Animal Microbiome Research

Unlock Comprehensive Microbial Insights in Animal Health and Disease

Leverage Cosmos-Hub for in depth analysis of gut, skin, and environmental microbes across the diverse animal species. By leveraging advanced sequencing technologies and multi-omics analyses, Cosmos-Hub enables researchers to profile and interpret gut microbiota composition, uncover molecular pathways, and connect microbial signatures to immune responses and production traits animal species such as dairy cattle, poultry, horses, pigs, and companion animals like cats and dogs.

Why Understanding Animal Microbiomes Matters

The microbiome plays a critical role in animal health, affecting digestion, immune function, and disease resistance. Livestock microbiomes influence productivity and food safety, while marine and wild animal microbiomes provide insights into ecological health. Domesticated and model organisms serve as valuable research tools for comparative microbiome studies. Cosmos-Hub enables researchers and veterinarians to harness microbiome data for applications ranging from agricultural improvements to veterinary medicine and wildlife conservation.

Our integrative approach supports animal microbiome studies relating to health, feed efficiency, and disease resilience, powering new discoveries at the intersection of microbiota, host physiology, and agricultural productivity.

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Applications in Animal Microbiome Research

Cosmos-Hub’s powerful analytical tools provide actionable insights into animal microbiomes, supporting:

Optimization of livestock health and productivity through gut microbiome modulation.
Understanding disease susceptibility and antimicrobial resistance in farm animals.
Comparative microbiome analysis in domesticated and wild animals.
Characterization of microbiome adaptations in marine species.
Use of model organisms to study host-microbiome interactions.

Gut Content Samples
- Livestock: Cows, pigs, sheep, goats – collected from feces or direct intestinal samples to study digestion, health, and antibiotic resistance.
- Poultry: Chickens, turkeys – intestinal and cecal samples for microbial diversity and disease prevention studies.
- Rodents: Mice, rats, cotton rats – used in controlled research models to study the gut microbiome’s impact on disease and therapy.
- Companion Animals: Cats & Dogs - fecal samples to better understand their health and/or impact of novel products on the gut microbiome for pet health and wellness.
Marine Animal Microbiomes
- Fish Gut Microbiomes: Understanding microbial adaptations in freshwater vs. saltwater environments.
- Coral Reef: Associated Microbiota: Studying marine microbiomes’ role in ecosystem health.
Skin and Fur Microbiomes
- Domesticated Animals: Dogs, cats, horses – analyzing skin microbiota to study dermatological health and disease susceptibility.
- Livestock and Poultry: Examining microbial populations on feathers, fur, and skin for insights into hygiene and biosecurity.
Model Organism Microbiomes
- Rodents: Mice, rats, cotton rats – controlled microbiome studies for human disease modeling.
- Other Models: Zebrafish, insects – used to explore host-microbe interactions in controlled settings.

Cosmos-Hub Features & Tools For Animal Microbiome Analysis

Harness Cosmos-Hub’s advanced analytics platform and cloud-based infrastructure to optimize every stage of animal microbiome profiling. Designed for researchers studying diverse host species and environments, Cosmos-Hub enables comprehensive, reproducible, and high-resolution insights into microbial communities—supporting the journey from raw sequence data to biological discovery.

Utilize our Kepler™ host-agnostic pipeline and database for rapid and precise data analysis to profile bacterial, fungal, and viral communities in animal microbiomes. Interpret findings according to your hypothesis with advanced statistical tools, such as MaAsLin, for exploring microbiome correlations with health outcomes.

All results are reported in user-friendly, exportable visualizations for easy interpretation of microbiome diversity and function.

Whether you are analyzing gut, skin, respiratory, or environmental microbiomes in agricultural, veterinary, wildlife, or comparative biology contexts, Cosmos-Hub provides a unified ecosystem of tools and data management solutions tailored to animal-focused research.

Platform Tools and Applications

Tool/Feature	Role in Animal Microbiome Profiling & Analysis
Statistics Toolbox	Build virtual cohorts across host species, breeds, production systems, or experimental conditions using categorical/continuous metadata. Perform advanced comparisons and meta-analyses across animal studies seamlessly.
RITA (AI Analysis)	AI-driven research assistant that interprets complex animal microbiome datasets, highlights host-specific microbial biomarkers, guides study design, and helps prepare results for veterinary, agricultural, and ecological applications.
EMU	High-precision taxonomic profiling of long-read amplicon data, enabling microbial classification and gene annotation in diverse animal hosts (from livestock to companion animals to wildlife).
Kepler™	Taxonomic profiling of microbial community structure across better understood animal groups or geographic regions—revealing host-specific core microbiomes and environmental influences, including the canine or mouse microbiome, for example.
DADA2	State-of-the-art processing pipeline for short-read 16S rRNA amplicon data, delivering accurate amplicon sequence variants (ASVs) for diversity analyses across animal microbiome studies.
Study & Data Management	Integrated dashboard that links raw sequence data, sample metadata (e.g., diet, species, housing conditions), and results. Supports collaboration across teams, secure AWS-based storage, and project continuity in multi-institutional research.

Species versatility

From livestock health monitoring to wildlife ecology, Cosmos-Hub handles heterogeneous datasets across multiple host species.

Cloud-based pipelines

No need for specialized infrastructure—projects scale seamlessly across research groups and institutions.

Collaboration & security

Intuitive dashboards promote team-based workflows while ensuring data integrity.

Benchmarking & discovery

With Cosmos-Hub, researchers can integrate their data with public microbiome datasets to validate findings and generate new hypotheses.

