201
|
McCarville JL, Chen GY, Cuevas VD, Troha K, Ayres JS. Microbiota Metabolites in Health and Disease. Annu Rev Immunol 2020; 38:147-170. [DOI: 10.1146/annurev-immunol-071219-125715] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolism is one of the strongest drivers of interkingdom interactions—including those between microorganisms and their multicellular hosts. Traditionally thought to fuel energy requirements and provide building blocks for biosynthetic pathways, metabolism is now appreciated for its role in providing metabolites, small-molecule intermediates generated from metabolic processes, to perform various regulatory functions to mediate symbiotic relationships between microbes and their hosts. Here, we review recent advances in our mechanistic understanding of how microbiota-derived metabolites orchestrate and support physiological responses in the host, including immunity, inflammation, defense against infections, and metabolism. Understanding how microbes metabolically communicate with their hosts will provide us an opportunity to better describe how a host interacts with all microbes—beneficial, pathogenic, and commensal—and an opportunity to discover new ways to treat microbial-driven diseases.
Collapse
Affiliation(s)
- Justin L. McCarville
- Molecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Grischa Y. Chen
- Molecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Víctor D. Cuevas
- Molecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Katia Troha
- Molecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Janelle S. Ayres
- Molecular and Systems Physiology Laboratory, Gene Expression Laboratory, NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| |
Collapse
|
202
|
Impact of deoxycholate on Clostridioides difficile growth, toxin production, and sporulation. Heliyon 2020; 6:e03717. [PMID: 32322715 PMCID: PMC7160582 DOI: 10.1016/j.heliyon.2020.e03717] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/27/2020] [Accepted: 03/30/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose Bile acids play an important role in Clostridioides difficile life cycle. Deoxycholate (DCA), one of the most abundant secondary bile acids, is known to inhibit vegetative growth and toxin production. However, limited data are available on the role of DCA on C. difficile sporulation. Here, we investigated the phenotypic and genotypic impact of DCA on the growth, toxin production, and sporulation of C. difficile. Methodology Four genetically divergent C. difficile strains were cultured in nutrient-rich broth with and without DCA at various concentrations, and growth activity was evaluated for each strain. Cytotoxicity assays using culture supernatants from cells grown in nutrient-rich broth with and without 0.01% DCA were conducted. Sporulation efficiency was determined using sporulation media with and without 0.01% DCA. Transcript levels of tcdB and spo0A were analyzed using quantitative reverse-transcription polymerase chain reaction. Results We found that DCA led to growth reduction in a dose-depended manner and regulated toxin production by repressing tcdB expression during vegetative growth. To our knowledge, we have also provided the first evidence that DCA reduces C. difficile sporulation efficiency through the downregulation of spo0A expression during the sporulation stage. Conclusions DCA modulates C. difficile sporulation, vegetative growth, and toxin production.
Collapse
|
203
|
Song M, Yang Q, Zhang F, Chen L, Su H, Yang X, He H, Liu F, Zheng J, Ling M, Lai X, Zhu X, Wang L, Gao P, Shu G, Jiang Q, Wang S. Hyodeoxycholic acid (HDCA) suppresses intestinal epithelial cell proliferation through FXR-PI3K/AKT pathway, accompanied by alteration of bile acids metabolism profiles induced by gut bacteria. FASEB J 2020; 34:7103-7117. [PMID: 32246800 DOI: 10.1096/fj.201903244r] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/03/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022]
Abstract
Bile acids (BAs) have been implicated in regulation of intestinal epithelial signaling and function. This study aimed to investigate the effects of hyodeoxycholic acid (HDCA) on intestinal epithelial cell proliferation and explore the underlying mechanisms. IPEC-J2 cells and weaned piglets were treated with HDCA and the contributions of cellular signaling pathways, BAs metabolism profiles and gut bacteria were assessed. In vitro, HDCA suppressed IPEC-J2 proliferation via the BAs receptor FXR but not TGR5. In addition, HDCA inhibited the PI3K/AKT pathway, while knockdown of FXR or constitutive activation of AKT eliminated the inhibitory effects of HDCA, suggesting that FXR-dependent inhibition of PI3K/AKT pathway was involved in HDCA-suppressed IPEC-J2 proliferation. In vivo, dietary HDCA inhibited intestinal expression of proliferative markers and PI3K/AKT pathway in weaned piglets. Meanwhile, HDCA altered the BAs metabolism profiles, with decrease in primary BA and increase in total and secondary BAs in feces, and reduction of conjugated BAs in serum. Furthermore, HDCA increased abundance of the gut bacteria associated with BAs metabolism, and thereby induced BAs profiles alternation, which might indirectly contribute to HDCA-suppressed cell proliferation. Together, HDCA suppressed intestinal epithelial cell proliferation through FXR-PI3K/AKT signaling pathway, accompanied by alteration of BAs metabolism profiles induced by gut bacteria.
