@misc{mcmillan_theriot_2024, title={Bile acids impact the microbiota, host, and <i>C. difficile</i> dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics}, volume={16}, ISSN={["1949-0984"]}, DOI={10.1080/19490976.2024.2393766}, abstractNote={Clostridioides difficile is a major nosocomial pathogen, causing significant morbidity and mortality worldwide. Antibiotic usage, a major risk factor for Clostridioides difficile infection (CDI), disrupts the gut microbiota, allowing C. difficile to proliferate and cause infection, and can often lead to recurrent CDI (rCDI). Fecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs) have emerged as effective treatments for rCDI and aim to restore colonization resistance provided by a healthy gut microbiota. However, much is still unknown about the mechanisms mediating their success. Bile acids, extensively modified by gut microbes, affect C. difficile's germination, growth, and toxin production while also shaping the gut microbiota and influencing host immune responses. Additionally, microbial interactions, such as nutrient competition and cross-feeding, contribute to colonization resistance against C. difficile and may contribute to the success of microbiota-focused therapeutics. Bile acids as well as other microbial mediated interactions could have implications for other diseases being treated with microbiota-focused therapeutics. This review focuses on the intricate interplay between bile acid modifications, microbial ecology, and host responses with a focus on C. difficile, hoping to shed light on how to move forward with the development of new microbiota mediated therapeutic strategies to combat rCDI and other intestinal diseases.}, number={1}, journal={GUT MICROBES}, author={McMillan, Arthur S. and Theriot, Casey M.}, year={2024}, month={Dec} }
 @article{mcmillan_zhang_dougherty_mcgill_gulati_baker_theriot_2024, title={Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent <i>Clostridioides difficile</i> infection}, ISSN={["2379-5042"]}, DOI={10.1128/msphere.00706-24}, abstractNote={ABSTRACT Recurrent C. difficile infection (rCDI) is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we use longitudinal stool samples collected from patients undergoing FMT to evaluate intra-individual changes in the microbiome, metabolome, and lipidome after successful FMTs relative to their baselines pre-FMT. We show changes in the abundance of many lipids, specifically a decrease in acylcarnitines post-FMT, and a shift from conjugated bile acids pre-FMT to deconjugated secondary bile acids post-FMT. These changes correlate with a decrease in Enterobacteriaceae, which encode carnitine metabolism genes, and an increase in Lachnospiraceae, which encode bile acid altering genes such as bile salt hydrolases (BSHs) and the bile acid-inducible ( bai ) operon, post-FMT. We also show changes in gut microbe-encoded amino acid biosynthesis genes, of which Enterobacteriaceae was the primary contributor to amino acids C. difficile is auxotrophic for. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT and generate hypotheses that require further experimental validation. This information is meant to help guide the development of new microbiota-focused therapeutics to treat rCDI. IMPORTANCE Recurrent C. difficile infection is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant. However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT. These changes correlate with Enterobacteriaceae pre-FMT, which encodes carnitine metabolism genes, and Lachnospiraceae post-FMT, which encodes bile salt hydrolases and baiA genes. There was also a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT, which we hope will help aid in the development of new microbiota-focused therapeutics to treat rCDI.}, journal={MSPHERE}, author={McMillan, Arthur S. and Zhang, Guozhi and Dougherty, Michael K. and McGill, Sarah K. and Gulati, Ajay S. and Baker, Erin S. and Theriot, Casey M.}, year={2024}, month={Oct} }
 @article{anderson_raskind_hissong_dougherty_mcgill_gulati_theriot_kennedy_evans_2024, title={Offline Two-Dimensional Liquid Chromatography-Mass Spectrometry for Deep Annotation of the Fecal Metabolome Following Fecal Microbiota Transplantation}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.4c00022}, abstractNote={Biological interpretation of untargeted LC-MS-based metabolomics data depends on accurate compound identification, but current techniques fall short of identifying most features that can be detected. The human fecal metabolome is complex, variable, incompletely annotated, and serves as an ideal matrix to evaluate novel compound identification methods. We devised an experimental strategy for compound annotation using multidimensional chromatography and semiautomated feature alignment and applied these methods to study the fecal metabolome in the context of fecal microbiota transplantation (FMT) for recurrent}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Anderson, Brady G. and Raskind, Alexander and Hissong, Rylan and Dougherty, Michael K. and McGill, Sarah K. and Gulati, Ajay S. and Theriot, Casey M. and Kennedy, Robert T. and Evans, Charles R.}, year={2024}, month={May} }
 @article{foley_walker_stewart_o'flaherty_gentry_patel_beaty_allen_pan_simpson_et al._2023, title={Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut}, volume={3}, ISSN={["2058-5276"]}, DOI={10.1038/s41564-023-01337-7}, abstractNote={AbstractBile acids (BAs) mediate the crosstalk between human and microbial cells and influence diseases including Clostridioides difficile infection (CDI). While bile salt hydrolases (BSHs) shape the BA pool by deconjugating conjugated BAs, the basis for their substrate selectivity and impact on C. difficile remain elusive. Here we survey the diversity of BSHs in the gut commensals Lactobacillaceae, which are commonly used as probiotics, and other members of the human gut microbiome. We structurally pinpoint a loop that predicts BSH preferences for either glycine or taurine substrates. BSHs with varying specificities were shown to restrict C. difficile spore germination and growth in vitro and colonization in pre-clinical in vivo models of CDI. Furthermore, BSHs reshape the pool of microbial conjugated bile acids (MCBAs) in the murine gut, and these MCBAs can further restrict C. difficile virulence in vitro. The recognition of conjugated BAs by BSHs defines the resulting BA pool, including the expansive MCBAs. This work provides insights into the structural basis of BSH mechanisms that shape the BA landscape and promote colonization resistance against C. difficile.}, journal={NATURE MICROBIOLOGY}, author={Foley, Matthew H. and Walker, Morgan E. and Stewart, Allison K. and O'Flaherty, Sarah and Gentry, Emily C. and Patel, Shakshi and Beaty, Violet V. and Allen, Garrison and Pan, Meichen and Simpson, Joshua B. and et al.}, year={2023}, month={Mar} }
 @article{icho_ward_tam_kociolek_theriot_melnyk_2023, title={Intestinal bile acids provide a surmountable barrier against C. difficile TcdB-induced disease pathogenesis}, volume={120}, ISSN={["1091-6490"]}, DOI={10.1073/pnas.2301252120}, abstractNote={
            Intestinal bile acids play an essential role in the
            Clostridioides difficile
            lifecycle having been shown in vitro to modulate various aspects of pathogenesis, including spore germination, vegetative growth, and more recently the action of the primary virulence determinant, TcdB. Here, we investigated whether physiological levels of the total pool of intestinal bile acids in mice and humans protect against TcdB action. Small molecules extracted from the lumenal contents of the small intestine, cecum, colon, and feces were found to inhibit TcdB in accordance with the differential amounts of total bile acids in each compartment. Extracts from antibiotic-treated and germ-free mice, despite harboring dramatically altered bile acid profiles, unexpectedly also prevented TcdB-induced cell rounding to similar extents. We show that protection, however, is surmountable and can be overcome at higher doses of TcdB—typical to those seen during severe
            C. difficile
            infection—suggesting that the protective properties of intestinal bile acids are operant primarily under low to moderate toxin levels. Taken together, these findings demonstrate a role for intestinal bile acids in attenuating virulence, provide insights into asymptomatic carriage of toxigenic
            C. difficile
            , and inform strategies to manipulate bile acid levels for therapeutic benefit.
          }, number={19}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Icho, Simoun and Ward, Jennifer S. and Tam, John and Kociolek, Larry K. and Theriot, Casey M. and Melnyk, Roman A.}, year={2023}, month={May} }
 @article{kisthardt_thanissery_pike_foley_theriot_2023, title={The microbial-derived bile acid lithocholate and its epimers inhibit <i>Clostridioides difficile</i> growth and pathogenicity while sparing members of the gut microbiota}, volume={205}, ISSN={["1098-5530"]}, DOI={10.1128/jb.00180-23}, abstractNote={ABSTRACT
          
            Clostridioides difficile
            is a Gram-positive, spore-forming anaerobe that causes clinical diseases ranging from diarrhea and pseudomembranous colitis to toxic megacolon and death.
            C. difficile
            infection (CDI) is associated with antibiotic usage, which disrupts the indigenous gut microbiota and causes the loss of microbial-derived secondary bile acids that normally provide protection against
            C. difficile
            colonization. Previous work has shown that the secondary bile acid lithocholate (LCA) and its epimer isolithocholate (iLCA) have potent inhibitory activity against clinically relevant
            C. difficile
            strains. To further characterize the mechanisms by which LCA and its epimers iLCA and isoallolithocholate (iaLCA) inhibit
            C. difficile,
            we tested their minimum inhibitory concentration against
            C. difficile
            R20291 and a commensal gut microbiota panel. We also performed a series of experiments to determine the mechanism of action by which LCA and its epimers inhibit
            C. difficile
            through bacterial killing and effects on toxin expression and activity. Additionally, we tested the cytotoxicity of these bile acids through Caco-2 cell apoptosis and viability assays to gauge their effects on the host. Here, we show that the epimers iLCA and iaLCA strongly inhibit
            C. difficile
            growth
            in vitro
            while sparing most commensal Gram-negative gut microbes. We also show that iLCA and iaLCA have bactericidal activity against
            C. difficile,
            and these epimers cause significant bacterial membrane damage at subinhibitory concentrations. Finally, we observe that iLCA and iaLCA decrease the expression of the large cytotoxin
            tcdA
            , while LCA significantly reduces toxin activity. Although iLCA and iaLCA are both epimers of LCA, they have distinct mechanisms for inhibiting
            C. difficile
            . LCA epimers, iLCA and iaLCA, represent promising compounds that target
            C. difficile
            with minimal effects on members of the gut microbiota that are important for colonization resistance.
          