Publications and Success Stories

Cosmos-Hub has been central to advancing animal microbiome research, providing researchers with the tools to explore host–microbiota interactions in diverse species. Studies have demonstrated how microbiome composition impacts physiology, performance, and adaptation in both experimental animal models and agricultural systems. Key investigations include:

Microbiome contributions to exercise adaptation and muscle physiology in laboratory mice.
Nutritional interventions and microbial modulation for animal health and productivity, including livestock species such as broiler chickens.

Highlighted publications:

Dysbiosis of the gut microbiome impairs mouse skeletal muscle adaptation to exercise. Valentino, T. R., Vechetti, I. J., Mobley, C. B., Dungan, C. M., Golden, L., Goh, J., & McCarthy, J. J. (2021). The Journal of Physiology, 600(1), 39-58. https://doi.org/10.1113/JP281788
Investigation into the supplementation of a ferric sillen core-linked polymer on the health and physiological performance of broiler chickens. Sehnal, L., Pristas, P., & Mizrahi, I. (2024). Animal Microbiome, 6(1), 45. https://pubmed.ncbi.nlm.nih.gov/39214059/
Khajanchi BK, Hasan NA, Choi SY, Han J, Zhao S, Colwell RR, Cerniglia CE, Foley SL. Comparative genomic analysis and characterization of incompatibility group FIB plasmid encoded virulence factors of Salmonella enterica isolated from food sources. BMC Genomics. 2017 Aug 2;18(1):570. doi: 10.1186/s12864-017-3954-5. PMID: 28768482; PMCID: PMC5541697.
Ishengoma, V.L.; Amachawadi, R.G.; Tokach, M.D.; Kang, Q.; Goodband, R.D.; DeRouchey, J.; Woodworth, J.; Nagaraja, T.G. The Impact of In-Water vs. In-Feed Chlortetracycline and Tiamulin Administration in Piglets on the Fecal Prevalence and Antimicrobial Resistance of Salmonella. Appl. Microbiol. 2024, 4, 297-311. https://doi.org/10.3390/applmicrobiol4010020
Chekabab, S.M.; Lawrence, J.R.; Alvarado, A.C.; Predicala, B.Z.; Korber, D.R. Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens. Antibiotics 2021, 10, 1152. https://doi.org/10.3390/antibiotics10101152
Vasco KA, Carbonell S, Sloup RE, Bowcutt B, Colwell RR, Graubics K, Erskine R, Norby B, Ruegg PL, Zhang L, Manning SD. Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle. Anim Microbiome. 2023 Nov 9;5(1):56. doi: 10.1186/s42523-023-00274-4. PMID: 37946266; PMCID: PMC10636827.
Oba PM, Sieja KM, Keating SCJ, Hristova T, Somrak AJ, Swanson KS. Oral microbiota populations of adult dogs consuming wet or dry foods. J Anim Sci. 2022 Aug 1;100(8):skac200. doi: 10.1093/jas/skac200. PMID: 35641105; PMCID: PMC9387596.
Ibekwe A, Durso L, Ducey TF, Oladeinde A, Jackson CR, Frye JG, Dungan R, Moorman T, Brooks JP, Obayiuwana A, Karathia H, Fanelli B, Hasan N. Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources. Microorganisms. 2021 May 13;9(5):1057. doi: 10.3390/microorganisms9051057. PMID: 34068339; PMCID: PMC8153348.
Connelly S, Fanelli B, Hasan NA, Colwell RR, Kaleko M. SYN-007, an Orally Administered Beta-Lactamase Enzyme, Protects the Gut Microbiome from Oral Amoxicillin/Clavulanate without Adversely Affecting Antibiotic Systemic Absorption in Dogs. Microorganisms. 2020 Jan 22;8(2):152. doi: 10.3390/microorganisms8020152. PMID: 31979034; PMCID: PMC7074739.
Fernández-Bravo A, Kilgore PB, Andersson JA, Blears E, Figueras MJ, Hasan NA, Colwell RR, Sha J, Chopra AK. T6SS and ExoA of flesh-eating Aeromonas hydrophila in peritonitis and necrotizing fasciitis during mono- and polymicrobial infections. Proc Natl Acad Sci U S A. 2019 Nov 26;116(48):24084-24092. doi: 10.1073/pnas.1914395116. Epub 2019 Nov 11. PMID: 31712444; PMCID: PMC6883842.
Connelly S, Fanelli B, Hasan NA, Colwell RR, Kaleko M. Oral Beta-Lactamase Protects the Canine Gut Microbiome from Oral Amoxicillin-Mediated Damage. Microorganisms. 2019 May 27;7(5):150. doi: 10.3390/microorganisms7050150. PMID: 31137766; PMCID: PMC6560916.
Khajanchi BK, Hasan NA, Choi SY, Han J, Zhao S, Colwell RR, Cerniglia CE, Foley SL. Comparative genomic analysis and characterization of incompatibility group FIB plasmid encoded virulence factors of Salmonella enterica isolated from food sources. BMC Genomics. 2017 Aug 2;18(1):570. doi: 10.1186/s12864-017-3954-5. PMID: 28768482; PMCID: PMC5541697.

Real-World Impact of Animal Microbiome Analysis with Cosmos-Hub

Cosmos-Hub empowers animal health, veterinary, and agricultural researchers to characterize host-associated microbial ecosystems, identify functional microbial signatures, and link microbiota composition to key outcomes such as animal performance, resilience, and wellbeing. From laboratory animal models that illuminate fundamental host–microbe mechanisms to applied livestock microbiome research driving innovation in nutrition, health management, and sustainable farming, Cosmos-Hub accelerates discovery and translation.

Unlock the potential of high-resolution animal microbiome profiling with Cosmos-Hub—advance understanding the role of microbial communities in animal health, yield and productivity.