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Mevada V, Patel R, Dudhagara P, Chaudhari R, Vohra M, Khan V, J. H. Shyu D, Chen YY, Zala D. Whole Genome Sequencing and Pan-Genomic Analysis of Multidrug-Resistant Vibrio cholerae VC01 Isolated from a Clinical Sample. Microorganisms 2023; 11:2030. [PMID: 37630590 PMCID: PMC10457874 DOI: 10.3390/microorganisms11082030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Cholera, a disease caused by the Vibrio cholerae bacteria, threatens public health worldwide. The organism mentioned above has a significant historical record of being identified as a prominent aquatic environmental pollutant capable of adapting its phenotypic and genotypic traits to react to host patients effectively. This study aims to elucidate the heterogeneity of the sporadic clinical strain of V. cholerae VC01 among patients residing in Silvasa. The study involved conducting whole-genome sequencing of the isolate obtained from patients exhibiting symptoms, including those not commonly observed in clinical practice. The strain was initially identified through a combination of biochemical analysis, microscopy, and 16s rRNA-based identification, followed by type strain-based identification. The investigation demonstrated the existence of various genetic alterations and resistance profiles against multiple drugs, particularly chloramphenicol (catB9), florfenicol (floR), oxytetracycline (tet(34)), sulfonamide (sul2), and Trimethoprim (dfrA1). The pan-genomic analysis indicated that 1099 distinct clusters were detected within the genome sequences of recent isolates worldwide. The present study helps to establish a correlation between the mutation and the coexistence of antimicrobial resistance toward current treatment.
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Affiliation(s)
- Vishal Mevada
- DNA Division, Directorate of Forensic Science, Gandhinagar 382007, India;
| | - Rajesh Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India;
| | - Pravin Dudhagara
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India;
| | - Rajesh Chaudhari
- School of Applied Sciences and Technology, Gujarat Technological University, Ahmedabad 382424, India;
| | - Mustafa Vohra
- Directorate of Medical & Health Services, UT of Dadra & Nagar Haveli and Daman & Diu, Silvassa 396230, India; (M.V.); (V.K.)
| | - Vikram Khan
- Directorate of Medical & Health Services, UT of Dadra & Nagar Haveli and Daman & Diu, Silvassa 396230, India; (M.V.); (V.K.)
| | - Douglas J. H. Shyu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan;
| | - Yih-Yuan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi City 600, Taiwan;
| | - Dolatsinh Zala
- School of Applied Sciences and Technology, Gujarat Technological University, Ahmedabad 382424, India;
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Quach NT, Nguyen Vu TH, Bui TL, Pham AT, An Nguyen TT, Xuan Le TT, Thuy Ta TT, Dudhagara P, Phi QT. Genome-Guided Investigation Provides New Insights into Secondary Metabolites of Streptomyces parvulus SX6 from Aegiceras corniculatum. Pol J Microbiol 2022; 71:381-394. [DOI: 10.33073/pjm-2022-034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/13/2022] [Indexed: 11/07/2022] Open
Abstract
Abstract
Whole-genome sequencing and genome mining are recently considered an efficient approach to shine more light on the underlying secondary metabolites of Streptomyces. The present study unearths the biosynthetic potential of endophytic SX6 as a promising source of biologically active substances and plant-derived compounds for the first time. Out of 38 isolates associated with Aegiceras corniculatum (L.) Blanco, Streptomyces parvulus SX6 was highly active against Pseudomonas aeruginosa ATCC® 9027™ and methicillin-resistant Staphylococcus epidermidis (MRSE) ATCC® 35984™. Additionally, S. parvulus SX6 culture extract showed strong cytotoxicity against Hep3B, MCF-7, and A549 cell lines at a concentration of 30 μg/ml, but not in non-cancerous HEK-293 cells. The genome contained 7.69 Mb in size with an average G + C content of 72.8% and consisted of 6,779 protein-coding genes. AntiSMASH analysis resulted in the identification of 29 biosynthetic gene clusters (BGCs) for secondary metabolites. Among them, 4 BGCs showed low similarity (28–67% of genes show similarity) to actinomycin, streptovaricin, and polyoxypeptin gene clusters, possibly attributed to antibacterial and anticancer activities observed. In addition, the complete biosynthetic pathways of plant-derived compounds, including daidzein and genistein were identified using genome mining and HPLC-DAD-MS analysis. These findings portray an exciting avenue for future characterization of promising secondary metabolites from mangrove endophytic S. parvulus.
