Allardet-Servent, A., Michaux-Charachon, S., Jumas-Bilak, E., Karayan, L., Ramuz, M. 1993. Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome. J Bacteriol. , 175(24), 7869- 74.
Ayer, W.A., Muir, D.J., Chakravarty, P. 1996. Phenolic and other metabolites of Phellinus pini, a fungus pathogenic to pine. Phytochemistry, 42(5), 1321- 1324.
Barka, E.A., Vatsa, P., Sanchez, L., Gaveau-Vaillant, N., Jacquard, C., Meier- Kolthoff, J.P., Klenk, H.P., Clement, C., Ouhdouch, Y., van Wezel, G.P. 2016. Taxonomy, Physiology, and Natural Products of Actinobacteria. Microbiol Mol Biol Rev, 80(1), 1-43.
Behera, B., Anil Vishnu, G.K., Chatterjee, S., Sitaramgupta, V.V., Sreekumar, N., Nagabhushan, A., Rajendran, N., Prathik, B.H., Pandya, H.J. 2019. Emerging technologies for antibiotic susceptibility testing. Biosens Bioelectron, 142, 111552.
Berdy, J. 2012. Thoughts and facts about antibiotics: where we are now and where we are heading. J Antibiot (Tokyo), 65(8), 385-95.
Berlinck, R.G.S., Monteiro, A.F., Bertonha, A.F., Bernardi, D.I., Gubiani, J.R., Slivinski, J., Michaliski, L.F., Tonon, L.A.C., Venancio, V.A., Freire, V.F. 2019. Approaches for the isolation and identification of hydrophilic, light- sensitive, volatile and minor natural products. Nat Prod Rep, 36(7), 981- 1004.
Besser, J., Carleton, H.A., Gerner-Smidt, P., Lindsey, R.L., Trees, E. 2018. Next- generation sequencing technologies and their application to the study and control of bacterial infections. Clin Microbiol Infect, 24(4), 335-341.
Bhattacharyya, P., Bose, S.K. 1967. Amino acid composition of cell wall and spore coat of Bacillus subtilis in relation to mycobacillin production. J Bacteriol. , 94(6), 2079–2080.
Bitok, J.K., Lemetre, C., Ternei, M.A., Brady, S.F. 2017. Identification of biosynthetic gene clusters from metagenomic libraries using PPTase complementation in a Streptomyces host. FEMS Microbiol Lett, 364(16).
Björnsson, L., Hugenholtz, P., Tyson, G.W., Blackall, L.L. 2002. Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology. , 148, 2309-18.
Blin, K., Shaw, S., Steinke, K., Villebro, R., Ziemert, N., Lee, S.Y., Medema, M.H., Weber, T. 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res.
Bloudoff, K., Fage, C.D., Marahiel, M.A., Schmeing, T.M. 2017. Structural and mutational analysis of the nonribosomal peptide synthetase heterocyclization domain provides insight into catalysis. Proc Natl Acad Sci U S A, 114(1), 95-100.
Bucar, F., Wube, A., Schmid, M. 2013. Natural product isolation--how to get from biological material to pure compounds. Nat Prod Rep, 30(4), 525-45.
Buston, H.W., Moss, M.O., Tyrrell, D. 1966. The influence of carbon dioxide on growth and sporulation of Chaetomium globosum. Transactions of the British Mycological Society, 49(3), 387-396.
Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., Knight, R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods., 7(5), 335-6.
Carver, T., Thomson, N., Bleasby, A., Berriman, M., Parkhill, J. 2009. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics., 25(1), 119-20.
Cavaletti, L., Monciardini, P., Bamonte, R., Schumann, P., Rohde, M., Sosio, M., Donadio, S. 2006. New lineage of filamentous, spore-forming, gram- positive bacteria from soil. Appl Environ Microbiol, 72(6), 4360-9.
Chakraborty, S., Rhee, K.Y. 2015. Tuberculosis Drug Development: History and Evolution of the Mechanism-Based Paradigm. Cold Spring Harb Perspect Med, 5(8), a021147.
Challis, G.L., Naismith, J.H. 2004. Structural aspects of non-ribosomal peptide biosynthesis. Current Opinion in Structural Biology, 14(6), 748-756.
Chang, Y.J., Land, M., Hauser, L., Chertkov, O., Del Rio, T.G., Nolan, M., Copeland, A., Tice, H., Cheng, J.F., Lucas, S., Han, C., Goodwin, L., Pitluck, S., Ivanova, N., Ovchinikova, G., Pati, A., Chen, A., Palaniappan, K., Mavromatis, K., Liolios, K., Brettin, T., Fiebig, A., Rohde, M., Abt, B., Goker, M., Detter, J.C., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H.P., Lapidus, A. 2011. Non- contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21). Stand Genomic Sci, 5(1), 97-111.
Charlesworth, B., Barton, N. 2004. Genome size: does bigger mean worse? Curr Biol, 14(6), R233-5.
Chaudhari, N.M., Gupta, V.K., Dutta, C. 2016. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep, 6, 24373.
Chen, L.Y., Lai, Y.M., Yang, Y.L., Zhao, X.Q. 2016. Genome mining reveals the biosynthetic potential of the marinederived strain Streptomyces marokkonensis M10. Synthetic and Systems Biotechnology, 1(1), 56-65.
Choulet, F., Aigle, B., Gallois, A., Mangenot, S., Gerbaud, C., Truong, C., Francou, F.X., Fourrier, C., Guerineau, M., Decaris, B., Barbe, V., Pernodet, J.L., Leblond, P. 2006a. Evolution of the terminal regions of the Streptomyces linear chromosome. Mol Biol Evol, 23(12), 2361-9.
Choulet, F., Gallois, A., Aigle, B., Mangenot, S., Gerbaud, C., Truong, C., Francou, F.X., Borges, F., Fourrier, C., Guerineau, M., Decaris, B., Barbe, V., Pernodet, J.L., Leblond, P. 2006b. Intraspecific variability of the terminal inverted repeats of the linear chromosome of Streptomyces ambofaciens. J Bacteriol, 188(18), 6599-610.
Chu, J., Vila-Farres, X., Inoyama, D., Ternei, M., Cohen, L.J., Gordon, E.A., Reddy, B.V., Charlop-Powers, Z., Zebroski, H.A., Gallardo-Macias, R., Jaskowski, M., Satish, S., Park, S., Perlin, D.S., Freundlich, J.S., Brady, S.F. 2016. Discovery of MRSA active antibiotics using primary sequence from the human microbiome. Nat Chem Biol, 12(12), 1004-1006.
Cody, W.L., Wilson, J.W., Hendrixson, D.R., McIver, K.S., Hagman, K.E., Ott, C.M., Nickerson, C.A., Schurr, M.J. 2008. Skim milk enhances the preservation of thawed -80 degrees C bacterial stocks. J Microbiol Methods, 75(1), 135- 8.
Collins, M.D., Pirouz, T., Goodfellow, M., Minnikin, D.E. 1977. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol. , 100(2), 221-30.
