Shotgun Metagenomics

Plasmidsaurus Shotgun Metagenomics is performed using the newest short-read sequencing technology from Illumina. We use transposase-mediated library preparation chemistry to profile the total genomic DNA present in your sample—capturing bacteria, archaea, fungi, and viruses in a single assay—and return a comprehensive taxonomic analysis of your microbial community.

We have tested our pipeline and analysis for a range of communities. We see strong reproducibility and correlation with known mock community abundances in Figure 1:

Raw paired-end reads undergo quality control which filters low-quality bases (Phred < 15), removes short reads (< 50 bp), auto-detects and trims adapters, and trims poly-G tails. Samples must pass a minimum read count threshold (1M reads after QC) to proceed.

Next, host-derived reads are removed by aligning against reference genomes (human and mouse by default) using minimap2. Only unmapped (non-host) read pairs are carried forward for taxonomic analysis.

Taxonomic profiling is performed using Sylph, an ultrafast abundance-corrected MinHash profiler. Reads are profiled against four databases covering bacteria/archaea (GTDB r226), fungi (FungiRefSeq), protists, and eukaryotic DNA viruses. 

Every order includes an interactive taxonomic report on the results page. These tools allow you to explore your community composition via dynamic sunburst charts and bar plots within minutes of receiving your results. You also receive raw FASTQ files, QC metrics, and detailed abundance tables for downstream use. 

When your order is ready, you'll receive an email with a download link and access to your interactive results on our website. We provide an order-level summary with exportable bar and area charts showing taxonomic abundances, plus individual sample reports with more detail. You can also download the raw data for custom analyses or visualizations.

The limit of detection depends on the species composition of your community and the level of host DNA present. In our testing, we have frequently detected community members with <0.1% abundance.

We recommend selecting the Big tier when profiling samples with significant host DNA, studying low abundance species or analyzing functional pathways in diverse samples. 

We can sequence samples with any level of host DNA. However, because this untargeted approach sequences all DNA present, host DNA will occupy a portion of the sequencing depth, proportionally reducing the data available for microbial profiling.

Results for the shotgun metagenomics services are typically returned within 6-8 days.

There are numerous approaches to extracting metagenomic DNA from the source material (swabs, soil, feces, et cetera), so we do not provide specific recommendations. Any extraction method that yields high quality, high purity, high molecular weight, double-stranded gDNA that is free of nicks, gaps, breaks, and contaminants (enzymatic inhibitors, RNA, etc.) is suitable for this service. 

See sample prep for more information.