Infant Microbiome
Explore Early-Life Microbiome Development with Advanced Metagenomics
Leverage Cosmos-Hub for comprehensive infant microbiome analysis to inform clinical studies, nutritional product development, and early-life interventions.
Why Infant Microbiome Research Matters
The infant microbiome critically shapes early-life health, immunity, and long-term developmental outcomes. From breastfeeding and infant formula to delivery methods and environmental exposures, understanding microbial composition and function during infancy provides essential insights for clinical interventions, nutritional formulations, and personalized pediatric care. Cosmos-Hub enables researchers to deeply explore infant microbiomes, empowering impactful research in digestive health, metabolic and immune system development, allergy prevention, and nutritional supplementation.
Applications in Infant Microbiome Research
Cosmos-Hub’s state-of-the-art microbiome profiling tools, including our CHAMP Human profiler, support comprehensive exploration of the infant gut microbiome. Key research areas include:
-
Infant formula studies
Evaluating how different nutritional formulations and supplements (e.g., human milk oligosaccharides) modulate gut microbiome composition, bringing infant microbiota closer to breastfed profiles and supporting gut maturation
-
Clinical trials
Investigating microbiota changes in response to extensively hydrolyzed formulas or amino acid-based formulas in infants with cow's milk protein allergy (CMPA), influencing both microbiome and metabolome
-
Immune and metabolic development
Understanding how microbiome modulation through human milk oligosaccharides (HMOs) reduces respiratory infections and promotes healthy gut development
-
Delivery mode studies
Comparing microbial diversity and functional


Popular Sample Types
-
Stool Samples
Stool samples provide critical insight into the gut microbiome of infants in the first 1000 days of life. Cosmos-Hub has been used for many research studies and for the purpose of developing new infant health products
-
Skin Swabs
Cosmos-Hub has been used to help identify the role of the microbiome in infant skin conditions such Atopic Dermatitis, diaper rash and rare diseases as well as part of understanding of the impact of the NICU on infant health and development.
-
Breast Milk
Understand the impact of HMO's on the infant microbiome as well track species and strains from mother to baby using CHAMP
How Cosmos-Hub Helps
Shotgun Metagenomics and CHAMP Profiling
Our shotgun metagenomics services provide high-resolution insights into the human microbiome. Using our proprietary CHAMP profiler—the most sensitive and accurate human microbiome profiler available—we offer detailed taxonomic and functional profiling to help researchers explore how microbial communities influence human health.
Functional Profiling
Our functional profiling for stool samples leverages curated gut-metabolic modules to explore microbial contributions to key processes, including:
- Short-chain fatty acid (SCFA) production for gut health.
- CAZyme analysis for fiber degradation and dietary metabolism.
- Bile acid metabolism for gut-liver interactions.
- KEGG module integration, offering a comprehensive overview of metabolic pathways affecting digestion and metabolic health.
- MetaCyc Database: A comprehensive metabolic pathway database that provides insights into microbial enzymatic functions and biochemical reactions.
- Enzyme Commission (EC) Classification: Organizes enzymes based on their catalytic activity, aiding in the identification of microbial enzymatic roles.
- Gene Ontology (GO): A framework for categorizing microbial genes based on their associated biological processes, molecular functions, and cellular components.
- Pfam Database: A collection of protein families and domains that helps characterize microbial proteins and their functional roles in metabolism and gene expression.
Publications and Success Stories
Real-World Impact of Human Microbiome Analysis with Cosmos-Hub
Cosmos-Hub has been instrumental in numerous studies exploring human microbiomes. Here are some key publications highlighting its impact:
- Shifts in Infant Skin Microbiome at 2 Months after Short-Term Emollient Use from Birth Are Associated with Reduced Prevalence of Atopic Dermatitis at 12 Months in a High-Risk Cohort. Stamatas GN, Insel R, Sørensen N, Palleja A, Moll JM, Oddos T, Chaoimh CN, O'B Hourihane J, Irvine AD. J Invest Dermatol. 2025. https://doi.org/10.1016/j.jid.2025.03.017
- Safety, efficacy, and impact on gut microbial ecology of a Bifidobacterium longum subspecies infantis LMG11588 supplementation in healthy term infants: a randomized, double-blind, controlled trial in the Philippines. Capeding MRZ, Phee LCM, Ming C, Noti M, Vidal K, Le Carrou G, Frézal A, Moll JM, Vogt JK, Myers PN, Nielsen BH, Boulangé CL, Samuel TM, Berger B, Cercamondi CI. Front Nutr. 2023. https://doi.org/10.3389/fnut.2023.1319873
- 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, Pedersen HK, Lukjancenko O, Eklund AC, Grathwohl D, Sprenger N, Berger B, Cercamondi CI; 5 HMO Study Investigator Consortium. Front Nutr. 2022. https://doi.org/10.3389/fnut.2022.920362
- Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease. Leonard MM, Karathia H, Pujolassos M, Troisi J, Valitutti F, Subramanian P, Camhi S, Kenyon V, Colucci A, Serena G, Cucchiara S, Montuori M, Malamisura B, Francavilla R, Elli L, Fanelli B, Colwell R, Hasan N, Zomorrodi AR, Fasano A; CD-GEMM Team. Microbiome. 2020. https://doi.org/10.1186/s40168-020-00906-w
- Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments. Hourigan SK, Subramanian P, Hasan NA, Ta A, Klein E, Chettout N, Huddleston K, Deopujari V, Levy S, Baveja R, Clemency NC, Baker RL, Niederhuber JE, Colwell RR. Front Microbiol. 2018. https://doi.org/10.3389/fmicb.2018.01361
Start Your Human Microbiome Research Today
Unlock the power of high-resolution microbiome analysis with Cosmos-Hub.