Cornelio, K., Espiritu, R.A., Hanashima, S., Todokoro, Y., Malabed, R., Kinoshita, M., Matsumori, N., Murata, M., Nishimura, S., Kakeya, H., Yoshida, M., Matsunaga, S. 2019. Theonellamide A, a marine-sponge-derived bicyclic peptide, binds to cholesterol in aqueous DMSO: Solution NMR-based analysis of peptide-sterol interactions using hydroxylated sterol. Biochim Biophys Acta Biomembr, 1861(1), 228-235.
Couch, J.N. 1949. A new group of organisms related to actinomyces. J. Elisha Mitchell Sci. Soc., 65, 315–318.
Crooks, G.E., Hon, G., Chandonia, J.M., Brenner, S.E. 2004. WebLogo: A sequence logo generator. Genome Research, 14, 1188-1190.
Darling, A.C., Mau, B., Blattner, F.R., Perna, N.T. 2004. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res., 14(7), 1394-403.
de Miera, L.E.S., Arroyo, P., de Luis Calabuig, E., Falagán, J., Ansola, G. 2014. High-throughput sequencing of 16S RNA genes of soil bacterial communities from a naturally occurring CO2 gas vent. International Journal of Greenhouse Gas Control, 29, 176-184.
Demain, A.L., Sanchez, S. 2009. Microbial drug discovery: 80 years of progress. J Antibiot (Tokyo). 62(1), 5-16.
Demharter, W., Hensel, R., Smida, J., Stackebrandt, E. 1989. Sphaerobacter thermophilus gen. nov., sp. nov. A Deeply Rooting Member of the Actinomycetes Subdivision Isolated from Thermophilically Treated Sewage Sludge. Systematic and Applied Microbiology, 11(3), 261-266.
den Hengst, C.D., Tran, N.T., Bibb, M.J., Chandra, G., Leskiw, B.K., Buttner, M.J. 2010. Genes essential for morphological development and antibiotic production in Streptomyces coelicolor are targets of BldD during vegetative growth. Mol Microbiol. , 78(2), 361-79.
Diender, M., Parera Olm, I., Gelderloos, M., Koehorst, J.J., Schaap, P.J., Stams, A.J.M., Sousa, D.Z. 2019. Metabolic shift induced by synthetic co-cultivation promotes high yield of chain elongated acids from syngas. Sci Rep, 9(1), 18081.
Ding, T., Yang, L.-J., Zhang, W.-D., Shen, Y.-H. 2019. The secondary metabolites of rare actinomycetes: chemistry and bioactivity. RSC Advances, 9(38), 21964-21988.
Domalaon, R., Idowu, T., Zhanel, G.G., Schweizer, F. 2018. Antibiotic Hybrids: the Next Generation of Agents and Adjuvants against Gram-Negative Pathogens? Clin Microbiol Rev, 31(2), e00077-17.
Dominici, F., Wang, Y., Correia, A.W., Ezzati, M., Pope, C.A., 3rd, Dockery, D.W. 2015. Chemical Composition of Fine Particulate Matter and Life Expectancy: In 95 US Counties Between 2002 and 2007. Epidemiology, 26(4), 556-64.
Donadio, S., Monciardini, P., Sosio, M. 2007. Polyketide synthases and nonribosomal peptide synthetases: the emerging view from bacterial genomics. Nat Prod Rep., 24(5), 1073-109.
Doroghazi, J.R., Metcalf, W.W. 2013. Comparative genomics of actinomycetes with a focus on natural product biosynthetic genes. BMC Genomics, 14(611).
Dutta, S., Whicher, J.R., Hansen, D.A., Hale, W.A., Chemler, J.A., Congdon, G.R., Narayan, A.R., Hakansson, K., Sherman, D.H., Smith, J.L., Skiniotis, G. 2014. Structure of a modular polyketide synthase. Nature, 510(7506), 512- 7.
Dziewit, L., Pyzik, A., Szuplewska, M., Matlakowska, R., Mielnicki, S., Wibberg, D., Schluter, A., Puhler, A., Bartosik, D. 2015. Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals. Front Microbiol, 6, 152.
Edgar, R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 32(5), 1792-7.
Edgar, R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26(19), 2460-1.
Edwards, D.J., Marquez, B.L., Nogle, L.M., McPhail, K., Goeger, D.E., Roberts, M.A., Gerwick, W.H. 2004. Structure and biosynthesis of the jamaicamides, new mixed polyketide-peptide neurotoxins from the marine cyanobacterium Lyngbya majuscula. Chem Biol, 11(6), 817-33.
Egermeier, M., Sauer, M., Marx, H. 2019. Golden Gate-based metabolic engineering strategy for wild-type strains of Yarrowia lipolytica. FEMS Microbiol Lett, 366(4).
El-Gebali, S., Mistry, J., Bateman, A., Eddy, S.R., Luciani, A., Potter, S.C., Qureshi, M., Richardson, L.J., Salazar, G.A., Smart, A., Sonnhammer, E.L.L., Hirsh, L., Paladin, L., Piovesan, D., Tosatto, S.C.E., Finn, R.D. 2019. The Pfam protein families database in 2019. Nucleic Acids Res, 47(D1), D427-D432.
Eldridge, D.J., Delgado-Baquerizo, M., Travers, S.K., Val, J., Oliver, I., Hamonts, K., Singh, B.K. 2017. Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores. Ecology. , 98(7), 1922-1931.
Ellis, G.A., Wyche, T.P., Fry, C.G., Braun, D.R., Bugni, T.S. 2014. Solwaric acids A and B, antibacterial aromatic acids from a marine Solwaraspora sp. Mar Drugs, 12(2), 1013-22.
Errington, J. 2003. Regulation of endospore formation in Bacillus subtilis. Nat Rev Microbiol, 1(2), 117-26.
Farver, D.K., Hedge, D.D., Lee, S.C. 2005. Ramoplanin: a lipoglycodepsipeptide antibiotic. Ann Pharmacother, 39(5), 863-8.
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol, 17, 368-376.
Finberg, R.W., Moellering, R.C., Tally, F.P., Craig, W.A., Pankey, G.A., Dellinger, E.P., West, M.A., Joshi, M., Linden, P.K., Rolston, K.V., Rotschafer, J.C., Rybak, M.J. 2004. The importance of bactericidal drugs: future directions in infectious disease. Clin Infect Dis. , 39(9), 1314-20.
Flärdh, K., Buttner, M.J. 2009. Streptomyces morphogenetics: dissecting differentiation in a filamentous bacterium. Nat Rev Microbiol, 7, 36-49.
Fouillaud, M., Venkatachalam, M., Girard-Valenciennes, E., Caro, Y., Dufosse, L. 2016. Anthraquinones and Derivatives from Marine-Derived Fungi: Structural Diversity and Selected Biological Activities. Mar Drugs, 14(4).
Funnell, B.E. 2014. Switching modes of chromosome dynamics in the bacterial cell cycle. Proc Natl Acad Sci U S A, 111(35), 12580-1.
Gaisin, V.A., Kalashnikov, A.M., Grouzdev, D.S., Sukhacheva, M.V., Kuznetsov, B.B., Gorlenko, V.M. 2017. Chloroflexus islandicus sp. nov., a thermophilic filamentous anoxygenic phototrophic bacterium from a geyser. Int J Syst Evol Microbiol, 67(5), 1381-1386.