          
            IMPORTANCE
            
              In the search for a novel therapeutic that targets
              Clostridioides difficile
              , bile acids have become a viable solution. Epimers of bile acids are particularly attractive as they may provide protection against
              C. difficile
              while leaving the indigenous gut microbiota largely unaltered. This study shows that LCA epimers isolithocholate (iLCA) and LCA epimers isoallolithocholate (iaLCA) specifically are potent inhibitors of
              C. difficile,
              affecting key virulence factors including growth, toxin expression, and activity. As we move toward the use of bile acids as therapeutics, further work will be required to determine how best to deliver these bile acids to a target site within the host intestinal tract.
            
          }, number={9}, journal={JOURNAL OF BACTERIOLOGY}, author={Kisthardt, Samantha C. and Thanissery, Rajani and Pike, Colleen M. and Foley, Matthew H. and Theriot, Casey M.}, year={2023}, month={Sep} }
 @article{stewart_foley_dougherty_mcgill_gulati_gentry_hagey_dorrestein_theriot_dodds_et al._2023, title={Using Multidimensional Separations to Distinguish Isomeric Amino Acid-Bile Acid Conjugates and Assess Their Presence and Perturbations in Model Systems}, volume={95}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.3c03057}, abstractNote={Bile acids play key roles in nutrient uptake, inflammation, signaling, and microbiome composition. While previous bile acid analyses have primarily focused on profiling 5 canonical primary and secondary bile acids and their glycine and taurine amino acid-bile acid (AA-BA) conjugates, recent studies suggest that many other microbial conjugated bile acids (or MCBAs) exist. MCBAs are produced by the gut microbiota and serve as biomarkers, providing information about early disease onset and gut health. Here we analyzed 8 core bile acids synthetically conjugated with 22 proteinogenic and nonproteogenic amino acids totaling 176 MCBAs. Since many of the conjugates were isomeric and only 42 different m/z values resulted from the 176 MCBAs, a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) was used for their separation. Their molecular characteristics were then used to create an in-house extended bile acid library for a combined total of 182 unique compounds. Additionally, ∼250 rare bile acid extracts were also assessed to provide additional resources for bile acid profiling and identification. This library was then applied to healthy mice dosed with antibiotics and humans having fecal microbiota transplantation (FMT) to assess the MCBA presence and changes in the gut before and after each perturbation.}, number={41}, journal={ANALYTICAL CHEMISTRY}, author={Stewart, Allison K. and Foley, Matthew H. and Dougherty, Michael K. and Mcgill, Sarah K. and Gulati, Ajay S. and Gentry, Emily C. and Hagey, Lee R. and Dorrestein, Pieter C. and Theriot, Casey M. and Dodds, James N. and et al.}, year={2023}, month={Oct}, pages={15357–15366} }
 @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}, abstractNote={Abstract
                Background
                Bile acids are known to be genotoxic and contribute to colorectal cancer (CRC). However, the link between CRC tumor bile acids to tumor location, patient sex, microbiome, immune-regulatory cells, and prognosis is not clear.
              
                Methods
                We conducted bile acid analysis using targeted liquid chromatography–mass spectrometry (LC–MS) on tumor tissues from CRC patients (n = 228) with survival analysis. We performed quantitative immunofluorescence (QIF) on tumors to examine immune cells.
              
                Results
                Twelve of the bile acids were significantly higher in right-sided colon tumors compared to left-sided colon tumors. Furthermore, in male patients, right-sided colon tumors had elevated secondary bile acids (deoxycholic acid, lithocholic acid, ursodeoxycholic acid) compared to left-sided colon tumors, but this difference between tumors by location was not observed in females. A high ratio of glycoursodeoxycholic to ursodeoxycholic was associated with 5-year overall survival (HR = 3.76, 95% CI = 1.17 to 12.1, P = 0.026), and a high ratio of glycochenodeoxycholic acid to chenodeoxycholic acid was associated with 5-year recurrence-free survival (HR = 3.61, 95% CI = 1.10 to 11.84, P = 0.034). We also show correlation between these bile acids and FoxP3 + T regulatory cells.
              
                Conclusions
                This study revealed that the distribution of bile acid abundances in colon cancer patients is tumor location-, age- and sex-specific, and are linked to patient prognosis. This study provides new implications for targeting bile acid metabolism, microbiome, and immune responses for colon cancer patients by taking into account primary tumor location and sex.
              }, 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}, abstractNote={ABSTRACT Acute intestinal mucositis is a common off-target effect of chemotherapy, leading to co-morbidities such as vomiting, diarrhea, sepsis, and death. We previously demonstrated that the presence of enteric bacteria modulates the extent of jejunal epithelial damage induced by doxorubicin (DXR) in mice. Despite conventional thinking of the crypt as a sterile environment, recent evidence suggests that bacterial signaling influences aISC function. In this study, we labeled aISCs using transgenic Lgr5-driven fluorescence or with immunostaining for OLFM4. We examined the effect of DXR in both germ free (GF) mice and mice depleted of microbiota using an established antimicrobial treatment protocol (AMBx). We found differences in DXR-induced loss of aISCs between GF mice and mice treated with AMBx. aISCs were decreased after DXR in GF mice, whereas AMBx mice retained aISC expression after DXR. Neither group of mice exhibited an inflammatory response to DXR, suggesting the difference in aISC retention was not due to differences in local tissue inflammation. Therefore, we suspected that there was a protective microbial signal present in the AMBx mice that was not present in the GF mice. 16S rRNA sequencing of jejunal luminal contents demonstrated that AMBx altered the fecal and jejunal microbiota. In the jejunal contents, AMBx mice had increased abundance of Ureaplasma and Burkholderia. These results suggest pro-survival signaling from microbiota in AMBx-treated mice to the aISCs, and that this signaling maintains aISCs in the face of chemotherapeutic injury. Manipulation of the enteric microbiota presents a therapeutic target for reducing the severity of chemotherapy-associated mucositis.}, 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}, abstractNote={
            C. difficile
            infection (CDI) is a highly inflammatory disease mediated by the production of two large toxins that weaken the intestinal epithelium and cause extensive colonic tissue damage. Antibiotic alternative therapies for CDI are urgently needed as current antibiotic regimens prolong the perturbation of the microbiota and lead to high disease recurrence rates.
          }, 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}, abstractNote={
            Proline is an essential environmental amino acid that
            C. difficile
            uses to support growth and cause significant disease. A posttranslationally modified form, hydroxyproline, is highly abundant in collagen, which is degraded by host proteases in response to
            C. difficile
            toxin activity.
          }, 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}, abstractNote={AbstractClostridioides difficile is a bacterial pathogen that causes a range of clinical disease from mild to moderate diarrhea, pseudomembranous colitis, and toxic megacolon. Typically, C. difficile infections (CDIs) occur after antibiotic treatment, which alters the gut microbiota, decreasing colonization resistance against C. difficile. Disease is mediated by two large toxins and the expression of their genes is induced upon nutrient depletion via the alternative sigma factor TcdR. Here, we use tcdR mutants in two strains of C. difficile and omics to investigate how toxin-induced inflammation alters C. difficile metabolism, tissue gene expression and the gut microbiota, and to determine how inflammation by the host may be beneficial to C. difficile. We show that C. difficile metabolism is significantly different in the face of inflammation, with changes in many carbohydrate and amino acid uptake and utilization pathways. Host gene expression signatures suggest that degradation of collagen and other components of the extracellular matrix by matrix metalloproteinases is a major source of peptides and amino acids that supports C. difficile growth in vivo. Lastly, the inflammation induced by C. difficile toxin activity alters the gut microbiota, excluding members from the genus Bacteroides that are able to utilize the same essential nutrients released from collagen degradation.}, 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}, abstractNote={Clostridioides difficile is an anaerobic pathogen that causes significant morbidity and mortality. Understanding the mechanisms of colonization resistance against C. difficile is important for elucidating the mechanisms by which C. difficile is able to colonize the gut after antibiotics. Commensal Clostridium play a key role in colonization resistance. They are able to modify bile acids which alter the C. difficile life cycle. Commensal Clostridium also produce other inhibitory metabolites including antimicrobials and short chain fatty acids. They also compete with C. difficile for vital nutrients such as proline. Understanding the mechanistic effects that these metabolites have on C. difficile and other gut pathogens is important for the development of new therapeutics against C. difficile infection (CDI), which are urgently needed.}, 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}, abstractNote={Significance
          
