Research in microbiology最新文献_第5页

Characterisation of a new virulent phage isolated from Hainan Island with potential against multidrug-resistant Pseudomonas aeruginosa infections 从海南岛分离出的一种新型毒性噬菌体的特征，该噬菌体具有抗耐多药型铜绿假单胞菌感染的潜力。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2025-01-01 DOI: 10.1016/j.resmic.2024.104250

Anyang Li , Chen Chen , Yanmei Li , Yanshuang Wang , Xuemiao Li , Qiao Zhu , Yue Zhang , Shen Tian , Qianfeng Xia

Multidrug-resistant (MDR) Pseudomonas aeruginosa is a serious life-threatening pathogen. The rise in P. aeruginosa resistance rates has renewed interest in phages as an alternative therapeutic approach for treating bacterial infections. In this study, we investigated the characteristics of the first Pseudomonas phage, vB_PaP_HN01, isolated from Hainan, the only tropical island in China. The lytic rate of this phage against P. aeruginosa reached 64.3 % (27/42). Under the optimal multiplicity of infection (MOI) of 0.1, more than 90 % of phage particles absorb onto the host cell within 10 min, with an eclipse period of around 15 min, and a high titer phage production (10¹¹ PFU/ml) within 90 min was demonstrated. vB_PaP_HN01 maintains a robust titer after 1 h exposure to pH values and temperatures (up to 50 °C). Genome annotation revealed that vB_PaP_HN01 did not contain drug-resistance or lysogeny-associated genes. It can effectively inhibit the formation of biofilms of MDR P. aeruginosa and eliminated aggressive biofilms (removal rate about 70 %). In the in vivo infection models, it was demonstrated that the survival rate and lifespan of Galleria mellonella larvae were increased alongside the injection of vB_PaP_HN01. These data revealed the potential of vB_PaP_HN01 against P. aeruginosa in clinic.

耐多药（MDR）铜绿假单胞菌是一种严重威胁生命的病原体。铜绿假单胞菌耐药率的上升再次激发了人们对噬菌体作为治疗细菌感染的替代疗法的兴趣。在这项研究中，我们研究了从中国唯一的热带岛屿海南分离出来的第一个假单胞菌噬菌体 vB_PaP_HN01 的特性。该噬菌体对铜绿假单胞菌的致死率达到 64.3%（27/42）。在最佳感染倍数（MOI）为 0.1 的情况下，超过 90% 的噬菌体颗粒在 10 分钟内吸收到宿主细胞上，食期约为 15 分钟，并在 90 分钟内产生高滴度噬菌体（1011 PFU/ml）。vB_PaP_HN01 在 pH 值（3-11）和温度（高达 50°C）下暴露 1 小时后仍能保持稳定的滴度。基因组注释显示，vB_PaP_HN01 不含抗药性基因或溶菌相关基因。它能有效抑制 MDR 铜绿假单胞菌生物膜的形成，并消除侵袭性生物膜（去除率约为 70%）。在体内感染模型中，结果表明在注射 vB_PaP_HN01 的同时，铜绿微囊藻幼虫的存活率和寿命也得到了提高。这些数据揭示了 vB_PaP_HN01 在临床上抗击铜绿假单胞菌的潜力。

{"title":"Characterisation of a new virulent phage isolated from Hainan Island with potential against multidrug-resistant Pseudomonas aeruginosa infections","authors":"Anyang Li , Chen Chen , Yanmei Li , Yanshuang Wang , Xuemiao Li , Qiao Zhu , Yue Zhang , Shen Tian , Qianfeng Xia","doi":"10.1016/j.resmic.2024.104250","DOIUrl":"10.1016/j.resmic.2024.104250","url":null,"abstract":"<div><div>Multidrug-resistant (MDR) <em>Pseudomonas aeruginosa</em> is a serious life-threatening pathogen. The rise in <em>P. aeruginosa</em> resistance rates has renewed interest in phages as an alternative therapeutic approach for treating bacterial infections. In this study, we investigated the characteristics of the first <em>Pseudomonas</em> phage, vB_PaP_HN01, isolated from Hainan, the only tropical island in China. The lytic rate of this phage against <em>P. aeruginosa</em> reached 64.3 % (27/42). Under the optimal multiplicity of infection (MOI) of 0.1, more than 90 % of phage particles absorb onto the host cell within 10 min, with an eclipse period of around 15 min, and a high titer phage production (10<sup>11</sup> PFU/ml) within 90 min was demonstrated. vB_PaP_HN01 maintains a robust titer after 1 h exposure to pH values and temperatures (up to 50 °C). Genome annotation revealed that vB_PaP_HN01 did not contain drug-resistance or lysogeny-associated genes. It can effectively inhibit the formation of biofilms of MDR <em>P. aeruginosa</em> and eliminated aggressive biofilms (removal rate about 70 %). In the in vivo infection models, it was demonstrated that the survival rate and lifespan of <em>Galleria mellonella</em> larvae were increased alongside the injection of vB_PaP_HN01. These data revealed the potential of vB_PaP_HN01 against <em>P. aeruginosa</em> in clinic.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"176 1","pages":"Article 104250"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142547123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Targeting MurG enzyme in Klebsiella pneumoniae: An in silico approach to novel antimicrobial discovery 以肺炎克雷伯氏菌中的 MurG 酶为靶标：新型抗菌药发现的硅学方法。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2025-01-01 DOI: 10.1016/j.resmic.2024.104257