Collapse
Affiliation(s)
- Min Song
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Qiang Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Fenglin Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Lin Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Han Su
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Xiaohua Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Haiwen He
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Fangfang Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Jisong Zheng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Mingfa Ling
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Xumin Lai
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Xiaotong Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Lina Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Ping Gao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Gang Shu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Qingyan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| | - Songbo Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, College of Animal Science, South China Agricultural University, Guangzhou, P. R. China.,National Engineering Research Center for Breeding Swine Industry and ALLTECH-SCAU Animal Nutrition Control Research Alliance, South China Agricultural University, Guangzhou, P. R. China
| |
Collapse
|
204
|
Bile Acid Profile and its Changes in Response to Cefoperazone Treatment in MR1 Deficient Mice. Metabolites 2020; 10:metabo10040127. [PMID: 32225042 PMCID: PMC7241087 DOI: 10.3390/metabo10040127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/08/2023] Open
Abstract
Mucosal associated invariant T-cells (MAIT cells) are activated following recognition of bacterial antigens (riboflavin intermediates) presented on major histocompatibility complex class I-related molecule (MR1). Our previous study showed that MR1−/− knock-out (KO) mice (lacking MAIT cells) harbor a unique microbiota that is resistant to antibiotic disruption and Clostridioides difficile colonization. While we have characterized the microbiota of this mouse strain, changes in global metabolic activity in these KO mice have not been assessed. Here, LC/MS-based untargeted metabolomics was applied to investigate the differences in the metabolome, specifically in the bile acid (BA) profile of wild-type (WT) and MR1−/− KO mice, as well as how antibiotics change these profiles. BA changes were evaluated in the intestinal content, cecum content, and stool samples from MR1−/− mice and WT mice treated with cefoperazone (Cef). Fecal pellets were collected daily and both intestinal and cecal contents were harvested at predetermined endpoints on day 0 (D0), day 1 (D1), day 3 (D3), and day 5 (D5). KO mice exhibited no changes in 6-hydroxymethyl-8-D-ribityllumazine (rRL-6-CH2OH; an MR1-restricted riboflavin derivative) in the stool samples at either time point vs. D0, while WT mice showed significant decreases in rRL-6-CH2OH in the stool samples on all treatment days vs. D0. Metabolomics analysis from cecal and stool samples showed that KO mice had more total BA intensity (KO/WT = ~1.7 and ~3.3 fold higher) than that from WT mice prior to Cef treatment, while the fold change difference (KO/WT = ~4.5 and ~4.4 fold) increased after five days of Cef treatment. Both KO and WT mice showed decreases in total BA intensity in response to Cef treatment, however, less dramatic decreases were present in KO vs. WT mice. Increases in taurocholic acid (TCA) intensity and decreases in deoxycholic acid (DCA) intensity in the stool samples from WT mice were associated with the depletion of certain gut bacteria, which was consistent with the previously reported microbiome data. Furthermore, the non-detected TCA and relatively higher DCA intensity in the KO mice might be related to Clostridioides difficile infection resistance, although this needs further investigation.
