Indian Journal of Microbiology最新文献

{"title":"Insights into Methylocucumis oryzae, a Large-sized, Phylogenetically Unique Type Ia Methanotroph with Biotechnological Potential","authors":"Monali C. Rahalkar, Jyoti A. Mohite, Kajal Pardhi, Shubha S. Manvi, Yash S. Kadam, Yukta V. Patil","doi":"10.1007/s12088-024-01347-x","DOIUrl":"https://doi.org/10.1007/s12088-024-01347-x","url":null,"abstract":"<p>The cultivation of microorganisms is important as it provides us an opportunity to explore the characteristics that can be used for a variety of applications. Methanotrophs oxidize methane and are one of the most challenging organisms to culture. In 2018, we cultured one of the largest methanotrophs within the gammaproteobacterial group (Type Ia), a novel genus and species, <i>Methylocucumis oryzae</i>, with large peculiar, elongated oval (cucumber-shaped) cells (~ 3–6 µm length × 1.5 µm breadth). We have described three strains of <i>Methylocucumis oryzae</i> (abbreviated as Mcu or <i>Mcu oryzae</i>) isolated from two flooded rice fields and recently from a stone quarry in Pune, all three locations are in Maharashtra state, Western India. Mcu is a mesophile and prefers lower temperatures for growth in the range 20–28 °C and does not grow above 37 °C. No other species of <i>Methylocucumis</i> have been reported from any other country and Mcu oryzae appears to be phylogenetically unique after 6 years of its initial report. Though the culture has certain challenges to grow on a larger scale due to its slow growth rate, it might have significant potential in methane mitigation, plant growth promotion, carotenoid production, etc. awaiting more detailed studies on this rare organism. Further optimization experiments to grow Mcu in large quantities might help us in developing environmental and biotechnological applications.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"25 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141576348","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":"Comparative Analysis of Vaginal Microbiome Associated with Oncogenic HPV Infection Among Different Ethnic Groups of Women of the Eastern Region of India","authors":"Anindita Goswami, Suvanjana Ghosh, Arghya Bandyopadhyay, Raju Gopal Saha, Prabir Sengupta, Utpal Bhuniya, Paramita Mandal","doi":"10.1007/s12088-024-01320-8","DOIUrl":"https://doi.org/10.1007/s12088-024-01320-8","url":null,"abstract":"<p>The study aimed to identify the influence of vaginal bacterial composition on HPV infection among tribal women of the eastern region of India compared to non-tribal women of the same region. For this study, 13 tribal women and 12 non-tribal women were recruited. DNA was isolated from vaginal swab samples, and subsequently, 16S rRNA gene analysis was performed. We identified two distinct clusters of samples based on taxonomic profiling and bacterial diversity. One cluster belonged to HPV negative samples and the other to HPV16/18 positive samples. The abundance of three bacterial species was significantly lower (<i>p</i> value &lt; 0.05) among oncogenic HPV positive samples (mean abundance = 4.33, 0, and 0, respectively) compared to HPV negative samples (mean abundance = 29.71, 45.73, and 19.01, respectively) irrespective of their ethnicities, such as <i>Lactobacillus amylolyticus, Bacillus coagulans, and Costridium </i>sensu stricto<i>.</i> HPV16/18 positive samples also represent the differential microbiome composition between the two ethnic groups of women. Ethnicity specific variations in human vaginal microbiome composition might be recommended for geographically tailored microbiome-based therapeutic strategies.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"71 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510982","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":"Presence and mRNA Expression of the sar Family Genes in Clinical and Non-clinical (Healthy Conjunctiva and Healthy Skin) Isolates of Staphylococcus epidermidis","authors":"Mario E. Cancino-Diaz, Fernando Gómez-Chávez, Juan C. Cancino-Diaz","doi":"10.1007/s12088-024-01339-x","DOIUrl":"https://doi.org/10.1007/s12088-024-01339-x","url":null,"abstract":"<p><i>Staphylococcus aureus</i> possesses <i>sar</i> family genes, including <i>sar</i>A, S, R, T, U, V, X, Y, Z, and <i>rot</i>, which are transcription factors involved in biofilm formation and quorum sensing. In contrast, <i>Staphylococcus epidermidis</i> has <i>sar</i>A, R, V, X, Y, Z, and <i>rot</i> genes; specifically, SarA, Z, and X are involved in biofilm formation. The expression of the <i>sar</i> family members in <i>S. epidermidis</i> isolated from clinical and non-clinical environments is unknown. This study aimed to establish if clinical and non-clinical isolates of <i>S. epidermidis</i> express the <i>sar</i> family members. We genotyped isolates from clinical ocular infections (n = 52), or non-clinical healthy conjunctiva (n = 40), and healthy skin (n = 50), using multilocus sequence typing (MLST) and the staphylococcal chromosomal cassette <i>mec</i> (SCC<i>mec</i>). We selected strains with different genotypes and representatives of each source of isolation, and the presence of the <i>sar</i> family genes was detected using PCR and RT-qPCR to determine their expression. The <i>sar</i> family genes were present in all selected strains, with no observed differences. The relative expression of the <i>sar</i> family showed that all selected strains expressed each gene weakly, with no significant differences observed between them or between different sources of isolation. In conclusion, the presence and relative expression of the <i>sar</i> family genes are very similar among strains, with no differences based on their origin of isolation and genotype.