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Pal Y, Mayilraj S, Krishnamurthi S. Uncovering the structure and function of specialist bacterial lineages in environments routinely exposed to explosives. Lett Appl Microbiol 2022; 75:1433-1448. [PMID: 35972393 DOI: 10.1111/lam.13810] [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: 09/21/2021] [Revised: 07/30/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
Environmental contamination by hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX), and Octahydro-1, 3, 5, 7-tetranitro-1, 3, 5, 7-tetrazocine (HMX), the two most widely used compounds for military operations, is a long-standing problem at the manufacturing and decommissioning plants. Since explosives contamination has previously been shown to favour the growth of specific bacterial communities, the present study attempts to identify the specialist bacterial communities and their potential functional and metabolic roles by using amplicon targeted and whole-metagenome sequencing approaches (WMS) in samples collected from two distinct explosives manufacturing sites. We hypothesize that the community structure and functional attributes of bacterial population are substantially altered by the concentration of explosives and physicochemical conditions. The results highlight the predominance of Planctomycetes in contrast to previous reports from similar habitats. The detailed phylogenetic analysis revealed the presence of OTU's related to bacterial members known for their explosives degradation. Further, the functional and metabolic analyses highlighted the abundance of putative genes and unidentified taxa possibly associated with xenobiotic biodegradation. Our findings suggest that microbial species capable of utilizing explosives as a carbon, energy, or electron source are favoured by certain selective pressures based on the prevailing physicochemical and geographical conditions.
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Affiliation(s)
- Yash Pal
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh, -160036
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh, -160036.,Director of Research, Bentoli AgriNutrition, India Pvt Ltd., 3F2, Third Floor, Front Block, Metro Tower, Building No.115, Poonamallee, High Road, Chennai, - 600 084
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh, -160036
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Kumar N, Gupta AK, Sudan SK, Pal D, Randhawa V, Sahni G, Mayilraj S, Kumar M. Abundance and Diversity of Phages, Microbial Taxa, and Antibiotic Resistance Genes in the Sediments of the River Ganges Through Metagenomic Approach. Microb Drug Resist 2021; 27:1336-1354. [PMID: 33913739 DOI: 10.1089/mdr.2020.0431] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In this study, we have analyzed the metagenomic DNA from the pooled sediment sample of the river Ganges to explore the abundance and diversity of phages, microbial community, and antibiotic resistance genes (ARGs). Utilizing data from Illumina platform, 4,174 (∼0.0013%) reads were classified for the 285 different DNA viruses largely dominated by the group of 260 distinctive phages (3,602 reads, ∼86.3%). Among all, Microcystis (782 hits), Haemophilus (403), Synechococcus (386), Pseudomonas (279), Enterococcus (232), Bacillus (196), Rhodococcus (166), Caulobacter (163), Salmonella (146), Enterobacteria (143), Mycobacterium and (128) phages show the highest abundance and account for ∼90% of the total identified phages. In addition, we have also identified corresponding host pertaining to these phages. Mainly, Proteobacteria (∼69.3%) dominates the microbial population structure. Primarily, orders such as Caulobacterales (∼28%), Burkholderiales (∼13.9%), Actinomycetales (∼13.7%), and Pseudomonadales (∼7.5%) signify the core section. Furthermore, 21,869 (∼0.00695%) reads were classified in 20 ARG types (classes) and 240 ARGs (subtypes), among which 4 ARG types, namely multidrug resistance (12,041 reads, ∼55%), bacitracin (3,202 reads, ∼15%), macrolide-lincosamide-streptogramin (1,744 reads, ∼7.98%), and fosmidomycin (990 reads, ∼4.53%), have the highest abundance. Simultaneously, six resistance mechanisms were also recognized with the dominance of antibiotic efflux (72.8%, 15,919 reads). The results unveil the distribution of (pro)-phages; microbial community; and various ARGs in the Ganges river sediments.
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Affiliation(s)
- Narender Kumar
- Division of Protein Science and Engineering, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Amit Kumar Gupta
- Virology Unit and Bioinformatics Centre, and Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Sarabjeet Kour Sudan
- Division of Protein Science and Engineering, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Deepika Pal
- MTCC-Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Vinay Randhawa
- Virology Unit and Bioinformatics Centre, and Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Girish Sahni
- Division of Protein Science and Engineering, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection and Gene Bank, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, and Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
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Chander AM, Kaur P, Sekhon PK, Kochhar R, Dhawan DK, Bhadada SK, Mayilraj S. Genome sequence and comparative genomics of multi-drug resistant strain Pseudomonas monteilii CD10_2 isolated from a type 1 diabetic-celiac disease patient. Gene Reports 2020. [DOI: 10.1016/j.genrep.2020.100734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Parvez S, Khan AU, Kaur G, Barakat M, Ortet P, Mayilraj S. An insight into the genome of extensively drug-resistant and uropathogenic Citrobacter werkmanii. J Glob Antimicrob Resist 2020; 22:785-791. [PMID: 32619689 DOI: 10.1016/j.jgar.2020.06.014] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/28/2020] [Accepted: 06/18/2020] [Indexed: 10/24/2022] Open
Abstract
OBJECTIVE Carbapenemase-producing bacteria pose a serious public-health threat. This study was performed to understand the emergence and genetic features of NDM-producers in hospital setting. METHODS Samples were collected from a tertiary-care hospital. Isolate identification was performed by 16S rRNA sequencing. The genome of Citrobacter werkmanii (AK-8) was sequenced on an Illumina NextSeq 500 platform. Resistance determinants and pathogenicity islands were determined by ResFinder and PathogenFinder, respectively. MLST, two-component systems and transcription factors were identified by P2RP server, whilst variant calling and insertion sequence (IS) elements were determined by Galaxy and ISfinder, respectively. The genome of AK-8 was compared with uropathogenic Escherichia coli strain 536. RESULTS This is the first report on whole-genome analysis of extensively drug-resistant NDM-6-producing uropathogenic C. werkmanii ST-104. Resistance genes for all antibiotics except colistin, fosfomycin, fusidic- acid, nitroimidazole, oxazolidinones, tetracycline and glycopeptides were detected in this strain. Genome analysis of AK-8 led to the identification of the BaeSR two-component system regulating production of multidrug efflux proteins. Virulence was regulated by CpxRA, ZraRS, RstAB, UhpAB, AcrAB, RcsBc and UvrY, whereas Bar-UvrY was found to control carbon metabolism, flagellum biosynthesis and biofilm formation. The AK-8 genome encodes 21 chemoreceptors involved in colonisation and pathogenesis. Fur family transcriptional regulator, cAMP receptor protein and RpoS were found to increase the virulence of AK-8. ntBLAST analysis showed 69.60% genetic identity with E. coli 536 as an adaptive feature for survival. CONCLUSION The emergence of extensively drug-resistant pathogenic C. werkmanii is alarming and it should not be ignored as commensal.
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Affiliation(s)
- Shadab Parvez
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University (AMU), Aligarh 202 002, Uttar Pradesh, India; Central Instrumentation Facility, Jamia Millia Islamia, New Delhi 110 025, India.
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit, Aligarh Muslim University (AMU), Aligarh 202 002, Uttar Pradesh, India.
| | - Gurwinder Kaur
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
| | - Mohamed Barakat
- Aix-Marseille Université, CEA, CNRS, LEMiRE, UMR 7265, BIAM, Saint-Paul-lez-Durance, France
| | - Philippe Ortet
- Aix-Marseille Université, CEA, CNRS, LEMiRE, UMR 7265, BIAM, Saint-Paul-lez-Durance, France
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
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Pal Y, Mayilraj S, Paul M, Schumann P, Krishnamurthi S. Indiicoccus explosivorum gen. nov., sp. nov., isolated from an explosives waste contaminated site. Int J Syst Evol Microbiol 2019; 69:2555-2564. [PMID: 31287396 DOI: 10.1099/ijsem.0.003541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pink-pigmented, Gram-stain-positive, aerobic, coccoid-shaped bacterial strain, designated as S5-TSA-19T, was isolated from an explosives contaminated site in Panchkula, Haryana, India. The 16S rRNA gene sequencing blast analysis indicated that the strain is a member of the family Planococcaceae with the highest sequence similarity to Planomicrobium soli XN13T (96.1 %), followed by Planococcus maitriensis S1T (95.6 %), Planococcus plakortidis DSM 23997T (95.6 %), Planomicrobium flavidum ISL-41T (95.6 %), Planococcus rifietoensis M8T (95.5 %), Planococcus salinus LCB217T (95.5 %) and Planococcus maritimus DSM 17275T (95.5 %). Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences (based on a conserved set of 400 proteins) retrieved the strain in a distinct branch indicating a separate lineage within the family Planococcaceae. Strain S5-TSA-19T had a distinctive chemotaxonomic pattern comprising A4α type peptidoglycan based on l-Lys-d-Asp, iso-C15 : 0 as the major fatty acid, absence of phosphatidylethanolamine as a major lipid and MK-7 and MK-6 as the major menaquinones, differentiating it from the genera Planococcus and Planomicrobium, thus supporting the findings of molecular phylogeny. Further, strain S5-TSA-19T was able to biotransform hexahydro-1,3,5,-trinitro-1,2,5-triazine (RDX) into nitrite derivatives under aerobic conditions in 2-4 days, whereas the closest reference strains did not possess this property. On the basis of polyphasic taxonomic characterization and a phylogenomics approach, strain S5-TSA-19T is proposed as the type strain of a novel species in a novel genus for which the name Indiicoccus explosivorum gen. nov., sp. nov. is proposed (=JCM 31737T=KCTC 33871T=MTCC 12608T).
