@article{cai_shen_lu_yan_huang_gaule_muca_theriot_rattray_rattray_et al._2022, title={Bile acid distributions, sex-specificity, and prognosis in colorectal cancer}, volume={13}, ISSN={["2042-6410"]}, DOI={10.1186/s13293-022-00473-9}, number={1}, journal={BIOLOGY OF SEX DIFFERENCES}, author={Cai, Yuping and Shen, Xinyi and Lu, Lingeng and Yan, Hong and Huang, Huang and Gaule, Patricia and Muca, Engjel and Theriot, Casey M. and Rattray, Zahra and Rattray, Nicholas J. W. and et al.}, year={2022}, month={Oct} }
 @article{sheahan_theriot_cortes_dekaney_2022, title={Prolonged oral antimicrobial administration prevents doxorubicin-induced loss of active intestinal stem cells}, volume={14}, ISSN={["1949-0984"]}, DOI={10.1080/19490976.2021.2018898}, number={1}, journal={GUT MICROBES}, author={Sheahan, Breanna J. and Theriot, Casey M. and Cortes, Jocsa E. and Dekaney, Christopher M.}, year={2022}, month={Dec} }
 @article{pike_tam_melnyk_theriot_2022, title={Tauroursodeoxycholic Acid Inhibits Clostridioides difficile Toxin-Induced Apoptosis}, ISSN={["1098-5522"]}, DOI={10.1128/iai.00153-22}, journal={INFECTION AND IMMUNITY}, author={Pike, Colleen M. and Tam, John and Melnyk, Roman A. and Theriot, Casey M.}, year={2022}, month={Jul} }
 @article{reed_fletcher_huang_thanissery_rivera_parsons_stewart_kountz_shen_balskus_et al._2022, title={The Stickland Reaction Precursor trans-4-Hydroxy-l-Proline Differentially Impacts the Metabolism of Clostridioides difficile and Commensal Clostridia}, volume={7}, ISSN={["2379-5042"]}, DOI={10.1128/msphere.00926-21}, number={2}, journal={MSPHERE}, author={Reed, A. D. and Fletcher, J. R. and Huang, Y. Y. and Thanissery, R. and Rivera, A. J. and Parsons, R. J. and Stewart, A. K. and Kountz, D. J. and Shen, A. and Balskus, E. P. and et al.}, year={2022}, month={Apr} }
 @article{fletcher_pike_parsons_rivera_foley_mclaren_montgomery_theriot_2021, title={Clostridioides difficile exploits toxin-mediated inflammation to alter the host nutritional landscape and exclude competitors from the gut microbiota}, volume={12}, ISSN={["2041-1723"]}, url={https://doi.org/10.1038/s41467-020-20746-4}, DOI={10.1038/s41467-020-20746-4}, number={1}, journal={NATURE COMMUNICATIONS}, author={Fletcher, Joshua R. and Pike, Colleen M. and Parsons, Ruth J. and Rivera, Alissa J. and Foley, Matthew H. and McLaren, Michael R. and Montgomery, Stephanie A. and Theriot, Casey M.}, year={2021}, month={Jan} }
 @misc{reed_theriot_2021, title={Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium}, volume={9}, ISSN={["2076-2607"]}, DOI={10.3390/microorganisms9020371}, number={2}, journal={MICROORGANISMS}, author={Reed, Amber D. and Theriot, Casey M.}, year={2021}, month={Feb} }
 @article{foley_o'flaherty_allen_rivera_stewart_barrangou_theriot_2021, title={Lactobacillus bile salt hydrolase substrate specificity governs bacterial fitness and host colonization}, volume={118}, ISSN={["1091-6490"]}, url={https://doi.org/10.1073/pnas.2017709118}, DOI={10.1073/pnas.2017709118}, number={6}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Foley, Matthew H. and O'Flaherty, Sarah and Allen, Garrison and Rivera, Alissa J. and Stewart, Allison K. and Barrangou, Rodolphe and Theriot, Casey M.}, year={2021}, month={Feb} }
 @article{pike_theriot_2021, title={Mechanisms of Colonization Resistance Against Clostridioides difficile}, volume={223}, ISSN={["1537-6613"]}, DOI={10.1093/infdis/jiaa408}, journal={JOURNAL OF INFECTIOUS DISEASES}, author={Pike, Colleen M. and Theriot, Casey M.}, year={2021}, month={Jun}, pages={S194–S200} }
 @article{winston_rivera_cai_patterson_theriot_2021, title={Secondary bile acid ursodeoxycholic acid alters weight, the gut microbiota, and the bile acid pool in conventional mice}, volume={16}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0246161}, number={2}, journal={PLOS ONE}, author={Winston, Jenessa A. and Rivera, Alissa and Cai, Jingwei and Patterson, Andrew D. and Theriot, Casey M.}, year={2021}, month={Feb} }
