Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylura

Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D (2007)
Microbiol Mol Biol Rev 71(3): 495-548.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Microbiol Mol Biol Rev
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71
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3
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495-548
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Ventura M, Canchaya C, Tauch A, et al. Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylura. Microbiol Mol Biol Rev. 2007;71(3):495-548.
Ventura, M., Canchaya, C., Tauch, A., Chandra, G., Fitzgerald, G. F., Chater, K. F., & van Sinderen, D. (2007). Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylura. Microbiol Mol Biol Rev, 71(3), 495-548. doi:10.1128/MMBR.00005-07
Ventura, M., Canchaya, C., Tauch, A., Chandra, G., Fitzgerald, G. F., Chater, K. F., and van Sinderen, D. (2007). Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylura. Microbiol Mol Biol Rev 71, 495-548.
Ventura, M., et al., 2007. Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylura. Microbiol Mol Biol Rev, 71(3), p 495-548.
M. Ventura, et al., “Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylura”, Microbiol Mol Biol Rev, vol. 71, 2007, pp. 495-548.
Ventura, M., Canchaya, C., Tauch, A., Chandra, G., Fitzgerald, G.F., Chater, K.F., van Sinderen, D.: Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylura. Microbiol Mol Biol Rev. 71, 495-548 (2007).
Ventura, Marco, Canchaya, Carlos, Tauch, Andreas, Chandra, Govind, Fitzgerald, Gerald F., Chater, Keith F., and van Sinderen, Douwe. “Genomics of Actinobacteria: Tracing the evolutionary history of an ancient phylura”. Microbiol Mol Biol Rev 71.3 (2007): 495-548.

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Lugli GA, Duranti S, Milani C, Turroni F, Viappiani A, Mangifesta M, van Sinderen D, Ventura M., Genome Announc 2(1), 2014
PMID: 24558236
Expression of fluorescent proteins in bifidobacteria for analysis of host-microbe interactions.
Grimm V, Gleinser M, Neu C, Zhurina D, Riedel CU., Appl Environ Microbiol 80(9), 2014
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Comparative genomics of the Bifidobacterium breve taxon.
Bottacini F, O'Connell Motherway M, Kuczynski J, O'Connell KJ, Serafini F, Duranti S, Milani C, Turroni F, Lugli GA, Zomer A, Zhurina D, Riedel C, Ventura M, van Sinderen D., BMC Genomics 15(), 2014
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Small non-coding RNAs in streptomycetes.
Heueis N, Vockenhuber MP, Suess B., RNA Biol 11(5), 2014
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International Space Station environmental microbiome - microbial inventories of ISS filter debris.
Venkateswaran K, Vaishampayan P, Cisneros J, Pierson DL, Rogers SO, Perry J., Appl Microbiol Biotechnol 98(14), 2014
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Actinomycetes from Red Sea sponges: sources for chemical and phylogenetic diversity.
Abdelmohsen UR, Yang C, Horn H, Hajjar D, Ravasi T, Hentschel U., Mar Drugs 12(5), 2014
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Bacterial phylogeny structures soil resistomes across habitats.
Forsberg KJ, Patel S, Gibson MK, Lauber CL, Knight R, Fierer N, Dantas G., Nature 509(7502), 2014
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Airway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease.
Huang YJ, Sethi S, Murphy T, Nariya S, Boushey HA, Lynch SV., J Clin Microbiol 52(8), 2014
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On the limits of computational functional genomics for bacterial lifestyle prediction.
Barbosa E, Röttger R, Hauschild AC, Azevedo V, Baumbach J., Brief Funct Genomics 13(5), 2014
PMID: 24855068
Transcription of two adjacent carbohydrate utilization gene clusters in Bifidobacterium breve UCC2003 is controlled by LacI- and repressor open reading frame kinase (ROK)-type regulators.
O'Connell KJ, Motherway MO, Liedtke A, Fitzgerald GF, Paul Ross R, Stanton C, Zomer A, van Sinderen D., Appl Environ Microbiol 80(12), 2014
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Copper Tube Pitting in Santa Fe Municipal Water Caused by Microbial Induced Corrosion.
Burleigh TD, Gierke CG, Fredj N, Boston PJ., Materials (Basel) 7(6), 2014
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Recovering glycoside hydrolase genes from active tundra cellulolytic bacteria.
Pinnell LJ, Dunford E, Ronan P, Hausner M, Neufeld JD., Can J Microbiol 60(7), 2014
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RND transporters protect Corynebacterium glutamicum from antibiotics by assembling the outer membrane.
Yang L, Lu S, Belardinelli J, Huc-Claustre E, Jones V, Jackson M, Zgurskaya HI., Microbiologyopen 3(4), 2014
PMID: 24942069
Bifidobacterium faecale sp. nov., isolated from human faeces.
Choi JH, Lee KM, Lee MK, Cha CJ, Kim GB., Int J Syst Evol Microbiol 64(pt 9), 2014
PMID: 24944342
Genomic characterization and transcriptional studies of the starch-utilizing strain Bifidobacterium adolescentis 22L.