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Affiliation(s)
- Yash Pal
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A Chandigarh 160036, Chandigarh 160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A Chandigarh 160036, Chandigarh 160036, India.,Present address: Bentoli AgriNutrition India Pvt Ltd, Chennai, India
| | - Mohit Paul
- CSIR-Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A Chandigarh 160036, Chandigarh 160036, India
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Sran KS, Bisht B, Mayilraj S, Roy Choudhury A. Structural characterization and antioxidant potential of a novel anionic exopolysaccharide produced by marine Microbacterium aurantiacum FSW-25. Int J Biol Macromol 2019; 131:343-352. [DOI: 10.1016/j.ijbiomac.2019.03.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/16/2019] [Accepted: 03/02/2019] [Indexed: 11/30/2022]
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Sekhon PK, Chander AM, Mayilraj S, Rishi P. Genomic analysis of Indian strains of Salmonella enterica subsp. enterica serovar Typhi indicates novel genetic repertoire for pathogenicity and adaptations. Mol Biol Rep 2019; 46:3967-3989. [DOI: 10.1007/s11033-019-04843-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 04/27/2019] [Indexed: 01/23/2023]
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Verma A, Pal Y, Ojha AK, Kumari M, Khatri I, Rameshkumar N, Schumann P, Dastager SG, Mayilraj S, Subramanian S, Krishnamurthi S. Taxonomic insights into the phylogeny of Bacillus badius and proposal for its reclassification to the genus Pseudobacillus as Pseudobacillus badius comb. nov. and reclassification of Bacillus wudalianchiensis Liu et al., 2017 as Pseudobacillus wudalianchiensis comb. nov. Syst Appl Microbiol 2019; 42:360-372. [DOI: 10.1016/j.syapm.2019.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/04/2019] [Accepted: 03/08/2019] [Indexed: 11/26/2022]
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Kaur N, Seuylemezian A, Patil PP, Patil P, Krishnamurti S, Varelas J, Smith DJ, Mayilraj S, Vaishampayan P. Paenibacillus xerothermodurans sp. nov., an extremely dry heat resistant spore forming bacterium isolated from the soil of Cape Canaveral, Florida. Int J Syst Evol Microbiol 2018; 68:3190-3196. [PMID: 30129919 DOI: 10.1099/ijsem.0.002967] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, motile, endospore-producing, facultative anaerobic bacterial strain, designated ATCC 27380T, was isolated from heat-stressed soil of Cape Canaveral, Florida, USA. Growth was observed at 20-42 °C (optimum, 37 °C), at pH 6.0-10.0 (optimum pH 7.0) and in the presence of 0.5-3 % NaCl (optimum 0.5 %). The cell wall contained meso-diaminopimelic acid as the diagnostic amino acid and the isoprenoid quinone was MK-7. The polar lipids present were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and one unknown phospholipid. The main fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing affiliated strain ATCC 27380T to the genus Paenibacillus, and showed the highest sequence similarity to Paenibacillus rigui JCM 16352T (97.0 %). The other closely related type strains exhibited 16S rRNA gene sequence similarity values below 95.9 %. The draft genome of ATCC 27380T had a size of 4,361,187 bases, with a G+C content of 51.0 %. The average nucleotide identity and in silico DNA-DNA hybridization values between strain ATCC 27380T and P. rigui JCM 16352T were 72.5% and 18.5 %, respectively, which were below the threshold suggested for species differentiation (96% and 70 %, respectively). The average amino acid identity between strain ATCC 27380T and P. rigui JCM 16352T was 68.72 %, which was above the suggested genus level demarcation of 65 %. Based on phenotypic, genotypic and chemotaxonomic data, strain ATCC 27380T represents a novel species in the genus Paenibacillus, for which the name Paenibacillusxerothermodurans sp. nov. (=DSM 520T=NRRL NRS-1629T=ATCC 27380T) is proposed.
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Affiliation(s)
- Navjot Kaur
- 1Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Arman Seuylemezian
- 2Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - Prashant P Patil
- 3Bacterial Genomics & Evolution Lab, CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
| | - Prabhu Patil
- 3Bacterial Genomics & Evolution Lab, CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
| | - Srinivasan Krishnamurti
- 1Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Joseph Varelas
- 4Universities Space Research Association, NASA Ames Research Center, Moffett Field, California, 94035, USA
| | - David J Smith
- 5NASA, Space Biosciences Research Branch, NASA Ames Research Center, Moffett Field, California, 94035, USA
| | - Shanmugam Mayilraj
- 1Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Parag Vaishampayan
- 2Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
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Pal D, Kaur N, Sudan SK, Bisht B, Krishnamurthi S, Mayilraj S. Acidovorax kalamii sp. nov., isolated from a water sample of the river Ganges. Int J Syst Evol Microbiol 2018; 68:1719-1724. [DOI: 10.1099/ijsem.0.002736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Deepika Pal
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Navjot Kaur
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Sarabjeet Kour Sudan
- Division of protein science and Engineering, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Bhawana Bisht
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Srinivasan Krishnamurthi
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
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Pal M, Kumari M, Kiran S, Salwan R, Mayilraj S, Chhibber S, Gulati A. Chryseobacterium glaciei sp. nov., isolated from the surface of a glacier in the Indian trans-Himalayas. Int J Syst Evol Microbiol 2018; 68:865-870. [PMID: 29458480 DOI: 10.1099/ijsem.0.002600] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mohinder Pal
- CSIR-Institute of Himalayan Bioresource Technology, Palampur (HP)-176 061, India
| | - Munesh Kumari
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shashi Kiran
- CSIR-Institute of Himalayan Bioresource Technology, Palampur (HP)-176 061, India
| | - Richa Salwan
- CSIR-Institute of Himalayan Bioresource Technology, Palampur (HP)-176 061, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160 036, India
| | - Sanjay Chhibber
- Department of Microbiology, Panjab University, Chandigarh 160 014, India
| | - Arvind Gulati
- CSIR-Institute of Himalayan Bioresource Technology, Palampur (HP)-176 061, India
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Takeo M, Kimura K, Mayilraj S, Inoue T, Tada S, Miyamoto K, Kashiwa M, Ikemoto K, Baranwal P, Kato D, Negoro S. Biosynthetic Pathway and Genes of Chitin/Chitosan-Like Bioflocculant in the Genus Citrobacter. Polymers (Basel) 2018; 10:polym10030237. [PMID: 30966272 PMCID: PMC6414854 DOI: 10.3390/polym10030237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 01/23/2018] [Revised: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 11/17/2022] Open
Abstract
Chitin/chitosan, one of the most abundant polysaccharides in nature, is industrially produced as a powder or flake form from the exoskeletons of crustaceans such as crabs and shrimps. Intriguingly, many bacterial strains in the genus Citrobacter secrete a soluble chitin/chitosan-like polysaccharide into the culture medium during growth in acetate. Because this polysaccharide shows strong flocculation activity for suspended solids in water, it can be used as a bioflocculant (BF). The BF synthetic pathway of C. freundii IFO 13545 is expected from known bacterial metabolic pathways to be as follows: acetate is metabolized in the TCA cycle and the glyoxylate shunt via acetyl-CoA. Next, fructose 6-phosphate is generated from the intermediates of the TCA cycle through gluconeogenesis and enters into the hexosamine synthetic pathway to form UDP-N-acetylglucosamine, which is used as a direct precursor to extend the BF polysaccharide chain. We conducted the draft genome sequencing of IFO 13545 and identified all of the candidate genes corresponding to the enzymes in this pathway in the 5420-kb genome sequence. Disruption of the genes encoding acetyl-CoA synthetase and isocitrate lyase by homologous recombination resulted in little or no growth on acetate, indicating that the cell growth depends on acetate assimilation via the glyoxylate shunt. Disruption of the gene encoding glucosamine 6-phosphate synthase, a key enzyme for the hexosamine synthetic pathway, caused a significant decrease in flocculation activity, demonstrating that this pathway is primarily used for the BF biosynthesis. A gene cluster necessary for the polymerization and secretion of BF, named bfpABCD, was also identified for the first time. In addition, quantitative RT-PCR analysis of several key genes in the expected pathway was conducted to know their expression in acetate assimilation and BF biosynthesis. Based on the data obtained in this study, an overview of the BF synthetic pathway is discussed.
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Affiliation(s)
- Masahiro Takeo
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Kazuyuki Kimura
- Hyogo Analysis Center Co., Ltd., 4-10-8 Seimondori, Hirohata, Himeji, Hyogo 671-1116, Japan.