Pragati Mahur, Amit Kumar Singh, Jayaraman Muthukumaran, Monika Jain

Antibiotic resistance poses a global crisis fuelled by widespread antibiotic use, particularly against Gram-negative bacteria like Klebsiella pneumoniae, a leading cause of hospital-acquired infections with high mortality rates. Urgent identification of effective drug targets is imperative, with a focus on metabolic pathways to inhibit bacterial growth. Targeting the crucial metabolic pathways of K. pneumoniae would be a more efficient way to prevent its growth and the diseases that it causes. The present study focused on inhibiting the UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (MurG) enzyme, which is a key enzyme in peptidoglycan biosynthesis pathway. A high throughput virtual screening was used to find possible lead molecules from Enamine -High-Throughput Screening Center library. The resulting high binding affinity ligands were further assessed for their drug-likeness and other pharmacokinetic properties. Based on these analyses, the three ligands Z95813755_1, Z324718246_1 and Z324718246_2 were selected for further molecular dynamic simulation studies. The molecular dynamic simulation results and MM/PBSA analysis predicted that both Z95813755_1 and Z324718246_2, molecules show higher binding affinity towards MurG. For the first time we are reporting potential candidate inhibitors against MurG from K. pneumoniae, providing new insights in management of multi drug resistant K. pneumoniae infections.

抗生素的广泛使用引发了抗生素耐药性这一全球性危机，尤其是针对肺炎克雷伯氏菌等革兰氏阴性菌的耐药性，肺炎克雷伯氏菌是医院感染的主要病因，死亡率很高。当务之急是确定有效的药物靶点，重点是抑制细菌生长的代谢途径。针对肺炎克雷伯菌的关键代谢途径将是防止其生长和引发疾病的更有效方法。本研究的重点是抑制 UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (MurG) 酶，它是肽聚糖生物合成途径中的一个关键酶。研究人员利用高通量虚拟筛选技术，从 Enamine 高通量筛选中心库中寻找可能的先导分子。对筛选出的高结合亲和力配体进一步评估了其药物相似性和其他药代动力学特性。在这些分析的基础上，选择了 Z95813755_1、Z324718246_1 和 Z324718246_2 这三种配体进行进一步的分子动力学模拟研究。分子动力学模拟结果和 MM/PBSA 分析表明，Z95813755_1 和 Z324718246_2 分子对 MurG 有更高的结合亲和力。我们首次报告了针对肺炎克雷伯菌 MurG 的潜在候选抑制剂，为治疗多重耐药肺炎克雷伯菌感染提供了新的思路。

{"title":"Targeting MurG enzyme in Klebsiella pneumoniae: An in silico approach to novel antimicrobial discovery","authors":"Pragati Mahur, Amit Kumar Singh, Jayaraman Muthukumaran, Monika Jain","doi":"10.1016/j.resmic.2024.104257","DOIUrl":"10.1016/j.resmic.2024.104257","url":null,"abstract":"<div><div>Antibiotic resistance poses a global crisis fuelled by widespread antibiotic use, particularly against Gram-negative bacteria like <em>Klebsiella pneumoniae</em>, a leading cause of hospital-acquired infections with high mortality rates. Urgent identification of effective drug targets is imperative, with a focus on metabolic pathways to inhibit bacterial growth. Targeting the crucial metabolic pathways of <em>K. pneumoniae</em> would be a more efficient way to prevent its growth and the diseases that it causes. The present study focused on inhibiting the UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol <em>N</em>-acetylglucosamine transferase (MurG) enzyme, which is a key enzyme in peptidoglycan biosynthesis pathway. A high throughput virtual screening was used to find possible lead molecules from Enamine -High-Throughput Screening Center library. The resulting high binding affinity ligands were further assessed for their drug-likeness and other pharmacokinetic properties. Based on these analyses, the three ligands Z95813755_1, Z324718246_1 and Z324718246_2 were selected for further molecular dynamic simulation studies. The molecular dynamic simulation results and MM/PBSA analysis predicted that both Z95813755_1 and Z324718246_2, molecules show higher binding affinity towards MurG. For the first time we are reporting potential candidate inhibitors against MurG from <em>K. pneumoniae</em>, providing new insights in management of multi drug resistant <em>K. pneumoniae</em> infections.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"176 1","pages":"Article 104257"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142626734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Characterization of tailocins of Pragia fontium 24613 and the tailocin loci within the family Budviciaceae Pragia fontium 24613 的尾丝素特征及芽苣苔科（Budviciaceae）内的尾丝素基因座。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2025-01-01 DOI: 10.1016/j.resmic.2024.104261

Kateřina Snopková , Eva Chaloupková , Matěj Hrala , David Šmajs

Tailocins are nano-scale phage tail-like protein complexes that can mediate antagonistic interactions between closely related bacterial species. While the capacity to produce R-type tailocin was found widely across Gammaproteobacteria, the production of F-type tailocins seems comparatively rare. In this study, we examined the freshwater isolate, Pragia fontium 24613, which can produce both R- and F-type tailocins. We investigated their inhibition spectrum, focusing on clinically relevant enterobacteria, and identified the associated tailocin gene cluster. Transmission electron microscopy confirmed that inactivation of the tape measure protein within the tailocin cluster disrupted R-tailocin production. Comparative analysis of Budviciaceae gene clusters showed high conservation of R-type tailocin genes, whereas F-type tailocin genes were found in only a few species, with little conservation. Our findings indicate a high prevalence of bacteriocin production among underexplored Enterobacteriales species. Detected tailocins showed potential as antimicrobials targeting clinically significant pathogens.

