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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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Khurana H, Sharma M, Verma H, Lopes BS, Lal R, Negi RK. Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential. Genomics 2020; 112:3191-3200. [PMID: 32512145 DOI: 10.1016/j.ygeno.2020.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/17/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.
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Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
| | - Bruno Silvester Lopes
- School of Medicine, Medical Sciences and Nutrition, Medical Microbiology, 0:025 Polwarth Building, Aberdeen AB25 2ZD, UK
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India.
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
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3
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Purohit HJ. Aligning Microbial Biodiversity for Valorization of Biowastes: Conception to Perception. Indian J Microbiol 2019; 59:391-400. [PMID: 31762500 DOI: 10.1007/s12088-019-00826-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022] Open
Abstract
Generation of biowastes is increasing rapidly and its uncontrolled, slow and persistent fermentation leads to the release of Green-house gases (GHGs) into the environment. Exploration and exploitation of microbial diversity for degrading biowastes can result in producing diverse range of bioactive molecules, which can act as a source of bioenergy, biopolymers, nutraceuticals and antimicrobials. The whole process is envisaged to manage biowastes, and reduce their pollution causing capacity, and lead to a sustainable society. A strategy has been proposed for: (1) producing bioactive molecules, and (2) achieving a zero-pollution emission by recycling of the GHGs through biological routes.
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Affiliation(s)
- Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental and Engineering Research Institute (CSIR-NEERI), Nehru Marg, Nagpur, Maharashtra 440020 India
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4
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Rapid Detection Device for Salmonella typhi in Milk, Juice, Water and Calf Serum. Indian J Microbiol 2018; 58:381-392. [PMID: 30013283 DOI: 10.1007/s12088-018-0730-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/20/2018] [Indexed: 10/17/2022] Open
Abstract
A limit of detection of 200 CFU/mL of Salmonella typhi spiked in various sample matrices were achieved in 30 min. The sample matrices were raw/unprocessed milk, commercially available milk, juice from packed bottles, fresh juice from carts, potable water, turbid water and calf serum. The complete protocol comprised of three steps: (a) cell lysis (b) nucleic acid amplification and (c) an in situ optical detection. The cell lysis was carried out using a simple heating based protocol, while the loop-mediated isothermal amplification of DNA was carried out by an in-house designed and fabricated system. The developed system consists of an aluminum block fitted with two cartridge heaters along with a thermocouple. The system was coupled to a light source and spectrometer for a simultaneous in situ detection. Primers specific for STY2879 gene were used to amplify the nucleic acid sequence, isolated from S. typhi cells. The protocol involves 15 min of cell lysis and DNA isolation followed by 15 min for isothermal amplification and simultaneous detection. No cross-reactivity of the primers were observed at 106 CFU/mL of Escherichia coli, Vibrio cholerae, Salmonella typhimurium, Salmonella paratyphi A, Pseudomonas aeruginosa, Bacillus cereus, Lysteria monocytogenes, Clostridium botulinum, Staphylococcus aureus and Salmonella havana. In addition, the system was able to detect S. typhi of 200 CFU/mL in a concoction of 106 CFU/mL of E. coli, 106 CFU/mL of V. cholerae, and 106 CFU/mL of hepatocyte-derived cellular carcinoma HUH7 cells. The proposed rapid diagnostic system shows a promising future in the field of food and medical diagnostics.
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Bhatt P. Insilico Tools to Study the Bioremediation in Microorganisms. HANDBOOK OF RESEARCH ON MICROBIAL TOOLS FOR ENVIRONMENTAL WASTE MANAGEMENT 2018. [DOI: 10.4018/978-1-5225-3540-9.ch018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bioinformatics is the new area of science to study various living organisms, plants and animals. Bioremediation is the removal of toxic pollutants from the environment using microorganisms. Many of the databases are available online and can be used for the study of the microorganism genomics, transcriptomics, proteomics. This chapter mainly focuses the uses of recent databases and tools for the exploration of microorganisms.
