Archives of Microbiology最新文献

{"title":"An improved DNA extraction method in okra for rapid PCR detection of Okra enation leaf curl virus from diverse Indian regions","authors":"Ankit Kumar,&nbsp;Jyoti Singh,&nbsp;Deepak Panwar,&nbsp;Anupma Singh,&nbsp;Ravi Singh Thapa,&nbsp;Rakesh Kumar,&nbsp;Dharmendra Pratap","doi":"10.1007/s00203-024-04176-0","DOIUrl":"10.1007/s00203-024-04176-0","url":null,"abstract":"<div><p>The extraction of DNA from okra (<i>Abelmoschus esculentus</i>) is challenging due to its high mucilage and polysaccharide content, which can hinder both the yield and quality of DNA. In this study, an improved DNA isolation method is described incorporating a key modification being the use of solution I (1 M NaCl and 2% Sarcosyl) as a pre-treatment before applying the CTAB buffer, resulting in high-purity genomic DNA in just 1 h and 45 min., making it suitable for handling large sample sizes due to its rapid processing capabilities. This enhanced DNA extraction method was crucial for the accurate and rapid molecular detection of <i>Okra enation leaf curl virus </i>(OELCuV), a monopartite begomovirus that has spread across various regions of India. Transmitted by the whitefly (<i>Bemisia tabaci</i>), OELCuV causes leaf curling, enations, and stunted growth in okra, leading to significant yield losses. The surveys conducted during the 2020–21 and 2021–22 sowing seasons revealed disease incidence ranging from 14.03 to 67.57%. The extracted DNA via the improved DNA extraction method enhanced the speed of PCR based molecular identification of OELCuV, using virus-specific coat protein primers. The amplified CP genes were cloned and sequenced to study the CP gene based diversity among OELCuV isolates from different states of India. The CP gene nucleotide identity among the studied OELCuV isolates ranged from 95.57 to 99.27%, while comparison with previously reported Indian OELCuV CP sequences, the nucleotide identity ranged from 89.35 to 98.83%. The successful application of this optimized DNA extraction method sped up the detection process but also holds promise for broader use in the molecular study of okra and other mucilaginous crops, particularly in the rapid and reliable identification of begomoviruses. The optimized DNA extraction method significantly accelerated the detection of OELCuV, demonstrating its efficiency and reliability. This method shows strong potential for broader applications in the molecular study of okra and other mucilaginous crops, making it a valuable tool for future research and disease management.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A step-by-step procedure for analysing the 16S rRNA-based microbiome diversity using QIIME 2 and comprehensive PICRUSt2 illustration for functional prediction","authors":"Ankita Srivastava,&nbsp;Yusuf Akhter,&nbsp;Digvijay Verma","doi":"10.1007/s00203-024-04177-z","DOIUrl":"10.1007/s00203-024-04177-z","url":null,"abstract":"<div><p>Short-read sequencing technology has emerged as a preferred tool to analyse the bacterial composition of a niche by targeting hypervariable regions of the 16S rRNA gene. It targets the short hypervariable regions of the 16S rRNA gene and uncovers the taxonomic profile and their associated pathways. QIIME 2 is preferred and ready-to-use pipelines that perform stepwise analysis of massive short reads of 16S rRNA genes. This wrapper comprises several tools that include quality checking, denoising, taxonomic classification, alignment, and diversity analysis. However, it demands huge bioinformatic analysis practices which are quite challenging to many microbiologists working in the field of traditional microbiology. This paper, therefore, aims to make microbiologists familiar with the steps of computational analysis for processing 16S rRNA-based sequences. Here, we are presenting stepwise processing of NGS sequences using the QIIME 2 platform along with their analyses, which include installing QIIME 2, importing and processing data, quality checks, taxonomy assignments, and diversity analysis. Besides, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States<b> (</b>PICRUSt2) has also been illustrated to understand the correlation between metabolic and physiological footprints of the different species observed during microbiome analysis. Therefore, this paper can be used as a handy toolkit for those researchers who are less familiar with its associated bioinformatic analysis.