As the name indicates, shotgun metagenomics is an attempt to capture fragments of eDNA dispersed at random within a microbial community, similar to the spray of a shotgun shell. The acquired DNA is expected to represent the microbial community surveyed and provides an opportunity to assemble whole microbial genomes, capture viral or pathogen interactions that may be missed by 16S/ITS studies, and collect information regarding the abundance of genes within a microbial community to determine putative metabolic activities. While the interpretation of 16S/ITS data is accessible to most, metagenomics poses a more complex challenge. Fortunately, many tutorials exist to help answer most metagenomics questions and represent the diversity of questions that can be addressed with a complex dataset.
At SeqCenter, we utilize our Illumina DNA Library Prep pipeline to perform Illumina shotgun WGS of your entire metagenomic sample. In our data analysis, we provide a basic community composition analysis and an annotated assembly of microbial genomes to help make the data more accessible to the greater scientific community. Shotgun metagenomics can be more costly than the 16S approach but can potentially offer more specific identification, functional gene information, and analytical possibilities for the user. For an example version of our shotgun metagenomics analysis methods, click here, and for an example of the analysis output, click here.