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh-160 036, India.
| | - Takuya Inoue
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Shohei Tada
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Kouki Miyamoto
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Masami Kashiwa
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Keishi Ikemoto
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Priyanka Baranwal
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
| | - Daiichiro Kato
- Department of Chemistry and Bioscience, Graduate School of Science and Engineering, Kagoshima 890-8580, Japan.
| | - Seiji Negoro
- Department of Applied Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
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Chander AM, Kochhar R, Dhawan DK, Bhadada SK, Mayilraj S. Genome sequence and comparative genomic analysis of a clinically important strain CD11-4 of Janibacter melonis isolated from celiac disease patient. Gut Pathog 2018; 10:2. [PMID: 29387173 PMCID: PMC5778662 DOI: 10.1186/s13099-018-0229-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/06/2018] [Indexed: 12/22/2022] Open
Abstract
Background Janibacter melonis and other member of this genus are known to cause bacteremia and serious clinical comorbidities, but there is no study reporting about pathogenicity attributes of J. melonis. Janibacter terrae is known to cause lethal infection. Reporting the genome of J. melonis CD11-4 and comparative genomics with other members of genus has provided some novel insights that can enable us to understand the mechanisms responsible for its pathogenicity in humans. Results Comparative genomic analysis by Rapid Annotation Server and Technology revealed the presence of similar virulence determinant genes in both J. terrae NBRC 107853T and J. melonis CD11-4. Like J. terrae NBRC 107853T, J. melonis CD11-4 contained two genes responsible for resistance against β-lactam class of antibiotics and two genes for resistance against fluoroquinolones. Interestingly, J. melonis CD11-4 contained a unique gene coding for multidrug resistance efflux pumps unlike all other members of this genus. It also contained two genes involved in Toxin-antitoxin Systems that were absent in J. terrae NBRC 107853T but were present in some other members of genus. Conclusions Genome annotations of J. melonis CD11-4 revealed that it contained similar or more virulence repertoire like J. terrae NBRC 107853T. Like other gut pathogens, J. melonis possesses key virulence determinant genes for antibiotic resistance, invasion, adhesion, biofilm formation, iron acquisition and to cope with stress response, thereby indicating that strain J. melonis CD11-4 could be a gut pathogen.
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Affiliation(s)
- Atul Munish Chander
- 1Department of Biophysics, Panjab University, Chandigarh, India.,3Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Kochhar
- 2Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Sanjay Kumar Bhadada
- 3Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Shanmugam Mayilraj
- 4Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh, 160036 India
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Sudan SK, Pal D, Bisht B, Kumar N, Chaudhry V, Patil P, Sahni G, Mayilraj S, Krishnamurthi S. Pseudomonas fluvialis sp. nov., a novel member of the genus Pseudomonas isolated from the river Ganges, India. Int J Syst Evol Microbiol 2018; 68:402-408. [DOI: 10.1099/ijsem.0.002520] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sarabjeet Kour Sudan
- Division of Protein Science and Engineering, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Deepika Pal
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Bhawana Bisht
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Narender Kumar
- Division of Protein Science and Engineering, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Vasvi Chaudhry
- Bacterial Genomics and Evolution Lab, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Prabhu Patil
- Bacterial Genomics and Evolution Lab, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Girish Sahni
- Division of Protein Science and Engineering, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Srinivasan Krishnamurthi
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, 160 036, India
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Pal D, Bhardwaj A, Sudan SK, Kaur N, Kumari M, Bisht B, Vyas B, Krishnamurthi S, Mayilraj S. Thauera propionica sp. nov., isolated from downstream sediment sample of the river Ganges, Kanpur, India. Int J Syst Evol Microbiol 2018; 68:341-346. [DOI: 10.1099/ijsem.0.002508] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Deepika Pal
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Ayanka Bhardwaj
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Sarabjeet Kour Sudan
- Division of Protein Science and Engineering, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Navjot Kaur
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Munesh Kumari
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Bhawana Bisht
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Bhawna Vyas
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Srinivasan Krishnamurthi
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shanmugam Mayilraj
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
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Pal D, Bhardwaj A, Kaur N, Sudan SK, Bisht B, Kumari M, Vyas B, Krishnamurthi S, Mayilraj S. Fictibacillus aquaticus sp. nov., isolated from downstream river water. Int J Syst Evol Microbiol 2017; 68:160-164. [PMID: 29116040 DOI: 10.1099/ijsem.0.002474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic bacterial strain, GDSW-R2A3T, was isolated from a downstream water sample collected from the river Ganges, India. Analysis of the 16S rRNA gene sequence of strain GDSW-R2A3T revealed its affiliation to the family Bacillaceae. Further analysis using a polyphasic approach revealed that strain GDSW-R2A3T was most closely related to the genus Fictibacillus. Analysis of the almost-complete (1488 bp) 16S rRNA gene sequence of strain GDSW-R2A3T revealed the highest level of sequence similarity with Fictibacillus phosphorivorans CCM 8426T (98.3 %) and Fictibacillus nanhaiensis KCTC 13712T (98.3 %) followed by Fictibacillus barbaricus DSM 14730T (98.0 %). The digital DNA-DNA hybridization and average nucleotide identity (ANI) values between strain GDSW-R2A3T and the most closely related taxon, F. phosphorivorans CCM 8426T, were 20.3 and 78.2 %, respectively. The DNA G+C content of the strain was 44.2 mol%. The cell-wall amino acid was meso-diaminopimelic acid. Polar lipids present were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, three aminophospholipids, two phospholipids and one unidentified lipid; the major menaquinone was MK-7; iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0 were the major fatty acids. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, it can be concluded that strain GDSW-R2A3T represents a novel species of the genus Fictibacillus, for which the name Fictibacillus aquaticus sp. nov. is proposed. The type strain is GDSW-R2A3T (=VTCC-B-910015T=CCM 8782T).
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Affiliation(s)
- Deepika Pal
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Ayanka Bhardwaj
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Navjot Kaur
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Sarabjeet Kour Sudan
- Division of Protein Science and Engineering, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Bhawana Bisht
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Munesh Kumari
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Bhawna Vyas
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Srinivasan Krishnamurthi
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shanmugam Mayilraj
- MTCC- Microbial Type Culture Collection and Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh 160 036, India
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Chander AM, Kaur G, Kaur G, Maurya SK, Nadeem S, Kochhar R, Dhawan DK, Bhadada SK, Agrewala JN, Mayilraj S. Comparative genomic analysis of Mycobacterium immunogenum strain CD11_6, a new potential vaccine strain against Mycobacterium tuberculosis. Can J Biotech 2017. [DOI: 10.24870/cjb.2017-a117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Verma A, Ojha AK, Pal Y, Kumari P, Schumann P, Gruber-Vodicka H, Dastager SG, Natarajan RK, Mayilraj S, Krishnamurthi S. An investigation into the taxonomy of “ Bacillus aminovorans ” and its reclassification to the genus Domibacillus as Domibacillus aminovorans sp. nov. Syst Appl Microbiol 2017; 40:458-467. [DOI: 10.1016/j.syapm.2017.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/11/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
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Verma A, Pal Y, Khatri I, Ojha AK, Gruber-Vodicka H, Schumann P, Dastager S, Subramanian S, Mayilraj S, Krishnamurthi S. Examination into the taxonomic position of Bacillus thermotolerans Yang et al., 2013, proposal for its reclassification into a new genus and species Quasibacillus thermotolerans gen. nov., comb. nov. and reclassification of B. encimensis Dastager et al., 2015 as a later heterotypic synonym of B. badius. Syst Appl Microbiol 2017; 40:411-422. [PMID: 28947104 DOI: 10.1016/j.syapm.2017.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 07/11/2017] [Accepted: 07/26/2017] [Indexed: 11/28/2022]
Abstract
Two novel Gram-staining positive, rod-shaped, moderately halotolerant, endospore forming bacterial strains 5.5LF 38TD and 5.5LF 48TD were isolated and taxonomically characterized from a landfill in Chandigarh, India. The analysis of 16S rRNA gene sequences of the strains confirmed their closest identity to Bacillus thermotolerans SgZ-8T with 99.9% sequence similarity. A comparative phylogenetic analysis of strains 5.5LF 38TD, 5.5LF 48TD and B. thermotolerans SgZ-8T confirmed their separation into a novel genus with B. badius and genus Domibacillus as the closest phylogenetic relatives. The major fatty acids of the strains are iso-C15:0 and iso-C16:0 and MK-7 is the only quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The digital DNA-DNA hybridization (DDH) and ortho average nucleotide identity (ANI) values calculated through whole genome sequences indicated that the three strains showed low relatedness with their phylogenetic neighbours. Based on evidences from phylogenomic analyses and polyphasic taxonomic characterization we propose reclassification of the species B. thermotolerans into a novel genus named Quasibacillus thermotolerans gen. nov., comb. nov with the type strain SgZ-8T (=CCTCC AB2012108T=KACC 16706T). Further our analyses also revealed that B. encimensis SGD-V-25T is a later heterotypic synonym of Bacillus badius DSM 23T.
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Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Yash Pal
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Indu Khatri
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Anup Kumar Ojha
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Harald Gruber-Vodicka
- Max-Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Peter Schumann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, GmBH, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
| | - Syed Dastager
- NCIM Resource Center, CSIR-National Chemical Laboratory, Pune 411 008, Maharashtra, India
| | | | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India.
