Improved efficiency of two-step amplicon PCR using an acoustic liquid handler.

Area of Science:

• Microbiology
• Molecular Biology
• Bioinformatics

Background:

• Next-generation sequencing (NGS) costs have decreased, but amplicon sequencing library preparation remains a bottleneck for microbiome studies.
• Acoustic liquid handlers offer miniaturization for molecular assays, including single-step PCR amplicon library preparation.
• Existing methods lack automation for two-step library preparation using acoustic liquid handling.

Purpose of the Study:

• To evaluate the efficiency of an acoustic liquid handler for automating a two-step amplicon library preparation process.
• To compare material usage, costs, and sequencing outcomes of an automated versus a manual library preparation method.
• To assess the impact of automation on bacterial community composition analysis.

Main Methods:

• Utilized an acoustic liquid handler to automate PCR, library quantification, and bead cleanup for amplicon library preparation.
• Compared an automated two-step protocol with a standard manual method for microbiome sample processing.
• Analyzed material consumption, cost-effectiveness, and sequencing data quality.

Main Results:

• Reduced PCR reaction volumes by fivefold using the automated method.
• Increased library preparation efficiency by approximately 32% compared to the manual method.
• Demonstrated no adverse effects on bacterial community composition or sequencing quality.

Conclusions:

• Automated acoustic liquid handling provides a cost-effective and efficient solution for microbiome amplicon library preparation.
• This automated approach enables higher throughput for sequencing large numbers of microbiome samples.
• The method maintains the integrity and quality of sequencing data for microbiome analysis.