Strategies for culture of ‘unculturable’ bacteria
Tóm tắt
Từ khóa
Tài liệu tham khảo
Aas, 2005, Defining the normal bacterial flora of the oral cavity, J Clin Microbiol, 43, 5721, 10.1128/JCM.43.11.5721-5732.2005
Alvarez-Barrientos, 2000, Applications of flow cytometry to clinical microbiology, Clin Microbiol Rev, 13, 167, 10.1128/CMR.13.2.167
Amann, 2001, The identification of microorganisms by fluorescence in situ hybridisation, Curr Opin Biotech, 12, 231, 10.1016/S0958-1669(00)00204-4
Amann, 1995, Phylogenetic identification and in situ detection of individual microbial cells without cultivation, Microbiol Rev, 59, 143, 10.1128/MMBR.59.1.143-169.1995
Auguet, 2010, Global ecological patterns in uncultured Archaea, ISME J, 4, 182, 10.1038/ismej.2009.109
Bae, 2005, Isolation of uncultivated anaerobic thermophiles from compost by supplementing cell extract of Geobacillus toebii in enrichment culture medium, Extremophiles, 9, 477, 10.1007/s00792-005-0467-y
Barcina, 1990, Survival strategy of Escherichia coli and Enterococcus faecalis in illuminated fresh and marine systems, J Appl Bacteriol, 68, 189, 10.1111/j.1365-2672.1990.tb02565.x
Belenguer, 2006, Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut, Appl Environ Microb, 72, 3593, 10.1128/AEM.72.5.3593-3599.2006
Ben-Dov, 2009, An in situ method for cultivating microorganisms using a double encapsulation technique, FEMS Microbiol Ecol, 68, 363, 10.1111/j.1574-6941.2009.00682.x
Bollmann, 2007, Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates, Appl Environ Microb, 73, 6386, 10.1128/AEM.01309-07
Bruns, 2002, Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea, Appl Environ Microb, 68, 3978, 10.1128/AEM.68.8.3978-3987.2002
Chen, 1985, Bacterial growth and the concentrations of cyclic nucleotides in Legionella pneumophila cultures, Curr Microbiol, 12, 23, 10.1007/BF01567748
Cohen-Gonsaud, 2005, The structure of a resuscitation-promoting factor domain from Mycobacterium tuberculosis shows homology to lysozymes, Nat Struct Mol Biol, 12, 270, 10.1038/nsmb905
Colwell, 2000, Viable but nonculturable bacteria, a survival strategy, 6, 121
Connon, 2002, High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates, Appl Environ Microb, 68, 3878, 10.1128/AEM.68.8.3878-3885.2002
Coppola, 1976, Interactions of N6-(delta2-isopentenyl)adenine with cyclic AMP on the regulation of growth and beta-galactosidase synthesis in Escherichia coli, J Gen Microbiol, 94, 436, 10.1099/00221287-94-2-436
Davey, 2008, Tracking dynamic interactions during plaque formation, J Bacteriol, 190, 7869, 10.1128/JB.01344-08
Davis, 2005, Effects of growth medium, inoculum size, and incubation time on culturability and isolation of soil bacteria, Appl Environ Microb, 71, 826, 10.1128/AEM.71.2.826-834.2005
De Kievit, 2001, Quorum-sensing genes in Pseudomonas aeruginosa biofilms, their role and expression patterns, 67, 1865
Ferrari, 2009, Cultivating fastidious bacteria, viability staining and micromanipulation from a soil substrate membrane system, 75, 3352
Ferrari, 2005, Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria, Appl Environ Microb, 71, 8714, 10.1128/AEM.71.12.8714-8720.2005
Ferrari, 2006, Catalyzed reporter deposition-fluorescence in situ hybridization allows for enrichment-independent detection of microcolony-forming soil bacteria, Appl Environ Microb, 72, 918, 10.1128/AEM.72.1.918-922.2006
Ferrari, 2008, Cultivating previously uncultured soil bacteria using a soil substrate membrane system, Nat Protoc, 3, 1261, 10.1038/nprot.2008.102