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Affiliation(s)
- Ngoc Tung Quach
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Hanh Nguyen Vu
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Lien Bui
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Anh Tuan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Thu An Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Thanh Xuan Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | | | - Pravin Dudhagara
- Department of Biosciences (UGC-SAP-II and DST-FIST-I), Veer Narmad South Gujarat University , Surat , India
| | - Quyet-Tien Phi
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
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Patel K, Patel N, Vaghamshi N, Shah K, Dugdirala SM, Dudhagara P. Trends and strategies in the effluent treatment of pulp and paper industries: A review highlighting reactor options. Curr Res Microb Sci 2021; 2:100077. [PMID: 34841366 PMCID: PMC8610311 DOI: 10.1016/j.crmicr.2021.100077] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 11/15/2022] Open
Abstract
From the beginning of the paper-making process, the pulp and paper industry has utilized a large amount of water and generated a vast amount of highly polluted wastewater. The paper industry faces global pressure to reduce water use and lower environmental pollution. However, traditional physicochemical methods of wastewater treatment need high energy input, and their ecological impact is questionable. Due to the zero discharged policy, the industries urgently require novel eco-friendly, sustainable, and efficient treatment techniques. Microbial technology is the most recommended option to treat wastewater and support sustainable growth. The present article describes the overview of traditional and novel methods, including membrane bioreactor (MBR) and moving-bed biofilm reactor (MBBR) technology's with their current state and their limits for treating pulp and paper wastewater. It is expected to integrate the novel methods with advanced hybrid technology to fulfill wastewater treatment criteria and prospects. Furthermore, coupling MBR and MBBR technology make energy and water recovery possible, and recycling wastewater will be economically and environmentally feasible.
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Affiliation(s)
- Kartik Patel
- Department of Biosciences (UGC-SAP-II & DST-FIST-I), Veer Narmard South Gujarat University, Surat 395007, India
| | - Niky Patel
- Department of Biosciences (UGC-SAP-II & DST-FIST-I), Veer Narmard South Gujarat University, Surat 395007, India
| | - Nilam Vaghamshi
- Department of Biosciences (UGC-SAP-II & DST-FIST-I), Veer Narmard South Gujarat University, Surat 395007, India
| | - Kamlesh Shah
- P.S. Science and H.D. Patel Arts College Kadi, Mahesana, Gujarat, India
| | - Srinivas Murthy Dugdirala
- Biogas Research Centre, Post-Graduate Department of Microbiology, M.D. Gramsewa Mahavidyalaya, Gujarat Vidyapith Sadra, Gandhinagar, Gujarat, India
| | - Pravin Dudhagara
- Department of Biosciences (UGC-SAP-II & DST-FIST-I), Veer Narmard South Gujarat University, Surat 395007, India
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Patel K, Dudhagara P. Optimization of xylanase production by Bacillus tequilensis strain UD-3 using economical agricultural substrate and its application in rice straw pulp bleaching. Biocatalysis and Agricultural Biotechnology 2020. [DOI: 10.1016/j.bcab.2020.101846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Patel K, Dudhagara P. Compatibility testing and enhancing the pulp bleaching process by hydrolases of the newly isolated thermophilic Isoptericola variabilis strain UD-6. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2019.1711067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Kartik Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, India
| | - Pravin Dudhagara
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, India
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Bhavsar S, Dudhagara P, Tank S. R software package based statistical optimization of process components to simultaneously enhance the bacterial growth, laccase production and textile dye decolorization with cytotoxicity study. PLoS One 2018; 13:e0195795. [PMID: 29718934 PMCID: PMC5931462 DOI: 10.1371/journal.pone.0195795] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/29/2018] [Indexed: 11/20/2022] Open
Abstract
The thermophilic bacterium, Bacillus licheniformis U1 is used for the optimization of bacterial growth (R1), laccase production (R2) and synthetic disperse blue DBR textile dye decolorization (R3) in the present study. Preliminary optimization has been performed by one variable at time (OVAT) approach using four media components viz., dye concentration, copper sulphate concentration, pH, and inoculum size. Based on OVAT result further statistical optimization of R1, R2 and R3 performed by Box–Behnken design (BBD) using response surface methodology (RSM) in R software with R Commander package. The total 29 experimental runs conducted in the experimental design study towards the construction of a quadratic model. The model indicated that dye concentration 110 ppm, copper sulphate 0.2 mM, pH 7.5 and inoculum size 6% v/v were found to be optimum to maximize the laccase production and bacterial growth. Whereas, maximum dye decolorization achieved in media containing dye concentration 110 ppm, copper sulphate 0.6 mM, pH 6 and inoculum size 6% v/v. R package predicted R2 of R1, R2 and R3 were 0.9917, 0.9831 and 0.9703 respectively; likened to Design-Expert (Stat-Ease) (DOE) predicted R2 of R1, R2, and R3 were 0.9893, 0.9822 and 0.8442 respectively. The values obtained by R software were more precise, reliable and reproducible, compared to the DOE model. The laccase production was 1.80 fold increased, and 2.24 fold enhancement in dye decolorization was achieved using optimized medium than initial experiments. Moreover, the laccase-treated sample demonstrated the less cytotoxic effect on L132 and MCF-7 cell lines compared to untreated sample using MTT assay. Higher cell viability and lower cytotoxicity observed in a laccase-treated sample suggest the impending application of bacterial laccase in the reduction of toxicity of dye to design rapid biodegradation process.
