Traditional Microbial Genomics

What is Metagenomics?

The Road to Metagenomics

Applications of Microbiome

Human Microbiome Project

Microbiome–innate-immune-system interactions are involved in multifactorial diseases

Gut microbiota enhance Parkinson's Disease

古籍糞便用藥

Metagenomic Approaches

16s-RNA Sequencing

Qiime2

EasyMAP

Whole Genome Shotgun Metagenomics

Operational Taxonomic Unit & Binning

DADA2 ( Divisive Amplicon Denoising Algorithm)

Analytic pipeline

Alpha diversity: species richness (and evenness) within a single sample [local scale] Beta diversity: change in species composition across a collection of samples [habitats]Gamma diversity: total species richness across an environmental gradient [landscap

Alpha Diversity: Observed OTU

Alpha Diversity: Faith's Phylogenetic Diversity

Alpha Diversity: Evenness

Example: Alpha Diversity

Plot: Alpha Diversity

Beta diversity

Principal Coordinate Analysis (PCoA)

Example: PCoA

Species Richness

Plot: beta diversity

Common Pitfalls in Comparing Relative Abundance

Linear discriminant analysis (LDA) Effect Size

Function Prediction: PICRUSt

Tax4Fun

Phneotypes classification

Microbial Colonization

In Vitro Functional Metagenomics

In Vivo Functional Metagenomics