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Affiliation(s)
- Pankaj Bhatt
- Dolphin (P.G.) Institute of Biomedical and Natural Sciences, India
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6
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Parmar KM, Hathi ZJ, Dafale NA. Control of Multidrug-Resistant Gene Flow in the Environment Through Bacteriophage Intervention. Appl Biochem Biotechnol 2016; 181:1007-1029. [PMID: 27723009 DOI: 10.1007/s12010-016-2265-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/23/2016] [Indexed: 02/06/2023]
Abstract
The spread of multidrug-resistant (MDR) bacteria is an emerging threat to the environment and public wellness. Inappropriate use and indiscriminate release of antibiotics in the environment through un-metabolized form create a scenario for the emergence of virulent pathogens and MDR bugs in the surroundings. Mechanisms underlying the spread of resistance include horizontal and vertical gene transfers causing the transmittance of MDR genes packed in different host, which pass across different food webs. Several controlling agents have been used for combating pathogens; however, the use of lytic bacteriophages proves to be one of the most eco-friendly due to their specificity, killing only target bacteria without damaging the indigenous beneficial flora of the habitat. Phages are part of the natural microflora present in different environmental niches and are remarkably stable in the environment. Diverse range of phage products, such as phage enzymes, phage peptides having antimicrobial properties, and phage cocktails also have been used to eradicate pathogens along with whole phages. Recently, the ability of phages to control pathogens has extended from the different areas of medicine, agriculture, aquaculture, food industry, and into the environment. To avoid the arrival of pre-antibiotic epoch, phage intervention proves to be a potential option to eradicate harmful pathogens generated by the MDR gene flow which are uneasy to cure by conventional treatments.
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Affiliation(s)
- Krupa M Parmar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Zubeen J Hathi
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India
| | - Nishant A Dafale
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nagpur, 440020, India.
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7
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Gene Specific Impedimetric Bacterial DNA Sensor for Rheumatic Heart Disease. Indian J Microbiol 2016; 57:112-115. [PMID: 28148987 DOI: 10.1007/s12088-016-0620-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 09/14/2016] [Indexed: 12/19/2022] Open
Abstract
An impedimetric mga gene specific DNA sensor was developed by immobilization of single stranded DNA probe onto the screen printed modified gold-dendrimer nanohybrid composite electrode for early and rapid detection of S. pyogenes in human throat swab samples causing rheumatic heart disease. Electrochemical impedance response was measured after hybridization with bacterial single stranded genomic DNA (ssG-DNA) with probe. The sensor was found highly specific to S. pyogenes and can detect as low as 0.01 ng ssDNA in 6 µL sample only in 30 min. The nanohybrid sensor was also tested with non-specific pathogens and characterized by FTIR. An early detection of the pathogen S. pyogenes in human can save damage of mitral and aortic heart valves (rheumatic heart disease) by proper medical care.
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8
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Puri A, Rai A, Dhanaraj PS, Lal R, Patel DD, Kaicker A, Verma M. An In Silico Approach for Identification of the Pathogenic Species, Helicobacter pylori and Its Relatives. Indian J Microbiol 2016; 56:277-86. [PMID: 27407291 PMCID: PMC4920758 DOI: 10.1007/s12088-016-0575-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 03/11/2016] [Indexed: 12/19/2022] Open
Abstract
Helicobacter is an economically important genus within the phylum Proteobacteria and include many species which cause many diseases in humans. With the conventional methods, it is difficult to identify them easily due to the high genetic similarity among its species. In the present study, 361 16S rRNA (rrs) gene sequences belonging to 45 species of genus Helicobacter were analyzed. Out of these, 264 sequences of 10 clinically relevant species (including Helicobacter pylori) were used. rrs gene sequences were analyzed to obtain a phylogenetic framework tree, in silico restriction enzyme analysis and species-specific conserved motifs. Protein sequences of another housekeeping gene, hsp60 were also subjected to phylogenetic analysis to supplement the data obtained using rrs sequences. Using these approaches, six out of ten species (including H. pylori) were easily segregated, whereas four species namely H. bilis, H. cinaedi, H. felis and Candidatus H. heilmannii were found to be heterogeneous. The above approaches have also helped in segregating unclassified sequences, thus proving them as an easy diagnostic method for identifying members of genus Helicobacter up to species level.
