Gut Microbiome Research Platform

Why Gut Microbiome Research Matters

The gut microbiome is a complex "hidden organ" consisting of approximately 100 trillion microorganisms residing in the human gastrointestinal tract. This dense ecosystem regulates host physiology and immunity through the production of essential metabolites, such as short-chain fatty acids (SCFAs), bile acids, and vitamins, which are critical for energy extraction and immune homeostasis

Disruptions to this microbial balance (known as dysbiosis) are increasingly linked to a wide range of chronic conditions. Research has established strong associations between altered gut microbiota and cardiovascular diseases (CVDs), type 2 diabetes, inflammatory bowel disease (IBD), and colorectal cancer. Furthermore, through the gut-brain axis, these microbial communities influence neurophysiology, impacting mental health conditions such as anxiety, depression, and autism spectrum disorders.

Our Gut Microbiome Data Analysis Services

Cosmos-Hub accelerates gut microbiome research with scalable, cloud-based pipelines designed for both human cohorts and in vivo models, from mice to livestock. The platform empowers researchers to integrate multi-omics data, combining taxonomic profiling with metadata on host factors, diet (e.g., plant polysaccharide-rich or Mediterranean diets), and immune responses. By leveraging these tools, you can unravel the complex interactions between human microbiota, immune cells, and microbial metabolites that drive health and disease outcomes.

Gut Microbiome Study Areas Enabled by Cosmos-Hub 

Our platform supports translational research across critical domains, including:

Gut–Immune Mechanisms & Inflammation

Exploring the role of pathobionts and commensals in Inflammatory Bowel Disease (IBD) and Irritable Bowel Syndrome (IBS). Uncover how dysbiosis affects intestinal barrier integrity ("leaky gut") and triggers immune responses involving cytokines like IL-17 and TNF-α.

Therapeutics & Fecal Microbiota Transplantation (FMT)

Supporting clinical trials and translational work for recurrent Clostridium difficile infection (rCDI) and beyond. Characterize donor feces efficacy, monitor engraftment, and assess microbiome recovery in patients treated for infectious diseases or metabolic disorders.

The Gut-Brain Axis & Mental Health

By facilitating longitudinal studies connecting microbiota composition to neurodevelopment and mental health. Investigate correlations between microbial metabolites (e.g., tryptophan, GABA) and conditions such as depression and anxiety, revealing how the gut modulates brain physiology.

Metabolic Disease & Diet Interactions

Investigating how dietary interventions (e.g., fiber-rich or ketogenic diets) reshape the microbiome to impact metabolic syndrome, obesity, and type 2 diabetes. Analyze the production of key metabolites like Trimethylamine N-oxide (TMAO) and SCFAs that mediate cardiovascular risk.

Gloved hand holding test tube near industrial water treatment facility

Sample Types in Gut Microbiome Research

Our platform supports diverse sample types to ensure comprehensive profiling:

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Cosmos-Hub Features & Tools For Gut Microbiome Analysis

 

Cosmos-Hub delivers a comprehensive suite of tools and cloud-based solutions that streamline every phase of gut microbiome profiling and analysis. 

Platform Tools and Applications

Tool/Feature

Role in Microbiome Profiling & Analysis

Statistics Toolbox

Create virtual cohorts from categorical/continuous metadata, run custom analyses, and conduct meta-analysis across studies with just a few clicks.

RITA (AI Assistant)

An AI-powered co-pilot that answers complex questions about microbiome data, reveals scientific insights, and assists with study design and manuscript prep.

CHAMP Human Microbiome Profiler

Perform high-resolution taxonomic and functional profiling for human microbiome datasets, enabling accurate detection of species and functional pathways.

MaAsLin3

Run advanced differential abundance testing to identify statistically significant associations between microbial features and metadata, suitable for longitudinal and complex study designs.

EMU

Long-read amplicon profiling pipeline for marker genes analysis (e.g., 16S, 18S, ITS) for accurate microbial diversity assessment.

Cosmos-Hub Atlas

Curated global database with 30,000+ public microbiome datasets, enabling comparison, meta-analysis, and new in silico research without sample collection.

Study & Data Management

Integrated dashboard links raw data, metadata, and results; supports team collaboration, data sharing, secure AWS-based storage, and seamless project continuity.

 

The Cosmos-Hub dashboard connects all project components in one secure, cloud-enabled workspace, supporting research teams as they analyze large, complex microbiome datasets. With security and team-based access at its core, Cosmos-Hub empowers researchers to focus on discovery and translational outcomes in gut health, from bioinformatic analysis to study publication.​

 

Ready to Transform Your Gut Microbiome Research?

Book a Demo today to see Cosmos-Hub in action and propel your research forward.

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All of Your Microbiome Studies. One Easy Platform.

Microbiome Profiling

Microbiome Profiling 

 

Industry-leading bioinformatics pipelines thhat let you analyze different types of sequencing data for multiple applications.

 

 
Popular Features
Import fastq's directly via UI or CLI 
Analysis of 16S, ITS & Shotgun data
Short & long-read compatibility 

 

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Statistics Toolbox

Statistical Analysis 

 

Comparative analysis workflows that leverage your study metadata to create virtual cohorts and analyze them with the latest statistical tools and visualizations.

 
Popular Features
Interactive charts & visualizations 
Univariate statistics like LeFSe, Wlicoxon Rank-Sum & PERMANOVA
Multivariate statistics like MaAsLin2 & MaAsLin3
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Integrated Data Management

Study Management 

 

A study dashboards that provides integrated storage of raw data, profiling data, and study metadata for secure and easy access. 

 

 
Popular Features
Easy-to-navigate dashboard
Upload and edit metadata directly
Single-sample reporting & visualization 

 

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Cosmos-Hub Atlas

Cosmos-Hub Atlas

 

A curated database of over 40,000 microbiome samples, with metadata, that users can compare their samples against. 

 

 
Popular Features
Standardized profilings
Curated metadata
Results shared in 2-3 days 
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AI Co-Pilot

AI Co-Pilot 

 

Cosmos-Hub's AI Co-Pilot, RITAi, supports the interpretation of results generated in the software by allowing researchers to make queries like when using their favorite GPT.

 
Popular Features
Publication insights with complete references  
Species Wizard
Support on how to use the Hub 
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Metabolomics (Coming Soon)

Metabolomics Module (Coming Soon) 

Cosmos-Hub is going multi-omics! In 2025, users will be able to import metabolomics data from any provider and conduct their analysis.

 

 
Popular Features
Support for targeted and untargeted metabolomics 
Additional statistics and visualizations
Multi-Omics Support

 

coming soon

Start Your Human Microbiome Research Today

 Unlock the power of high-resolution microbiome analysis with Cosmos-Hub.