尾蛋白是纳米级的噬菌体尾部蛋白复合物，可介导密切相关的细菌物种之间的拮抗相互作用。虽然 R 型尾蛋白的产生能力广泛存在于伽马蛋白杆菌中，但 F 型尾蛋白的产生似乎相对罕见。在本研究中，我们研究了淡水分离物 Pragia fontium 24613，它既能产生 R 型尾丝菌素，也能产生 F 型尾丝菌素。我们研究了它们对临床相关肠杆菌的抑制谱，并确定了相关的尾丝菌素基因簇。透射电子显微镜证实，尾球菌素基因簇中的胶带测量蛋白失活会破坏 R 型尾球菌素的产生。对芽胞杆菌科基因簇的比较分析表明，R型尾丝菌素基因的保存率很高，而F型尾丝菌素基因仅在少数物种中发现，保存率很低。我们的研究结果表明，在未被充分开发的肠杆菌属菌株中，细菌素的产生率很高。检测到的尾丝菌素具有作为针对临床上重要病原体的抗菌素的潜力。

{"title":"Characterization of tailocins of Pragia fontium 24613 and the tailocin loci within the family Budviciaceae","authors":"Kateřina Snopková , Eva Chaloupková , Matěj Hrala , David Šmajs","doi":"10.1016/j.resmic.2024.104261","DOIUrl":"10.1016/j.resmic.2024.104261","url":null,"abstract":"<div><div>Tailocins are nano-scale phage tail-like protein complexes that can mediate antagonistic interactions between closely related bacterial species. While the capacity to produce R-type tailocin was found widely across Gammaproteobacteria, the production of F-type tailocins seems comparatively rare. In this study, we examined the freshwater isolate, <em>Pragia fontium</em> 24613, which can produce both R- and F-type tailocins. We investigated their inhibition spectrum, focusing on clinically relevant enterobacteria, and identified the associated tailocin gene cluster. Transmission electron microscopy confirmed that inactivation of the tape measure protein within the tailocin cluster disrupted R-tailocin production. Comparative analysis of <em>Budviciaceae</em> gene clusters showed high conservation of R-type tailocin genes, whereas F-type tailocin genes were found in only a few species, with little conservation. Our findings indicate a high prevalence of bacteriocin production among underexplored Enterobacteriales species. Detected tailocins showed potential as antimicrobials targeting clinically significant pathogens.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"176 1","pages":"Article 104261"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The roots of the Institut Pasteur's “Grand Cours” 巴斯德研究所“大课程”的根源。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2025-01-01 DOI: 10.1016/j.resmic.2024.104259

Antoine Dampierre , Sandra Legout , Emmanuel Drouin

The article presents an analysis of the history of the microbiology course delivered during the inaugural operational year of the Institut Pasteur in Paris. The year 1889 is examined through the lens of three hitherto unknown volumes that bring together the microbiology lectures delivered at the end of the 19th century.

The course was entirely independent from the teaching provided by the universities or faculties of medicine and rapidly gained international recognition. Indeed, the course provided the students with the theoretical knowledge of Pasteurian theories regarding the completely new discipline of microbiology and the specific techniques used to cultivate, conserve, and observe microbes. The steady increase in the number of lectures between 1889 and 1914 reflects the expansion of microbiological knowledge during this period. The contributions of researchers such as Émile Roux (1853–1933), Élie Metchnikoff (1845–1916), and Amédée Borrel (1867–1936) illuminated the collaboration and the growing diversification of expertise at the heart of the Institut Pasteur (IP).

Furthermore, this study highlights the international influence of the course, as evidenced by the participation of foreign students. It examines the history of the course as a powerful tool for disseminating knowledge of new microbiological techniques and the results of research carried out in Pasteur's laboratories. It also examines how the course served as a political instrument, asserting the authority of the Institut Pasteur in the field of microbiology in France and extending its influence worldwide.

文章介绍了微生物学课程的历史分析期间交付的巴斯德研究所在巴黎的首次操作年。1889年是通过三本迄今未知的书的镜头来检查的，这些书汇集了19世纪末发表的微生物学讲座。该课程完全独立于大学或医学院提供的教学，并迅速获得国际认可。事实上，这门课程为学生提供了关于巴氏理论的理论知识，这是一门全新的微生物学学科，以及用于培养、保存和观察微生物的具体技术。1889年至1914年间讲座数量的稳步增长反映了这一时期微生物知识的扩展。研究人员如Émile Roux (1853-1933)， Élie Metchnikoff（1845-1916）和amsamdsamade Borrel（1867-1936）的贡献阐明了巴斯德研究所（IP）核心的合作和日益多样化的专业知识。此外，本研究突出了该课程的国际影响力，这可以从外国学生的参与中得到证明。它考察了这门课程的历史，作为传播新微生物技术知识和巴斯德实验室研究成果的有力工具。它还考察了该课程如何作为一种政治工具，在法国微生物学领域维护巴斯德研究所的权威，并扩大其在世界范围内的影响力。

{"title":"The roots of the Institut Pasteur's “Grand Cours”","authors":"Antoine Dampierre , Sandra Legout , Emmanuel Drouin","doi":"10.1016/j.resmic.2024.104259","DOIUrl":"10.1016/j.resmic.2024.104259","url":null,"abstract":"<div><div>The article presents an analysis of the history of the microbiology course delivered during the inaugural operational year of the Institut Pasteur in Paris. The year 1889 is examined through the lens of three hitherto unknown volumes that bring together the microbiology lectures delivered at the end of the 19th century.</div><div>The course was entirely independent from the teaching provided by the universities or faculties of medicine and rapidly gained international recognition. Indeed, the course provided the students with the theoretical knowledge of Pasteurian theories regarding the completely new discipline of microbiology and the specific techniques used to cultivate, conserve, and observe microbes. The steady increase in the number of lectures between 1889 and 1914 reflects the expansion of microbiological knowledge during this period. The contributions of researchers such as Émile Roux (1853–1933), Élie Metchnikoff (1845–1916), and Amédée Borrel (1867–1936) illuminated the collaboration and the growing diversification of expertise at the heart of the Institut Pasteur (IP).</div><div>Furthermore, this study highlights the international influence of the course, as evidenced by the participation of foreign students. It examines the history of the course as a powerful tool for disseminating knowledge of new microbiological techniques and the results of research carried out in Pasteur's laboratories. It also examines how the course served as a political instrument, asserting the authority of the Institut Pasteur in the field of microbiology in France and extending its influence worldwide.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"176 1","pages":"Article 104259"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Both GacS-regulated lipopeptides and the type three secretion system contribute to Pseudomonas cichorii induced necrosis in lettuce and chicory GacS调控的脂肽和三型分泌系统都有助于cichorii假单胞菌诱导莴苣和菊苣坏死。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2025-01-01 DOI: 10.1016/j.resmic.2024.104249

