Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

Area of Science:

• Environmental science
• Microbiology
• Genomics

Background:

• Next-generation sequencing (NGS) is crucial for modern environmental DNA (eDNA) studies.
• Evaluating the performance of different NGS techniques is essential for accurate biodiversity assessments.

Purpose of the Study:

• To compare amplicon and shotgun sequencing for eDNA analysis in Brazilian river systems.
• To assess the impact of sequencing methods on biodiversity and community ecology metrics.
• To investigate the influence of environmental factors on eDNA data.

Main Methods:

• Water samples were collected from four major Brazilian river floodplain systems.
• Two NGS techniques, amplicon and shotgun sequencing, were employed.
• Environmental data (pH, temperature, nutrients) were integrated with sequencing data.

Main Results:

• Amplicon sequencing identified significantly more phyla and families than shotgun sequencing.
• Amplicon data demonstrated greater robustness in biodiversity and community ecology analyses.
• Environmental data showed divergent correlations depending on the sequencing method used.

Conclusions:

• Amplicon sequencing may be more effective for comprehensive biodiversity assessment in these environments.
• Previous biodiversity studies using shotgun data with specific algorithms may require re-evaluation.
• The choice between amplicon and shotgun sequencing depends on project-specific advantages and goals.