{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T17:30:03Z","timestamp":1782149403558,"version":"3.54.5"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,8,9]],"date-time":"2019-08-09T00:00:00Z","timestamp":1565308800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,8,9]],"date-time":"2019-08-09T00:00:00Z","timestamp":1565308800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001409","name":"Department of Science and Technology, Ministry of Science and Technology","doi-asserted-by":"publisher","award":["SB\/YS\/LS-09\/2014"],"award-info":[{"award-number":["SB\/YS\/LS-09\/2014"]}],"id":[{"id":"10.13039\/501100001409","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Antibiotic-resistance is ever growing burden on our society for the past many years. Many synthetic chemistry approaches and rational drug-design have been unable to pace up and tackle this problem. Natural resources, more specifically, the microbial diversity, on the other hand, make a traditional and still the best platform to search for new chemical scaffolds and compounds. Here, we report the antimicrobial characteristics of novel bacterial isolate from a salt lake in India. We screened the bacterial isolates for their inhibitory activity against indicator bacteria and found that four novel species were able to prevent the growth of test strains studied <jats:italic>in vitro<\/jats:italic>. Further, we characterized one novel species (SMB1<jats:sup>T<\/jats:sup>\u2009=\u2009SL4-2) using polyphasic taxonomic approaches and also purified the active ingredient from this bacterium. We successfully characterized the antimicrobial compound using mass spectroscopy and amino acid analysis. We also allocated two novel biosynthetic gene clusters for putative bacteriocins and one novel non-ribosomal peptide gene cluster in its whole genome. We concluded that the strain SMB1<jats:sup>T<\/jats:sup> belonged to the genus <jats:italic>Paenibacilllus<\/jats:italic> with the pairwise sequence similarity of 98.67% with <jats:italic>Paenibacillus tarimensis<\/jats:italic> DSM 19409<jats:sup>T<\/jats:sup> and we proposed the name <jats:italic>Paenibacillus sambharensis<\/jats:italic> sp. nov. The type strain is SMB1<jats:sup>T<\/jats:sup> (=MTCC 12884\u2009=\u2009KCTC 33895<jats:sup>T<\/jats:sup>).<\/jats:p>","DOI":"10.1038\/s41598-019-47879-x","type":"journal-article","created":{"date-parts":[[2019,8,9]],"date-time":"2019-08-09T10:02:38Z","timestamp":1565344958000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Antimicrobial properties of the novel bacterial isolate Paenibacilllus sp. SMB1 from a halo-alkaline lake in India"],"prefix":"10.1038","volume":"9","author":[{"given":"Harjodh","family":"Singh","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manpreet","family":"Kaur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manoj","family":"Jangra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunita","family":"Mishra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hemraj","family":"Nandanwar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anil Kumar","family":"Pinnaka","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,8,9]]},"reference":[{"key":"47879_CR1","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/j.molmed.2012.03.003","volume":"18","author":"P Nordmann","year":"2012","unstructured":"Nordmann, P., Dortet, L. & Poirel, L. Carbapenem resistance in Enterobacteriaceae: here is the storm! Trends in molecular medicine 18, 263\u2013272 (2012).","journal-title":"Trends in molecular medicine"},{"key":"47879_CR2","unstructured":"WHO. Worldwide country situation analysis: response to antimicrobial resistance. (2015)."},{"key":"47879_CR3","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1038\/nrd2201","volume":"6","author":"DJ Payne","year":"2007","unstructured":"Payne, D. J., Gwynn, M. N., Holmes, D. J. & Pompliano, D. L. Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nature reviews Drug discovery 6, 29 (2007).","journal-title":"Nature reviews Drug discovery"},{"key":"47879_CR4","doi-asserted-by":"publisher","first-page":"13184","DOI":"10.1002\/anie.201708133","volume":"56","author":"MF Chellat","year":"2017","unstructured":"Chellat, M. F. & Riedl, R. Pseudouridimycin: The First Nucleoside Analogue That Selectively Inhibits Bacterial RNA Polymerase. Angewandte Chemie International Edition 56, 13184\u201313186 (2017).","journal-title":"Angewandte Chemie International Edition"},{"key":"47879_CR5","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1002\/ardp.201600064","volume":"349","author":"KM Fisch","year":"2016","unstructured":"Fisch, K. M. & Schaeberle, T. F. Toolbox for Antibiotics Discovery from Microorganisms. Archiv der Pharmazie 349, 683\u2013691 (2016).","journal-title":"Archiv der Pharmazie"},{"key":"47879_CR6","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1038\/nature14098","volume":"517","author":"LL Ling","year":"2015","unstructured":"Ling, L. L. et al. A new antibiotic kills pathogens without detectable resistance. Nature 517, 455 (2015).","journal-title":"Nature"},{"key":"47879_CR7","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.molcel.2018.03.001","volume":"70","author":"L Pantel","year":"2018","unstructured":"Pantel, L. et al. Odilorhabdins, antibacterial agents that cause miscoding by binding at a new ribosomal site. Molecular cell 70, 83\u201394. e87 (2018).","journal-title":"Molecular cell"},{"key":"47879_CR8","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1038\/nature18634","volume":"535","author":"A Zipperer","year":"2016","unstructured":"Zipperer, A. et al. Human commensals producing a novel antibiotic impair pathogen colonization. Nature 535, 511 (2016).","journal-title":"Nature"},{"key":"47879_CR9","unstructured":"Kamat, T. & Kerkar, S. Bacteria from Salt Pans: a potential resource of antibacterial metabolites. Recent Research in Science and Technology 3 (2011)."},{"key":"47879_CR10","unstructured":"Hashemi, T., Baseri, S. M. & Bahador, N. Isolation of Halophilic Bacteria from Maharlu salt Lake-Iran and their evaluation for the production of bioactive compounds (2014)."},{"key":"47879_CR11","first-page":"506","volume":"3","author":"A Sawale","year":"2014","unstructured":"Sawale, A., Kadam, T., Karale, M. & Kadam, O. Antimicrobial activity of secondary metabolites from halophilic Bacillus pumilus sp. Int. J. Curr. Microbiol. App. Sci 3, 506\u2013512 (2014).","journal-title":"Int. J. Curr. Microbiol. App. Sci"},{"key":"47879_CR12","first-page":"831","volume":"4","author":"A Azemin","year":"2015","unstructured":"Azemin, A., Klappa, P. & Omar, M. S. S. Bacteriocin isolated from Halomonas sp.: a bacterial DING protein. The Malaysian Journal of Analytical Sciences 4, 831\u2013840 (2015).","journal-title":"The Malaysian Journal of Analytical Sciences"},{"key":"47879_CR13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4172\/2157-7471.1000214","volume":"5","author":"B Essghaier","year":"2014","unstructured":"Essghaier, B. et al. Antimicrobial behavior of intracellular proteins from two moderately halophilic bacteria: strain J31 of Terribacillus halophilus and strain M3-23 of Virgibacillus marismortui. Journal of Plant Pathology & Microbiology 5, 1 (2014).","journal-title":"Journal of Plant Pathology & Microbiology"},{"key":"47879_CR14","doi-asserted-by":"crossref","unstructured":"Singh, H. et al. Salibacterium nitratireducens sp. nov., a haloalkalitolerant bacterium isolated from a water sample from Sambhar salt lake, India. International journal of systematic and evolutionary microbiology (2018).","DOI":"10.1099\/ijsem.0.003021"},{"key":"47879_CR15","doi-asserted-by":"crossref","unstructured":"Singh, H. et al. Bacillus alkalilacus sp. nov., isolated from a sediment sample from a lake in India. International journal of systematic and evolutionary microbiology (2018).","DOI":"10.1099\/ijsem.0.002726"},{"key":"47879_CR16","doi-asserted-by":"crossref","unstructured":"Singh, H. et al. Bacillus lacus sp. nov., isolated from a water sample of a salt lake in India. International journal of systematic and evolutionary microbiology (2018).","DOI":"10.1099\/ijsem.0.002588"},{"key":"47879_CR17","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1042\/bj0580633","volume":"58","author":"I Lockhart","year":"1954","unstructured":"Lockhart, I. & Abraham, E. The amino acid sequence in bacitracin A. Biochemical Journal 58, 633 (1954).","journal-title":"Biochemical Journal"},{"key":"47879_CR18","doi-asserted-by":"publisher","first-page":"3223","DOI":"10.1073\/pnas.68.12.3223","volume":"68","author":"KJ Stone","year":"1971","unstructured":"Stone, K. J. & Strominger, J. L. Mechanism of action of bacitracin: complexation with metal ion and C55-isoprenyl pyrophosphate. Proceedings of the National Academy of Sciences 68, 3223\u20133227 (1971).","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"47879_CR19","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1093\/bioinformatics\/btm009","volume":"23","author":"AL Delcher","year":"2007","unstructured":"Delcher, A. L., Bratke, K. A., Powers, E. C. & Salzberg, S. L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673\u2013679 (2007).","journal-title":"Bioinformatics"},{"key":"47879_CR20","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1007\/BF00873085","volume":"64","author":"C Ash","year":"1993","unstructured":"Ash, C., Priest, F. G. & Collins, M. D. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Antonie van Leeuwenhoek 64, 253\u2013260 (1993).","journal-title":"Antonie van Leeuwenhoek"},{"key":"47879_CR21","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1099\/00207713-37-4-463","volume":"37","author":"L Wayne","year":"1987","unstructured":"Wayne, L. et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic and Evolutionary Microbiology 37, 463\u2013464 (1987).","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"47879_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00792-012-0493-5","volume":"17","author":"J Hamedi","year":"2013","unstructured":"Hamedi, J., Mohammadipanah, F. & Ventosa, A. Systematic and biotechnological aspects of halophilic and halotolerant actinomycetes. Extremophiles 17, 1\u201313 (2013).","journal-title":"Extremophiles"},{"key":"47879_CR23","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1099\/00207713-52-1-131","volume":"52","author":"L Daane","year":"2002","unstructured":"Daane, L. et al. PAH-degradation by Paenibacillus spp. and description of Paenibacillus naphthalenovorans sp. nov., a naphthalene-degrading bacterium from the rhizosphere of salt marsh plants. International journal of systematic and evolutionary microbiology 52, 131\u2013139 (2002).","journal-title":"International journal of systematic and evolutionary microbiology"},{"key":"47879_CR24","doi-asserted-by":"publisher","first-page":"1909","DOI":"10.1099\/ijs.0.015271-0","volume":"60","author":"KH Kishore","year":"2010","unstructured":"Kishore, K. H., Begum, Z., Pathan, A. A. K. & Shivaji, S. Paenibacillus glacialis sp. nov., isolated from the Kafni glacier of the Himalayas, India. International journal of systematic and evolutionary microbiology 60, 1909\u20131913 (2010).","journal-title":"International journal of systematic and evolutionary microbiology"},{"key":"47879_CR25","doi-asserted-by":"publisher","first-page":"1521","DOI":"10.1099\/ijs.0.63078-0","volume":"54","author":"MJ Montes","year":"2004","unstructured":"Montes, M. J., Mercad\u00e9, E., Bozal, N. & Guinea, J. Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment. International journal of systematic and evolutionary microbiology 54, 1521\u20131526 (2004).","journal-title":"International journal of systematic and evolutionary microbiology"},{"key":"47879_CR26","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1099\/ijs.0.02822-0","volume":"54","author":"P Scheldeman","year":"2004","unstructured":"Scheldeman, P. et al. Paenibacillus lactis sp. nov., isolated from raw and heat-treated milk. International Journal of Systematic and Evolutionary Microbiology 54, 885\u2013891 (2004).","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"47879_CR27","doi-asserted-by":"publisher","DOI":"10.1186\/s12934-016-0603-7","volume":"15","author":"EN Grady","year":"2016","unstructured":"Grady, E. N., MacDonald, J., Liu, L., Richman, A. & Yuan, Z.-C. Current knowledge and perspectives of Paenibacillus: a review. Microbial cell factories 15, 203 (2016).","journal-title":"Microbial cell factories"},{"key":"47879_CR28","doi-asserted-by":"publisher","first-page":"19540","DOI":"10.1021\/ja3089229","volume":"134","author":"CT Lohans","year":"2012","unstructured":"Lohans, C. T. et al. Structural characterization of the highly cyclized lantibiotic paenicidin A via a partial desulfurization\/reduction strategy. Journal of the American Chemical Society 134, 19540\u201319543 (2012).","journal-title":"Journal of the American Chemical Society"},{"key":"47879_CR29","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1128\/AAC.01813-15","volume":"60","author":"P Baindara","year":"2016","unstructured":"Baindara, P. et al. Characterization of the antimicrobial peptide penisin, a class Ia novel lantibiotic from Paenibacillus sp. strain A3. Antimicrobial agents and chemotherapy 60, 580\u2013591 (2016).","journal-title":"Antimicrobial agents and chemotherapy"},{"key":"47879_CR30","first-page":"e00727","volume":"4","author":"Y Li","year":"2016","unstructured":"Li, Y., Li, Q., Li, Y., Gao, J. & Fan, X. Draft genome sequence of Paenibacillus polymyxa KF-1, an excellent producer of microbicides. Genome announcements 4, e00727\u201300716 (2016).","journal-title":"Genome announcements"},{"key":"47879_CR31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/BF02788897","volume":"42","author":"E Azevedo","year":"1993","unstructured":"Azevedo, E., Rios, E., Fukushima, K. & Campos-Takaki, G. Bacitracin production by a new strain ofBacillus subtilis. Applied biochemistry and biotechnology 42, 1 (1993).","journal-title":"Applied biochemistry and biotechnology"},{"key":"47879_CR32","doi-asserted-by":"publisher","first-page":"1347","DOI":"10.1007\/s00726-016-2228-x","volume":"48","author":"N Zhao","year":"2016","unstructured":"Zhao, N., Pan, Y., Cheng, Z. & Liu, H. Lasso peptide, a highly stable structure and designable multifunctional backbone. Amino acids 48, 1347\u20131356 (2016).","journal-title":"Amino acids"},{"key":"47879_CR33","doi-asserted-by":"publisher","first-page":"13662","DOI":"10.1074\/jbc.M116.722108","volume":"291","author":"S Zhu","year":"2016","unstructured":"Zhu, S. et al. Insights into the unique phosphorylation of the lasso peptide paeninodin. Journal of Biological Chemistry 291, 13662\u201313678 (2016).","journal-title":"Journal of Biological Chemistry"},{"key":"47879_CR34","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/s41564-018-0110-1","volume":"3","author":"BM Hover","year":"2018","unstructured":"Hover, B. M. et al. Culture-independent discovery of the malacidins as calcium-dependent antibiotics with activity against multidrug-resistant Gram-positive pathogens. Nature microbiology 3, 415 (2018).","journal-title":"Nature microbiology"},{"key":"47879_CR35","doi-asserted-by":"publisher","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","volume":"29","author":"A Gurevich","year":"2013","unstructured":"Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072\u20131075 (2013).","journal-title":"Bioinformatics"},{"key":"47879_CR36","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-75","volume":"9","author":"RK Aziz","year":"2008","unstructured":"Aziz, R. K. et al. The RAST Server: rapid annotations using subsystems technology. BMC genomics 9, 75 (2008).","journal-title":"BMC