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Volumn 4, Issue MAY, 2014, Pages

Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients

Author keywords

16S rDNA profiling; Bacterial communities; Endotracheal aspirate; Microbiota; Supraglottic secretions

Indexed keywords

DNA 16S; RNA 16S;

EID: 84907172085     PISSN: None     EISSN: 22352988     Source Type: Journal    
DOI: 10.3389/fcimb.2014.00065     Document Type: Note
Times cited : (24)

References (33)
  • 1
    • 0000374167 scopus 로고    scopus 로고
    • Capacity of nine thermostable DNA polymerases To mediate DNA amplification in the presence of PCR-inhibiting samples
    • Al-Soud, A. W., and Rådström, P. (1998). Capacity of nine thermostable DNA polymerases To mediate DNA amplification in the presence of PCR-inhibiting samples. Appl. Environ. Microbiol. 64, 3748-3753.
    • (1998) Appl. Environ. Microbiol , vol.64 , pp. 3748-3753
    • Al-Soud, A.W.1    Rådström, P.2
  • 2
    • 84863292680 scopus 로고    scopus 로고
    • Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection
    • Biesbroek, G., Sanders, E. A., Roeselers, G., Wang, X., Caspers, M. P., Trzcinski, K., et al. (2012). Deep sequencing analyses of low density microbial communities: working at the boundary of accurate microbiota detection. PLoS ONE 7:e32942. doi: 10.1371/journal.pone.0032942
    • (2012) PLoS ONE , vol.7
    • Biesbroek, G.1    Sanders, E.A.2    Roeselers, G.3    Wang, X.4    Caspers, M.P.5    Trzcinski, K.6
  • 3
    • 79952298772 scopus 로고    scopus 로고
    • Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis
    • Bogaert, D., Keijser, B., Huse, S., Rossen, J., Veenhoven, R., van Gils, E., et al. (2011). Variability and diversity of nasopharyngeal microbiota in children: a metagenomic analysis. PLoS ONE 6:e17035. doi: 10.1371/journal.pone.0017035
    • (2011) PLoS ONE , vol.6
    • Bogaert, D.1    Keijser, B.2    Huse, S.3    Rossen, J.4    Veenhoven, R.5    van Gils, E.6
  • 4
  • 5
    • 84867563577 scopus 로고    scopus 로고
    • Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease
    • Cabrera-Rubio, R., Garcia-Nunez, M., Seto, L., Anto, J. M., Moya, A., Monso, E., et al. (2012). Microbiome diversity in the bronchial tracts of patients with chronic obstructive pulmonary disease. J. Clin. Microbiol. 50, 3562-3568. doi: 10.1128/JCM.00767-12
    • (2012) J. Clin. Microbiol , vol.50 , pp. 3562-3568
    • Cabrera-Rubio, R.1    Garcia-Nunez, M.2    Seto, L.3    Anto, J.M.4    Moya, A.5    Monso, E.6
  • 6
    • 80053122563 scopus 로고    scopus 로고
    • Topographical continuity of bacterial populations in the healthy human respiratory tract
    • Charlson, E. S., Bittinger, K., Haas, A. R., Fitzgerald, A. S., Frank, I., Yadav, A., et al. (2011). Topographical continuity of bacterial populations in the healthy human respiratory tract. Am. J. Res. Crit. Care Med. 184, 957-963. doi: 10.1164/rccm.201104-0655OC
    • (2011) Am. J. Res. Crit. Care Med , vol.184 , pp. 957-963
    • Charlson, E.S.1    Bittinger, K.2    Haas, A.R.3    Fitzgerald, A.S.4    Frank, I.5    Yadav, A.6
  • 7
    • 69249109724 scopus 로고    scopus 로고
    • Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine
    • Claesson, M. J., O'Sullivan, O., Wang, Q., Nikkila, J., Marchesi, J. R., Smidt, H., et al. (2009). Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 4:e6669. doi: 10.1371/journal.pone.0006669
    • (2009) PLoS ONE , vol.4
    • Claesson, M.J.1    O'Sullivan, O.2    Wang, Q.3    Nikkila, J.4    Marchesi, J.R.5    Smidt, H.6
  • 8
    • 0028120237 scopus 로고