            The transformation of bile acids (BAs) by the gut microbiota is increasingly recognized as an important factor shaping host health. The prerequisite step of BA metabolism is carried out by bile salt hydrolases (BSHs), which are encoded by select gut and probiotic bacteria. Despite their prevalence, the utility of harboring a
            bsh
            is unclear. Here, we investigate the role of BSHs encoded by
            Lactobacillus acidophilus
            and
            Lactobacillus gasseri
            . We show that BA type and BSH substrate preferences affect in vitro and in vivo growth of both species. These findings contribute to a mechanistic understanding of bacterial survival in various BA-rich niches and inform future efforts to leverage BSHs as a therapeutic tool for manipulating the gut microbiota.
          }, 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{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}, abstractNote={Ursodeoxycholic acid (commercially available as ursodiol) is a naturally occurring bile acid that is used to treat a variety of hepatic and gastrointestinal diseases. Ursodiol can modulate bile acid pools, which have the potential to alter the gut microbiota community structure. In turn, the gut microbial community can modulate bile acid pools, thus highlighting the interconnectedness of the gut microbiota-bile acid-host axis. Despite these interactions, it remains unclear if and how exogenously administered ursodiol shapes the gut microbial community structure and bile acid pool in conventional mice. This study aims to characterize how ursodiol alters the gastrointestinal ecosystem in conventional mice. C57BL/6J wildtype mice were given one of three doses of ursodiol (50, 150, or 450 mg/kg/day) by oral gavage for 21 days. Alterations in the gut microbiota and bile acids were examined including stool, ileal, and cecal content. Bile acids were also measured in serum. Significant weight loss was seen in mice treated with the low and high dose of ursodiol. Alterations in the microbial community structure and bile acid pool were seen in ileal and cecal content compared to pretreatment, and longitudinally in feces following the 21-day ursodiol treatment. In both ileal and cecal content, members of the Lachnospiraceae Family significantly contributed to the changes observed. This study is the first to provide a comprehensive view of how exogenously administered ursodiol shapes the healthy gastrointestinal ecosystem in conventional mice. Further studies to investigate how these changes in turn modify the host physiologic response are important.}, 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}, abstractNote={The relationship between the gut microbiota and Clostridioides difficile, and its role in the severity of C. difficile infection in humans is an area of active research. Intestinal carriage of toxigenic and non-toxigenic C. difficile strains, with and without clinical signs, is reported in animals, however few studies have looked at the risk factors associated with C. difficile carriage and the role of the host gut microbiota. Here, we isolated and characterized C. difficile strains from different animal species (predominantly canines (dogs), felines (cats), and equines (horses)) that were brought in for tertiary care at North Carolina State University Veterinary Hospital. C. difficile strains were characterized by toxin gene profiling, fluorescent PCR ribotyping, and antimicrobial susceptibility testing. 16S rRNA gene sequencing was done on animal feces to investigate the relationship between the presence of C. difficile and the gut microbiota in different hosts. Here, we show that C. difficile was recovered from 20.9% of samples (42/201), which included 33 canines, 2 felines, and 7 equines. Over 69% (29/42) of the isolates were toxigenic and belonged to 14 different ribotypes including ones known to cause CDI in humans. The presence of C. difficile results in a shift in the fecal microbial community structure in both canines and equines. Commensal Clostridium hiranonis was negatively associated with C. difficile in canines. Further experimentation showed a clear antagonistic relationship between the two strains in vitro, suggesting that commensal Clostridia might play a role in colonization resistance against C. difficile in different hosts.}, 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} }
 @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}, abstractNote={Significance
          