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"12 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510983","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":"Molecular Analysis of Classical Swine Fever Virus Associated Field Infections Evidence Novel CSFV Sub Genotype in Tamil Nadu, Southern India","authors":"S. Parthiban, B. Kowsalya, M. Parthiban, A. Ramesh, P. Raja, K. Gopal, S. Jaisree, R. Thangathurai, K. Senthilkumar","doi":"10.1007/s12088-024-01345-z","DOIUrl":"https://doi.org/10.1007/s12088-024-01345-z","url":null,"abstract":"<p>Classical swine fever (CSF) is an endemic and major viral infection of Indian swine husbandry, contributing to great economic losses with multiple genotypes associated with vast clinical and subclinical outcomes. Molecular detection and genotyping of CSF virus directly from field samples has great application in disease monitoring and control measures hence this study aimed to isolate and characterize CSFV genotypes circulating in southern states of India. Fifty-seven porcine post-mortem tissues (lymph nodes, spleens, livers, lungs, and kidneys) collected from pigs suspected of systemic infections and sudden death with the history of live attenuated CSF vaccination from different regions of Tamil Nadu were used in this study. An <i>NS5B</i> gene based CSFV specific RT-PCR screening confirmed CSFV positivity in 7% (4/57) of samples with a specific amplicon of 449 bp. Further molecular screening for other viral co-infections such as PCV2, PPV and PRRSV done by specific individual PCR assays to all the samples. Non-involvement of above screened three viral pathogens in all four field samples which showed positivity for CSFV confirming CSFV as primary pathogen<b>.</b> Two RT-PCR positive samples (TNI-4 and CHNL-2) selected randomly and sequenced. Aligned contig sequences of both samples were subjected to BLAST homology search and phylogentic characterization. BLAST study of TNI-4 sequence revealed 99% sequence identity with Indian CSFV sequences of genotype 1 and CHNL-2 showed 98% sequence identity with Indian CSFV sequences of genotype 2. Phylogenetic analysis of the TNI-4 and CHNL-2 sequences obtained in this study along with 38 published CSFV sequences consisting of all 5 new genotypes and 14 sub genotypes through the Maximum Likelihood tree method in MEGA 11 revealed that TNI-4 clustering together with 1.7 sub genotypes and CHNL-2 clustering together with 2.2 sub genotypes. TNI-4 and CHNL-2 partial <i>NS5B</i> gene sequences obtained in this study deposited in the GenBank database under accession numbers of MW822568 and MW822569 respectively. The study is the first to report CSF infections associated with the newer 1.7 sub genotype in Tamil Nadu, southern India. It is possible that vaccination could affect the genetic diversity of the CSFV through recombination and point mutations for immune evasion.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"61 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510959","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":"Role of Gut Microbiome in Cancer Treatment","authors":"Vijay Mishra, Yachana Mishra","doi":"10.1007/s12088-024-01340-4","DOIUrl":"https://doi.org/10.1007/s12088-024-01340-4","url":null,"abstract":"<p>The gut microbiota influences the effectiveness and side effects of cancer treatments, particularly immunotherapy and associated immune-related complications. This important involvement of the microbiome is supported by the patients receiving antibiotics responding poorly to immunotherapy. Relatively few research has examined the underlying processes, and until recently, data regarding the detection of the microbial organisms that trigger these effects were inconsistent. Since then, a deeper comprehension of the processes of action and taxonomic classification of the relevant species has been attained. It's been demonstrated that certain bacterial species can enhance the body’s reaction to immune checkpoint inhibitors through the release of distinct metabolites or products. Nonetheless, in certain patients who are not responding, Gram-negative bacteria may have a dominating suppressive impact. Patients' propensity to react to immunotherapy can be somewhat accurately predicted by machine learning techniques based on their microbiome makeup. Consequently, there has been an increase in interest in modifying the microbiome makeup to enhance patient