Chien-Jui Huang , Ellen Pauwelyn , Marc Ongena , Peter Bleyaert , Monica Höfte

Pseudomonas cichorii SF1-54, the causal agent of lettuce midrib rot disease, produces lipopeptides cichofactins and cichopeptins which are important virulence factors. The GacS/GacA two-component system is well known to regulate production of lipopeptides in pseudomonads. Additionally, the functions of the type three secretion system (T3SS) in P. cichorii-plant interactions are not clarified. In this study, we investigated the role of the GacS-regulated lipopeptides and the T3SS in pathogenicity of P. cichorii SF1-54 on two host plants, chicory and lettuce, by constructing mutants in hrpL, which encodes the key sigma factor to control T3SS expression, and gacS. Compared with the wildtype, the hrpL mutant produced lipopeptides at a similar level but the gacS mutant was strongly impaired in lipopeptide production. The mutant deficient in hrpL did not significantly differ from the wildtype in virulence on chicory and lettuce. The gacS mutant exhibited significantly less symptoms on both host plants compared to the wildtype and the hrpL mutant. Intriguingly, the gacS hrpL-double mutant no longer produced lipopeptides, lost virulence and showed impaired colonization on chicory, but was still weakly virulent on lettuce. Thus, contribution of both the GacS-regulated lipopeptides and T3SS to virulence of P. cichorii SF1-54 is host plant dependent.

莴苣中肋腐烂病的病原菌 Pseudomonas cichorii SF1-54 能产生脂肽 cichofactins 和 cichopeptins，它们是重要的毒力因子。众所周知，GacS/GacA 双组分系统可以调节假单胞菌脂肽的产生。此外，三型分泌系统（T3SS）在 P. cichorii- 植物相互作用中的功能尚未明确。在本研究中，我们通过构建编码控制 T3SS 表达的关键 sigma 因子 hrpL 和 gacS 的突变体，研究了 GacS 调控的脂肽和 T3SS 在 P. cichorii SF1-54 对菊苣和莴苣两种寄主植物的致病性中的作用。与野生型相比，hrpL 突变体产生脂肽的水平相似，但 gacS 突变体产生脂肽的能力严重受损。缺乏 hrpL 的突变体对菊苣和莴苣的毒力与野生型没有显著差异。与野生型和 hrpL 突变体相比，gacS 突变体在两种寄主植物上表现出的症状明显较少。耐人寻味的是，gacS hrpL 双突变体不再产生脂肽，失去了毒力，在菊苣上的定殖能力受损，但在莴苣上仍有弱毒力。因此，GacS 调控的脂肽和 T3SS 对 P. cichorii SF1-54 的毒力都有依赖性。

{"title":"Both GacS-regulated lipopeptides and the type three secretion system contribute to Pseudomonas cichorii induced necrosis in lettuce and chicory","authors":"Chien-Jui Huang , Ellen Pauwelyn , Marc Ongena , Peter Bleyaert , Monica Höfte","doi":"10.1016/j.resmic.2024.104249","DOIUrl":"10.1016/j.resmic.2024.104249","url":null,"abstract":"<div><div><em>Pseudomonas cichorii</em> SF1-54, the causal agent of lettuce midrib rot disease, produces lipopeptides cichofactins and cichopeptins which are important virulence factors. The GacS/GacA two-component system is well known to regulate production of lipopeptides in pseudomonads. Additionally, the functions of the type three secretion system (T3SS) in <em>P. cichorii</em>-plant interactions are not clarified. In this study, we investigated the role of the GacS-regulated lipopeptides and the T3SS in pathogenicity of <em>P. cichorii</em> SF1-54 on two host plants, chicory and lettuce, by constructing mutants in <em>hrpL</em>, which encodes the key sigma factor to control T3SS expression, and <em>gacS</em>. Compared with the wildtype, the <em>hrpL</em> mutant produced lipopeptides at a similar level but the <em>gacS</em> mutant was strongly impaired in lipopeptide production. The mutant deficient in <em>hrpL</em> did not significantly differ from the wildtype in virulence on chicory and lettuce. The <em>gacS</em> mutant exhibited significantly less symptoms on both host plants compared to the wildtype and the <em>hrpL</em> mutant. Intriguingly, the <em>gacS hrpL</em>-double mutant no longer produced lipopeptides, lost virulence and showed impaired colonization on chicory, but was still weakly virulent on lettuce. Thus, contribution of both the GacS-regulated lipopeptides and T3SS to virulence of <em>P. cichorii</em> SF1-54 is host plant dependent.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"176 1","pages":"Article 104249"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metabolic complexities and heterogeneity in quorum sensing signaling molecules in bacteria isolated from black band disease in a Caribbean coral 从加勒比珊瑚黑带病中分离出的细菌的代谢复杂性和法定量感应信号分子的异质性。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2025-01-01 DOI: 10.1016/j.resmic.2024.104248

Laura Ripe-Jaime , Erika Díaz , Ángel G. Franco , Catherine Keim , Daniela Burgos , Valeria Pizarro , Luis F. Cadavid , Anny Cárdenas , Catalina Arévalo-Ferro