            Clostridioides difficile
            is a bacterial pathogen of global importance that is a major cause of hospital-acquired diarrhea. Antibiotic-mediated disruptions to the gut microbiota and associated metabolome promote
            C. difficile
            growth and infection through mechanisms that are poorly understood. Here, we show that intestinal bile acids, which are known to play a role in
            C. difficile
            germination and outgrowth, also directly bind and inhibit TcdB toxin, the primary virulence determinant of
            C. difficile
            . Bile acid binding induces a major conformational change in TcdB structure that prevents receptor binding and uptake into cells. In addition to suggesting a role for bile acids in protecting against
            C. difficile
            pathogenesis, these findings highlight an approach to block
            C. difficile
            virulence.
          }, 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{pike_theriot_2021, title={Mechanisms of Colonization Resistance Against Clostridioides difficile}, volume={223}, ISSN={["1537-6613"]}, DOI={10.1093/infdis/jiaa408}, abstractNote={Abstract
               Clostridioides difficile is an urgent antimicrobial-resistant bacterium, causing mild to moderate and sometimes life-threatening disease. Commensal gut microbes are critical for providing colonization resistance against C difficile and can be leveraged as non-antibiotic alternative therapeutics for the prevention and treatment of C difficile infection.}, journal={JOURNAL OF INFECTIOUS DISEASES}, author={Pike, Colleen M. and Theriot, Casey M.}, year={2021}, month={Jun}, pages={S194–S200} }
 @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}, abstractNote={In this issue of Cell, Alavi et al. report that infection by Vibrio cholerae is blocked by gut microbiome-mediated hydrolysis of bile acids. Cholera therefore joins amebic dysentery and Clostridioides difficile colitis as enteric infections profoundly influenced by the microbiome’s impact on bile acid metabolism. In this issue of Cell, Alavi et al. report that infection by Vibrio cholerae is blocked by gut microbiome-mediated hydrolysis of bile acids. Cholera therefore joins amebic dysentery and Clostridioides difficile colitis as enteric infections profoundly influenced by the microbiome’s impact on bile acid metabolism. Vibrio cholerae causes watery diarrhea so severe that it kills by dehydration within hours. We are now experiencing the 7th pandemic of cholera, all 7 of which likely originated in the Indian subcontinent, with current estimates of up to 3 million cases and 100,000 deaths annually. That cholera is water-borne was established by the physician John Snow in 1854 by linking victims of the London Broad Street cholera epidemic not to bad air but to the Broad Street water pump. V. cholerae exists in aquatic environments on the surface and in the intestine of copepods (a type of small crustacean). This leads to sporadic outbreaks near rivers in the Indian subcontinent, amplified by human fecal-oral spread of the bacteria during outbreaks causing pandemics. Diarrhea is caused by cholera toxin, an enzyme that ADP-ribosylates the Gs protein that regulates adenylate cyclase, leading to a cyclic AMP (cAMP)-mediated chloride ion (Cl−) secretion. Cholera toxin and the toxin coregulated pili (TCP) are regulated by TcpP, a membrane bound transcriptional activator. There is substantial person-to-person variation in the severity of cholera, with one explanation being personal differences in the microbiome regulating virulence gene expression by TcpP. However, we still lack a complete understanding of the factors that cause person-to-person variation on severity of cholera. In this issue of Cell, Ansel Hsiao and colleagues demonstrate that hydrolysis of the bile acid taurocholate to cholate by the gut microbiome blocks TcpP activation and cholera colonization. This paper adds to emerging literature on how the microbiome impacts infectious diseases via microbial metabolism of bile acids in the gut. The primary bile acids cholate (CA) and chenodeoxycholate (CDCA) are made by the liver, where they are conjugated with a glycine or taurine before being secreted into the duodenum. As they make their way through the small intestine, 95% of bile acids are absorbed in the terminal ileum through the enterohepatic system, a majority being conjugated bile acids (Figure 1). Gut microbes that encode bacterial bile salt hydrolase bsh genes can deconjugate or cleave the glycine and taurine from conjugated bile acids to yield deconjugated bile acids (e.g., taurocholate [TCA]→taurine and CA). This is a critical first step in microbial bile acid metabolism that leads to all subsequent biotransformations. The deconjugated bile acids that reach the large intestine are then metabolized by members of the gut microbiota into secondary bile acids, including deoxycholate (DCA). (Foley et al., 2019Foley M.H. O’Flaherty S. Barrangou R. Theriot C.M. Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract.PLoS Pathog. 2019; 15: e1007581Crossref PubMed Scopus (44) Google Scholar). Here, Alavi et al., 2020Alavi S. Mitchell J.D. Cho J.Y. Liu R. MacBeth J.C. Hsiao A. Interpersonal gut microbiome variation drives susceptibility and resistance to Vibrio cholerae.Cell. 2020; 181 (this issue): 1533-1546Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar demonstrate that the composition of the gut microbiome contributes to resistance to cholera. By reconstituting germ-free mice with defined communities of human microbiome bacteria, they discovered that the commensal bacterium Blautia obeum mediates resistance. They show that B. obeum mediates resistance in mice through degrading TCA to CA and that the abundance of the B. obeum BSH enzyme correlated with resistance in humans. In the absence of B. obeum-dependent degradation, TCA induces the TcpP virulence regulator to cause disease. Cholera therefore joins a list of enteropathogens whose ability to cause disease is regulated by microbiome metabolism of bile acids. A second example is the parasite Entamoeba histolytica, an ameba that invades the intestine by eating the epithelial lining in a process called trogocytosis. Burgess et al., 2020Burgess S.L. Leslie J.L. Uddin M.J. Oakland D.N. Gilchrist C.A. Moreau G.B. Watanabe K. Saleh M.M. Simpson M. Thompson B.A. et al.Gut microbiome communication with bone marrow regulates susceptibility to amebiasis.J. Clin. Invest. 2020; https://doi.org/10.1172/JCI133605Crossref Scopus (8) Google Scholar recently identified the intestinal bacterium Clostridium scindens as providing protection from amebic colitis. Introduction of C. scindens into the microbiome of a mouse altered the bone marrow by inducing expansion of granulocyte-monocyte progenitors (GMPs). C. scindens-mediated protection from amebiasis could be transferred with adoptive transfer of bone marrow to a naive mouse and act via an increased recruitment of polymorphonuclear neutrophils to the colon. Because C. scindens can dehydroxylate CA to DCA, Burgess et al., 2020Burgess S.L. Leslie J.L. Uddin M.J. Oakland D.N. Gilchrist C.A. Moreau G.B. Watanabe K. Saleh M.M. Simpson M. Thompson B.A. et al.Gut microbiome communication with bone marrow regulates susceptibility to amebiasis.J. Clin. Invest. 2020; https://doi.org/10.1172/JCI133605Crossref Scopus (8) Google Scholar tested if this mediated alteration of the marrow. In fact, administration of DCA alone provided complete protection from amebiasis via GMP expansion, demonstrating microbiome-to-bone-marrow communication via bile acids. A final example relates to Clostridioides difficile infection (CDI). C. difficile is a Gram-positive spore forming bacillus and the most common cause of hospital-acquired, antibiotic-associated diarrhea. Ingestion of the spore form of C. difficile in an individual with a dysbiotic microbiome (usually due to prior antibiotic therapy) leads to infection of the large intestine by the vegetative stage of C. difficile. Primary and secondary bile acids have been shown to impact C. difficile vegetative growth as well as spore germination and toxin activity. For example, the primary bile acid TCA induces spore germination, and DCA inhibits C. difficile growth. Like the amebic colitis example, C. scindens is implicated as having a protective role in CDI. First, depletion of C. scindens is associated with more severe disease in humans and mice. Moreover, in the mouse model of CDI, reconstitution of C. scindens was able to partially restore colonization resistance against CDI in mice, and colonization resistance was associated with secondary bile acid synthesis (Buffie et al., 2015Buffie C.G. Bucci V. Stein R.R. McKenney P.T. Ling L. Gobourne A. No D. Liu H. Kinnebrew M. Viale A. et al.Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.Nature. 2015; 517: 205-208Crossref PubMed Scopus (855) Google Scholar). In patients with recurrent CDI, high levels of conjugated primary bile acids and reduced secondary bile acids were observed in feces when compared to healthy individuals. Successful treatment of recurrent CDI with fecal microbial transplant restored the level of fecal secondary bile acids, specifically, DCA and LCA (Weingarden et al., 2015Weingarden A. González A. Vázquez-Baeza Y. Weiss S. Humphry G. Berg-Lyons D. Knights D. Unno T. Bobr A. Kang J. et al.Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.Microbiome. 2015; 3: 10https://doi.org/10.1186/s40168-015-0070-0Crossref PubMed Scopus (145) Google Scholar, Seekatz et al., 2018Seekatz A.M. Theriot C.M. Rao K. Chang Y.M. Freeman A.E. Kao J.Y. Young V.B. Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection.Anaerobe. 2018; 53: 64-73Crossref PubMed Scopus (60) Google Scholar). Most recently, Reed et al., 2020Reed A.D. Nethery M.A. Stewart A. Barrangou R. Theriot C.M. Strain-dependent inhibition of Clostridioides difficile by commensal Clostridia encoding the bile acid inducible (bai) operon.J Bacteriol. 2020; https://doi.org/10.1128/JB.00039-20Crossref PubMed Scopus (7) Google Scholar have shown that several commensal Clostridia encoding the bai operon (which encodes enzymes that convert cholate into the secondary bile acid deoxycholate), but not all, are able to inhibit C. difficile growth due to the conversion of CA to DCA, which should provide protection. To summarize, there is strong in vitro and supportive in vivo evidence that microbial metabolism of bile acids has a direct impact on C. difficile spore germination, growth, and toxin production and activity. Bile acids also regulate the immune system, as demonstrated in amebic dysentery with DCA protecting by increasing marrow GMPs. Additional examples of a direct impact of bile acids on the immune system include the secondary bile acid LCA regulating Th17 responses by interfering with RORyT transcriptional activity (Hang et al., 2019Hang S. Paik D. Yao L. Kim E. Trinath J. Lu J. Ha S. Nelson B.N. Kelly S.P. Wu L. et al.Bile acid metabolites control TH17 and Treg cell differentiation.Nature. 2019; 576: 143-148Crossref PubMed Scopus (164) Google Scholar) and, in the context of colitis, bile acids interacting with macrophages to induce IL-10, which polarizes T cells to a regulatory phenotype (Biagioli et al., 2017Biagioli M. Carino A. Cipriani S. Francisci D. Marchianò S. Scarpelli P. Sorcini D. Zampella A. Fiorucci S. The bile acid receptor GPBAR1 regulates the M1/M2 phenotype of intestinal macrophages and activation of GPBAR1 rescues mice from murine colitis.J. Immunol. 2017; 199: 718-733Crossref PubMed Scopus (85) Google Scholar). In summary, Alavi et al., 2020Alavi S. Mitchell J.D. Cho J.Y. Liu R. MacBeth J.C. Hsiao A. Interpersonal gut microbiome variation drives susceptibility and resistance to Vibrio cholerae.Cell. 2020; 181 (this issue): 1533-1546Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar have deepened our understanding of how composition of the gut microbiome protects from cholera by the discovery of the role of bacterially encoded bile salt hydrolases. As microbiome science moves from description to mechanism, bile acids synthesized by the host and further converted by the microbiota are becoming central players, both for their direct impact on enteropathogens and for their impact on the immune system. Work from the authors’ labs is supported by National Institutes of Health grants R35 GM119438 (to C.M.T.), 2R37 AI026649-31 , and R01 AI043596-22 (to W.A.P.) and the Henske and McGrath families. Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera InfectionAlavi et al.CellJune 16, 2020In BriefDifferences in the gut microbiome between individuals determine resistance to cholera infection through the effects on the activity of a bile salt enzyme. Full-Text PDF Open Archive}, 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}, abstractNote={Clostridioides difficile infection (CDI) causes serious and sometimes fatal symptoms like diarrhea and pseudomembraneous colitis. Although antibiotics for CDI exist, they are either expensive or cause recurrence of the infection due to their altering the colonic microbiota which is necessary to suppress the infection. Here, we leverage a class of known membrane-targeting compounds that we previously showed to have broad inhibitory activity across multiple C. difficile strains while preserving the microbiome to develop an efficacious agent. A new series of salicylanilides was synthesized and the most potent analog was selected through an in vitro inhibitory assay to evaluate its pharmacokinetic parameters and potency in a CDI mouse model. The results revealed reduced recurrence of CDI and disturbance of the microbiota in mice compared to standard-of-care vancomycin, thus paving the way for novel therapy that can potentially target the cell membrane of C. difficile to minimize relapse in the recovering patient.}, 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}, abstractNote={Clostridioides difficileinfection (CDI) is associated with increasing morbidity and mortality posing an urgent threat to public health. Recurrence of CDI after successful treatment with antibiotics is high, thus necessitating discovery of novel therapeutics against this enteric pathogen. Administration of the secondary bile acid ursodeoxycholic acid (UDCA; ursodiol) inhibits the life cycles of various strains ofC. difficilein vitro, suggesting that the FDA-approved formulation of UDCA, known as ursodiol, may be able to restore colonization resistance againstC. difficilein vivo.}, 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}, abstractNote={Research on bile acids has increased dramatically due to recent studies demonstrating their ability to significantly impact the host, microbiome, and various disease states [1–3]. Although these liver-synthesized molecules assist in the absorption and digestion of dietary fat in the intestine, their reabsorption and recirculation also gives them access to peripheral organs [4] (Fig 1A). Bile acids serve as substrates for bile acid receptors (BARs) found throughout the body that control critical regulatory and metabolic processes and therefore represent an important class of bioactive molecules [5]. Despite the importance of bile acids to host health, there remain gaps in our knowledge about the bacterial enzymes driving their composition and modification. 
 
 
 
 
 