genomics"},{"key":"47879_CR37","doi-asserted-by":"publisher","first-page":"W448","DOI":"10.1093\/nar\/gkt391","volume":"41","author":"AJ van Heel","year":"2013","unstructured":"van Heel, A. J., de Jong, A., Montalban-Lopez, M., Kok, J. & Kuipers, O. P. BAGEL3: automated identification of genes encoding bacteriocins and (non-) bactericidal posttranslationally modified peptides. Nucleic acids research 41, W448\u2013W453 (2013).","journal-title":"Nucleic acids research"},{"key":"47879_CR38","doi-asserted-by":"publisher","first-page":"W237","DOI":"10.1093\/nar\/gkv437","volume":"43","author":"T Weber","year":"2015","unstructured":"Weber, T. et al. antiSMASH 3.0\u2014a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic acids research 43, W237\u2013W243 (2015).","journal-title":"Nucleic acids research"},{"key":"47879_CR39","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1016\/j.syapm.2017.07.005","volume":"40","author":"S Kiran","year":"2017","unstructured":"Kiran, S., Swarnkar, M. K., 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. Systematic and applied microbiology 40, 430\u2013439 (2017).","journal-title":"Systematic and applied microbiology"},{"key":"47879_CR40","doi-asserted-by":"publisher","first-page":"320","DOI":"10.1016\/j.syapm.2012.04.004","volume":"35","author":"A Kumar","year":"2012","unstructured":"Kumar, A. et al. Shivajiella indica gen. nov., sp. nov., a marine bacterium of the family \u201cCyclobacteriaceae\u201d with nitrate reducing activity. Systematic and applied microbiology 35, 320\u2013325 (2012).","journal-title":"Systematic and applied microbiology"},{"key":"47879_CR41","unstructured":"Wayne, P. Performance standards for antimicrobial susceptibility testing: Twenty Fifth International Supplement M100-S25. Clinical and Laboratory Standards Institute (2015)."},{"key":"47879_CR42","unstructured":"Sasser, M. Identification of bacteria by gas chromatography of cellular fatty acids. (1990)."},{"key":"47879_CR43","doi-asserted-by":"crossref","unstructured":"Mandel, M. & Marmur, J. In Methods in enzymology Vol. 12 195\u2013206 (Elsevier, 1968).","DOI":"10.1016\/0076-6879(67)12133-2"},{"key":"47879_CR44","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1139\/W10-121","volume":"57","author":"J Loveland-Curtze","year":"2011","unstructured":"Loveland-Curtze, J., Miteva, V. I. & Brenchley, J. E. Evaluation of a new fluorimetric DNA\u2013DNA hybridization method. Canadian journal of microbiology 57, 250\u2013255 (2011).","journal-title":"Canadian journal of microbiology"},{"key":"47879_CR45","first-page":"133","volume":"12","author":"JD Ley","year":"1970","unstructured":"Ley, J. D., Cattoir, H. & Reynaerts, A. The quantitative measurement of DNA hybridization from renaturation rates. The FEBS Journal 12, 133\u2013142 (1970).","journal-title":"The FEBS Journal"},{"key":"47879_CR46","first-page":"143","volume":"12","author":"M Gillis","year":"1970","unstructured":"Gillis, M., Ley, J. D. & Cleene, M. D. The determination of molecular weight of bacterial genome DNA from renaturation rates. The FEBS Journal 12, 143\u2013153 (1970).","journal-title":"The FEBS Journal"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-47879-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-47879-x","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-47879-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T12:23:49Z","timestamp":1671279829000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-47879-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,8,9]]},"references-count":46,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["47879"],"URL":"https:\/\/doi.org\/10.1038\/s41598-019-47879-x","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,8,9]]},"assertion":[{"value":"12 October 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 July 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"9 August 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"11561"}}