Coral diseases contribute to the worldwide loss of coral reefs, with the Black Band Disease (BBD) being a prominent example. BBD is an infectious condition with lesions with a pigmented mat composed of cyanobacteria, sulphate-reducing, sulphide-oxidizing, and heterotrophic bacteria. We compared the heterotrophic bacterial communities of healthy and BBD-affected colonies of the Caribbean coral Orbicella faveolata using culture-dependent and -independent techniques. Twenty and 23 bacterial isolates were identified from healthy and diseased tissues, respectively, which differed in their capacities to metabolize carbohydrates and citrate, either anaerobically or aerobically. They also differed in their quorum-sensing (QS) activity, as QS signaling molecules were found exclusively, and QS-inhibition was found primarily, in isolates from diseased tissues. Screening of bacterial diversity by 16SrDNA metabarcoding showed that members of the bacterial genera Muricauda and Maritimimonas were dominant in healthy tissues whereas members of the cyanobacterial genus Roseofilum were dominant in diseased tissues. These results suggest that bacterial dysbiosis can be linked with altered bacterial communication, likely leading to diachrony and imbalance that may participate in the progression of BBD. Investigating physiological traits and QS-based communication offers insights into the onset and progression of coral infections, paving the way for novel strategies to mitigate their impact.

珊瑚疾病是造成全球珊瑚礁消失的原因之一，黑带病（BBD）就是一个突出的例子。黑带病是一种由蓝藻、硫酸盐还原菌、硫氧化菌和异养菌组成的色素垫层病变的传染性疾病。我们使用独立和非独立培养技术，比较了加勒比海珊瑚 Orbicella faveolata 健康珊瑚群和受 BBD 影响珊瑚群的异养细菌群落。分别从健康组织和患病组织中鉴定出了 20 和 23 个细菌分离物，它们在厌氧或需氧条件下代谢碳水化合物和柠檬酸盐的能力各不相同。它们在法定人数感应（QS）活性方面也存在差异，因为在病变组织的分离物中只发现了 QS 信号分子，而在病变组织的分离物中主要发现了 QS 抑制因子。通过 16SrDNA 代谢编码筛选细菌多样性的结果表明，健康组织中主要是 Muricauda 和 Maritimimonas 细菌属的成员，而病变组织中主要是 Roseofilum 蓝藻属的成员。这些结果表明，细菌失调与细菌交流的改变有关，很可能导致异步和失衡，从而参与 BBD 的发展。通过研究生理特征和基于 QS 的交流，可以深入了解珊瑚感染的发生和发展过程，为制定减轻其影响的新策略铺平道路。

{"title":"Metabolic complexities and heterogeneity in quorum sensing signaling molecules in bacteria isolated from black band disease in a Caribbean coral","authors":"Laura Ripe-Jaime , Erika Díaz , Ángel G. Franco , Catherine Keim , Daniela Burgos , Valeria Pizarro , Luis F. Cadavid , Anny Cárdenas , Catalina Arévalo-Ferro","doi":"10.1016/j.resmic.2024.104248","DOIUrl":"10.1016/j.resmic.2024.104248","url":null,"abstract":"<div><div>Coral diseases contribute to the worldwide loss of coral reefs, with the Black Band Disease (BBD) being a prominent example. BBD is an infectious condition with lesions with a pigmented mat composed of cyanobacteria, sulphate-reducing, sulphide-oxidizing, and heterotrophic bacteria. We compared the heterotrophic bacterial communities of healthy and BBD-affected colonies of the Caribbean coral <em>Orbicella faveolat</em><em>a</em> using culture-dependent and -independent techniques. Twenty and 23 bacterial isolates were identified from healthy and diseased tissues, respectively, which differed in their capacities to metabolize carbohydrates and citrate, either anaerobically or aerobically. They also differed in their quorum-sensing (QS) activity, as QS signaling molecules were found exclusively, and QS-inhibition was found primarily, in isolates from diseased tissues. Screening of bacterial diversity by 16SrDNA metabarcoding showed that members of the bacterial genera <em>Muricauda</em> and <em>Maritimimonas</em> were dominant in healthy tissues whereas members of the cyanobacterial genus <em>Roseofilum</em> were dominant in diseased tissues. These results suggest that bacterial dysbiosis can be linked with altered bacterial communication, likely leading to diachrony and imbalance that may participate in the progression of BBD. Investigating physiological traits and QS-based communication offers insights into the onset and progression of coral infections, paving the way for novel strategies to mitigate their impact.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"176 1","pages":"Article 104248"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142506871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Influence of 5′-UTR nucleotide composition on translation efficiency in Escherichia coli 5'-UTR 核苷酸组成对大肠杆菌翻译效率的影响

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2025-01-01 DOI: 10.1016/j.resmic.2024.104260

Jinjin Li , Jiaojiao Li , Peixian Li , Jie Zhang , Qian Liu , Hao Qi

Translation initiation for 5′-UTR contributes primarily to the efficient protein expression in Escherichia coli. Many studies have focused on constructing random 5′-UTR libraries to investigate the impact of mRNA features on protein translation efficiency. However, the study on the effect of the absence of specific types of nucleotides in the entire 5′-UTR region on translation efficiency has not yet been reported. Here, we constructed four reporter plasmid libraries encoding the sfGFP fluorescent protein, each preceded by 5′-UTRs that lack one specific nucleotide (25B, 25D, 25H, 25V). Each library was transformed into E. coli cells, and the fluorescence distribution among the different libraries was analyzed by flow cytometer. Additionally, we quantified the activity of 256 unique 5′-UTR sequences and analyzed the impact of the corresponding mRNA sequence features on translation efficiency. We found that the 25D library, which lacks the C nucleotide, exhibited the highest overall translation efficiency compared to the other three libraries. Moreover, the minimum free energy and 16S rRNA hybridization energy of the 5′-UTR sequence could work coordinately to influence translation efficiency. The 5′-UTR sequences lacking the C nucleotide also achieve efficient protein translation. These findings may provide several guiding principles for precisely tuning protein expression.

