Uncover the Microbial World: Shotgun & Amplicon-Based Metagenomics Analyses Tailored to Your Research
Metagenomes: From microbial diversity to metabolic potential, explore microbial diversity, taxonomy, and function.
What is Metagenomics. Definition and Why Does It Matter
Metagenomics is the study of genetic material recovered directly from environmental or biological samples, enabling the analysis of entire microbial communities without the need for culturing. By sequencing and interpreting DNA from complex mixtures, with our metagenomics services you will reveal what organisms are present, what they are doing and how they interact. This approach has transformed microbiology, with applications in environmental research, clinical diagnostics, agriculture, biotechnology, and more.
What Can You Achieve with our Metagenomics Services?
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Taxonomic Profiling
Identify bacteria, archaea, viruses, and eukaryotes with high-resolution methods (16S, whole-genome).
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Functional Prediction
Predict metabolic pathways, gene clusters, and ecosystem roles via tools like eggNOG and KEGG.
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Agricultural Metagenomics
Reveal the functional potential of microbial communities, including their metabolic pathways, nutrient cycling, and interactions with plants.
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Ecological Interactions
Explore community structure, diversity, and interspecies relationships.
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Genome Reconstructions
Recover MAGs (Metagenome-Assembled Genomes) through binning and assembly workflows.
Applications of Metagenomics
It is estaimated that only 1% of microbes can be cultured in the lab. Metagenomics analysis allows recovering genetic material of microbes and study them. Metagenomics has revolutionized our understanding of microbial life, offering valuable insights across a wide range of fields. From environmental ecosystems to food or agricultural samples, our metagenomics services allow not only to to analyze single microbial genomes, but explore entire microbial communities and open new possibilities for discovery, monitoring, and innovation.
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.
Biotechnology
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
Initial steps include adapter trimming, quality filtering, and optional host DNA removal. Tools used: FastQC, Trimmomatic, KneadData.
Amplicon-Based Microbiome Analysis
Marker-gene (16S/18S/ITS) denoising, taxonomic classification, and diversity analysis using DADA2 and QIIME2. Customizable for all major databases (SILVA, Greengenes, UNITE).
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.
Amplicon & Shotgun Sequencing Metagenomics
We offer specialized pipelines for both 16S/ITS rRNA gene sequencing and whole-genome metagenomics, depending on your goals and dataset.
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.
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 Asqued 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 accept raw .fastq or .fastq.gz files directly from sequencing centers. Our workflow includes quality control, trimming, filtering, and (if needed) host genome removal before proceeding to taxonomic or functional analysis.
Q3: Which tools and databases do you include in your metagenomics services?
Q4: Do I need to provide a reference genome or metadata?
It’s not required, but if you have sample metadata, experimental groupings, or a host reference genome, it can greatly improve interpretation and allow for more targeted analyses (e.g., differential abundance testing or host DNA filtering).
Q5: Will I receive publication-ready results?
Yes. You’ll get a full report with figures (e.g., bar plots, diversity metrics, PCA), tables (e.g., taxa abundance, KEGG pathways), etc. We can also assist with methods sections for publication if requested.