Galperin, M.Y. 2001. Conserved ‘Hypothetical’ Proteins: New Hints and New Puzzles. Comp Funct Genomics, 2(1), 14-18.
Genilloud, O. 2017. Actinomycetes: still a source of novel antibiotics. Natural Product Reports, 34(10), 1203-1232.
Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol, 57(Pt 1), 81- 91.
Grazziotin, A.L., Vidal, N.M., Venancio, T.M. 2015. Uncovering major genomic features of essential genes in Bacteria and a methanogenic Archaea. FEBS J, 282(17), 3395-3411.
Gregory, T.R. 2005. Synergy between sequence and size in large-scale genomics. Nat Rev Genet, 6(9), 699-708.
Griffiths, S., Mesarich, C.H., Saccomanno, B., Vaisberg, A., De Wit, P.J., Cox, R., Collemare, J. 2016. Elucidation of cladofulvin biosynthesis reveals a cytochrome P450 monooxygenase required for anthraquinone dimerization. Proc Natl Acad Sci U S A, 113(25), 6851-6.
Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Window 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
Han, K., Li, Z.F., Peng, R., Zhu, L.P., Zhou, T., Wang, L.G., Li, S.G., Zhang, X.B., Hu, W., Wu, Z.H., Qin, N., Li, Y.Z. 2013a. Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Sci Rep, 3, 2101.
Han, K., Li, Z.F., Peng, R., Zhu, L.P., Zhou, T., Wang, L.G., Li, S.G., Zhang, X.B., Hu, W., Wu, Z.H., Qin, N., Li, Y.Z. 2013b. Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Sci Rep., 3, 2101.
Hanada, S., Hiraishi, A., Shimada, K., Matsuura, K. 1995. Chloroflexus aggregans sp. nov., a filamentous phototrophic bacterium which forms dense cell aggregates by active gliding movement. Int J Syst Bacteriol. , 45(4), 676- 81.
Harper, J.J., Davis, G.H.G. 1979. Two-dimensional thin-layer chromatography for amino acid analysis of bacterial cell walls. Int J Syst Bacteriol, 29, 56-58.
Hasegawa, T., Takizawa, M., Tanida, S. 1983. A rapid analysis for chemical grouping of aerobic actinomycetes. Gen. Appl. Microbiol., 29, 319–322.
Hayashi, T., Kitamura, Y., Funa, N., Ohnishi, Y., Horinouchi, S. 2011. Fatty acyl- AMP ligase involvement in the production of alkylresorcylic acid by a Myxococcus xanthus type III polyketide synthase. Chembiochem, 12(14), 2166-76.
Hertweck, C., Luzhetskyy, A., Rebets, Y., Bechthold, A. 2007. Type II polyketide synthases: gaining a deeper insight into enzymatic teamwork. Nat Prod Rep, 24(1), 162-90.
Hisanaga, Y., Ago, H., Nakagawa, N., Hamada, K., Ida, K., Yamamoto, M., Hori, T., Arii, Y., Sugahara, M., Kuramitsu, S., Yokoyama, S., Miyano, M. 2004. Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer. J Biol Chem, 279(30), 31717-26.
Hodgkiss, I.J., Harvey, R. 1972. Effect of carbon dioxide on the growth and sporulation of certain coprophilous pyrenomycetes. Transactions of the British Mycological Society, 59(3), 409-418.
Hong, K., Gao, A.H., Xie, Q.Y., Gao, H., Zhuang, L., Lin, H.P., Yu, H.P., Li, J., Yao, X.S., Goodfellow, M., Ruan, J.S. 2009. Actinomycetes for marine drug discovery isolated from mangrove soils and plants in China. Mar Drugs, 7(1), 24-44.
Hrouzek, P., Kuzma, M., Cerny, J., Novak, P., Fiser, R., Simek, P., Lukesova, A., Kopecky, J. 2012. The cyanobacterial cyclic lipopeptides puwainaphycins F/G are inducing necrosis via cell membrane permeabilization and subsequent unusual actin relocalization. Chem Res Toxicol, 25(6), 1203-11.
Hug, L.A., Baker, B.J., Anantharaman, K., Brown, C.T., Probst, A.J., Castelle, C.J., Butterfield, C.N., Hernsdorf, A.W., Amano, Y., Ise, K., Suzuki, Y., Dudek, N., Relman, D.A., Finstad, K.M., Amundson, R., Thomas, B.C., Banfield, J.F. 2016. A new view of the tree of life. Nat Microbiol, 1, 16048.
Hugenholtz, P., Stackebrandt, E. 2004. Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol, 54(Pt 6), 2049-51.
Ibal, J.C., Pham, H.Q., Park, C.E., Shin, J.H. 2019. Information about variations in multiple copies of bacterial 16S rRNA genes may aid in species identification. PLoS One, 14(2), e0212090.
Izhaki, I. 2002. Emodin: A Secondary Metabolite with Multiple Ecological Functions in Higher Plants. The New Phytologist, 155(2), 205-217.
Jansen, G., Aktipis, C.A. 2014. Resistance Is Mobile: The Accelerating Evolution of Mobile Genetic Elements Encoding Resistance. Journal of Evolutionary Medicine, 2, 1-3.
Jenke-Kodama, H., Dittmann, E. 2009. Evolution of metabolic diversity: insights from microbial polyketide synthases. Phytochemistry, 70(15-16), 1858-66.
Jiang, X., Ellabaan, M.M.H., Charusanti, P., Munck, C., Blin, K., Tong, Y., Weber, T., Sommer, M.O.A., Lee, S.Y. 2017. Dissemination of antibiotic resistance genes from antibiotic producers to pathogens. Nat Commun, 8, 15784.
Jiang, Z., Li, P., Jiang, D., Dai, X., Zhang, R., Wang, Y., Wang, Y. 2016. Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor- Formed Spring in Tengchong Geothermal Area, China. PLoS One, 11(1), e0146331.
Ju, K.S., Gao, J., Doroghazi, J.R., Wang, K.K., Thibodeaux, C.J., Li, S., Metzger, E., Fudala, J., Su, J., Zhang, J.K., Lee, J., Cioni, J.P., Evans, B.S., Hirota, R., Labeda, D.P., van der Donk, W.A., Metcalf, W.W. 2015. Discovery of phosphonic acid natural products by mining the genomes of 10,000 actinomycetes. Proc Natl Acad Sci U S A, 112(39), 12175-80.
Jung, H.M., Jeya, M., Kim, S.Y., Moon, H.J., Kumar Singh, R., Zhang, Y.W., Lee, J.K. 2009. Biosynthesis, biotechnological production, and application of teicoplanin: current state and perspectives. Appl Microbiol Biotechnol, 84(3), 417-28.
Kaster, A.K., Mayer-Blackwell, K., Pasarelli, B., Spormann, A.M. 2014. Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin. ISME J, 8(9), 1831-42.
Kato, M. 1934. Studies on "Tengu-no-Mugimeshi" [Japanese]. Rpt. Imp. Govt. Inst. for Nutrition, 7, 88-129.
