Polyphasic Characterization and Comparative Genomics of a Newly Isolated Strain of Kocuria soli from Wild Ass Sanctuary, Gujarat, India

Sasikala Chintalapati, Jagadeeshwari Uppada

Abstract


From soil sample collected from Little Rann of Kutch-Wild Ass Wild Life Sanctuary, Gujarat a bacterial strain that is non-motile, cocci in shape, obligate aerobic, gram positive, catalase and oxidase positive was isolated and named as strain JC486. Strain JC486T was related to Kocuria soli M5W7-7T (99.7%) belonging to genus Kocuria according to sequence similarity and comparison data of 16S rRNA gene. The strain JC486T had a G+C content (DNA) of 71 mol% and was found to have one amino phospholipid (APL), one aminolipid (AL), one phospholipid (PL), and five polar lipids which are unidentified, respiratory quinone MK-7, and the fatty acids (major) of strain JC486 include anteiso-C15:0 and anteiso-C17:0. Lysine and alanine are found in peptidoglycan of cell wall. Both strains have ANI and dDDH scores of 98 and 80.2, respectively. Based on physiological, chemotaxonomic and phylotaxogenomic studies, it is determined strain JC486 (= KCTC49118 = LMG 30604) is a strain of Kocuria soli


References


Stackebrandt E, Koch C, Gvozdiak O, Schumann P. Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol. 1995; 45, 682–692.

Li WJ, Zhang YQ, Schumann P, Chen HH, Hozzein WN, et al. Kocuria aegyptia sp. nov., a novel actinobacterium isolated from a saline, alkaline desert soil in Egypt. Int J Syst Evol Microbiol. 2006; 56: 733–737.

Kovács G, Burghardt J, Pradella S, Schumann P, Stackebrandt E, et al. Kocuria palustris sp. nov. and Kocuria rhizophila sp. nov., isolated from the rhizoplane of the narrow-leaved cattail (Typha angustifolia). Int J Syst Bacteriol. 1999; 49: 167–173. 4. Camacho M, Redondo-gomez S, Rodriguez-llorente I, Rohde M, Sproer C, Schumann P, Klenk HP, Montero-calasanz MDC. Kocuria salina sp. nov., an actinobacterium isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum and emended description of Kocuria turfanensis. Int J Syst Evol Microbiol. 2017; 67: 5006–5012.

Park EJ, Kim MS, Roh SW, Jung MJ, Bae JW. Kocuria atrinae sp. nov., isolated from traditional Korean fermented seafood. Int J Syst Evol Microbiol. 2010; 60: 914–918.

Park EJ, Roh SW, Kim MS, Jung MJ, Shin KS, et al. Kocuria koreensis sp. nov., isolated from fermented seafood. Int J Syst Evol Microbiol. 2010; 60: 140–143.

Bala M, Kaur C, Kaur I, Khan F, Mayilraj S. Kocuria sediminis sp. nov., isolated from a marine sediment sample. Antonie van Leeuwenhoek. 2012; 101: 469–478.

Dastager SG, Tang SK, Srinivasan K, Lee JC, Li WJ. Kocuria indica sp. nov., isolated from a sediment sample. Int J Syst Evol Microbiol. 2014; 64: 869–874.

Kim SB, Nedashkovskaya OI, Mikhailov VV, Han SK, Kim KO, et al. Kocuria marina sp. nov., a novel actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol. 2004; 54: 1617–1620.

Tuo L, Li FN, Bao YX, Yan XR, Sun CH. Kocuria soli sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol. 2019; 69(7): 2064–2068.

Kaur C, Kaur I, Raichand R, Bora TC, Mayilraj S. Description of a novel actinobacterium Kocuria assamensis sp. nov., isolated from a water sample collected from the river Brahmaputra, Assam, India. Antonie van Leeuwenhoek. 2011; 99: 721–726.

Stackebrandt E, Schumann P. Genus V. Kocuria gen. nov. Stackebrandt & Schumann 1995, 690VP. In Bergey’s Manual of Systematic Bacteriology, vol. 5, pp. 626–635. Edited by W. B. Whitman, (2012).

Divyasree B, Lakshmi KVNS, Bharti Dave, Sasikala Ch, Ramana Ch.V. Rhodovulum aestuarii sp. nov., isolated from a brackish water body. Int J Syst Evol Microbiol. 2016; 66: 165–171.

Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol. 2017; 67: 1613–1617.

Rodriguez-R LM, Konstantinidis KT The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. Peer J Preprints. 2016; 4: 1.

Auch AF, Jan M, Klenk H-P, et al. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci. 2010; 2: 117–134. https://doi.org/10.4056/sigs.531120.

Meier-Kolthoff JP, Auch AF, Klenk HP, Göker Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinf. 2013; 14: 60. https://doi.org/10.1186/1471-2105-14-60 M.

Auch AF, Klenk HP, Göker M Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci. 2010; 28: 142–148. https://doi.org/10.4056/sigs.541628.

Venkataramana K, Padmavali P, Ritu V, Adnan Bashir B, Vinod K, Maheshwar K, Mohan Rao B. Emerging bacterial infection: identification and clinical Significance of Kocuria species. Cureus. 2016; 8(8): e731.

Cosentino S1, Voldby Larsen M, Møller Aarestrup F, Lund O. PathogenFinder-distinguishing friend from foe using bacterial whole genome sequence data. PLoS One. 2013; 28; 8(10): e77302.

Tamura S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016; 33: 1870–1874.

Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980; 16: 111–120.

Biebl H, Pfennig N. Isolation of members of the family Rhodospirillaceae. In The Prokaryotes: A Handbook on Habitats, Isolation, and Identification of Bacteria, Vol. 1, pp. 267–273. Edited by Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HG. New York: Springer (1981).

Cappuccino JG, Sherman N. Microbiology–A laboratory manual. Fifth edition Benjamin/Cummings Science Publishing, California. (1998).

Smibert RM, Krieg NR. General characterization. In Manual of Methods for General Microbiology, pp. 409–443. Edited by Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA, Krieg NR, Phillips GB. Washington, DC: American Society for Microbiology, (1981).

Smibert RM, Krieg NR. Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by Gerhardt P. Washington, DC: American Society for Microbiology. (1994).

Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids.; Newark, DE: MIDI Inc. (1990).

Xie C, Yokota A. Phylogenetic analysis of Lampropedia hyaline based on the 16SrRNA gene sequence. J Gen Appl Microbiol. 2003; 49: 345–349.

Schleifer, K.H. Analysis of the chemical composition and primary structure of murein. Methods Microbiol. 1985; 18: 123–156.

Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev. 1972; 36: 407–477.

McKerrow J, Vagg S, McKinney T, Seviour EM, Maszenan AM, Brooks P, Seviour RJ. A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram positive bacteria. Lett Appl Microbiol. 2000; 30: 178–182.


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