Microbiome Sequencing Techniques: 16S to Shotgun Metagenomics


From 16S to shotgun metagenomics, you can explore how microbiome sequencing works, compare methods, and choose the best approach for your research—click to dive in. Understanding microbiome sequencing techniques helps tailor study design to your goals, budget, and turnaround. Traditional microbiome sequencing techniques like 16S rRNA gene profiling target bacteria, while whole-genome shotgun sequencing analyzes all genetic material in a sample to reveal taxonomic, functional, and even strain-level information. Your choice shapes downstream analysis, data interpretation, and potential applications. 16S sequencing is a cost-effective way to survey large numbers of samples. By amplifying a short region of the 16S rRNA gene, this approach delivers quick microbial profiles with typically genus- or sometimes species-level resolution. It requires relatively modest computational resources and simpler pipelines, making it ideal for broad community surveys and initial exploratory studies. However, 16S provides limited insight into function and typically misses non-bacterial members, so it cannot directly reveal metabolic capabilities or precise strain differences. If your research focuses on broad shifts in community composition across many samples, this microbiome sequencing technique is often a smart starting point. Shotgun metagenomics offers deeper insights at a higher resolution. By sequencing all DNA in a sample, it enables species- or strain-level taxonomic assignments and direct functional profiling of genes and pathways, capturing bacteria, viruses, fungi, and archaea. This approach unlocks functional potential and metabolic interactions, which is valuable for studies linking the microbiome to health outcomes, personalized nutrition, or targeted probiotic strategies. The trade-offs include higher costs, more complex library prep, greater computational demands, and greater sensitivity to host DNA contamination. For research questions about mechanisms and functional pathways, shotgun metagenomics is frequently the preferred microbiome sequencing technique. For teams and organizations advancing gut-health programs, InnerBuddies offers a powerful platform to operationalize sequencing insights. Our white-label Gut Health Operating System is modular and feature-rich, designed to power your own microbiome testing products. Features like the Gut Microbiome Health Index (0–100)—supported by an exclusive IP deal with EAFIT University—plus actionable insights on Bacteria Abundances and Bacteria Functions help you benchmark against a healthy cohort. Target Group Analysis and personalized nutrition and probiotic/prebiotic advice translate sequencing results into practical guidance tailored to Healthy Aging, Endurance Sport, Skin & Hair Health, and more. To see these capabilities in action, explore the InnerBuddies microbiome test page: InnerBuddies microbiome test, or learn about ongoing access through our Gut Health Membership. If you’re considering a partner-led model, our B2B program can help you co-create solutions with customers: Become an InnerBuddies partner.