Thiopseudomonas acetoxidans sp. nov., một loại vi khuẩn oxy hóa axit axetic và axit butyric được phân lập từ dung dịch lên men kỵ khí của thực phẩm thải

Alanjary M, Steinke K, Ziemert N (2019) AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 47:W276-w282. https://doi.org/10.1093/nar/gkz282 Antonov IV (2020) Two cobalt chelatase subunits can be generated from a single chlD gene via programed frameshifting. Mol Biol Evol 37:2268–2278. https://doi.org/10.1093/molbev/msaa081 Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, EdwarRA FK, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeilLK PD, Paczian T, Parrello B, Pusch GD, ReichC SR, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations usingsubsystemstechnology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75 Becker D, Popp D, Bonk F, Kleinsteuber S, Harms H, Centler F (2023) Metagenomic analysis of anaerobic microbial communities degrading short-chain fatty acids as sole carbon sources. Microorganisms 11:420. https://doi.org/10.3390/microorganisms11020420 Bertelli C, Laird MR, Williams KP, Simon Fraser University ResearchComputing Group, Lau BY, Hoad G, Winsor GL, Brinkman FSL (2017) IslandViewer 4: expandedprediction of genomic islands for larger-scale datasets. Nucleic Acids Res 45:W30-35. https://doi.org/10.1093/nar/gkx343 Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F, Alanjary M, Fetter A, Terlouw BR, Metcalf WW, Helfrich EJN, van Wezel GP, Medema MH, Weber T (2023) antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 51:W46–W50. https://doi.org/10.1093/nar/gkad344 Chan PP, Lowe TM (2019) tRNAscan-SE: Searching for tRNA genes in genomic sequences. Methods Mol Biol 1962:1–14. https://doi.org/10.1007/978-1-4939-9173-0_1 Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH (2019) GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36:1925–1927. https://doi.org/10.1093/bioinformatics/btz848 Chen S, Zhou Y, Chen Y, Gu J (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884–i890. https://doi.org/10.1093/bioinformatics/bty560 Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney AP, Yi H, Xu XW, De Meyer S, Trujillo ME (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516 Drobish AM, Emery BD, Whitney AM, Lauer AC, Metcalfe MG, McQuiston JR (2016) Oblitimonas alkaliphila gen. nov., sp. nov., in the family Pseudomonadaceae, recovered from a historical collection of previously unidentified clinical strains. Int J Syst Evol Microbiol 66:3063–3070. https://doi.org/10.1099/ijsem.0.001147 Fatollahi P, Ghasemi M, Yazdian F, Sadeghi A (2021) Ectoine production in bioreactor by Halomonas elongata DSM2581: Using MWCNT and Fe-nanoparticle. Biotechnol Prog 37:e3073. https://doi.org/10.1002/btpr.3073 Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416. https://doi.org/10.2307/2412116 Gervasoni S, Malloci G, Bosin A, Vargiu AV, Zgurskaya HI, Ruggerone P (2022) Recognition of quinolone antibiotics by the multidrug efflux transporter MexB of Pseudomonas aeruginosa. Phys Chem Chem Phys 24:16566–16575. https://doi.org/10.1039/d2cp00951j Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181-184. https://doi.org/10.1093/nar/gkn179 Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P (2019) eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47:D309–D314. https://doi.org/10.1093/nar/gky1085 Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, TsangKK LBA, Dave BM, Pereira S, Sharma AN, DoshiS CM, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS, Wright GD, McArthur AG (2017) CARD2017: expansion and model-centric curation of the comprehensiveantibiotic resistance database. Nucleic AcidsRes 45:D566-573. https://doi.org/10.1093/nar/gkw1004 Jiang CY, Liu Y, Liu YY, You XY, Guo X, Liu SJ (2008) Alicyclobacillus ferrooxydans sp. nov., a ferrous-oxidizing bacterium from solfataric soil. Int J Syst Evol Microbiol 58:2898–2903. https://doi.org/10.1099/ijs.0.2008/000562-0 Kellogg JA, Bankert DA, Withers GS, Sweimler W, Kiehn TE, Pfyffer GE (2001) Application of the Sherlock Mycobacteria Identification System using high-performance liquid chromatography in a clinical laboratory. J Clin Microbiol 39:964–970. https://doi.org/10.1128/jcm.39.3.964-970.2001 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 Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096 Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. https://doi.org/10.1093/nar/gkm160 Liu W, Cong B, Lin J, Zhao L, Liu S (2022) Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment. BMC Genomics 