Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil

Ali, Z., Cousin, S., Frühling, A., Brambilla, E., Schumann, P., Yang, Y., & Stackebrandt, E. (2009). Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. International Journal of Systematic and Evolutionary Microbiology, 59, 2610–2617.

Article  CAS  PubMed  Google Scholar 

Baek, C., Shin, S. K., & Yi, H. (2018). Flavobacterium magnum sp. nov., Flavobacterium pallidum sp. nov., Flavobacterium crocinum sp. nov. and Flavobacterium album sp. nov. International Journal of Systematic and Evolutionary Microbiology, 68, 3837–3843.

Article  CAS  PubMed  Google Scholar 

Baker, G. C., Smith, J. J., & Cowan, D. A. (2003). Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods, 55, 541–555.

Article  CAS  PubMed  Google Scholar 

Bayliss, S. C., Thorpe, H. A., Coyle, N. M., Sheppard, S. K., & Feil, E. J. (2019). PIRATE: a fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. Gigascience, 8, 119.

Article  Google Scholar 

Bergey, D., Harrison, F., Breed, R., Hammer, B., & Huntoon, F. (1923). Genus II. Flavobacterium gen. nov. Bergey’s manual of determinative bacteriology (pp. 97–117). Baltimore: The Williams & Wilkins Co.

Google Scholar 

Bernardet, J. F., & Bowman, J. P. (2006). The genus Flavobacterium. In M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer, & E. Stackebrandt (Eds.), The prokaryotes: The biology of bacteria (3rd ed., pp. 481–531). Springer.

Chapter  Google Scholar 

Bernardet, J. F., 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. International Journal of Systematic and Evolutionary Microbiology, 52, 1049–1070.

CAS  PubMed  Google Scholar 

Bernardet, J. F., 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). International Journal of Systematic and Evolutionary Microbiology, 46, 128–148.

Google Scholar 

Blin, K., Shaw, S., Kloosterman, A. M., Charlop-Powers, Z., van Wezel, G. P., Medema, M. H., & Weber, T. (2021). antiSMASH 6.0: Improving cluster detection and comparison capabilities. Nucleic Acids Research, 49, W29–W35.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bu, J. H., & Cha, C. J. (2018). Flavobacterium foetidum sp. nov., isolated from ginseng soil. International Journal of Systematic and Evolutionary Microbiology, 68, 616–622.

Article  CAS  PubMed  Google Scholar 

Chan, P. P., Lin, B. Y., Mak, A. J., & Lowe, T. M. (2021). tRNAscan-SE 2.0: Improved detection and functional classification of transfer RNA genes. Nucleic Acids Research, 49, 9077–9096.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chaudhary, D. K., & Kim, J. (2018). Flavobacterium naphthae sp. nov., isolated from oil-contaminated soil. International Journal of Systematic and Evolutionary Microbiology, 68, 305–309.

Article  CAS  PubMed  Google Scholar 

Chen, W. M., Chen, W. T., Young, C. C., & Sheu, S. Y. (2019). Flavobacterium niveum sp. nov., isolated from a freshwater creek. International Journal of Systematic and Evolutionary Microbiology, 69, 271–277.

Article  CAS  PubMed  Google Scholar 

Chin, C. S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., et al. (2013). Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 10, 563–569.

Article  CAS  PubMed  Google Scholar 

Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D. R., da Costa, M. S., Rooney, A. P., Yi, H., Xu, X. W., De Meyer, S., et al. (2018). Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 68, 461–466.

Article  CAS  PubMed  Google Scholar 

Collins, M. D. (1985). Analysis of isoprenoid quinones. In T. Bergan (Ed.), Methods in microbiology (Vol. 18, pp. 329–366). Academic Press.

Google Scholar 

Declercq, A. M., Haesebrouck, F., Van den Broeck, W., Bossier, P., & Decostere, A. (2013). Columnaris disease in fish: A review with emphasis on bacterium-host interactions. Veterinary Research, 44, 27.

Article  PubMed  PubMed Central  Google Scholar 

Dong, K., Chen, F., Du, Y., & Wang, G. (2013a). Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense, Flavobacterium saliperosum and Flavobacterium suncheonense. International Journal of Systematic and Evolutionary Microbiology, 63, 886–892.