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Kiran S, Swarnkar MK, Mayilraj S, Tewari R, Gulati A. Paenibacillus ihbetae sp. nov., a cold-adapted antimicrobial producing bacterium isolated from high altitude Suraj Tal Lake in the Indian trans-Himalayas. Syst Appl Microbiol 2017; 40:430-439. [PMID: 28882448 DOI: 10.1016/j.syapm.2017.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 01/02/2017] [Revised: 05/01/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
The assessment of bacterial diversity and bioprospection of the high-altitude lake Suraj Tal microorganisms for potent antimicrobial activities revealed the presence of two Gram-stain-variable, endospore-forming, rod-shaped, aerobic bacteria, namely IHBB 9852T and IHBB 9951. Phylogenetic analysis based on 16S rRNA gene sequence showed the affiliation of strains IHBB 9852T and IHBB 9951 within the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus lactis DSM 15596T (97.8% and 97.7%) and less than 95.9% similarity to other species of the genus Paenibacillus. DNA-DNA relatedness among strains IHBB 9852T and IHBB 9951 was 90.2%, and with P. lactis DSM 15596T, was 52.7% and 52.4%, respectively. The novel strains contain anteiso-C15:0, iso-C15:0, C16:0 and iso-C16:0 as major fatty acids, and phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol were predominant polar lipids. The DNA G+C content for IHBB 9852T and IHBB 9951 was 52.1 and 52.2mol%. Based on the results of phenotypic and genomic characterisations, we concluded that strains IHBB 9852T and IHBB 9951 belong to a novel Paenibacillus species, for which the name Paenibacillus ihbetae sp. nov. is proposed. The type strain is IHBB 9852T (=MTCC 12459T=MCC 2795T=JCM 31131T=KACC 19072T; DPD TaxonNumber TA00046) and IHBB 9951 (=MTCC 12458=MCC 2794=JCM 31132=KACC 19073) is a reference strain.
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Affiliation(s)
- Shashi Kiran
- Microbial Prospection Division, CSIR-Institute of Himalayan Bioresource Technology, P.O. Box 6, Palampur, H.P. 176 061, India; Department of Microbial Biotechnology, Panjab University, Chandigarh 160 014, India
| | - Mohit Kumar Swarnkar
- Microbial Prospection Division, CSIR-Institute of Himalayan Bioresource Technology, P.O. Box 6, Palampur, H.P. 176 061, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - Rupinder Tewari
- Department of Microbial Biotechnology, Panjab University, Chandigarh 160 014, India
| | - Arvind Gulati
- Microbial Prospection Division, CSIR-Institute of Himalayan Bioresource Technology, P.O. Box 6, Palampur, H.P. 176 061, India.
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Ojha AK, Verma A, Pal Y, Bhatt D, Mayilraj S, Krishnamurthi S. Marinomonas epiphytica sp. nov., isolated from a marine intertidal macroalga. Int J Syst Evol Microbiol 2017; 67:2746-2751. [PMID: 28771118 DOI: 10.1099/ijsem.0.002014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, aerobic marine bacterial strain, SAB-3T, was isolated from brown macroalgae (Dictyota sp.) growing in the Arabian sea, Goa, India. The strain grew optimally at 30 °C, with 2.0-4.0 % (w/v) NaCl and at pH 7.0 on marine agar medium. Strain SAB-3T was unable to hydrolyse aesculin and did not grow in the presence of rifamycin but showed resistance to antibiotics such as cefadroxil and co-trimoxazole. The major fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 0, and Q-8 was the major ubiquinone. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.0 mol%. 16S rRNA gene sequencing and phylogenetic analysis indicated that the strain was a member of the genus Marinomonas with Marinomonas aquiplantarum IVIA-Po-159T (97.6 % similarity), Marinomonas posidonica IVIA-Po-181T (97.5 %) and Marinomonas dokdonensis DSM 17202T (97.4 %) as the closest relatives. Whole genome relatedness determined through DNA-DNA hybridization revealed values of 40-50 % (below the 70 % threshold recommended for species delineation) with the above three species, thus confirming it as representing a distinct and novel species of the genus Marinomonas for which the name Marinomonas epiphytica sp. nov. is proposed. The type strain is SAB-3T (=JCM 31365T=KCTC 52293T=MTCC 12569T).
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Affiliation(s)
- Anup Kumar Ojha
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Ashish Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Yash Pal
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Deepak Bhatt
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
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Verma A, Ojha AK, Dastager SG, Natarajan R, Mayilraj S, Krishnamurthi S. Domibacillus mangrovi sp. nov. and Domibacillus epiphyticus sp. nov., isolated from marine habitats of the central west coast of India. Int J Syst Evol Microbiol 2017; 67:3063-3070. [DOI: 10.1099/ijsem.0.002085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Anup Kumar Ojha
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Syed G. Dastager
- NCIM-Resource Centre, CSIR-National Chemical Laboratory, Pune-411008, Maharashtra, India
| | - Rameshkumar Natarajan
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram-695019, Kerala, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
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Checinska Sielaff A, Kumar RM, Pal D, Mayilraj S, Venkateswaran K. Solibacillus kalamii sp. nov., isolated from a high-efficiency particulate arrestance filter system used in the International Space Station. Int J Syst Evol Microbiol 2017; 67:896-901. [DOI: 10.1099/ijsem.0.001706] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Rajendran Mathan Kumar
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Deepika Pal
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
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Chander AM, Nair RG, Kaur G, Kochhar R, Dhawan DK, Bhadada SK, Mayilraj S. Genome Insight and Comparative Pathogenomic Analysis of Nesterenkonia jeotgali Strain CD08_7 Isolated from Duodenal Mucosa of Celiac Disease Patient. Front Microbiol 2017; 8:129. [PMID: 28210247 PMCID: PMC5288335 DOI: 10.3389/fmicb.2017.00129] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 07/26/2016] [Accepted: 01/18/2017] [Indexed: 12/30/2022] Open
Abstract
Species of the genus Nesterenkonia have been isolated from different ecological niches, especially from saline habitats and reported as weak human pathogens causing asymptomatic bacteraemia. Here, for the first time we are reporting the genome sequence and pathogenomic analysis of a strain designated as CD08_7 isolated from the duodenal mucosa of a celiac disease patient, identified as Nesterenkonia jeotgali. To date, only five strains of the genus Nesterenkonia (N. massiliensis strain NP1T, Nesterenkonia sp. strain JCM 19054, Nesterenkonia sp. strain F and Nesterenkonia sp. strain AN1) have been whole genome sequenced and annotated. In the present study we have mapped and compared the virulence profile of N. jeotgali strain CD08_7 along with other reference genomes which showed some characteristic features that could contribute to pathogenicity. The RAST (Rapid Annotation using Subsystem Technology) based genome mining revealed more genes responsible for pathogenicity in strain CD08_7 when compared with the other four sequenced strains. The studied categories were resistance to antibiotic and toxic compounds, invasion and intracellular resistance, membrane transport, stress response, osmotic stress, oxidative stress, phages and prophages and iron acquisition. A total of 1431 protein-encoding genes were identified in the genome of strain CD08_7 among which 163 were predicted to contribute for pathogenicity. Out of 163 genes only 59 were common to other genome, which shows the higher levels of genetic richness in strain CD08_7 that may contribute to its functional versatility. This study provides a comprehensive analysis on genome of N. jeotgali strain CD08_7 and possibly indicates its importance as a clinical pathogen.
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Affiliation(s)
- Atul M Chander
- Department of Biophysics, Panjab UniversityChandigarh, India; Department of Endocrinology, Postgraduate Institute of Medical Education and ResearchChandigarh, India
| | - Ramesan G Nair
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology Chandigarh, India
| | - Gurwinder Kaur
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology Chandigarh, India
| | - Rakesh Kochhar
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research Chandigarh, India
| | | | - Sanjay K Bhadada
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research Chandigarh, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology Chandigarh, India
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Pal D, Mathan Kumar R, Kaur N, Kumar N, Kaur G, Singh NK, Krishnamurthi S, Mayilraj S. Bacillus maritimus sp. nov., a novel member of the genus Bacillus isolated from marine sediment. Int J Syst Evol Microbiol 2017; 67:60-66. [DOI: 10.1099/ijsem.0.001569] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Deepika Pal
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Rajendran Mathan Kumar
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Navjot Kaur
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Narender Kumar
- Division of Protein Science and Engineering, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Gurwinder Kaur
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Nitin Kumar Singh
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Srinivasan Krishnamurthi
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shanmugam Mayilraj
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR – Institute of Microbial Technology, Chandigarh 160 036, India
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Verma A, Ojha AK, Kumari P, Sundharam SS, Mayilraj S, Krishnamurthi S. Luteimonas padinae sp. nov., an epiphytic bacterium isolated from an intertidal macroalga. Int J Syst Evol Microbiol 2016; 66:5444-5451. [DOI: 10.1099/ijsem.0.001539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Anup Kumar Ojha
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Parveen Kumari
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Shiva S. Sundharam
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
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Kaur G, Arora A, Sathyabama S, Mubin N, Verma S, Mayilraj S, Agrewala JN. Genome sequencing, assembly, annotation and analysis of Staphylococcus xylosus strain DMB3-Bh1 reveals genes responsible for pathogenicity. Gut Pathog 2016; 8:55. [PMID: 27833663 PMCID: PMC5101723 DOI: 10.1186/s13099-016-0139-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 11/01/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Staphylococcus xylosus is coagulase-negative staphylococci (CNS), found occasionally on the skin of humans but recurrently on other mammals. Recent reports suggest that this commensal bacterium may cause diseases in humans and other animals. In this study, we present the first report of whole genome sequencing of S. xylosus strain DMB3-Bh1, which was isolated from the stool of a mouse. RESULTS The draft genome of S. xylosus strain DMB3-Bh1 consisted of 2,81,0255 bp with G+C content of 32.7 mol%, 2623 predicted coding sequences (CDSs) and 58 RNAs. The final assembly contained 12 contigs of total size 2,81,0255 bp with N50 contig length of 4,37,962 bp and the largest contig assembled measured 7,61,338 bp. Further, an interspecies comparative genomic analysis through rapid annotation using subsystem technology server was achieved with Staphylococcus aureus RF122 that revealed 36 genes having similarity with S. xylosus DMB3-Bh1. 35 genes encoded for virulence, disease and defense and 1 gene encoded for phages, prophages and transposable elements. CONCLUSIONS These results suggest co linearity in genes between S. xylosus DMB3-Bh1 and S. aureus RF122 that contribute to pathogenicity and might be the result of horizontal gene transfer. The study indicates that S. xylosus DMB3-Bh1 may be a potential emerging pathogen for rodents.