Duranti S, Turroni F, Lugli GA, Milani C, Viappiani A, Mangifesta M, Gioiosa L, Palanza P, van Sinderen D, Ventura M., Appl Environ Microbiol 80(19), 2014
PMID: 25063659
Thaxtomin A production and virulence are controlled by several bld gene global regulators in Streptomyces scabies.
Bignell DR, Francis IM, Fyans JK, Loria R., Mol Plant Microbe Interact 27(8), 2014
PMID: 24678834
Improved group-specific primers based on the full SILVA 16S rRNA gene reference database.
Pfeiffer S, Pastar M, Mitter B, Lippert K, Hackl E, Lojan P, Oswald A, Sessitsch A., Environ Microbiol 16(8), 2014
PMID: 25229098
Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics.
Lugli GA, Milani C, Turroni F, Duranti S, Ferrario C, Viappiani A, Mancabelli L, Mangifesta M, Taminiau B, Delcenserie V, van Sinderen D, Ventura M., Appl Environ Microbiol 80(20), 2014
PMID: 25107967
Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil.
Pan Y, Cassman N, de Hollander M, Mendes LW, Korevaar H, Geerts RH, van Veen JA, Kuramae EE., FEMS Microbiol Ecol 90(1), 2014
PMID: 25046442
Bifidobacterium bifidum as an example of a specialized human gut commensal.
Turroni F, Duranti S, Bottacini F, Guglielmetti S, Van Sinderen D, Ventura M., Front Microbiol 5(), 2014
PMID: 25191315
Diversity, ecology and intestinal function of bifidobacteria.
Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M., Microb Cell Fact 13 Suppl 1(), 2014
PMID: 25186128
Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae.
Rebets Y, Tokovenko B, Lushchyk I, Rückert C, Zaburannyi N, Bechthold A, Kalinowski J, Luzhetskyy A., BMC Genomics 15(), 2014
PMID: 25301375
Bacteria as vitamin suppliers to their host: a gut microbiota perspective.
LeBlanc JG, Milani C, de Giori GS, Sesma F, van Sinderen D, Ventura M., Curr Opin Biotechnol 24(2), 2013
PMID: 22940212
Density parameter estimation for finding clusters of homologous proteins--tracing actinobacterial pathogenicity lifestyles.
Röttger R, Kalaghatgi P, Sun P, Soares Sde C, Azevedo V, Wittkop T, Baumbach J., Bioinformatics 29(2), 2013
PMID: 23142964
Transcriptional and functional characterization of genetic elements involved in galacto-oligosaccharide utilization by Bifidobacterium breve UCC2003.
O'Connell Motherway M, Kinsella M, Fitzgerald GF, van Sinderen D., Microb Biotechnol 6(1), 2013
PMID: 23199239
Microbial mechanisms mediating increased soil C storage under elevated atmospheric N deposition.
Eisenlord SD, Freedman Z, Zak DR, Xue K, He Z, Zhou J., Appl Environ Microbiol 79(4), 2013
PMID: 23220961
Phylogenetic distribution of potential cellulases in bacteria.
Berlemont R, Martiny AC., Appl Environ Microbiol 79(5), 2013
PMID: 23263967
Proteome turnover in bacteria: current status for Corynebacterium glutamicum and related bacteria.
Trötschel C, Albaum SP, Poetsch A., Microb Biotechnol 6(6), 2013
PMID: 23425033
Diversity of bacteria in surface ice of Austre Lovénbreen glacier, Svalbard.
Zeng YX, Yan M, Yu Y, Li HR, He JF, Sun K, Zhang F., Arch Microbiol 195(5), 2013
PMID: 23474777
The multifaceted roles of antibiotics and antibiotic resistance in nature.
Sengupta S, Chattopadhyay MK, Grossart HP., Front Microbiol 4(), 2013
PMID: 23487476
Bacillus subtilis SC02 supplementation causes alterations of the microbial diversity in grass carp water.
Zhang X, Fu L, Deng B, Liang Q, Zheng J, Sun J, Zhu H, Peng L, Wang Y, Wenying S, Li W., World J Microbiol Biotechnol 29(9), 2013
PMID: 23539150
Antibacterial activity of actinomycetes isolated from different soil samples of Sheopur (A city of central India).
Chaudhary HS, Yadav J, Shrivastava AR, Singh S, Singh AK, Gopalan N., J Adv Pharm Technol Res 4(2), 2013
PMID: 23833752
The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase.
Tabib-Salazar A, Liu B, Doughty P, Lewis RA, Ghosh S, Parsy ML, Simpson PJ, O'Dwyer K, Matthews SJ, Paget MS., Nucleic Acids Res 41(11), 2013
PMID: 23605043
Phylogenetic analyses of phylum Actinobacteria based on whole genome sequences.
Verma M, Lal D, Kaur J, Saxena A, Kaur J, Anand S, Lal R., Res Microbiol 164(7), 2013
PMID: 23608518
The Nocardia cyriacigeorgica GUH-2 genome shows ongoing adaptation of an environmental Actinobacteria to a pathogen's lifestyle.