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Affiliation(s)
- Sunil Bhavsar
- Department of Biosciences (UGC-SAP-II), Veer Narmad South Gujarat University, Surat, Gujarat, INDIA
- * E-mail:
| | - Pravin Dudhagara
- Department of Biosciences (UGC-SAP-II), Veer Narmad South Gujarat University, Surat, Gujarat, INDIA
- Bioinformatics and Supercomputer Laboratory, Department of Biosciences (UGC-SAP-II), Veer Narmad South Gujarat University, Surat, Gujarat, INDIA
| | - Shantilal Tank
- Department of Biosciences (UGC-SAP-II), Veer Narmad South Gujarat University, Surat, Gujarat, INDIA
- Bioinformatics and Supercomputer Laboratory, Department of Biosciences (UGC-SAP-II), Veer Narmad South Gujarat University, Surat, Gujarat, INDIA
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Bhagat C, Dudhagara P, Tank S. Trends, application and future prospectives of microbial carbonic anhydrase mediated carbonation process for CCUS. J Appl Microbiol 2017; 124:316-335. [PMID: 28921830 DOI: 10.1111/jam.13589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 06/17/2017] [Accepted: 09/06/2017] [Indexed: 12/21/2022]
Abstract
Growing industrialization and the desire for a better economy in countries has accelerated the emission of greenhouse gases (GHGs), by more than the buffering capacity of the earth's atmosphere. Among the various GHGs, carbon dioxide occupies the first position in the anthroposphere and has detrimental effects on the ecosystem. For decarbonization, several non-biological methods of carbon capture, utilization and storage (CCUS) have been in use for the past few decades, but they are suffering from narrow applicability. Recently, CO2 emission and its disposal related problems have encouraged the implementation of bioprocessing to achieve a zero waste economy for a sustainable environment. Microbial carbonic anhydrase (CA) catalyses reversible CO2 hydration and forms metal carbonates that mimic the natural phenomenon of weathering/carbonation and is gaining merit for CCUS. Thus, the diversity and specificity of CAs from different micro-organisms could be explored for CCUS. In the literature, more than 50 different microbial CAs have been explored for mineral carbonation. Further, microbial CAs can be engineered for the mineral carbonation process to develop new technology. CA driven carbonation is encouraging due to its large storage capacity and favourable chemistry, allowing site-specific sequestration and reusable product formation for other industries. Moreover, carbonation based CCUS holds five-fold more sequestration capacity over the next 100 years. Thus, it is an eco-friendly, feasible, viable option and believed to be the impending technology for CCUS. Here, we attempt to examine the distribution of various types of microbial CAs with their potential applications and future direction for carbon capture. Although there are few key challenges in bio-based technology, they need to be addressed in order to commercialize the technology.
