ovina had the richest species composition of endophytic fungi, and the endophytic fungi were most abundant in their roots compared to shoots. Chao, Margalef, Shannon, Simpson, Berger–Parker, Menhinick, and Camargo indices showed that F. ovina roots had the most endophytic fungal species. The frequency distribution of fungal species isolated from Ferula spp. fell into the log-series model, and F. ovina roots had the highest Fisher alpha. The dominance indices showed that there are no dominant species in the endophytic fungal community isolated from Ferula spp., indicating community stability. Evenness values were 0.69, 0.90, 0.94, and 0.57 for endophytic fungi isolated from F. ovina roots, F. ovina shoots, F. galbaniflua roots, and F. persica roots, respectively, indicating a species distribution that tends toward evenness. The fungal species community isolated from each of F. ovina roots, F. ovina shoots, F. galbaniflua roots, and F. persica roots was a diverse species group originating from a homogeneous habitat. Their distribution followed a log-normal distribution, suggesting that the interactions of numerous independent environmental factors multiplicatively control species abundances. Principal component analysis showed that the highest species diversity and dominance were observed in the endophytic fungal community isolated from F. ovina and F. persica roots, respectively.
{"title":"Culture-based diversity of endophytic fungi of three species of Ferula grown in Iran","authors":"N. Safaie, M. Salehi, Mona Felegari, S. Farhadi, Samira Karimzadeh, Sadegh Asadi, Jun-Li Yang, Mohammad-Reza Naghavi","doi":"10.3389/fmicb.2024.1363158","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1363158","url":null,"abstract":"A total of 1,348 endophytic fungal strains were isolated from Ferula ovina, F. galbaniflua, and F. persica. They included Eurotiales (16 species), Pleosporales (11 species), Botryosphaeriales (1 species), Cladosporiales (2 species), Helotiales (6 species), Hypocreales (31 species), Sordariales (7 species), Glomerellales (2 species), and Polyporales (1 species). F. ovina had the richest species composition of endophytic fungi, and the endophytic fungi were most abundant in their roots compared to shoots. Chao, Margalef, Shannon, Simpson, Berger–Parker, Menhinick, and Camargo indices showed that F. ovina roots had the most endophytic fungal species. The frequency distribution of fungal species isolated from Ferula spp. fell into the log-series model, and F. ovina roots had the highest Fisher alpha. The dominance indices showed that there are no dominant species in the endophytic fungal community isolated from Ferula spp., indicating community stability. Evenness values were 0.69, 0.90, 0.94, and 0.57 for endophytic fungi isolated from F. ovina roots, F. ovina shoots, F. galbaniflua roots, and F. persica roots, respectively, indicating a species distribution that tends toward evenness. The fungal species community isolated from each of F. ovina roots, F. ovina shoots, F. galbaniflua roots, and F. persica roots was a diverse species group originating from a homogeneous habitat. Their distribution followed a log-normal distribution, suggesting that the interactions of numerous independent environmental factors multiplicatively control species abundances. Principal component analysis showed that the highest species diversity and dominance were observed in the endophytic fungal community isolated from F. ovina and F. persica roots, respectively.","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141107756","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 : 2024-05-23DOI: 10.3389/fmicb.2024.1360343
Mariana Gonda, Caterina Rufo, Jose L. Gonzalez-Andujar, Silvana Vero
Aspergillus flavus (A. flavus), a frequent contaminant in silage, is a significant producer of aflatoxins, notably the potent carcinogen aflatoxin B1. This contaminant poses a potential risk during the initial aerobic phase of ensiling. The present work studied the impact of temperature on A. flavus growth and aflatoxin B1 production in laboratory-scale sorghum silos during the initial aerobic phase. Growth curves of A. flavus were generated at various temperatures and modeled with the Gompertz model. Results indicated that the optimal temperature range for the maximum growth rate in sorghum mini-silos is between 25 and 30°C. Mold biomass and aflatoxin B1 levels were quantified using qPCR and HPLC, respectively. A predictive model for aflatoxin B1 synthesis in the initial ensiling phase was established, in function of grain moisture, external temperature, and time. Within the studied range, A. flavus’s initial concentration did not significantly influence aflatoxin B1 production. According to the model maximum aflatoxin production is expected at 30% moisture and 25°C temperature, after 6 days in the aerobic phase. Aflatoxin B1 production in such conditions was corroborated experimentally. Growth curves and aflatoxin B1 production highlighted that at 48 h of incubation under optimal conditions, aflatoxin B1 concentrations in mini-silos exceeded national legislation limits, reaching values close to 100 ppb. These results underscore the risk associated with A. flavus presence in ensiling material, emphasizing the importance of controlling its development in sorghum silos.
{"title":"Mitigating aflatoxin B1 in high-moisture sorghum silage: Aspergillus flavus growth and aflatoxin B1 prediction","authors":"Mariana Gonda, Caterina Rufo, Jose L. Gonzalez-Andujar, Silvana Vero","doi":"10.3389/fmicb.2024.1360343","DOIUrl":"https://doi.org/10.3389/fmicb.2024.1360343","url":null,"abstract":"Aspergillus flavus (A. flavus), a frequent contaminant in silage, is a significant producer of aflatoxins, notably the potent carcinogen aflatoxin B1. This contaminant poses a potential risk during the initial aerobic phase of ensiling. The present work studied the impact of temperature on A. flavus growth and aflatoxin B1 production in laboratory-scale sorghum silos during the initial aerobic phase. Growth curves of A. flavus were generated at various temperatures and modeled with the Gompertz model. Results indicated that the optimal temperature range for the maximum growth rate in sorghum mini-silos is between 25 and 30°C. Mold biomass and aflatoxin B1 levels were quantified using qPCR and HPLC, respectively. A predictive model for aflatoxin B1 synthesis in the initial ensiling phase was established, in function of grain moisture, external temperature, and time. Within the studied range, A. flavus’s initial concentration did not significantly influence aflatoxin B1 production. According to the model maximum aflatoxin production is expected at 30% moisture and 25°C temperature, after 6 days in the aerobic phase. Aflatoxin B1 production in such conditions was corroborated experimentally. Growth curves and aflatoxin B1 production highlighted that at 48 h of incubation under optimal conditions, aflatoxin B1 concentrations in mini-silos exceeded national legislation limits, reaching values close to 100 ppb. These results underscore the risk associated with A. flavus presence in ensiling material, emphasizing the importance of controlling its development in sorghum silos.","PeriodicalId":509565,"journal":{"name":"Frontiers in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141105325","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}
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