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Affiliation(s)
- Ayush Puri
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - Arshiya Rai
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - P. S. Dhanaraj
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - Rup Lal
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110 007 India
| | - Dev Dutt Patel
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - Anju Kaicker
- />Department of Biochemistry, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
| | - Mansi Verma
- />Department of Zoology, Sri Venkateswara College, University of Delhi, South Campus, New Delhi, 110 021 India
- />Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110 007 India
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9
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Brambila-Tapia AJL, Poot-Hernández AC, Perez-Rueda E, Rodríguez-Vázquez K. Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics. Indian J Microbiol 2016; 56:134-41. [PMID: 27570304 DOI: 10.1007/s12088-015-0562-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/23/2015] [Indexed: 11/29/2022] Open
Abstract
DNA methylation plays an important role in gene expression and virulence in some pathogenic bacteria. In this report, we describe DNA methyltransferases (MTases) present in human pathogenic bacteria and compared them with related species, which are not pathogenic or less pathogenic, based in comparative genomics. We performed a search in the KEGG database of the KEGG database orthology groups associated with adenine and cytosine DNA MTase activities (EC: 2.1.1.37, EC: 2.1.1.113 and EC: 2.1.1.72) in 37 human pathogenic species and 18 non/less pathogenic relatives and performed comparisons of the number of these MTases sequences according to their genome size, the DNA MTase type and with their non-less pathogenic relatives. We observed that Helicobacter pylori and Neisseria spp. presented the highest number of MTases while ten different species did not present a predicted DNA MTase. We also detected a significant increase of adenine MTases over cytosine MTases (2.19 vs. 1.06, respectively, p < 0.001). Adenine MTases were the only MTases associated with restriction modification systems and DNA MTases associated with type I restriction modification systems were more numerous than those associated with type III restriction modification systems (0.84 vs. 0.17, p < 0.001); additionally, there was no correlation with the genome size and the total number of DNA MTases, indicating that the number of DNA MTases is related to the particular evolution and lifestyle of specific species, regulating the expression of virulence genes in some pathogenic bacteria.
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Affiliation(s)
- Aniel Jessica Leticia Brambila-Tapia
- Departamento de Fisiología, Centro Universitario de Ciencias de La Salud (CUCS), Universidad de Guadalajara, Sierra Mojada #800, Colonia Independencia, 44340 Guadalajara, Jalisco Mexico ; Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y Sistemas (IIMAS), Universidad Nacional Autónoma de México (UNAM), Escolar #300, 04510 Ciudad Universitaria, Distrito Federal Mexico
| | - Augusto Cesar Poot-Hernández
- Departamento de Ingeniería celular y biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
| | - Ernesto Perez-Rueda
- Departamento de Ingeniería celular y biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos Mexico
| | - Katya Rodríguez-Vázquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigación en Matemáticas Aplicadas y Sistemas (IIMAS), Universidad Nacional Autónoma de México (UNAM), Escolar #300, 04510 Ciudad Universitaria, Distrito Federal Mexico
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10
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Comparative Genomics Reveals Biomarkers to Identify Lactobacillus Species. Indian J Microbiol 2016; 56:265-76. [PMID: 27407290 DOI: 10.1007/s12088-016-0605-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/09/2016] [Indexed: 12/19/2022] Open
Abstract
Bacteria possessing multiple copies of 16S rRNA (rrs) gene demonstrate high intragenomic heterogeneity. It hinders clear distinction at species level and even leads to overestimation of the bacterial diversity. Fifty completely sequenced genomes belonging to 19 species of Lactobacillus species were found to possess 4-9 copies of rrs each. Multiple sequence alignment of 268 rrs genes from all the 19 species could be classified into 20 groups. Lactobacillus sanfranciscensis TMW 1.1304 was the only species where all the 7 copies of rrs were exactly similar and thus formed a distinct group. In order to circumvent the problem of high heterogeneity arising due to multiple copies of rrs, 19 additional genes (732-3645 nucleotides in size) common to Lactobacillus genomes, were selected and digested with 10 Type II restriction endonucleases (RE), under in silico conditions. The following unique gene-RE combinations: recA (1098 nts)-HpyCH4 V, CviAII, BfuCI and RsaI were found to be useful in identifying 29 strains representing 17 species. Digestion patterns of genes-ruvB (1020 nts), dnaA (1368 nts), purA (1290 nts), dnaJ (1140 nts), and gyrB (1944 nts) in combination with REs-AluI, BfuCI, CviAI, Taq1, and Tru9I allowed clear identification of an additional 14 strains belonging to 8 species. Digestion pattern of genes recA, ruvB, dnaA, purA, dnaJ and gyrB can be used as biomarkers for identifying different species of Lactobacillus.
