Multiple Microbiome Organisms

Several CMB Faculty are interested in characterizing and understanding microbial communities in healthy, sick, and even dead plants, humans and animals.  They are part of a larger group at CSU known as the Microbiome Network.  This research area relies heavily on next – generation sequencing and bioinformatics analysis.


Zaid AbdoZaid Abdo
Associate Professor (Microbiology, Immunology, and Pathology)
Microbiome interaction and function.  Relationship between the immune system and the microbiome.  Viral evolution. Antimicrobial resistance. Computational tools

Corey Broeckling
Faculty Affiliate (College of Agriculture)

Stephen ColemanStephen Coleman
Associate Professor (Animal Sciences)
Development and dynamics of the equine microbiome

Gregg Dean 
Professor (Microbiology, Immunology, and Pathology)
Development of a probiotic vaccine platform utilizing the probiotic organism Lactobacillus acidophilus.  Relationship between the host microbiome and mucosal immunity

Karen Dobos
Professor (Microbiology, Immunology, and Pathology)
Her lab primarily uses biochemical approaches to study the physiology of microbial diseases. While she and her team are most known for their work in biomarker discovery and systems biology for Mycobacterium tuberculosis, they also actively work and collaborate to address novel questions around pathogen inactivation, vector-mycobacteria intersections, and pathogen/vector cryopreservation.

Christopher GentileChristopher Gentile
Associate Professor (Food Science & Human Nutrition)
Metabolic and vascular dysfunction in obesity and Type II diabetes

Jess MetcalfJessica Metcalf
Associate Professor (Animal Sciences)
Interactions between microbes and vertebrates during life and after death.  Dynamics of microbial community change over time.

Jessica Prenni
Associate Professor (Agricultural Sciences)
Novel methods and applications using mass spectrometry to address important issues in food and agricultural crop quality and safety.


Ken ReardonKenneth Reardon
Professor  (Chemical Engineering)
Proteomics, systems biology, metabolic engineering, and enzyme-based biosensors.

Elizabeth RyanElizabeth Ryan
Associate Professor (Environmental & Radiological Health Sciences)
Interactions between diet and cancer. Toxicology, immunology, oncology and nutrition.

Erika Szymanski
Assistant Professor (Microbiome Initiative Hire)

Investigating words as tools for making scientific knowledge, especially around how humans practice multispecies working relationships; social dimensions of emerging biotechnologies; science communication strategies for building relationships among scientists/science and others/other ways of knowing

Henry Thompson
Professor (Plant sciences)

Biochemical and molecular approaches to cancer prevention; preclinical models and clinical investigations.

Stuart TobetStuart A. Tobet
Professor (Biomedical Sciences)
Interactions of neuro, immune, and microbial components of the mammalian intestine

Pankaj Trivedi

Assistant Professor (C034 Plant Science)

Multitrophic interactions among and between microbiome and the plant environment that influence the health and productivity of managed and natural systems, especially in response to environmental change

Tiffany Weir  Tiffany Weir
Associate Professor (Food Science & Human Nutrition)
Role of microbes in ecosystems ranging from soils to processed food products to the human gut.

Kelly WrightonKelly Wrighton
Associate Professor (Soil & Crop Sciences)
Microbial communities across ecosystems ranging from 2,500 meter deep fractured shales, rivers, and soils, to human guts.

Affiliate Faculty

Jan Leach
Professor (Agricultural Biology)
Plant interactions with microbial pathogens that result in resistance or disease


Certificate Overview and Course Requirements

Microbiome related coursework can be found here.

Facilities & Resources

CMB Students

Valerie Seitz Valerie Seitz (Prenni Lab)
(PhD, 2019 Cohort, OVPR Fellow 2022-23)

Victoria Nieciecki (Metcalf Lab)
(PhD, 2020 Cohort, qCMB NIH T32 fellow 2021 – 22)

Tymofiy Lutsiv  Tymofiy Lutsiv (Thompson Lab)

(PhD, 2019 Cohort)

Kayl Ecton (Abdo / Dean Lab)
(PhD, 2019 Cohort)
Recipient NSF GRFP (2021)

Heather Deel Heather Deel (Metcalf Lab)
NIJ Fellow 2019 – 21
Vice President for Research Fellow 2019