Katsuyama, Y., Sone, K., Satou, R., Izumikawa, M., Takagi, M., Fujie, M., Satoh, N., Shin-Ya, K., Ohnishi, Y. 2016. Involvement of the Baeyer-Villiger Monooxygenase IfnQ in the Biosynthesis of Isofuranonaphthoquinone Scaffold of JBIR-76 and -77. Chembiochem, 17(11), 1021-8.
Kautsar, S.A., Blin, K., Shaw, S., Navarro-Munoz, J.C., Terlouw, B.R., van der Hooft, J.J.J., van Santen, J.A., Tracanna, V., Suarez Duran, H.G., Pascal Andreu, V., Selem-Mojica, N., Alanjary, M., Robinson, S.L., Lund, G., Epstein, S.C., Sisto, A.C., Charkoudian, L.K., Collemare, J., Linington, R.G., Weber, T., Medema, M.H. 2019. MIBiG 2.0: a repository for biosynthetic gene clusters of known function. Nucleic Acids Res.
Kawamura, T. 1916. Studies on "Tengu-no-Mugimeshi", a massy bacterial vegetation [Japanese]. Bot. Mag. [Tokyo], 30, 109-119, 133-150.
Kelly, S.L., Kelly, D.E. 2013. Microbial cytochromes P450: biodiversity and biotechnology. Where do cytochromes P450 come from, what do they do and what can they do for us? Philos Trans R Soc Lond B Biol Sci, 368(1612), 20120476.
Khan, Z.A., Siddiqui, M.F., Park, S. 2019. Current and Emerging Methods of Antibiotic Susceptibility Testing. Diagnostics (Basel), 9(2).
Kim, M., Cho, A., Lim, H.S., Hong, S.G., Kim, J.H., Lee, J., Choi, T., Ahn, T.S., Kim, O.S. 2015. Highly heterogeneous soil bacterial communities around Terra Nova Bay of Northern Victoria Land, Antarctica. PLoS One, 10(3), e0119966.
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. Int J Syst Evol Microbiol, 64(Pt 2), 346-51.
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.
King, C.E., King, G.M. 2014. Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria. International Journal of Systematic and Evolutionary Microbiology, 64(Pt 4), 1244-1251.
Komaki, H., Hosoyama, A., Yabe, S., Yokota, A., Uchino, Y., Takano, H. 2016. Draft Genome Sequence of Thermogemmatispora onikobensis NBRC 111776T, an Aerial Mycelium- and Spore-Forming Thermophilic Bacterium Belonging to the Class Ktedonobacteria. Genome Announc, 4(5), e01156- 16.
Kouprina, N., Larionov, V. 2008. Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat Protoc, 3(3), 371-7.
Kouprina, N., Larionov, V. 2016. Transformation-associated recombination (TAR) cloning for genomics studies and synthetic biology. Chromosoma, 125(4), 621-32.
Kumar, S., Stecher, G., Tamura, K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol, 33(7), 1870-4.
Kuroda, M., Ohta, T., Uchiyama, I., Baba, T., Yuzawa, H., Kobayashi, I., Cui, L., Oguchi, A., Aoki, K.-i., Nagai, Y., Lian, J., Ito, T., Kanamori, M., Matsumaru, H., Maruyama, A., Murakami, H., Hosoyama, A., Mizutani-Ui, Y., Takahashi, N.K., Sawano, T., Inoue, R.-i., Kaito, C., Sekimizu, K., Hirakawa, H., Kuhara, S., Goto, S., Yabuzaki, J., Kanehisa, M., Yamashita, A., Oshima, K., Furuya, K., Yoshino, C., Shiba, T., Hattori, M., Ogasawara, N., Hayashi, H., Hiramatsu, K. 2001. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. The Lancet, 357(9264), 1225-1240.
Lam, J.K., Sargent, M.V., Elix, J.A., Smith, D.O. 1972. Synthesis of Valsarin and 5,7-Dichloroemodin. J Chem Soc Perkin 1. , 12, 1466-70.
Landwehr, W., Wolf, C., Wink, J. 2016. Actinobacteria and Myxobacteria-Two of the Most Important Bacterial Resources for Novel Antibiotics. Curr Top Microbiol Immunol, 398, 273-302.
Lane, D. 1991. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. Chichester, United Kingdom: John Wiley and Sons, pp. 115-175.
Larson, C.B., Crusemann, M., Moore, B.S. 2017. PCR-Independent Method of Transformation-Associated Recombination Reveals the Cosmomycin Biosynthetic Gene Cluster in an Ocean Streptomycete. J Nat Prod, 80(4), 1200-1204.
Lee, J.C., Park, H.R., Park, D.J., Lee, H.B., Kim, Y.B., Kim, C.J. 2003. Improved production of teicoplanin using adsorbent resin in fermentations. Lett Appl Microbiol, 37(3), 196-200.
Letunic, I., Bork, P. 2019. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res, 47(W1), W256-W259.
Letzel, A.C., Pidot, S.J., Hertweck, C. 2014. Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in anaerobic bacteria. BMC Genomics, 15(983).
Li, B., Walsh, C.T. 2010. Identification of the gene cluster for the dithiolopyrrolone antibiotic holomycin in Streptomyces clavuligerus. . Proc Natl Acad Sci U S A., 107(46), 19731-5.
Li, Y., Li, Z., Yamanaka, K., Xu, Y., Zhang, W., Vlamakis, H., Kolter, R., Moore, B.S., Qian, P.Y. 2015. Directed natural product biosynthesis gene cluster capture and expression in the model bacterium Bacillus subtilis. Sci Rep, 5, 9383.
Liu, F., Garneau, S., Walsh, C.T. 2004. Hybrid nonribosomal peptide-polyketide interfaces in epothilone biosynthesis: minimal requirements at N and C termini of EpoB for elongation. Chem Biol, 11(11), 1533-42.
Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P.M., Henrissat, B. 2014. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res, 42(Database issue), D490-5.
Lu, J.J., Perng, C.L., Lee, S.Y., Wan, C.C. 2000. Use of PCR with universal primers and restriction endonuclease digestions for detection and identification of common bacterial pathogens in cerebrospinal fluid. J Clin Microbiol. , 38(6), 2076-80.
Lynch, R.C., King, A.J., Farías, M.E., Sowell, P., Vitry, C., Schmidt, S.K. 2012. The potential for microbial life in the highest-elevation (>6000 m.a.s.l.) mineral soils of the Atacama region. Journal of Geophysical Research: Biogeosciences, 117(G2), n/a-n/a.
Magalon, A., Alberge, F. 2016. Distribution and dynamics of OXPHOS complexes in the bacterial cytoplasmic membrane. Biochim Biophys Acta, 1857(3), 198-213.
Magoc, T., Salzberg, S.L. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics, 27(21), 2957-63.
Makela, M.R., Donofrio, N., de Vries, R.P. 2014. Plant biomass degradation by fungi. Fungal Genet Biol, 72, 2-9.
Manivasagan, P., Venkatesan, J., Sivakumar, K., Kim, S.K. 2014. Pharmaceutically active secondary metabolites of marine actinobacteria. Microbiol Res, 169(4), 262-78.