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Kumar R, Koul S, Kumar P, Kalia VC. Searching Biomarkers in the Sequenced Genomes of Staphylococcus for their Rapid Identification. Indian J Microbiol 2016; 56:64-71. [PMID: 26843698 DOI: 10.1007/s12088-016-0565-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 01/11/2016] [Indexed: 12/19/2022] Open
Abstract
Bacterial identification using rrs (16S rRNA) gene is widely reported. Bacteria possessing multiple copies of rrs lead to overestimation of its diversity. Staphylococcus genomes carries 5-6 copies of rrs showing high similarity in their nucleotide sequences, which lead to ambiguous results. The genomes of 31 strains of Staphylococcus representing 7 species were searched for the presence of common genes. In silico digestion of 34 common genes using 10 restriction endonucleases (REs) lead to select gene-RE combinations, which could be used as biomarkers. RE digestion of recA allowed unambiguous identification of 13 genomes representing all the 7 species. In addition, a few more genes (argH, argR, cysS, gyrB, purH, and pyrE) and RE combinations permitted further identification of 12 strains. By employing additional RE and genes unique to a particular strain, it was possible to identify the rest 6 Staphylococcus aureus strains. This approach has the potential to be utilized for rapid detection of Staphylococcus strains.
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Affiliation(s)
- Ravi Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
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12
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Kalia VC, Kumar R, Kumar P, Koul S. A Genome-Wide Profiling Strategy as an Aid for Searching Unique Identification Biomarkers for Streptococcus. Indian J Microbiol 2015; 56:46-58. [PMID: 26843696 DOI: 10.1007/s12088-015-0561-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 11/13/2015] [Indexed: 12/19/2022] Open
Abstract
The use of rrs (16S rRNA) gene is widely regarded as the "gold standard" for identifying bacteria and determining their phylogenetic relationships. Nevertheless, multiple copies of this gene in a genome is likely to give an overestimation of the bacterial diversity. In each of the 50 Streptococcus genomes (16 species, 50 strains), 4-7 copies of rrs are present. The nucleotide sequences of these rrs genes show high similarity within and among genomes, which did not allow unambiguous identification. A genome-wide search revealed the presence of 27 gene sequences common to all the Streptococcus species. Digestion of these 27 gene sequences with 10 type II restriction endonucleases (REs) showed that unique RE digestion in purH gene is sufficient for clear cut identification of 30 genomes belonging to 16 species. Additional gene-RE combinations allowed identification of another 15 strains belonging to S. pneumoniae, S. pyogenes, and S. suis. For the rest 5 strains, a combination of 2 genes was required for identifying them. The proposed strategy is likely to prove helpful in proper detection of pathogens like Streptococcus.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Ravi Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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Koul S, Prakash J, Mishra A, Kalia VC. Potential Emergence of Multi-quorum Sensing Inhibitor Resistant (MQSIR) Bacteria. Indian J Microbiol 2015; 56:1-18. [PMID: 26843692 DOI: 10.1007/s12088-015-0558-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 10/28/2015] [Indexed: 12/15/2022] Open
Abstract
Expression of certain bacterial genes only at a high bacterial cell density is termed as quorum-sensing (QS). Here bacteria use signaling molecules to communicate among themselves. QS mediated genes are generally involved in the expression of phenotypes such as bioluminescence, biofilm formation, competence, nodulation, and virulence. QS systems (QSS) vary from a single in Vibrio spp. to multiple in Pseudomonas and Sinorhizobium species. The complexity of QSS is further enhanced by the multiplicity of signals: (1) peptides, (2) acyl-homoserine lactones, (3) diketopiperazines. To counteract this pathogenic behaviour, a wide range of bioactive molecules acting as QS inhibitors (QSIs) have been elucidated. Unlike antibiotics, QSIs don't kill bacteria and act at much lower concentration than those of antibiotics. Bacterial ability to evolve resistance against multiple drugs has cautioned researchers to develop QSIs which may not generate undue pressure on bacteria to develop resistance against them. In this paper, we have discussed the implications of the diversity and multiplicity of QSS, in acting as an arsenal to withstand attack from QSIs and may use these as reservoirs to develop multi-QSI resistance.
