CHAMP: Microbiome Analysis Software Features

CHAMP is a next-generation human microbiome profiling  pipeline delivering the most accurate, user-friendly taxonomic and functional analysis for a wide range of human-associated microbial studies. 

Researchers use CHAMP for comprehensive, high-accuracy profiling across all major domains that leverages an internal database generated from real world microbiome data. Outputs include bacteria, archaea, eukaryotes, and viral species, Gut-Brain/Gut-Metabolic functional modules, all optimised for understanding microbial communities in diverse human body sites and low biomass samples.

What sets CHAMP apart is its capacity to accurately detect, quantify, and functionally annotate a vast array of microbial taxa, supporting advanced human microbiome research and rare species identification in human microbiome data.

"CHAMP is a next-generation microbiome analysis software known for its exceptional sensitivity, specificity, and taxonomic breadth, optimized specifically for human-associated microbial profiling".

Download our CHAMP Whitepaper today

What does CHAMP do? What makes it different?

CHAMP integrates an expansive, proprietary reference database and advanced algorithms to enable sensitive marker gene identification and accurate taxonomic annotation of human microbiome samples.

The platform consistently delivers up to 16% higher recall for microbial species (including rare conspecific genetic diversity) and up to 400 times fewer false positives (false positive relative abundance) than alternative local tools such as MetaPhlAn4 and Bracken.

It is particularly adept at differentiating closely related species and covering primarily unknown or rarely profiled microbial communities.

CHAMP provides robust human microbiome profiling for various human body sites—including gut, vaginal, skin, and oral—unlocking multi-domain insights and facilitating microbiome research on diverse and complex communities.

Database Breadth and Scalability

CHAMP’s reference database is built from over 400,000 metagenome-assembled genomes (MAGs) derived from more than 30,000 human microbiome samples across nine key body sites. 

The database includes ~6,567 prokaryotic species clusters, 244 eukaryotic species, and 64,003 viral/bacteriophage genomes, forming one of the most comprehensive curated collections for human microbiome research. 

In total, the non-redundant gene catalog contains over 25 million genes. This scale ensures robust species- and sub-species-level profiling across all human body niches and supports comparative meta-analysis across global populations.

Taxonomic and Functional Profiling Capabilities

CHAMP by Cmbio integrates GTDB annotation references and is evaluated via CAMI and NIBSC international benchmarks. It is available through Cosmos-HUB, a secure, AWS-based platform that democratizes microbiome analysis—making advanced profiling tools available to users regardless of bioinformatics expertise. Each species is represented by signature genes for precise abundance estimation, even in low-biomass or complex samples. Functional profiling is integrated with curated databases and includes KEGG modules, Gut-Brain Modules (GBMs), and Gut Metabolic Modules (GMMs), linking species to metabolic pathways, neuroactive compound synthesis/degradation, and other key microbial functions. 

This enables a comprehensive understanding of microbial communities and their potential influence on human health.

Options for Strain, Clonal, and Viral Phage Profiling

CHAMP can also be employed forstrain- and clonal-level resolution for closely related microbial species, alongside comprehensive virome and bacteriophage profiling, including:

• Over 64,000 viral and phage genomes, enabling differentiation of virulent and temperate phages with lifestyle annotation (lytic vs. lysogenic) and host genus mapping for more than 55% of tailed phages. 
• Clonal-level analysis tracks dynamics of both probiotic and endogenous populations, while virome profiling supports robust detection in shotgun metagenomic datasets. 

This unified approach ensures that closely related strains, bacteriophages, and rare species are accurately resolved across human microbiome samples. This data can be further analyzed through our strain-tracking capabilities (StrainQ).

Benchmarking and Validation

CHAMP consistently demonstrates benchmark-leading performance in CAMI and NIBSC datasets, achieving the highest species recall and F1 scores compared to MetaPhlAn4, Bracken, mOTUs3, and Phanta. Its false positive relative abundance is up to 400× lower than competitor tools, ensuring reliable detection even at low sequencing depths and in low-biomass samples. 

CHAMP is optimized exclusively for human-associated microbiomes, and its benchmarking results are recognized across peer-reviewed publications and international research consortia.

Integration and User Experience

CHAMP is available via Cosmos-Hub: a secure, AWS-based cloud computing software for human microbiome analysis featuring no-code, user-friendly workflows for both novice and experienced researchers. The platform democratizes access to high-quality microbiome profiling tools, comparative/statistical analysis, and supports data interpretation with RITA AI Co-Pilot for rapid microbiome data interpretation.

CHAMP Technology: Technical Supported Use Cases

CHAMP supports diverse human microbiome research applications, enabling studies that push the boundaries of translational science. CHAMP is the preferred solution for:

• Population health studies
• Next-generation probiotic and biotherapeutic design
• Neurology and mental health microbiome testing
• Infectious disease studies
• Human nutrition studies

Comparison Table: CHAMP vs. Additional Microbiome Profilers

Unlock CHAMP Microbiome Analysis Tools With Cosmos-Hub

At every stage, CHAMP’s focus on sensitivity, specificity, and taxonomic breadth supports leading-edge human microbiome research, particularly in complex and low-biomass environments.

Ready to experience industry-leading microbiome analysis? Book a demo of CHAMP via Cosmos-Hub, or contact us to discuss tailored research solutions.

Interested in emerging multi-omics? Join the metabolomics waitlist for new 2025 features.

CHAMP Microbiome Research FAQs

How accurate is CHAMP compared to other tools?

CHAMP sets industry standards in species recall, F1 score, and low false positives. Benchmarks show up to 110x fewer false positives and unmatched robustness for low biomass samples.

Can CHAMP detect rare or low biomass organisms?

Yes. CHAMP’s heightened sensitivity enables reliable detection and quantification of rare and low-biomass species even at minimal sequencing depths.