 @article{thanissery_mclaren_rivera_reed_betrapally_burdette_winston_jacob_callahan_theriot_2020, title={Clostridioides difficile carriage in animals and the associated changes in the host fecal microbiota}, volume={66}, ISSN={["1095-8274"]}, DOI={10.1016/j.anaerobe.2020.102279}, journal={ANAEROBE}, author={Thanissery, R. and McLaren, M. R. and Rivera, A. and Reed, A. D. and Betrapally, N. S. and Burdette, T. and Winston, J. A. and Jacob, M. and Callahan, B. J. and Theriot, C. M.}, year={2020}, month={Dec} }
 @misc{winston_theriot_2020, title={Diversification of host bile acids by members of the gut microbiota}, volume={11}, ISSN={["1949-0984"]}, DOI={10.1080/19490976.2019.1674124}, number={2}, journal={GUT MICROBES}, author={Winston, Jenessa A. and Theriot, Casey M.}, year={2020}, month={Mar}, pages={158–171} }
 @article{tam_icho_utama_orrell_gomez-biagi_theriot_kroh_rutherford_lacy_melnyk_2020, title={Intestinal bile acids directly modulate the structure and function of C. difficile TcdB toxin}, volume={117}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1916965117}, number={12}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Tam, John and Icho, Simoun and Utama, Evelyn and Orrell, Kathleen E. and Gomez-Biagi, Rodolfo F. and Theriot, Casey M. and Kroh, Heather K. and Rutherford, Stacey A. and Lacy, D. Borden and Melnyk, Roman A.}, year={2020}, month={Mar}, pages={6792–6800} }
 @article{theriot_petri_2020, title={Role of Microbiota-Derived Bile Acids in Enteric Infections}, volume={181}, ISSN={["1097-4172"]}, DOI={10.1016/j.cell.2020.05.033}, number={7}, journal={CELL}, author={Theriot, Casey M. and Petri, William A., Jr.}, year={2020}, month={Jun}, pages={1452–1454} }
 @article{blake_thanissery_rivera_hixon_lin_theriot_janda_2020, title={Salicylanilide Analog Minimizes Relapse of Clostridioides difficile Infection in Mice}, volume={63}, ISSN={["1520-4804"]}, DOI={10.1021/acs.jmedchem.0c00123}, number={13}, journal={JOURNAL OF MEDICINAL CHEMISTRY}, author={Blake, Steven and Thanissery, Rajani and Rivera, Alissa J. and Hixon, Mark S. and Lin, Mingliang and Theriot, Casey M. and Janda, Kim D.}, year={2020}, month={Jul}, pages={6898–6908} }
 @article{winston_rivera_cai_thanissery_montgomery_patterson_theriot_2020, title={Ursodeoxycholic Acid (UDCA) Mitigates the Host Inflammatory Response during Clostridioides difficile Infection by Altering Gut Bile Acids}, volume={88}, ISSN={["1098-5522"]}, DOI={10.1128/IAI.00045-20}, number={6}, journal={INFECTION AND IMMUNITY}, author={Winston, Jenessa A. and Rivera, Alissa J. and Cai, Jingwei and Thanissery, Rajani and Montgomery, Stephanie A. and Patterson, Andrew D. and Theriot, Casey M.}, year={2020}, month={May} }
 @article{foley_o'flaherty_barrangou_theriot_2019, title={Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract}, volume={15}, ISSN={["1553-7374"]}, url={https://doi.org/10.1371/journal.ppat.1007581}, DOI={10.1371/journal.ppat.1007581}, number={3}, journal={PLOS PATHOGENS}, author={Foley, Matthew H. and O'Flaherty, Sarah and Barrangou, Rodolphe and Theriot, Casey M.}, editor={Knoll, Laura J.Editor}, year={2019}, month={Mar} }
 @article{foster_jacob_farmer_callahan_theriot_kathariou_cernicchiaro_prange_papich_2019, title={Ceftiofur formulation differentially affects the intestinal drug concentration, resistance of fecal Escherichia coli, and the microbiome of steers}, volume={14}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0223378}, number={10}, journal={PLOS ONE}, author={Foster, Derek M. and Jacob, Megan E. and Farmer, Kyle A. and Callahan, Benjamin J. and Theriot, Casey M. and Kathariou, Sophia and Cernicchiaro, Natalia and Prange, Timo and Papich, Mark G.}, year={2019}, month={Oct} }