23:713. https://doi.org/10.1186/s12864-022-08942-6 Liu T, Ning L, Mei C, Li S, Zheng L, Qiao P, Wang H, Hu T, Zhong W (2023) Synthetic bacterial consortia enhanced the degradation of mixed priority phthalate ester pollutants. Environ Res 235:116666. https://doi.org/10.1016/j.envres.2023.116666 Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18. https://doi.org/10.1186/2047-217x-1-18 Luo C, Rodriguez RL, Konstantinidis KT (2014) MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 42:e73. https://doi.org/10.1093/nar/gku169 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. https://doi.org/10.1186/1471-2105-14-60 Nagakubo S, Nishino K, Hirata T, Yamaguchi A (2002) The putative response regulator BaeR stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, MdtABC. J Bacteriol 184:4161–4167. https://doi.org/10.1128/jb.184.15.4161-4167.2002 Orans J, Johnson MD, Coggan KA, Sperlazza JR, Heiniger RW, Wolfgang MC, Redinbo MR (2010) Crystal structure analysis reveals Pseudomonas PilY1 as an essential calcium-dependent regulator of bacterial surface motility. Proc Natl Acad Sci U S A 107:1065–1070. https://doi.org/10.1073/pnas.0911616107 Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW (2015) CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. https://doi.org/10.1101/gr.186072.114 Qin H, Wang D, Xing X, Tang Y, Wei X, Chen X, Zhang W, Chen A, Li L, Liu Y, Zhu B (2021) A few key nirK- and nosZ-denitrifier taxa play a dominant role in moisture-enhanced N2O emissions in acidic paddy soil. Geoderma 385:114917. https://doi.org/10.1016/j.geoderma.2020.114917 Richter M, Rosselló-Móra R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131. https://doi.org/10.1073/pnas.0906412106 Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9:111–118. https://doi.org/10.1128/microbe.9.111.1 Rudra B, Gupta RS (2021) Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera. Int J Syst Evol Microbiol 71:005011. https://doi.org/10.1099/ijsem.0.005011 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 Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: Tarnished gold standards. Microbiol Today 8:6–9 Suvorova IA, Ravcheev DA, Gelfand MS (2012) Regulation and evolution of malonate and propionate catabolism in proteobacteria. J Bacteriol 194:3234–3240. https://doi.org/10.1128/JB.00163-12 Tan W-B, Jiang Z, Chen C, Yuan Y, Gao L-F, Wang H-F, Cheng J, Li WJ, Wang A-J (2015) Thiopseudomonas denitrificans gen. nov., sp. nov., isolated from anaerobic activated sludge. Int J Syst Evol Microbiol 65:225–229. https://doi.org/10.1099/ijs.0.064634-0 Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569 Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL (2013) Microbial genomic taxonomy. BMC Genomics 14:913. https://doi.org/10.1186/1471-2164-14-913 Tindall BJ (1990) Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66:199–202. https://doi.org/10.1016/0378-1097(90)90282-U Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR et al (eds) Methods for general and molecular bacteriology, 3rd. American Society for Microbiology, Washington, pp 330–393 Torrents E, Eliasson R, Wolpher H, Gräslund A, Reichard P (2001) The anaerobic ribonucleotide reductase from Lactococcus lactis. Interactions between the two proteins NrdD and NrdG. J Biol Chem 276:33488–33494. https://doi.org/10.1074/jbc.M103743200 Truchon AN, Hendrich CG, Bigott AF, Dalsing BL, Allen C (2022) NorA, HmpX, and NorB cooperate to reduce NO toxicity during denitrification and plant pathogenesis in Ralstonia solanacearum. Microbiol Spectr 10:e0026422. https://doi.org/10.1128/spectrum.00264-22 van den Berg J, Galbiati H, Rasmussen A, Miller S, Poolman B (2016) On the mobility, membrane location and functionality of mechanosensitive channels in Escherichia coli. Sci Rep 6:32709. https://doi.org/10.1038/srep32709 Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703. https://doi.org/10.1128/jb.173.2.697-703.1991 Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755 Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4 Zhang J, Liu Y-X, Guo X, Qin Y, Garrido-Oter R, Schulze-Lefert P, Bai Y (2021) High-throughput cultivation and identification of bacteria from the plant root microbiota. Nat Protoc 16:988–1012. https://doi.org/10.1038/s41596-020-00444-7 Zhang H, Liang Z, Zhao M, Ma Y, Luo Z, Li S, Xu H (2022) Metabolic engineering of Escherichia coli for ectoine production with a fermentation strategy of supplementing the amino donor. Front Bioeng Biotechnol 10:824859. https://doi.org/10.3389/fbioe.2022.824859