reaction to medication. Clinical proof-of-concept studies demonstrate that dietary modifications or fecal microbiota transplantation (FMT) might be used therapeutically to increase the efficacy of immunotherapy in cancer patients. Current developments and new approaches for microbiota-based cancer treatments have been emphasized. In conclusion, preclinical research on animals and human clinical trials has made tremendous progress in our understanding of the function of the gut microbiome in health and illness. These investigations have shed light on the effects of food, FMT, probiotics, prebiotics, and microbiome-disease connections. However, there are still a lot of issues and restrictions that must be resolved before this research can be used in real-world clinical settings.</p><h3 data-test=\"abstract-sub-heading\">Graphical Abstract</h3>\u0000","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"205 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530237","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":"Synthetic p72 Peptide-Based Indirect- Enzyme-Linked Immunosorbent Assay for Diagnosis of African Swine Fever Virus Infection","authors":"Navdeep Kaur Dhiman, M. Manu, Vinay G. Joshi, Yashpal Singh Malik","doi":"10.1007/s12088-024-01334-2","DOIUrl":"https://doi.org/10.1007/s12088-024-01334-2","url":null,"abstract":"<p>In the present study, we explored the potential diagnostic application of B cell linear peptides derived from the p72 protein of African Swine Fever Virus (ASFV) using a two-step bioinformatics approach for developing an indirect enzyme-linked immunosorbent assay (ELISA) for ASF detection. Through computational analysis, eight linear B cell epitopes with significant conservation across various ASFV genotypes were identified. These peptides were chemically synthesized and evaluated for their immunoreactivity using specific rabbit hyperimmune serum against the ASFV p72 protein. The synthesized peptides displayed notable reactivity in dot-ELISA and subsequently in indirect-ELISA. Validation of the indirect ELISA was conducted using samples collected during ASFV outbreaks in the northern states of India from 2022 to 2023, and further corroborated using a commercial kit. The P1 peptide-based indirect ELISA demonstrated a sensitivity of 100% and a specificity of 86%. Additionally, peptides P3, P4, P5, P7, and P8 exhibited a specificity of 100%, while peptides P2, P3, P4, P6, and P7 displayed a sensitivity greater than 70% in the indirect ELISA. These results underscore the diagnostic potential of p72 protein-specific B cell epitopes for the detection of ASFV infection in field settings. The developed assay holds promise for ASFV infection detection, as well as for seromonitoring and serosurveillance applications.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"146 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510956","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":"Antimicrobial and Computational Studies of Newly Synthesized Benzotriazoles","authors":"Navneet Singh, Vanika Mahant, Ridhima Bhasin, Kunika Verma, Anupam Kumar, Ashish Vyas","doi":"10.1007/s12088-024-01344-0","DOIUrl":"https://doi.org/10.1007/s12088-024-01344-0","url":null,"abstract":"<p>Antimicrobial Resistance (AMR) due to non-responding viruses, fungi, bacteria and parasites leads to discovery of new antimicrobial medicines which can control the risk of disease spread, severe illness, disability and death. Heterocyclic chemistry has always been a continuous supplier of novel antimicrobial agents which are in great demand in pharma sector. Therefore, compounds such as 1-(Chloromethyl)-1H-Benzotriazole, 1; 1-((1-H-benzo[d][1,2,3]triazol-1-yl)methyl)phenyl hydrazine, 2; 1-((1-H-benzo[d][1,2,3]triazol-1-yl)methyl)hydrazine, 3; and N-(benzo[e][1,2,4]triazin-4(3-H)-ylmethylbenzenamine, 4 were designed, and synthesized through conventional and microwave-assisted methods. All of these novel benzotriazoles were explored through in-vitro antimicrobial studies and in silico studies. Antimicrobial activity was carried out against bacterial strains <i>Escherichia coli</i>, <i>Bacillus subtilis</i>, and fungal strains <i>Aspergillus niger</i> and <i>Candida albicans</i> at concentrations 5, 10 and 15 mg/ml. In silico studies was carried out with 4CAW: <i>Aspergillus fumigatus</i> N-myristoyl transferase in complex with myristoyl CoA and a pyrazole sulphonamide ligand. Our antimicrobial and molecular docking studies revealed that all of the derivatives showed promising activity, moreover molecular docking gave significant values of ligand posed energy and docking run elapsed time which further endorsed the astonishing characteristic of benzotriazole derivatives esp. N-(benzo[e]a[1,2,4] triazin-4(3-H)-ylmethylbenzenamine for biological and therapeutic leads.