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Affiliation(s)
- Gurwinder Kaur
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036 India
| | - Amit Arora
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036 India
| | - Sathyaseelan Sathyabama
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036 India
| | - Nida Mubin
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036 India
| | - Sheenam Verma
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036 India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036 India
| | - Javed N. Agrewala
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036 India
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Bajaj A, Kumar A, Yadav S, Kaur G, Bala M, Singh NK, Mathan Kumar R, Manickam N, Mayilraj S. Isolation and characterization of a novel Gram-negative bacterium Chromobacterium alkanivorans sp. nov., strain IITR-71T degrading halogenated alkanes. Int J Syst Evol Microbiol 2016; 66:5228-5235. [PMID: 27619232 DOI: 10.1099/ijsem.0.001500] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a Gram-stain negative, non-violaceinpigmented bacterium isolated from an insecticide-contaminated site was characterized by a polyphasic approach. The bacterium was able to grow on three different halogenated compounds namely 1-hlorobutane, 1-hloropropane and 1,2-ichloroethane. As a critical step in the degradation of these haloalkanes, stoichiometric amounts of dechlorination were estimated. Based on selective enrichment method for three months, using a highly contaminated mixed chemical soil, a bacterium was obtained and designated as IITR-71T. Its versatility and novelty led us to further characterize it by polyphasic taxonomy. The 16S rRNA gene sequence (1446 bases) comparison showed highest similarity with those of members of the genus Chromobacterium with the most closely related species to strain IITR-71T being Chromobacterium aquaticum (99.3 %) followed by Chromobacterium haemolyticum (98.6 %) and Chromobacterium piscinae (97.1 %). The major ubiquinone was Q-8. Predominant polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The DNA G+C content of IITR-71T was estimated to be 61.2 mol%. The genotypic and phenotypic distinctiveness of IITR-71T and its phylogenetic relationships indicate that IITR-71T represents a novel species, for which the name Chromobacterium alkanivorans sp. nov. is proposed. The type strain is IITR-71T (=MTCC 11059T=JCM 30068T=KCTC 52433T).
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Affiliation(s)
- Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Anand Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Shivani Yadav
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Gurwinder Kaur
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Monu Bala
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Nitin Kumar Singh
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Rajendran Mathan Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, 160 036, India
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Kaur G, Sathyabama S, Arora A, Verma S, Mubin N, Agrewala JN, Mayilraj S. Erratum to: Genome sequencing, annotation and comparative genomic analysis of Shigella dysenteriae strain SD1D. Gut Pathog 2016; 8:38. [PMID: 27516810 PMCID: PMC4980780 DOI: 10.1186/s13099-016-0120-6] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 07/28/2016] [Indexed: 11/10/2022] Open
Abstract
[This corrects the article DOI: 10.1186/1757-4749-6-28.].
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Affiliation(s)
- Gurwinder Kaur
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Sathyaseelan Sathyabama
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Amit Arora
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Sheenam Verma
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Nida Mubin
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Javed N Agrewala
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036 India
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Kaur G, Kumar N, Mual P, Kumar A, Kumar RM, Mayilraj S. Brachybacterium aquaticum sp. nov., a novel actinobacterium isolated from seawater. Int J Syst Evol Microbiol 2016; 66:4705-4710. [PMID: 27514821 DOI: 10.1099/ijsem.0.001414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A pale-yellowish bacterium, strain KWS-1T, was isolated from seawater during a study of the bacterial diversity of the marine environment of the Kanyakumari coastal region of the Bay of Bengal, India, and was studied by using a polyphasic taxonomic approach. Strain KWS-1T had morphological and chemotaxonomic properties (cell-wall diamino acid, menaquinone and fatty acid profile) consistent with its classification in the genus Brachybacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain KWS-1T was related most closely to Brachybacterium paraconglomeratum JCM 17781T, followed by Brachybacterium saurashtrense DSM 23186T, Brachybacterium gingengisoli JCM 19356T, Brachybacterium faecium JCM 11609T and Brachybacterium conglomeratum JCM 11608T (98.45, 98.24, 98.12, 98.10 and 98.10 % similarity, respectively), whereas the sequence similarity values with respect to the other Brachybacterium species with validly published names were between 97.4 and 94.2 %. However, the DNA-DNA hybridization values between strain KWS-1T and the five most closely related species were less than the threshold value for species discrimination. The major lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine and the major quinone was menaquinone MK-7. The DNA G+C content of strain KWS-1T was 71.8 mol%. The above data in combination with the phenotypic distinctiveness of strain KWS-1T from other reference strains clearly indicate that the strain represents a novel species, for which the name Brachybacterium aquaticum sp. nov. is proposed. The type strain is KWS-1T (=MTCC 11836T=DSM 28796T=JCM 30059T).
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Affiliation(s)
- Gurwinder Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Narender Kumar
- Division of Protein Science & Engineering, CSIR - Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Poonam Mual
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Anand Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Rajendran Mathan Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Shanmugam Mayilraj
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh, 160 036, India
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Kaur G, Mual P, Kumar N, Verma A, Kumar A, Krishnamurthi S, Mayilraj S. Microbacterium aureliae sp. nov., a novel actinobacterium isolated from Aurelia aurita, the moon jellyfish. Int J Syst Evol Microbiol 2016; 66:4665-4670. [PMID: 27506590 DOI: 10.1099/ijsem.0.001407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a lemon-yellow-pigmented actinobacterium, strain JF-6T, isolated from Aurelia aurita, the moon jellyfish, collected from the Bay of Bengal coast, Kanyakumari, India, was determined using a polyphasic approach. The strain had phenotypic and chemotaxonomic properties that were consistent with its classification in the genus Microbacterium. Alignment of the 16S rRNA gene sequence of strain JF-6T with sequences from Microbacterium arthrosphaerae CC-VM-YT, Microbacterium yannicii G72T, Microbacterium trichothecenolyticum IFO 15077T, Microbacterium flavescens DSM 20643T, Microbacterium insulae DS-66T, Microbacterium resistens DMMZ 1710T and Microbacterium thalassium IFO 16060T revealed similarities of 98.95, 98.76, 98.43, 98.41, 98.41, 98.26 and 98.22 %, respectively. However, the levels of DNA-DNA relatedness with its closest phylogenetic neighbours confirmed that it represents a novel species within the genus. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The major menaquinones detected for strain JF-6T were MK-13 and MK-12. The diamino acid in the cell-wall peptidoglycan was ornithine and the peptidoglycan was type B2β (Glu/Hyg-Gly-d-Orn). The DNA G+C content was 69.4 mol%. Based on these differences, strain JF-6T (=MTCC 11843T=JCM 30060T=KCTC 39828T) should be classified as the type strain of a novel species of Microbacterium, for which the name Microbacterium aureliae sp. nov. is proposed.
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Affiliation(s)
- Gurwinder Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160 036, India
| | - Parveen Mual
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160 036, India
| | - Narender Kumar
- Division of Protein Science & Engineering, CSIR - Institute of Microbial Technology, Chandigarh 160 036, India
| | - Ashish Verma
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160 036, India
| | - Anand Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160 036, India
| | - Srinivasan Krishnamurthi
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160 036, India
| | - Shanmugam Mayilraj
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160 036, India
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Mual P, Singh NK, Verma A, Schumann P, Krishnamurthi S, Dastager S, Mayilraj S. Reclassification of Bacillus isronensis Shivaji et al. 2009 as Solibacillus isronensis comb. nov. and emended description of genus Solibacillus Krishnamurthi et al. 2009. Int J Syst Evol Microbiol 2016; 66:2113-2120. [DOI: 10.1099/ijsem.0.000982] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Poonam Mual
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
| | - Nitin Kumar Singh
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
| | - Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
| | - Peter Schumann
- Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen,Inhoffenstrasse 7b, D-38124, Braunschweig,Germany
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
| | - Syed Dastager
- NCIM Resource Center, CSIR – National Chemical Laboratory,Pune 411 008, Maharashtra,India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), Institute of Microbial Technology,Sector 39A, Chandigarh 160 036,India
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Kumar RM, Kaur G, Kumar A, Bala M, Singh NK, Kaur N, Kumar N, Mayilraj S. Taxonomic description and genome sequence of Bacillus campisalis sp. nov., a member of the genus Bacillus isolated from a solar saltern. Int J Syst Evol Microbiol 2016; 65:3235-3240. [PMID: 26296567 DOI: 10.1099/ijsem.0.000400] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of a Gram-stain positive bacterium isolated from a solar saltern sample collected from Kanyakumari, coastal region of the Bay of Bengal, India, was analysed by using a polyphasic approach. The isolated strain, designated SA2-6T, had phenotypic characteristics that matched those of the genus Bacillus. The 16S rRNA gene sequence (1493 bases) of the novel strain was compared with those of previously studied Bacillus type strains and confirmed that the strain belongs to the genus Bacillus and was moderately closely related to the type strain of Bacillus foraminis at 97.5 % 16S rRNA gene sequence similarity, followed by those of Bacillus thioparans (96.9 %), Bacillus subterraneus (96.8 %), Bacillus jeotgali (96.6 %), Bacillus selenatarsenatis (96.6 %) and Bacillus boroniphilus (96.6 %). 16S rRNA gene sequence analysis indicated that strain SA2-6T differs from all other species of the genus Bacillus by at least 2.5 %. It contained MK-7 as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, and iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids. Major lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data from this polyphasic study, strain SA2-6T is considered to represent a novel species of the genus Bacillus, for which the name Bacillus campisalis sp. nov. is proposed. The type strain is SA2-6T ( = MTCC 11848T = DSM 28801T). The draft genome of strain SA2-6T consisted of 5 183 363 bp with G+C content of 45.44 mol%, 5352 predicted coding sequences, 191 RNAs and 479 subsystems.