 @article{theriot_fletcher_2019, title={Human fecal metabolomic profiling could inform Clostridioides difficile infection diagnosis and treatment}, volume={129}, ISSN={["1558-8238"]}, DOI={10.1172/JCI130008}, number={9}, journal={JOURNAL OF CLINICAL INVESTIGATION}, author={Theriot, Casey M. and Fletcher, Joshua R.}, year={2019}, month={Sep}, pages={3539–3541} }
 @article{thanissery_zeng_doyle_theriot_2018, title={A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile}, volume={9}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2018.01206}, journal={FRONTIERS IN MICROBIOLOGY}, author={Thanissery, Rajani and Zeng, Daina and Doyle, Raul G. and Theriot, Casey M.}, year={2018}, month={Jun} }
 @article{theriot_2018, title={Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics}, volume={3}, ISSN={["2379-5077"]}, DOI={10.1128/msystems.00173-17}, number={2}, journal={MSYSTEMS}, author={Theriot, Casey M.}, year={2018} }
 @article{ferguson_jacob_theriot_callahan_prange_papich_foster_2018, title={Dosing Regimen of Enrofloxacin Impacts Intestinal Pharmacokinetics and the Fecal Microbiota in Steers}, volume={9}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2018.02190}, DOI={10.3389/fmicb.2018.02190}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Ferguson, Kaitlyn M. and Jacob, Megan E. and Theriot, Casey M. and Callahan, Benjamin J. and Prange, Timo and Papich, Mark G. and Foster, Derek M.}, year={2018}, month={Sep} }
 @article{ma_han_heinrich_fu_zhang_sandhu_agdashian_terabe_berzofsky_fako_et al._2018, title={MICROBIOME Gut microbiome-mediated bile acid metabolism regulates liver cancer via NKT cells}, volume={360}, number={6391}, journal={Science}, author={Ma, C. and Han, M. J. and Heinrich, B. and Fu, Q. and Zhang, Q. F. and Sandhu, M. and Agdashian, D. and Terabe, M. and Berzofsky, J. A. and Fako, V. and et al.}, year={2018}, pages={876-} }
 @article{seekatz_theriot_rao_chang_freeman_kao_young_2018, title={Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection}, volume={53}, ISSN={["1095-8274"]}, DOI={10.1016/j.anaerobe.2018.04.001}, journal={ANAEROBE}, author={Seekatz, Anna M. and Theriot, Casey M. and Rao, Krishna and Chang, Yu-Ming and Freeman, Alison E. and Kao, John Y. and Young, Vincent B.}, year={2018}, month={Oct}, pages={64–73} }
 @article{fletcher_erwin_lanzas_theriot_2018, title={Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model}, volume={3}, ISSN={["2379-5042"]}, url={http://europepmc.org/articles/PMC5874438}, DOI={10.1128/msphere.00089-18}, number={2}, journal={MSPHERE}, author={Fletcher, Joshua R. and Erwin, Samantha and Lanzas, Cristina and Theriot, Casey M.}, year={2018} }
 @article{o'flaherty_crawley_theriot_barrangou_2018, title={The Lactobacillus Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation}, volume={3}, ISSN={["2379-5042"]}, url={https://doi.org/10.1128/mSphere.00140-18}, DOI={10.1128/msphere.00140-18}, number={3}, journal={MSPHERE}, publisher={American Society for Microbiology}, author={O'Flaherty, Sarah and Crawley, Alexandra Briner and Theriot, Casey M. and Barrangou, Rodolphe}, editor={Ellermeier, Craig D.Editor}, year={2018} }
 @article{thanissery_winston_theriot_2017, title={Inhibition of spore germination, growth, and toxin activity of clinically relevant C-difficile strains by gut microbiota derived secondary bile acids}, volume={45}, ISSN={["1095-8274"]}, DOI={10.1016/j.anaerobe.2017.03.004}, journal={ANAEROBE}, author={Thanissery, Rajani and Winston, Jenessa A. and Theriot, Casey M.}, year={2017}, month={Jun}, pages={86–100} }
 @article{cox_theriot_fichorova_2017, title={Introduction to the special issue highlighting Anaerobe 2016}, volume={45}, ISSN={["1095-8274"]}, DOI={10.1016/j.anaerobe.2017.05.002}, journal={ANAEROBE}, author={Cox, Laura M. and Theriot, Casey M. and Fichorova, Raina N.}, year={2017}, month={Jun}, pages={1–2} }
