Microbial diversity in the sputum of a cystic fibrosis patient studied with 16S rDNA pyrosequencing.
Recent studies using 16S rRNA gene amplification followed by clonal Sanger sequencing in cystic fibrosis demonstrated that cultured microorganisms are only part of the infecting flora. The purpose of this paper was to compare pyrosequencing and clonal Sanger sequencing on sputum. The sputum of a patient with cystic fibrosis was analysed by culture, Sanger clone sequencing and pyrosequencing after 16S rRNA gene amplification. A total of 4,499 sequencing reads were obtained, which could be attributed to six consensus sequences, but the length of reads leads to fastidious data analysis. Compared to clonal Sanger sequencing and to cultivation results, pyrosequencing recovers greater species richness and gives a more reliable estimate of the relative abundance of bacterial species. The 16S pyrosequencing approach expands our knowledge of the microbial diversity of cystic fibrosis sputum. The current lack of phylogenetic resolution at the species level for the GS 20 sequencing reads will be overcome with the next generation of pyrosequencing apparatus.
Armougom
F
F
URMITE-UMR CNRS 6236, IRD 3R198, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13005 Marseille, France.
Bittar
F
F
Stremler
N
N
Rolain
J-M
JM
Robert
C
C
Dubus
J-C
JC
Sarles
J
J
Raoult
D
D
La Scola
B
B
D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification; D001424:Bacterial Infections / Q000382:microbiology*; D044822:Biodiversity; D003550:Cystic Fibrosis / Q000150:complications*; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D006801:Humans; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013183:Sputum / Q000382:microbiology*
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S