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Affiliation(s)
- Rajendran Mathan Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Gurwinder Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Anand Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Monu Bala
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Nitin Kumar Singh
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Navjot Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Narender Kumar
- Division of Protein Science & Engineering, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
| | - Shanmugam Mayilraj
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR- Institute of Microbial Technology, Chandigarh, 160 036, India
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Kumar RM, Kaur G, Kumar N, Kumar A, Singh NK, Bala M, Kaur N, Mayilraj S. Taxonomic description and genome sequence of Salinicoccus sediminis sp. nov., a halotolerant bacterium isolated from marine sediment. Int J Syst Evol Microbiol 2016; 65:3794-3799. [PMID: 26956594 DOI: 10.1099/ijsem.0.000495] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, coccoid, halotolerant bacterial strain, designated SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurred at temperatures in the range 25-37 °C (optimum 30 °C), at pH 7.0-11.0 (optimum pH 8.0) and at NaCl concentrations of up to 25.0% (optimum 15.0%). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6%) followed by Salinicoccus halodurans W24T (96.6%). The predominant polar lipids were diphosphatidylglycerol, phosphatidylinositol and phosphatidylglycerol. The major cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0 and anteiso-C17:0. The draft genome of strain SV-16T consisted of 2,591,284 bp with a DNA G+C content of 48.7 mol%. On the basis of the phenotypic characteristics and genotypic distinctiveness of strain SV-16T, it should be classified within a novel species of the genus Salinicoccus, for which the name Salinicoccus sediminis sp. nov. is proposed. The type strain is SV-16T ( = MTCC 11832T = DSM 28797T).
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Affiliation(s)
- Rajendran Mathan Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Gurwinder Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Narender Kumar
- Division of protein science & Engineering, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Anand Kumar
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Nitin Kumar Singh
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Monu Bala
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Navjot Kaur
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
| | - Shanmugam Mayilraj
- MTCC - Microbial Type Culture Collection & Gene Bank, CSIR - Institute of Microbial Technology, Chandigarh 160036, India
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Gahlawat G, Shikha S, Chaddha BS, Chaudhuri SR, Mayilraj S, Choudhury AR. Microbial glycolipoprotein-capped silver nanoparticles as emerging antibacterial agents against cholera. Microb Cell Fact 2016; 15:25. [PMID: 26829922 PMCID: PMC4736657 DOI: 10.1186/s12934-016-0422-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/13/2016] [Indexed: 11/17/2022] Open
Abstract
Background With the increased number of cholera outbreaks and emergence of multidrug resistance in Vibrio cholerae strains it has become necessary for the scientific community to devise and develop novel therapeutic approaches against cholera. Recent studies have indicated plausibility of therapeutic application of metal nano-materials. Among these, silver nanoparticles (AgNPs) have emerged as a potential antimicrobial agent to combat infectious diseases. At present nanoparticles are mostly produced using physical or chemical techniques which are toxic and hazardous. Thus exploitation of microbial systems could be a green eco-friendly approach for the synthesis of nanoparticles having similar or even better antimicrobial activity and biocompatibility. Hence, it would be worth to explore the possibility of utilization of microbial silver nanoparticles and their conjugates as potential novel therapeutic agent against infectious diseases like cholera. Results The present study attempted utilization of Ochrobactrum rhizosphaerae for the production of AgNPs and focused on investigating their role as antimicrobial agents against cholera. Later the exopolymer, purified from the culture supernatant, was used for the synthesis of spherical shaped AgNPs of around 10 nm size. Further the exopolymer was characterized as glycolipoprotein (GLP). Antibacterial activity of the novel GLP–AgNPs conjugate was evaluated by minimum inhibitory concentration, XTT reduction assay, scanning electron microscopy (SEM) and growth curve analysis. SEM studies revealed that AgNPs treatment resulted in intracellular contents leakage and cell lysis. Conclusion The potential of microbially synthesized nanoparticles, as novel therapeutic agents, is still relatively less explored. In fact, the present study first time demonstrated that a glycolipoprotein secreted by the O. rhizosphaerae strain can be exploited for production of AgNPs which can further be employed to treat infectious diseases. Although this type of polymer has been obtained earlier from marine fungi and bacteria, none of these reports have studied the role of this polymer in AgNPs synthesis and its application in cholera therapy. Interestingly, the microbial GLP-capped AgNPs exhibited antibacterial activity against V. cholerae comparable to ciprofloxacin. Thus the present study may open up new avenues for development of novel therapeutic agents for treatment of infectious diseases.Development of novel therapeutic agents for treatment of cholera ![]()
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Affiliation(s)
- Geeta Gahlawat
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
| | - Sristy Shikha
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
| | | | | | - Shanmugam Mayilraj
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
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Kaur N, Arora A, Kumar N, Mayilraj S. Genome sequencing and annotation of Laceyella sacchari strain GS 1-1, isolated from hot spring, Chumathang, Leh, India. Genom Data 2015; 2:18-9. [PMID: 26484058 PMCID: PMC4535657 DOI: 10.1016/j.gdata.2013.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 09/18/2013] [Revised: 10/23/2013] [Accepted: 10/23/2013] [Indexed: 10/29/2022]
Abstract
We report the 3.3-Mb draft genome of Laceyella sacchari strain GS 1-1, isolated from hot spring water sample, Chumathang, Leh, India. Draft genome of strain GS 1-1 consists of 3, 324, 316 bp with a G + C content of 48.8% and 3429 predicted protein coding genes and 75 RNAs. Geobacillus thermodenitrificans strain NG80-2, Geobacillus kaustophilus strain HTA426 and Geobacillus sp. Strain G11MC16 are the closest neighbors of the strain GS 1-1.
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Affiliation(s)
- Navjot Kaur
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Amit Arora
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Narender Kumar
- Division of Protein Science & Engineering, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Chandigarh 160036, India
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Kumar A, Bajaj A, Mathan Kumar R, Kaur G, Kaur N, Kumar Singh N, Manickam N, Mayilraj S. Taxonomic description and genome sequence of Rheinheimera mesophila sp. nov., isolated from an industrial waste site. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijsem.0.000471] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-staining-negative gammaproteobacterium, designated IITR-13T, was isolated from a pesticide-contaminated soil and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, the strain showed the closest similarity (98.7 %) to Rheinheimera tangshanensis JA3-B52T followed by Rheinheimera texasensis A62-14BT (97.7 %) and Rheinheimera soli BD-d46T (97.3 %). The 16S rRNA gene sequence similarity of the novel strain to other members of the genus Rheinheimera was < 97.3 %. However, DNA–DNA hybridization between strain IITR-13T and the type strains of R. tangshanensis, R. texasensis and R. soli was 47.5 ± 0.6, 42.4 ± 0.4 and 39.8 ± 0.3 %, respectively; these values are less than 70 %, a threshold value for delineation of a novel species. The strain had C12 : 0 3-OH, C16 : 0, C17 : 1ω8c, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C18 : 1ω6c as the major fatty acids. The major isoprenoid quinones detected for strain IITR-13T were ubiquinone Q-8 and menaquinone MK-7.The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and seven unknown phospholipids. Based on phenotypic and chemotaxonomic characteristics and analysis of the 16S rRNA gene sequence, the novel strain should be assigned to a novel species, for which the name Rheinheimera mesophila sp. nov. is proposed, with the type strain IITR-13T ( = MTCC 12064T = DSM 29723T). Also, we report the draft genome sequence of Rheinheimera mesophila IITR-13T; the draft genome sequence includes 3 749 903 bases and comprises 3449 predicted coding sequences, with a G+C content of 47.8 %. It consists of 102 contigs (>1000 bp).
