Khan ST, Hiraishi A (2002) Diaphorobacter nitroreducens gen. nov., sp. nov., a poly(3-hydroxybutyrate)-degrading denitrifying bacterium isolated from activated sludge. J Gen Appl Microbiol 48:299–308

Kim SJ, Moon JY, Ahn JH et al (2014) Diaphorobacter aerolatus sp. nov., isolated from air, and emended description of the genus Diaphorobacter. Int J Syst Evol Microbiol 64:513–517. https://doi.org/10.1099/ijs.0.051060-0

Article  CAS  PubMed  Google Scholar 

Pham VH, Park SJ, Roh Y et al (2009) Diaphorobacter oryzae sp. nov., isolated from a thiosulfate-oxidizing enrichment culture. Int J Syst Evol Microbiol 59:218–221. https://doi.org/10.1099/ijs.0.001669-0

Article  CAS  PubMed  Google Scholar 

Liu Y, Zhu HH (2019) Diaphorobacter polyhydroxybutyrativorans Qiu et al. 2015 is a later heterotypic synonym of Diaphorobacter nitroreducens Khan and Hiraishi 2003. Int J Syst Evol Microbiol 69:2954–2957. https://doi.org/10.1099/ijsem.0.003582

Article  CAS  PubMed  Google Scholar 

Ruan Z, Cao W, Zhu J et al (2022) Comparative genomic analysis of Pseudoxanthomonas sp. X-1, a bromoxynil octanoate-degrading bacterium, and its related type strains. Curr Microbiol 79:65. https://doi.org/10.1007/s00284-021-02735-y

Chung J hui, Lee JY, Choi GH, et al (2022) Horticoccus luteus gen. nov., sp. nov., a novel member of the phylum Verrucomicrobia isolated from a Dichlorodiphenyltrichloroethane (DDT)-contaminated orchard soil. Curr Microbiol 79:340. https://doi.org/10.1007/s00284-022-03036-8

Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2014) Phenotypic characterization and the principles of comparative systematics. Methods Gen Mol Microbiol 330–393. https://doi.org/10.1128/9781555817497.ch15

Tindall BJ (1990) A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 13:128–130. https://doi.org/10.1016/S0723-2020(11)80158-X

Article  CAS  Google Scholar 

Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202. https://doi.org/10.1016/0378-1097(90)90282-U

Article  CAS  Google Scholar 

Miller LT (1982) Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586

Article  CAS  PubMed  PubMed Central  Google Scholar 

Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 3:208–218

Article  CAS  Google Scholar 

Heo J, Cho HY, Heo I et al (2019) Pulveribacter suum gen. nov., sp. nov., isolated from a pig farm dust collector. Int J Syst Evol Microbiol 69:1864–1869. https://doi.org/10.1099/ijsem.0.003082

Article  CAS  PubMed  Google Scholar 

Du H, Jiao N, Hu Y, Zeng Y (2006) Diversity and distribution of pigmented heterotrophic bacteria in marine environments. FEMS Microbiol Ecol 57:92–105. https://doi.org/10.1111/j.1574-6941.2006.00090.x

Article  CAS  PubMed  Google Scholar 

Kim OS, Cho YJ, Lee K et al (2012) Introducing EzTaxon-e: A prokaryotic 16s rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721. https://doi.org/10.1099/ijs.0.038075-0

Article  CAS  PubMed  Google Scholar 

Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

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 

Rzhetsky A, Nei M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10(5):1073–1095. https://doi.org/10.1093/oxfordjournals.molbev.a040056

Article  CAS  PubMed  Google Scholar 

Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38(7):3022–3027. https://doi.org/10.1093/molbev/msab120

Article  CAS  PubMed  PubMed Central  Google Scholar 

Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics (Oxford, England) 30(14):2068–2069. https://doi.org/10.1093/bioinformatics/btu153

Article  CAS  PubMed  Google Scholar 

Yoon SH, HaLim SJ et al (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek, Int J Gen Mol Microbiol 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4

Article  CAS  Google Scholar 

Auch AF, von Jan M et al (2010) Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2(1):117–134. https://doi.org/10.4056/sigs.531120

Article  PubMed  PubMed Central  Google Scholar 

Gu Z, Gu L, Eils R, Schlesner M, Brors B (2014) circlize Implements and enhances circular visualization in R. Bioinformatics (Oxford, England) 30(19):2811–2812. https://doi.org/10.1093/bioinformatics/btu393

Article  CAS  PubMed  Google Scholar 

Ebenhoh O, Handorf T, Heinrich R (2004) Structural analysis of expanding metabolic networks. Genome Inform 15(1):35–45. https://doi.org/10.11234/GI1990.15.35

Tal O, Bartuv R, Vetcos M et al (2021) NetCom: a network-based tool for predicting metabolic activities of microbial communities based on interpretation of metagenomics data. Microorganisms 9(9):1838. https://doi.org/10.3390/microorganisms9091838

Article  CAS  PubMed  PubMed Central  Google Scholar 

Team RC (2010) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. Computing 14:12–21

Stackebrandt E, Frederiksen W, Garrity GM et al (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047. https://doi.org/10.1099/ijs.0.02360-0.02360

Richter M et al (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106(45):19126–19131. https://doi.org/10.1073/pnas.0906412106

Article  PubMed  PubMed Central  Google Scholar