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Affiliation(s)
- C Bhagat
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - P Dudhagara
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - S Tank
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, India
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Thapa R, Bhagat C, Shrestha P, Awal S, Dudhagara P. Enzyme-mediated formulation of stable elliptical silver nanoparticles tested against clinical pathogens and MDR bacteria and development of antimicrobial surgical thread. Ann Clin Microbiol Antimicrob 2017; 16:39. [PMID: 28511708 PMCID: PMC5434635 DOI: 10.1186/s12941-017-0216-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/12/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Silver nanoparticles (AgNPs) are believed to be emerging tool against various infectious diseases including multi-drug resistant (MDR) bacteria. In the present study, in vitro synthesis of AgNPs was optimized using 1:50 ratio of macerozyme (25 μg/μl) and 1 mM AgNO3 incubated at 80 °C for 8 h. AgNPs were characterized by UV-Visible spectroscopy, dynamic light scattering (DLS), scanning electron microscopy, energy-dispersive X-ray spectroscopy, transmission electron microscopy (TEM) and X-ray diffraction (XRD). RESULTS Characterization studies suggest the synthesis of elliptical, stable and crystalline AgNPs with an average size of 38.26 ± 0.4 nm calculated using TEM. The XRD pattern revealed the face-centered-cubic (fcc) form of metallic silver. Good shape integrity and dispersion of AgNPs after 1 year of incubation confirmed their stability. AgNPs were exibited the antimicrobial property against ten pathogenic bacteria, three molds and one yeast. The AgNPs also revealed remarkable antimicrobial activity against three MDR strains i.e. Extended spectrum beta-lactamase positive Escherichia coli, Staphylococcus aureus (MRSA) and Teicoplanin resistant Streptococcus Pneumoniae. The AgNPs coated surgical threads (suture) were revealed the remarkble antibacterial activity against three MDR strains. This is the first report to synthesize antimicrobial elliptical AgNPs using enzymes. CONCLUSION The results suggest the possibilities to develop the nanoparticles coated antimicrobial medical fabric to combat against MDR infection.
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Affiliation(s)
- Rupak Thapa
- Department of Biotechnology, Veer Narmad South Gujarat University, Surat, Gujarat, 395007, India
| | - Chintan Bhagat
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, 395007, India
| | - Pragya Shrestha
- Department of Biotechnology, Veer Narmad South Gujarat University, Surat, Gujarat, 395007, India
| | - Suvash Awal
- Department of Biotechnology, Veer Narmad South Gujarat University, Surat, Gujarat, 395007, India
| | - Pravin Dudhagara
- Department of Biosciences (UGC-SAP-DRS-II), Veer Narmad South Gujarat University, Surat, Gujarat, 395007, India.
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Dudhagara P, Bhavsar S, Bhagat C, Ghelani A, Bhatt S, Patel R. Web Resources for Metagenomics Studies. Genomics Proteomics Bioinformatics 2015; 13:296-303. [PMID: 26602607 PMCID: PMC4678780 DOI: 10.1016/j.gpb.2015.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/09/2015] [Accepted: 10/13/2015] [Indexed: 10/26/2022]
Abstract
The development of next-generation sequencing (NGS) platforms spawned an enormous volume of data. This explosion in data has unearthed new scalability challenges for existing bioinformatics tools. The analysis of metagenomic sequences using bioinformatics pipelines is complicated by the substantial complexity of these data. In this article, we review several commonly-used online tools for metagenomics data analysis with respect to their quality and detail of analysis using simulated metagenomics data. There are at least a dozen such software tools presently available in the public domain. Among them, MGRAST, IMG/M, and METAVIR are the most well-known tools according to the number of citations by peer-reviewed scientific media up to mid-2015. Here, we describe 12 online tools with respect to their web link, annotation pipelines, clustering methods, online user support, and availability of data storage. We have also done the rating for each tool to screen more potential and preferential tools and evaluated five best tools using synthetic metagenome. The article comprehensively deals with the contemporary problems and the prospects of metagenomics from a bioinformatics viewpoint.
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Affiliation(s)
- Pravin Dudhagara
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India.
| | - Sunil Bhavsar
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India
| | - Chintan Bhagat
- Department of Biosciences, Veer Narmad South Gujarat University, Surat 395007, India
| | - Anjana Ghelani
- Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat 395001, India
| | - Shreyas Bhatt
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India
| | - Rajesh Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan 384265, India
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Abstract
The data in this article contains the sequences of fungal Internal Transcribed Spacer (ITS) and 18S rRNA gene from a metagenome of Lonar soda lake, India. Sequences were amplified using fungal specific primers, which amplified the amplicon lined between the 18S and 28S rRNA genes. Data were obtained using Fungal tag-encoded FLX amplicon pyrosequencing (fTEFAP) technique and used to analyze fungal profile by the culture-independent method. Primary analysis using PlutoF 454 pipeline suggests the Lonar lake mycobiome contained the 29 different fungal species. The raw sequencing data used to perform this analysis along with FASTQ file are located in the NCBI Sequence Read Archive (SRA) under accession No. SRX889598 (http://www.ncbi.nlm.nih.gov/sra/SRX889598).
