Microbiome Sequencing Options: A Quick Guide to Choosing the Right Method


When considering microbiome sequencing options, researchers typically weigh 16S rRNA gene sequencing, shotgun metagenomics, and targeted sequencing panels. 16S rRNA sequencing is affordable and fast, great for surveying broad bacterial composition but typically limited to genus-level resolution and lacks direct functional data. Shotgun metagenomics sequences all DNA in a sample, enabling species- and sometimes strain-level taxonomy and insights into metabolic pathways, but at higher cost and with more demanding data analysis. Targeted sequencing panels offer a middle ground, focusing on predefined genes or pathways to balance cost with actionable functional information. Your choice should align with whether your goal is taxonomic profiling, functional inference, or both, as well as your budget and project scale. Costs and accuracy vary across these microbiome sequencing options. 16S sequencing can run a few dollars to tens per sample when batching large numbers, while shotgun metagenomics can cost significantly more per sample due to sequencing depth and data processing needs. Accuracy depends on read depth, reference databases, and pipeline choices; shotgun provides richer data but requires careful QC and bioinformatics support. When planning a study, clarify the questions you want to answer (who’s there, what they’re doing, and how that relates to health or product outcomes), the required resolution, and how results will be used in clinical, consumer, or research contexts. To turn microbiome sequencing options into a practical product, InnerBuddies offers a white-label Gut Health Operating System designed to power your microbiome testing program. The platform includes a Gut Microbiome Health Index (0–100), based on an exclusive IP deal with EAFIT University in Colombia, plus Bacteria Abundances for a top 40 taxa with healthy-cohort benchmarking and Bacteria Functions categorized and labeled as positive or negative. It also provides Target Group Analysis for domains like Healthy Aging, Endurance Sport, and Skin & Hair Health, along with Personalized Nutrition advice and personalized probiotics and prebiotics recommendations that draw on diet and stool data. InnerBuddies serves both consumer gut test solutions and B2B partnerships, with all B2B options also accessible directly to consumers. Learn more about their microbiome testing solution on the product page here: InnerBuddies microbiome test product page. For teams evaluating how to implement microbiome sequencing options at scale, consider pairing data generation with a platform that translates findings into practical actions. If you’re exploring a white-label route or consumer-ready program, check InnerBuddies’ B2B opportunities or membership services: InnerBuddies B2B page and InnerBuddies Gut Health Membership.