 @inbook{fleming-davies_jabbari_robertson_asih_lanzas_lenhart_theriot_2017, title={Mathematical Modeling of the Effects of Nutrient Competition and Bile Acid Metabolism by the Gut Microbiota on Colonization Resistance Against Clostridium difficile}, ISBN={9783319603025 9783319603049}, ISSN={2364-5733 2364-5741}, url={http://dx.doi.org/10.1007/978-3-319-60304-9_8}, DOI={10.1007/978-3-319-60304-9_8}, booktitle={Association for Women in Mathematics Series}, publisher={Springer International Publishing}, author={Fleming-Davies, Arietta and Jabbari, Sara and Robertson, Suzanne L. and Asih, Tri Sri Noor and Lanzas, Cristina and Lenhart, Suzanne and Theriot, Casey M.}, year={2017}, pages={137–161} }
 @article{theriot_bowman_young_2016, title={Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for
                    Clostridium difficile
                    Spore Germination and Outgrowth in the Large Intestine}, volume={1}, ISSN={2379-5042}, url={http://dx.doi.org/10.1128/mSphere.00045-15}, DOI={10.1128/msphere.00045-15}, abstractNote={ABSTRACT
                  <jats:p>
                    It is hypothesized that the depletion of microbial members responsible for converting primary bile acids into secondary bile acids reduces resistance to
                    <jats:italic>Clostridium difficile
                    colonization. To date, inhibition of
                    <jats:italic>C. difficile
                    growth by secondary bile acids has only been shown
                    <jats:italic>in vitro
                    . Using targeted bile acid metabolomics, we sought to define the physiologically relevant concentrations of primary and secondary bile acids present in the murine small and large intestinal tracts and how these impact
                    <jats:italic>C. difficile
                    dynamics. We treated mice with a variety of antibiotics to create distinct microbial and metabolic (bile acid) environments and directly tested their ability to support or inhibit
                    <jats:italic>C. difficile
                    spore germination and outgrowth
                    <jats:italic>ex vivo.
                    Susceptibility to
                    <jats:italic>C. difficile
                    in the large intestine was observed only after specific broad-spectrum antibiotic treatment (cefoperazone, clindamycin, and vancomycin) and was accompanied by a significant loss of secondary bile acids (deoxycholate, lithocholate, ursodeoxycholate, hyodeoxycholate, and ω-muricholate). These changes were correlated to the loss of specific microbiota community members, the
                    <jats:italic>Lachnospiraceae
                    and
                    <jats:italic>Ruminococcaceae
                    families. Additionally, physiological concentrations of secondary bile acids present during
                    <jats:italic>C. difficile
                    resistance were able to inhibit spore germination and outgrowth
                    <jats:italic>in vitro
                    . Interestingly, we observed that
                    <jats:italic>C. difficile
                    spore germination and outgrowth were supported constantly in murine small intestinal content regardless of antibiotic perturbation, suggesting that targeting growth of
                    <jats:italic>C. difficile
                    will prove most important for future therapeutics and that antibiotic-related changes are organ specific. Understanding how the gut microbiota regulates bile acids throughout the intestine will aid the development of future therapies for
                    <jats:italic>C. difficile
                    infection and other metabolically relevant disorders such as obesity and diabetes.
