Microbiome Profiling

Streamline Microbiome Profiling with Cosmos-Hub

Cosmos-Hub allows researchers to import their raw sequencing data directly into the platform and run a number of available bioinformatics pipelines for microbiome analysis.

CHAMP™ Human Microbiome Profiling

Introduction to Human Microbiome Sequencing and Profiling

Human microbiome profiling is crucial for identifying and quantifying diverse microbial communities, including bacteria, archaea, eukaryotes, and viruses, across various body sites. Advanced sequencing has made this analysis accessible, but accurate taxonomic identification is vital for linking microbes to health, especially in challenging low-biomass samples.

Species-Level Resolution

Accurately identify and quantify human-specific microbes at the species level across all human body sites based on GTDB-based taxonomy.

Low-Biomass Sample Compatibility

Achieve superior performance in challenging samples with limited microbial content or high host DNA contamination.

Human-Specific Optimization

Utilize tailored databases and algorithms designed specifically for human-associated microbiomes across diverse body sites.

Functional Profiling Integration

Go beyond taxonomy to analyze metabolic pathways via Gut-Metabolic Module and Gut-Brain Module.

Microbiome Profiling

Streamline Microbiome Profiling with Cosmos-Hub

Cosmos-Hub allows researchers to import their raw sequencing data directly into the platform and run a number of available bioinformatics pipelines for microbiome analysis.

In just a few easy steps, users can run industry-leading bioinformatics pipelines for a wide range of different data types:

Import data from their computer, from Illumina BaseSpace, directly from NCBI SRA or via Command Line Import (CLI).
Select the type of data they’d like to import: Shotgun, 16S or ITS
Select from 1 of 9 different host genomes to run automated host read depletion
Upload your study metadata
Choose your pipeline and primers

In just a few easy steps, users can run industry-leading bioinformatics pipelines for a wide range of different data types:

Import data from their computer, from Illumina BaseSpace, directly from NCBI SRA or via Command Line Import (CLI).
Select the type of data they’d like to import: Shotgun, 16S or ITS
Select from 1 of 9 different host genomes to run automated host read depletion
Upload your study metadata
Choose your pipeline and primers

Cosmos-Hub CHAMP™ Pipeline Overview

The Cosmos-Hub + Cmbio team has developed CHAMP, an advanced profiling tool for precise taxonomic profiling of prokaryotes, eukaryotes, and viruses across all human body sites. CHAMP utilizes a signature gene-based methodology with shotgun-metagenomic data with proprietary algorithms, refined across thousands of samples, to deliver exceptional accuracy and minimize false discoveries in human microbiome analysis.

Unlike general profilers, CHAMP employs a human-specific, curated database compiled from over 30,382 human microbiome samples spanning nine body sites. This database encompasses 6,567 prokaryotic, 244 eukaryotic, and 64,003 viral species. This human-centric approach ensures superior accuracy for clinical research, population health studies, and therapeutic development, where precise human microbiome characterization is crucial.

CHAMP's strength lies in its sophisticated marker gene-based profiling, combining extensive database curation with dynamic, sample-specific signal filtering. This minimizes false positives while maximizing species detection sensitivity, particularly in low-biomass samples where other profilers often fail.

This includes:

Bacteria: Extensive coverage of human-associated bacterial species with strain-level resolution, enabling detailed community structure analysis and accurate pathogen detection.
Archaea: Comprehensive profiling of methanogenic and non-methanogenic archaeal species common in human microbiomes, especially in the gut.
Functional Modules: Human-relevant functional profiling, including Gut-Brain Modules, Gut Metabolic Modules as well as KEGG Modules and KEGG Orthologs.

Databases and Outputs

The Cosmos-Hub team have curated our proprietary Human Microbiome Reference (HMR05) database containing over 6,567 prokaryotic species, 244 eukaryotic species, and 64,003 viral genomes derived from the world's largest collection of human microbiome samples. This gives users the opportunity to leverage the most comprehensive human-specific reference data available to maximize discovery and minimize false signals. The CHAMP taxonomic profiling outputs can be exported directly from the platform as well as plugged directly into the Cosmos-Hub Statistics Toolbox.