Marmann, A., Aly, A.H., Lin, W., Wang, B., Proksch, P. 2014. Co-cultivation--a powerful emerging tool for enhancing the chemical diversity of microorganisms. Mar Drugs, 12(2), 1043-65.
Marti, T., Hu, Z., Pohl, N.L., Shah, A.N., Khosla, C. 2000. Cloning, nucleotide sequence, and heterologous expression of the biosynthetic gene cluster for R1128, a non-steroidal estrogen receptor antagonist. Insights into an unusual priming mechanism. J Biol Chem, 275(43), 33443-8.
Masschelein, J., Jenner, M., Challis, G.L. 2017. Antibiotics from Gram-negative bacteria: a comprehensive overview and selected biosynthetic highlights. Natural Product Reports, 34(7), 712-783.
McCutcheon, J.P., von Dohlen, C.D. 2011. An interdependent metabolic patchwork in the nested symbiosis of mealybugs. Curr Biol, 21(16), 1366- 72.
Melander, R.J., Zurawski, D.V., Melander, C. 2018. Narrow-Spectrum Antibacterial Agents. Medchemcomm. , 9, 12-21.
Miller, D.A., Luo, L., Hillson, N., Keating, T.A., Walsh, C.T. 2002. Yersiniabactin Synthetase: A Four-Protein Assembly Line Producing the Nonribosomal Peptide/ Polyketide Hybrid Siderophore of Yersinia pestis. Chem Biol, 9(3), 333-44.
Miller, S.I. 2016. Antibiotic Resistance and Regulation of the Gram-Negative Bacterial Outer Membrane Barrier by Host Innate Immune Molecules. MBio, 7(5).
Mitani, T., Kadota, H. 1976. Incorporation of Glycine and Serine into Sporulating Cells ofBacillus subtilis. Agr. BioI. Chern., 40(4), 677-682.
Molisch, H. 1926. Pflanzenbiologie in Japan. Jena.
Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A.C., Kanehisa, M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res, 35(Web Server issue), W182-5.
Mouri, Y., Jang, M.S., Konishi, K., Hirata, A., Tezuka, T., Ohnishi, Y. 2018. Regulation of sporangium formation by the orphan response regulator TcrA in the rare actinomycete Actinoplanes missouriensis. Mol Microbiol, 107(6), 718-733.
Mouri, Y., Konishi, K., Fujita, A., Tezuka, T., Ohnishi, Y. 2017. Regulation of Sporangium Formation by BldD in the Rare Actinomycete Actinoplanes missouriensis. J. Bacteriol., 199, 1-17.
Nakashima, T., Takahashi, Y., Omura, S. 2017. Search for new compounds from Kitasato microbial library by physicochemical screening. Biochem Pharmacol, 134, 42-55.
Naughton, L.M., Romano, S., O'Gara, F., Dobson, A.D.W. 2017. Identification of Secondary Metabolite Gene Clusters in the Pseudovibrio Genus Reveals Encouraging Biosynthetic Potential toward the Production of Novel Bioactive Compounds. Front Microbiol, 8, 1494.
Newman, D.J., Cragg, G.M. 2016. Natural products as sources of new drugs from 1981 to 2014. J Nat Prod. , 79(3), 629-61.
Nindita, Y., Cao, Z., Fauzi, A.A., Teshima, A., Misaki, Y., Muslimin, R., Yang, Y., Shiwa, Y., Yoshikawa, H., Tagami, M., Lezhava, A., Ishikawa, J., Kuroda, M., Sekizuka, T., Inada, K., Kinashi, H., Arakawa, K. 2019. The genome sequence of Streptomyces rochei 7434AN4, which carries a linear chromosome and three characteristic linear plasmids. Sci Rep, 9(1), 10973.
Noblin, X., Rojas, N.O., Westbrook, J., Llorens, C., Argentina, M., Dumais, J. 2012. The fern sporangium: a unique catapult. Science, 335(6074), 1322.
Northup, D.E., Melim, L.A., Spilde, M.N., Hathaway, J.J., Garcia, M.G., Moya, M., Stone, F.D., Boston, P.J., Dapkevicius, M.L., Riquelme, C. 2011. Lava cave microbial communities within mats and secondary mineral deposits: implications for life detection on other planets. Astrobiology, 11(7), 601-18.
Okada, K., Iida, T., Kita-Tsukamoto, K., Honda, T. 2005. Vibrios commonly possess two chromosomes. J Bacteriol, 187(2), 752-7.
Okada, Y. 1937. OCCURRENCE OF MASSES OF GELATINOUS MICROBES IN THE SOIL. Soil Science, 43(5), 367-374.
Omura, S., Ikeda, H., Ishikawa, J., Hanamoto, A., Takahashi, C., Shinose, M., Takahashi, Y., Horikawa, H., Nakazawa, H., Osonoe, T., Kikuchi, H., Shiba, T., Sakaki, Y., Hattori, M. 2001. Genome sequence of an industrial microorganism Streptomyces avermitilis: Deducing the ability of producing secondary metabolites. Proceedings of the National Academy of Sciences, 98(21), 12215-12220.
Ono, N. 1916. Untersuchungen über "Tengu-no-Mugimeshi" [Japanese]. Bot. Mag. [Tokyo], 30, 59-65.
Ortega, M.A., van der Donk, W.A. 2016. New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products. Cell Chem Biol, 23(1), 31-44.
Pandey, A. 2009. Handbook of Plant-Based Biofuels. CRC Press, Boca Raton. Pandey, R.P. 2017. Diversifying Natural Products with Promiscuous Glycosyltransferase Enzymes via a Sustainable Microbial Fermentation Approach. Front Chem, 5, 110.
Park, J.S., Kagaya, N., Hashimoto, J., Izumikawa, M., Yabe, S., Shin-Ya, K., Nishiyama, M., Kuzuyama, T. 2014. Identification and biosynthesis of new acyloins from the thermophilic bacterium Thermosporothrix hazakensis SK20-1(T). Chembiochem, 15(4), 527-32.
Park, J.S., Yabe, S., Shin-ya, K., Nishiyama, M., Kuzuyama, T. 2015. New 2-(1'H- indole-3'-carbonyl)-thiazoles derived from the thermophilic bacterium Thermosporothrix hazakensis SK20-1(T). J Antibiot (Tokyo), 68(1), 60-2.
Parks, D.H., Imelfort, M., Skennerton, C.T., Hugenholtz, P., Tyson, G.W. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res, 25(7), 1043-55.
PINE, L., HOWELL Jun, A. 1956. Comparison of Physiological and Biochemical Characters of Actinomyces spp. with those of Lactobacillus bifidus. J . gen. Microbiol., 15(3), 428-445.
Procópio, R.E., Silva, I.R., Martins, M.K., Azevedo, J.L., Araújo, J.M. 2012. Antibiotics produced by Streptomyces. Braz J Infect Dis., 16(5), 466-71.
Rausch, C., Hoof, I., Weber, T., Wohlleben, W., Huson, D.H. 2007. Phylogenetic analysis of condensation domains in NRPS sheds light on their functional evolution. BMC Evolutionary Biology, 7(1), 78.
