What is metagenomics and how is metagenomic data analyzed?

Metagenomics is the study of genetic material recovered directly from environmental samples, enabling analysis of microbial communities without cultivation. Analysis approaches include: 1) Amplicon sequencing (16S/18S/ITS) - PCR-amplify marker genes, cluster into OTUs or ASVs (DADA2, QIIME2), assign taxonomy. 2) Shotgun metagenomics - sequence all DNA, provides functional information. Reads are assembled (metaSPAdes, MEGAHIT), binned into MAGs (MetaBAT, CONCOCT), and annotated. Taxonomic profiling uses MetaPhlAn, Kraken, or Kaiju. Functional profiling uses HUMAnN, MEGAN, or MG-RAST. Applications include: gut microbiome studies, environmental monitoring, antibiotic resistance surveillance, and novel enzyme discovery.