Journal of microbiological methods最新文献

{"title":"Current advancements in nanoparticles for vaccines and drug delivery for the treatment of tuberculosis","authors":"Dinesh Kumar Sharma","doi":"10.1016/j.mimet.2025.107138","DOIUrl":"10.1016/j.mimet.2025.107138","url":null,"abstract":"<div><div>Since the early centuries until the present, tuberculosis has been a global illness with no cure. However, the sickness remains dormant in the afflicted individuals in certain circumstances. Due to the thick lipid mycobacterial wall and the challenging medication delivery into the bacterial cell, treatment is complex at this point. Over the past utics., there has been a growth in the function of nanomaterials in tuberculosis (TB) management, especially in the domains of early diagnosis, vaccine, and therapy. It has been demonstrated that nanomaterials are effective in quickly and accurately identifying tuberculosis germs. Additionally, novel nanocarriers have shown great promise for improved medication delivery and immunization, possibly increasing drug concentrations in target organs while lowering the frequency of treatments. Furthermore, the engineering of antigen carriers is a promising area of tuberculosis research that may lead to the successful creation of a novel class of potent TB vaccines. This article addresses tuberculosis infection diagnosis, pathophysiology, immunology, and advanced nanoparticles to deliver TB vaccines and anti-TB drugs. The challenges and prospects for the future in creating secure and functional nanoparticles for tuberculosis treatment and diagnosis for the good health and well-being of the patient are also discussed.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107138"},"PeriodicalIF":1.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143869841","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}

{"title":"Optimizing α-amylase production by an extremely halophilic archaeon Haloferax mucosum MS1.4, using response surface methodology","authors":"Kannapally Punjumpiduka Neethu ,&nbsp;Kizhakkecheruvil Sivadas Sobhana ,&nbsp;Rajendra Babu Keerthi ,&nbsp;Eldho Varghese ,&nbsp;Lakshmanan Ranjith ,&nbsp;Salma Jasmine ,&nbsp;Kunnummel Krishnan Joshi ,&nbsp;Grinson George","doi":"10.1016/j.mimet.2025.107136","DOIUrl":"10.1016/j.mimet.2025.107136","url":null,"abstract":"<div><div>This study investigated α-amylase production potential of the haloarchaeal strain <em>Haloferax mucosum</em> MS1.4 (NCBI GenBank Acc. No. OL780830), isolated from a solar saltpan located in Tamil Nadu, southern India. The enzyme was partially purified and characterized, employing SDS-PAGE analysis indicating a molecular mass of approximately 67 kDa. In order to optimize the conditions for maximizing α-amylase production, a two-step statistical approach was adopted. The initial phase involved using a Plackett-Burman Design (PBD) to determine the primary factors affecting enzyme production. PBD identified incubation time, starch concentration and NaCl concentration as the most significant variables influencing enzyme yield. These factors were further optimized using Box-Behnken Design (BBD) under Response Surface Methodology (RSM). Maximum α-amylase production of 955.97 units min⁻¹ was obtained under the optimized conditions of 1.62 % starch; 29.88 % NaCl and an incubation period of 144 h (6 days). The findings highlight the potential of <em>H. mucosum</em> MS1.4 as a promising candidate for industrial enzyme production under high-saline conditions.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107136"},"PeriodicalIF":1.7,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143878458","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}

{"title":"Exploring omics approaches in probiotics: Contemporary developments and prospective pathways","authors":"Ishita Verma,&nbsp;Bhargabi Banerjee,&nbsp;Arushi Singh,&nbsp;Priya Kannan,&nbsp;Lilly M. Saleena","doi":"10.1016/j.mimet.2025.107135","DOIUrl":"10.1016/j.mimet.2025.107135","url":null,"abstract":"<div><div>The application of omics technologies in combination with bench investigations has brought about a significant transformation in the field of probiotics, enabling a thorough investigation of the basic elements contributing to the probiotic activity. Genomics studies have decoded the complete set of genes of probiotic organisms, shedding light on beneficial traits and mechanisms of probiotic action. Transcriptomics analyses focus on gene expression patterns and investigate probiotic adaptation and functionality. Proteomic studies have revealed the intricate connections between proteins in probiotic cells and their relationship with the host environment. Metabolomic profiling has provided a comprehensive perspective on the metabolic pathways related to probiotic metabolism and the production of bioactive substances. The ongoing development of omics technology presents exciting opportunities for probiotic research, as it allows for a deeper exploration of probiotic-host interactions and the creation of advanced and tailored probiotics that offer specific health advantages. A comprehensive analysis of recent progress in genomics, transcriptomics, proteomics, and metabolomics related to probiotics is presented in this review.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107135"},"PeriodicalIF":1.7,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873865","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}

