Abstract
Strain 6021061333T was isolated from the sputum of 16-year-old girl with cystic fibrosis following a pulmonary exacerbation. This bacterial strain could not be identified by our systematic MALDI-TOF mass spectrometry screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 97.83% sequence identity with Chryseobacterium kwangjuense strain KJ1R5T, the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. Colonies are yellow, circular and 0.5–1 mm in diameter after cultivation at 28 °C for 24 h on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 28–37 °C (optimally at 28 °C). Strain 6021061333T is Gram-negative, non-motile and strictly aerobic bacillus. It is catalase and oxidase positive. The 4,864,678 bp-long genome, composed of five contigs, has a G+C content of 38.86%. Out of the 4427 predicted genes, 4342 were protein-coding genes and 85 were RNAs. The major fatty acids are branched (13-methyl-tetradecanoic acid and 15-methyl-hexadecenoic acid). Digital DNA–DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of the strain 6021061333T against genomes of the type strains of related species ranged between 23.60 and 50.40% and between 79.31 and 93.06%, respectively. According to our taxonogenomics results, we propose the creation of Chryseobacterium phocaeense sp. nov. that contains the type strain 6021061333T (= CSUR P2660, = CECT 9670).
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Auch AF, von Jan M, Klenk H-P, Göker M (2010) Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2:117–134. https://doi.org/10.4056/sigs.531120
Aziz RK, Bartels D, Best AA et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75
Bankevich A, Nurk S, Antipov D et al (2012) SPAdes—a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
Bernardet JF, Vancanneyt M, Matte-Tailliez O et al (2005) Polyphasic study of Chryseobacterium strains isolated from diseased aquatic animals. Syst Appl Microbiol 28:640–660. https://doi.org/10.1016/j.syapm.2005.03.016
Bittar F, Keita MB, Lagier J-C et al (2014) Gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools. Sci Rep 4:7174. https://doi.org/10.1038/srep07174
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
De Beer H, Hugo CJ, Jooste PJ et al (2005) Chryseobacterium vrystaatense sp. nov., isolated from raw chicken in a chicken-processing plant. Int J Syst Evol Microbiol 55:2149–2153. https://doi.org/10.1099/ijs.0.63746-0
Deng L, Li MF, Li YH et al (2015) Chryseobacterium indologenes in four patients with leukemia. Transpl Infect Dis 17:583–587. https://doi.org/10.1111/tid.12400
Dione N, Sankar SA, Lagier JC et al (2016) Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 10:66–76. https://doi.org/10.1016/j.nmni.2016.01.002
Dugas JE, Zurek L, Paster BJ et al (2001) Isolation and characterization of a Chryseobacterium strain from the gut of the American cockroach, Periplaneta americana. Arch Microbiol 175:259–262. https://doi.org/10.1007/s002030000243
Green BT, Nolan PE (2001) Cellulitis and bacteraemia due to Chryseobacterium indologenes. J Infect 42:219–220. https://doi.org/10.1053/jinf.2001.0822
Gupta SK, Padmanabhan BR, Diene SM et al (2014) ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 58:212–220. https://doi.org/10.1128/AAC.01310-13
Hadjadj L, Rathored J, Keita MB et al (2016) Non contiguous-finished genome sequence and description of Microbacterium gorillae sp. nov. Stand Genomic Sci 11:32. https://doi.org/10.1186/s40793-016-0152-z
Hantsis-Zacharov E, Halpern M (2007) Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk. Int J Syst Evol Microbiol 57:2344–2348. https://doi.org/10.1099/ijs.0.65115-0
Hantsis-Zacharov E, Shaked T, Senderovich Y, Halpern M (2008) Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow’s milk. Int J Syst Evol Microbiol 58:2635–2639. https://doi.org/10.1099/ijs.0.65819-0
Hernandez-Divers SJ, Hensel P, Gladden J et al (2009) Investigation of shell disease in map turtles (Graptemys spp.). J Wildl Dis 45:637–652. https://doi.org/10.7589/0090-3558-45.3.637
Holmes B, Owen RJ, Steigerwalt AG et al (1984) Flavobacterium gleum, a new species found in human clinical specimens. Int J Syst Evol Microbiol 34:21–25. https://doi.org/10.1099/00207713-34-1-21
Holmes B, Steigerwalt AG, Nicholson AC (2013) DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov. Int J Syst Evol Microbiol 63:4639–4662. https://doi.org/10.1099/ijs.0.054353-0
Hsueh PR, Hsiue TR, Wu JJ et al (1996) Flavobacterium indologenes bacteremia: clinical and microbiological characteristics. Clin Infect Dis 23:550–555. https://doi.org/10.1093/clinids/23.3.550
Hyatt D, Chen G-L, LoCascio PF et al (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119. https://doi.org/10.1186/1471-2105-11-119
Kämpfer P, McInroy JA, Glaeser SP (2013) Chryseobacterium zeae sp. nov., Chryseobacterium arachidis sp. nov., and Chryseobacterium geocarposphaerae sp. nov. isolated from the rhizosphere environment. Antonie van Leeuwenhoek 105:491–500. https://doi.org/10.1007/s10482-013-0101-4