    • Inhibition of the polymerase chain reaction by mucolytic agents
    • Deneer, H. G., and Knight, I. (1994). Inhibition of the polymerase chain reaction by mucolytic agents. Clin. Chem. 40, 171-172.
    • (1994) Clin. Chem , vol.40 , pp. 171-172
    • Deneer, H.G.1    Knight, I.2
  • 9
    • 84886624088 scopus 로고    scopus 로고
    • A method for selectively enriching microbial DNA from contaminating vertebrate host DNA
    • Feehery, G. R., Yigit, E., Oyola, S. O., Langhorst, B. W., Schmidt, V. T., Stewart, F. J., et al. (2013). A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. PLoS ONE 8:e76096. doi: 10.1371/journal.pone.0076096
    • (2013) PLoS ONE , vol.8
    • Feehery, G.R.1    Yigit, E.2    Oyola, S.O.3    Langhorst, B.W.4    Schmidt, V.T.5    Stewart, F.J.6
  • 11
    • 63249099357 scopus 로고    scopus 로고
    • Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples
    • Kermekchiev, M. B., Kirilova, L. I., Vail, E. E., and Barnes, W. M. (2009). Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res. 37, e40. doi: 10.1093/nar/gkn1055
    • (2009) Nucleic Acids Res , vol.37
    • Kermekchiev, M.B.1    Kirilova, L.I.2    Vail, E.E.3    Barnes, W.M.4
  • 12
    • 84877077675 scopus 로고    scopus 로고
    • Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome
    • Krych, L., Hansen, C. H., Hansen, A. K., van den Berg, F. W., and Nielsen, D. S. (2013). Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome. PLoS ONE 8:e62578. doi: 10.1371/journal.pone.0062578
    • (2013) PLoS ONE , vol.8
    • Krych, L.1    Hansen, C.H.2    Hansen, A.K.3    van den Berg, F.W.4    Nielsen, D.S.5
  • 13
    • 84879755675 scopus 로고    scopus 로고
    • Comparison of DNA extraction methods in analysis of salivary bacterial communities
    • Lazarevic, V., Gaia, N., Girard, M., Francois, P., and Schrenzel, J. (2013a). Comparison of DNA extraction methods in analysis of salivary bacterial communities. PLoS ONE 8:e67699. doi: 10.1371/journal.pone.0067699
    • (2013) PLoS ONE , vol.8
    • Lazarevic, V.1    Gaia, N.2    Girard, M.3    Francois, P.4    Schrenzel, J.5
  • 14
    • 84880506369 scopus 로고    scopus 로고
    • Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media
    • Lazarevic, V., Manzano, S., Gaia, N., Girard, M., Whiteson, K., Hibbs, J., et al. (2013b). Effects of amoxicillin treatment on the salivary microbiota in children with acute otitis media. Clin. Microbiol. Infect. 19, E335-E342. doi: 10.1111/1469-0691.12213
    • (2013) Clin. Microbiol. Infect , vol.19 , pp. E335-E342
    • Lazarevic, V.1    Manzano, S.2    Gaia, N.3    Girard, M.4    Whiteson, K.5    Hibbs, J.6
  • 15
    • 84988012964 scopus 로고    scopus 로고
    • The salivary microbiome assessed by a high-throughput and culture-independent approach
    • Lazarevic, V., Whiteson, K., François, P., and Schrenzel, J. (2011). The salivary microbiome assessed by a high-throughput and culture-independent approach. J. Integr. Omics 1, 25-35. doi: 10.5584/jiomics.v1i1.43
    • (2011) J. Integr. Omics , vol.1 , pp. 25-35
    • Lazarevic, V.1    Whiteson, K.2    François, P.3    Schrenzel, J.4
  • 17
    • 77957168527 scopus 로고    scopus 로고
    • Study of inter-and intra-individual variations in the salivary microbiota
    • Lazarevic, V., Whiteson, K., Hernandez, D., François, P., and Schrenzel, J. (2010). Study of inter-and intra-individual variations in the salivary microbiota. BMC Genomics 11:523. doi: 10.1186/1471-2164-11-523
    • (2010) BMC Genomics , vol.11 , pp. 523
    • Lazarevic, V.1    Whiteson, K.2    Hernandez, D.3    François, P.4    Schrenzel, J.5
  • 18
