Abstract
The Gram-positive, nonmotile, rod-shaped bacterium EF45044T was isolated from a hot spring in Chungju, South Korea. The strain was able to grow at concentrations of 0‒5% (w/v) NaCl, at pH 6.0‒10.0 and in the temperature range of 18‒50 °C. Strain EF45044T showed the highest 16S rRNA gene sequence similarity (98.2%) with Microbacterium ketosireducens DSM 12510T, and the digital DNA‒DNA hybridization (dDDH), average amino acid identity (AAI), and average nucleotide identity (ANI) values were all lower than the accepted species threshold. Strain EF45044T contained MK‒12 and MK‒13 as the predominant respiratory quinones and anteiso‒C17:0, anteiso‒C15:0, and iso‒C16:0 as the major fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, and glycolipid were detected as the major polar lipids. The cell-wall peptidoglycan contained ornithine. The DNA G + C content was 71.4 mol%. Based on the polyphasic data, strain EF45044T (= KCTC 49703T) presents a novel species of the genus Microbacterium, for which the name Microbacterium neungamense sp. nov. is proposed.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability statement
The 16S rRNA gene sequence and the whole-genome sequence of strain EF45044 have been deposited in GenBank/EMBL/DDBJ with the accession numbers MW139252 and CP069717, respectively.
References
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75
Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA, Stevens R, Vonstein V, Wattam AR, Xia F (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365. https://doi.org/10.1038/srep08365
Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. https://doi.org/10.1038/nmeth.2474
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68(1):461–466. https://doi.org/10.1099/ijsem.0.002516
Collins MD, Jones D, Keddie RM, Kroppenstedt RM, Schleifer KH (1983) Classification of some coryneform bacteria in a new genus Aureobacterium. Syst Appl Microbiol 4:236–252. https://doi.org/10.1016/S0723-2020(83)80053-8
Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N, Levy S, Granger S (2008) Consensus generation and variant detection by Celera Assembler. Bioinformatics 24(8):1035–1040. https://doi.org/10.1093/bioinformatics/btn074
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376. https://doi.org/10.1007/BF01734359
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
Hall TA (1999) BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
Hiraishi A (1988) Respiratory quinone profiles as tools for identifying different bacterial populations in activated sludge. J Gen Appl Microbiol 34:39–56. https://doi.org/10.2323/jgam.34.39
Kämpfer P, Rekha PD, Schumann P, Arun AB, Young CC, Chen WM (2011) Microbacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems. Int J Syst Evol Microbiol 61(6):1334–1337. https://doi.org/10.1099/ijs.0.026401-0
Kim D, Park S, Chun J (2021) Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 59:476–480. https://doi.org/10.1007/s12275-021-1154-0
Kook MC, Son HM, Yi TH (2014) Microbacterium kyungheense sp. nov. and Microbacterium jejuense sp. nov., isolated from salty soil. Int J Syst Evol Microbiol 64(7):2267–2273. https://doi.org/10.1099/ijs.0.054973-0
Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108. https://doi.org/10.1093/nar/gkm160
Meier-Kolthoff JP, Sardà Carbasse J, Peinado-Olarte RL, Göker M (2022) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50:D801–D807. https://doi.org/10.1093/nar/gkab902
Minnikin DE, O’Donnell AG, Goodfellow M, Alderso G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2(5):233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Nei M, Kumar S, Takahashi K (1998) The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc Natl Acad Sci USA 95(21):12390–12397. https://doi.org/10.1073/pnas.95.21.12390
Nguyen NL, Kim YJ, Hoang VA, Min JW, Hwang KH, Yang DC (2015) Microbacterium panaciterrae sp. nov., isolated from the rhizosphere of ginseng. Int J Syst Evol Microbiol 65:927–933. https://doi.org/10.1099/ijs.0.000041
Orla-Jensen S (1919) The Latic Acid Bacteria. Andr. Fred. Host and Son, Copenhagen
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R (2014) The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42(D1):D206–D214. https://doi.org/10.1093/nar/gkt1226
Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genom Proteom Bioinform 13(5):278–289. https://doi.org/10.1016/j.gpb.2015.08.002
Roberts RJ, Carneiro MO, Schatz MC (2017) Erratum to: the advantages of SMRT sequencing. Genome Biol 18(1):2–5. https://doi.org/10.1186/s13059-017-1295-y
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical note 101. MIDI Inc., Newark
Schädler S, Burkhardt C, Kappler A (2008) Evaluation of electron microscopic sample preparation methods and imaging techniques for characterization of cell-mineral aggregates. Geomicrobiol J 25(5):228–239. https://doi.org/10.1080/01490450802153462
Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407–477. https://doi.org/10.1128/br.36.4.407-477.1972
Takeuchi M, Hatano K (1998a) Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium. Int J Syst Bacteriol 48:739–747. https://doi.org/10.1099/00207713-48-3-739
Takeuchi M, Hatano K (1998b) Proposal of six new species in the genus Microbacterium and transfer of Flavobacterium marinotypicum ZoBell and Upham to the genus Microbacterium as Microbacterium maritypicum comb. Nov. Int J Syst Bacteriol 48(3):973–982. https://doi.org/10.1099/00207713-48-3-973
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729. https://doi.org/10.1093/molbev/mst197
Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28(1):33–36. https://doi.org/10.1093/nar/28.1.33
Yokota A, Takeuchi M, Sakane T, Weiss N (1993) Proposal of six new species in the genus Aureobacterium and transfer of Flavobacterium esteraromaticum Omelianski to the genus Aureobacterium as Aureobacterium esteraromaticum comb. nov. Int J Syst Bacteriol 43(3):555–564. https://doi.org/10.1099/00207713-43-3-555
Yoon SH, Ha SM, Kwon SJ, Lim JM, Kim YS, Seo HS, Chun JS (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
Yoon SH, Ha SM, Lim JM, Kwon SJ, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Funding
This work was supported by the National Institute of Biological Resources funded by the Ministry of Environment (NIBR202102109), Basic Research of the NRF (NRF-2020R1F1A1076624), grant from the Ministry of Ocean and Fisheries (PM62830), and grant from the Technology Innovation Program (20015807) funded by the Ministry of Trade, Industry & Energy.
Author information
Authors and Affiliations
Contributions
DG carried out most of the experiments, contributed to data interpretation, and wrote the manuscript; GEJ and DO contributed to the experimental design and performed isolation & identification and characteristic experiments of EF45044; D-WL, Y-JL and S-BK contributed to data interpretation and study conception; I-TC and W-JC contributed to the experiments regarding the differential characteristics of strain EF45044; S-KP contributed to the fatty acid composition experiments of strain EF45044; and J-SL and S-JL contributed to the conception and design of the entire study and wrote the manuscript. All authors have read and agreed to the published version of the manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no conflicts of interest.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Ganbat, D., Jeong, G.E., Oh, D. et al. Description of Microbacterium neungamense sp. nov. isolated from a hot spring. Arch Microbiol 205, 23 (2023). https://doi.org/10.1007/s00203-022-03343-5
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-022-03343-5