                  
                  <jats:p>
                     <jats:bold>IMPORTANCE
                    Antibiotics alter the gastrointestinal microbiota, allowing for
                    <jats:italic>Clostridium difficile
                    infection, which is a significant public health problem. Changes in the structure of the gut microbiota alter the metabolome, specifically the production of secondary bile acids. Specific bile acids are able to initiate
                    <jats:italic>C. difficile
                    spore germination and also inhibit
                    <jats:italic>C. difficile
                    growth
                    <jats:italic>in vitro
                    , although no study to date has defined physiologically relevant bile acids in the gastrointestinal tract. In this study, we define the bile acids
                    <jats:italic>C. difficile
                    spores encounter in the small and large intestines before and after various antibiotic treatments. Antibiotics that alter the gut microbiota and deplete secondary bile acid production allow
                    <jats:italic>C. difficile
                    colonization, representing a mechanism of colonization resistance. Multiple secondary bile acids in the large intestine were able to inhibit
                    <jats:italic>C. difficile
                    spore germination and growth at physiological concentrations and represent new targets to combat
                    <jats:italic>C. difficile
                    in the large intestine.
                  }, number={1}, journal={mSphere}, publisher={American Society for Microbiology}, author={Theriot, Casey M. and Bowman, Alison A. and Young, Vincent B.}, editor={Ellermeier, Craig D.Editor}, year={2016}, month={Jan} }
 @article{winston_thanissery_montgomery_theriot_2016, title={Cefoperazone-treated Mouse Model of Clinically-relevant Clostridium difficile Strain R20291}, ISSN={["1940-087X"]}, DOI={10.3791/54850}, number={118}, journal={JOVE-JOURNAL OF VISUALIZED EXPERIMENTS}, author={Winston, Jenessa A. and Thanissery, Rajani and Montgomery, Stephanie A. and Theriot, Casey M.}, year={2016}, month={Dec} }
 @article{winston_theriot_2016, title={Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract}, volume={41}, ISSN={["1095-8274"]}, DOI={10.1016/j.anaerobe.2016.05.003}, journal={ANAEROBE}, author={Winston, Jenessa A. and Theriot, Casey M.}, year={2016}, month={Oct}, pages={44–50} }
 @article{noecker_eng_srinivasan_theriot_young_jansson_fredricks_borenstein_2016, title={Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation}, volume={1}, ISSN={2379-5077}, url={http://dx.doi.org/10.1128/mSystems.00013-15}, DOI={10.1128/msystems.00013-15}, abstractNote={ABSTRACT
                  <jats:p>Multiple molecular assays now enable high-throughput profiling of the ecology, metabolic capacity, and activity of the human microbiome. However, to date, analyses of such multi-omic data typically focus on statistical associations, often ignoring extensive prior knowledge of the mechanisms linking these various facets of the microbiome. Here, we introduce a comprehensive framework to systematically link variation in metabolomic data with community composition by utilizing taxonomic, genomic, and metabolic information. Specifically, we integrate available and inferred genomic data, metabolic network modeling, and a method for predicting community-wide metabolite turnover to estimate the biosynthetic and degradation potential of a given community. Our framework then compares variation in predicted metabolic potential with variation in measured metabolites’ abundances to evaluate whether community composition can explain observed shifts in the community metabolome, and to identify key taxa and genes contributing to the shifts. Focusing on two independent vaginal microbiome data sets, each pairing 16S community profiling with large-scale metabolomics, we demonstrate that our framework successfully recapitulates observed variation in 37% of metabolites. Well-predicted metabolite variation tends to result from disease-associated metabolism. We further identify several disease-enriched species that contribute significantly to these predictions. Interestingly, our analysis also detects metabolites for which the predicted variation negatively correlates with the measured variation, suggesting environmental control points of community metabolism. Applying this framework to gut microbiome data sets reveals similar trends, including prediction of bile acid metabolite shifts. This framework is an important first step toward a system-level multi-omic integration and an improved mechanistic understanding of the microbiome activity and dynamics in health and disease.