Article  CAS  PubMed  Google Scholar 

Dong, K., Chen, F., Du, Y., & Wang, G. (2013b). Flavobacterium hauense sp. nov., isolated from soil and emended descriptions of Flavobacterium subsaxonicum, Flavobacterium beibuense and Flavobacterium rivuli. International Journal of Systematic and Evolutionary Microbiology, 63, 3237–3242.

Article  CAS  PubMed  Google Scholar 

Dusa, A. (2021). Venn: Draw venn diagrams. https://github.com/dusadrian/venn.

Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Feldgarden, M., Brover, V., Gonzalez-Escalona, N., Frye, J. G., Haendiges, J., Haft, D. H., Hoffmann, M., Pettengill, J. B., Prasad, A. B., Tillman, G. E., et al. (2021). AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific Reports, 11, 12728.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783–791.

Article  PubMed  Google Scholar 

Frank, J. A., Reich, C. I., Sharma, S., Weisbaum, J. S., Wilson, B. A., & Olsen, G. J. (2008). Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Applied and Environmental Microbiology, 74, 2461–2470.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Holmes, B., & Owen, R. (1979). Proposal that Flavobacterium breve be substituted as the type species of the genus in place of Flavobacterium aquatile and emended description of the genus Flavobacterium. International Journal of Systematic and Evolutionary Microbiology, 29, 416–426.

Google Scholar 

Hyatt, D., Chen, G. L., Locascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010). Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.

Article  PubMed  PubMed Central  Google Scholar 

Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018). High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nature Communications, 9, 5114.

Article  PubMed  PubMed Central  Google Scholar 

Jukes, T. H., & Cantor, C. R. (1969). Evolution of protein molecules. In H. N. Munro (Ed.), Mammalian protein metabolism (Vol. 3, pp. 21–132). Academic Press.

Chapter  Google Scholar 

Kalvari, I., Nawrocki, E. P., Ontiveros-Palacios, N., Argasinska, J., Lamkiewicz, K., Marz, M., Griffiths-Jones, S., Toffano-Nioche, C., Gautheret, D., Weinberg, Z., et al. (2021). Rfam 14: Expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Research, 49, D192–D200.

Article  CAS  PubMed  Google Scholar 

Kang, J. Y., Chun, J., & Jahng, K. Y. (2013). Flavobacterium aciduliphilum sp. nov., isolated from freshwater, and emended description of the genus Flavobacterium. International Journal of Systematic and Evolutionary Microbiology, 63, 1633–1638.

Article  CAS  PubMed  Google Scholar 

Kim, J., Na, S. I., Kim, D., & Chun, J. (2021). UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. Journal of Microbiology, 59, 609–615.

Article  CAS  PubMed  Google Scholar 

Kim, M., Oh, H. S., Park, S. C., & Chun, J. (2014). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 64, 346–351.

Article  CAS  PubMed  Google Scholar 

Kuo, I., Saw, J., Kapan, D. D., Christensen, S., Kaneshiro, K. Y., & Donachie, S. P. (2013). Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai ‘i, and emended description of the genus Flavobacterium. International Journal of Systematic and Evolutionary Microbiology, 63, 3280–3286.

Article  CAS  PubMed  Google Scholar 

Laslett, D., & Canback, B. (2004). ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research, 32, 11–16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee, K., Kim, D. W., & Cha, C. J. (2021). Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data. Journal of Microbiology, 59, 270–280.

Article  CAS  PubMed  Google Scholar 

Li, A., Liu, H., Sun, B., Zhou, Y., & Xin, Y. (2014). Flavobacterium lacus sp. nov., isolated from a high-altitude lake, and emended description of Flavobacterium filum. International Journal of Systematic and Evolutionary Microbiology, 64, 933–939.

Article  CAS  PubMed  Google Scholar 

Liu, Y., Le Han, H., Zou, Y., & Kim, S. G. (2019). Flavobacterium ustbae sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia. International Journal of Systematic and Evolutionary Microbiology, 69, 3955–3960.

Article  CAS  PubMed  Google Scholar 

Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). BUSCO: assessing genomic data quality and beyond. Current Protocols, 1, e323.

留言 (0)

沒有登入
gif