{"title":"Recovery of Clostridium from soil using Heat Shock enrichment technique and Agar Deeps","authors":"Hironobu Ootsuchi,&nbsp;Misaki Nakajima,&nbsp;Yuji Hatada","doi":"10.1016/j.mimet.2025.107133","DOIUrl":"10.1016/j.mimet.2025.107133","url":null,"abstract":"<div><div>Some members of the genus <em>Clostridium</em> can produce butanol and hydrogen from renewable substrates contributing to biofuel production. In recent years, there has been a growing social demand for its utilization to realize a sustainable society. <em>Clostridium</em> is also attracting attention in the medical field, and research is being conducted to use it as a prodrug treatment and an intestinal bacterium to reduce cancer. <em>Clostridium</em> is a very attractive research subject. However, because <em>Clostridium</em> is an obligatory anaerobe, it requires expensive equipment not used to culture aerobic bacteria, making it difficult to start research on it. In this study, we developed an inexpensive and highly selective method for isolating <em>Clostridium</em> that does not require special equipment. This method combines two methods to increase the selectivity of <em>Clostridium</em>: the heat shock enrichment method, which selects non-spore-forming bacteria, and the agar deep method, which selects anaerobic bacteria based on their oxygen requirement. Using the isolation method developed in this study, we succeeded in isolating 11 new species of <em>Clostridium</em>. In total, 17 species of 3 genera were obtained from soil samples (0.2 g each) from only eight locations. Surprisingly, this represents 7.5 % of <em>Clostridium</em> reported to date.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107133"},"PeriodicalIF":1.7,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859086","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}

{"title":"Targeting SufC ATPase in Staphylococcus aureus AR465: Insights from an in silico and molecular docking approach","authors":"Sounak Sinha ,&nbsp;Birsing Murmu ,&nbsp;Arya Ketan Roy ,&nbsp;Piyush Jagdish Balgote ,&nbsp;Jayanthi Sivaraman","doi":"10.1016/j.mimet.2025.107134","DOIUrl":"10.1016/j.mimet.2025.107134","url":null,"abstract":"<div><div><em>Staphylococcus aureus</em> AR465 (<em>S. aureus</em> AR465) is a deadly pathogen that often inherits multidrug resistance, where the antibiotics become ineffective against it. The iron‑sulfur (Fe<img>S) cluster assembly pathway has the potential to serve as a new drug target, allowing for the modification of these molecules to be susceptible to oxidative conditions. Our study focuses on the preliminary stage of the Fe<img>S pathway inhibition by inhibiting the SufC protein, unlike previous studies that targeted the final stage. SufC has an Adenosine triphosphate (ATP) binding site. The main goal of this study is to inhibit the SufBCD complex of <em>S. aureus</em> AR465 to bind with other subunits to form an Fe<img>S cluster. The Sulfur Utilization Factor (SUF) system plays a massive role in the survival of this pathogen by producing electron carrier proteins which possess Fe<img>S cofactors. The SufC protein from the SufBCD system was chosen as the main target for the potential inhibitor molecules. SufC is an ATP-binding cassette (ABC) that transfers an Fe<img>S cluster to SufA, which then transports it to an apoprotein involved in electron transport processes. In this research, several drugs were selected which can block this particular stage of the Fe<img>S cluster formation pathway. The idea was to competitively inhibit the binding of ATP with the help of inhibitors so that it cannot bind to the desired site of SufC. Eventually, the inhibitor molecule blocks the transfer of the Fe<img>S cluster to a newly synthesized apo-protein and kills the pathogen.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107134"},"PeriodicalIF":1.7,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859085","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}