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sublethal injury and recovery of Escherichia coli O157:H7 after dielectric barrier discharge plasma treatment","authors":"Yafei Zhai,&nbsp;Yuhao Wang,&nbsp;Bohua Wang,&nbsp;Liyuan Niu,&nbsp;Qisen Xiang,&nbsp;Yanhong Bai","doi":"10.1007/s00203-024-04193-z","DOIUrl":"10.1007/s00203-024-04193-z","url":null,"abstract":"<div><p>Dielectric barrier discharge (DBD) plasma can be used to control food spoilage and food pathogens. However, DBD plasma may induce sublethal injury in microorganisms, constituting a considerable risk to food safety. This research was designed to investigate the sublethal injury and recovery of <i>Escherichia coli</i> O157:H7 after DBD plasma treatment. The results indicated that the sublethal injury ratios of cells rose along with the augmentation of treatment time and input power of DBD plasma under mild treatment conditions, whereas injury accumulation ultimately culminated in cell death. The highest sublethal ratio of 99.3% was obtained after DBD plasma treatment at 18 W for 40 s. When solutions such as phosphate buffered saline (PBS), peptone water, glucose solution, and tryptic soy broth (TSB) were used for cell recovery, TSB was proven to be the most efficacious, facilitating the completion of recovery within 2 h. The repair ratio of injured cells increased as the recovery pH (3.0–7.0) and temperature (4–37 ºC) increased. Moreover, Mg²⁺ and Zn²⁺ were demonstrated to be necessary for the recovery process, while Ca²⁺ presented a weak effect. Understanding the sublethal injury of bacteria resulting from DBD plasma treatment and their repair conditions can provide useful insight into avoiding the occurrence of sublethal injury as well as inhibiting the occurrence of recovery during food processing and storage.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142613893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring secretory signal sequences useful in excreting recombinant proteins in Beauveria bassiana as biocontrol fungus","authors":"Kang Wei,&nbsp;Jin-Li Ding,&nbsp;Hang-Rong Xu,&nbsp;Ming-Guang Feng,&nbsp;Sheng-Hua Ying","doi":"10.1007/s00203-024-04190-2","DOIUrl":"10.1007/s00203-024-04190-2","url":null,"abstract":"<div><p>Entomopathogenic fungi excrete a group of proteins to assimilate nutrients and defeat the host immune defense. Functional secretory signal sequences are needed for efficient secretion of the virulence-related proteins in recombinant strain. In this study, secretome analysis was used to explore the secreted proteins of <i>Beauveria bassiana</i>. Enrichment analysis indicated that <i>B. bassiana</i> secretome was mainly associated with metabolism of glucoside, polysaccharide, extracellular ester compound, and so on. In addition, proteins associated with biogenesis of cellular components were also enriched, including those involved in biogenesis of cell wall and vacuole. Then, four secretory signal sequences were functionally verified with green fluorescent protein as reporter. Finally, a signal sequence was used to excrete three insect venom protein serpins in <i>B. bassiana</i>, in which over-expression of serpin 8 gene resulted in a significant increase in fungal virulence. This study highlights that functional secretory signal sequences are potential molecular elements useful in excretion of virulence-related proteins in insect pathogenic fungi.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteome modulation triggers potent antiviral response in Japanese Encephalitis Virus infected human macrophages","authors":"Manas Ranjan Praharaj,&nbsp;Harshavardhan Budamgunta,&nbsp;Tejaswi Ambati,&nbsp;Raja Ishaq Nabi Khan,&nbsp;Bappaditya Dey,&nbsp;Ravi Kumar Gandham,&nbsp;G. Taru Sharma,&nbsp;Subeer S. Majumdar","doi":"10.1007/s00203-024-04167-1","DOIUrl":"10.1007/s00203-024-04167-1","url":null,"abstract":"<div><p>Japanese encephalitis virus (JEV) is a mosquito-borne neurotropic virus that claims thousands of children’s lives globally every year, causing neuropsychiatric sequelae. While neuronal cell pathogenesis is a terminal consequence of JEV infection, the virus hijacks macrophages during initial replication and propagation, making macrophages critical cells of host immune defense that dictate the outcomes of infection. Though a plethora of studies have been reported using various neuronal and immune cells, a global response of human macrophages to JEV infection is yet to be explored. In this study, we assessed the kinetics of global proteome dysregulation employing an in vitro JEV infection model using human monocyte-derived macrophages (THP-1). A comparative assessment of the proteome of the infected THP-1 cells revealed differential regulation of 428 proteins at 24 h post-infection (hpi), which was later increased to 443 by 48 h post-infection. Global gene ontology analysis of the differentially expressed proteins highlighted several critical pathways related to immune and metabolic processes that are known to play either proviral or antiviral effects during infection. Notably, several antiviral proteins, including STAT2, OAS1, MX1, MX2, RIG-I, ISG15, and ISG20, were significantly upregulated at both time points post-infection. In contrast, a considerable downregulation of BCL-2, an anti-apoptotic protein at 48hpi indicates the activation of cell death pathways. Further, gene set enrichment analysis identified the type I interferon signaling pathway as one of the top upregulated pathways following JEV infection in human macrophages. Altogether, this study demonstrates human macrophage responses to JEV infection at the proteome level for the first time, highlighting several critical and novel antiviral proteins and pathways that not only advance our understanding of anti-JEV immunity but also aid in developing strategies to control this acute global public health menace.