                  <jats:p>
                     <jats:bold>IMPORTANCE
                    Studies characterizing both the taxonomic composition and metabolic profile of various microbial communities are becoming increasingly common, yet new computational methods are needed to integrate and interpret these data in terms of known biological mechanisms. Here, we introduce an analytical framework to link species composition and metabolite measurements, using a simple model to predict the effects of community ecology on metabolite concentrations and evaluating whether these predictions agree with measured metabolomic profiles. We find that a surprisingly large proportion of metabolite variation in the vaginal microbiome can be predicted based on species composition (including dramatic shifts associated with disease), identify putative mechanisms underlying these predictions, and evaluate the roles of individual bacterial species and genes. Analysis of gut microbiome data using this framework recovers similar community metabolic trends. This framework lays the foundation for model-based multi-omic integrative studies, ultimately improving our understanding of microbial community metabolism.
                  }, number={1}, journal={mSystems}, publisher={American Society for Microbiology}, author={Noecker, Cecilia and Eng, Alexander and Srinivasan, Sujatha and Theriot, Casey M. and Young, Vincent B. and Jansson, Janet K. and Fredricks, David N. and Borenstein, Elhanan}, editor={Sanchez, Laura M.Editor}, year={2016}, month={Jan} }
 @article{seekatz_theriot_molloy_wozniak_bergin_young_2015, title={Fecal Microbiota Transplantation Eliminates Clostridium difficile in a Murine Model of Relapsing Disease}, volume={83}, ISSN={0019-9567 1098-5522}, url={http://dx.doi.org/10.1128/IAI.00459-15}, DOI={10.1128/iai.00459-15}, abstractNote={Recurrent<jats:named-content content-type="genus-species">Clostridium difficile}, number={10}, journal={Infection and Immunity}, publisher={American Society for Microbiology}, author={Seekatz, Anna M. and Theriot, Casey M. and Molloy, Caitlyn T. and Wozniak, Katherine L. and Bergin, Ingrid L. and Young, Vincent B.}, editor={McCormick, B. A.Editor}, year={2015}, month={Jul}, pages={3838–3846} }
 @article{theriot_young_2015, title={Interactions Between the Gastrointestinal Microbiome and Clostridium difficile}, volume={69}, ISSN={0066-4227 1545-3251}, url={http://dx.doi.org/10.1146/annurev-micro-091014-104115}, DOI={10.1146/annurev-micro-091014-104115}, number={1}, journal={Annual Review of Microbiology}, publisher={Annual Reviews}, author={Theriot, Casey M. and Young, Vincent B.}, year={2015}, month={Oct}, pages={445–461} }
 @article{sadighi akha_mcdermott_theriot_carlson_frank_mcdonald_falkowski_bergin_young_huffnagle_2015, title={Interleukin-22 and CD160 play additive roles in the host mucosal response to Clostridium difficile infection in mice}, volume={144}, ISSN={0019-2805}, url={http://dx.doi.org/10.1111/imm.12414}, DOI={10.1111/imm.12414}, number={4}, journal={Immunology}, publisher={Wiley}, author={Sadighi Akha, Amir A. and McDermott, Andrew J. and Theriot, Casey M. and Carlson, Paul E., Jr and Frank, Charles R. and McDonald, Roderick A. and Falkowski, Nicole R. and Bergin, Ingrid L. and Young, Vincent B. and Huffnagle, Gary B.}, year={2015}, month={Mar}, pages={587–597} }
 @article{bassis_theriot_young_2014, title={Alteration of the Murine Gastrointestinal Microbiota by Tigecycline Leads to Increased Susceptibility to Clostridium difficile Infection}, volume={58}, ISSN={0066-4804 1098-6596}, url={http://dx.doi.org/10.1128/AAC.02262-13}, DOI={10.1128/AAC.02262-13}, number={5}, journal={Antimicrobial Agents and Chemotherapy}, publisher={American Society for Microbiology}, author={Bassis, C. M. and Theriot, C. M. and Young, V. B.}, year={2014}, month={Mar}, pages={2767–2774} }
