micropita

micropita selects representative samples for two-stage microbial community studies by applying purposive sampling methods to 16S ribosomal RNA gene sequencing datasets to prioritize taxa and sample properties for follow-up metagenomic or other omics analyses.

Key Features:

• Purposeful sample selection: Provides purposive selection criteria including choosing samples typical of the surveyed population, targeting specific microbial clades or rare species, maximizing community diversity, representing extreme or deviant communities, and identifying communities that discriminate among environmental or host phenotypes.
• Two-stage study design support: Implements purposive sampling methods tailored for two-stage study designs to guide selection for follow-up assays.
• Evaluation and validation: Validated on simulated and experimental datasets, including 318 paired 16S amplicon and whole-community metagenomic samples from the Human Microbiome Project.
• Impact on sample representation: Supports strategies that either minimize discrepancies between selected and original surveys (representative selection) or intentionally emphasize non-representative properties such as maximal diversity.

Scientific Applications:

• Metagenomic follow-up: Selecting samples from 16S surveys for whole-community metagenomic sequencing follow-up analyses.
• Metabolomic profiling: Choosing biologically relevant samples for metabolomic analyses linked to microbial community composition.
• High-throughput microbial community studies: Informing sample selection in large-scale microbial community investigations to prioritize biologically meaningful follow-up assays.

Methodology:

Implements purposive sampling methods for two-stage study designs and was evaluated on simulated and experimental datasets, including 318 paired 16S amplicon and whole-community metagenomic samples from the Human Microbiome Project.