Zoropogui A, Pujic P, Normand P, Barbe V, Belli P, Graindorge A, Roche D, Vallenet D, Mangenot S, Boiron P, Rodriguez-Nava V, Ribun S, Richard Y, Cournoyer B, Blaha D., BMC Genomics 14(), 2013
PMID: 23622346
Changes in diversity, abundance, and structure of soil bacterial communities in Brazilian Savanna under different land use systems.
Rampelotto PH, de Siqueira Ferreira A, Barboza AD, Roesch LF., Microb Ecol 66(3), 2013
PMID: 23624541
Comparative genomics of Bifidobacterium animalis subsp. lactis reveals a strict monophyletic bifidobacterial taxon.
Milani C, Duranti S, Lugli GA, Bottacini F, Strati F, Arioli S, Foroni E, Turroni F, van Sinderen D, Ventura M., Appl Environ Microbiol 79(14), 2013
PMID: 23645200
Mobilome and genetic modification of bifidobacteria.
Guglielmetti S, Mayo B, Álvarez-Martín P., Benef Microbes 4(2), 2013
PMID: 23271067
Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol.
Milani C, Hevia A, Foroni E, Duranti S, Turroni F, Lugli GA, Sanchez B, Martín R, Gueimonde M, van Sinderen D, Margolles A, Ventura M., PLoS One 8(7), 2013
PMID: 23869230
Metabolism of four α-glycosidic linkage-containing oligosaccharides by Bifidobacterium breve UCC2003.
O'Connell KJ, O'Connell Motherway M, O'Callaghan J, Fitzgerald GF, Ross RP, Ventura M, Stanton C, van Sinderen D., Appl Environ Microbiol 79(20), 2013
PMID: 23913435
Bacillus subtilis SC02 supplementation causes alterations of the microbial diversity in grass carp water
Zhang X, Fu L, Deng B, Liang Q, Zheng J, Sun J, Zhu H, Peng L, Wang Y, Wenying S, Li W., World J Microbiol Biotechnol 29(9), 2013
PMID: IND500684735
WhiB7, an Fe-S-dependent transcription factor that activates species-specific repertoires of drug resistance determinants in actinobacteria.
Ramón-García S, Ng C, Jensen PR, Dosanjh M, Burian J, Morris RP, Folcher M, Eltis LD, Grzesiek S, Nguyen L, Thompson CJ., J Biol Chem 288(48), 2013
PMID: 24126912
Phylogenetic perspectives of nitrogen-fixing actinobacteria.
Gtari M, Ghodhbane-Gtari F, Nouioui I, Beauchemin N, Tisa LS., Arch Microbiol 194(1), 2012
PMID: 21779790
The influence of the discharging sewage on microbial diversity in sludge from Dongting Lake.
Yang Y, Wang X, Shi J, Li J., World J Microbiol Biotechnol 28(2), 2012
PMID: 22806836
Prokaryotic systematics in the genomics era.
Zhi XY, Zhao W, Li WJ, Zhao GP., Antonie Van Leeuwenhoek 101(1), 2012
PMID: 22116211
Signals and regulators that govern Streptomyces development.
McCormick JR, Flärdh K., FEMS Microbiol Rev 36(1), 2012
PMID: 22092088
Streptomyces as symbionts: an emerging and widespread theme?
Seipke RF, Kaltenpoth M, Hutchings MI., FEMS Microbiol Rev 36(4), 2012
PMID: 22091965
The early settlers: intestinal microbiology in early life.
Scholtens PA, Oozeer R, Martin R, Amor KB, Knol J., Annu Rev Food Sci Technol 3(), 2012
PMID: 22224552
Investigating conservation of the albaflavenone biosynthetic pathway and CYP170 bifunctionality in streptomycetes.
Moody SC, Zhao B, Lei L, Nelson DR, Mullins JG, Waterman MR, Kelly SL, Lamb DC., FEBS J 279(9), 2012
PMID: 22151149
Safety assessment of Bifidobacterium longum JDM301 based on complete genome sequences.
Wei YX, Zhang ZY, Liu C, Malakar PK, Guo XK., World J Gastroenterol 18(5), 2012
PMID: 22346255
The influence of the discharging sewage on microbial diversity in sludge from Dongting Lake
Yang Y, Wang X, Shi J, Li J., World J Microbiol Biotechnol 28(2), 2012
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Cytoskeletal proteins of actinobacteria.
Letek M, Fiuza M, Villadangos AF, Mateos LM, Gil JA., Int J Cell Biol 2012(), 2012
PMID: 22481946
Composition, diversity, and origin of the bacterial community in grass carp intestine.
Wu S, Wang G, Angert ER, Wang W, Li W, Zou H., PLoS One 7(2), 2012
PMID: 22363439
Biodiscovery from rare actinomycetes: an eco-taxonomical perspective.
Kurtböke DI., Appl Microbiol Biotechnol 93(5), 2012
PMID: 22297430
Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia.
Trost E, Blom J, Soares Sde C, Huang IH, Al-Dilaimi A, Schröder J, Jaenicke S, Dorella FA, Rocha FS, Miyoshi A, Azevedo V, Schneider MP, Silva A, Camello TC, Sabbadini PS, Santos CS, Santos LS, Hirata R, Mattos-Guaraldi AL, Efstratiou A, Schmitt MP, Ton-That H, Tauch A., J Bacteriol 194(12), 2012
PMID: 22505676
The role of Corynebacterium glutamicum spiA gene in whcA-mediated oxidative stress gene regulation.
