A Gram-strain negative, aerobic, catalase and oxidase positive, non-motile, short rod-shaped bacterium, designated 17mud1-8T, was isolated from mud collected from Nowon-gu, Seoul, South Korea. The strain was found to be able to grow at 10–40 °C (optimum 28–30 °C), pH 5.0–8.0 (optimum 7.0), and in the absence of NaCl. The nearly full-length 16S rRNA gene of strain 17mud1-8T exhibits sequence similarity of 94.1% with that of Panacibacter ginsenosidivorans Gsoil 1550T, followed by 93.6% sequence similarity with Parafilimonas terrae DSM 28286T. Phylogenetic analysis indicated that strain 17mud1-8T belongs to the family Chitinophagaceae, sharing approximately 94.1–91.9% sequence similarity with members of closely related genera. The respiratory quinone was identified as MK-7. The predominant fatty acids were found to consist of iso-C15:0, iso-C17:1ω5c and iso-C15:1 G. The polar lipids were identified as phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, ten unidentified aminolipids and seven unidentified lipids. The draft genome of 17mud1-8T has G+C content of 40.9 mol% and a 5.8 Mb chromosome. On the basis of the phenotypic and genotypic properties, and phylogenetic inference, strain 17mud1-8T was found to represent a novel genus in the family Chitinophagaceae, for which the name Ilyomonas limi gen. nov., sp. nov. is proposed, with the type strain 17mud1-8T(=KCTC 52874T = NBRC 112826T).
This is a preview of subscription content, log in to check access.
This work was supported by a research grant from Seoul Women’s University (2018) and the Project on Survey of Indigenous Species of Korea of the National Institute of Biological Resources (NIBR) under the Ministry of Environment (MOE) (NIBR201701206). We thank Prof Dr. Bernhard Schink (University of Konstanz, Konstanz, Germany) for advice concerning the species name.
GC isolated the bacterium, designed the study, performed the phenotypic and biochemical characterization, wrote the original draft; JK, HK and IK helped the analysis of taxonomic data; MKK and TS designed and supervised the study, edited the original draft.
Compliance with ethical standards
Conflict of interest
The authors declare that there is no conflict of interest.
This study does not describe any experimental work related to human.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75CrossRefGoogle Scholar
Bernardet JF, Nakagawa Y, Holmes B, Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070Google Scholar
Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology, Washington, DC, pp 309–329Google Scholar
Buck JD (1982) Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993Google Scholar
Chaudhary DK, Dahal RH, Kim J (2018) Nemorella caseinilytica gen. nov., sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 68:474–481CrossRefGoogle Scholar
Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354Google Scholar
Dahal RH, Chaudhary DK, Kim J (2017) Rurimicrobium arvi gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from farmland soil. Int J Syst Evol Microbiol 67:5235–5243CrossRefGoogle Scholar
Fautz E, Reichenbach H (1980) A simple test for flexirubin-type pigments. FEMS Microbiol Ecol 8:87–91CrossRefGoogle Scholar
Felsenstein J (1985) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefGoogle Scholar
Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57CrossRefGoogle Scholar
Hall T (1997) BioEdit. Biological sequence alignment editor for Win 95/98/NT/2 K/XP. Ibis Therapeutics, CarlsbadGoogle Scholar
Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469CrossRefGoogle Scholar
Jiang F, Qiu X, Chang X, Qu Z, Ren L et al (2014) Terrimonas arctica sp. nov., isolated from Arctic tundra soil. Int J Syst Evol Microbiol 64:3798–3803CrossRefGoogle Scholar
Jin D, Wang P, Bai Z, Jin B, Yu Z et al (2013) Terrimonas pekingensis sp. nov., isolated from bulking sludge, and emended descriptions of the genus Terrimonas, Terrimonas ferruginea, Terrimonas lutea and Terrimonas aquatica. Int J Syst Evol Microbiol 63:1658–1664CrossRefGoogle Scholar
Kämpfer P, Lodders N, Falsen E (2011) Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 61:518–523CrossRefGoogle Scholar
Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH et al (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbial 62:716–721CrossRefGoogle Scholar
Kim SJ, Park JH, Lim JM, Ahn JH, Anandham R, Weon HY, Kwon SW (2014) Parafilimonas terrae gen. nov., sp. nov., isolated from greenhouse soil. Int J Syst Evol Microbiol 64:3040–3045CrossRefGoogle Scholar
Kim Y, Kim B, Kang K, Ahn TY (2016) Sediminibacterium aquarii sp. nov., isolated from sediment in a fishbowl. Int J Syst Evol Microbiol 66:4501–4505CrossRefGoogle Scholar
Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefGoogle Scholar
Komagata K, Suzuki KI (1987) Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19:161–205CrossRefGoogle Scholar
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefGoogle Scholar
Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evol Microbiol 38:358–361Google Scholar
Madhaiyan M, Poonguzhali S, Senthilkumar M, Pragatheswari D, Lee JS et al (2015) Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil. Int J Syst Evol Microbiol 65:578–586CrossRefGoogle Scholar
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al (1984) An integrated procedure for the extraction of bacterial isoprenoidquinones and polar lipids. J Microbiol Methods 2:233–241CrossRefGoogle Scholar
Qu JH, Yuan HL (2008) Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 58:2191–2194CrossRefGoogle Scholar
Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425Google Scholar
Sheu SY, Cho NT, Arun AB, Chen WM (2010) Terrimonas aquatica sp. nov., isolated from a freshwater spring. Int J Syst Evol Microbiol 60:2705–2709CrossRefGoogle Scholar
Siddiqi MZ, Muhammad Shafi S, Choi KD, Im WT (2016) Panacibacter ginsenosidivorans gen. nov., sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field. Int J Syst Evol Microbiol 66:4039–4045CrossRefGoogle Scholar
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654Google Scholar
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefGoogle Scholar