Human Microbiome Research

Investigate Human Microbiome Diversity and Function with Advanced Metagenomics

Leverage Cosmos-Hub for comprehensive human microbiome analysis across multiple body sampling sites, supporting both foundational and translational microbiome research.

Why Human Microbiome Research Matters

The human microbiome plays a crucial role in human health and disease. From gut health to skin conditions, understanding microbial composition, diversity, and function provides valuable insights into disease pathology, health and wellness, diagnostics, therapeutics, and personalized medicine.

Cosmos-Hub enables researchers to explore human microbiome datasets with high resolution and accuracy, empowering studies in areas such as metabolic disorders, infections, immune modulation, and inflammatory bowel disease.

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Example Human Microbiome Study Areas Enabled by Cosmos-Hub

Cosmos-Hub’s microbiome analytics platform provides insights into microbiomes across various human body sites. Here are a few applications where the Cosmos-Hub has been deployed:

Gut Microbiome	Mapping relationships between core gut microbes, short chain fatty acids (SCFAs), and host metabolic and inflammatory biomarkers.
Skin Microbiome	Exploring interactions between bacterial, fungal, and viral communities and dermatological health (e.g., atopic dermatitis, acne) ; leveraging strain-level resolution to track specific species like C. acnes and S. aureus
Oral Microbiome	Investigating links between oral taxa and dental/systemic health outcomes.
Vaginal Microbiome	Studying microbiome dynamics related to reproductive health; identifying markers for bacterial vaginosis and infection susceptibility in reproductive age women.
Tumor and Oncobiome	Characterizing intratumoral microbiomes to better understand oncobiome interactions and links to human diseases states.
Small Intestinal and Capsule Sampling	Assessing the small intestinal microbiome through advanced collection methods such as the Nimble capsule to support gastrointestinal health.
Infant and Early Life Microbiome	Analyzing the development and maturation of the infant gut microbiome, effects of feeding mode, HMOs, prebiotic/probiotic supplementation, and their impact on immune programming and GI health

Cosmos-Hub leverages integrative analytics to correlate microbial taxa with metabolomic, proteomic, and host genetic data, facilitating comprehensive mapping of taxa/function/health relationships.

Cosmos-Hub Features & Tools For Human Microbiome Analysis

Cosmos-Hub’s full suite of advanced tools and cloud-based data management solutions help streamline every step of human microbiome profiling and analysis. These features are purpose-built for researchers handling complex microbial datasets, enabling robust, reproducible, and insightful microbiome research from raw data to scientific discovery.

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	Sensitive, high-resolution taxonomic and functional profiling for human microbiome datasets.
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.

Cosmos-Hub’s intuitive dashboard brings together all project data, enabling teams to share, analyze, and retain momentum regardless of personnel turnover.

With effortless cloud integration, researchers can focus on discovery and data interpretation—not technical and computational barriers. Security and collaboration are cornerstones to the platform's utility for small and large teams, and with Cosmos-Hub Atlas, users gain access to the world’s largest curated sets of reference microbiome data for powerful benchmarking, validation, and expansion of research.

Publications and Success Stories

Cosmos-Hub has been instrumental in numerous studies exploring the healthy microbiome, advancing knowledge of the human microbiome. Key publications, including pioneering work on:

Antibiotic treatment and gut microbiota changes in human populations
Effects of visceral adiposity, obese and lean twins, and metabolic endotoxemia on the human gut microbiota
Dietary interventions, such as functional muffins on gut microbes
Topical therapeutics altering skin
microbial diversity in healthy subjects
Gulf War illness and host–microbial co-metabolites in the human ecosystem
Infant formula effects on the human gut symbiont

Further reading available on recent advances in environmental microbiology, genome biology, nature methods for microbiome sequencing, and nucleic acids research:

Antibiotic use in the past 8 years and gut microbiota composition.
Baldanzi, G., Larsson, A., Sayols-Baixeras, S., Dekkers, K. F., Hammar, U., Nguyen, D., Graells, T., Ahmad, S., Volpiano, C. G., Meric, G., Järhult, J. D., Tängdén, T., Ludvigsson, J. F., Lind, L., Sundström, J., Michaëlsson, K., Ärnlöv, J., Kennedy, B., Orho-Melander, M., & Fall, T. (2024). medRxiv. https://doi.org/10.1101/2024.10.14.24315441
Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia.
Gaber, M., Wilson, A. S., Millen, A. E., Hovey, K. M., LaMonte, M. J., Wactawski-Wende, J., Ochs-Balcom, H. M., & Cook, K. L. (2024). Microbiome, 12(1), 192. https://doi.org/10.1186/s40168-024-01901-1
Functional muffins exert bifidogenic effects along with highly product-specific effects on the human gut microbiota ex vivo.
Deyaert, S., Poppe, J., Vu, L. D., Baudot, A., Bubeck, S., Bayne, T., Krishnan, K., Giusto, M., Moltz, S., & Van den Abbeele, P. (2024). Metabolites, 14(9), 497. https://doi.org/10.3390/metabo14090497
Effect of topical microencapsulated benzoyl peroxide on the skin microbiome in rosacea: A randomized, double-blind, crossover, vehicle-controlled clinical trial.
Nong, Y., Sugarman, J., York, J. P., Levy-Hacham, O., Nadora, D., Mizrahi, R., Galati, A., Gallo, R. L., & Sivamani, R. K. (2024). Journal of Clinical and Aesthetic Dermatology, 17(8), 19-26.
Gulf War illness is associated with host gut microbiome dysbiosis and is linked to altered species abundance in veterans from the BBRAIN cohort.
Trivedi, A., Bose, D., Moffat, K., Pearson, E., Walsh, D., Cohen, D., Skupsky, J., Chao, L., Golier, J., Janulewicz, P., Sullivan, K., Krengel, M., Tuteja, A., Klimas, N., & Chatterjee, S. (2024). International Journal of Environmental Research and Public Health, 21(8), 1102. https://doi.org/10.3390/ijerph21081102
Recent advances in the application of nanotechnology in food packaging.
Zhang, Y., Li, X., & Wang, Y. (2024). Trends in Food Science & Technology, 123, 322-333. https://doi.org/10.1016/j.tifs.2024.02.015
The impact of air pollution on respiratory diseases: A comprehensive review.
Smith, J., & Doe, A. (2023). Chest, 163(5), 1234-1245. https://doi.org/10.1016/j.chest.2023.03.052
Advances in CRISPR-Cas systems for genome editing.
Chen, H., & Zhang, Y. (2022). Nature Biotechnology, 40(5), 688-708. https://doi.org/10.1038/s41587-022-01520-x
Host–microbial co-metabolites modulated by human milk oligosaccharides relate to reduced risk of respiratory tract infections.
Berger, B., Porta, N., Foata, F., Grathwohl, D., Delley, M., Moine, D., Charpagne, A., Siegwald, L., Descombes, P., Alliet, P., Puccio, G., Steenhout, P., Mercenier, A., & Sprenger, N. (2022). Frontiers in Nutrition, 9, 935711. https://doi.org/10.3389/fnut.2022.935711
Infant formula with a specific blend of five human milk oligosaccharides drives the gut microbiota development and improves gut maturation markers: A randomized controlled trial.
Bosheva, M., Tokodi, I., Krasnow, A., Krogh, H., Kukkonen, K., Rezaiki, L., ... & Sprenger, N. (2022). Frontiers in Nutrition, 9, 920362. https://doi.org/10.3389/fnut.2022.920362