在大肠杆菌中，5'-UTR 的翻译起始是高效表达蛋白质的主要因素。许多研究都侧重于构建随机 5'-UTR 文库，以研究 mRNA 特征对蛋白质翻译效率的影响。然而，关于整个 5'-UTR 区域缺少特定类型核苷酸对翻译效率影响的研究尚未见报道。在此，我们构建了四个编码 sfGFP 荧光蛋白的报告质粒文库，每个文库前面的 5'-UTR 都缺少一个特定的核苷酸（25B、25D、25H、25V）。将每个文库转化到大肠杆菌细胞中，用流式细胞仪分析不同文库的荧光分布。此外，我们还量化了 256 个独特的 5'-UTR 序列的活性，并分析了相应的 mRNA 序列特征对翻译效率的影响。我们发现，与其他三个文库相比，缺少 C 核苷酸的 25D 文库的整体翻译效率最高。此外，5'-UTR序列的最小自由能和16S rRNA杂交能可以协同影响翻译效率。缺少 C 核苷酸的 5'-UTR 序列也能实现高效的蛋白质翻译。这些发现可能为精确调整蛋白质表达提供了一些指导原则。

{"title":"Influence of 5′-UTR nucleotide composition on translation efficiency in Escherichia coli","authors":"Jinjin Li , Jiaojiao Li , Peixian Li , Jie Zhang , Qian Liu , Hao Qi","doi":"10.1016/j.resmic.2024.104260","DOIUrl":"10.1016/j.resmic.2024.104260","url":null,"abstract":"<div><div>Translation initiation for 5′-UTR contributes primarily to the efficient protein expression in <em>Escherichia coli</em>. Many studies have focused on constructing random 5′-UTR libraries to investigate the impact of mRNA features on protein translation efficiency. However, the study on the effect of the absence of specific types of nucleotides in the entire 5′-UTR region on translation efficiency has not yet been reported. Here, we constructed four reporter plasmid libraries encoding the sfGFP fluorescent protein, each preceded by 5′-UTRs that lack one specific nucleotide (25B, 25D, 25H, 25V). Each library was transformed into <em>E. coli</em> cells, and the fluorescence distribution among the different libraries was analyzed by flow cytometer. Additionally, we quantified the activity of 256 unique 5′-UTR sequences and analyzed the impact of the corresponding mRNA sequence features on translation efficiency. We found that the 25D library, which lacks the C nucleotide, exhibited the highest overall translation efficiency compared to the other three libraries. Moreover, the minimum free energy and 16S rRNA hybridization energy of the 5′-UTR sequence could work coordinately to influence translation efficiency. The 5′-UTR sequences lacking the C nucleotide also achieve efficient protein translation. These findings may provide several guiding principles for precisely tuning protein expression.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"176 1","pages":"Article 104260"},"PeriodicalIF":2.5,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evolutionary trends indicate a coherent organization of sap operons 进化趋势表明，树液操作子的组织是一致的。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2024-11-01 DOI: 10.1016/j.resmic.2024.104228

Pratik Dasgupta, Kavya Vinil, Shankar Prasad Kanaujia

Human hosts possess a complex network of immune responses against microbial pathogens. The production of antimicrobial peptides (AMPs), which target the pathogen cell membranes and inhibit them from inhabiting the hosts, is one such mechanism. However, pathogens have evolved systems that encounter these host-produced AMPs. The Sap (sensitivity to antimicrobial peptides) transporter uptakes AMPs inside the microbial cell and proteolytically degrades them. The Sap transporters comprise five subunits encoded by genes in an operon. Despite its ubiquitous nature, its subunits are not found to be in tandem with many organisms. In this study, a total of 421 Sap transporters were analyzed for their operonic arrangement. Out of 421, a total of 352 operons were found to be in consensus arrangement, while the remaining 69 show a varying arrangement of genes. The analysis of the intergenic distance between the subunits of the sap operon suggests a signature pattern with sapAB (-4), sapBC (-14), sapCD (-1), and sapDF (-4 to 1). An evolutionary analysis of these operons favors the consensus arrangement of the Sap transporter systems, substantiating its prevalence in most of the Gram-negative pathogens. Overall, this study provides insight into bacterial evolution, favoring the maintenance of the genetic organization of essential pathogenicity factors.

人类宿主对微生物病原体具有复杂的免疫反应网络。抗菌肽（AMPs）的产生就是其中一种机制，它以病原体细胞膜为目标，抑制病原体在宿主体内栖息。然而，病原体也进化出了与宿主产生的这些抗菌肽对抗的系统。Sap（对抗菌肽的敏感性）转运体在微生物细胞内吸收 AMPs，并对其进行蛋白分解。Sap 转运体由基因编码的五个亚基组成一个操作子。尽管Sap转运体无处不在，但其亚基在许多生物体内并不串联。本研究共分析了 421 个 Sap 转运体的操作子排列。在 421 个操作子中，发现共有 352 个操作子采用了一致的排列方式，其余 69 个操作子的基因排列方式各不相同。对 sap 操作子亚基间基因距离的分析表明，sapAB（-4）、sapBC（-14）、sapCD（-1）和 sapDF（-4 到 1）是一种特征模式。对这些操作子的进化分析表明，Sap 转运体系统的一致排列方式证明了它在大多数革兰氏阴性病原体中的普遍性。总之，这项研究为细菌进化提供了深入的见解，有利于维持重要致病因子的遗传组织。