Collapse
|
205
|
Kester JC, Brubaker DK, Velazquez J, Wright C, Lauffenburger DA, Griffith LG. Clostridioides difficile-Associated Antibiotics Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms. Antimicrob Agents Chemother 2020; 64:e01404-19. [PMID: 31988098 PMCID: PMC7179307 DOI: 10.1128/aac.01404-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/04/2020] [Indexed: 12/16/2022] Open
Abstract
A clinically relevant risk factor for Clostridioides difficile-associated disease (CDAD) is recent antibiotic treatment. Although broad-spectrum antibiotics have been shown to disrupt the structure of the gut microbiota, some antibiotics appear to increase CDAD risk without being highly active against intestinal anaerobes, suggesting direct nonantimicrobial effects. We examined cell biological effects of antibiotic exposure that may be involved in bacterial pathogenesis using an in vitro germfree human colon epithelial culture model. We found a marked loss of mucosal barrier and immune function with exposure to the CDAD-associated antibiotics clindamycin and ciprofloxacin, distinct from the results of pretreatment with an antibiotic unassociated with CDAD, tigecycline, which did not reduce innate immune or mucosal barrier functions. Importantly, pretreatment with CDAD-associated antibiotics sensitized mucosal barriers to C. difficile toxin activity in primary cell-derived enteroid monolayers. These data implicate commensal-independent gut mucosal barrier changes in the increased risk of CDAD with specific antibiotics and warrant further studies in in vivo systems. We anticipate this work to suggest potential avenues of research for host-directed treatment and preventive therapies for CDAD.
Collapse
Affiliation(s)
- Jemila C Kester
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jason Velazquez
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Charles Wright
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
206
|
Valdés-Duque BE, Giraldo-Giraldo NA, Jaillier-Ramírez AM, Giraldo-Villa A, Acevedo-Castaño I, Yepes-Molina MA, Barbosa-Barbosa J, Barrera-Causil CJ, Agudelo-Ochoa GM. Stool Short-Chain Fatty Acids in Critically Ill Patients with Sepsis. J Am Coll Nutr 2020; 39:706-712. [PMID: 32163012 DOI: 10.1080/07315724.2020.1727379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Objective: To determine the concentration of stool short-chain fatty acids (SCFAs) in critically ill patients with sepsis and to compare the results between the critically ill patient and the control group.Methods: This descriptive, multicenter, observational study was conducted in five health institutions. Over a 6-month study period, critically ill patients with sepsis who were admitted to the intensive care unit (ICU) and met the inclusion criteria were enrolled, and a control, paired by age and sex, was recruited for each patient. A spontaneous stool sample was collected from each participant and a gas chromatograph coupled to a mass spectrometer (Agilent 7890/MSD 5975 C) was used to measure the concentrations SCFAs.Results: The final sample included 44 patients and 45 controls. There were no differences in the age and sex distributions between the groups (p > 0.05). According to body mass index (BMI), undernutrition was more prevalent among critically ill patients, and BMI in control subjects was most frequently classified as overweight (p = 0.024). Propionic acid, acetic acid, butyric acid, and isobutyric acid concentrations were significantly lower in the critically ill patient group than in the control group (p = 0.000). No association with outcome variables (complications, ICU stay, and discharge condition) was found in the patients, and patients diagnosed with infection on ICU admission showed significant decreases in butyric and isobutyric acid concentrations with respect to other diagnostic criteria (p < 0.05).Conclusions: The results confirm significantly lower concentrations of stool SCFAs in critically ill patients with sepsis than in control subjects. Due to its role in intestinal integrity, barrier function, and anti-inflammatory effect, maintaining the concentration of SCFAs may be important in the ICU care protocols of the critical patient.
Collapse
Affiliation(s)
- Beatriz E Valdés-Duque
- Bioscience Research Group, Institución Universitaria Colegio Mayor de Antioquia - IUCMA, Medellín, Antioquia, Colombia
| | - Nubia A Giraldo-Giraldo
- Food and Human Nutrition Research Group, Universidad de Antioquia - UdeA, Medellín, Antioquia, Colombia
| | - Ana M Jaillier-Ramírez
- Departamento de nutrición, Hospital Universitario San Vicente Fundación Rionegro, Rionegro, Antioquia, Colombia
| | - Adriana Giraldo-Villa
- Departamento de nutrición clínica, Hospital Pablo Tobón Uribe, Medellín, Antioquia, Colombia
| | - Irene Acevedo-Castaño
- Departamento de nutrición y dietética, Hospital General, Medellín, Antioquia, Colombia
| | - Mónica A Yepes-Molina
- Departamento de nutrición y dietética, Hospital Universitario San Vicente Fundación Medellín, Medellín, Antioquia, Colombia
| | - Janeth Barbosa-Barbosa
- Departamento de nutrición, área de soporte nutricional, Clínica Las Américas, Medellín, Antioquia, Colombia
| | - Carlos J Barrera-Causil
- Research Group in Teaching and Modeling in Applied Exact Sciences, Instituto Tecnológico Metropolitano - ITM, Medellín, Antioquia, Colombia
| | - Gloria M Agudelo-Ochoa