Park JS, Lee JY, Kim HJ, Kim ES, Kim P, Kim Y, Lee HS., FEMS Microbiol Lett 331(1), 2012
PMID: 22443283
Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient.
Schröder J, Maus I, Meyer K, Wördemann S, Blom J, Jaenicke S, Schneider J, Trost E, Tauch A., BMC Genomics 13(), 2012
PMID: 22524407
Analysis of predicted carbohydrate transport systems encoded by Bifidobacterium bifidum PRL2010.
Turroni F, Strati F, Foroni E, Serafini F, Duranti S, van Sinderen D, Ventura M., Appl Environ Microbiol 78(14), 2012
PMID: 22562993
Characterization of soil bacterial assemblies in Brazilian savanna-like vegetation reveals acidobacteria dominance.
Araujo JF, de Castro AP, Costa MM, Togawa RC, Júnior GJ, Quirino BF, Bustamante MM, Williamson L, Handelsman J, Krüger RH., Microb Ecol 64(3), 2012
PMID: 22570118
Diversity of bifidobacteria within the infant gut microbiota.
Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, Kerr C, Hourihane J, Murray D, Fuligni F, Gueimonde M, Margolles A, De Bellis G, O'Toole PW, van Sinderen D, Marchesi JR, Ventura M., PLoS One 7(5), 2012
PMID: 22606315
An efficient and reproducible method for transformation of genetically recalcitrant bifidobacteria.
Serafini F, Turroni F, Guglielmetti S, Gioiosa L, Foroni E, Sanghez V, Bartolomucci A, Motherway MO, Palanza P, van Sinderen D, Ventura M., FEMS Microbiol Lett 333(2), 2012
PMID: 22640171
Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing.
Wirth R, Kovács E, Maróti G, Bagi Z, Rákhely G, Kovács KL., Biotechnol Biofuels 5(), 2012
PMID: 22673110
Three pathway-specific regulators control streptolydigin biosynthesis in Streptomyces lydicus.
Gómez C, Olano C, Méndez C, Salas JA., Microbiology 158(pt 10), 2012
PMID: 22820841
Bifidobacterium asteroides PRL2011 genome analysis reveals clues for colonization of the insect gut.
Bottacini F, Milani C, Turroni F, Sánchez B, Foroni E, Duranti S, Serafini F, Viappiani A, Strati F, Ferrarini A, Delledonne M, Henrissat B, Coutinho P, Fitzgerald GF, Margolles A, van Sinderen D, Ventura M., PLoS One 7(9), 2012
PMID: 23028506
The pupylation pathway and its role in mycobacteria.
Barandun J, Delley CL, Weber-Ban E., BMC Biol 10(), 2012
PMID: 23198822
Methods of combinatorial optimization to reveal factors affecting gene length.
Bolshoy A, Tatarinova T., Bioinform Biol Insights 6(), 2012
PMID: 23300345
Metabolism of a plant derived galactose-containing polysaccharide by Bifidobacterium breve UCC2003.
O'Connell Motherway M, Fitzgerald GF, van Sinderen D., Microb Biotechnol 4(3), 2011
PMID: 21375716
Prolonged environmental persistence requires efficient disinfection procedures to control Devriesea agamarum-associated disease in lizards.
Hellebuyck T, Pasmans F, Blooi M, Haesebrouck F, Martel A., Lett Appl Microbiol 52(1), 2011
PMID: 21091522
Candidate gene and genome-wide association studies of Mycobacterium avium subsp. paratuberculosis infection in cattle and sheep: a review.
Purdie AC, Plain KM, Begg DJ, de Silva K, Whittington RJ., Comp Immunol Microbiol Infect Dis 34(3), 2011
PMID: 21216466
A combined approach for comparative exoproteome analysis of Corynebacterium pseudotuberculosis.
Pacheco LG, Slade SE, Seyffert N, Santos AR, Castro TL, Silva WM, Santos AV, Santos SG, Farias LM, Carvalho MA, Pimenta AM, Meyer R, Silva A, Scrivens JH, Oliveira SC, Miyoshi A, Dowson CG, Azevedo V., BMC Microbiol 11(1), 2011
PMID: 21241507
Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis.
Sojka L, Kouba T, Barvík I, Sanderová H, Maderová Z, Jonák J, Krásny L., Nucleic Acids Res 39(11), 2011
PMID: 21303765
Bisubstrate specificity in histidine/tryptophan biosynthesis isomerase from Mycobacterium tuberculosis by active site metamorphosis.
Due AV, Kuper J, Geerlof A, von Kries JP, Wilmanns M., Proc Natl Acad Sci U S A 108(9), 2011
PMID: 21321225
Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils.
Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, Schöning I, Schrumpf M, Daniel R., PLoS One 6(2), 2011
PMID: 21359220
The actinobacteria-specific gene wblA controls major developmental transitions in Streptomyces coelicolor A3(2).
Fowler-Goldsworthy K, Gust B, Mouz S, Chandra G, Findlay KC, Chater KF., Microbiology 157(pt 5), 2011
PMID: 21330440
Ovine ruminal microbes are capable of biotransforming hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX).