{"title":"Evolutionary trends indicate a coherent organization of sap operons","authors":"Pratik Dasgupta, Kavya Vinil, Shankar Prasad Kanaujia","doi":"10.1016/j.resmic.2024.104228","DOIUrl":"10.1016/j.resmic.2024.104228","url":null,"abstract":"<div><div><span>Human hosts possess a complex network of immune responses against microbial pathogens. The production of antimicrobial peptides (AMPs), which target the pathogen cell membranes and inhibit them from inhabiting the hosts, is one such mechanism. However, pathogens have evolved systems that encounter these host-produced AMPs. The Sap (</span><u>s</u>ensitivity to <u>a</u>ntimicrobial <u>p</u>eptides) transporter uptakes AMPs inside the microbial cell and proteolytically degrades them. The Sap transporters comprise five subunits encoded by genes in an operon. Despite its ubiquitous nature, its subunits are not found to be in tandem with many organisms. In this study, a total of 421 Sap transporters were analyzed for their operonic arrangement. Out of 421, a total of 352 operons were found to be in consensus arrangement, while the remaining 69 show a varying arrangement of genes. The analysis of the intergenic distance between the subunits of the <em>sap</em> operon suggests a signature pattern with <em>sapAB</em> (-4), <em>sapBC</em> (-14), <em>sapCD</em> (-1), and <em>sapDF</em><span> (-4 to 1). An evolutionary analysis of these operons favors the consensus arrangement of the Sap transporter systems, substantiating its prevalence in most of the Gram-negative pathogens. Overall, this study provides insight into bacterial evolution, favoring the maintenance of the genetic organization of essential pathogenicity factors.</span></div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 8","pages":"Article 104228"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Biosynthetic capabilities of Antarctic yeast Sporobolomyces roseus AL103: Temperature influence on intracellular metabolites and characterization of the exopolysaccharide 南极酵母 Sporobolomyces roseus AL103 的生物合成能力：温度对胞内代谢物的影响和外多糖的特征。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2024-11-01 DOI: 10.1016/j.resmic.2024.104247

Snezhana Rusinova-Videva , Manol Ognyanov , Kalina Alipieva , Stefka Nachkova , Dessislava Gerginova , Ani Petrova , Maria Marudova , Sofia Milenkova , Tsvetelina Paunova-Krasteva , Dragomir Mateev

The purpose of the study was to investigate the biosynthetic properties of the Antarctic yeast strain Sporobolomyces roseus AL₁₀₃ in response to temperature changes, to perform intracellular metabolic profiling, and to reveal the chemical and functional characteristics of the synthesized exopolysaccharide (EPS). The results show that the yeast strain needed a shorter time to reach a stationary phase at 22 °C contrary to that of 5 °C. An NMR analysis revealed differences in metabolic profiles of amino acids, glucose, trehalose, glycerol, uridine, etc. EPS (2.9 g/L) was characterized by high–molecular-weight with total carbohydrate, uronic acids, and protein content of 66 %, 10.5 %, and 2.5 %, respectively. Mannose (74 mol%) and galactose (19 mol%) were the major constituents. The FT-IR data suggested the presence of β-(1–4)-mannan. DSC thermogram, WVTR, mechanical properties, and moisture sorption of the EPS film showed thermal stability up to 220 °C and hydrophilic behavior. The newly obtained polymer film was studied for the first time and the data showed possibilities for its successful application as a film-forming material in the preparation of packaging materials. In conclusion, the temperature influenced the metabolic profile of the Antarctic yeast producer. The biotechnological process could be directed to obtain the target intracellular or extracellular metabolites.

本研究旨在研究南极酵母菌株 Sporobolomyces roseus AL103 对温度变化的生物合成特性，进行细胞内代谢分析，并揭示合成的外多糖（EPS）的化学和功能特性。结果表明，酵母菌株在 22 ℃ 达到静止期所需的时间比在 5 ℃ 达到静止期所需的时间短。核磁共振分析表明，氨基酸、葡萄糖、三卤糖、甘油、尿苷等代谢谱存在差异。EPS（2.9 克/升）具有高分子量的特点，总碳水化合物、尿酸和蛋白质含量分别为 66%、10.5% 和 2.5%。主要成分是甘露糖（74 摩尔%）和半乳糖（19 摩尔%）。傅立叶变换红外光谱数据表明存在β-(1-4)-甘露聚糖。EPS 薄膜的 DSC 热图、WVTR、机械性能和吸湿性能表明，其热稳定性可达 220 ℃，并具有亲水性。对新获得的聚合物薄膜进行了首次研究，研究数据表明，该薄膜可成功用作制备包装材料的成膜材料。总之，温度影响了南极酵母生产者的新陈代谢曲线。生物技术过程可以定向获得目标细胞内或细胞外代谢物。

