amplysis: an R package for microbial composition and diversity analysis using 16S rRNA amplicon data

Area of Science:

• Microbial Ecology
• Bioinformatics
• Environmental Genomics

Background:

• Analyzing 16S rRNA sequencing data presents bioinformatics challenges for many researchers.
• Existing methods often require expertise in diverse, complex tools.
• A need exists for streamlined, user-friendly microbiome data analysis.

Purpose of the Study:

• To introduce amplysis, an R package designed to simplify 16S rRNA amplicon data analysis.
• To provide an intuitive, code-light workflow for microbiome data processing and visualization.
• To lower the barrier for researchers in exploring microbiome data.

Main Methods:

• Developed amplysis as an R package integrating data import, processing, statistical analysis, and visualization.
• Implemented features for data normalization, microbial composition profiling, and diversity analysis.
• Utilized Principal Component Analysis and Principal Coordinates Analysis for ordination.
• Demonstrated utility through three case studies, including environmental samples.

Main Results:

• amplysis successfully streamlined the analysis and visualization of 16S rRNA data.
• Case studies showed efficient generation of abundance plots, diversity indices, and ordination plots.
• Analysis revealed significant microbial community shifts in response to environmental stressors (HCH degradation).
• The package ensured reproducibility and high-quality output for complex microbiome analyses.

Conclusions:

• amplysis significantly simplifies complex 16S rRNA data analysis and visualization.
• The R package enhances reproducibility and accessibility for microbiome research.
• amplysis is a valuable resource for microbial ecology and environmental genomics researchers.