 @inbook{theriot_young_2014, title={Antibiotic-Associated Diarrhea}, ISBN={9781461464181}, url={http://dx.doi.org/10.1007/978-1-4614-6418-1_64-3}, DOI={10.1007/978-1-4614-6418-1_64-3}, booktitle={Encyclopedia of Metagenomics}, publisher={Springer New York}, author={Theriot, Casey and Young, Vincent B.}, year={2014}, pages={1–7} }
 @article{theriot_koenigsknecht_carlson_hatton_nelson_li_huffnagle_z. li_young_2014, title={Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection}, volume={5}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/ncomms4114}, DOI={10.1038/ncomms4114}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Koenigsknecht, Mark J. and Carlson, Paul E. and Hatton, Gabrielle E. and Nelson, Adam M. and Li, Bo and Huffnagle, Gary B. and Z. Li, Jun and Young, Vincent B.}, year={2014}, month={Jan} }
 @article{trindade_theriot_leslie_carlson_bergin_peters-golden_young_aronoff_2014, title={Clostridium difficile-induced colitis in mice is independent of leukotrienes}, volume={30}, ISSN={1075-9964}, url={http://dx.doi.org/10.1016/j.anaerobe.2014.09.006}, DOI={10.1016/j.anaerobe.2014.09.006}, journal={Anaerobe}, publisher={Elsevier BV}, author={Trindade, Bruno C. and Theriot, Casey M. and Leslie, Jhansi L. and Carlson, Paul E., Jr. and Bergin, Ingrid L. and Peters-Golden, Marc and Young, Vincent B. and Aronoff, David M.}, year={2014}, month={Dec}, pages={90–98} }
 @article{koenigsknecht_theriot_bergin_schumacher_schloss_young_2014, title={Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract}, volume={83}, ISSN={0019-9567 1098-5522}, url={http://dx.doi.org/10.1128/IAI.02768-14}, DOI={10.1128/IAI.02768-14}, abstractNote={<jats:named-content content-type="genus-species">Clostridium difficile}, number={3}, journal={Infection and Immunity}, publisher={American Society for Microbiology}, author={Koenigsknecht, Mark J. and Theriot, Casey M. and Bergin, Ingrid L. and Schumacher, Cassie A. and Schloss, Patrick D. and Young, Vincent B.}, editor={McCormick, B. A.Editor}, year={2014}, month={Dec}, pages={934–941} }
 @article{theriot_schumacher_bassis_seekatz_young_2014, title={Effects of Tigecycline and Vancomycin Administration on Established Clostridium difficile Infection}, volume={59}, ISSN={0066-4804 1098-6596}, url={http://dx.doi.org/10.1128/aac.04296-14}, DOI={10.1128/aac.04296-14}, abstractNote={ABSTRACT}, number={3}, journal={Antimicrobial Agents and Chemotherapy}, publisher={American Society for Microbiology}, author={Theriot, Casey M. and Schumacher, Cassie A. and Bassis, Christine M. and Seekatz, Anna M. and Young, Vincent B.}, year={2014}, month={Dec}, pages={1596–1604} }
 @article{sadighi akha_theriot_erb-downward_mcdermott_falkowski_tyra_rutkowski_young_huffnagle_2013, place={McDonald, D.T. Rutkowski, V.B. Young, G.B}, title={Acute infection of mice with Clostridium difficile leads to eIF2α phosphorylation and pro-survival signalling as part of the mucosal inflammatory response}, volume={140}, ISSN={0019-2805}, url={http://dx.doi.org/10.1111/imm.12122}, DOI={10.1111/imm.12122}, number={1}, journal={Immunology}, publisher={Wiley}, author={Sadighi Akha, Amir A. and Theriot, Casey M. and Erb-Downward, John R. and McDermott, Andrew J. and Falkowski, Nicole R. and Tyra, Heather M. and Rutkowski, D. Thomas and Young, Vincent B. and Huffnagle, Gary B.}, year={2013}, month={Aug}, pages={111–122} }
 @article{theriot_young_2013, title={Microbial and metabolic interactions between the gastrointestinal tract and Clostridium difficile infection}, volume={5}, ISSN={1949-0976 1949-0984}, url={http://dx.doi.org/10.4161/gmic.27131}, DOI={10.4161/gmic.27131}, number={1}, journal={Gut Microbes}, publisher={Informa UK Limited}, author={Theriot, Casey M and Young, Vincent B}, year={2013}, month={Dec}, pages={86–95} }
