Abstract
A bacterial strain designated KDG-16 T is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16 T are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20–25 °C, pH 6–7, and with 0% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set reveal that strain KDG-16 T is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16 T shares the highest similarity with Flavobacterium terrigena DSM 17934 T (97.7%). The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between strain KDG-16 T and the closely related Flavobacterium species are below the cut-off values of 95–96, 90 and 70%, respectively, used for species demarcation. Strain KDG-16 T contains iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized phospholipid, two uncharacterized aminolipids and two uncharacterized lipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. Genomic DNA G + C content of strain KDG-16 T is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16 T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium difficile sp. nov. is proposed. The type strain is KDG-16 T (= BCRC 81194 T = LMG 31332 T).
Similar content being viewed by others
Abbreviations
- eggNOG:
-
Evolutionary genealogy of genes: Nonsupervised Orthologous Groups
- UBCG:
-
Up-to-date bacterial core gene set
- ANI:
-
Average nucleotide identity
- AAI:
-
Average amino acid identity
- dDDH:
-
Digital DNA–DNA hybridization
- PE:
-
Phosphatidylethanolamine
- APL:
-
Uncharacterized aminophospholipid
- PL:
-
Uncharacterized phospholipid
- AL:
-
Uncharacterized aminolipid
- L:
-
Uncharacterized lipid
- HSPD:
-
Homospermidine
- SPD:
-
Spermidine; MK-6, menaquinone-6
References
Anzai Y, Kudo Y, Oyaizu H (1997) The phylogeny of genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 47:249–251
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477
Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM (1923) Genus II. Flavobacterium gen. nov. In: Bergey’s Manual of Determinative Bacteriology, 1st edn. Williams & Wilkins, Baltimore, p 97–117
Bernardet JF, Bowman JP (2011) Genus I. Flavobacterium. In: Whitman W (ed) Bergey’s Manual of Systematic Bacteriology, vol 4, 2nd edn. Williams & Wilkins, Baltimore, p 112–154
Bernardet JF, Nakagawa Y, Holmes B (2002) Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 52:1049–1070
Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P (1996) Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 46:128–148
Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A (2016) EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 44:W22–W28
Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868
Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology, Washington, DC, pp 309–329
Busse HJ, Auling G (1988) Polyamine pattern as chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol 11:1–8
Busse HJ, Bunka S, Hensel A, Lubitz W (1997) Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 47:698–708
Chang SC, Wang JT, Vandamme P, Hwang JH, Chang PS, Chen WM (2004) Chitinimonas taiwanensis gen. nov., sp. nov., a novel chitinolytic bacterium isolated from a freshwater pond for shrimp culture. Syst Appl Microbiol 27:43–49
Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 265–309
Dong K, Chen F, Du Y, Wang G (2013) Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense. Int J Syst Evol Microbiol 63:886–892
Embley TM, Wait R (1994) Structural lipids of eubacteria. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 121–161
Ewels P, Magnusson M, Lundin S, Käller M (2016) MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32:3047–3048
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
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
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
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol Biol Evol 34:2115–2122
Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P (2016) eggNOG4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 44:D286–D293
Kämpfer P, Rossellό-Mora R, Hermansson M, Persson F, Huber B, Falsen E, Busse HJ (2007) Undibacterium pigrum gen. nov., sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 57:1510–1515
Kang JY, Chun J, Jahng KY (2013) Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 63:1633–1638
Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY, Donachie SP (2013) Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium. Int J Syst Evol Microbiol 63:3280–3286
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
Lee I, Ouk Kim Y, Park SC, Chun J (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103
Ludwig W, Euzéby J, Whitman WB (2011) Taxonomic outlines of the phyla Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. In: Whitman W (ed) Bergey’s Manual of Systematic Bacteriology, vol 4, 2nd edn. Williams & Wilkins, Baltimore, p 21–24
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60
Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285
Nokhal TH, Schlegel HG (1983) Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 33:26–37
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards R, 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 Acid Res 42:D206–D214
Reichenbach H (1992) The order Cytophagales. In: Balows A, Trüper HG, Dworkin M, Harder W, Schleifer KH et al (eds) The prokaryotes, a handbook on the biology of bacteria: ecophysiology, isolation, identification, applications, 2nd edn. Springer, New York, NY, pp 3631–3675
Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131
Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe Magazine 9:111–118
Saitou N, Nei M (1987) The neighbor-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406–425
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc, Newark, DE
Schmidt K, Connor A, Britton G (1994) Analysis of pigments: carotenoids and related polyenes. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 403–461
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069
Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al (eds) Methods for general and molecular bacteriology, 3rd. American Society for Microbiology, Washington, DC, pp 330–393
Weisburg WG, Burns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
Wen CM, Tseng CS, Cheng CY, Li YK (2002) Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 35:213–219
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
Funding
The authors received no specific grant from any funding agency.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflicts of interest
The authors declare that there are 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
About this article
Cite this article
Chen, WM., You, YX., Young, CC. et al. Flavobacterium difficile sp. nov., isolated from a freshwater waterfall. Arch Microbiol 203, 4449–4459 (2021). https://doi.org/10.1007/s00203-021-02440-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00203-021-02440-1