NEXTFLEX 16S V1-V3 rRNA Amplicon-seq Kits, 48 Barcodes

Streamlined 16S V1-V3 workflow, cleanup beads included, and flexible multiplexing

The kit follows a two-step PCR design: PCR I amplifies the V1–V3 region from genomic DNA, followed by a bead cleanup to remove excess primers and short fragments. PCR II adds barcoded PCR II primers for indexing, with a final cleanup step before pooling. NEXTFLEXNGS Cleanup Beads are supplied with the kit. This helps reduce variability and avoids separate consumables purchase.

The NEXTFLEX 16S V1–V3 Kit supports multiplexing of up to 384 samples, helping reduce per-sample sequencing costs. Barcodes are available in sets of 12, 48, or 96, each supplied with two reactions per index to support projects of any scale.

Confident V1–V3 taxonomic resolution with flexible input and quality-aware outputs

Paired-end 2×300 sequencing spans the full V1–V3 amplicon (~500–580 bp), with overlapping forward and reverse reads that support read merging, chimera removal, and model-based error correction. This improves your ability to distinguish between closely related taxa and helps reduce classification errors.

Accurate taxonomic calls are essential for interpreting microbiome data, whether analyzing community structure, relative abundance, or shifts across study conditions. Using amplicon sequence variants (ASVs) instead of broad operational taxonomic units (OTUs) enables higher resolution and comparability, which is valuable in longitudinal studies, method validation, and standardized pipelines.

The protocol supports 1–50 ng DNA input, so most extraction methods yield sufficient material without additional concentration steps. Cycle number guidance is included to adjust amplification for different input levels, helping maintain consistent results while minimizing over-amplification artifacts.

Unsure whether 16S or shotgun metagenomics is right for your study? Explore a brief comparison highlighting key differences and use cases.

Cosmos-Hub 16S analysis (included with "S" variants)

Product variants with an "S" in the SKU number include access to Cosmos-Hub®, an online platform for streamlined 16S analysis. This tool processes your V1–V3 FASTQ files through a standardized, version-controlled DADA2 workflow with SILVA taxonomy, producing a quality-filtered ASV table along with clear QC summaries and interactive visualizations.

Built-in comparative tools include tables, heatmaps, bar and stacked plots, alpha and beta diversity metrics, abundance distributions, differential abundance testing, and statistical comparisons between groups. Results export as tab-separated files and PDFs, with each chart available for download in PNG or SVG formats for easy integration into downstream analysis or reports. Learn more about Cosmos-Hub.

Revvity 16S rRNA analysis - schedule a live demo

Interested in seeing Cosmos-Hub® in action? Book a one-on-one 30-minute online demonstration to explore how this analysis platform works with the NEXTFLEX 16S rRNA Amplicon-Seq Kits. You'll get a guided walkthrough of the workflow, results, and visualization tools, plus a chance to ask questions tailored to your study. 

Automation-ready

Validated scripts are available for the Sciclone NGS and NGSx platforms, including the G3 NGSx iQ® system, which enables walkaway 96-well library prep with built-in thermocycling. These automation protocols help standardize results, reduce hands-on time, and support higher-throughput workflows using the same validated kit chemistry.

Choose the 16S rRNA region that fits your study

Revvity offers 16S amplicon kits for V1–V3, V3–V4, and V4 regions, allowing you to align region selection with your research goals. Use V1–V3 when your study or standard operating procedures prioritize this region for its enhanced resolution in specific clades. Choose V3–V4 when you want broader coverage across two hypervariable domains, or go with V4 for a shorter, well-established insert compatible with legacy datasets and widely adopted protocols.

Human cohort and clinical studies

L’Heureux, J. E., Corbett, A., Ballard, C., et al. (2025). Oral microbiome and nitric oxide biomarkers in older individuals with APOE4 genotype and mild cognitive impairment. PNAS Nexus. https://doi.org/10.1093/pnasnexus/pgae543

Vanhatalo, A., Curtis, K. J., Littlewood, J., et al. (2021). Network analysis of the nitrate-sensitive oral microbiome reveals interactions with cognitive and cardiovascular health. Redox Biology. https://doi.org/10.1016/j.redox.2021.101933

Cato, L. E., McKay, A. K. A., L’Heureux, J. E., et al. (2023). Low-carbohydrate, high-fat diet alters the oral microbiome without negating the nitrite response to beetroot juice. Nutrients. https://doi.org/10.3390/nu15245123

Yegorov, S., Babenko, D., Kozhakhmetov, S., et al. (2020). Psoriasis is associated with elevated gut IL-1α and intestinal microbiome alterations. Frontiers in Immunology. https://doi.org/10.3389/fimmu.2020.571319

Mechanistic and preclinical studies

Roje, B., Casemiro, S., Watson, J. F., et al. (2024). Gut microbiota carcinogen metabolism causes distal tissue tumours. Nature. https://doi.org/10.1038/s41586-024-07754-w

Quereda, J. J., Dussurget, O., Nahori, M.-A., et al. (2016). Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1523899113