- Food and Human Nutrition Research Group, Universidad de Antioquia - UdeA, Medellín, Antioquia, Colombia
| |
Collapse
|
207
|
Shen A. Clostridioides difficile Spores: Bile Acid Sensors and Trojan Horses of Transmission. Clin Colon Rectal Surg 2020; 33:58-66. [PMID: 32104157 DOI: 10.1055/s-0040-1701230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Gram-positive, spore-forming bacterium, Clostridioides difficile is the leading cause of healthcare-associated infections in the United States, although it also causes a significant number of community-acquired infections. C. difficile infections, which range in severity from mild diarrhea to toxic megacolon, cost more to treat than matched infections, with an annual treatment cost of approximately $6 billion for almost half-a-million infections. These high-treatment costs are due to the high rates of C. difficile disease recurrence (>20%) and necessity for special disinfection measures. These complications arise in part because C. difficile makes metabolically dormant spores, which are the major infectious particle of this obligate anaerobe. These seemingly inanimate life forms are inert to antibiotics, resistant to commonly used disinfectants, readily disseminated, and capable of surviving in the environment for a long period of time. However, upon sensing specific bile salts in the vertebrate gut, C. difficile spores transform back into the vegetative cells that are responsible for causing disease. This review discusses how spores are ideal vectors for disease transmission and how antibiotics modulate this process. We also describe the resistance properties of spores and how they create challenges eradicating spores, as well as promote their spread. Lastly, environmental reservoirs of C. difficile spores and strategies for destroying them particularly in health care environments will be discussed.
Collapse
Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts
| |
Collapse
|
208
|
Donlan A, Petri WA. The Inflammasome and Type-2 Immunity in Clostridium difficile Infection. Clin Colon Rectal Surg 2020; 33:67-72. [PMID: 32104158 DOI: 10.1055/s-0040-1701231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Clostridium difficile (reclassified as " Clostridioides ") is the leading cause of hospital-acquired infections in the United States, and is associated with high-patient mortality and high rates of recurrence. Inflammasome priming and activation by the bacterial toxins, TcdA , TcdB , and C. difficile transferase (CDT), initiates a potent immune response that is characterized by interleukin- (IL) 8, IL-1β, and neutrophil recruitment, and is required for pathogen killing. However, it is becoming clearer that a strong inflammatory response during C. difficile infection can result in host tissue damage, and is associated with worse patient outcome. Recent work has begun to show that a type-2 immune response, most often associated with helminth infections, allergy, and asthma, may be protective during C. difficile infection. While the mechanisms through how this response protect are still unclear, there is evidence that it is mediated through eosinophil activity. This chapter will review the immune response to C. difficile, how the inflammasome signaling during infection can deleterious to the host, as well as the current understanding of a protective type-2 immunity. Understanding the host immune response may help to provide insight into novel approaches to prognosis markers, as well as how treat patient C. difficile infection without, or in addition to, antibiotics.
Collapse
Affiliation(s)
- Alexandra Donlan
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia
| | - William A Petri
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia.,Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia
| |
Collapse
|
209
|
Sinha SR, Haileselassie Y, Nguyen LP, Tropini C, Wang M, Becker LS, Sim D, Jarr K, Spear ET, Singh G, Namkoong H, Bittinger K, Fischbach MA, Sonnenburg JL, Habtezion A. Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation. Cell Host Microbe 2020; 27:659-670.e5. [PMID: 32101703 DOI: 10.1016/j.chom.2020.01.021] [Citation(s) in RCA: 405] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 12/22/2019] [Accepted: 01/24/2020] [Indexed: 12/24/2022]
Abstract
Secondary bile acids (SBAs) are derived from primary bile acids (PBAs) in a process reliant on biosynthetic capabilities possessed by few microbes. To evaluate the role of BAs in intestinal inflammation, we performed metabolomic, microbiome, metagenomic, and transcriptomic profiling of stool from ileal pouches (surgically created resevoirs) in colectomy-treated patients with ulcerative colitis (UC) versus controls (familial adenomatous polyposis [FAP]). We show that relative to FAP, UC pouches have reduced levels of lithocholic acid and deoxycholic acid (normally the most abundant gut SBAs), genes required to convert PBAs to SBAs, and Ruminococcaceae (one of few taxa known to include SBA-producing bacteria). In three murine colitis models, SBA supplementation reduces intestinal inflammation. This anti-inflammatory effect is in part dependent on the TGR5 bile acid receptor. These data suggest that dysbiosis induces SBA deficiency in inflammatory-prone UC patients, which promotes a pro-inflammatory state within the intestine that may be treated by SBA restoration.