Eaton HL, De Lorme M, Chaney RL, Craig AM., Microb Ecol 62(2), 2011
PMID: 21340737
A guide to the natural history of freshwater lake bacteria.
Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson S., Microbiol Mol Biol Rev 75(1), 2011
PMID: 21372319
Insights into physiological and genetic mupirocin susceptibility in bifidobacteria.
Serafini F, Bottacini F, Viappiani A, Baruffini E, Turroni F, Foroni E, Lodi T, van Sinderen D, Ventura M., Appl Environ Microbiol 77(9), 2011
PMID: 21421794
Core gene set as the basis of multilocus sequence analysis of the subclass Actinobacteridae.
Adékambi T, Butler RW, Hanrahan F, Delcher AL, Drancourt M, Shinnick TM., PLoS One 6(3), 2011
PMID: 21483493
The extracellular proteome of Bifidobacterium animalis subsp. lactis BB-12 reveals proteins with putative roles in probiotic effects.
Gilad O, Svensson B, Viborg AH, Stuer-Lauridsen B, Jacobsen S., Proteomics 11(12), 2011
PMID: 21598393
Proteomics of corynebacteria: From biotechnology workhorses to pathogens.
Poetsch A, Haussmann U, Burkovski A., Proteomics 11(15), 2011
PMID: 21674800
Comparative genome-scale metabolic modeling of actinomycetes: the topology of essential core metabolism.
Alam MT, Medema MH, Takano E, Breitling R., FEBS Lett 585(14), 2011
PMID: 21712033
Granaticins and their biosynthetic gene cluster from Streptomyces vietnamensis: evidence of horizontal gene transfer.
Deng MR, Guo J, Li X, Zhu CH, Zhu HH., Antonie Van Leeuwenhoek 100(4), 2011
PMID: 21732034
Ability of Bifidobacterium breve to grow on different types of milk: exploring the metabolism of milk through genome analysis.
Turroni F, Foroni E, Serafini F, Viappiani A, Montanini B, Bottacini F, Ferrarini A, Bacchini PL, Rota C, Delledonne M, Ottonello S, van Sinderen D, Ventura M., Appl Environ Microbiol 77(20), 2011
PMID: 21856831
Genetic analysis and morphological identification of pilus-like structures in members of the genus Bifidobacterium.
Foroni E, Serafini F, Amidani D, Turroni F, He F, Bottacini F, O'Connell Motherway M, Viappiani A, Zhang Z, Rivetti C, van Sinderen D, Ventura M., Microb Cell Fact 10 Suppl 1(), 2011
PMID: 21995649
Mycobacterium chelonae-abscessus complex associated with sinopulmonary disease, Northeastern USA.
Simmon KE, Brown-Elliott BA, Ridge PG, Durtschi JD, Mann LB, Slechta ES, Steigerwalt AG, Moser BD, Whitney AM, Brown JM, Voelkerding KV, McGowan KL, Reilly AF, Kirn TJ, Butler WR, Edelstein PH, Wallace RJ, Petti CA., Emerg Infect Dis 17(9), 2011
PMID: 21888796
Global genome transcription profiling of Bifidobacterium bifidum PRL2010 under in vitro conditions and identification of reference genes for quantitative real-time PCR.
Turroni F, Foroni E, Montanini B, Viappiani A, Strati F, Duranti S, Ferrarini A, Delledonne M, van Sinderen D, Ventura M., Appl Environ Microbiol 77(24), 2011
PMID: 22003014
Complete genome sequence of Bifidobacterium animalis subsp. lactis BLC1.
Bottacini F, Dal Bello F, Turroni F, Milani C, Duranti S, Foroni E, Viappiani A, Strati F, Mora D, van Sinderen D, Ventura M., J Bacteriol 193(22), 2011
PMID: 22038957
Genome sequence of Brachybacterium squillarum M-6-3(T), isolated from salt-fermented seafood.
Park SK, Roh SW, Whon TW, Bae JW., J Bacteriol 193(22), 2011
PMID: 22038973
Ribose utilization by the human commensal Bifidobacterium breve UCC2003.
Pokusaeva K, Neves AR, Zomer A, O'Connell-Motherway M, MacSharry J, Curley P, Fitzgerald GF, van Sinderen D., Microb Biotechnol 3(3), 2010
PMID: 21255330
Genome sequence of the Fleming strain of Micrococcus luteus, a simple free-living actinobacterium.
Young M, Artsatbanov V, Beller HR, Chandra G, Chater KF, Dover LG, Goh EB, Kahan T, Kaprelyants AS, Kyrpides N, Lapidus A, Lowry SR, Lykidis A, Mahillon J, Markowitz V, Mavromatis K, Mukamolova GV, Oren A, Rokem JS, Smith MC, Young DI, Greenblatt CL., J Bacteriol 192(3), 2010
PMID: 19948807
Genome-based phylogenetic analysis of Streptomyces and its relatives.
Alam MT, Merlo ME, Takano E, Breitling R., Mol Phylogenet Evol 54(3), 2010
PMID: 19948233
The complex extracellular biology of Streptomyces.