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142596067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteria carrying mobile colistin resistance genes and their control measures, an updated review","authors":"Qi Zhang","doi":"10.1007/s00203-024-04188-w","DOIUrl":"10.1007/s00203-024-04188-w","url":null,"abstract":"<div><p>The plasmid encoded mobile colistin resistance (MCRs) enzyme poses a significant challenge to the clinical efficacy of colistin, which is frequently employed as a last resort antibiotic for treating infections caused by multidrug resistant bacteria. This transferase catalyzes the addition of positively charged phosphoethanolamine to lipid A of the outer membrane of gram-negative bacteria, thereby facilitating the acquired colistin resistance. This review aims to summarize and critically discuss recent advancements in the distribution and pathogenesis of <i>mcr</i>-positive bacteria, as well as the various control measures available for treating these infections. In addition, the ecology of <i>mcr</i> genes, colistin-resistance mechanism, co-existence with other antibiotic resistant genes, and their impact on clinical treatment are also analyzed to address the colistin resistance crisis. These insights provide a comprehensive perspective on MCRs and serve as a valuable reference for future therapeutic approaches to effectively combat <i>mcr</i>-positive bacterial infections.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142595952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Different transcriptomic and metabolomic analysis of Saccharomyces cerevisiae BY4742 and CEN.PK2-1C strains","authors":"Meihong Zhang,&nbsp;Shujuan Zhao","doi":"10.1007/s00203-024-04178-y","DOIUrl":"10.1007/s00203-024-04178-y","url":null,"abstract":"<div><p>To establish efficient yeast cell factories, it is necessary to understand the transcriptional and metabolic changes among different yeasts. <i>Saccharomyces cerevisiae</i> BY4742 and CEN.PK2-1C strains are originated from different yeast strains and are commonly used as model organisms and chassis cells in molecular biology study and synthetic biology-based natural production. Metabolomic analysis showed that the BY4742 strain produced higher levels of phenylalanine, tyrosine than CEN.PK2-1C, while CEN.PK2-1C produced high levels of indoleacetaldehyde, indolepyruvate. Transcriptomic analysis showed that the two strains showed large differences in the glycolysis pathway and pyruvate metabolism pathway. CEN.PK2-1C had greater glycolysis flux than BY4742, whereas BY4742 has greater flux in the pathway of pyruvate metabolism to produce fumarate. These findings provide a basis knowledge of the metabolomic and transcriptomic differences between BY4742 and CEN.PK2-1C strains, and also provide preliminary information for strain selection for molecular biology study and synthetic biology-based natural product production.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142595290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polysaccharides of natural products alleviate antibiotic-associated diarrhea by regulating gut microbiota: a review","authors":"Yong Lai,&nbsp;Xin Lan,&nbsp;Yahui Qin,&nbsp;Yuankui Wei,&nbsp;Xi Li,&nbsp;Jianan Feng,&nbsp;Junping Jiang","doi":"10.1007/s00203-024-04184-0","DOIUrl":"10.1007/s00203-024-04184-0","url":null,"abstract":"<div><p>Antibiotic-associated diarrhea (AAD) is diarrhea caused by disturbances in intestinal microbiota and metabolism following inappropriate use of antibiotics. With the over-reliance on antibiotics, the incidence of AAD is increasing worldwide. Recently, the role of probiotics and prebiotic preparations in the prevention and treatment of AAD has received increasing attention. Various prebiotics can not only reduce the incidence of AAD, but also effectively shorten the course of the disease and alleviate the symptoms. Notably, many polysaccharides derived from plants and fungi are a class of biologically active and rich prebiotics with great potential to alleviate AAD. Therefore, this review aims to summarize the latest research on natural product polysaccharides to alleviate antibiotic-associated diarrhea by modulating the gut microbiota. It provides a theoretical basis for exploring the mechanism of natural product modulation of gut microbiota to alleviate AAD, and provides a reference for further development of active prebiotics.