Collapse
Affiliation(s)
- Sidhartha R Sinha
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Yeneneh Haileselassie
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Linh P Nguyen
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carolina Tropini
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Min Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Laren S Becker
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Davis Sim
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karolin Jarr
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Estelle T Spear
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gulshan Singh
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hong Namkoong
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael A Fischbach
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Justin L Sonnenburg
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Aida Habtezion
- Department of Medicine, Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
210
|
Jia ET, Liu ZY, Pan M, Lu JF, Ge QY. Regulation of bile acid metabolism-related signaling pathways by gut microbiota in diseases. J Zhejiang Univ Sci B 2020; 20:781-792. [PMID: 31489798 DOI: 10.1631/jzus.b1900073] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Over the past decade, there has been increasing attention on the interaction between microbiota and bile acid metabolism. Bile acids are not only involved in the metabolism of nutrients, but are also important in signal transduction for the regulation of host physiological activities. Microbial-regulated bile acid metabolism has been proven to affect many diseases, but there have not been many studies of disease regulation by microbial receptor signaling pathways. This review considers findings of recent research on the core roles of farnesoid X receptor (FXR), G protein-coupled bile acid receptor (TGR5), and vitamin D receptor (VDR) signaling pathways in microbial-host interactions in health and disease. Studying the relationship between these pathways can help us understand the pathogenesis of human diseases, and lead to new solutions for their treatments.
Collapse
Affiliation(s)
- Er-Teng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhi-Yu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing 210097, China
| | - Jia-Feng Lu
- Center of Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou 215002, China
| | - Qin-Yu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| |
Collapse
|
211
|
Bogatyrev SR, Rolando JC, Ismagilov RF. Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine. MICROBIOME 2020; 8:19. [PMID: 32051033 PMCID: PMC7017497 DOI: 10.1186/s40168-020-0785-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/05/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND The upper gastrointestinal tract plays a prominent role in human physiology as the primary site for enzymatic digestion and nutrient absorption, immune sampling, and drug uptake. Alterations to the small intestine microbiome have been implicated in various human diseases, such as non-alcoholic steatohepatitis and inflammatory bowel conditions. Yet, the physiological and functional roles of the small intestine microbiota in humans remain poorly characterized because of the complexities associated with its sampling. Rodent models are used extensively in microbiome research and enable the spatial, temporal, compositional, and functional interrogation of the gastrointestinal microbiota and its effects on the host physiology and disease phenotype. Classical, culture-based studies have documented that fecal microbial self-reinoculation (via coprophagy) affects the composition and abundance of microbes in the murine proximal gastrointestinal tract. This pervasive self-reinoculation behavior could be a particularly relevant study factor when investigating small intestine microbiota. Modern microbiome studies either do not take self-reinoculation into account, or assume that approaches such as single housing mice or housing on wire mesh floors eliminate it. These assumptions have not been rigorously tested with modern tools. Here, we used quantitative 16S rRNA gene amplicon sequencing, quantitative microbial functional gene content inference, and metabolomic analyses of bile acids to evaluate the effects of self-reinoculation on microbial loads, composition, and function in the murine upper gastrointestinal tract. RESULTS In coprophagic mice, continuous self-exposure to the fecal flora had substantial quantitative and qualitative effects on the upper gastrointestinal microbiome. These differences in microbial abundance and community composition were associated with an altered profile of the small intestine bile acid pool, and, importantly, could not be inferred from analyzing large intestine or stool samples. Overall, the patterns observed in the small intestine of non-coprophagic mice (reduced total microbial load, low abundance of anaerobic microbiota, and bile acids predominantly in the conjugated form) resemble those typically seen in the human small intestine. CONCLUSIONS Future studies need to take self-reinoculation into account when using mouse models to evaluate gastrointestinal microbial colonization and function in relation to xenobiotic transformation and pharmacokinetics or in the context of physiological states and diseases linked to small intestine microbiome and to small intestine dysbiosis. Video abstract.