Rogers, E.W., Molinski, T.F. 2007. Asymmetric synthesis of diastereomeric diaminoheptanetetraols. A proposal for the configuration of (+)-zwittermicin a. Org Lett, 9(3), 437-40.
Romaniuk, K., Golec, P., Dziewit, L. 2018. Insight Into the Diversity and Possible Role of Plasmids in the Adaptation of Psychrotolerant and Metalotolerant Arthrobacter spp. to Extreme Antarctic Environments. Front Microbiol, 9, 3144.
Ross, A.C., Gulland, L.E., Dorrestein, P.C., Moore, B.S. 2015. Targeted capture and heterologous expression of the Pseudoalteromonas alterochromide gene cluster in Escherichia coli represents a promising natural product exploratory platform. ACS Synth Biol, 4(4), 414-20.
Rozwandowicz, M., Brouwer, M.S.M., Fischer, J., Wagenaar, J.A., Gonzalez-Zorn, B., Guerra, B., Mevius, D.J., Hordijk, J. 2018. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother, 73(5), 1121-1137.
Russo, I., Del Mese, P., Viretto, M., Doronzo, G., Mattiello, L., Trovati, M., Anfossi, G. 2008. Sodium azide, a bacteriostatic preservative contained in commercially available laboratory reagents, influences the responses of human platelets via the cGMP/PKG/VASP pathway. Clin Biochem, 41(4-5), 343-9.
Rytioja, J., Hilden, K., Yuzon, J., Hatakka, A., de Vries, R.P., Makela, M.R. 2014. Plant-polysaccharide-degrading enzymes from Basidiomycetes. Microbiol Mol Biol Rev, 78(4), 614-49.
Sabath, N., Ferrada, E., Barve, A., Wagner, A. 2013. Growth temperature and genome size in bacteria are negatively correlated, suggesting genomic streamlining during thermal adaptation. Genome Biol Evol, 5(5), 966-77.
Saitou, N., Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 4, 406-425.
Sasser, M. 1990. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101. Newark: DE: MIDI Inc.
Schleifer, K.H., Kandler, O. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev, 36, 407-477.
Schmid, J., Heider, D., Wendel, N.J., Sperl, N., Sieber, V. 2016. Bacterial Glycosyltransferases: Challenges and Opportunities of a Highly Diverse Enzyme Class Toward Tailoring Natural Products. Front Microbiol, 7, 182.
Seki, M., Honda, I., Fujita, I., Yano, I., Yamamoto, S., Koyama, A. 2009. Whole genome sequence analysis of Mycobacterium bovis bacillus Calmette- Guerin (BCG) Tokyo 172: a comparative study of BCG vaccine substrains. Vaccine, 27(11), 1710-6.
Sekiguchi, Y., Yamada, T., Hanada, S., Ohashi, A., Harada, H., Kamagata, Y. 2003. Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol, 53(Pt 6), 1843-51.
Shen, B. 2003. Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms. Current Opinion in Chemical Biology, 7(2), 285-295.
Shirling, E.B., Gottlieb, D. 1966. Methods for characterization of Streptomyces species. Int J Syst Bacteriol, 16, 313–340.
Shou, Q., Feng, L., Long, Y., Han, J., Nunnery, J.K., Powell, D.H., Butcher, R.A. 2016. A hybrid polyketide-nonribosomal peptide in nematodes that promotes larval survival. Nat Chem Biol, 12(10), 770-2.
Silva, C.E.d.F., Bertucco, A. 2019. Bioethanol from Microalgal Biomass: A Promising Approach in Biorefinery. Brazilian Archives of Biology and Technology, 62.
Sisler, H.D., Coursen, B.W. 1960. Effect of Cycloheximide (Actidione) on the Metabolism and Growth of Fungi. Developments in Industrial Microbiology 181-186.
Smibert, R.M., Krieg, N.L. 1994. Phenotypic characterization. In. Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
Soupene, E., Kuypers, F.A. 2008. Mammalian long-chain acyl-CoA synthetases. Exp Biol Med (Maywood), 233(5), 507-21.
Stackebrandt, E.a.G., B.M. 1994. Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology. Int J Syst Evol Microbiol, 44, 846-849.
Stevenson, L.J., Owen, J.G., Ackerley, D.F. 2019. Metagenome Driven Discovery of Nonribosomal Peptides. ACS Chem Biol, 14(10), 2115-2126.
Sticher, O. 2008. Natural product isolation. Nat Prod Rep, 25(3), 517-54.
Stott, M.B., Crowe, M.A., Mountain, B.W., Smirnova, A.V., Hou, S., Alam, M., Dunfield, P.F. 2008. Isolation of novel bacteria, including a candidate division, from geothermal soils in New Zealand. Environ Microbiol, 10(8), 2030-41.
Stres, B., Sul, W.J., Murovec, B., Tiedje, J.M. 2013. Recently deglaciated high- altitude soils of the Himalaya: diverse environments, heterogenous bacterial communities and long-range dust inputs from the upper troposphere. PLoS One, 8(9), e76440.
Subramani, R., Sipkema, D. 2019. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs, 17(5).
Tacconelli, E., Carrara, E., Savoldi, A., Harbarth, S., Mendelson, M., Monnet, D.L., Pulcini, C., Kahlmeter, G., Kluytmans, J., Carmeli, Y., Ouellette, M., Outterson, K., Patel, J., Cavaleri, M., Cox, E.M., Houchens, C.R., Grayson, M.L., Hansen, P., Singh, N., Theuretzbacher, U., Magrini, N., Aboderin, A.O., Al-Abri, S.S., Awang Jalil, N., Benzonana, N., Bhattacharya, S., Brink, A.J., Burkert, F.R., Cars, O., Cornaglia, G., Dyar, O.J., Friedrich, A.W., Gales, A.C., Gandra, S., Giske, C.G., Goff, D.A., Goossens, H., Gottlieb, T., Guzman Blanco, M., Hryniewicz, W., Kattula, D., Jinks, T., Kanj, S.S., Kerr, L., Kieny, M.-P., Kim, Y.S., Kozlov, R.S., Labarca, J., Laxminarayan, R., Leder, K., Leibovici, L., Levy-Hara, G., Littman, J., Malhotra-Kumar, S., Manchanda, V., Moja, L., Ndoye, B., Pan, A., Paterson, D.L., Paul, M., Qiu, H., Ramon-Pardo, P., Rodríguez-Baño, J., Sanguinetti, M., Sengupta, S., Sharland, M., Si-Mehand, M., Silver, L.L., Song, W., Steinbakk, M., Thomsen, J., Thwaites, G.E., van der Meer, J.W.M., Van Kinh, N., Vega, S., Villegas, M.V., Wechsler-Fördös, A., Wertheim, H.F.L., Wesangula, E., Woodford, N., Yilmaz, F.O., Zorzet, A. 2018. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. The Lancet Infectious Diseases, 18(3), 318-327.