Frohlich, 2000, New techniques for isolation of single prokaryotic cells, FEMS Microbiol Rev, 24, 567, 10.1111/j.1574-6976.2000.tb00558.x
Giovannoni, 1990, Genetic diversity in Sargasso Sea bacterioplankton, Nature, 345, 60, 10.1038/345060a0
Graber, 2005, Folate cross-feeding supports symbiotic homoacetogenic spirochetes, Appl Environ Microb, 71, 1883, 10.1128/AEM.71.4.1883-1889.2005
Hackstadt, 1981, Biochemical stratagem for obligate parasitism of eukaryotic cells by Coxiella burnetii, P Natl Acad Sci USA, 78, 3240, 10.1073/pnas.78.5.3240
Hahn, 2004, The filtration-acclimatization method for isolation of an important fraction of the not readily cultivable bacteria, J Microbiol Meth, 57, 379, 10.1016/j.mimet.2004.02.004
Hall-Stoodley, 2004, Bacterial biofilms, from the natural environment to infectious diseases, 2, 95
Huang, 2009, Raman tweezers sorting of single microbial cells, Environ Microbiol Reports, 1, 44, 10.1111/j.1758-2229.2008.00002.x
Huber, 1995, Isolation of a hyperthermophilic archaeum predicted by in situ RNA analysis, Nature, 376, 57, 10.1038/376057a0
Hugenholtz, 2002, Exploring prokaryotic diversity in the genomic era, Genome Biol, 3, 1, 10.1186/gb-2002-3-2-reviews0003
Hugenholtz, 1998, Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, J Bacteriol, 180, 4765, 10.1128/JB.180.18.4765-4774.1998
Hugenholtz, 2009, Focus, synergistetes, 11, 1327
Janssen, 2003, Selective enrichment and purification of cultures of Methanosaeta spp, J Microbiol Methods, 52, 239, 10.1016/S0167-7012(02)00181-1
Kaeberlein, 2002, Isolating ‘uncultivable’ microorganisms in pure culture in a simulated natural environment, Science, 296, 1127, 10.1126/science.1070633
Kana, 2009, Resuscitation-promoting factors as lytic enzymes for bacterial growth and signaling, FEMS Immunol Med Mic, 58, 39, 10.1111/j.1574-695X.2009.00606.x
Kell, 2000, Bacterial dormancy and culturability, the role of autocrine growth factors, 3, 238
Kim, 2008a, Isolation of uncultivable anaerobic thermophiles of the family Clostridiaceae requiring growth-supporting factors, J Microbiol Biotechn, 18, 611
Kim, 2008b, Characterization of growth-supporting factors produced by Geobacillus toebii for the commensal thermophile Symbiobacterium toebii, J Microbiol Biotechn, 18, 490
Koch, 1997, Microbial physiology and ecology of slow growth, Microbiol Mol Biol R, 61, 305, 10.1128/.61.3.305-318.1997
Konaklieva, 2006, Chemical communication - do we have a quorum?, Mini Rev Med Chem, 6, 817, 10.2174/138955706777698589
Kopke, 2005, Microbial diversity in coastal subsurface sediments, a cultivation approach using various electron acceptors and substrate gradients, 71, 7819
Lewis, 2007, Persister cells, dormancy and infectious disease, Nat Rev Microbiol, 5, 48, 10.1038/nrmicro1557
Marsh, 2005, Dental plaque, biological significance of a biofilm and community life-style, 32, 7
Mikx, 1975, Symbiosis of Streptococcus mutans and Veillonella alcalescens in mixed continuous cultures, Arch Oral Biol, 20, 407, 10.1016/0003-9969(75)90224-1
Munson, 2002, Molecular and cultural analysis of the microflora associated with endodontic infections, J Dent Res, 81, 761, 10.1177/0810761
Nichols, 2008, Short peptide induces an ‘uncultivable’ microorganism to grow in vitro, Appl Environ Microb, 74, 4889, 10.1128/AEM.00393-08
Ohno, 1999, Establishing the independent culture of a strictly symbiotic bacterium Symbiobacterium thermophilum from its supporting Bacillus strain, Biosci Biotech Bioch, 63, 1083, 10.1271/bbb.63.1083