{"title":"Biosynthetic capabilities of Antarctic yeast Sporobolomyces roseus AL103: Temperature influence on intracellular metabolites and characterization of the exopolysaccharide","authors":"Snezhana Rusinova-Videva , Manol Ognyanov , Kalina Alipieva , Stefka Nachkova , Dessislava Gerginova , Ani Petrova , Maria Marudova , Sofia Milenkova , Tsvetelina Paunova-Krasteva , Dragomir Mateev","doi":"10.1016/j.resmic.2024.104247","DOIUrl":"10.1016/j.resmic.2024.104247","url":null,"abstract":"<div><div>The purpose of the study was to investigate the biosynthetic properties of the Antarctic yeast strain <em>Sporobolomyces roseus</em> AL<sub>103</sub> in response to temperature changes, to perform intracellular metabolic profiling, and to reveal the chemical and functional characteristics of the synthesized exopolysaccharide (EPS). The results show that the yeast strain needed a shorter time to reach a stationary phase at 22 °C contrary to that of 5 °C. An NMR analysis revealed differences in metabolic profiles of amino acids, glucose, trehalose, glycerol, uridine, etc. EPS (2.9 g/L) was characterized by high–molecular-weight with total carbohydrate, uronic acids, and protein content of 66 %, 10.5 %, and 2.5 %, respectively. Mannose (74 mol%) and galactose (19 mol%) were the major constituents. The FT-IR data suggested the presence of β-(1–4)-mannan. DSC thermogram, WVTR, mechanical properties, and moisture sorption of the EPS film showed thermal stability up to 220 °C and hydrophilic behavior. The newly obtained polymer film was studied for the first time and the data showed possibilities for its successful application as a film-forming material in the preparation of packaging materials. In conclusion, the temperature influenced the metabolic profile of the Antarctic yeast producer. The biotechnological process could be directed to obtain the target intracellular or extracellular metabolites.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 8","pages":"Article 104247"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142473523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Construction of core genome multi-locus sequence typing schemes for population structure analyses of Nocardia species 构建用于诺卡氏菌种群结构分析的核心基因组多焦点序列分型方案。

IF 2.5 4区生物学 Q3 MICROBIOLOGY

Research in microbiology

Pub Date : 2024-11-01 DOI: 10.1016/j.resmic.2024.104246

Yizhak Hershko , Matan Slutzkin , Daniel Barkan , Amos Adler

Nocardia, a member of the Actinobacteria phylum, populates diverse habitats globally, with certain species being the cause of various clinical infections in humans. There is paucity of data regarding the population structure of this genus and of established genomic-based phylogenetic methods. We examined the whole genome sequences of 193 isolates spanning five major pathogenic Nocardia species sourced from public databases, encompassing diverse geographic regions. Using the chewBBACA pipeline, a species-specific core genome multilocus sequence typing (cgMLST) schema was created for N. cyriacigeorgica, N. farcinica, N. brasiliensis, N. wallacei, and N. abscessus. Additional genomic features that were examined included virulence factor (VF) profile, total length and open-reading frame count, the core genome length and core gene count, and GC content. Our findings indicated that: (i) N. brasiliensis diverges significantly from the other four species, underscoring its distinct evolutionary trajectory; (ii) the population structures of all species were polyclonal, with phylogenetic clustering occurring in the minority of isolates; (iii) clonal complexes were largely restricted to specific geographical locations, rather than demonstrating a global distribution, and (iv) initial evidence suggests no direct common-source transmission amongst the studied strains. Our study establishes a comprehensive genome-based phylogenetic methodology for population structure of Nocardia species.

诺卡氏菌（Nocardia）是放线菌门（Actinobacteria）的成员之一，在全球不同的栖息地都有分布，其中某些种类是导致人类各种临床感染的原因。有关该菌属种群结构和基于基因组的系统发育方法的数据十分匮乏。我们研究了从公共数据库中获取的 193 个分离株的全基因组序列，这些分离株横跨五个主要致病性诺卡氏菌物种，涵盖不同的地理区域。利用 chewBBACA 管道，为 N. cyriacigeorgica、N. farcinica、N. brasiliensis、N. wallacei 和 N. abscessus 创建了物种特异性核心基因组多焦点序列分型（cgMLST）模式。检查的其他基因组特征包括毒力因子（VF）特征、总长度和开放读码框数量、核心基因组长度和核心基因数量以及 GC 含量。我们的研究结果表明(i) N. brasiliensis 与其他四个物种存在显著差异，突显了其独特的进化轨迹；(ii) 所有物种的种群结构都是多克隆的，少数分离株出现了系统发育聚类；(iii) 克隆复合体主要局限于特定的地理位置，而不是全球分布；(iv) 初步证据表明，所研究的菌株之间没有直接的共源传播。我们的研究为诺卡氏菌的种群结构建立了一套全面的基于基因组的系统发育方法。

{"title":"Construction of core genome multi-locus sequence typing schemes for population structure analyses of Nocardia species","authors":"Yizhak Hershko , Matan Slutzkin , Daniel Barkan , Amos Adler","doi":"10.1016/j.resmic.2024.104246","DOIUrl":"10.1016/j.resmic.2024.104246","url":null,"abstract":"<div><div>Nocardia, a member of the Actinobacteria phylum, populates diverse habitats globally, with certain species being the cause of various clinical infections in humans. There is paucity of data regarding the population structure of this genus and of established genomic-based phylogenetic methods. We examined the whole genome sequences of 193 isolates spanning five major pathogenic <em>Nocardia</em> species sourced from public databases, encompassing diverse geographic regions. Using the chewBBACA pipeline, a species-specific core genome multilocus sequence typing (cgMLST) schema was created for <em>N. cyriacigeorgica</em>, <em>N. farcinica</em>, <em>N. brasiliensis</em>, <em>N. wallacei</em>, and <em>N. abscessus</em>. Additional genomic features that were examined included virulence factor (VF) profile, total length and open-reading frame count, the core genome length and core gene count, and GC content. Our findings indicated that: (i) <em>N. brasiliensis</em> diverges significantly from the other four species, underscoring its distinct evolutionary trajectory; (ii) the population structures of all species were polyclonal, with phylogenetic clustering occurring in the minority of isolates; (iii) clonal complexes were largely restricted to specific geographical locations, rather than demonstrating a global distribution, and (iv) initial evidence suggests no direct common-source transmission amongst the studied strains. Our study establishes a comprehensive genome-based phylogenetic methodology for population structure of <em>Nocardia</em> species.</div></div>","PeriodicalId":21098,"journal":{"name":"Research in microbiology","volume":"175 8","pages":"Article 104246"},"PeriodicalIF":2.5,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406741","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0