 @article{taveirne_theriot_livny_dirita_2013, title={The Complete Campylobacter jejuni Transcriptome during Colonization of a Natural Host Determined by RNAseq}, volume={8}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0073586}, DOI={10.1371/journal.pone.0073586}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Taveirne, Michael E. and Theriot, Casey M. and Livny, Jonathan and DiRita, Victor J.}, editor={Rasko, David AEditor}, year={2013}, month={Aug}, pages={e73586} }
 @article{theriot_koumpouras_carlson_bergin_aronoff_young_2011, title={Cefoperazone-treated mice as an experimental platform to assess differential virulence of Clostridium difficile strains}, volume={2}, ISSN={1949-0976 1949-0984}, url={http://dx.doi.org/10.4161/gmic.19142}, DOI={10.4161/gmic.19142}, number={6}, journal={Gut Microbes}, publisher={Informa UK Limited}, author={Theriot, Casey M. and Koumpouras, Charles C. and Carlson, Paul E. and Bergin, Ingrid I. and Aronoff, David M. and Young, Vincent B.}, year={2011}, month={Nov}, pages={326–334} }
 @article{theriot_semcer_shah_grunden_2011, title={Improving the Catalytic Activity of Hyperthermophilic Pyrococcus horikoshii Prolidase for Detoxification of Organophosphorus Nerve Agents over a Broad Range of Temperatures}, volume={2011}, ISSN={1472-3646 1472-3654}, url={http://dx.doi.org/10.1155/2011/565127}, DOI={10.1155/2011/565127}, journal={Archaea}, publisher={Hindawi Limited}, author={Theriot, Casey M. and Semcer, Rebecca L. and Shah, Saumil S. and Grunden, Amy M.}, editor={C.M., B.Semcer and Shah, S.Editors}, year={2011}, pages={1–9} }
 @article{reeves_theriot_bergin_huffnagle_schloss_young_2011, title={The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection}, volume={2}, ISSN={1949-0976 1949-0984}, url={http://dx.doi.org/10.4161/gmic.2.3.16333}, DOI={10.4161/gmic.2.3.16333}, number={3}, journal={Gut Microbes}, publisher={Informa UK Limited}, author={Reeves, Angela E. and Theriot, Casey M. and Bergin, Ingrid L. and Huffnagle, Gary B. and Schloss, Patrick D. and Young, Vincent B.}, year={2011}, month={May}, pages={145–158} }
 @article{theriot_grunden_2010, title={Hydrolysis of organophosphorus compounds by microbial enzymes}, volume={89}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-010-2807-9}, DOI={10.1007/s00253-010-2807-9}, number={1}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Grunden, Amy M.}, year={2010}, month={Oct}, pages={35–43} }
 @article{theriot_du_tove_grunden_2010, title={Improving the catalytic activity of hyperthermophilic Pyrococcus prolidases for detoxification of organophosphorus nerve agents over a broad range of temperatures}, volume={87}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-010-2614-3}, DOI={10.1007/s00253-010-2614-3}, number={5}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Du, Xuelian and Tove, Sherry R. and Grunden, Amy M.}, year={2010}, month={Apr}, pages={1715–1726} }
 @article{theriot_tove_grunden_2009, title={Characterization of two proline dipeptidases (prolidases) from the hyperthermophilic archaeon Pyrococcus horikoshii}, volume={86}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-009-2235-x}, DOI={10.1007/s00253-009-2235-x}, number={1}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Tove, Sherry R. and Grunden, Amy M.}, year={2009}, month={Sep}, pages={177–188} }
 @article{theriot_tove_grunden_2009, title={Erratum to: Characterization of two proline dipeptidases (prolidases) from the hyperthermophilic archaeon Pyrococcus horikoshii}, volume={86}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/S00253-009-2300-5}, DOI={10.1007/S00253-009-2300-5}, number={1}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Tove, Sherry R. and Grunden, Amy M.}, year={2009}, month={Oct}, pages={393–393} }
 @misc{theriot_tove_grunden_2009, title={biotechnological applications of recombinant microbial prolidases}, volume={68}, journal={Advances in applied microbiology, vol 68}, author={Theriot, C. M. and Tove, S. R. and Grunden, A. M.}, year={2009}, pages={99-} }