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Core for Integrated Microbiota Research

About the Core for Integrated Microbiota Research

The human microbiota is inextricably linked to health and disease. These trillions of bacteria, viruses and fungi contribute millions of additional genes and metabolites to a host’s own genetic and biochemical repertoire. Healthy microbiota is an essential partner that benefits overall host physiology, metabolism, development and immune homeostasis. Not surprisingly, perturbation of microbiota abundance or diversity (dysbiosis) accompanies many human diseases such as obesity, inflammatory bowel disease, diabetes, cancer, neurological disorders and many others. The growing toolkit to manipulate the human microbiome presents an attractive and underexplored avenue for new therapeutic development and personalized medicine.

The goal of the Core for Integrated Microbiota Research (CIMR) is to facilitate new and innovative research that empowers investigators to remain highly competitive for extramural federal and foundation grants. To this end, the CIMR integrates facilities and expertise of three core components — gnotobiotics, metabolomics and metagenomics — to provide users a seamless, comprehensive workflow for the complete analysis of the microbiota.


The CIMR is supported by and administratively headquartered in the Department of Microbial Pathogenesis and Immunology. CIMR is a core resource of and received support from the Center for Translational and Environmental Health Research. The CIMR also received generous, multi-year seed-investments from the College of Medicine, TAMHSC Vice President for Research, and the Texas A&M College of Veterinary Medicine.

Research Impact

To help visualize the far reaching impact of microbiota across numerous fields of research, we've mined PubMed for microbiota disease terms. The following chart displays the number of papers containing microbiota disease terms in PubMed organized by topic.


About Gnobiotics

In the microbiota field, a germ-free animal is akin to a “microbiota knockout”. It is a powerful tool for dissecting the contribution of a particular microbe or a community of microbes to specific aspects of health or disease. Many microbiota studies begin with this in vivo model so that the intimate host-microbe relationship can be established and manipulated. More and more researchers in diverse fields now appreciate the impact of microbiota, creating a need for germ-free animal housing and expert care staff.

The CIMR Gnotobiotic Animal Facility offers highly specialized housing and germ-free mice for germ-free and gnotobiotic studies, as well as study design consultation and assistance with experiment implementation, data interpretation and research compliance. The Core for Integrated Microbiota Research at Texas A&M Health Science Center is one of only two core gnotobiotic facilities in Texas, and additionally provides research support, resources and intellectual community.Lorem ipsum dolor amet


The CIMR Gnotobiotic Animal Core facility is housed within a state-of-the-art vivarium at the Texas A&M Health Science Center. Currently, we have germ-free isolators for maintaining breeder colonies and for experimental use, and we are developing single cage isolators for use in short-term and multiple-association experiments.

Germ-free / Gnotobiotic Core

  • (2) CBC Flexible Film Isolators, housing 18 cages each
  • (4) CBC Flexible Film Isolators, quad units, housing 5 cages each
  • (1) Tecniplast Bioexclusion System double-sided rack, housing 60 isocages
  • Procedure room

Microbiota Microbiology Lab

Our microbiology lab accommodates the culture of both aerobic and anaerobic microbes for gnotobiotic studies, as well as facilitating on-site quality analysis of the Gnotobiotic Core facility.

  • Biosafety Level 2 status
  • Coy 2-person Anaerobic Chamber
  • Biosafety Cabinet
  • In-house Quality Control Analysis

Services and Fees

Subject to change. Please contact us for more info.