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Affiliation(s)
- Anand Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160 036, India
| | - Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow 226 001, India
| | - Rajendran Mathan Kumar
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160 036, India
| | - Gurwinder Kaur
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160 036, India
| | - Navjot Kaur
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160 036, India
| | - Nitin Kumar Singh
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160 036, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow 226 001, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology (IMTECH), Chandigarh 160 036, India
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Verma A, Mual P, Mayilraj S, Krishnamurthi S. Tamilnaduibacter salinus gen. nov., sp. nov., a halotolerant gammaproteobacterium within the family Alteromonadaceae, isolated from a salt pan in Tamilnadu, India. Int J Syst Evol Microbiol 2015; 65:3248-3255. [PMID: 26296662 DOI: 10.1099/ijsem.0.000401] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-negative, slow-growing, halotolerant strains with rod-shaped cells, designated as strains Mi-7T and Mi-8, which formed pin-point colonies on halophilic media were isolated during a study into the microbial diversity of a salt pan in the state of Tamilnadu, India. Both the strains had an obligate requirement for 1 % (w/v) NaCl for growth and were halotolerant, growing at NaCl concentrations of up to 20 % (w/v) in media. The strains, however, showed an inability to utilize the majority of substrates tested as sole carbon sources for growth and in fermentation reactions. Molecular phylogenetic analyses, based on 16S rRNA gene sequence revealed their closest phylogenetic neighbours to be members of the genus Marinobacter, with whom they showed the highest sequence similarity of 93.6 % and even less with the type strain of the type species, Marinobacter hydrocarbonoclasticus DSM 8798T (91.1 %). Similarities with other genera within the family Alteromonadaceae were below 91.0 %. However, the two strains were very closely related to each other with 99.9 % sequence similarity, and DNA–DNA hybridization analyses confirmed their placement in the same species. The DNA G+C content of both strains was 65 mol%. Using the polyphasic taxonomic data obtained from this study, strains Mi-7T and Mi-8 represent two strains of the same species of a novel genus for which the name Tamilnaduibacter salinus gen. nov., sp. nov., is proposed; the type strain of the novel species is Mi-7T ( = MTCC 12009T = DSM 28688T).
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Affiliation(s)
- Ashish Verma
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Poonam Mual
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
| | - Srinivasan Krishnamurthi
- Microbial Type Culture Collection & Gene Bank (MTCC), CSIR-Institute of Microbial Technology, Sec-39A, Chandigarh-160036, India
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Kaur H, Dolma K, Kaur N, Malhotra A, Kumar N, Dixit P, Sharma D, Mayilraj S, Choudhury AR. Marine microbe as nano-factories for copper biomineralization. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0432-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Khatri I, Singh NK, Subramanian S, Mayilraj S. Genome sequencing and annotation of Acinetobacter junii strain MTCC 11364. Genomics Data 2014; 2:13-5. [PMID: 26484056 PMCID: PMC4536018 DOI: 10.1016/j.gdata.2013.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 10/23/2013] [Accepted: 10/23/2013] [Indexed: 11/28/2022]
Abstract
The genus Acinetobacter consists of 31 validly published species ubiquitously distributed in nature and primarily associated with nosocomial infection. We report the 3.5 Mb draft genome of the Acinetobacter junii strain MTCC 11364. The genome has a G + C content of 38.0% and includes 3 rRNA genes (5S, 23S, 16S) and 64 aminoacyl-tRNA synthetase genes.
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Singh NK, Khatri I, Subramanian S, Mayilraj S. Genome sequencing and annotation of Acinetobacter gerneri strain MTCC 9824T. Genomics Data 2014; 2:7-9. [PMID: 26484054 PMCID: PMC4536119 DOI: 10.1016/j.gdata.2013.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 10/23/2013] [Accepted: 10/23/2013] [Indexed: 11/29/2022]
Abstract
The genus Acinetobacter consists of 31 validly published species ubiquitously distributed in nature and primarily associated with nosocomial infection. We report the 4.4 Mb genome of Acinetobacter gerneri strain MTCC 9824T. The genome has a G + C content of 38.0% and includes 3 rRNA genes (5S, 23S16S) and 64 aminoacyl-tRNA synthetase genes.
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Affiliation(s)
- Nitin Kumar Singh
- Microbial Type Culture Collection and Gene Bank (MTCC), Chandigarh 160036, India
| | - Indu Khatri
- Protein Science and Engineering, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
| | - Srikrishna Subramanian
- Protein Science and Engineering, CSIR-Institute of Microbial Technology, Chandigarh 160036, India
- Corresponding authors at: CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India. Tel.: + 91 1726665483, + 91 172 6665166; fax: + 91 172 2695215.
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), Chandigarh 160036, India
- Corresponding authors at: CSIR-Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India. Tel.: + 91 1726665483, + 91 172 6665166; fax: + 91 172 2695215.
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Bajaj A, Mayilraj S, Mudiam MKR, Patel DK, Manickam N. Isolation and functional analysis of a glycolipid producing Rhodococcus sp. strain IITR03 with potential for degradation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT). Bioresour Technol 2014; 167:398-406. [PMID: 25000395 DOI: 10.1016/j.biortech.2014.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 05/31/2014] [Accepted: 06/03/2014] [Indexed: 06/03/2023]
Abstract
A 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degrading bacterium strain IITR03 producing trehalolipid was isolated and characterized from a pesticides contaminated soil. The strain IITR03 was identified as a member of the genus Rhodococcus based on polyphasic studies. Under aqueous culture conditions, the strain IITR03 degraded 282 μM of DDT and could also utilize 10mM concentration each of 4-chlorobenzoic acid, 3-chlorobenzoic acid and benzoic acid as sole carbon and energy source. The catechol 1,2-dioxygenase enzyme activity resulted in conversion of catechol to form cis,cis-muconic acid. Cloning and sequencing of partial nucleotide sequence of catechol 1,2-dioxygenase gene (cat) from strain IITR03 revealed its similarity to catA gene present in Rhodococcus sp. strain Lin-2 (97% identity) and Rhodococcus strain AN22 (96% identity) degrading benzoate and aniline, respectively. The results suggest that the strain IITR03 could be useful for field bioremediation studies of DDT-residues and chlorinated aromatic compounds present in contaminated sites.
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Affiliation(s)
- Abhay Bajaj
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Shanmugam Mayilraj
- MTCC-Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | | | - Devendra Kumar Patel
- Analytical Chemistry Section, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicology Research, Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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Vaishampayan P, Roberts AH, Augustus A, Pukall R, Schumann P, Schwendner P, Mayilraj S, Salmassi T, Venkateswaran K. Deinococcus phoenicis sp. nov., an extreme ionizing-radiation-resistant bacterium isolated from the Phoenix Lander assembly facility. Int J Syst Evol Microbiol 2014; 64:3441-3446. [PMID: 25030518 DOI: 10.1099/ijs.0.063107-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated 1P10ME(T), which was resistant to extreme doses of ionizing radiation, pale-pink, non-motile, and a tetrad-forming coccoid was isolated from a cleanroom at the Kennedy Space Center, where the Phoenix spacecraft was assembled. Strain 1P10ME(T) showed optimum growth at 30 °C, with a pH range for growth of 6.5-9.0 and was highly sensitive to sodium chloride, growing only in medium with no added NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1P10ME(T) represents a novel member of the genus Deinococcus, with low sequence similarities (<93.5%) to recognized species of the genus Deinococcus. The predominant cellular fatty acid was C15:1ω6c. This novel strain exhibits extreme resistance to gamma radiation (D10 >8 kGy) and UV (D10 >1000 Jm(-2)). The results of our polyphasic taxonomic analyses suggest that strain 1P10ME(T) represents a novel species of the genus Deinococcus, for which the name Deinococcus phoenicis sp. nov. is proposed. The type strain is 1P10ME(T) ( = NRRL B-59546(T) = DSM 27173(T)).
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Affiliation(s)
- Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California, Institute of Technology, Pasadena, CA 91109, USA
| | - Anne Hayden Roberts
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Angela Augustus
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Petra Schwendner
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Tina Salmassi
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California, Institute of Technology, Pasadena, CA 91109, USA
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Kaur G, Sathyabama S, Arora A, Verma S, Mubin N, Agrewala JN, Mayilraj S. Genome sequencing, annotation and comparative genomic analysis of Shigella dysenteriae strain SD1D. Gut Pathog 2014; 6:28. [PMID: 25028600 PMCID: PMC4099087 DOI: 10.1186/1757-4749-6-28] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/02/2014] [Indexed: 11/15/2022] Open
Abstract
Background Shigellosis is an acute form of gastroenteritis caused by the bacteria belonging to the genus Shigella. It is the most common cause of morbidity and mortality in children. Shigella belongs to the family Enterobactericeae, which is a Gram-negative and rod shaped bacterium. In the present study, we report the draft genome of Shigella dysenteriae strain SD1D, which was isolated from the stool sample of a healthy individual. Results Based on 16S rRNA gene sequence and phylogenetic analysis, the strain SD1D was identified as Shigella dysenteriae. The draft genome of SD1D consisted of 45, 93, 159 bp with a G + C content of 50.7%, 4, 960 predicted CDSs, 75 tRNAs and 2 rRNAs. The final assembly contained 146 contigs of total length 45, 93, 159 bp with N50 contig length of 77, 053 bp; the largest contig assembled measured 3, 85, 550 bp. Conclusions We have for the first time performed the whole genome sequencing of Shigella dysenteriae strain SD1D. The comparative genomic analysis revealed several genes responsible for the pathogenesis, virulence, defense, resistance to antibiotics and toxic compounds, multidrug resistance efflux pumps and other genomic features of the bacterium.