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Affiliation(s)
- Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Jyotsana Prakash
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
| | - Anjali Mishra
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India ; Academy for Scientific and Innovative Research (AcSIR), 2 Rafi Marg, New Delhi, 110001 India
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14
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Kalia VC, Kumar P. Genome Wide Search for Biomarkers to Diagnose Yersinia Infections. Indian J Microbiol 2015; 55:366-74. [PMID: 26543261 DOI: 10.1007/s12088-015-0552-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 09/01/2015] [Indexed: 01/12/2023] Open
Abstract
Bacterial identification on the basis of the highly conserved 16S rRNA (rrs) gene is limited by its presence in multiple copies and a very high level of similarity among them. The need is to look for other genes with unique characteristics to be used as biomarkers. Fifty-one sequenced genomes belonging to 10 different Yersinia species were used for searching genes common to all the genomes. Out of 304 common genes, 34 genes of sizes varying from 0.11 to 4.42 kb, were selected and subjected to in silico digestion with 10 different Restriction endonucleases (RE) (4-6 base cutters). Yersinia species have 6-7 copies of rrs per genome, which are difficult to distinguish by multiple sequence alignments or their RE digestion patterns. However, certain unique combinations of other common gene sequences-carB, fadJ, gluM, gltX, ileS, malE, nusA, ribD, and rlmL and their RE digestion patterns can be used as markers for identifying 21 strains belonging to 10 Yersinia species: Y. aldovae, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. pestis, Y. pseudotuberculosis, Y. rohdei, Y. ruckeri, and Y. similis. This approach can be applied for rapid diagnostic applications.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, Delhi, 110007 India
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15
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Kalia VC, Kumar P, Kumar R, Mishra A, Koul S. Genome Wide Analysis for Rapid Identification of Vibrio Species. Indian J Microbiol 2015; 55:375-83. [PMID: 26543262 DOI: 10.1007/s12088-015-0553-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 12/17/2022] Open
Abstract
The highly conserved 16S rRNA (rrs) gene is generally used for bacterial identification. In organisms possessing multiple copies of rrs, high intra-genomic heterogeneity does not allow easy distinction among different species. In order to identify Vibrio species, a wide range of genes have been employed. There is an urgent requirement of a consensus gene, which can be used as biomarker for rapid identification. Eight sequenced genomes of Vibrio species were screened for selecting genes which were common among all the genomes. Out of 108 common genes, 24 genes of sizes varying from 0.11 to 3.94 kb were subjected to in silico digestion with 10 type II restriction endonucleases (RE). A few unique genes-dapF, fadA, hisD, ilvH, lpxC, recF, recR, rph and ruvB in combination with certain REs provided unique digestion patterns, which can be used as biomarkers. This protocol can be exploited for rapid diagnosis of Vibrio species.
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Affiliation(s)
- Vipin Chandra Kalia
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
| | - Prasun Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Ravi Kumar
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Anjali Mishra
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India
| | - Shikha Koul
- Microbial Biotechnology and Genomics, CSIR - Institute of Genomics and Integrative Biology (IGIB), Delhi University Campus, Mall Road, New Delhi, 110007 India ; Academy of Scientific and Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi, 110001 India
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