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142595291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring biodegradable alternatives: microorganism-mediated plastic degradation and environmental policies for sustainable plastic management","authors":"Rita de Cássia Garcia Simão,&nbsp;Paula Maria Carneiro Rocha,&nbsp;Júlia Thays Kava Martins,&nbsp;Maurício Turkiewicz,&nbsp;Jacqueline Plewka,&nbsp;José Luis da-Conceição Silva,&nbsp;Alexandre Maller,&nbsp;Marina Kimiko Kadowaki,&nbsp;Álvaro Pereira Sampaio Costa-Júnior","doi":"10.1007/s00203-024-04170-6","DOIUrl":"10.1007/s00203-024-04170-6","url":null,"abstract":"<div><p>Plastics offer versatility, durability and low production costs, but they also pose environmental and health risks due to improper disposal, accumulation in water bodies, low recycling rates and temporal action that causes physicochemical changes in plastics and the release of toxic products to animal health and nature. Some microorganisms may play crucial roles in improving plastic waste management in the future. <i>Cunningamella echinulata</i> has been identified as a promising candidate that remains viable for long periods and produces a cutinase that is capable of degrading plastic. Other recent approaches involving the use of microorganisms are discussed in this review. However, there does not seem to be a single science that is efficient or most appropriate for solving the problem of plastic pollution on the planet at present. Regulations, especially the implementation of different laws that address the entire plastic cycle in different countries, such as Brazil, the USA, China and the European Union, play important roles in the management of this waste and can contribute to reducing this problem. In the context of the transversality of the information compiled here, the current limitations are discussed, and an effective plan is proposed to reduce plastic pollution. Although it is challenging, it involves implementing legislation, promoting sustainable alternatives, improving collection and recycling systems, encouraging reuse, supporting research and technological innovation, promoting corporate responsibility, collaborating globally, raising public awareness, optimizing waste management and, above all, continuously monitoring the progress of actions based on measurable metrics.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142579394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into molecular mechanisms of phytochemicals in quorum sensing modulation for bacterial biofilm control","authors":"Anh Ngoc Xuan Nguyen,&nbsp;Krit Thirapanmethee,&nbsp;Teerawit Audshasai,&nbsp;Piyatip Khuntayaporn,&nbsp;Mullika Traidej Chomnawang","doi":"10.1007/s00203-024-04171-5","DOIUrl":"10.1007/s00203-024-04171-5","url":null,"abstract":"<div><p>Biofilm formation is a common mechanism by which bacteria undergo phenotypic changes to adapt to environmental stressors. The formation of biofilms has a detrimental impact in clinical settings by contributing to chronic infections and promoting antibiotic resistance. Delving into the molecular mechanisms, the quorum sensing (QS) system involves the release of chemical signals for bacterial cell-to-cell communication, which activates and regulates the expression of various genes and virulence factors, including those related to biofilm formation. Accordingly, the QS system becomes a potential target for combating biofilm-associated concerns. Natural products derived from plants have a long history of treating infectious diseases in humans due to their antimicrobial properties, making them valuable resources for screening anti-biofilm agents. This review aims to discover the mechanisms by which phytochemical agents inhibit QS, potentially offering promising new therapies for treating biofilm-associated infections. By targeting the QS system, these phytochemical agents can prevent bacterial aggregation and biofilm formation while also diminishing other bacterial virulence factors. Additionally, it is important to focus on the advancement of techniques and experiments to investigate their molecular mechanisms. A thorough understanding of these mechanisms may encourage further studies to evaluate the safety and efficacy of phytochemical agents used alone or in combination with other strategies.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"206 12","pages":""},"PeriodicalIF":2.3,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581565","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}