Skin Microbiome Research

The Cosmos-Hub platform delivers advanced metagenomic insights and bioinformatics processing to reveal the true diversity of skin microbes in every sample, helping you profile both common and rare commensal skin bacteria with unmatched accuracy.

Our end-to-end platform empowers labs and researchers to identify, quantify, and understand key microbial players shaping the skin’s ecosystem. This enables confident, data-driven decisions in skin microbiome studies. Whether you are investigating health, disease, or therapeutic interventions, Cosmos-Hub is built to accelerate your breakthroughs in skin microbiome research.​

 

Why Skin Microbiome Research Matters

The human skin microbiome is a diverse ecosystem of microorganisms that resides on the surface of healthy human skin and within unique niches like hair follicles and sebaceous glands. Far from being passive passengers, these human skin commensal bacteria and other commensal microbes play a crucial role in maintaining skin health, supporting the skin barrier, and communicating with the cutaneous immune system to defend against skin disease and skin disorders.​

Recent skin microbiome studies reveal that the skin microbial communities impact skin barrier function, modulate skin inflammation, and protect against infection by pathogens such as Staphylococcus aureus and Staphylococcus epidermidis. Commensal bacteria like S. epidermidis produce antimicrobial peptides, which limits S. aureus colonization and protects against pathogenic overgrowth.

Disruptions to the balance of skin microorganisms, whether due to antibiotic treatment, environmental factors, or underlying skin diseases like atopic dermatitis and acne vulgaris, can lead to bacterial skin infections and complicate wound healing.​

Our Oral Microbiome Data Analysis Services

Harness the power of advanced oral microbiome analysis with our comprehensive bioinformatics pipelines . Analyze oral samples from buccal mucosa, saliva, dental plaque, tongue swabs, and gingival crevicular fluid directly from FASTQ files to profile the interventional changes in bacterial communities. Bioinformatics capabilities include:

 

Long-read and Short-read Amplicon sequencing (16S rRNA)

 

Shotgun Metagenomics for strain-and-species-level  analysis, facilitating identification of pathogenic microorganisms associated with oral disease

 

Long-read and short-read ITS sequencing to assess fungal diversity within oral microbial communities

 

Metabolomics integration, combining microbiome and metabolic data for a holistic view of human health and systemic health

 

Skin Microbiome Study Areas Enabled by Cosmos-Hub 

Cosmos-Hub’s advanced microbiome analytics platform unlocks in-depth exploration of microbial communities across a vast range of skin microbiome research applications. Some areas enabled by the platform include:

Atopic Dermatitis & Inflammatory Skin Diseases

  • Investigation of skin microbiota composition in healthy skin versus atopic dermatitis or other skin diseasesStrain-level S. aureus tracking with StrainQ™ to differentiate endogenous vs. intervention-derived clonesCorrelation of microbiome diversity with disease severity and lesional status
  • Functional profiling revealing metabolic shifts contributing to AD pathogenesis
  • Psoriasis & Chronic Dermatological ConditionsStudies of Staphylococcus aureus colonization and biofilm formation as they relate to chronic dermatological conditionsPhageome analysis identifying Staphylococcus-related bacteriophages in affected vs. unaffected skinFunctional gene profiling (vitamin B12 production, antimicrobial peptide synthesis)
  • Acne Vulgaris & Sebaceous DisordersMulti-omics characterization of facial skin microbiome shifts during puberty
  • Cutibacterium acnes (formerly Propionibacterium acnes) strain differentiation using Single Locus Sequence Typing (SLST)
  • Integration of bacterial, fungal, and functional metagenome data for mechanistic insights
  • Skin Barrier Function & Immune ModulationComparative analysis of skin barrier and immune system function in skin disorders and in the context of antibiotic treatment
  • Understanding complex interactions between commensal microbes and skin bacteria in connection to skin inflammation and wound healing
  • Analysis of antimicrobial peptides, their regulation, and efficacy within the human body, and their impact on skin health

Topical Therapeutic Development

  • Pre/probiotic skincare efficacy validation through multi-omics integration
  • Probiotic strain engraftment tracking and persistence monitoring with StrainQ™
  • Correlation of microbiome modulation with clinical endpoints (hydration, inflammation markers)

Sample-Agnostic Profiling

  • Profiling the skin metagenome from a wide range of sample types, including swabs from skin surface, hair follicles, and sebaceous glands, to reveal the diversity of skin microorganisms
  • Low-biomass sample optimization leveraging CHAMP's superior sensitivity at shallow sequencing depths

Gloved hand holding test tube near industrial water treatment facility

Sample Types in Skin Microbiome Research

Cosmos-Hub supports diverse sample types relevant to skin microbiome research, enabling robust investigation across:

Cosmos-Hub Features & Tools For Skin Microbiome Analysis

 

Cosmos-Hub delivers a comprehensive suite of tools and cloud-based solutions that streamline every phase of skin microbiome profiling and analysis. Each feature is designed specifically for the challenges of microbiome research, from raw data acquisition via 16S rRNA sequencing to detailed taxonomic and functional annotation of human skin microbiota. 

Platform Tools and Applications

Tool/Feature

Role in Microbiome Profiling & Analysis

CHAMP™ Human Microbiome Profiler

Sensitive, high-resolution taxonomic and functional profiling for human microbiome datasets. Benchmarking demonstrates 16% greater sensitivity and 400× lower false positives vs. competitors. Specifically optimized for low-biomass skin samples.

Statistics Toolbox

Create virtual cohorts from categorical/continuous metadata (lesional vs. non-lesional, acne vs. healthy), 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. Ask RITA about skin-specific organisms like "What is known about C. acnes phylotypes in acne pathogenesis?"

EMU

Long-read amplicon profiling pipeline for marker genes analysis (e.g.,  16S, 18S, ITS) for accurate microbial diversity assessment. Full-length 16S achieves species-level resolution critical for skin microbiome studies.

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 from skin microbiome studies. With security and team-based access at its core, Cosmos-Hub empowers researchers to focus on discovery and translational outcomes in skin health, from bioinformatic analysis to study publication.​

Cosmos-Hub leverages the world's largest curated sets of reference skin microbiome data—empowering dermatology, immunology, pharmaceutical, and academic researchers to benchmark, validate, and expand knowledge of human skin commensal bacteria, microbial communities, and their role in skin barrier function, immunity, and disease..​

 

Publications and Success Stories

Ready to Transform Your Oral Microbiome Research?

Join the forefront of oral health research with Cosmos-Hub. Our platform's unique capabilities and user-friendly design make it the ideal choice for researchers aiming to unlock new insights without needing specialized bioinformatics resources.

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

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 

 

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
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 

 

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 
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 
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

 

Start Your Human Microbiome Research Today

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