Prokaryotes: Over 400,000 high-quality metagenome-assembled genomes (MAGs) from 30,382 human samples across nine body sites, representing 6,567 bacterial and archaeal species. This database undergoes strict quality filtering for completeness and contamination.
Eukaryotes: A curated collection of 244 human-relevant eukaryotic species, including gut fungi, opportunistic pathogens, and commensal eukaryotes, manually selected for clinical relevance and based on human microbiome literature.
Viromes (Coming soon to Cosmos-Hub): A comprehensive viral database containing 64,003 viruses, including bacteriophages, with host prediction, lifestyle annotation, and integration of public viral databases with de novo discoveries.
CHAMP™ Human-Specific: The integrated HMR05 database, combining all kingdoms with human-specific curation and optimization, provides unmatched accuracy for human microbiome profiling across all body sites.

Gut-Brain Modules: Curated functional modules specifically designed to assess microbial contributions to the gut-brain axis, including neurotransmitter biosynthesis and neuroactive compound production.
Gut Metabolic Modules: Specialized metabolic pathway collections focused on human health-relevant functions, such as short-chain fatty acid production, bile acid metabolism, and dietary fiber degradation.

CARD Integration: Comprehensive Antibiotic Resistance Database integration, providing clinical relevance scoring and horizontal gene transfer assessment for detected resistance genes.
VFDB Integration: Virulence Factor Database integration, enabling pathogenicity assessment and clinical risk evaluation for detected virulence determinants.

Pipeline Performance, Benchmarking & References

CHAMP has undergone extensive benchmarking against established profiling tools including MetaPhlAn 4, Bracken 2, mOTUs 3, and Phanta using diverse sets of in silico metagenomes and DNA mock communities. CHAMP demonstrated unparalleled species recall, F1 score, and significantly reduced false positives, with false positive relative abundance (FPRA) averaging 50-fold lower than the second-best performing profiler. More information on the method and comprehensive benchmarking results can be found in our recently published Frontiers in Microbiology paper and detailed documentation.

Learn More

Direct fast upload

Simply drag and drop your fastq's or use the command line to upload your samples directly to the cloud platform in a matter of minutes.

Taxonomic and Functional Integration

Simultaneous detection of microbial communities, Gut-Metabolic Modules, and Gut-Brain Modules in a single comprehensive pipeline, all with GTDB based nomenclature of high-quality MAGs and reference genomes.

Increased Sensitivity

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 that it is there.

Human-Specific Microbiome Results

CHAMP employs over 400,000 metagenome-assembled genomes (MAGs), derived from more than 30,000 microbiome samples sourced from 9 distinct human body sites-including gut, vagina, skin, and mouth. This provides superior sensitivity and specificity for human microbiome samples relative to host-agnostic pipelines.

Time to results

Generate comprehensive taxonomic and functional results in a matter of hours once files are successfully uploaded.

Integrated with the Cosmos-Hub Statistics Toolbox

Once profiling is complete, leverage your metadata to create groups and generate statistical analyses and interactive visualizations.

Finally, the Cosmos-Hub Support team is on hand to provide personalized parameter recommendations, data interpretation guidance, and technical support across all time zones to ensure your research success.

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Applications and sample types

Decision-making on when and how to implement CHAMP human microbiome analysis is determined by the research application, sample characteristics, and the need for accurate human-specific microbiome characterization.

While CHAMP is optimized specifically for human-associated samples, it has particular advantages over general-purpose profilers in:

Clinical microbiome studies requiring accurate species identification for biomarker discovery, diagnostic development, and therapeutic monitoring with minimal false positive signals.
Population health research demanding robust profiling across diverse human populations, geographic locations, and demographic groups with standardized, reproducible results.

Therapeutic microbiome development needing precise strain-level identification for probiotic development, live biotherapeutic products, and microbiome-based interventions.
Low-biomass human samples requiring superior sensitivity for accurate profiling in challenging sample types including tissue biopsies, urine, and respiratory samples.