Také, A., Nakashima, T., Inahashi, Y., Shiomi, K., Takahashi, Y., Ōmura, S., Matsumoto, A. 2016. Analyses of the cell-wall peptidoglycan structures in three genera Micromonospora, Catenuloplanes, and Couchioplanes belonging to the family Micromonosporaceae by derivatization with FDLA and PMP using LC/MS. The Journal of General and Applied Microbiology, 62(4), 199-205.
Takada, Y., Furuya, M. 2010. Aseismic slip during the 1996 earthquake swarm in and around the Onikobe geothermal area, NE Japan. Earth and Planetary Science Letters, 290(3-4), 302-310.
Takahashi, M. 1935. Studies on "Tengu-no-Mugimeshi". Botany and Zoology, 3, 761-768, 925-931, 1128-1134.
Takatori, J., et al. 2009. Deep comparison of the microbial community structure of "Tengu−no −mugimeshi". Oral report at 25th Japanese Society of Microbial Ecology, 2009-11-21.
Takenaka, M., Lee, J.M., Kahar, P., Ogino, C., Kondo, A. 2019. Efficient and Supplementary Enzyme Cocktail from Actinobacteria and Plant Biomass Induction. Biotechnol J, 14(3), e1700744.
Tanizawa, Y., Fujisawa, T., Nakamura, Y. 2018. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics, 34(6), 1037-1039.
Tazzyman, S.J., Bonhoeffer, S. 2015. Why There Are No Essential Genes on Plasmids. Mol Biol Evol, 32(12), 3079-88.
Tebo, B.M., Davis, R.E., Anitori, R.P., Connell, L.B., Schiffman, P., Staudigel, H. 2015. Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica. Front Microbiol, 6, 179.
Tettelin, H., Masignani, V., Cieslewicz, M.J., Donati, C., Medini, D., Ward, N.L., Angiuoli, S.V., Crabtree, J., Jones, A.L., Durkin, A.S., Deboy, R.T., Davidsen, T.M., Mora, M., Scarselli, M., Margarit y Ros, I., Peterson, J.D., Hauser, C.R., Sundaram, J.P., Nelson, W.C., Madupu, R., Brinkac, L.M., Dodson, R.J., Rosovitz, M.J., Sullivan, S.A., Daugherty, S.C., Haft, D.H., Selengut, J., Gwinn, M.L., Zhou, L., Zafar, N., Khouri, H., Radune, D., Dimitrov, G., Watkins, K., O'Connor, K.J., Smith, S., Utterback, T.R., White, O., Rubens, C.E., Grandi, G., Madoff, L.C., Kasper, D.L., Telford, J.L., Wessels, M.R., Rappuoli, R., Fraser, C.M. 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A, 102(39), 13950-5.
Thaxter, R. 1982. On the Myxobacteriaceae, a new order of Schizomycetes. Bot. Gaz., 17, 389–406.
Thomas, C.M., Summers, D. 2008. Bacterial Plasmids.
Tiberi, S., Munoz-Torrico, M., Duarte, R., Dalcolmo, M., D'Ambrosio, L., Migliori, G.B. 2018. New drugs and perspectives for new anti-tuberculosis regimens. Pulmonology, 24(2), 86-98.
Tindall, B.J. 1990a. A Comparative Study of the Lipid Composition of Halobacterium saccharovorum from Various Sources. Systematic and Applied Microbiology, 13(2), 128-130.
Tindall, B.J. 1990b. Lipid composition of Halobacterium lacusprofundi. . FEMS Microbiol Lett, 66, 199–202.
Tindall, B.J., Sikorski, J., Smibert , R.M., Kreig, N.R. 2007. Phenotypic characterization and the principles of comparative systematics. . In Methods for General and Molecular Microbiology 3rd edn., 330-393.
Tsakos, M., Clement, L.L., Schaffert, E.S., Olsen, F.N., Rupiani, S., Djurhuus, R., Yu, W., Jacobsen, K.M., Villadsen, N.L., Poulsen, T.B. 2016. Total Synthesis and Biological Evaluation of Rakicidin A and Discovery of a Simplified Bioactive Analogue. Angew Chem Int Ed Engl, 55(3), 1030-5.
Uchida, K., Jang, M.S., Ohnishi, Y., Horinouchi, S., Hayakawa, M., Fujita, N., Aizawa, S. 2011. Characterization of Actinoplanes missouriensis Spore Flagella. Appl Environ Microbiol. , 77(7), 2559–2562.
Ur-Rehman, S., Mushtaq, Z., Zahoor, T., Jamil, A., Murtaza, M.A. 2015. Xylitol: a review on bioproduction, application, health benefits, and related safety issues. Crit Rev Food Sci Nutr, 55(11), 1514-28.
van Heel, A.J., de Jong, A., Song, C., Viel, J.H., Kok, J., Kuipers, O.P. 2018. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res, 46(W1), W278-W281.
Van Leuven, J.T., Meister, R.C., Simon, C., McCutcheon, J.P. 2014. Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one. Cell, 158(6), 1270-1280.
Vila-Farres, X., Chu, J., Inoyama, D., Ternei, M.A., Lemetre, C., Cohen, L.J., Cho, W., Reddy, B.V., Zebroski, H.A., Freundlich, J.S., Perlin, D.S., Brady, S.F. 2017. Antimicrobials Inspired by Nonribosomal Peptide Synthetase Gene Clusters. J Am Chem Soc, 139(4), 1404-1407.
Volff, J.N., Altenbuchner, J. 2000. A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol Lett. , 186(2), 143-50.
Vyssotski, M., Ryan, J., Lagutin, K., Wong, H., Morgan, X., Stott, M. 2012. A novel fatty acid, 12,17-dimethyloctadecanoic acid, from the extremophile Thermogemmatispora sp. (Strain T81). Lipids, 47(6), 601-11.
Wang, C.M., Zheng, Y., Sakai, Y., Toyoda, A., Minakuchi, Y., Abe, K., Yokota, A., Yabe, S. 2019. Tengunoibacter tsumagoiensis gen. nov., sp. nov., Dictyobacter kobayashii sp. nov., Dictyobacter alpinus sp. nov. and description of Dictyobacteraceae fam. nov. within the order Ktedonobacterales isolated from Tengu-no-mugimeshi, a soil-like granular mass of microorganisms, and emended descriptions of the genera Ktedonobacter and Dictyobacter. Int J Syst Evol Microbiol, in press.
Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol, 73(16), 5261-7.
Wattam, A.R., Williams, K.P., Snyder, E.E., Almeida, N.F., Jr., Shukla, M., Dickerman, A.W., Crasta, O.R., Kenyon, R., Lu, J., Shallom, J.M., Yoo, H., Ficht, T.A., Tsolis, R.M., Munk, C., Tapia, R., Han, C.S., Detter, J.C., Bruce, D., Brettin, T.S., Sobral, B.W., Boyle, S.M., Setubal, J.C. 2009. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol, 191(11), 3569-79.
Winterstein, C., Ludwig, B. 1998. Genes coding for respiratory complexes map on all three chromosomes of the Paracoccus denitrificans genome. Arch Microbiol. , 169(4), 275-81.
