Uncover the Microbial World: Metagenomics Services for Shotgun and Amplicon Sequencing Projects
Analyze complex microbial communities from environmental, host-associated, agricultural, food, or industrial samples. From taxonomic composition to functional potential and genome recovery, we deliver interpretable, publication-ready metagenomics results.
What is Metagenomics and Why Does It Matter
Metagenomics is the study of genetic material recovered directly from environmental or biological samples, allowing researchers to analyze entire microbial communities without culturing individual organisms. By sequencing DNA from complex samples, metagenomics can reveal which organisms are present, what functions they may perform, and how microbial communities change across environments or conditions. To learn more about metagenomics you can explore the dedicated post in our blog!
What Can You Achieve with our Metagenomics Services?
- Taxonomic profiling
Identify bacteria, archaea, viruses, and microbial eukaryotes in complex communities using amplicon-based or shotgun approaches. - Functional profiling and pathway analysis
Explore metabolic potential, enzyme repertoires, resistance genes, and ecological functions using curated annotation databases. - Metagenome assembly and genome recovery
Assemble metagenomic reads and recover metagenome-assembled genomes (MAGs) through binning and quality-control workflows. - Community diversity and comparative analysis
Compare microbial communities across samples, environments, treatments, or time points using alpha/beta diversity and multivariate statistics. - Ecological and host-associated interpretation
Investigate microbial interactions, environmental adaptation, and community shifts in host-associated or environmental systems.
- Taxonomic profiling
Applications of Metagenomics
Metagenomics has expanded our ability to study microbial life beyond culturable isolates, providing insight into community composition, functional potential, and ecological dynamics across a wide range of sample types. Our metagenomics services support projects in environmental microbiology, agriculture, biotechnology, food systems, and host-associated microbiome research.
Environmental Microbiology
Understand the structure and function of microbial communities in soil, water, marine ecosystems, and extreme environments.
Agriculture & Plant Science
Assess soil health, promote sustainable practices, and optimize plant-microbe interactions to improve crop yield and resistance.
Biotechnology
Discover enzymes, gene clusters, and biosynthetic pathways with industrial or pharmaceutical potential.
Food Safety & Fermentation
Monitor microbial populations in fermented products or detect contamination in food production systems.
Evolutionary & Comparative Genomics
Explore microbial evolution, gene flow, and adaptation by comparing communities across space and time.
Enzymology
Metagenomics helps identify microbial enzymes with industrial applications, such as in biofuel production, wastewater treatment, etc.
A typical Metagenomics Services workflow
Our Metagenomics Services
We offer tailored pipelines for both amplicon-based and shotgun sequencing metagenomics projects. Whether you’re working with environmental, clinical, or experimental samples, our services are designed to provide robust, interpretable, and publication-ready results.
Quality Control and Preprocessing
Adapter trimming, quality filtering, and optional host DNA removal. Tools used: FastQC, Trimmomatic, KneadData.
Amplicon-Based Microbiome Analysis
Denoising, ASV inference, taxonomic classification, and diversity analysis using tools such as DADA2 and QIIME2.
Custom Pipelines & Reporting
Need something specific? We offer modular pipelines, data interpretation support, and publication-ready reporting tailored to your goals.
Why Choose Our Metagenomics Services?
We combine scientific expertise with robust, transparent pipelines to deliver results that are not only accurate but also ready for publication or regulatory use. Here’s what sets us apart:
End-to-End Workflow
From raw sequencing files to annotated pathways and statistical comparisons, we handle every step of the metagenomic analysis.
Shotgun and Amplicon support
We offer tailored workflows for both shotgun metagenomics and marker-gene community analysis, depending on your dataset and research goals.
Interpretable, Actionable Results
You receive clear summary reports, high-resolution figures, and annotated tables — all ready to support publication, grant applications, or regulatory submissions.
Transparent and Reproducible Pipelines
All steps are documented, version-controlled, and available on request. We prioritize reproducibility and data integrity in every analysis.
Tailored to Your Questions
We don’t run “one-size-fits-all” scripts — our pipelines are customized to your hypotheses, study design, and organismal focus.
Direct Communication & Support
From project kickoff to final report, you’re in contact with the scientists doing the analysis — not a black box service.
Deliverables – What You’ll Receive
Our metagenomics services provide a comprehensive suite of outputs, tailored to your specific research objectives. All deliverables are structured for reproducibility and downstream usability.
Assembly / MAG outputs (if included)
MAG bins, quality summaries, taxonomic assignments, and associated statistics.
Assembled & Annotated Contigs
For shotgun metagenomics, we deliver assembled contigs (FASTA), annotated with gene predictions, functional roles (e.g., KEGG, EggNog), and taxonomy.
Taxonomic & Functional Profiles
Detailed tables of taxonomic composition and gene function abundance (e.g., using MetaPhlAn or Kaiju), including relative and absolute abundance formats.
Visualizations & Figures
Publication-ready bar plots, heatmaps, pathway enrichment charts, ordination (PCA/NMDS), and clustering figures.
Summary Report (PDF)
Step-by-step documentation of your analysis pipeline, tools used, and key biological insights.
Metadata-Linked Results
Results structured and labeled according to your sample metadata (e.g., site, depth, treatment), for easy correlation and interpretation.
Frequently Asked Questions (F.A.Q.)
Q1: What types of metagenomic data do you analyze?
We analyze both amplicon-based (e.g., 16S, 18S, ITS) and shotgun metagenomic datasets. If you’re unsure about the format or best approach for your project, feel free to contact us — we can help you decide based on your research goals.
Q2: Can you process raw fastq files from sequencing facilities?
Yes. We can start from raw FASTQ files and perform preprocessing, quality control, and downstream analysis
Q3: Which tools and databases do you include in your metagenomics services?
Q4: Do I need to provide a reference genome or metadata?
A reference genome is not required for most metagenomics analyses. Metadata is strongly recommended, since it improves interpretation and supports group comparisons, diversity analysis, and ecological context.
Q5: Will I receive publication-ready results?
Yes. Deliverables typically include processed tables, figures, annotated outputs, and a structured report suitable for manuscripts, grant reporting, or collaboration.