{"title":"Comparison of molecular serotyping methods for Actinobacillus pleuropneumoniae and analysis of atypical serotypes detected in routine diagnostics","authors":"Henning Lindhaus ,&nbsp;Henning Bischoff ,&nbsp;Madita Harms ,&nbsp;Theresa Menke ,&nbsp;Carina Helmer ,&nbsp;Isabel Hennig-Pauka","doi":"10.1016/j.mimet.2025.107132","DOIUrl":"10.1016/j.mimet.2025.107132","url":null,"abstract":"<div><div>Clinical outbreaks due to <em>Actinobacillus pleuropneumoniae</em> (APP) and subclinical infections have high impact on swine health status worldwide although several commercial vaccines are available. Autogenous vaccination programs are implemented when APP outbreaks occur in commercially vaccinated herds. The identification and characterization of the involved APP serotypes is therefore crucial for the implementation of preventive strategies and antimicrobial usage reduction on the farm. Interpretation of serotyping results obtained by different methods might be difficult in case of mismatching results or untypable APP isolates. In this study results of two routine serotyping methods- a capsular gene based and an <em>apx</em> toxin gene PCR- were compared in 151 APP field and 19 APP reference strains. APP species was identified after bacterial culture by MALDI-TOF-MS followed by serotyping. Toxin profiles were not in accordance with the serotype defined by capsule gene PCR in 37 % of APP field strains which were grouped in those with (1) atypical capsule (<em>cps</em>) gene patterns (22 %) and those with (2) atypical <em>apxIV</em> toxin gene length (78 %). Selected atypical APP strains were further analysed by whole genome sequencing. The toxin gene-based PCR robustly identified the <em>apxI-III</em> toxin genes in all strains and revealed highly variable <em>apxIV</em> toxin gene patterns. For thirteen isolates a <em>cps</em>-gene type 6 and <em>apxIV</em> toxin gene pattern of serotype 2/8/15 could be confirmed via WGS. For three serotype 9/11 isolates the failure of the <em>cps</em> gene typing was found to be due to a deletion at the 3′ of the cpsF gene. A standardized, precise description of the <em>apx</em>-toxin gene pattern as well as the <em>cps</em>-gene-based serotype for APP strains can be recommended (e.g. APP cps type 2, <em>apx</em> gene profile <em>apxIB, apxII, apxIII</em>).</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107132"},"PeriodicalIF":1.7,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851529","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}

{"title":"Using pathology images and artificial intelligence to identify bacterial infections and their types","authors":"Xinggong Liang ,&nbsp;Gongji Wang ,&nbsp;Zhengyang Zhu ,&nbsp;Wanqing Zhang ,&nbsp;Yuqian Li ,&nbsp;Jianliang Luo ,&nbsp;Han Wang ,&nbsp;Shuo Wu ,&nbsp;Run Chen ,&nbsp;Mingyan Deng ,&nbsp;Hao Wu ,&nbsp;Chen Shen ,&nbsp;Gengwang Hu ,&nbsp;Kai Zhang ,&nbsp;Qinru Sun ,&nbsp;Zhenyuan Wang","doi":"10.1016/j.mimet.2025.107131","DOIUrl":"10.1016/j.mimet.2025.107131","url":null,"abstract":"<div><div>Bacterial infections pose a significant biosafety concern, making early and accurate diagnosis essential for effective treatment and prognosis. Traditional diagnostic methods, while reliable, are often slow and fail to meet urgent clinical demands. In contrast, emerging technologies offer greater efficiency but are often costly and inaccessible. In this study, we utilized easily accessible pathology images to diagnose bacterial infections. Our initial findings indicate that, in the absence of postmortem phenomena, microscopic examination of pathological images can confirm the presence of a bacterial infection. However, distinguishing between different types of bacterial infections remains challenging due to similarities in pathological changes. To address this limitation, we applied a computational pathology approach by integrating pathology images with artificial intelligence (AI) algorithms. Our model classified bacterial infections at both the patch-level and whole slide image (WSI)-level. The results demonstrated strong performance, with an overall AUC consistently above 0.950 across training, testing, and external validation datasets, indicating high accuracy, robustness, and generalizability. This study highlights AI's potential in identifying bacterial infection types and provides valuable technical support for clinical diagnostics, paving the way for faster and more precise infection management.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107131"},"PeriodicalIF":1.7,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143829779","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}