 
Open in a separate window 
 
 
Fig 1 
 
Bile salt hydrolases act on circulating conjugated bile acids in the gut-liver axis. 
(A) Bile acids synthesized in the liver and stored in the gall bladder enter the small intestine through the duodenum where they reach millimolar concentrations. The majority of bile acids (95%) are reabsorbed in the ileum and recirculate to the liver through the portal vein. The remaining population transit to the colon as they continue to be reabsorbed, and a small (<5%) amount exit through the feces. Recirculating bile acids access host tissues outside the intestines to impart systemic effects on host physiology. (B) BSHs cleave the amide bond in conjugated bile acids to open up the bile acid pool to increased complexity. The gut microbiota performs additional chemistry on deconjugated bile acids to generate the secondary bile acid pool, which can undergo enterohepatic circulation and be reconjugated in the liver. These transformations are illustrated to the right as conjugated CA is deconjugated, subjected to 7 α-dehydroxylation to become DCA, and subsequently reconjugated. (C) Monomeric BSH overlay from Bifidobacterium longum (PDB ID 2HEZ), Enteroccocus faecalis (PDB ID 4WL3), Lactobacillus salivarius (PDB ID 5HKE), and Clostridium perfringens (PDB ID 2BJF). Hydrolyzed TDCA in the CpBSH active site is coordinated by several loops that contain the most variation in the peptide backbone compared to the other structures. BSH, bile salt hydrolase; CA, cholic acid; CpBSH, C. perfringens BSH; DCA,; TDCA, taurodeoxycholic acid; PDB ID, Protein Data Bank ID.}, 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}, abstractNote={Antimicrobial drug concentrations in the gastrointestinal tract likely drive antimicrobial resistance in enteric bacteria. Our objective was to determine the concentration of ceftiofur and its metabolites in the gastrointestinal tract of steers treated with ceftiofur crystalline-free acid (CCFA) or ceftiofur hydrochloride (CHCL), determine the effect of these drugs on the minimum inhibitory concentration (MIC) of fecal Escherichia coli, and evaluate shifts in the microbiome. Steers were administered either a single dose (6.6 mg/kg) of CCFA or 2.2 mg/kg of CHCL every 24 hours for 3 days. Ceftiofur and its metabolites were measured in the plasma, interstitium, ileum and colon. The concentration and MIC of fecal E. coli and the fecal microbiota composition were assessed after treatment. The maximum concentration of ceftiofur was higher in all sampled locations of steers treated with CHCL. Measurable drug persisted longer in the intestine of CCFA-treated steers. There was a significant decrease in E. coli concentration (P = 0.002) within 24 hours that persisted for 2 weeks after CCFA treatment. In CHCL-treated steers, the mean MIC of ceftiofur in E. coli peaked at 48 hours (mean MIC = 20.45 ug/ml, 95% CI = 10.29–40.63 ug/ml), and in CCFA-treated steers, mean MIC peaked at 96 hours (mean MIC = 10.68 ug/ml, 95% CI = 5.47–20.85 ug/ml). Shifts in the microbiome of steers in both groups were due to reductions in Firmicutes and increases in Bacteroidetes. CCFA leads to prolonged, low intestinal drug concentrations, and is associated with decreased E. coli concentration, an increased MIC of ceftiofur in E. coli at specific time points, and shifts in the fecal microbiota. CHCL led to higher intestinal drug concentrations over a shorter duration. Effects on E. coli concentration and the microbiome were smaller in this group, but the increase in the MIC of ceftiofur in fecal E. coli was similar.}, 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} }
 @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}, abstractNote={ABSTRACT Bile acid biotransformation is a collaborative effort by the host and the gut microbiome. Host hepatocytes synthesize primary bile acids from cholesterol. Once these host-derived primary bile acids enter the gastrointestinal tract, the gut microbiota chemically modify them into secondary bile acids. Interest into the gut-bile acid-host axis is expanding in diverse fields including gastroenterology, endocrinology, oncology, and infectious disease. This review aims to 1) describe the physiologic aspects of collaborative bile acid metabolism by the host and gut microbiota; 2) to evaluate how gut microbes influence bile acid pools, and in turn how bile acid pools modulate the gut microbial community structure; 3) to compare species differences in bile acid pools; and lastly, 4) discuss the effects of ursodeoxycholic acid (UDCA) administration, a common therapeutic bile acid, on the gut microbiota-bile acid-host axis.}, number={2}, journal={GUT MICROBES}, author={Winston, Jenessa A. and Theriot, Casey M.}, year={2020}, month={Mar}, pages={158–171} }
 @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}, abstractNote={Clostridioides difficile is a significant public health threat, and diagnosis of this infection is challenging due to a lack of sensitivity in current diagnostic testing. In this issue of the JCI, Robinson et al. use a logistic regression model based on the fecal metabolome that is able to distinguish between patients with non-C. difficile diarrhea and C. difficile infection, and to some degree, patients who are asymptomatically colonized with C. difficile. The authors construct a metabolic definition of human C. difficile infection, which could improve diagnostic accuracy and aid in the development of targeted therapeutics against this pathogen.}, 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}, abstractNote={Antibiotics are considered to be the first line of treatment for mild to moderately severe Clostridium difficile infection (CDI) in humans. However, antibiotics are also risk factors for CDI as they decrease colonization resistance against C. difficile by altering the gut microbiota and metabolome. Finding compounds that selectively inhibit different stages of the C. difficile life cycle, while sparing the indigenous gut microbiota is important for the development of alternatives to standard antibiotic treatment. 2-aminoimidazole (2-AI) molecules are known to disrupt bacterial protection mechanisms in antibiotic resistant bacteria such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus, but are yet to be evaluated against C. difficile. A comprehensive small molecule-screening pipeline was developed to investigate how novel small molecules affect different stages of the C. difficile life cycle (growth, toxin, and sporulation) in vitro, and a library of commensal bacteria that are associated with colonization resistance against C. difficile. The initial screening tested the efficacy of eleven 2-AI molecules (compound 1 through 11) against C. difficile R20291 compared to a vancomycin (2 μg/ml) control. Molecules were selected for their ability to inhibit C. difficile growth, toxin activity, and sporulation. Further testing included growth inhibition of other C. difficile strains (CD196, M68, CF5, 630, BI9, M120) belonging to distinct PCR ribotypes, and a commensal panel (Bacteroides fragilis, B. thetaiotaomicron, C. scindens, C. hylemonae, Lactobacillus acidophilus, L. gasseri, Escherichia coli, B. longum subsp. infantis). Three molecules compound 1 and 2, and 3 were microbicidal, whereas compounds 4, 7, 9, and 11 inhibited toxin activity without affecting the growth of C. difficile strains and the commensal microbiota. The antimicrobial and anti-toxin effects of 2-AI molecules need to be further characterized for mode of action and validated in a mouse model of CDI.}, 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}, abstractNote={Over the past 10 years, microbiome research has focused on defining the structures associated with different disease states in multiple systems, but has fallen short on showing causation. Prior omic studies have generated many new hypotheses, but moving forward we need to start dissecting the function of each bacterium alone and in concert with complex bacterial communities in well-characterized systems.}, 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}, abstractNote={Objective: The intestinal concentrations of antimicrobial drugs that select for resistance in fecal bacteria of cattle are poorly understood. Our objective was to associate active drug concentrations in the intestine of steers with changes in the resistance profile and composition of the fecal microbiome. Methods: Steers were administered either a single dose (12.5 mg/kg) or 3 multiple doses (5 mg/kg) of enrofloxacin subcutaneously every 24 h. Enrofloxacin and ciprofloxacin concentrations in intestinal fluid were measured over 96 h, and the abundance and MIC of E. coli in culture and the composition of the fecal microbiota by 16S rRNA gene sequencing were assessed over 192 h after initial treatment. Results: Active drug concentrations in the ileum and colon exceeded plasma and interstitial fluid concentrations, but were largely eliminated by 48 h after the last dose. The concentration of E. coli in the feces significantly decreased during peak drug concentrations, but returned to baseline by 96 h in both groups. The median MIC of E. coli isolates increased for 24 h in the single dose group, and for 48 h in the multiple dose group. The median MIC was higher in the multiple dose group when compared to the single dose group starting 12 h after the initial dose. The diversity of the fecal microbiota did not change in either treatment group, and taxa-specific changes were primarily seen in phyla commonly associated with the rumen. Conclusions: Both dosing regimens of enrofloxacin achieve high concentrations in the intestinal lumen, and the rapid elimination mitigates long-term impacts on fecal E. coli resistance and the microbiota.}, 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}, abstractNote={A significant proportion of individuals develop recurrent Clostridium difficile infection (CDI) following initial disease. Fecal microbiota transplantation (FMT), a highly effective treatment method for recurrent CDI, has been demonstrated to induce microbiota recovery. One of the proposed functions associated with restoration of colonization resistance against C. difficile has been recovery of bile acid metabolism. In this study, we aimed to assess recovery of short chain fatty acids (SCFAs) in addition to bile acids alongside microbial community structure in six patients with recurrent CDI following treatment with FMT over time. Using 16S rRNA gene-based sequencing, we observed marked similarity of the microbiota between recipients following FMT (n = 6, sampling up to 6 months post-FMT) and their respective donors. Sustained increases in the levels of the SCFAs butyrate, acetate, and propionate were observed post-FMT, and variable recovery over time was observed in the secondary bile acids deoxycholate and lithocholate. To correlate these changes with specific microbial taxa at an individual level, we applied a generalized estimating equation approach to model metabolite concentrations with the presence of specific members of the microbiota. Metabolites that increased following FMT were associated with bacteria classified within the Lachnospiraceae, Ruminococcaceae, and unclassified Clostridiales families. In contrast, members of these taxa were inversely associated with primary bile acids. The longitudinal aspect of this study allowed us to characterize individualized patterns of recovery, revealing variability between and within patients following FMT.}, 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}, abstractNote={
            Clostridium difficile
            is a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring
            C. difficile
            growth. Here we used metabolomics and transcriptomics to define the gut environment after antibiotics and during the initial stages of
            C. difficile
            colonization and infection. We show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time and that
            C. difficile
            gene expression is consistent with their utilization by the bacterium
            in vivo
            . We employed an integrated approach to analyze the metabolome and transcriptome to identify associations between metabolites and transcripts. This highlighted the importance of key nutrients in the early stages of colonization, and the data provide a rationale for the development of therapies based on the use of bacteria that specifically compete for nutrients that are essential for
            C. difficile
            colonization and disease.
          }, 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}, abstractNote={
            Bile acids play an integral role in shaping the gut microbiota and host physiology by regulating metabolic signaling, weight gain, and serum cholesterol and liver triglyceride levels. Given these important roles of bile acids, we investigated the presence of bile salt hydrolase (BSH) in
            Lactobacillus
            genomes representing 170 different species, determined strain- and species-specific patterns of occurrences, and expanded on the diversity of the BSH repertoire in this genus. While our data showed that 28% of
            Lactobacillus
            species encode BSH proteins, these species are associated mainly with vertebrate-adapted niches, demonstrating selective pressure on lactobacilli to evolve to adapt to specific environments. These new data will allow targeted selection of specific strains of lactobacilli and BSH proteins for future mechanistic studies to explore their therapeutic potential for treating metabolic disorders.
          }, 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}, abstractNote={The changing epidemiology of Clostridium difficile infection over the past decades presents a significant challenge in the management of C. difficile associated diseases. The gastrointestinal tract microbiota provides colonization resistance against C. difficile, and growing evidence suggests that gut microbial derived secondary bile acids (SBAs) play a role. We hypothesized that the C. difficile life cycle; spore germination and outgrowth, growth, and toxin production, of strains that vary by age and ribotype will differ in their sensitivity to SBAs. C. difficile strains R20291 and CD196 (ribotype 027), M68 and CF5 (017), 630 (012), BI9 (001) and M120 (078) were used to define taurocholate (TCA) mediated spore germination and outgrowth, growth, and toxin activity in the absence and presence of gut microbial derived SBAs (deoxycholate, isodeoxycholate, lithocholate, isolithocholate, ursodeoxycholate, ω-muricholate, and hyodeoxycholate) found in the human and mouse large intestine. C. difficile strains varied in their rates of germination, growth kinetics, and toxin activity without the addition of SBAs. C. difficile M120, a highly divergent strain, had robust germination, growth, but significantly lower toxin activity compared to other strains. Many SBAs were able to inhibit TCA mediated spore germination and outgrowth, growth, and toxin activity in a dose dependent manner, but the level of inhibition and resistance varied across all strains and ribotypes. This study illustrates how clinically relevant C. difficile strains can have different responses when exposed to SBAs present in the gastrointestinal tract.}, 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}, abstractNote={Mounting evidence in humans supports an etiological role for the microbiota in inflammatory atherosclerosis. Atherosclerosis is a progressive disease characterized by accumulation of inflammatory cells and lipids in vascular tissue. While retention of lipoprotein into the sub-endothelial vascular layer is believed to be the initiating stimulus leading to the development of atherosclerosis, activation of multiple pathways related to vascular inflammation and endothelial dysfunction sustain the process by stimulating recruitment of leukocytes and immune cells into the sub-endothelial layer. The Gram-negative oral pathogen Porphyromonas gingivalis has been associated with the development and acceleration of atherosclerosis in humans and these observations have been validated in animal models. It has been proposed that common mechanisms of immune signaling link stimulation by lipids and pathogens to vascular inflammation. Despite the common outcome of P. gingivalis and lipid feeding on atherosclerosis progression, we established that these pro-atherogenic stimuli induced distinct gene signatures in the ApoE−/− mouse model of atherosclerosis. In this study, we further defined the distinct roles of dietary lipids and P. gingivalis infection on atherosclerosis progression and the gut microbiota. We demonstrate that diet-induced lipid lowering resulted in less atherosclerotic plaque in ApoE−/− mice compared to ApoE−/− mice continuously fed a Western diet. However, the effect of diet-induced lipid lowering on plaque accumulation was blunted by P. gingivalis infection. Using principal component analysis and hierarchical clustering, we demonstrate that dietary intervention as well as P. gingivalis infection result in distinct bacterial communities in fecal and cecal samples of ApoE−/− mice as compared to ApoE−/− mice continuously fed either a Western diet or a normal chow diet. Collectively, we identified distinct microbiota changes accompanying atherosclerotic plaque, suggesting a future avenue for investigation on the impact of the gut microbiota, diet, and P. gingivalis infection on atherosclerosis.}, 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}, abstractNote={Clostridium difficile is the leading cause of infectious diarrhea in hospitals and one of the most common healthcare associated infections. Antibiotics alter the normal gut microbiota and facilitate the colonization of enteric pathogens such as C. difficile. Our objective is to elucidate the role of bile acids and other mechanisms in providing colonization resistance against C. difficile. We formulated and analyzed differential equation models for microbial interactions in the gut and bile acid dynamics, as well as a combined model including both mechanisms. Our analysis indicates that bile acids do not prevent C. difficile colonization, but they regulate the onset of C. difficile colonization and growth after antibiotic perturbation. These results have implications in the development of novel ways to inhibit C. difficile infection.}, 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={
            Antibiotics alter the gastrointestinal microbiota, allowing for
            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
            C. difficile
            spore germination and also inhibit
            C. difficile
            growth
            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
            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
            C. difficile
            colonization, representing a mechanism of colonization resistance. Multiple secondary bile acids in the large intestine were able to inhibit
            C. difficile
            spore germination and growth at physiological concentrations and represent new targets to combat
            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}, abstractNote={Clostridium difficile is an anaerobic, gram-positive, spore-forming enteric pathogen that is associated with increasing morbidity and mortality and consequently poses an urgent threat to public health. Recurrence of a C. difficile infection (CDI) after successful treatment with antibiotics is high, occurring in 20-30% of patients, thus necessitating the discovery of novel therapeutics against this pathogen. Current animal models of CDI result in high mortality rates and thus do not approximate the chronic, insidious disease manifestations seen in humans with CDI. To evaluate therapeutics against C. difficile, a mouse model approximating human disease utilizing a clinically-relevant strain is needed. This protocol outlines the cefoperazone mouse model of CDI using a clinically-relevant and genetically-tractable strain, R20291. Techniques for clinical disease monitoring, C. difficile bacterial enumeration, toxin cytotoxicity, and histopathological changes throughout CDI in a mouse model are detailed in the protocol. Compared to other mouse models of CDI, this model is not uniformly lethal at the dose administered, allowing for the observation of a prolonged clinical course of infection concordant with the human disease. Therefore, this cefoperazone mouse model of CDI proves a valuable experimental platform to assess the effects of novel therapeutics on the amelioration of clinical disease and on the restoration of colonization resistance against C. difficile.}, 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}, abstractNote={Clostridium difficile is an anaerobic, Gram positive, spore-forming bacillus that is the leading cause of nosocomial gastroenteritis. Clostridium difficile infection (CDI) is associated with increasing morbidity and mortality, consequently posing an urgent threat to public health. Recurrence of CDI after successful treatment with antibiotics is high, thus necessitating discovery of novel therapeutics against this pathogen. Susceptibility to CDI is associated with alterations in the gut microbiota composition and bile acid metabolome, specifically a loss of microbial derived secondary bile acids. This review aims to summarize in vitro, ex vivo, and in vivo studies done by our group and others that demonstrate how secondary bile acids affect the different stages of the C. difficile life cycle. Understanding the dynamic interplay of C. difficile and microbial derived secondary bile acids within the gastrointestinal tract will shed light on how bile acids play a role in colonization resistance against C. difficile. Rational manipulation of secondary bile acids may prove beneficial as a treatment for patients with CDI.}, 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={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={ABSTRACT
          
