Taxonomic Profiling is a microbiome analysis service that provides the identities and relative abundances of the microorganisms present in a sample.
Taxonomic Profiling is a microbiome analysis service that identifies and quantifies the microorganisms present in a sample, enabling researchers to understand the composition and diversity of microbial communities. Depending on the scientific question, BaseClear offers both amplicon sequencing and shotgun metagenomics approaches to characterize bacteria, archaea, fungi, and other microorganisms across a wide range of sample types. The service provides insights into which organisms are present, their relative abundances, and how microbial communities differ between samples, treatments, environments, or time points.
This service is designed for biotechnology companies, food and feed organizations, personal care and consumer health companies, pharmaceutical developers, academic researchers, and environmental scientists investigating the role of microbiomes. Typical applications include clinical microbiome studies, probiotic and microbial ingredient development, skin and gut microbiome research, agricultural and environmental microbiology, product efficacy studies, and microbial monitoring programs. Taxonomic profiling is often the first step in understanding how microbial communities respond to health, product performance, environmental conditions, or biological processes.
BaseClear applies validated sequencing and bioinformatics workflows tailored to the study objectives. Amplicon sequencing targets conserved genetic markers such as the 16S rRNA gene for bacteria and archaea or ITS regions for fungi, providing a cost-effective method for profiling large sample cohorts. For higher taxonomic resolution and broader biological insights, shotgun metagenomic sequencing analyzes all DNA present in a sample, enabling species- and strain-level classification while simultaneously supporting downstream functional analyses. Sequencing is performed using high-quality Illumina platforms, supported by robust quality control, curated reference databases, and state-of-the-art bioinformatics pipelines.
Clients receive a comprehensive project report describing the methods, quality metrics, and key findings of the study. Deliverables typically include raw sequencing data, taxonomic abundance tables, alpha and beta diversity analyses, statistical comparisons between sample groups, publication-ready visualizations such as bar charts, heatmaps, ordination plots, and diversity metrics, as well as expert interpretation from BaseClear’s microbiome specialists. The result is a reliable and actionable understanding of microbial community composition that supports research, development, and data-driven decision-making.
Discuss your research objectives, sample types, and desired level of taxonomic resolution with our microbiome experts. Together, we determine whether amplicon sequencing, shotgun metagenomics, or a combination of approaches best fits your project.
Send your biological samples or extracted DNA to BaseClear together with the relevant project and metadata information. Our team verifies sample suitability and confirms the analysis plan before processing begins.
Your samples are processed using validated DNA extraction, library preparation, and Illumina sequencing workflows. Depending on the selected approach, we generate either targeted amplicon data (e.g. 16S or ITS) or untargeted shotgun metagenomic sequencing data.
BaseClear applies advanced bioinformatics pipelines to identify and quantify microorganisms present in each sample. Taxonomic profiles, diversity metrics, statistical comparisons, and visualizations are generated to reveal meaningful differences and patterns within your microbiome dataset.
You receive a comprehensive report containing relative taxonomic abundance profiles, diversity analyses, publication-ready figures, and expert interpretation. The results provide actionable insights into microbial community composition and support research, product development, and scientific decision-making.
End-to-end microbial safety assessment capabilities
Regulatory-ready data generation and interpretation
Integrated wet-lab and bioinformatics expertise
Structured support for EFSA and global submissions
Amplicon sequencing is the preferred approach when cost-effective taxonomic profiling of large sample cohorts is the primary objective. By targeting conserved marker genes such as 16S rRNA for bacteria and archaea or ITS regions for fungi, amplicon sequencing provides reliable community composition data while requiring significantly less sequencing depth than shotgun metagenomics. Shotgun metagenomics is generally recommended when higher taxonomic resolution, strain-level classification, or downstream functional analysis is required.
Taxonomic resolution depends on both the sequencing approach and the complexity of the microbial community being analyzed. Amplicon sequencing typically provides reliable classification at the genus level and, in some cases, species-level assignment depending on the target region and reference database. Shotgun metagenomics generally offers higher resolution and can often distinguish organisms at the species or strain level while also providing information on genes and functional potential.
Robust quality control and standardized bioinformatics workflows are essential for generating reproducible taxonomic profiling results. BaseClear applies validated laboratory protocols, sequencing quality controls, curated reference databases, and standardized analysis pipelines to minimize technical variation and maximize comparability between samples. Quality metrics are monitored throughout the workflow to ensure reliable taxonomic assignments and defensible biological conclusions.
Taxonomic profiling is widely used to identify differences in microbial community composition across experimental conditions, treatments, or longitudinal studies. BaseClear performs alpha diversity, beta diversity, and differential abundance analyses to evaluate how microbial communities change between groups or over time. These statistical analyses help researchers identify microbial taxa that may be associated with specific phenotypes, interventions, environmental conditions, or product effects.
A taxonomic profiling project delivers both the underlying sequencing data and the analytical outputs required for interpretation and reporting. Clients typically receive raw sequencing data, taxonomic abundance tables, alpha and beta diversity metrics, statistical comparison results, and publication-ready visualizations such as stacked bar charts, heatmaps, principal coordinate analysis (PCoA) plots, and diversity analyses. A comprehensive project report summarizes the methodology, quality metrics, and key biological findings.
SERVICES
Phenotypic assessment of antimicrobial resistance aligned with EFSA guidelines
SERVICES
Phenotypic assessment of antimicrobial and cytotoxic production
Speak with our experts to design a WGS strategy aligned with your regulatory needs. Your first consultation is free and without obligation.