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Affiliation(s)
- Gurwinder Kaur
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Sathyaseelan Sathyabama
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Amit Arora
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Sheenam Verma
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Nida Mubin
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Javed N Agrewala
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene bank, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
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Göker M, Lu M, Fiebig A, Nolan M, Lapidus A, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Mayilraj S, Rohde M, Detter JC, Bunk B, Spring S, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279(T)), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Stand Genomic Sci 2014; 9:1076-88. [PMID: 25197484 PMCID: PMC4149034 DOI: 10.4056/sigs.5138968] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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] [Indexed: 02/05/2023] Open
Abstract
Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847(T), turned out to be misclassified and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pre-genome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and annotation of the type strain, M3(T). The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the G enomic E ncyclopedia of B acteria and Archaea project.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Megan Lu
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matt Nolan
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Alla Lapidus
- T. Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia
- Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | - Hope Tice
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Jan-Fang Cheng
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Cliff Han
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Sam Pitluck
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Ioanna Pagani
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Krishna Palaniappan
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Shanmugam Mayilraj
- MTCC – Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Boyke Bunk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Reinhard Wirth
- University of Regensburg, Microbiology – Archaeenzentrum, Regensburg, Germany
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - James Bristow
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Jonathan A. Eisen
- DOE Joint Genome Institute, Walnut Creek, California, USA
- University of California Davis Genome Center, Davis, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Nikos C. Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Dkhar HK, Nanduri R, Mahajan S, Dave S, Saini A, Somavarapu AK, Arora A, Parkesh R, Thakur KG, Mayilraj S, Gupta P. Mycobacterium tuberculosis keto-mycolic acid and macrophage nuclear receptor TR4 modulate foamy biogenesis in granulomas: a case of a heterologous and noncanonical ligand-receptor pair. J Immunol 2014; 193:295-305. [PMID: 24907344 DOI: 10.4049/jimmunol.1400092] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The cell wall of Mycobacterium tuberculosis is configured of bioactive lipid classes that are essential for virulence and potentially involved in the formation of foamy macrophages (FMs) and granulomas. Our recent work established crosstalk between M. tuberculosis cell wall lipids and the host lipid-sensing nuclear receptor TR4. In this study, we have characterized, identified, and adopted a heterologous ligand keto-mycolic acid from among M. tuberculosis lipid repertoire for the host orphan NR TR4. Crosstalk between cell wall lipids and TR4 was analyzed by transactivation and promoter reporter assays. Mycolic acid (MA) was found to transactivate TR4 significantly compared with other cell wall lipids. Among the MA, the oxygenated form, keto-MA, was responsible for transactivation, and the identity was validated by TR4 binding assays followed by TLC and nuclear magnetic resonance. Isothermal titration calorimetry revealed that keto-MA binding to TR4 is energetically favorable. This keto-MA-TR4 axis seems to be essential to this oxygenated MA induction of FMs and granuloma formation as evaluated by in vitro and in vivo model of granuloma formation. TR4 binding with keto-MA features a unique association of host nuclear receptor with a bacterial lipid and adds to the presently known ligand repertoire beyond dietary lipids. Pharmacologic modulation of this heterologous axis may hold promise as an adjunct therapy to frontline tuberculosis drugs.
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Affiliation(s)
- Hedwin Kitdorlang Dkhar
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Ravikanth Nanduri
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Sahil Mahajan
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Sandeep Dave
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Ankita Saini
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Arun Kumar Somavarapu
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Ashish Arora
- Council of Scientific and Industrial Research-Central Drug Research Institute, Lucknow 226031, India
| | - Raman Parkesh
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Krishan Gopal Thakur
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Shanmugam Mayilraj
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Pawan Gupta
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
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Manickam N, Singh NK, Bajaj A, Kumar RM, Kaur G, Kaur N, Bala M, Kumar A, Mayilraj S. Bacillus mesophilum sp. nov., strain IITR-54T, a novel 4-chlorobiphenyl dechlorinating bacterium. Arch Microbiol 2014; 196:517-23. [PMID: 24807729 DOI: 10.1007/s00203-014-0988-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 04/02/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
Abstract
The taxonomic position of a Gram-positive, endospore-forming bacterium isolated from soil sample collected from an industrial site was analyzed by a polyphasic approach. The strain designated as IITR-54T matched most of the phenotypic and chemical characteristics of the genus Bacillus and represents a novel species. It was found to biodegrade 4-chlorobiphenyl through dechlorination and was isolated through enrichment procedure from an aged polychlorinated biphenyl-contaminated soil. Both resting cell assay and growth under aerobic liquid conditions using 4-chlorobiphenyl as sole source of carbon along with 0.01% yeast extract, formation of chloride ions was measured. 16S rRNA (1,489 bases) nucleotide sequence of isolated strain was compared with those of closely related Bacillus type strains and confirmed that the strain belongs to the genus Bacillus. Strain IITR-54T differs from all other species of Bacillus by at least 2.1% at the 16S rRNA level, and the moderately related species are Bacillus oceanisediminis (97.9%) followed by Bacillus infantis (97.7%), Bacillus firmus (97.4%), Bacillus drentensis (97.3%), Bacillus circulans (97.2%), Bacillus soli (97.1%), Bacillus horneckiae (97.1%), Bacillus pocheonensis (97.1%) and Bacillus bataviensis (97.1%), respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid and the major isoprenoid quinone was MK-7. Major fatty acids are iso-C15:0 (32.4%) and anteiso-C15:0 (27.4%). Predominant polar lipids are diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The results of physiological and biochemical tests allowed the genotypic and phenotypic distinctiveness of strain IITR-54T with its phylogenetic relatives and suggest that the strain IITR-54T should be recognized as a novel species, for which the name Bacillus mesophilum sp. nov. is proposed. The type strain is IITR-54T (=MTCC 11060T=JCM 19208T).
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Affiliation(s)
- Natesan Manickam
- Environmental Biotechnology Division, CSIR-Indian Institute of Toxicological Research (IITR), Lucknow, 226 001, India
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Sathyabama S, Kaur G, Arora A, Verma S, Mubin N, Mayilraj S, Agrewala JN. Genome sequencing, annotation and analysis of Salmonella enterica sub species salamae strain DMA-1. Gut Pathog 2014; 6:8. [PMID: 24721679 PMCID: PMC4108123 DOI: 10.1186/1757-4749-6-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The genus Salmonella is Gram-negative which belongs to the family Enterobacteriaceae. In this study, we have sequenced the whole genome of the strain DMA-1, which was isolated from mouse stool sample and identified as Salmonella enterica subspecies salamae. RESULTS The strain DMA-1 was closely related at the 16S rRNA gene sequence level with the members of the genus Salmonella: Salmonella enterica subspecies salamae DSM 9220T (100%), followed by Salmonella enterica subspecies diarizonae (99.1%), Salmonella enterica subspecies enterica (99.0%) and Salmonella enterica subspecies indica (98.5%). We obtained the draft genome of S. enterica subspecies salamae strain DMA-1 with a size of 4,826,209 bp and mean G+C content of 52.0 mol%. CONCLUSIONS We for the first time, sequenced the entire genome of the strain DMA-1 which was isolated from the mouse stool sample and identified it as Salmonella enterica, sub species salamae. Further, we subjected the whole genome sequencing data for annotation that revealed several genes responsible for the pathogenesis, virulence, defense, metabolism and other genomic features.
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Affiliation(s)
- Sathyaseelan Sathyabama
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Gurwinder Kaur
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Amit Arora
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Sheenam Verma
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Nida Mubin
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
| | - Javed N Agrewala
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, India
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Sharma D, Mayilraj S, Manhas RK. Streptomyces amritsarensis sp. nov., exhibiting broad-spectrum antimicrobial activity. Antonie Van Leeuwenhoek 2014; 105:943-9. [PMID: 24664662 DOI: 10.1007/s10482-014-0151-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 03/10/2014] [Indexed: 11/30/2022]
Abstract
A new actinobacterium strain, designated 2A(T), was isolated from a soil sample collected from Guru Nanak Dev University, Punjab (India) and characterized using a polyphasic taxonomic approach. It showed antimicrobial activity against various Gram-positive and Gram-negative bacteria including drug resistant bacteria and fungi. The strain had chemotaxononomic and morphological properties typical of the genus Streptomyces. The 16S rRNA gene sequence of the strain showed 99.9, 99.5 and 99.5 % similarity with Streptomyces flavotricini DSM 40152(T), Streptomyces toxytricini DSM 40178(T) and Streptomyces globosus DSM 40815(T), respectively. This strain formed a coherent cluster with them and shared DNA-DNA homology of 37.6 ± 0.6, 34.4 ± 0.5 and 33.1 ± 0.4 % with type strains, S. flavotricini DSM 40152(T), S. globosus DSM 40815(T) and S. toxytricini DSM 40178(T), respectively. Further, the strain was readily distinguished from the phylogenetic close relatives in a variety of morphological, physiological and biochemical properties. Based on the genotypic and phenotypic characteristics, it is proposed that strain 2A(T) represents a novel species in the genus Streptomyces, for which the name Streptomyces amritsarensis sp. nov. is proposed, with the type strain 2A(T) (=MTCC 11845(T)=JCM 19660(T)).
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Affiliation(s)
- Deepika Sharma
- Department of Microbiology, Guru Nanak Dev University, Amritsar, 143005, India
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