Confused by taxonomy shifts, functional predictions, or conflicting results across tools?

We help researchers make sense of microbiome data from 16S rRNA and shotgun metagenomics - and integrate those insights with host biology, clinical metadata, or multi-omics measurements.

⚠️ Common Pitfalls in Microbiome Projects

• ❌ Choosing 16S or shotgun without understanding the downstream impact
• ❌ Contamination in low-biomass samples leading to false conclusions
• ❌ Taxonomic misclassification depending on database or tool
• ❌ Overpredicted pathways from functional inference tools like HUMAnN3 or PICRUSt2
• ❌ Batch effects from extraction kits or library prep methods
• ❌ Machine learning models that overfit and fail to replicate
• ❌ Lack of integration between microbiome shifts and host response

🔍 What We Help You Analyze

🧬 16S vs. Shotgun: Choosing the Right Approach
We don’t just run your data - we help you choose the right method based on your biological question. Whether you need genus-level trends, strain-level resolution, or functional context, we guide you toward the most appropriate strategy.

🧫 Decontamination, QC, and Batch Correction
Microbiome datasets are highly sensitive to contaminants, especially in lung, skin, and blood samples. We apply rigorous filtering, include proper controls, and use tools like Decontam to flag and mitigate unwanted noise.

🧬 Functional Profiling and Pathway Inference
We support metabolic pathway prediction and gene family profiling using tools like HUMAnN3 and MetaCyc - but always contextualize predictions with caution, limitations, and validation plans.

🤝 Host-Microbe Multi-Omics Integration
We specialize in integrating microbiome data with host transcriptomic, proteomic, or epigenomic profiles. Whether you’re mapping immune responses, identifying microbial triggers, or exploring metabolic networks, we support end-to-end modeling and visualization.

🧪 Predictive Modeling and Association Testing
Our team has built validated statistical models linking microbiome composition or function to clinical variables. We help you avoid overfitting, interpret results conservatively, and build reproducible models that reviewers trust.

💡 Why Clients Choose Us

- Unmatched expertise across microbial ecology, immunology, and human health
- Deep experience handling diverse sample types - from stool to oral, skin, blood, and placenta
- Judgment-driven support when it comes to contamination, functional prediction, and interpretation
- Custom pipelines for 16S, shotgun, strain-resolved profiling, and integration with host -omics
- Publication support including reviewer response and method clarification
- Backed by our team’s 150+ years of combined bioinformatics experience

📚 Want to go deeper?

Read our article → Microbiome Data Analysis: From 16S rRNA to Functional Integration with Host Biology

Explore the 10 Reasons Why Clients Choose Us →

Reason #1: 150 years of combined experience in bioinformatics
Reason #2: Deep understanding of both the biology and the computer
Reason #3: Top-level expertise possessed by our bioinformaticians
Reason #4: Wide range of bioinformatics and data modeling solutions that we cover
Reason #5: Researchers from 80 organizations can't all be wrong!
Reason #6: We are cost-effective
Reason #7: We guarantee to do it "right"!
Reason #8: We will assist you in paper reviews
Reason #9: We will assist you in grant writing
Reason #10: See how researchers have evaluated us

Find out more about our company, or check out our FAQ page!

Send us an inquiry, chat with us online (during our business hours 9–5 Mon–Fri U.S. Central Time), or reach us in other ways!