Germ-free, C57BL/6 mouse (bred in-house) $100 each
Vendor-supplied mouse list price + shipping
Per diem (standard) $5/cage
Per diem (Tecniplast isocage) TBA
Isolator use (small / large) $200/$400 ea
Injections $5/cage
Gavage $10/cage
Blood collection $10/cage
Fecal sample collection, 1x per week no charge
Fecal sample collection into Mo-Bio kit $15/sample
Necropsy/Tissue harvest (at endpoint) $75/hr
Ex vivo tissue processing $25/hr
Germ free re-derivation coming soon
Endoscopy/Image recording coming soon
Additional port manipulation $25/port
Additional consultation/training $100/hr

About Metabolomics

The microbiota contributes hundreds of thousands of additional genes to its host organism. This in turn has a tremendous impact on the number and diversity of metabolic reactions that can occur within the host. As the microbiota field moves from initial, descriptive studies to more functional and mechanistic analyses, metabolomics is emerging as an important enabling technology. Metabolomics is the identification and quantification of small molecules that can provide a snapshot of the functional state of a cell/tissue. Metabolites produced by the intestinal microbiota, for example, are important modulators of host physiology. As we probe deeper into the human microbiome, a core microbial population remains elusive, but metabolomics data are beginning to define a core function profile that may one day be diagnostic for homeostasis or dysbiosis.

The Integrated Metabolomics Analysis Core (IMAC) at Texas A&M University is a state-of-the-art facility that provides investigators in diverse fields, including microbiome research, with metabolomic workflows for the identification, characterization and quantitation of small molecules. The instrumentation panel at IMAC includes state-of-the-art LC-MS and GC-MS. Users will be able to discover and characterize metabolites with high resolution and accuracy using a Q Exactive Plus mass spectrometer. A TSQ Quantiva mass spectrometer and a TSQ 8000EVO gas chromatography mass spectrometer will also be available for quantitation of identified molecules.

The IMAC is co-directed by Dr. Arul Jayaraman from the Department of Chemical Engineering and Dr. Lawrence Dangott from the Protein Chemistry Laboratory (PCL). The IMAC was established through funding from the Texas A&M University Research Development Fund (RDF). The IMAC is housed in the PCL in the Biochemistry & Biophysics Building at Texas A&M. For more information on IMAC and to discuss projects, contact Jayaraman or Dangott.

About Metagenomics

Next-generation sequencing, metagenomics analysis and bioinformatics services are provided by the Texas A&M Institute for Genomic Science and Society (TIGSS) at Texas A&M University, directed by Dr. David Threadgill of the Department of Molecular and Cellular Medicine.

More information coming soon. Until then, visit the Texas A&M Institute for Genome Sciences and Society - TIGSS website.