    • 84878708884 scopus 로고    scopus 로고
    • Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates
    • Ling, Z., Liu, X., Luo, Y., Yuan, L., Nelson, K. E., Wang, Y., et al. (2013). Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates. BMC Genomics 14:390. doi: 10.1186/1471-2164-14-390
    • (2013) BMC Genomics , vol.14 , pp. 390
    • Ling, Z.1    Liu, X.2    Luo, Y.3    Yuan, L.4    Nelson, K.E.5    Wang, Y.6
  • 20
    • 84926418348 scopus 로고    scopus 로고
    • Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome
    • Marine, R., McCarren, C., Vorrasane, V., Nasko, D., Crowgey, E., Polson, S. W., et al. (2014). Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome. Microbiome 2, 3. doi: 10.1186/2049-2618-2-3
    • (2014) Microbiome , vol.2 , pp. 3
    • Marine, R.1    McCarren, C.2    Vorrasane, V.3    Nasko, D.4    Crowgey, E.5    Polson, S.W.6
  • 21
    • 84857122937 scopus 로고    scopus 로고
    • An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
    • McDonald, D., Price, M. N., Goodrich, J., Nawrocki, E. P., Desantis, T. Z., Probst, A., et al. (2012). An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618. doi: 10.1038/ismej.2011.139
    • (2012) ISME J , vol.6 , pp. 610-618
    • McDonald, D.1    Price, M.N.2    Goodrich, J.3    Nawrocki, E.P.4    Desantis, T.Z.5    Probst, A.6
  • 22
    • 77958006512 scopus 로고    scopus 로고
    • Probiotic prophylaxis of ventilator-associated pneumonia: a blinded, randomized, controlled trial
    • Morrow, L. E., Kollef, M. H., and Casale, T. B. (2010). Probiotic prophylaxis of ventilator-associated pneumonia: a blinded, randomized, controlled trial. Am. J. Res. Crit. Care Med. 182, 1058-1064. doi: 10.1164/rccm.200912-1853OC
    • (2010) Am. J. Res. Crit. Care Med , vol.182 , pp. 1058-1064
    • Morrow, L.E.1    Kollef, M.H.2    Casale, T.B.3
  • 23
    • 80053900916 scopus 로고    scopus 로고
    • Molecular identification of bacteria in tracheal aspirate fluid from mechanically ventilated preterm infants
    • Mourani, P. M., Harris, J. K., Sontag, M. K., Robertson, C. E., and Abman, S. H. (2011). Molecular identification of bacteria in tracheal aspirate fluid from mechanically ventilated preterm infants. PLoS ONE 6:e25959. doi: 10.1371/journal.pone.0025959
    • (2011) PLoS ONE , vol.6
    • Mourani, P.M.1    Harris, J.K.2    Sontag, M.K.3    Robertson, C.E.4    Abman, S.H.5
  • 24
    • 0027508905 scopus 로고
    • Detection of Pneumocystis carinii DNA in sputum and bronchoalveolar lavage samples by polymerase chain reaction
    • Olsson, M., Elvin, K., Lofdahl, S., and Linder, E. (1993). Detection of Pneumocystis carinii DNA in sputum and bronchoalveolar lavage samples by polymerase chain reaction. J. Clin. Microbiol. 31, 221-226.
    • (1993) J. Clin. Microbiol , vol.31 , pp. 221-226
    • Olsson, M.1    Elvin, K.2    Lofdahl, S.3    Linder, E.4
  • 25
    • 69349087447 scopus 로고    scopus 로고
    • Can bacteriological upper airway samples obtained at intensive care unit admission guide empiric antibiotherapy for ventilator-associated pneumonia?
    • Pirracchio, R., Mateo, J., Raskine, L., Rigon, M. R., Lukaszewicz, A. C., Mebazaa, A., et al. (2009). Can bacteriological upper airway samples obtained at intensive care unit admission guide empiric antibiotherapy for ventilator-associated pneumonia? Crit. Care Med. 37, 2559-2563. doi: 10.1097/CCM.0b013e3181a57b48
    • (2009) Crit. Care Med , vol.37 , pp. 2559-2563
    • Pirracchio, R.1    Mateo, J.2    Raskine, L.3    Rigon, M.R.4    Lukaszewicz, A.C.5    Mebazaa, A.6
  • 26
    • 84867427320 scopus 로고    scopus 로고
