Microbiome Analysis Service

Computer with graphs on screen
  • Complete Solution for Unbiased Microbiome Profiling
  • Quick Turnaround as Little as 2 Weeks
  •  Species-Level Resolution with 16S Sequencing

Focus on discoveries. We take care of everything else.

Comprehensive & User-Friendly Report

Let Us Do the Work.

Watch a brief walkthrough of the final report or download a full example report below.

Publication-Ready Data at Your Fingertips

All of Zymo Research’s Microbiome Analysis Services include comprehensive bioinformatics and statistical analyses as well as group comparisons, presented in a user-friendly and interactive report. Let Zymo Research do the bioinformatics so that you don’t have to!

Varies Graph

Typical Analyses for Targeted Services Include:

  • Composition Bar Plots
  • Taxonomy Heatmap
  • Alpha-Diversity
  • Beta-Diversity
  • LEfSe Biomarker Discovery
  • Taxa2SV Decomposer
  • Absolute Abundance Quantification

Typical Analyses for Shotgun Services Include:

  • Functional Profiling
  • Taxa Identification to Strain Level
  • Antibiotic Resistance Gene Identification
  • Virulence Factor Identification
  • Clustering Heatmap
  • Alpha-Diversity
  • Beta-Diversity
  • LEfSe Biomarker Discovery

Cited in Major Publications

Read peer-reviewed citations to discover how scientists are using these services.

Bullman et al. used the ZymoBIOMICS Targeted Sequencing Service to show that Fusobacterium and other pathogenic microbes are frequently found in both the primary and distant metastatic sites of the most aggressive and deadliest colon cancers. The authors demonstrated the potential for antibiotics to help fight Fusobacterium-positive metastatic colon cancer in a mouse model containing patient-derived xenografts.

Akyol et al. performed 16S and 18S analysis of anaerobic digestates using the ZymoBIOMICS Targeted Sequencing Service to assess microbial diversity in lignocellulose-rich digestates. The most abundant bacterial and fungal genera were consistent across digestate samples.

The authors investigated the role of the mucosal immune system, the commensal gut microbiota, and the intestinal epithelium in the loss of intestinal homeostasis that drives inflammatory bowel disease (IBD). The ZymoBIOMICS Targeted Sequencing Service was used to determine altered microbiome diversity in mice with different types of inflammation and to demonstrate that rapamycin, the drug used to inhibit mTOR signaling in mice in vivo, did not affect the commensal gut microbiota.

Microbiomics-Grade Technologies

Any sample. Ultra-clean. Rigorous controls.

Infinity Dna

Human samples, water, soil, food testing, pathogen surveillance, and more.

Certification Of Ultra-Clean Certified

Certified low bioburden reagents limit sample contamination.

Theoretical Graph

Zymo Research’s mock microbial communities deemed “Regulatory-grade genomes” by FDA.

Unbiased Microbiome Profiling

Microbiome Standards Included in Every Project.

microbiome composition graph

All Sources of Bias Taken Into Account

Microbiome graph with unbiased and biased results
Zymo Research’s Microbiome Analysis Services use unparalleled DNA extraction protocols: the ZymoBIOMICS DNA Kits. These kits are commonly reported in literature and are certified to have unbiased microbial lysis, resulting in the most accurate microbiome profiling. Other common DNA extraction protocols and kits reported in literature have a dramatic bias toward certain microbes.

Preserve Microbiome Samples at Ambient Temperature with DNA/RNA Shield
Microbiome Fecal Sample graph
Various sample collection devices prefilled with DNA/RNA Shield are available to help streamline your collection process.
Controlling PCR Chimera during 16S Library Preparation
Microbiome Quick 16S graph
The innovative use of real-time PCR during library preparation minimizes PCR chimera formation.

Redefining Targeted Sequencing

Species-Level Resolution with 16S Sequencing.

Species level Pie Chart
species level chart

Reshape the Coverage of 16S Primers

Microbiome Reshape Chart
The phylogenetic coverage of 16S sequencing is determined by the targeted 16S primer set used. As more microbes are newly discovered, the design of 16S primer sets becomes even more critical to successful identification of all bacteria, and archaea, in the microbiome. The 16S primer sets designed and used by Zymo Research Microbiome Analysis Services significantly improve the V1-V2 and V3-V4 regions. Other regions of the 16S gene, such as V1-V3 or V4, can also be targeted.

Shotgun Metagenomic Service

Take your samples further.

Microbiome CosmosID

Shotgun Metagenomic Service

Shotgun metagenomic sequencing offers strain-level resolution, multiple-kingdom identification, and functional gene profiling.

The Zymo Research Shotgun Metagenomic Service provides the most complete and sophisticated solution for shotgun metagenomics. The bioinformatics analysis for this service features:


  • Identification with industry-leading sensitivity and precision
  • Strain-level resolution of all microbial kingdoms (bacteria, archaea, viruses, protists, fungi)
Microbiome Shotgun Service

World’s Largest Curated Database

  • 150,000+ genomes and gene sequences
  • 100s of millions of biomarkers
  • Data structure follows the phylogenetic hierarchy of genomes, enabling accurate classification, even of unknown strains, based on this virtual tree of life

  Target Organisms Sequencing Platform
Targeted Sequencing Service: 16S
(V1-V2, V1-V3, V3-V4, V4, or V6-V8)
Bacteria, Archaea Illumina MiSeq
Targeted Sequencing Service: ITS Fungi Illumina MiSeq
Targeted Sequencing Service: 18S Eukaryotes Illumina MiSeq
Shotgun Metagenomic Service Bacteria, Viruses, Fungi, Protists Illumina NovaSeq
Fill out my online form.