  • Nod2: A Critical Regulator of Ileal Microbiota and Crohn's Disease.
    Sidiq T, Yoshihama S, Downs I, Kobayashi KS.
    Front Immunol. 2016 Sep 20;7:367. Review.
    Free PMC Article
  • Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis).
    Xie Y, Xia P, Wang H, Yu H, Giesy JP, Zhang Y, Mora MA, Zhang X.
    Sci Rep. 2016 Sep 15;6:33350. doi: 10.1038/srep33350.
    Free PMC Article
  • Interferon Tau Affects Mouse Intestinal Microbiota and Expression of IL-17.
    Ren W, Chen S, Zhang L, Liu G, Hussain T, Hao X, Yin J, Duan J, Tan B, Wu G, Bazer FW, Yin Y.
    Mediators Inflamm. 2016;2016:2839232. doi: 10.1155/2016/2839232. Epub 2016 Aug 17.
    Free PMC Article
  • Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing.
    Garcia-Mazcorro JF, Castillo-Carranza SA, Guard B, Gomez-Vazquez JP, Dowd SE, Brightsmith DJ.
    Microb Ecol. 2016 Aug 27. [Epub ahead of print]
  • Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing. Meason-Smith C, Diesel A, Patterson AP, Older CE, Johnson TJ, Mansell JM, Suchodolski JS, Rodrigues Hoffmann A. Vet Dermatol. 2016 Aug 23. doi: 10.1111/vde.12373. [Epub ahead of print]
  • Bacterial Communities: Interactions to Scale.
    Stubbendieck RM, Vargas-Bautista C, Straight PD. Front Microbiol. 2016 Aug 8;7:1234. doi: 10.3389/fmicb.2016.01234. eCollection 2016. Review. PMID:27551280 Free PMC Article
  • The skin microbiome in allergen-induced canine atopic dermatitis.
    Pierezan F, Olivry T, Paps JS, Lawhon SD, Wu J, Steiner JM, Suchodolski JS, Rodrigues Hoffmann A.
    Vet Dermatol. 2016 Aug 3.
  • The Pathogenesis of Nonalcoholic Fatty Liver Disease: Interplay between Diet, Gut Microbiota, and Genetic Background.
    Yu J, Marsh S, Hu J, Feng W, Wu C.
    Gastroenterol Res Pract. 2016;2016:2862173. Review.
  • Diagnosis and interpretation of intestinal dysbiosis in dogs and cats.
    Suchodolski JS.
    Vet J. 2016 Apr 25. pii: S1090-0233(16)30033-8. Review.
  • The effects of feeding and withholding food on the canine small intestinal microbiota.
    Kasiraj AC, Harmoinen J, Isaiah A, Westermarck E, Steiner JM, Spillmann T, Suchodolski JS.
    FEMS Microbiol Ecol. 2016 Jun;92(6). pii: fiw085.
  • The microbiota-derived metabolite indole decreases mucosal inflammation and injury in a murine model of NSAID enteropathy.
    Whitfield-Cargile CM, Cohen ND, Chapkin RS, Weeks BR, Davidson LA, Goldsby JS, Hunt CL, Steinmeyer SH, Menon R, Suchodolski JS, Jayaraman A, Alaniz RC.
    Gut Microbes. 2016 May 3;7(3):246-61.
  • Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice.
    Garcia-Mazcorro JF, Ivanov I, Mills DA, Noratto G.
    PeerJ. 2016 Feb 15;4:e1702..
  • Effect of Quorum Sensing by Staphylococcus epidermidis on the Attraction Response of Female Adult Yellow Fever Mosquitoes, Aedes aegypti aegypti (Linnaeus) (Diptera: Culicidae), to a Blood-Feeding Source.
    Zhang X, Crippen TL, Coates CJ, Wood TK, Tomberlin JK.
    PLoS One. 2015 Dec 16;10(12):e0143950.
  • What is living on your dog's skin? Characterization of the canine cutaneous mycobiota and fungal dysbiosis in canine allergic dermatitis.
    Meason-Smith C, Diesel A, Patterson AP, Older CE, Mansell JM, Suchodolski JS, Rodrigues Hoffmann A. FEMS Microbiol Ecol. 2015 Dec;91(12)
  • Selective Manipulation of the Gut Microbiota Improves Immune Status in Vertebrates.
    Montalban-Arques A, De Schryver P, Bossier P, Gorkiewicz G, Mulero V, Gatlin DM 3rd, Galindo-Villegas J. Front Immunol. 2015 Oct 9;6:512. Review
  • Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals.
    Whitfield-Cargile CM, Cohen ND, Suchodolski J, Chaffin MK, McQueen CM, Arnold CE, Dowd SE, Blodgett GP. PLoS One. 2015 Aug 25;10(8):e0136586.