Lagesen K, Hallin P, Rødland EA et al (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. https://doi.org/10.1093/nar/gkm160
Lagier JC, Armougom F, Million M et al (2012) Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18:1185–1193. https://doi.org/10.1111/1469-0691.12023
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964
Luo R, Liu B, Xie Y et al (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1(1):18. https://doi.org/10.1186/2047-217x-1-18
McKew G (2014) Severe sepsis due to Chryseobacterium indologenes in an immunocompetent adventure traveler. J Clin Microbiol 52:4100–4101. https://doi.org/10.1128/JCM.01691-14
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013a) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P (2013b) When should a DDH experiment be mandatory in microbial taxonomy? Arch Microbiol 195:413–418. https://doi.org/10.1007/s00203-013-0888-4
Montero-Calasanz MDC, Goker M, Rohde M et al (2013) Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. Int J Syst Evol Microbiol 63:4386–4395. https://doi.org/10.1099/ijs.0.052456-0
Montero-Calasanz MDC, Göker M, Rohde M et al (2014) Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense. Syst Appl Microbiol 37:342–350. https://doi.org/10.1016/j.syapm.2014.04.004
Ouk Kim Y, Chun J, Lee I, Park S-C (2016) OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
Ramasamy D, Mishra AK, Lagier J-C et al (2014) A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 64:384–391. https://doi.org/10.1099/ijs.0.057091-0
Sang MK, Kim HS, Myung IS et al (2013) Chryseobacterium kwangjuense sp. nov., isolated from pepper (Capsicum annuum L.) root. Int J Syst Evol Microbiol 63:2835–2840. https://doi.org/10.1099/ijs.0.048496-0
Sasser, M (2006) Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). MIDI, Technical Note 101
Seck EH, Beye M, Traore SI et al (2017) Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics. MicrobiologyOpen 55:e00535. https://doi.org/10.1002/mbo3.535
Sharma P, Gupta SK, Diene SM, Rolain JM (2015) Whole-genome sequence of Chryseobacterium oranimense, a colistin-resistant bacterium isolated from a cystic fibrosis patient in France. Antimicrob Agents Chemother 59:1696–1706. https://doi.org/10.1128/AAC.02417-14
Tai CJ, Kuo HP, Lee FL et al (2006) Chryseobacterium taiwanense sp. nov., isolated from soil in Taiwan. Int J Syst Evol Microbiol 56:1771–1776. https://doi.org/10.1099/ijs.0.64294-0
Vandamme P, Bernardet JF, Segers P et al (1994) NOTES: new perspectives in the classification of the Flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Evol Microbiol 44:827–831. https://doi.org/10.1099/00207713-44-4-827
Vaneechoutte M, Kampfer P, De Baere T et al (2007) Chryseobacterium hominis sp. nov., to accommodate clinical isolates biochemically similar to CDC groups II-h and II-c. Int J Syst Evol Microbiol 57:2623–2628. https://doi.org/10.1099/ijs.0.65158-0
Wang X, Hu Z, Fan Y, Wang H (2013) Chryseobacterium indologenes catheter-related meningitis in an elderly patient after intracranial aneurysm clipping surgery. Neurol Sci 35:113–115. https://doi.org/10.1007/s10072-013-1500-z
Xu L, Huo Y-Y, Li Z-Y et al (2015) Chryseobacterium profundimaris sp. nov., a new member of the family Flavobacteriaceae isolated from deep-sea sediment. Antonie van Leeuwenhoek 107:979–989. https://doi.org/10.1007/s10482-015-0390-x
Yang F, Liu H-M, Zhang R et al (2015) Chryseobacterium shandongense sp. nov., isolated from soil. Int J Syst Evol Microbiol 65:1860–1865. https://doi.org/10.1099/ijs.0.000186
Young CC, Kämpfer P, Shen FT et al (2005) Chryseobacterium formosense sp. nov., isolated from the rhizosphere of Lactuca sativa L. (garden lettuce). Int J Syst Evol Microbiol 55:423–426. https://doi.org/10.1099/ijs.0.63331-0
Zdanowski MK, Weglenski P, Golik P et al (2004) Bacterial diversity in Adélie penguin, Pygoscelis adeliae, guano: molecular and morpho-physiological approaches. FEMS Microbiol Ecol 50:163–173. https://doi.org/10.1016/j.femsec.2004.06.012
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. https://doi.org/10.1101/gr.074492.107
Acknowledgements
This work was supported by the IHU Méditerranée Infection and by the French Government under the «Investissements d’avenir» (Investments for the Future) program managed by the Agence Nationale de la Recherche (ANR, fr: National Agency for Research) (reference: Méditerranée Infection 10-IAHU-03). This work was also supported by Région Provence Alpes Côte d’Azur and European funding FEDER PRIMI.
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Abou Abdallah, R., Okdah, L., Bou Khalil, J. et al. Draft genome and description of Chryseobacterium phocaeense sp. nov.: a new bacterial species isolated from the sputum of a cystic fibrosis patient. Arch Microbiol 201, 1361–1368 (2019). https://doi.org/10.1007/s00203-019-01704-1
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DOI: https://doi.org/10.1007/s00203-019-01704-1