Short pyrosequencing reads suffice for accurate microbial community analysis

The results show that sequencing effort is best focused on gathering more short sequences rather than fewer longer ones, provided that the primers are chosen wisely, and that community comparison methods such as UniFrac are surprisingly robust to variation in the region sequenced

Z. Liu; C. Lozupone; M. Hamady; F. D. Bushman; R. Knight


Scholarcy highlights

  • The vast majority of life on earth is microbial, and the vast majority of these microbial species have not been cultured in the laboratory
  • We have shown that short sequence fragments from the 16S ribosomal RNA, including 100-base reads similar to those used in pyrosequencing, allow substantial resolution of biologically meaningful similarities and differences between microbial samples
  • We have demonstrated that it is possible to recapture the conclusions obtained from full-length sequences
  • Accurate use of these short sequence reads for community comparisons requires judicious choice of primers, and requires that the sequences be placed in the context of a larger phylogenetic tree based on full-length 16S rRNA sequences
  • The trade-off between obtaining more sequences and obtaining longer sequences is clear: 100-base sequences from R357 covering only 8% of the length of the near-full-length 16S rRNA sequences we used for this study provided comparable resolution to 70% jackknifes with the full-length sequences
  • Number inside each bubble indicates the cluster recovery above. UniFrac principal coordinates anaylsis clustering of the full-length sequences. UniFrac PCoA clustering of an example of good cluster recovery, F517 with 200-base reads

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