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Affiliation(s)
- Pravin Dudhagara
- Department of Biotechnology, Veer Narmad South Gujarat University, Surat 395007, India
| | - Anjana Ghelani
- Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Science, Surat, India
| | - Sunil Bhavsar
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, India
| | - Shreyas Bhatt
- Department of Life Sciences, Hemchandrachrya North Gujarat University, Patan, India
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Mangrola A, Dudhagara P, Koringa P, Joshi CG, Parmar M, Patel R. Deciphering the microbiota of Tuwa hot spring, India using shotgun metagenomic sequencing approach. Genom Data 2015; 4:153-5. [PMID: 26484204 PMCID: PMC4535658 DOI: 10.1016/j.gdata.2015.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/12/2015] [Indexed: 01/22/2023]
Abstract
Here, we report metagenome from the Tuwa hot spring, India using shotgun sequencing approach. Metagenome consisted of 541,379 sequences with 98.7 Mbps size with 46% G + C content. Metagenomic sequence reads were deposited into the EMBL database under accession number ERP009321. Community analysis presented 99.1% sequences belong to bacteria, 0.3% of eukaryotic origin, 0.2% virus derived and 0.05% from archea. Unclassified and unidentified sequences were 0.4% and 0.07% respectively. A total of 22 bacterial phyla include 90 families and 201 species were observed in the hot spring metagenome. Firmicutes (97.0%), Proteobacteria (1.3%) and Actinobacteria (0.4%) were reported as dominant bacterial phyla. In functional analysis using Cluster of Orthologous Group (COG), 21.5% drops in the poorly characterized group. Using subsystem based annotation, 4.0% genes were assigned for stress responses and 3% genes were fit into the metabolism of aromatic compounds. The hot spring metagenome is very rich with novel sequences affiliated to unclassified and unidentified lineages, suggesting the potential source for novel microbial species and their products.
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Affiliation(s)
- Amitsinh Mangrola
- Department of Biochemistry, Shri Alpesh N. Patel Post Graduate Institute, Anand, India
| | - Pravin Dudhagara
- Department of Biotechnology, Veer Narmad South Gujarat University, Surat, India
| | - Prakash Koringa
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - C G Joshi
- Department of Animal Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Mansi Parmar
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Rajesh Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
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Dudhagara P, Ghelani A, Patel R, Chaudhari R, Bhatt S. Bacterial tag encoded FLX titanium amplicon pyrosequencing (bTEFAP) based assessment of prokaryotic diversity in metagenome of Lonar soda lake, India. Genom Data 2015; 4:8-11. [PMID: 26484168 PMCID: PMC4535755 DOI: 10.1016/j.gdata.2015.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 01/29/2015] [Indexed: 11/29/2022]
Abstract
Bacterial diversity and archaeal diversity in metagenome of the Lonar soda lake sediment were assessed by bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). Metagenome comprised 5093 sequences with 2,531,282 bp and 53 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA218849. Metagenome sequence represented the presence of 83.1% bacterial and 10.5% archaeal origin. A total of 14 different bacteria demonstrating 57 species were recorded with dominating species like Coxiella burnetii (17%), Fibrobacter intestinalis (12%) and Candidatus Cloacamonas acidaminovorans (11%). Occurrence of two archaeal phyla representing 24 species, among them Methanosaeta harundinacea (35%), Methanoculleus chikugoensis (12%) and Methanolinea tarda (11%) were dominating species. Significant presence of 11% sequences as an unclassified indicated the possibilities for unknown novel prokaryotes from the metagenome.
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Affiliation(s)
- Pravin Dudhagara
- Department of Biotechnology, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Anjana Ghelani
- Department of Microbiology, Shree Ramkrishna Institute of Computer Education and Applied Sciences, Surat, India
| | - Rajesh Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Rajesh Chaudhari
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Shreyas Bhatt
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
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