Ohno, 2000, Symbiobacterium thermophilum gen. nov., sp. nov., a symbiotic thermophile that depends on co-culture with a Bacillus strain for growth, Int J Syst Evol Micr, 50, 1829, 10.1099/00207713-50-5-1829
Omsland, 2008, Sustained axenic metabolic activity by the obligate intracellular bacterium Coxiella burnetii, J Bacteriol, 190, 3203, 10.1128/JB.01911-07
Ormsbee, 1964, Metabolic activity in Coxiella burnetii, J Bacteriol, 88, 1205, 10.1128/JB.88.5.1205-1210.1964
Pace, 1997, A molecular view of microbial diversity and the biosphere, Science, 276, 734, 10.1126/science.276.5313.734
Podar, 2007, Targeted access to the genomes of low-abundance organisms in complex microbial communities, Appl Environ Microb, 73, 3205, 10.1128/AEM.02985-06
Rappe, 2003, The uncultured microbial majority, Annu Rev Microbiol, 57, 369, 10.1146/annurev.micro.57.030502.090759
Rappe, 2002, Cultivation of the ubiquitous SAR11 marine bacterioplankton clade, Nature, 418, 630, 10.1038/nature00917
Ravagnani, 2005, A novel firmicute protein family related to the actinobacterial resuscitation-promoting factors by non-orthologous domain displacement, BMC Genomics, 6, 39, 10.1186/1471-2164-6-39
Sait, 2002, Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys, Environ Microbiol, 4, 654, 10.1046/j.1462-2920.2002.00352.x
Salama, 1993, Isolation of Lactococcus lactis subsp. cremoris from nature by colony hybridization with rRNA probes, Appl Environ Microb, 59, 3941, 10.1128/AEM.59.11.3941-3945.1993
Shah, 2008, A eukaryotic-like Ser/Thr kinase signals bacteria to exit dormancy in response to peptidoglycan fragments, Cell, 135, 486, 10.1016/j.cell.2008.08.039
Song, 2009, Improved culturability of SAR11 strains in dilution-to-extinction culturing from the East Sea, West Pacific Ocean, FEMS Microbiol Lett, 295, 141, 10.1111/j.1574-6968.2009.01623.x
Staley, 1985, Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats, Annu Rev Microbiol, 39, 321, 10.1146/annurev.mi.39.100185.001541
Stingl, 2008, Dilution-to-extinction culturing of psychrotolerant planktonic bacteria from permanently ice-covered lakes in the McMurdo Dry Valleys, Antarctica, Microb Ecol, 55, 395, 10.1007/s00248-007-9284-4
Stoodley, 2002, Biofilms as complex differentiated communities, Annu Rev Microbiol, 56, 187, 10.1146/annurev.micro.56.012302.160705
Tamaki, 2005, Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques, Appl Environ Microb, 71, 2162, 10.1128/AEM.71.4.2162-2169.2005
Tanaka, 2004, Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth, Int J Syst Evol Micr, 54, 955, 10.1099/ijs.0.02750-0
Ten Cate, 2006, Biofilms, a new approach to the microbiology of dental plaque, Odontology, 94, 1, 10.1007/s10266-006-0063-3
Tripp, 2008, SAR11 marine bacteria require exogenous reduced sulphur for growth, Nature, 452, 741, 10.1038/nature06776
Vartoukian, 2009, Diversity and morphology of members of the phylum ‘Synergistetes’ in periodontal health and disease, Appl Environ Microb, 75, 3777, 10.1128/AEM.02763-08
Vartoukian, 2010, Cultivation of a Synergistetes strain representing a previously uncultivated lineage, Environ Microbiol, 12, 916, 10.1111/j.1462-2920.2009.02135.x
Wang, 2009, Isolation and characterization of low nucleic acid (LNA)-content bacteria, ISME J, 3, 889, 10.1038/ismej.2009.46
Watve, 2000, The ‘K’ selected oligophilic bacteria, a key to uncultured diversity?, 78, 1535
Wyss, 1989, Dependence of proliferation of Bacteroides forsythus on exogenous N-acetylmuramic acid, Infect Immun, 57, 1757, 10.1128/IAI.57.6.1757-1759.1989