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"177 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510984","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 In-Silico Immunoepitope Landscape and Genetic Diversity in p72 and CD2v Proteins Across Asian African Swine Fever Virus Isolates","authors":"Kalpana Singh, Nagendra Nath Barman, Lukumoni Buragohain, Sachin Kumar, Yashpal Singh Malik","doi":"10.1007/s12088-024-01305-7","DOIUrl":"https://doi.org/10.1007/s12088-024-01305-7","url":null,"abstract":"<p>African swine fever (ASF) is a highly lethal infectious disease affecting pigs caused by the African swine fever virus (ASFV). The p72 is the major capsid protein and has strong immunogenicity. Another, outer envelope protein, CD2-like (CD2v), plays a pivotal role in viral pathogenesis. Despite the grave threat posed by ASFV, efficient vaccines and diagnostic assays remain elusive. In this study, genetic diversity of p72 and CD2v at protein and gene levels was analysed in-silico among most of the isolates of ASFV across Asia, including India, by assessing sequence similarity, phylogeny, and selection pressure. Further, in-silico prediction of immunogenic epitopes was done within stabilized (by MD-simulation) predicted structures of p72 and CD2v proteins by assessing variability in terms of Shannon entropy, relative solvent accessibility, and prediction of B and T-cell epitope peptides. The present study highlights the conservation of both p72 and CD2v proteins across prevalent ASFV isolates in Asia, including India, and suggests for their potential utility in developing diagnostic assays, as both can induce robust immunogenic responses. Consequently, these proteins emerge as promising vaccine candidates against ASFV.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"20 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141530153","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":"Nanomaterial-Based Biosensors for the Detection of COVID-19","authors":"Manju Tewari, Prerna Rana, Veena Pande","doi":"10.1007/s12088-024-01336-0","DOIUrl":"https://doi.org/10.1007/s12088-024-01336-0","url":null,"abstract":"<p>The COVID-19 outbreak began in December 2019 and has affected people worldwide. It was declared a pandemic in 2020 by the World Health Organization. Developing rapid and reliable diagnostic techniques is crucial for identifying COVID-19 early and preventing the disease from becoming severe. In addition to conventional diagnostic techniques such as RT-PCR, computed tomography, serological assays, and sequencing methods, biosensors have become widely accepted for identifying and screening COVID-19 infection with high accuracy and sensitivity. Their low cost, high sensitivity, specificity, and portability make them ideal for diagnostics. The use of nanomaterials improves the performance of biosensors by increasing their sensitivities and limiting detection by several orders of magnitude. This manuscript briefly reviews the COVID-19 outbreak and its pathogenesis. Furthermore, it comprehensively discusses the currently available biosensors for SARS-CoV-2 detection, with a special emphasis on nanomaterials-based biosensors developed to detect this emerging virus and its variants efficiently.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"96 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510963","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":"Cross-Species Insights into PR Proteins: A Comprehensive Study of Arabidopsis thaliana, Solanum lycopersicum, and Solanum tuberosum","authors":"Karun Wilson, Sathiavelu Arunachalam","doi":"10.1007/s12088-024-01343-1","DOIUrl":"https://doi.org/10.1007/s12088-024-01343-1","url":null,"abstract":"<p>This study provides a comprehensive analysis of pathogenesis-related (PR) proteins, focusing on PR1, PR5, and PR10, in three plant species: <i>Arabidopsis thaliana</i> (At), <i>Solanum lycopersicum</i> (Sl), and <i>Solanum tuberosum</i> (St). We investigated various physico-chemical properties, including protein length, molecular weight, isoelectric point (pI), hydrophobicity, and structural characteristics, such as RMSD, using state-of-the-art tools like AlphaFold and PyMOL. Our analysis found that the SlPR10-StPR10 protein pair had the highest sequence identity (80.00%), lowest RMSD value (0.307 Å), and a high number of overlapping residues (160) among all other protein pairs, indicating their remarkable similarity. Additionally, we used bioinformatics tools such as Cello, Euk-mPLoc 2.0, and Wolfpsort to predict subcellular localization, with AtPR1, AtPR5, and SlPR5 proteins predicted to be located in the extracellular space in both <i>Arabidopsis</i> and <i>S. lycopersicum</i>, while AtPR10 was predicted to be located in the cytoplasm. This comprehensive analysis, including the use of cutting-edge structural prediction and subcellular localization tools, enhances our understanding of the structural, functional, and localization aspects of PR proteins, shedding light on their roles in plant defense mechanisms across different plant species.</p>","PeriodicalId":13316,"journal":{"name":"Indian Journal of Microbiology","volume":"50 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2024-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141510957","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}