    • The lung microbiome in moderate and severe chronic obstructive pulmonary disease
    • Pragman, A. A., Kim, H. B., Reilly, C. S., Wendt, C., and Isaacson, R. E. (2012). The lung microbiome in moderate and severe chronic obstructive pulmonary disease. PLoS ONE 7:e47305. doi: 10.1371/journal.pone.0047305
    • (2012) PLoS ONE , vol.7
    • Pragman, A.A.1    Kim, H.B.2    Reilly, C.S.3    Wendt, C.4    Isaacson, R.E.5
  • 27
    • 79952390994 scopus 로고    scopus 로고
    • Fast identification and removal of sequence contamination from genomic and metagenomic datasets
    • Schmieder, R., and Edwards, R. (2011). Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS ONE 6:e17288. doi: 10.1371/journal.pone.0017288
    • (2011) PLoS ONE , vol.6
    • Schmieder, R.1    Edwards, R.2
  • 28
    • 84862162269 scopus 로고    scopus 로고
    • Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples
    • Segata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., et al. (2012). Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol. 13, R42. doi: 10.1186/gb-2012-13-6-r42
    • (2012) Genome Biol , vol.13
    • Segata, N.1    Haake, S.K.2    Mannon, P.3    Lemon, K.P.4    Waldron, L.5    Gevers, D.6
  • 29
    • 0001582862 scopus 로고
    • The reduction in vitro in viscosity of mucoprotein solutions by a new mucolytic agent, N-acetyl-L-cysteine
    • Sheffner, A. L. (1963). The reduction in vitro in viscosity of mucoprotein solutions by a new mucolytic agent, N-acetyl-L-cysteine. Ann. N.Y. Acad. Sci. 106, 298-310. doi: 10.1111/j.1749-6632.1963.tb16647.x
    • (1963) Ann. N.Y. Acad. Sci , vol.106 , pp. 298-310
    • Sheffner, A.L.1
  • 30
    • 0031904685 scopus 로고    scopus 로고
    • Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants
    • Tanner, M. A., Goebel, B. M., Dojka, M. A., and Pace, N. R. (1998). Specific ribosomal DNA sequences from diverse environmental settings correlate with experimental contaminants. Appl. Environ. Microbiol. 64, 3110-3113.
    • (1998) Appl. Environ. Microbiol , vol.64 , pp. 3110-3113
    • Tanner, M.A.1    Goebel, B.M.2    Dojka, M.A.3    Pace, N.R.4
  • 31
    • 0026328502 scopus 로고
    • Reduction of salivary bacteria by pre-procedural rinses with chlorhexidine 0.12%
    • Veksler, A. E., Kayrouz, G. A., and Newman, M. G. (1991). Reduction of salivary bacteria by pre-procedural rinses with chlorhexidine 0.12%. J. Periodontol. 62, 649-651. doi: 10.1902/jop.1991.62.11.649
    • (1991) J. Periodontol , vol.62 , pp. 649-651
    • Veksler, A.E.1    Kayrouz, G.A.2    Newman, M.G.3
  • 32
    • 84859726078 scopus 로고    scopus 로고
    • Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples
    • Willner, D., Daly, J., Whiley, D., Grimwood, K., Wainwright, C. E., and Hugenholtz, P. (2012). Comparison of DNA extraction methods for microbial community profiling with an application to pediatric bronchoalveolar lavage samples. PLoS ONE 7:e34605. doi: 10.1371/journal.pone.0034605
    • (2012) PLoS ONE , vol.7
    • Willner, D.1    Daly, J.2    Whiley, D.3    Grimwood, K.4    Wainwright, C.E.5    Hugenholtz, P.6
  • 33
    • 74949134895 scopus 로고    scopus 로고
    • Defining the healthy core microbiome of oral microbial communities
    • Zaura, E., Keijser, B. J., Huse, S. M., and Crielaard, W. (2009). Defining the healthy core microbiome of oral microbial communities. BMC Microbiol. 9:259. doi: 10.1186/1471-2180-9-259
    • (2009) BMC Microbiol , vol.9 , pp. 259
    • Zaura, E.1    Keijser, B.J.2    Huse, S.M.3    Crielaard, W.4


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