Chater KF, Biró S, Lee KJ, Palmer T, Schrempf H., FEMS Microbiol Rev 34(2), 2010
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Bifidobacterium stercoris sp. nov., isolated from human faeces.
Kim MS, Roh SW, Bae JW., Int J Syst Evol Microbiol 60(pt 12), 2010
PMID: 20081020
Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion.
Trost E, Götker S, Schneider J, Schneiker-Bekel S, Szczepanowski R, Tilker A, Viehoever P, Arnold W, Bekel T, Blom J, Gartemann KH, Linke B, Goesmann A, Pühler A, Shukla SK, Tauch A., BMC Genomics 11(), 2010
PMID: 20137072
Intertwinement of stress response regulons in Bifidobacterium breve UCC2003.
Zomer A, van Sinderen D., Gut Microbes 1(2), 2010
PMID: 21326917
Call of the wild: antibiotic resistance genes in natural environments.
Allen HK, Donato J, Wang HH, Cloud-Hansen KA, Davies J, Handelsman J., Nat Rev Microbiol 8(4), 2010
PMID: 20190823
Analyses of bifidobacterial prophage-like sequences.
Ventura M, Turroni F, Foroni E, Duranti S, Giubellini V, Bottacini F, van Sinderen D., Antonie Van Leeuwenhoek 98(1), 2010
PMID: 20229290
Characterization of the serpin-encoding gene of Bifidobacterium breve 210B.
Turroni F, Foroni E, O'Connell Motherway M, Bottacini F, Giubellini V, Zomer A, Ferrarini A, Delledonne M, Zhang Z, van Sinderen D, Ventura M., Appl Environ Microbiol 76(10), 2010
PMID: 20348296
Stress-induced synthesis of phosphatidylinositol 3-phosphate in mycobacteria.
Morita YS, Yamaryo-Botte Y, Miyanagi K, Callaghan JM, Patterson JH, Crellin PK, Coppel RL, Billman-Jacobe H, Kinoshita T, McConville MJ., J Biol Chem 285(22), 2010
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A framework for classification of prokaryotic protein kinases.
Tyagi N, Anamika K, Srinivasan N., PLoS One 5(5), 2010
PMID: 20520783
A guide to successful bioprospecting: informed by actinobacterial systematics.
Goodfellow M, Fiedler HP., Antonie Van Leeuwenhoek 98(2), 2010
PMID: 20582471
Comparative genomics of the genus Bifidobacterium.
Bottacini F, Medini D, Pavesi A, Turroni F, Foroni E, Riley D, Giubellini V, Tettelin H, van Sinderen D, Ventura M., Microbiology 156(pt 11), 2010
PMID: 20634238
Performance of a sulfidogenic bioreactor and bacterial community shifts under different alkalinity levels.
Zhao YG, Li XW, Wang JC, Bai J, Tian WJ., Bioresour Technol 101(23), 2010
PMID: 20688512
Actinobacteria: the good, the bad, and the ugly.
Miao V, Davies J., Antonie Van Leeuwenhoek 98(2), 2010
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Genomic insights into bifidobacteria.
Lee JH, O'Sullivan DJ., Microbiol Mol Biol Rev 74(3), 2010
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Origins and evolution of antibiotic resistance.
Davies J, Davies D., Microbiol Mol Biol Rev 74(3), 2010
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Role of porins in iron uptake by Mycobacterium smegmatis.
Jones CM, Niederweis M., J Bacteriol 192(24), 2010
PMID: 20952578
Genome analysis of Bifidobacterium bifidum PRL2010 reveals metabolic pathways for host-derived glycan foraging.
Turroni F, Bottacini F, Foroni E, Mulder I, Kim JH, Zomer A, Sánchez B, Bidossi A, Ferrarini A, Giubellini V, Delledonne M, Henrissat B, Coutinho P, Oggioni M, Fitzgerald GF, Mills D, Margolles A, Kelly D, van Sinderen D, Ventura M., Proc Natl Acad Sci U S A 107(45), 2010
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Kateete DP, Okee M, Katabazi FA, Okeng A, Asiimwe J, Boom HW, Eisenach KD, Joloba ML., BMC Microbiol 10(), 2010
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Structural analysis of the 6 kb cryptic plasmid pFAJ2600 from Rhodococcus erythropolis NI86/21 and construction of Escherichia coli-Rhodococcus shuttle vectors.
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A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model.
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AUTHOR UNKNOWN, 1973
Evidence for symmetric chromosomal inversions around the replication origin in bacteria.
Eisen JA, Heidelberg JF, White O, Salzberg SL., Genome Biol. 1(6), 2000
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Elliot MA, Talbot NJ., Curr. Opin. Microbiol. 7(6), 2004
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The molecular phylogeny and systematics of the actinomycetes.
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Epidemiology of infection by nontuberculous mycobacteria.
Falkinham JO 3rd., Clin. Microbiol. Rev. 9(2), 1996
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Fang Z, Doig C, Kenna DT, Smittipat N, Palittapongarnpim P, Watt B, Forbes KJ., J. Bacteriol. 181(3), 1999
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Fernandez-Garayzabal JF, Vela AI, Egido R, Hutson RA, Lanzarot MP, Fernandez-Garcia M, Collins MD., Int. J. Syst. Evol. Microbiol. 54(Pt 6), 2004
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Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set.
Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbon MH, Bobadilla del Valle M, Fyfe J, Garcia-Garcia L, Rastogi N, Sola C, Zozio T, Guerrero MI, Leon CI, Crabtree J, Angiuoli S, Eisenach KD, Durmaz R, Joloba ML, Rendon A, Sifuentes-Osornio J, Ponce de Leon A, Cave MD, Fleischmann R, Whittam TS, Alland D., J. Bacteriol. 188(2), 2006
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Whole genome-based phylogenetic analysis of free-living microorganisms.
Fitz-Gibbon ST, House CH., Nucleic Acids Res. 27(21), 1999
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Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.
Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR Jr, Venter JC, Fraser CM., J. Bacteriol. 184(19), 2002
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Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats.
Frothingham R, Meeker-O'Connell WA., Microbiology (Reading, Engl.) 144 ( Pt 5)(), 1998
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Corynebacterium efficiens sp. nov., a glutamic-acid-producing species from soil and vegetables.
Fudou R, Jojima Y, Seto A, Yamada K, Kimura E, Nakamatsu T, Hiraishi A, Yamanaka S., Int. J. Syst. Evol. Microbiol. 52(Pt 4), 2002
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Clinical microbiology of coryneform bacteria.
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The complete genome sequence of Mycobacterium bovis.
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Identification, cloning, and expression of the CAMP factor gene (cfa) of group A streptococci.
Gase K, Ferretti JJ, Primeaux C, McShan WM., Infect. Immun. 67(9), 1999
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Isolation by genetic labeling of a new mycobacterial plasmid, pJAZ38, from Mycobacterium fortuitum.
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Mycolactone: a polyketide toxin from Mycobacterium ulcerans required for virulence.
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Metagenomic analysis of the human distal gut microbiome.
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The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome.
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The microaerophily and photosensitivity of Propionibacterium acnes.
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Molecular characterization of Bifidobacterium longum biovar longum NAL8 plasmids and construction of a novel replicon screening system.
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The pathology of diphtheria.
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Crohn's disease and Mycobacterium avium subsp. paratuberculosis: current issues.
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Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence.
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Propionibacterium acnes and acne.
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Biology and molecular epidemiology of diphtheria toxin and the tox gene.
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Phylogenetic analysis based on genome-scale metabolic pathway reaction content.
Hong SH, Kim TY, Lee SY., Appl. Microbiol. Biotechnol. 65(2), 2004
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Systems biology and new technologies enable predictive and preventative medicine.
Hood L, Heath JR, Phelps ME, Lin B., Science 306(5696), 2004
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AUTHOR UNKNOWN, 2007
Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex.
Huard RC, Fabre M, de Haas P, Lazzarini LC, van Soolingen D, Cousins D, Ho JL., J. Bacteriol. 188(12), 2006
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Nocardia species as an etiologic agent in Parkinson's disease: serological testing in a case-control study.
Hubble JP, Cao T, Kjelstrom JA, Koller WC, Beaman BL., J. Clin. Microbiol. 33(10), 1995
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The sulfur-regulated arylsulfatase gene cluster of Pseudomonas aeruginosa, a new member of the cys regulon.
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Huson DH, Steel M., Bioinformatics 20(13), 2004
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Sensing and responding to diverse extracellular signals? Analysis of the sensor kinases and response regulators of Streptomyces coelicolor A3(2).
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Propionibacterium acnes endocarditis.
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Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis.
Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S., Nat. Biotechnol. 21(5), 2003
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Multiple novel promoters from the early region in the Streptomyces temperate phage phi C31 are activated during lytic development.
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The immunology of Propionibacterium acnes and acne.
Ingham E., Curr. Opin. Infect. Dis. 12(3), 1999
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The complete genomic sequence of Nocardia farcinica IFM 10152.
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AUTHOR UNKNOWN, 1987
Leprosy.
Jacobson RR, Krahenbuhl JL., Lancet 353(9153), 1999
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Severe infections caused by Propionibacterium acnes: an underestimated pathogen in late postoperative infections.
Jakab E, Zbinden R, Gubler J, Ruef C, von Graevenitz A, Krause M., Yale J Biol Med 69(6), 1996
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Evidence that the Streptomyces developmental protein WhiD, a member of the WhiB family, binds a [4Fe-4S] cluster.
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Out of the iron age: new insights into the critical role of manganese homeostasis in bacteria.
Jakubovics NS, Jenkinson HF., Microbiology (Reading, Engl.) 147(Pt 7), 2001
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Analysis of nucleotide methylation in DNA from Corynebacterium glutamicum and related species.
Jang KH, Chambers PJ, Britz ML., FEMS Microbiol. Lett. 136(3), 1996
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Identification of genes that are associated with DNA repeats in prokaryotes.
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Propionibacterium acnes and inflammation in acne; P. acnes has T-cell mitogenic activity.
Jappe U, Ingham E, Henwood J, Holland KT., Br. J. Dermatol. 146(2), 2002
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New approach to phylogenetic analysis of the genus Bifidobacterium based on partial HSP60 gene sequences.