Collapse
Affiliation(s)
- Said R Bogatyrev
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Justin C Rolando
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, USA
| | - Rustem F Ismagilov
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, USA.
| |
Collapse
|
212
|
Ocvirk S, Wilson AS, Posma JM, Li JV, Koller KR, Day GM, Flanagan CA, Otto JE, Sacco PE, Sacco FD, Sapp FR, Wilson AS, Newton K, Brouard F, DeLany JP, Behnning M, Appolonia CN, Soni D, Bhatti F, Methé B, Fitch A, Morris A, Gaskins HR, Kinross J, Nicholson JK, Thomas TK, O'Keefe SJD. A prospective cohort analysis of gut microbial co-metabolism in Alaska Native and rural African people at high and low risk of colorectal cancer. Am J Clin Nutr 2020; 111:406-419. [PMID: 31851298 PMCID: PMC6997097 DOI: 10.1093/ajcn/nqz301] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/14/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Alaska Native (AN) people have the world's highest recorded incidence of sporadic colorectal cancer (CRC) (∼91:100,000), whereas rural African (RA) people have the lowest risk (<5:100,000). Previous data supported the hypothesis that diet affected CRC risk through its effects on the colonic microbiota that produce tumor-suppressive or -promoting metabolites. OBJECTIVES We investigated whether differences in these metabolites may contribute to the high risk of CRC in AN people. METHODS A cross-sectional observational study assessed dietary intake from 32 AN and 21 RA healthy middle-aged volunteers before screening colonoscopy. Analysis of fecal microbiota composition by 16S ribosomal RNA gene sequencing and fecal/urinary metabolites by 1H-NMR spectroscopy was complemented with targeted quantification of fecal SCFAs, bile acids, and functional microbial genes. RESULTS Adenomatous polyps were detected in 16 of 32 AN participants, but not found in RA participants. The AN diet contained higher proportions of fat and animal protein and less fiber. AN fecal microbiota showed a compositional predominance of Blautia and Lachnoclostridium, higher microbial capacity for bile acid conversion, and low abundance of some species involved in saccharolytic fermentation (e.g., Prevotellaceae, Ruminococcaceae), but no significant lack of butyrogenic bacteria. Significantly lower concentrations of tumor-suppressive butyrate (22.5 ± 3.1 compared with 47.2 ± 7.3 SEM µmol/g) coincided with significantly higher concentrations of tumor-promoting deoxycholic acid (26.7 ± 4.2 compared with 11 ± 1.9 µmol/g) in AN fecal samples. AN participants had lower quantities of fecal/urinary metabolites than RA participants and metabolite profiles correlated with the abundance of distinct microbial genera in feces. The main microbial and metabolic CRC-associated markers were not significantly altered in AN participants with adenomatous polyps. CONCLUSIONS The low-fiber, high-fat diet of AN people and exposure to carcinogens derived from diet or environment are associated with a tumor-promoting colonic milieu as reflected by the high rates of adenomatous polyps in AN participants.
Collapse
Affiliation(s)
- Soeren Ocvirk
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Annette S Wilson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joram M Posma
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, London, United Kingdom
| | - Jia V Li
- Section of Nutritional Research, Division of Digestive Diseases, Department of Metabolism, Digestion, and Reproduction, Imperial College, London, United Kingdom
- Centre for Digestive and Gut Health, Institution of Global Health Innovation, Imperial College, London, United Kingdom
| | - Kathryn R Koller
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Gretchen M Day
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Christie A Flanagan
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Jill Evon Otto
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Pam E Sacco
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Frank D Sacco
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Flora R Sapp
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Amy S Wilson
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Keith Newton
- Division of Gastroenterology, University of KwaZulu-Natal, Durban, South Africa
| | - Faye Brouard
- Manguzi Hospital, Manguzi, KwaZulu-Natal, South Africa
| | - James P DeLany
- Division of Endocrinology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Translational Research Institute for Metabolism and Diabetes, Advent Health, Orlando, FL, USA
| | - Marissa Behnning
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Corynn N Appolonia
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Devavrata Soni
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Faheem Bhatti
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Barbara Methé
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alison Morris
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - H Rex Gaskins
