Microbiome Profiling

Overview:

Microbiome sequencing characterizes microbial communities from complex samples such as stool, soil, water, skin, or environmental swabs. Approaches include 16S rRNA gene sequencing for bacteria, ITS sequencing for fungi, and whole-genome shotgun metagenomics for comprehensive taxonomic and functional profiling. Illumina short-read sequencing provides high reproducibility and accuracy; Nanopore long-read sequencing enables full-length 16S or whole-genome resolution. DNA input needs vary from 1 ng (amplicon-based) to >50 ng (shotgun). Microbiome profiling supports studies of community composition, diversity metrics, antimicrobial resistance genes, metabolic pathways, host–microbiota interactions, and environmental microbiology. While 16S/ITS are cost-effective and widely used for taxonomic profiling, only shotgun metagenomics provides functional gene content and strain-level resolution.

Workflow:

DNA extraction, amplification of 16S rRNA gene (amplicon-based) or direct sequencing (shotgun metagenomics), sequencing.

Methods:

16S rRNA amplicon

full-length 16S

shotgun metagenomics