  • Microbial influences on hormesis, oncogenesis, and therapy: A review of the literature
    Clanton R, Saucier D, Ford J, Akabani G.
    Environ Res. 2015 Oct;142:239-56. Review.
  • The Microbiome: The Trillions of Microorganisms That Maintain Health and Cause Disease in Humans and Companion Animals.
    Hoffmann AR, Proctor LM, Surette MG, Suchodolski JS.
    Vet Pathol. 2016 Jan;53(1):10-21. Review. ( PDF)
  • Microbiota regulates type 1 diabetes through Toll-like receptors
    Burrows MP, Volchkov P, Kobayashi KS, Chervonsky AV.
    Proc Natl Acad Sci USA. 2015 Aug 11; 112(32):9973-7 ( PDF)
  • Fecal microbiota composition of breast-fed infants is correlated with human milk oligosaccharides consumed
    Wang M, Li M, Wu S, Lebrilla CB, Chapkin RS , Ivanov I, Donovan SM.
    J Pediatr Gastroenterol Nutr. 2015 Jun;60(6):825-33. ( PDF)
  • Space Environmental Factor Impacts upon Murine Colon Microbiota and Mucosal Homeostasis.
    Ritchie LE, Taddeo SS, Weeks BR, Lima F, Bloomfield SA, Azcarate-Peril MA, Zwart SR, Smith SM, Turner ND.
    PLoS One. 2015 Jun 17;10(6):e0125792. eCollection 2015. ( PDF)
  • Microbiota metabolite regulation of host immune homeostasis: a mechanistic missing link.
    Steinmeyer S, Lee K, Jayaraman A, Alaniz RC.
    Curr Allergy Asthma Rep. 2015 May;15(5):24. Review. ( PDF)
  • Aryl Hydrocarbon Receptor Activity of Tryptophan Metabolites in Young Adult Mouse Colonocytes.
    Cheng Y, Jin UH, Allred CD, Jayaraman A, Chapkin RS, Safe S.
    Drug Metab Dispos. 2015 Oct;43(10):1536-43. ( PDF)
  • Characterization of microbial dysbiosis and metabolomic changes in dogs with acute diarrhea.
    Guard BC, Barr JW, Reddivari L, Klemashevich C, Jayaraman A, Steiner JM, Vanamala J, Suchodolski JS.
    PLoS One. 2015 May 22;10(5):e0127259. ( PDF)
  • Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis.
    Ritchie LE, Sturino JM, Carroll RJ, Rooney LW, Azcarate-Peril MA, Turner ND.
    FEMS Microbiol Ecol. 2015 Mar;91(3). ( PDF)
  • Mitigation of colitis with NovaSil clay therapy.
    Zychowski KE, Elmore SE, Rychlik KA, Ly HJ, Pierezan F, Isaiah A, Suchodolski JS, Hoffmann AR, Romoser AA, Phillips TD.
    Dig Dis Sci. 2015 Feb;60(2):382-92. ( PDF)
  • A gnotobiotic mouse model demonstrates that dietary fiber protects against colorectal tumorigenesis in a microbiota- and butyrate-dependent manner.
    Donohoe DR, Holley D, Collins LB, Montgomery SA, Whitmore AC, Hillhouse A, Curry KP, Renner SW, Greenwalt A, Ryan EP, Godfrey V, Heise MT, Threadgill DS, Han A, Swenberg JA, Threadgill DW, Bultman SJ. Cancer Discovery. Dec. 4, 2014 ( PDF)
  • Noninvasive molecular fingerprinting of host-microbiome interactions in neonates.
    Donovan SM, Wang M, Monaco MH, Martin CR , Davidson LA, Ivanov I, Chapkin RS.
    FEBS Lett. 2014 Nov 17;588(22):4112-9. Review. ( PDF)
  • Microbial bile acid metabolic clusters: the bouncers at the bar. Sorg JA.
    Cell Host Microbe. 2014 Nov 12;16(5):551-2. ( PDF)
  • Prediction and quantification of bioactive microbiota metabolites in the mouse gut.
    Sridharan GV, Choi K, Klemashevich C, Wu C, Prabakaran D, Pan LB, Steinmeyer S, Mueller C, Yousofshahi M, Alaniz RC, Lee K, Jayaraman A.
    Nat Commun. 2014 Nov 20;5:5492. ( PDF)
  • Microbiome-derived tryptophan metabolites and their aryl hydrocarbon receptor-dependent agonist and antagonist activities.
    Jin UH, Lee SO, Sridharan G, Lee K, Davidson LA, Jayaraman A, Chapkin RS, Alaniz R, Safe S.
    Mol Pharmacol. 2014 May;85(5):777-88. ( PDF)
  • Rational identification of diet-derived postbiotics for improving intestinal microbiota function
    Klemashevich C, Wu C, Howsmon D, Alaniz RC, Lee K, Jayaraman A.
