Microbiome data analysis services for 16S, 18S, and ITS sequencing projects.
Understand who is present in your samples, estimate diversity, compare microbial communities, and receive publication-ready figures, tables, and reports.
What is Microbiome Data Analysis and Why Does It Matter
Unlike metagenomics, microbiome data analysis focuses on microbial communities through sequencing of conserved genetic markers — most commonly the 16S rRNA gene for bacteria and archaea, the 18S rRNA gene for eukaryotes, and the ITS region for fungi.. If you want to learn more about microbiome profiling, you can read the dedicated post in our blog!
This approach enables researchers to explore:
Community composition: who’s there?
Alpha and beta diversity: how rich and varied the communities are
Taxonomic resolution: from phyla to genus or even species (depending on region and quality)
Whether your project involves environmental microbiomes, host-associated samples such as gut, skin, or soil, or built environments, amplicon-based microbiome analysis is a cost-effective and widely adopted approach for studying microbial ecology, community shifts, and health-associated dysbiosis.
What Can You Achieve with our Microbiome Data Analysis Services?
Bacterial and archaeal profiling (16S rRNA)
Accurately characterize prokaryotic communities using full‑length or variable-region 16S sequences.
Fungal community analysis (ITS)
Leverage ITS1/ITS2 sequencing to explore fungal diversity in environmental, agricultural, or host-associated samples.
Eukaryotic microbial diversity (18S)
Identify protists and other microeukaryotes with 18S‑based profiling — ideal for ecological and marine studies.
Alpha/Beta diversity metrics
Assess within- and between-sample diversity using richness, Shannon index, PCoA, and other ordination methods. Compare balance – unbalanced (i.e. health – dysbiosis) microbial communities across samples, treatments or conditions.
Taxonomic assignment and relative abundances
Assign taxonomy using curated databases (e.g., SILVA, Greengenes, UNITE) and generate intuitive abundance plots.
Data visualization and interpretation
Get publication-ready figures (e.g., barplots, heatmaps, PCA) and expert commentary tailored to your study design.
Applications of Microbiome Data Analysis
Biomedical Research
Study the human microbiome across body sites to understand disease associations, immune responses, dysbiosis, and treatment effects.
Agriculture & Soil Health
Profile microbial communities in soil to improve crop yield, monitor plant-microbe interactions, and evaluate biofertilizers.
Food Safety & Quality Control
Track microbial diversity in food products or production environments to ensure quality, safety, and regulatory compliance.
Environmental Monitoring
Assess microbial ecosystems in marine, freshwater, or terrestrial habitats to detect pollution, biodiversity changes, or ecosystem health.
Biotechnology & Industrial Microbiology
Monitor microbial populations in bioreactors and fermentation processes to optimize production and process stability.
Host-Associated Microbiomes
Profile the microbiota of animals, plants, or humans to explore host–microbe interactions in health, development, and adaptation.
A typical Microbiome data analysis workflow
Our Microbiome Data Analysis Services
We offer end-to-end microbiome data analysis services using 16S, 18S, and ITS amplicon sequencing data. Whether you’re studying environmental, host-associated, or engineered microbial communities, our pipelines ensure accurate ASV inference, taxonomic assignment, diversity analysis, and insightful visualization.
Quality Control
We perform rigorous quality filtering and trimming of raw reads using tools like fastp, Trimmomatic or Cutadapt, ensuring high-confidence results from the start.
ASV Inference & Taxonomic Assignment
Using tools such as DADA2, we infer accurate amplicon sequence variants (ASVs) and assign taxonomy using trusted databases (e.g., SILVA, Greengenes).
Diversity & Community Analysis
We assess alpha diversity and beta diversity with tools like Phyloseq, Mia, or MicrobiomeAnalyst, with visualizations including ordination plots (PCA, NMDS, PCoA).
Differential Abundance Testing
We identify taxa that differ significantly across conditions or sample groups using non-parametric statistical methods implemented in Mia or MicrobiomeAnalyst.
Integration with Sample Metadata
We integrate microbiome data with sample-specific variables (e.g., pH, health status, location) to explore correlations and generate insights through multivariate analysis.
Custom Pipelines & Reporting
Need something specific? We offer modular pipelines, data interpretation support, and publication-ready reporting tailored to your goals.
Why Choose Our Microbiome Data Analysis Services?
We combine microbial ecology expertise with proven, transparent workflows tailored to amplicon-based microbiome studies. Whether your goal is academic publication, environmental monitoring, or exploratory research, here’s what sets us apart:
Scientific Expertise
Our team brings extensive experience in microbiome ecology, high-throughput sequencing, and advanced statistical analysis.
Tailored Pipelines
Every project is unique — we customize each workflow based on your needs, environment, and research goals. We do not rely on “one-size-fits-all” pipelines. Each workflow is adapted to your samples, metadata, and research questions.
End-to-End Service
We handle the full analysis process, from raw FASTQ files to final figures and deliverables, saving you time and effort.
Insightful Visualizations
We generate publication-quality plots for taxonomic composition, diversity metrics, and multivariate comparisons.
Transparent and Reproducible Pipelines
All steps are documented and version-controlled. We prioritize reproducibility and data integrity in every analysis.
Fast Turnaround & Support
We aim for fast turnaround times and remain available to clarify results, adapt outputs, and assist with figure preparation.
Deliverables – What You’ll Receive
Every microbiome data analysis project includes a comprehensive set of deliverables designed for transparency, reproducibility, and ease of interpretation. All outputs are tailored to your research goals and preferred format.
Raw Sequencing Data (optional)
If available, we provide access to the raw FASTQ files generated from your amplicon sequencing runs (16S, 18S, ITS).
Processed Abundance & Taxonomic Tables
Cleaned and filtered ASV/OTU tables with taxonomic assignments (kingdom to genus/species level), including relative abundance metrics.
Visualizations & Figures
Publication-ready plots such as bar charts, stacked plots, heatmaps, alpha/beta diversity plots, and ordination (e.g., PCoA, NMDS).
Summary Report (PDF)
Clear and structured documentation outlining the methodology, pipeline steps, and key biological interpretations of your dataset.
- Diversity & Statistical Analyses
Results from alpha and beta diversity metrics, group comparisons, and (if applicable) differential abundance tests using tools like Phyloseq, Mia, or MicrobiomeAnalyst.
Metadata-Linked Results
All outputs are organized and linked to your experimental metadata (e.g., sample types, conditions, collection sites) for easy downstream integration.
Frequently Asked Questions (F.A.Q.)
Q1. What type of sequencing data do you accept for microbiome profiling?
We primarily work with 16S rRNA, 18S rRNA, and ITS amplicon sequencing data in FASTQ format.
Q2: What tools or platforms do you use?
We primarly use open source programs, like DADA2, Phyloseq, Mia, or MicrobiomeAnalyst for processing, analysis, and visualization. You’ll receive a transparent report with all the tools used and their software versions. Other tools of preference can be implemented too.
Q3: How long does the analysis take?
Turnaround time typically ranges from 3 to 10 business days from start confirmation, depending on data volume, complexity, and additional customizations.
Q4: Can I request custom analyses or visualizations?
Yes! Our workflows are modular and can be adapted to your project, including specific comparisons, metadata integration, and customized figure outputs.
Q5: What kind of deliverables will I receive?
You will receive a structured report, publication-ready figures, and tabular outputs such as ASV tables, taxonomy assignments and diversity metrics.