            Recurrent
            Clostridium difficile
            infection (CDI) is of particular concern among health care-associated infections. The role of the microbiota in disease recovery is apparent given the success of fecal microbiota transplantation (FMT) for recurrent CDI. Here, we present a murine model of CDI relapse to further define the microbiota recovery following FMT. Cefoperazone-treated mice were infected with
            C. difficile
            630 spores and treated with vancomycin after development of clinical disease. Vancomycin treatment suppressed both
            C. difficile
            colonization and cytotoxin titers. However,
            C. difficile
            counts increased within 7 days of completing treatment, accompanied by relapse of clinical signs. The administration of FMT immediately after vancomycin cleared
            C. difficile
            and decreased cytotoxicity within 1 week. The effects of FMT on the gut microbiota community were detectable in recipients 1-day posttransplant. Conversely, mice not treated with FMT remained persistently colonized with high levels of
            C. difficile
            , and the gut microbiota in these mice persisted at low diversity. These results suggest that full recovery of colonization resistance against
            C. difficile
            requires the restoration of a specific community structure.
          }, 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}, abstractNote={ Antibiotics have significant and long-lasting effects on the intestinal microbiota and consequently reduce colonization resistance against pathogens, including Clostridium difficile. By altering the community structure of the gut microbiome, antibiotics alter the intestinal metabolome, which includes both host- and microbe-derived metabolites. The mechanisms by which antibiotics reduce colonization resistance against C. difficile are unknown yet important for development of preventative and therapeutic approaches against this pathogen. This review focuses on how antibiotics alter the structure of the gut microbiota and how this alters microbial metabolism in the intestine. Interactions between gut microbial products and C. difficile spore germination, growth, and toxin production are discussed. New bacterial therapies to restore changes in bacteria-driven intestinal metabolism following antibiotics will have important applications for treatment and prevention of C. difficile infection. }, 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{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}, abstractNote={ABSTRACT
          