Wu , D., Raymond, J., Wu, M., Chatterji, S., Ren, Q., Graham, J.E., Bryant, D.A., Robb, F., Colman, A., Tallon, L.J., Badger, J.H., Madupu, R., Ward, N.L., Eisen, J.A. 2009. Complete genome sequence of the aerobic CO-oxidizing thermophile Thermomicrobium roseum. PLoS One, 4(1), e4207.
Xu, B., Aitken, E.J., Baker, B.P., Turner, C.A., Harvey, J.E., Stott, M.B., Power, J.F., Harris, P.W.R., Keyzers, R.A., Brimble, M.A. 2018. Genome mining, isolation, chemical synthesis and biological evaluation of a novel lanthipeptide, tikitericin, from the extremophilic microorganism Thermogemmatispora strain T81. Chem Sci, 9(37), 7311-7317.
Xu, Y., Kersten, R.D., Nam, S.J., Lu, L., Al-Suwailem, A.M., Zheng, H., Fenical, W., Dorrestein, P.C., Moore, B.S., Qian, P.Y. 2012. Bacterial biosynthesis and maturation of the didemnin anti-cancer agents. J Am Chem Soc, 134(20), 8625-32.
Yabe, S., Aiba, Y., Sakai, Y., Hazaka, M., Yokota, A. 2010a. A life cycle of branched aerial mycelium- and multiple budding spore-forming bacterium Thermosporothrix hazakensis belonging to the phylum Chloroflexi. J Gen Appl Microbiol, 56(2), 137-41.
Yabe, S., Aiba, Y., Sakai, Y., Hazaka, M., Yokota, A. 2011. Thermogemmatispora onikobensis gen. nov., sp. nov. and Thermogemmatispora foliorum sp. nov., isolated from fallen leaves on geothermal soils, and description of Thermogemmatisporaceae fam. nov. and Thermogemmatisporales ord. nov. within the class Ktedonobacteria. Int J Syst Evol Microbiol, 61(Pt 4), 903-10.
Yabe, S., Aiba, Y., Sakai, Y., Hazaka, M., Yokota, A. 2010b. Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria. Int J Syst Evol Microbiol, 60(Pt 8), 1794-801.
Yabe, S., Sakai, Y., Abe, K., Yokota, A. 2017a. Diversity of Ktedonobacteria with Actinomycetes-Like Morphology in Terrestrial Environments. Microbes Environ, 32(1), 61-70.
Yabe, S., Sakai, Y., Abe, K., Yokota, A., Také, A., Matsumoto, A., Sugiharto, A., Susilowati, D., Hamada, M., Nara, K., Made, S., Otsuka, S. 2017b. Dictyobacter aurantiacus gen. nov., sp. nov., a member of the family Ktedonobacteraceae, isolated from soil, and emended description of the genus Thermosporothrix. Int J Syst Evol Microbiol, 67(8), 2615-2621.
Yabe, S., Sakai, Y., Yokota, A. 2016. Thermosporothrix narukonensis sp. nov., belonging to the class Ktedonobacteria, isolated from fallen leaves on geothermal soil, and emended description of the genus Thermosporothrix. International Journal of Systematic and Evolutionary Microbiology, 66(6), 2152-57.
Yabe, S., Wang, C., Zheng, Y., Sakai, Y., Abe, K., Yokota, A. 2019. Formation of sporangiospores in Dictyobacter aurantiacus (class Ktedonobacteria in phylum Chloroflexi). The Journal of General and Applied Microbiology, 65, in press.
Yahya, M.F.Z.R., Hamid, U.M.A., Norfatimah, M.Y., Kambol, R. 2014. In silico Analysis of Essential Tricarboxylic Acid Cycle Enzymes from Biofilm- forming Bacteria. Trends in Bioinformatics, 7(1), 19-26.
Yamada, T., Sekiguchi, Y., Hanada, S., Imachi, H., Ohashi, A., Harada, H., Kamagata, Y. 2006. Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol, 56(Pt 6), 1331-40.
Yamanaka, K., Reynolds, K.A., Kersten, R.D., Ryan, K.S., Gonzalez, D.J., Nizet, V., Dorrestein, P.C., Moore, B.S. 2014. Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. Proc Natl Acad Sci U S A, 111(5), 1957-62.
Yan, X., Probst, K., Linnenbrink, A., Arnold, M., Paululat, T., Zeeck, A., Bechthold, A. 2012. Cloning and heterologous expression of three type II PKS gene clusters from Streptomyces bottropensis. Chembiochem, 13(2), 224-30.
Yang, M., Yun, J., Zhang, H., Magocha, T.A., Zabed, H., Xue, Y., Fokum, E., Sun, W., Qi, X. 2018. Genetically Engineered Strains: Application and Advances for 1,3-Propanediol Production from Glycerol. Food Technol Biotechnol, 56(1), 3-15.
Yoon, S.H., Ha, S.M., Lim, J., Kwon, S., Chun, J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek, 110(10), 1281-1286.
Yosioka, I., Yamauchi, H., Morimoto, K., Kitagawa, I. 1968. Three new chlorine containing bisanthronylz from a lichen, anaptychia obscurata vain. Tetrahedron Letters, 9(34), 3749-3752.
Zhang, C.S., Stratmann, A., Block, O., Bruckner, R., Podeschwa, M., Altenbach, H.J., Wehmeier, U.F., Piepersberg, W. 2002. Biosynthesis of the C(7)- cyclitol moiety of acarbose in Actinoplanes species SE50/110. 7-O- phosphorylation of the initial cyclitol precursor leads to proposal of a new biosynthetic pathway. J Biol Chem, 277(25), 22853-62.
Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P.K., Xu, Y., Yin, Y. 2018a. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res, 46(W1), W95-W101.
Zhang, Q., Yu, Y., Velasquez, J.E., van der Donk, W.A. 2012. Evolution of lanthipeptide synthetases. Proc Natl Acad Sci U S A, 109(45), 18361-6.
Zhang, Q.W., Lin, L.G., Ye, W.C. 2018b. Techniques for extraction and isolation of natural products: a comprehensive review. Chin Med, 13, 20.
Zhang, Z., Pan, H.X., Tang, G.L. 2017. New insights into bacterial type II polyketide biosynthesis. F1000Res, 6, 172.
Zhao, J., Jiang, X. 2018. The application of sulfur-containing peptides in drug discovery. Chinese Chemical Letters, 29(7), 1079-1087.
Zhou, Q., Brauer, A., Adihou, H., Schmalhofer, M., Saura, P., Grammbitter, G.L.C., Kaila, V.R.I., Groll, M., Bode, H.B. 2019. Molecular mechanism of polyketide shortening in anthraquinone biosynthesis of Photorhabdus luminescens. Chem Sci, 10(25), 6341-6349.
Zhou, Z., Gu, J., Li, Y.Q., Wang, Y. 2012. Genome plasticity and systems evolution in Streptomyces. BMC Bioinformatics, 13 Suppl 10, S8.
Ziemert, N., Podell, S., Penn, K., Badger, J.H., Allen, E., Jensen, P.R. 2012. The natural product domain seeker NaPDoS: a phylogeny based bioinformatic tool to classify secondary metabolite gene diversity. PLoS One, 7(3), e34064.
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