Primer selection impacts the evaluation of microecological patterns in environmental microbiomes.

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Primer selection is critical for accurate microbial community profiling using high-throughput sequencing.
• Existing methods may not fully account for biases introduced by primer choice.
• Understanding these biases is essential for reliable ecological interpretations.

Purpose of the Study:

• To investigate the influence of primer selection on microbial community composition and functional predictions.
• To assess the impact of primer bias on microecological pattern characterization.
• To identify factors contributing to primer bias in amplicon sequencing.

Main Methods:

• Comparative analysis of microbial community data generated with different primer sets.
• Evaluation of taxonomic and functional profiling methods.
• Assessment of bias consistency across various habitats and clustering techniques.

Main Results:

• Primer selection significantly altered taxonomic and predicted functional composition.
• Primer bias was not resolved by close-reference clustering.
• Biases in community profiling were consistent across habitats, but microecological patterns showed variability.
• Primer bias is linked to taxa specificity, regional hypervariability, and amplification efficiency.

Conclusions:

• Primer choice is a major determinant of microbial community structure and function outcomes.
• Standardized primer selection or bias correction methods are needed for robust ecological studies.
• Primer biases present a challenge for consistent microecological pattern analysis across different environments.