            Antibiotics can play dual roles in
            Clostridium difficile
            infection (CDI); antibiotic treatment increases the risk of CDI, and antibiotics are used to treat CDI. The glycylcycline antibiotic tigecycline has broad antimicrobial activity, yet it is rarely associated with the development of CDI, presumably due to its activity against
            C. difficile
            . In this study, we investigated how tigecycline treatment affects the structure of the gut microbiota and susceptibility to CDI by treating mice with tigecycline (
            n
            = 20) or saline (
            n
            = 8) for 10 days. A sequence analysis of the bacterial 16S rRNA gene amplicons was used to monitor changes in the fecal microbiota. A subset of the mice was followed for 5 weeks after the end of treatment. The remaining mice were challenged with
            C. difficile
            strain VPI 10463 spores 2 days after the tigecycline treatment ended. Tigecycline treatment resulted in major shifts in the gut microbiota, including large decreases in
            Bacteroidetes
            levels and large increases in
            Proteobacteria
            levels. Mice with tigecycline-altered microbial communities were susceptible to challenge with
            C. difficile
            spores and developed clinical signs of severe CDI. Five weeks after the cessation of tigecycline treatment, the recovery of the bacterial community was incomplete and diversity was lower than in the untreated controls. Antibiotics with intrinsic activity against
            C. difficile
            can still alter the microbiota in a way that leads to susceptibility to CDI after discontinuation of the drug. These results indicate that microbiotic dynamics are key in the development of CDI, and a better understanding of these dynamics may lead to better strategies to prevent and treat this disease.
          }, 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}, abstractNote={Antibiotics can have significant and long-lasting effects on the gastrointestinal tract microbiota, reducing colonization resistance against pathogens including Clostridium difficile. Here we show that antibiotic treatment induces substantial changes in the gut microbial community and in the metabolome of mice susceptible to C. difficile infection. Levels of secondary bile acids, glucose, free fatty acids and dipeptides decrease, whereas those of primary bile acids and sugar alcohols increase, reflecting the modified metabolic activity of the altered gut microbiome. In vitro and ex vivo analyses demonstrate that C. difficile can exploit specific metabolites that become more abundant in the mouse gut after antibiotics, including the primary bile acid taurocholate for germination, and carbon sources such as mannitol, fructose, sorbitol, raffinose and stachyose for growth. Our results indicate that antibiotic-mediated alteration of the gut microbiome converts the global metabolic profile to one that favours C. difficile germination and growth. Antibiotics alter the intestinal microbiota and facilitate colonization of pathogens such as Clostridium difficile. Here, the authors show that antibiotic-induced shifts in the mouse gut microbiome are correlated with changes in levels of certain metabolites that C. difficilecan use for germination and growth.}, 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}, abstractNote={Clostridium difficile is the major cause of antibiotic-associated diarrhea and pseudomembranous colitis in healthcare settings. However, the host factors involved in the intestinal inflammatory response and pathogenesis of C. difficile infection (CDI) are largely unknown. Here we investigated the role of leukotrienes (LTs), a group of pro-inflammatory lipid mediators, in CDI. Notably, the neutrophil chemoattractant LTB4, but not cysteinyl (cys) LTs, was induced in the intestine of C57BL/6 mice infected with either C. difficile strain VPI 10463 or strain 630. Genetic or pharmacological ablation of LT production did not ameliorate C. difficile colitis or clinical signs of disease in infected mice. Histological analysis demonstrated that intestinal neutrophilic inflammation, edema and tissue damage in mice during acute and severe CDI were not modulated in the absence of LTs. In addition, CDI induced a burst of cytokines in the intestine of infected mice in a LT-independent manner. Serum levels of anti-toxin A immunoglobulin (Ig) G levels were also not modulated by endogenous LTs. Collectively, our results do not support a role for LTs in modulating host susceptibility to CDI in mice.}, 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={ABSTRACT
          
            Clostridium difficile
            infection (CDI) following antibiotic therapy is a major public health threat. While antibiotic disruption of the indigenous microbiota underlies the majority of cases of CDI, the early dynamics of infection in the disturbed intestinal ecosystem are poorly characterized. This study defines the dynamics of infection with
            C. difficile
            strain VPI 10463 throughout the gastrointestinal (GI) tract using a murine model of infection. After inducing susceptibility to
            C. difficile
            colonization via antibiotic administration, we followed the dynamics of spore germination, colonization, sporulation, toxin activity, and disease progression throughout the GI tract.
            C. difficile
            spores were able to germinate within 6 h postchallenge, resulting in the establishment of vegetative bacteria in the distal GI tract. Spores and cytotoxin activity were detected by 24 h postchallenge, and histopathologic colitis developed by 30 h. Within 36 h, all infected mice succumbed to infection. We correlated the establishment of infection with changes in the microbiota and bile acid profile of the small and large intestines. Antibiotic administration resulted in significant changes to the microbiota in the small and large intestines, as well as a significant shift in the abundance of primary and secondary bile acids.
            Ex vivo
            analysis suggested the small intestine as the site of spore germination. This study provides an integrated understanding of the timing and location of the events surrounding
            C. difficile
            colonization and identifies potential targets for the development of new therapeutic strategies.
          }, 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
          