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James Kinross
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Jeremy K Nicholson
- Centre for Digestive and Gut Health, Institution of Global Health Innovation, Imperial College, London, United Kingdom
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Timothy K Thomas
- Clinical & Research Services, Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, AK, USA
| | - Stephen J D O'Keefe
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| |
Collapse
|
213
|
Insights into the Role of Human Gut Microbiota in Clostridioides difficile Infection. Microorganisms 2020; 8:microorganisms8020200. [PMID: 32023967 PMCID: PMC7074861 DOI: 10.3390/microorganisms8020200] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/29/2020] [Accepted: 01/31/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile infection (CDI) has emerged as a major health problem worldwide. A major risk factor for disease development is prior antibiotic use, which disrupts the normal gut microbiota by altering its composition and the gut’s metabolic functions, leading to the loss of colonization resistance and subsequent CDI. Data from human studies have shown that the presence of C. difficile, either as a colonizer or as a pathogen, is associated with a decreased level of gut microbiota diversity. The investigation of the gut’s microbial communities, in both healthy subjects and patients with CDI, elucidate the role of microbiota and improve the current biotherapeutics for patients with CDI. Fecal microbiota transplantation has a major role in managing CDI, aiming at re-establishing colonization resistance in the host gastrointestinal tract by replenishing the gut microbiota. New techniques, such as post-genomics, proteomics and metabolomics analyses, can possibly determine in the future the way in which C. difficile eradicates colonization resistance, paving the way for the development of new, more successful treatments and prevention. The aim of the present review is to present recent data concerning the human gut microbiota with a focus on its important role in health and disease.
Collapse
|
214
|
Schnizlein MK, Vendrov KC, Edwards SJ, Martens EC, Young VB. Dietary Xanthan Gum Alters Antibiotic Efficacy against the Murine Gut Microbiota and Attenuates Clostridioides difficile Colonization. mSphere 2020; 5:e00708-19. [PMID: 31915217 PMCID: PMC6952194 DOI: 10.1128/msphere.00708-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/06/2019] [Indexed: 01/16/2023] Open
Abstract
Dietary fiber provides a variety of microbiota-mediated benefits ranging from anti-inflammatory metabolites to pathogen colonization resistance. A healthy gut microbiota protects against Clostridioides difficile colonization. Manipulation of these microbes through diet may increase colonization resistance to improve clinical outcomes. The primary objective of this study was to identify how the dietary fiber xanthan gum affects the microbiota and C. difficile colonization. We added 5% xanthan gum to the diet of C57BL/6 mice and examined its effect on the microbiota through 16S rRNA gene amplicon sequencing and short-chain fatty acid analysis. Following either cefoperazone or an antibiotic cocktail administration, we challenged mice with C. difficile and measured colonization by monitoring the CFU. Xanthan gum administration is associated with increases in fiber-degrading taxa and short-chain fatty acid concentrations. However, by maintaining both the diversity and absolute abundance of the microbiota during antibiotic treatment, the protective effects of xanthan gum administration on the microbiota were more prominent than the enrichment of these fiber-degrading taxa. As a result, mice that were on the xanthan gum diet experienced limited to no C. difficile colonization. Xanthan gum administration alters mouse susceptibility to C. difficile colonization by maintaining the microbiota during antibiotic treatment. While antibiotic-xanthan gum interactions are not well understood, xanthan gum has previously been used to bind drugs and alter their pharmacokinetics. Thus, xanthan gum may alter the activity of the oral antibiotics used to make the microbiota susceptible. Future research should further characterize how this and other common dietary fibers interact with drugs.IMPORTANCE A healthy gut bacterial community benefits the host by breaking down dietary nutrients and protecting against pathogens. Clostridioides difficile capitalizes on the absence of this community to cause diarrhea and inflammation. Thus, a major clinical goal is to find ways to increase resistance to C. difficile colonization by either supplementing with bacteria that promote resistance or a diet to enrich for those already present in the gut. In this study, we describe an interaction between xanthan gum, a human dietary additive, and the microbiota resulting in an altered gut environment that is protective against C. difficile colonization.