    Curr Opin Biotechnol. 2014 Apr;26:85-90. Review. ( PDF)
  • PGRP-SC2 promotes gut immune homeostasis to limit commensal dysbiosis and extend lifespan.
    Guo L, Karpac J, Tran SL, Jasper H.
    Cell. 2014 Jan 16;156(1-2):109-22. ( PDF)
  • The microbiome and colorectal neoplasia: environmental modifiers of dysbiosis.
    Turner ND, Ritchie LE, Bresalier RS, Chapkin RS.
    Curr Gastroenterol Rep. 2013 Sep;15(9):346. Review. ( PDF)
  • Regulation of intestinal microbiota by the NLR protein family
    Biswas A, Kobayashi KS.
    Int Immunol. 2013 Apr;25(4):207-14. Review. ( PDF)
  • Ancient T-independence of mucosal IgX/A: gut microbiota unaffected by larval thymectomy in Xenopus laevis.
    Mashoof S, Goodroe A, Du CC, Eubanks JO, Jacobs N, Steiner JM, Tizard I, Suchodolski JS, Criscitiello MF.
    Mucosal Immunol. 2013 Mar;6(2):358-68. doi: 10.1038/mi.2012.78. ( PDF)
  • Host-microbe interactions in the neonatal intestine: role of human milk oligosaccharides.
    Donovan SM, Wang M, Li M, Friedberg I, Schwartz SL, Chapkin RS.
    Adv Nutr. 2012 May 1;3(3):450S-5S. Review. ( PDF)
  • A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response.
    Schwartz S, Friedberg I, Ivanov IV, Davidson LA, Goldsby JS, Dahl DB, Herman D, Wang M, Donovan SM, Chapkin RS.
    Genome Biol. 2012 Apr 30;13(4) ( PDF)
  • Nod2: a key regulator linking microbiota to intestinal mucosal immunity.
    Biswas A, Petnicki-Ocwieja T, Kobayashi KS.
    J Mol Med (Berl). 2012 Jan;90(1):15-24. Review. ( PDF)
  • Recent advances in the field of nutritional immunology.
    Monk JM, Hou TY, Chapkin RS.
    Expert Rev Clin Immunol. 2011 Nov;7(6):747-9. Review. ( PDF)
  • The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation.
    Bansal T, Alaniz RC, Wood TK, Jayaraman A.
    Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):228-33. ( PDF)
  • Nod2 is required for the regulation of commensal microbiota in the intestine.
    Petnicki-Ocwieja T, Hrncir T, Liu YJ, Biswas A, Hudcovic T, Tlaskalova-Hogenova H, Kobayashi KS.
    Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15813-8. ( PDF)
  • Metabolism of bile salts in mice influences spore germination in Clostridium difficile.
    Giel JL, Sorg JA, Sonenshein AL, Zhu J.
    PLoS One. 2010 Jan 15;5(1):e8740. ( PDF)
  • The gastrointestinal microbiome: a malleable, third genome of mammals.
    Carroll IM, Threadgill DW, Threadgill DS.
    Mammalian Genome. 2009 Jul:20(7):395-403 ( PDF)
  • Quantitative PCR assays for mouse enteric flora reveal strain-dependent differences in composition that are influences by the microenvironment.
    Deloris Alexander A, Orcutt RP, Henry JC, Baker J Jr, Bissahoyo AC, Threadgill DW.
    Mammalian Genome. 2006 Nov; 17(11):1093-104 ( PDF)

National Microbiome Initiative announced, $500 million pledged for microbiome studies

The White House Office of Science and Technology Policy announced on May 13, 2016, the launch of the National Microbiome Initiative (NMI) — an ambitious plan to advance the understanding of microbiomes across different ecosystems including human, animals, oceans, crops and the atmosphere. Federal agencies have pledged $121 million over the next two years. More than 100 external sources spanning universities, companies and non-profits have committed an additional $400 million in new efforts to support microbiome science. NMI will focus on supporting interdisciplinary microbiome research, developing platform technologies and expanding the microbiome workforce. Read More »

In the News

Discoveries, developments and new funding for microbiota research at Texas A&M are making the news. Find out what the buzz is about.