            The glycylcycline antibiotic tigecycline was approved in 2005 for the treatment of complicated skin and soft tissue infections and complicated intra-abdominal infections. Tigecycline is broadly active against both Gram-negative and Gram-positive microorganisms, including
            Clostridium difficile
            . Tigecycline has a low MIC against
            C. difficile
            in vitro
            and thus may represent an alternate treatment for
            C. difficile
            infection (CDI). To assess the use of tigecycline for treatment of established CDI, 5- to 8-week-old C57BL/6 mice were colonized with
            C. difficile
            strain 630. After
            C. difficile
            colonization was established, mice (
            n
            = 10 per group) were treated with either a 5-day course of tigecycline (6.25 mg/kg every 12 h subcutaneously) or a 5-day course of vancomycin (0.4 mg/ml in drinking water) and compared to infected, untreated control mice. Mice were evaluated for clinical signs of CDI throughout treatment and at 1 week posttreatment to assess potential for disease development. Immediately following a treatment course,
            C. difficile
            was not detectable in the feces of vancomycin-treated mice but remained detectable in feces from tigecycline-treated and untreated control mice. Toxin activity and histopathological inflammation and edema were observed in the ceca and colons of untreated mice; tigecycline- and vancomycin-treated mice did not show such changes directly after treatment. One week after the conclusion of either antibiotic treatment,
            C. difficile
            load, toxin activity, and histopathology scores increased in the cecum and colon, indicating that
            C. difficile
            -associated disease occurred.
            In vitro
            growth studies confirmed that subinhibitory concentrations of tigecycline were able to suppress toxin activity and spore formation of
            C. difficile
            , whereas vancomycin did not. Taken together, these data show how tigecycline is able to alter
            C. difficile
            pathogenesis in a mouse model of CDI.
          }, 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_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}, abstractNote={SummaryOur previous work has shown the significant up‐regulation of Il22 and increased phosphorylation of signal transducer and activator of transcription 3 (STAT3) as part of the mucosal inflammatory response to Clostridium difficile infection in mice. Others have shown that phosphorylation of STAT3 at mucosal surfaces includes interleukin‐22 (IL‐22) and CD160‐mediated components. The current study sought to determine the potential role(s) of IL‐22 and/or CD160 in the mucosal response to C. difficile infection. Clostridium difficile‐infected mice treated with anti‐IL‐22, anti‐CD160 or a combination of the two showed significantly reduced STAT3 phosphorylation in comparison to C. difficile‐infected mice that had not received either antibody. In addition, C. difficile‐infected mice treated with anti‐IL‐22/CD160 induced a smaller set of genes, and at significantly lower levels than the untreated C. difficile‐infected mice. The affected genes included pro‐inflammatory chemokines and cytokines, and anti‐microbial peptides. Furthermore, histopathological and flow cytometric assessments both showed a significantly reduced influx of neutrophils in C. difficile‐infected mice treated with anti‐IL‐22/CD160. These data demonstrate that IL‐22 and CD160 are together responsible for a significant fraction of the colonic STAT3 phosphorylation in C. difficile infection. They also underscore the additive effects of IL‐22 and CD160 in mediating both the pro‐inflammatory and pro‐survival aspects of the host mucosal response in this infection.}, 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{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}, abstractNote={SummaryThe current study sought to delineate the gene expression profile of the host response in the caecum and colon during acute infection with Clostridium difficile in a mouse model of infection, and to investigate the nature of the unfolded protein response in this process. The infected mice displayed a significant up‐regulation in the expression of chemokines (Cxcl1, Cxcl2 and Ccl2), numerous pro‐inflammatory cytokines (Ifng, Il1b, Il6, and Il17f), as well as Il22 and a number of anti‐microbial peptides (Defa1, Defa28, Defb1, Slpi and Reg3g) at the site(s) of infection. This was accompanied by a significant influx of neutrophils, dendritic cells, cells of the monocyte/macrophage lineage and all major subsets of lymphocytes to these site(s). However, CD4 T cells of the untreated and C. difficile‐infected mice expressed similar levels of CD69 and CD25. Neither tissue had up‐regulated levels of Tbx21, Gata3 or Rorc. The caeca and colons of the infected mice showed a significant increase in eukaryotic initiation factor 2α (eIF2α) phosphorylation, but neither the splicing of Xbp1 nor the up‐regulation of endoplasmic reticulum chaperones, casting doubt on the full‐fledged induction of the unfolded protein response by C. difficile. They also displayed significantly higher phosphorylation of AKT and signal transducer and activator of transcription 3 (STAT3), an indication of pro‐survival signalling. These data underscore the local, innate, pro‐inflammatory nature of the response to C. difficile and highlight eIF2α phosphorylation and the interleukin‐22–pSTAT3–RegIIIγ axis as two of the pathways that could be used to contain and counteract the damage inflicted on the intestinal epithelium.}, 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}, abstractNote={Antibiotics disturb the gastrointestinal tract microbiota and in turn reduce colonization resistance against Clostridium difficile. The mechanism for this loss of colonization resistance is still unknown but likely reflects structural (microbial) and functional (metabolic) changes to the gastrointestinal tract. Members of the gut microbial community shape intestinal metabolism that provides nutrients and ultimately supports host immunity. This review will discuss how antibiotics alter the structure of the gut microbiota and how this impacts bacterial metabolism in the gut. It will also explore the chemical requirements for C. difficile germination, growth, toxin production and sporulation. Many of the metabolites that influence C. difficile physiology are products of gut microbial metabolism including bile acids, carbohydrates and amino acids. To restore colonization resistance against C. difficile after antibiotics a targeted approach restoring both the structure and function of the gastrointestinal tract is needed.}, 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}, abstractNote={Campylobacter jejuni is a major human pathogen and a leading cause of bacterial derived gastroenteritis worldwide. C. jejuni regulates gene expression under various environmental conditions and stresses, indicative of its ability to survive in diverse niches. Despite this ability to highly regulate gene transcription, C. jejuni encodes few transcription factors and its genome lacks many canonical transcriptional regulators. High throughput deep sequencing of mRNA transcripts (termed RNAseq) has been used to study the transcriptome of many different organisms, including C. jejuni; however, this technology has yet to be applied to defining the transcriptome of C. jejuni during in vivo colonization of its natural host, the chicken. In addition to its use in profiling the abundance of annotated genes, RNAseq is a powerful tool for identifying and quantifying, as-of-yet, unknown transcripts including non-coding regulatory RNAs, 5’ untranslated regulatory elements, and anti-sense transcripts. Here we report the complete transcriptome of C. jejuni during colonization of the chicken cecum and in two different in vitro growth phases using strand-specific RNAseq. Through this study, we identified over 250 genes differentially expressed in vivo in addition to numerous putative regulatory RNAs, including trans-acting non-coding RNAs and anti-sense transcripts. These latter potential regulatory elements were not identified in two prior studies using ORF-based microarrays, highlighting the power and value of the RNAseq approach. Our results provide new insights into how C. jejuni responds and adapts to the cecal environment and reveals new functions involved in colonization of its natural host.}, 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}, abstractNote={The toxin-producing bacterium C. difficile is the leading cause of antibiotic-associated colitis, with an estimated 500,000 cases C. difficile infection (CDI) each year in the US with a cost approaching 3 billion dollars. Despite the significance of CDI, the pathogenesis of this infection is still being defined. The recent development of tractable murine models of CDI will help define the determinants of C. difficile pathogenesis in vivo. To determine if cefoperazone-treated mice could be utilized to reveal differential pathogenicity of C. difficile strains, 5–8 week old C57BL/6 mice were pretreated with a 10 d course of cefoperazone administered in the drinking water. Following a 2-d recovery period without antibiotics, the animals were orally challenged with C. difficile strains chosen to represent the potential range of virulence of this organism from rapidly fatal to nonpathogenic. Animals were monitored for loss of weight and clinical signs of colitis. At the time of harvest, C. difficile strains were isolated from cecal contents and the severity of colitis was determined by histopathologic examination of the cecum and colon. Cefoperazone treated mice challenged with C. difficile strains VPI 10463 and BI1 exhibited signs of severe colitis while infection with 630 and F200 was subclinical. This increased clinical severity was correlated with more severe histopathology with significantly more edema, inflammation and epithelial damage encountered in the colons of animals infected with VPI 10463 and BI1. Disease severity also correlated with levels of C. difficile cytotoxic activity in intestinal tissues and elevated blood neutrophil counts. Cefoperazone treated mice represent a useful model of C. difficile infection that will help us better understand the pathogenesis and virulence of this re-emerging pathogen.}, 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}, abstractNote={Prolidases hydrolyze Xaa-Pro dipeptides and can also cleave the P-F and P-O bonds found in organophosphorus (OP) compounds, including the nerve agents soman and sarin.Ph1prol (PH0974) has previously been isolated and characterized fromPyrococcus horikoshiiand was shown to have higher catalytic activity over a broader pH range, higher affinity for metal, and increased thermostability compared toP. furiosusprolidase,Pfprol (PF1343). To obtain a better enzyme for OP nerve agent decontamination and to investigate the structural factors that may influence protein thermostability and thermoactivity, randomly mutatedPh1prol enzymes were prepared. FourPh1prol mutants (A195T/G306S-, Y301C/K342N-, E127G/E252D-, and E36V-Ph1prol) were isolated which had greater thermostability and improved activity over a broader range of temperatures against Xaa-Pro dipeptides and OP nerve agents compared to wild typePyrococcusprolidases.}, 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}, abstractNote={Clostridium difficile infection (CDI) arises in the setting of antibiotic administration where disruption of the normal indigenous gut microbiota leads to susceptibility to C. difficile colonization and colitis. Using a murine model of CDI, we demonstrate that changes in the community structure of the indigenous gut microbiota are associated with the loss of colonization resistance against C. difficile. Several antibiotic regimens were tested in combination for the ability to overcome colonization resistance, including a five antibiotic cocktail consisting of kanamycin, gentamicin, colistin, metronidazole, and vancomycin administered in drinking water for three days, a single intraperitoneal dose of clindamycin or 10 days of cefoperazone in drinking water. Following antibiotic treatment animals were challenged with 105 colony forming units of C. difficile strain VPI 10463 via oral gavage. Animals that received the antibiotic cocktail and clindamycin prior to C. difficile challenge followed one of two clinical courses, either becoming clinically ill and moribund within 2-4 days post challenge, or remaining clinically well. Animals that became clinically ill developed histologically severe colitis. These histopathologic findings were significantly less severe in animals that remained clinically well. Analysis of 16S rRNA gene sequences retrieved from gut tissue at necropsy demonstrated that Proteobacteria dominated the gut microbiota in clinically ill animals. In contrast, the gut microbial community of clinically well animals more closely resembled untreated animals, which were dominated by members of the Firmicutes. All animals that received cefoperazone treatment prior to C. difficile challenge were clinically ill and moribund by 2-5 days post challenge in a dose dependent manner. The gut communities in these animals were dominated by C.difficile suggesting that cefoperazone treatment resulted in a greater loss in colonization resistance. Thus, the severity of colitis that arises in this system reflects the interplay between the expansion of C. difficile in the gut community and the ecologic dynamics of the indigenous microbial community as it recovers from antibiotic perturbation. We demonstrate that altering the balance of these two opposing processes alters clinical outcome and thus may lead to novel preventative and therapeutic approaches for CDI.}, 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}, abstractNote={There are classes of microbial enzymes that have the ability to degrade harmful organophosphorus (OP) compounds that are present in some pesticides and nerve agents. To date, the most studied and potentially important OP-degrading enzymes are organophosphorus hydrolase (OPH) and organophosphorus acid anhydrolase (OPAA), which have both been characterized from a number of organisms. Here we provide an update of what is experimentally known about OPH and OPAA to include their structures, substrate specificity, and catalytic properties. Current and future potential applications of these enzymes in the hydrolysis of OP compounds are also addressed.}, 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}, abstractNote={Prolidase isolated from the hyperthermophilic archaeon Pyrococcus furiosus has potential for application for decontamination of organophosphorus compounds in certain pesticides and chemical warfare agents under harsh conditions. However, current applications that use an enzyme-based cocktail are limited by poor long-term enzyme stability and low reactivity over a broad range of temperatures. To obtain a better enzyme for OP nerve agent decontamination and to investigate structural factors that influence protein thermostability and thermoactivity, randomly mutated P. furiosus prolidases were prepared by using XL1-red-based mutagenesis and error-prone PCR. An Escherichia coli strain JD1 (lambdaDE3) (auxotrophic for proline [DeltaproA] and having deletions in pepQ and pepP dipeptidases with specificity for proline-containing dipeptides) was constructed for screening mutant P. furiosus prolidase expression plasmids. JD1 (lambdaDE3) cells were transformed with mutated prolidase expression plasmids and plated on minimal media supplemented with 50 muM Leu-Pro as the only source of proline. By using this positive selection, Pyrococcus prolidase mutants with improved activity over a broader range of temperatures were isolated. The activities of the mutants over a broad temperature range were measured for both Xaa-Pro dipeptides and OP nerve agents, and the thermoactivity and thermostability of the mutants were determined.}, 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}, abstractNote={Prolidases hydrolyze the unique bond between X-Pro dipeptides and can also cleave the P-F and P-O bonds found in organophosphorus compounds, including the nerve agents, soman and sarin. The advantages of using hyperthermophilic enzymes in biodetoxification strategies are based on their enzyme stability and efficiency. Therefore, it is advantageous to examine new thermostable prolidases for potential use in biotechnological applications. Two thermostable prolidase homologs, PH1149 and PH0974, were identified in the genome of Pyrococcus horikoshii based on their sequences having conserved metal binding and catalytic amino acid residues that are present in other known prolidases, such as the previously characterized Pyrococcus furiosus prolidase. These P. horikoshii prolidases were expressed recombinantly in the Escherichia coli strain BL21 (lambdaDE3), and both were shown to function as proline dipeptidases. Biochemical characterization of these prolidases shows they have higher catalytic activities over a broader pH range, higher affinity for metal and are more stable compared to P. furiosus prolidase. This study has important implications for the potential use of these enzymes in biotechnological applications and provides further information on the functional traits of hyperthermophilic proteins, specifically metalloenzymes.}, 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-} }