microbiome

microbiome analyzes microbial community profiling data, extending the phyloseq class to investigate phylogenetic relationships and abundance patterns, including bistable and temporal stability features, in human intestinal microbiota.

Key Features:

• Phyloseq extension: Extends the phyloseq class to support additional analyses of microbial community profiling and metadata integration.
• Phylogenetic Analysis: Supports deep phylogenetic analysis to explore relationships and distributions of bacterial communities.
• Bistable Abundance Distributions: Identifies bacterial groups exhibiting bistable abundance patterns, characterized by being either highly abundant or nearly absent across individuals.
• Temporal Stability Analysis: Assesses temporal stability and highlights decreased stability at intermediate bacterial abundances.

Scientific Applications:

• Health Implications: Identifies bistable bacterial groups as potential tipping elements to study critical transitions and their associations with human health.
• Host Factor Associations: Enables investigation of associations between bacterial abundance distributions and host factors such as aging and overweight, supporting potential diagnostic research.

Methodology:

Uses data from extensive cohort studies, including analysis of intestinal microbiota in a thousand Western adults. Employs robust statistical methods to discern patterns and correlations within microbial communities, with analyses reported to be independent of short-term dietary interventions.