Microbiome Profiling Services

With our next-generation human microbiome profiler, CHAMP™, we offer high-resolution taxonomic and functional profiling that is unparalleled in accuracy, precision, and coverage to maximize insights from your study.

CHAMP™ employs over 400,000 metagenome-assembled genomes (MAGs), created from a collection of more than 30,000 microbiome samples from individuals across the world. These samples were sourced from 9 different human body sites including but not limited to: gut (stool and small intestine), vagina, skin and mouth. From this extensive human microbiome data collection, we have identified almost 7000 bacteria, archaea, and eukaryote species, including many newly discovered species. This is the foundation of our microbiome analysis services.

A more accurate future for microbiome research

CHAMP™ provides the most accurate and sensitive microbiome profiling data thanks to the following features:

• High sensitivity: Detects low abundant and rare species in samples.
• Superior specificity: Exclusively detects species actually present in samples.
• Abundance accuracy: Provides correct abundance estimations.
• Accurate taxonomic annotation: Microorganisms correctly annotated at species resolution.

CHAMP™ demonstrates best-in-class performance using both CAMI and NIBSC benchmarks against the best and most widely used profiling pipelines in the field.

Compared to MetaPhlAn4, CHAMP™ showed 16% greater sensitivity (recall) across different human body sites and showed an astounding 400 times lower false signal in the NIBSC mock community benchmark compared to state-of-the-art profilers (MetaPhlAn4, Centrifuge, Kraken, and Bracken). This means that when CHAMP™ detects something, you can trust it’s there.

CHAMP™ uses the latest GTDB annotation which includes more rare species and, compared to NCBI, often classifies sub-species as species in their own right.

Best-in-class microbiome profiling data

Combining the world’s most comprehensive reference catalogue for human-associated microbes with a proprietary algorithm for detection and abundance estimation of species, CHAMP™ provides you with the best microbiome data for further analysis.

For analyzing low biomass samples, searching for very rare species, profiling the microbiome of large-scale population health studies, or designing next generation probiotics or live biotherapeutics, CHAMP™ sets new standards in sensitivity and accuracy for microbiome research.

CHAMP™ also provides phage and virome profiling and advanced functional annotations. Furthermore, with the addition of our clonal-level analysis tool, it can separate very closely related strains, helping researchers understand the dynamics between probiotics/therapeutic microbes and endogenous populations of the same species.

Understanding which microorganisms are present in a microbiome is essential, but it only tells part of the story. To truly comprehend how microbial communities influence health and disease, it's crucial to explore what these microorganisms are capable of doing—their functional potential.

Functional microbiome analysis goes beyond identifying microbial species. It predicts what microorganisms are equipped to do based on the genes they possess, providing deeper insights into their contributions to various physiological states.

Our Functional Profiling Services

We offer comprehensive functional profiling using:

• Kyoto Encyclopedia of Genes and Genomes (KEGG): Mapping genes to metabolic pathways and cellular processes.

• Curated Databases:

  • Gut Metabolic Modules

  • Gut-Brain Modules

  • Bile Acid Metabolism

  • Human Milk Oligosaccharide (HMO) Metabolism

  • Antimicrobial Resistance Genes (CARD)

  • Virulence Factors

  • And More

By leveraging these resources, we help you decode the functional capabilities of microbial communities, shedding light on how they contribute to health and disease.

Functional Species Groups (FSG)

Understanding Functional Redundancy

Different microbial species can occupy the same functional niche in various hosts—a phenomenon known as functional redundancy. Through our Functional Species Group (FSG) tool, we group species that share similar functional potentials regarding metabolic pathways, enzymatic activities, or disease associations. For example, species encoding the molecular pathway for butyrate production via transferase are grouped together.

Enrichment Testing for Functional Associations

Sometimes, a group of functionally related species may be associated with a treatment or condition, even if none of the individual species show significant abundance changes on their own. Our FSG enrichment tests can identify such associations by statistically evaluating whether multiple species within the same FSG collectively have a stronger link to a treatment group.

The power of this approach lies in its ability to identify functional enrichment even when there is no significant change at the species or strain level—pinpointing critical functions or pathways relevant to specific phenotypes or treatments.

We continually expand our FSG sets based on the latest scientific developments and our clients' interests. Functional analysis and FSG enrichment serve as natural extensions of taxonomic analysis, bringing you closer to understanding the mechanisms linking the microbiome to phenotypes, diseases, and treatment responses.

Applications

By including functional microbiome analysis in your study, you can:

Identify Potential Biomarkers

• Disease Diagnosis and Progression: Discover functional biomarkers associated with specific phenotypes or disease states.

• Machine Learning Integration: Use functional profiles as input for machine learning models to enhance predictive accuracy.

Understand Microbiome Adaptation

• Environmental Responses: Explore how microbial communities adapt to environmental changes like toxin exposure, antibiotic use, or dietary shifts.

• Mechanistic Insights: Gain a deeper understanding of microbial resilience and adaptation mechanisms.

Inform Treatment Development

• Mechanistic Understanding: Increase knowledge of how microbial functions impact health conditions, guiding the development of new treatments.

• Actionable Hypotheses: Generate testable hypotheses for follow-up in vivo or in vitro studies.

• Multi-Omics Integration: Combine functional analysis with other omics data (genomics, metabolomics) for a holistic view.