Gledhill WE, Casida LE (1969) Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia. Appl Microbiol 18(3):340–349. https://doi.org/10.1128/am.18.3.340-349.1969
Article PubMed PubMed Central CAS Google Scholar
Ortiz-Martinez A, Gonzalez JM, Evtushenko LI, Jurado V, Laiz L, Groth I, Saiz-Jimenez C (2004) Reclassification of Agromyces fucosus subsp. hippuratus as Agromyces hippuratus sp. nov., comb. nov. and emended description of Agromyces fucosus. Int J Syst Evol Microbiol 54(5):1553–1556. https://doi.org/10.1099/ijs.0.02856-0
Article PubMed CAS Google Scholar
Zgurskaya HI, Evtushenko LI, Akimov VN, Voyevoda HV, Dobrovolskaya TG, Lysak LV, Kalakoutskii LV (1992) Emended description of the genus Agromyces and description of Agromyces cerinus subsp. cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov. Int J Syst Evol Microbiol 42(4):635–641. https://doi.org/10.1099/00207713-42-4-635
Parte AC, Carbasse JS, Meier-Kolthoff JP, Reimer LC, Göker M (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607–5612. https://doi.org/10.1099/ijsem.0.004332
Article PubMed PubMed Central Google Scholar
Chen J, Chen HM, Zhang YQ et al (2011) Agromyces flavus sp. nov., an actinomycete isolated from soil. Int J Syst Evol Microbiol 61(7):1705–1709. https://doi.org/10.1099/ijs.0.023242-0
Article PubMed CAS Google Scholar
Dastager SG, Qiang ZL, Damare S, Tang SK, Li WJ (2012) Agromyces indicus sp. nov., isolated from mangroves sediment in Chorao Island, Goa, India. Antonie Van Leeuwenhoek 102:345–352. https://doi.org/10.1007/s10482-012-9744-9
Article PubMed CAS Google Scholar
Hamada M, Shibata C, Ishida Y, Tamura T, Yamamura H, Hayakawa M, Suzuki KI (2014) Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil. Int J Syst Evol Microbiol 64(Pt3):833–838. https://doi.org/10.1099/ijs.0.057349-0
Article PubMed CAS Google Scholar
Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C (2005) Agromyces subbeticus sp. nov., isolated from a cave in southern Spain. Int J Syst Evol Microbiol 55(5):1897–1901. https://doi.org/10.1099/ijs.0.63637-0
Article PubMed CAS Google Scholar
Sun TY, Cao P, Sun KX et al (2019) Agromyces tardus sp. nov., an actinobacterium isolated from the rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 69(10):3268–3275. https://doi.org/10.1099/ijsem.0.003621
Article PubMed CAS Google Scholar
Heo J, Hamada M, Tamura T et al (2020) Agromyces protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis. Int J Syst Evol Microbiol 70(2):1259–1265. https://doi.org/10.1099/ijsem.0.003908
Article PubMed CAS Google Scholar
Serwecinska L (2020) Antimicrobials and antibiotic-resistant bacteria: a risk to the environment and to public health. Water 12(12):3313. https://doi.org/10.3390/w12123313
Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173(2):697–703. https://doi.org/10.1128/jb.173.2.697-703.1991
Article PubMed PubMed Central CAS Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096
Article PubMed PubMed Central CAS Google Scholar
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/bf01731581
Article PubMed CAS Google Scholar
Golosova O, Henderson R, Vaskin Y et al (2014) Unipro UGENE NGS pipelines and components for variant calling. RNA-seq and ChIP-seq data analyses PeerJ 2(8):e644. https://doi.org/10.7717/peerj.644
Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A (2020) Using SPAdes De Novo assembler. Curr Protoc Bioinformatics 70:e102–e102. https://doi.org/10.1002/cpbi.102
Article PubMed CAS Google Scholar
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S (2018) High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. https://doi.org/10.1038/s41467-018-07641-9
Article PubMed PubMed Central Google Scholar
Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M (2022) TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 50(D17):D801–D807. https://doi.org/10.1093/nar/gkab902
Article PubMed CAS Google Scholar
Tatiana T, Michael DC, Azat B et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44(14):6614–6624. https://doi.org/10.1093/nar/gkw569
Huerta-Cepas J, Szklarczyk D, Heller D et al (2019) eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47(D1):D309–D314. https://doi.org/10.1093/nar/gky1085
Article PubMed CAS Google Scholar
Zhang DF, He W, Shao ZZ, Ahmed I et al (2023) Corrigendum: phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae. Int J Syst Evol Microbiol 73(12):006156. https://doi.org/10.1099/ijsem.0.006207
Mistry J, Finn R (2007) Pfam: a domain-centric method for analyzing proteins and proteomes. Methods Mol Biol 396:43–58. https://doi.org/10.1385/1-59745-515-6:43
Article PubMed CAS Google Scholar
Potter SC, Luciani A, Eddy SR, Park Y, Lopez R, Finn RD (2018) HMMER web server: 2018 update. Nucleic Acids Res 46(W1):W200–W204. https://doi.org/10.1093/nar/gky448
Article PubMed PubMed Central CAS Google Scholar
Sievers F, Higgins DG (2021). The Clustal Omega Multiple Alignment Package. In: Katoh K (eds) Multiple Sequence Alignment, Methods in Molecular Biology. Humana, New York, NY.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) Trimal: a tool for automated alignment trimming in large-scale phylogenetic analyses. BioinformaticsI 25(15):1972–1973. https://doi.org/10.1093/bioinformatics/btp348
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37(5):1530–1534. https://doi.org/10.1093/molbev/msaa015
Article PubMed PubMed Central CAS Google Scholar
Zhang DF, He W, Shao ZZ, Ahmed I, Zhang YQ, Li WJ, Zhao Z (2023) Easycgtree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets. Bmc BioinformaticsI 24:390. https://doi.org/10.1186/s12859-023-05527-2
Athalye M, Noble WC, Minnikin DE (1985) Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 58(5):507–512. https://doi.org/10.1111/j.1365-2672.1985.tb01491.x
Article PubMed CAS Google Scholar
Hiraishi A, Ueda Y, Ishihara J, Mori T (1996) Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42(6):457–469. https://doi.org/10.2323/jgam.42.457
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(5):233–241. https://doi.org/10.1016/0167-7012(84)90018-6
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