Auch AF, von JM, Klenk HP, 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):29. https://doi.org/10.4056/sigs.531120
Beveridge T (2001) Use of the Gram stain in microbiology. Biotech Histochem 76(3):111–118
Article CAS PubMed Google Scholar
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
Article CAS PubMed PubMed Central Google Scholar
Chaudhary DK, Lee SD, Kim J (2017) Lysobacter olei sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 67:4660–4666. https://doi.org/10.1099/ijsem.0.002348
Article CAS PubMed Google Scholar
Choi H, Im WT, Park JS (2018) Lysobacter spongiae sp. nov. isolated from spongin. J Microbiol 56(2):97–103. https://doi.org/10.1007/s12275-018-7462-3
Christensen P, Cook FD (1978) Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28:367–393. https://doi.org/10.1099/00207713-28-3-367
Coil D, Jospin G, Darling AE (2014) A5-MiSeq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31:587–589. https://doi.org/10.1093/bioinformatics/btu661
Article CAS PubMed Google Scholar
Farris MH, Olson JB (2007) Detection of Actinobacteria cultivated from environmental samples reveals bias in universal primers. Lett Appl Microbiol 45(4):376–381. https://doi.org/10.1111/j.1472-765X.2007.02198.x
Article CAS PubMed Google Scholar
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Article CAS PubMed Google Scholar
Gross H, Trappen S-V, Cleenwerck I, Miess H, Vos PD (2016) Reclassification of Pseudomonas sp. PB-6250t as Lysobacter firmicutimachus sp. nov. Int J Syst Evol Microbiol 66(10):4162–4166. https://doi.org/10.1099/ijsem.0.001329
Kates M (1972) Techniques of lipidology: isolation, analysis and identification of lipids. In: Work TS, Work E (eds) Laboratory techniques in biochemistry and molecular biology, vol 3. Elsevier, Amsterdam, pp 269–610
Kimura MA (1980) Simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120
Article CAS PubMed Google Scholar
Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2367
Lee I, Ouk KY, Park SC, Chun J (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
Article CAS PubMed Google Scholar
Lee SY, Kim PS, Sung H, Hyun DW, Bae JW (2022) Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork. J Microbiol 60:469–477. https://doi.org/10.1007/s12275-022-1647-5
Article CAS PubMed Google Scholar
Liu ZY, Jiang PQ, Niu GJ, Wang WJ, Li J (2022) Lysobacter antarcticus sp. nov., an SUF-system-containing bacterium from Antarctic coastal sediment. Int J Syst Evol Microbiol 72(2):1466–5034. https://doi.org/10.1099/ijsem.0.005250
Margesin R, Zhang DC, Albuquerque L, Froufe HJC, Egas C, da Costa MS (2018) Lysobacter silvestris sp. nov., isolated from alpine forest soil, and reclassification of Luteimonas tolerans as Lysobacter tolerans comb. nov. Int J Syst Evol Microbiol 68:1571–1577. https://doi.org/10.1099/ijsem.0.002710
Article CAS PubMed Google Scholar
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):1471–2105. https://doi.org/10.1186/1471-2105-14-60
Mikkel S (2016) Adapter Removal v2: rapid adapter trimming, identification, and read merging. BMC Res Notes 9:88. https://doi.org/10.1186/s13104-016-1900-2
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Mobley HL, Doyle RJ, Streips UN, Langemeier SO (1982) Transport and incorporation of N-acetyl-D-glucosamine in Bacillus subtilis. J Bacteriol 150(1):8–15. https://doi.org/10.1128/jb.150.1.8-15.1982
Article CAS PubMed PubMed Central Google Scholar
Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y (2013) Assembling genomes and mini-metagenomes from highly chimeric reads. Lect N Bioinformat 7821:158–170. https://doi.org/10.1007/978-3-642-37195-0_13
Park JH, Kim R, Aslam Z, Jeon CO, Chung YR (2008) Lysobacter capsici sp. nov., with antimicrobial activity, isolated from the rhizosphere of pepper, and emended description of the genus Lysobacter. Int J Syst Evol Microbiol 58(Pt 2):387–92. https://doi.org/10.1099/ijs.0.65290-0
Raj PS, Ramaprasad EV, Vaseef S, Sasikala C, Ramana C (2013) Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream. Int J Syst Evol Microbiol 63:181–186. https://doi.org/10.1099/ijs.0.038471-0
Article CAS PubMed Google Scholar
Richter M, RossellóMóra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131. https://doi.org/10.1073/pnas.0906412106
Article PubMed PubMed Central Google Scholar
Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9:945–967
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Article CAS PubMed Google Scholar
Sang EJ, Hyo JL, Che OJ (2016) Lysobacter aestuarii sp nov. isolated from estuary sediment. Int J Syst Evol Microbiol 66:1346–1351. https://doi.org/10.1099/ijsem.0.000884
Siddiqi MZ, Im WT (2016) Lysobacter pocheonensis sp. nov., isolated from soil of a ginseng field. Arch Microbiol 198:551–557
Article CAS PubMed Google Scholar
Srinivasan S, Kim MK, Sathiyaraj G, Kim HB, Kim YJ, Yang DC (2009) Lysobacter soli sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 60(7):1543–1547. https://doi.org/10.1099/ijs.0.016428-0
Weon HY, Kim BY, Baek YK, Yoo SH, Kwon SW, Stackebrandt E, Go SJ (2006) Two novel species, Lysobacter daejeonensis sp. nov. and Lysobacter yangpyeongensis sp. nov., isolated from Korean greenhouse soils. Int J Syst Evol Microbiol 56(Pt 5):947–951. https://doi.org/10.1099/ijs.0.64095-0
Xiao M, Zhou XK, Chen X, Duan YQ, Alkhalifah DHM, Im WT, Hozzein WN, Chen W, Li WJ (2019) Lysobacter tabacisoli sp. nov. isolated from rhizosphere soil of Nicotiana tabacum. Int J Syst Evol 69(7):1875–1880. https://doi.org/10.1099/ijsem.0.003164
Xu L, Huang XX, Fan DL, Sun JQ (2020) Lysobacter alkalisoli sp. nov., a chitin-degrading strain isolated from saline-alkaline soil. Int J Syst Evol Microbiol 70:1273–1281. https://doi.org/10.1099/ijsem.0.003911
Article CAS PubMed Google Scholar
Ye XM, Chu CW, Shi C, Zhu JC, He Q, He J (2015) Lysobacter caeni sp. nov., isolated from the sludge of a pesticide manufacturing factory. Int J Syst Evol Microbiol 65(Pt 3):845–850. https://doi.org/10.1099/ijs.0.000024
Zhang L, Bai J, Wang Y, Wu GL, Dai J, Fang CX (2011) Lysobacter korlensis sp. nov. and Lysobacter bugurensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 61(Pt 9):2259–2265. https://doi.org/10.1099/ijs.0.024448-0
Zhang XJ, Yao Q, Wang YH, Yang SZ, Feng GD, Zhu HH (2019) Lysobacter silvisoli sp. nov. isolated from forest soil. Int J Syst Evol Microbiol 69:93–98. https://doi.org/10.1099/ijsem.0.003105
留言 (0)