Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• High-throughput sequencing of 16S rRNA gene amplicons is crucial for microbial community profiling.
• The 454-pyrosequencing platform is favored for its phylogenetic resolution due to longer reads.
• Pacific Biosciences (PacBio) offers longer reads and lower costs but has historically high error rates.

Discussion:

• PacBio's circular consensus sequencing (CCS) technology enables accurate, genus-level microbiome characterization.
• This study details successful 16S rRNA gene amplicon profiling using PacBio.
• Significant modifications to standard bioinformatic quality control workflows were necessary for effective analysis.

Key Insights:

• PacBio sequencing, particularly with CCS, provides a viable and affordable alternative for microbial community profiling.
• The platform's longer reads, despite initial error rate concerns, can yield valuable phylogenetic insights.
• Adaptations in bioinformatics are key to leveraging PacBio data for microbiome studies.

Outlook:

• Further optimization of bioinformatic pipelines can enhance PacBio's utility in microbial ecology.
• This approach democratizes microbiome research by reducing costs.
• Future studies can explore PacBio for deeper phylogenetic resolution in complex microbial communities.