{"title":"Development of novel and efficient Corynebacterium glutamicum gene expression systems for industrial enzyme production","authors":"Miao Wang ,&nbsp;Xiaoxin Ren ,&nbsp;Ziqi Wu,&nbsp;Daqing Xu,&nbsp;Liqiang Wu","doi":"10.1016/j.mimet.2025.107130","DOIUrl":"10.1016/j.mimet.2025.107130","url":null,"abstract":"<div><div>An ideal microbial gene expression system for industrial enzyme production should possess a function complementary selection marker, a cost-effective inducer, and the ability for extracellular protein secretion. In this study，we employed CRISPR-Cpf1 gene editing technology to construct an engineered <em>Corynebacterium glutamicum</em> host strain, <em>C. glutamicum</em> Δ<em>alr∷araE</em> Δ<em>murI</em>, by deleting the alanine racemase-encoding gene <em>alr</em> and the glutamate racemase-encoding gene <em>murI</em>, and by integrating the <em>Bacillus subtilis</em> arabinose-related compounds permease-encoding gene <em>araE</em> into the chromosome. The two secretion-type expression vectors pAU30S (Sec-type) and pAU30T (Tat-type) that both employ <em>alr</em> as selection marker, the T7 transcription system to transcribe target genes, and the <em>B. subtilis</em> AraR-<em>OR</em>_<em>A1</em><em>/OR</em>_<em>A2</em> negative control system to control gene transcription, were constructed. The α-amylase AmyF from <em>Geobacillus stearothermophilus</em> was used as reporter protein to test the applicability of the L-arabinose-induced gene expression systems <em>C. glutamicum</em>/pAU30S and <em>C. glutamicum</em> Δ<em>alr∷araE</em> Δ<em>murI</em>/pAU30T. The results of transparent circle investigation, SDS-PAGE and amylase activity analysis demonstrated that the recombinant AmyF was efficiently expressed and completely secreted into the culture medium in its active form. The <em>C. glutamicum</em> Δ<em>alr∷araE</em> Δ<em>murI</em>/pAU30S and <em>C. glutamicum</em> Δ<em>alr∷araE</em> Δ<em>murI</em>/pAU30T systems represent highly efficient gene expression platforms suitable for the secretory production of industrial enzymes.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107130"},"PeriodicalIF":1.7,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143829711","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}

{"title":"Pancreatic stone protein levels accurately predict severity in sepsis of various causes earlier than other biomarkers","authors":"Dimitrios Kouroupis ,&nbsp;Charalampos Zarras ,&nbsp;Theocharis Koufakis ,&nbsp;Maria Terzaki ,&nbsp;Panagiotis Pateinakis ,&nbsp;Aristeidis Chalvantzis ,&nbsp;Konstantina Mpani ,&nbsp;Anthi Issa ,&nbsp;Prodromos Soukiouroglou ,&nbsp;Anastasia Sarvani ,&nbsp;Athina Pyrpasopoulou ,&nbsp;Michail Doumas ,&nbsp;Eleni Vagdatli","doi":"10.1016/j.mimet.2025.107129","DOIUrl":"10.1016/j.mimet.2025.107129","url":null,"abstract":"<div><div>The aim of this study was to compare the prognostic value of PSP in different types of sepsis, with common biomarkers. PSP levels were higher in bacteremia and Gram-negative sepsis and correlated with worse outcome (<em>p</em> = 0,006) earlier than WBC, CRP and PCT. It may aid for risk stratification in sepsis.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107129"},"PeriodicalIF":1.7,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143815539","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}

{"title":"Subtractive genomics approach: A guide to unveiling therapeutic targets across pathogens","authors":"Bhavya Mudgal ,&nbsp;Devvret Verma ,&nbsp;Divya Venogopal ,&nbsp;Suraj V. Atram ,&nbsp;Debasis Mitra ,&nbsp;Sugam Gupta","doi":"10.1016/j.mimet.2025.107127","DOIUrl":"10.1016/j.mimet.2025.107127","url":null,"abstract":"<div><div>Subtractive genomics is an adaptable bioinformatics technique that is used to identify potential therapeutic targets by differentiating essential genes in pathogens and non-pathogenic genes. Since, identification of therapeutic targets and understanding of their structure, function, and role in pathogenesis is important in development of drug design. Therefore, this review will provide a comprehensive look at the subtractive genomics technique which was applied to various pathogens, often highlighting the effectiveness of the methodology in drug target discovery and novel therapeutics development. Tools and software such as BLAST, Roary, and AutoDock Vina are widely utilized in this methodology for various aspects such as, genome comparison, essential gene identification, clustering, subcellular localization, pathway analysis, molecular docking <em>etc.</em> Diseases such as tuberculosis, botulism, staphylococcal infections, ventilator-associated pneumonia, secondary meningitis, gonorrhoea, septicaemia, <em>etc.,</em> are among the infectious diseases targeted using subtractive genomics. Comparison of basic principles, tools, and advancements use these subtractive genomics studies, will provide insight into the adaptable nature of this technique and the diversity of pathogens, which have benefited with this methodology into providing successful results. The main focus is on the genome sequencing advancements, annotation and validation through <em>in-</em>silico techniques, to find effective drug targets while, decreasing the possibility of toxicity in the host. We have also discussed the possibility of taking a multi-omics approach and incorporating AI and machine learning to expand on the current data and finding effective therapeutics for helping globally on health challenges.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"232 ","pages":"Article 107127"},"PeriodicalIF":1.7,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143815540","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}