Jian W, Zhu L, Dong X., Int. J. Syst. Evol. Microbiol. 51(Pt 5), 2001
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Efficient transformation system for Propionibacterium freudenreichii based on a novel vector.
Jore JP, van Luijk N, Luiten RG, van der Werf MJ, Pouwels PH., Appl. Environ. Microbiol. 67(2), 2001
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Jost BH, Field AC, Trinh HT, Songer JG, Billington SJ., Antimicrob. Agents Chemother. 47(11), 2003
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AUTHOR UNKNOWN, 2005
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
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Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum.
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The terminal structures of linear plasmids from Rhodococcus opacus.
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Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences.
Kasai H, Ezaki T, Harayama S., J. Clin. Microbiol. 38(1), 2000
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Molecular cloning and characterization of Bifidobacterium bifidum 1,2-alpha-L-fucosidase (AfcA), a novel inverting glycosidase (glycoside hydrolase family 95).
Katayama T, Sakuma A, Kimura T, Makimura Y, Hiratake J, Sakata K, Yamanoi T, Kumagai H, Yamamoto K., J. Bacteriol. 186(15), 2004
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The nature and consequence of genetic variability within Mycobacterium tuberculosis.
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The Five "Classical" Plant Hormones.
Kende H, Zeevaart J., Plant Cell 9(7), 1997
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AUTHOR UNKNOWN, 1984
Plasmids in group JK coryneform bacteria isolated in a single hospital.
Kerry-Williams SM, Noble WC., J Hyg (Lond) 97(2), 1986
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Molecular epidemiology of group JK Corynebacterium on a cancer ward: lack of evidence for patient-to-patient transmission.
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Characterization of pRGO1, a plasmid from Propionibacterium acidipropionici, and its use for development of a host-vector system in propionibacteria.
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AUTHOR UNKNOWN, 2000
Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB).
Kim BJ, Lee SH, Lyu MA, Kim SJ, Bai GH, Chae GT, Kim EC, Cha CY, Kook YH., J. Clin. Microbiol. 37(6), 1999
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The whcE gene of Corynebacterium glutamicum is important for survival following heat and oxidative stress.
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AUTHOR UNKNOWN, 1957
Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue.
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rRNA operon copy number reflects ecological strategies of bacteria.
Klappenbach JA, Dunbar JM, Schmidt TM., Appl. Environ. Microbiol. 66(4), 2000
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Evolution of minimal-gene-sets in host-dependent bacteria.
Klasson L, Andersson SG., Trends Microbiol. 12(1), 2004
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Lessons from the genomes of bifidobacteria.
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Dynamic bacterial genome organization.
Kolsto AB., Mol. Microbiol. 24(2), 1997
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Trends between gene content and genome size in prokaryotic species with larger genomes.
Konstantinidis KT, Tiedje JM., Proc. Natl. Acad. Sci. U.S.A. 101(9), 2004
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SHOT: a web server for the construction of genome phylogenies.
Korbel JO, Snel B, Huynen MA, Bork P., Trends Genet. 18(3), 2002
PMID: 11858840
The role of innate immunity in the pathogenesis of acne.
Koreck A, Pivarcsi A, Dobozy A, Kemeny L., Dermatology (Basel) 206(2), 2003
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A small cryptic plasmid from Rhodococcus erythropolis: characterization and utility for gene expression.
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Biochemistry of homologous recombination in Escherichia coli.
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Extensive surface diversity of a commensal microorganism by multiple DNA inversions.
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Comparison of mammalian cell entry operons of mycobacteria: in silico analysis and expression profiling.
Kumar A, Chandolia A, Chaudhry U, Brahmachari V, Bose M., FEMS Immunol. Med. Microbiol. 43(2), 2005
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The balance of driving forces during genome evolution in prokaryotes.
Kunin V, Ouzounis CA., Genome Res. 13(7), 2003
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The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
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Determination of a 15437 bp nucleotide sequence around the inhA gene of Mycobacterium avium and similarity analysis of the products of putative ORFs.
Labo M, Gusberti L, Rossi ED, Speziale P, Riccardi G., Microbiology (Reading, Engl.) 144 ( Pt 3)(), 1998
PMID: 9534249
Cytochrome p450 complement (CYPome) of the avermectin-producer Streptomyces avermitilis and comparison to that of Streptomyces coelicolor A3(2).
Lamb DC, Ikeda H, Nelson DR, Ishikawa J, Skaug T, Jackson C, Omura S, Waterman MR, Kelly SL., Biochem. Biophys. Res. Commun. 307(3), 2003
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AUTHOR UNKNOWN, 1997
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Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology.
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Cloning and sequencing of the hyaluronate lyase gene from Propionibacterium acnes.
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Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
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AUTHOR UNKNOWN, 2001
Mycobacteria in soil and their relation to disease-associated strains.
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A new subfamily of the Nudix hydrolase superfamily active on 5-methyl-UTP (ribo-TTP) and UTP.
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The superoxide dismutase gene, a target for detection and identification of mycobacteria by PCR.
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A 12.7 kb fragment of the Mycobacterium tuberculosis genome is not present in Mycobacterium bovis.
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