Reed WoydaReed Woyda (Abdo Lab)
(PHD, 2019 Cohort)
qCMB NIH T32 Fellowship
USDA – ORISE Fellow 2019 – 20

Ikaia Leleiwi (Wrighton Lab)
(PhD, 2019 Cohort)
qCMB T32 Fellow 2020-21

Khalid Al-Lakhen (Metcalf Lab)
(PhD 2021 Cohort)


Nora Jean Nealon (PhD 2019, Ryan Lab) – Post-doc at the Ohio State University
Heather Deel (PhD 2022, Metcalf Lab) – Bioinformaticist USDA-APHIS, Fort Collins

1: A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. Deel H, Emmons AL, Kiely J, Damann FE, Carter DO, Lynne A, Knight R, Xu ZZ, Bucheli S, Metcalf JL.  mSphere. 2021 Aug 25;6(4):e0045521. doi: 10.1128/mSphere.00455-21 PMID: 34259562; PMCID: PMC8386422.

2: Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. Dillon MR, Bolyen E, Adamov A, Belk A, Borsom E, Burcham Z, Debelius JW, Deel H, Emmons A, Estaki M, Herman C, Keefe CR, Morton JT, Oliveira RRM, Sanchez A, Simard A, Vázquez-Baeza Y, Ziemski M, Miwa HE, Kerere TA, Coote C, Bonneau R, Knight R, Oliveira G, Gopalasingam P, Kaehler BD, Cope EK, Metcalf JL, Robeson Ii MS, Bokulich NA, Caporaso JG. PLoS Comput Biol. 2021 Jun 24;17(6):e1009056. doi: 10.1371/journal.pcbi.1009056. PMID: 34166363; PMCID: PMC8224931.

3: A pilot study characterizing gravesoil bacterial communities a decade after swine decomposition. Burcham ZM, Weitzel MA, Hodges LD, Deel HL, Metcalf JL.  Forensic Sci Int. 2021 Apr 21;323:110782. doi: 10.1016/j.forsciint.2021.110782. PMID: 33894685.

4: Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg. Oladeinde A, Abdo Z, Press MO, Cook K, Cox NA, Zwirzitz B, Woyda R, Lakin SM, Thomas JC 4th, Looft T, Cosby DE, Hinton A Jr, Guard J, Line E, Rothrock MJ, Berrang ME, Herrington K, Zock G, Plumblee Lawrence J, Cudnik D, House S, Ingram K, Lariscy L, Wagner M, Aggrey SE, Chai L, Ritz C.  mSystems. 2021 Aug 31;6(4):e0072921. doi: 10.1128/mSystems.00729-21.. PMID: 34427525; PMCID: PMC8409728.

5: Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca. Oladeinde A, Cook K, Lakin SM, Woyda R, Abdo Z, Looft T, Herrington K, Zock G, Lawrence JP, Thomas JC 4th, Beaudry MS, Glenn T. Appl Environ Microbiol. 2019 Oct 30;85(22):e01903-19. doi: 10.1128/AEM.01903-19. PMID: 31471306; PMCID: PMC6821953.

6: Effects of differing withdrawal times from ractopamine hydrochloride on residue concentrations of beef muscle, adipose tissue, rendered tallow, and large intestine. Davis HE, Geornaras I, Lindstrom V, Chaparro JM, Nair MN, Delmore RJ, Engle TE, Belk KE, Prenni JE.  PLoS One. 2020 Dec 2;15(12):e0242673. doi: 10.1371/journal.pone.0242673. PMID: 33264353; PMCID: PMC7710041.

7: Compositional Changes of the High-Fat Diet-Induced Gut Microbiota upon Consumption of Common Pulses. Lutsiv T, Weir TL, McGinley JN, Neil ES, Wei Y, Thompson HJ. Nutrients. 2021 Nov 9;13(11):3992. doi: 10.3390/nu13113992. PMID: 34836246; PMCID: PMC8625176.

8: Optimization of proteomics sample preparation for identification of host and bacterial proteins in mouse feces. Baniasad M, Kim Y, Shaffer M, Sabag-Daigle A, Leleiwi I, Daly RA, Ahmer BMM, Wrighton KC, Wysocki VH. Anal Bioanal Chem. 2022 Mar;414(7):2317-2331. doi: 10.1007/s00216-022-03885-z. PMID: 35106611.