Collapse
Affiliation(s)
- Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kimberly C Vendrov
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Summer J Edwards
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
215
|
Martinez-Guryn K, Leone V, Chang EB. Regional Diversity of the Gastrointestinal Microbiome. Cell Host Microbe 2020; 26:314-324. [PMID: 31513770 DOI: 10.1016/j.chom.2019.08.011] [Citation(s) in RCA: 222] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The role of gut microbes in health and disease has often been surmised from stool, which is easily sampled and rich in microbial diversity, density, and abundance. Microbial analyses of stool have been accepted as measures to determine the relationship of gut microbiomes with host health and disease, based on the belief that it represents all microbial populations throughout the gut. However, functional heterogeneity of each gastrointestinal tract (GIT) segment gives rise to regional differences in gut microbial populations. Herein, we summarize the literature regarding the microbial landscape along the rostral to caudal, i.e., horizontal mouth to anus, axis of the GIT. We aim to identify gaps in the literature, particularly regarding small intestinal microbiota abundance and diversity, highlight the importance of regional microbiota on host health and disease, as well as discuss opportunities to advance this line of research.
Collapse
Affiliation(s)
- Kristina Martinez-Guryn
- Biomedical Sciences Department, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA
| | - Vanessa Leone
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
216
|
Guthrie G, Stoll B, Chacko S, Lauridsen C, Plat J, Burrin D. Rifampicin, not vitamin E, suppresses parenteral nutrition-associated liver disease development through the pregnane X receptor pathway in piglets. Am J Physiol Gastrointest Liver Physiol 2020; 318:G41-G52. [PMID: 31604032 PMCID: PMC6985848 DOI: 10.1152/ajpgi.00193.2019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Infants receiving long-term parenteral nutrition (PN) develop PN-associated liver disease (PNALD). We previously (Ng K et al. JPEN J Parenter Enteral Nutr 40: 656-671, 2016. doi:10.1177/0148607114567900.) showed that PN containing soy-based lipid supplemented with vitamin E (α-tocopherol) prevents the development of PNALD. We hypothesize that this occurs via vitamin E activation of pregnane X receptor (PXR)-mediated pathways involved in bile acid metabolism. Neonatal piglets received PN for 14 days containing Intralipid (IL; soy-based lipid emulsion), IL supplemented with 12.6 mg·kg-1·day-1 vitamin E (VITE), or IL with 10 mg·kg-1·day-1 Rifadin IV (RIF), a PXR agonist. Pigs treated with IL and VITE, but not RIF, developed cholestasis and hyperbilirubinemia, markers of liver disease. The hepatic PXR target genes CYP3A29 and UGT1A6 increased during RIF treatment. RIF also modestly increased metabolism of chenodeoxycholic acid to the more hydrophilic bile acid hyocholic acid. Serum fibroblast growth factor (FGF)-19, a key regulator in suppressing hepatic bile acid synthesis, significantly increased in the RIF group. We conclude rifampicin modified markers of PNALD development by increased metabolism of bile acids and potentially suppressed bile acid synthesis. Vitamin E was ineffective at high lipid doses in preventing PNALD.NEW & NOTEWORTHY Intravenous vitamin E and rifampicin were administered to neonatal piglets receiving parenteral nutrition to determine their efficacy in reducing the progression of parenteral nutrition-associated liver disease (PNALD). Rifampicin increased serum FGF-19 concentrations and synthesis of the bile acid hyocholic acid which led to a reduction of PNALD parameters at 2 wk of administration. This result has potential clinical implications for the use of rifampicin as a safe and inexpensive treatment for short-term development of PNALD.
Collapse
Affiliation(s)
- Gregory Guthrie
- 1United States Department of Agriculture Agricultural Research Service, Children’s Nutrition Research Center, Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Barbara Stoll
- 1United States Department of Agriculture Agricultural Research Service, Children’s Nutrition Research Center, Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Shaji Chacko
- 1United States Department of Agriculture Agricultural Research Service, Children’s Nutrition Research Center, Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | | | - Jogchum Plat
- 3Department of Nutrition and Movement Sciences, School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Douglas Burrin
- 1United States Department of Agriculture Agricultural Research Service, Children’s Nutrition Research Center, Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
217
|
Jiang D, Armour CR, Hu C, Mei M, Tian C, Sharpton TJ, Jiang Y. Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Front Genet 2019; 10:995. [PMID: 31781153 PMCID: PMC6857202 DOI: 10.3389/fgene.2019.00995] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/18/2019] [Indexed: 12/21/2022] Open
Abstract
The advent of large-scale microbiome studies affords newfound analytical opportunities to understand how these communities of microbes operate and relate to their environment. However, the analytical methodology needed to model microbiome data and integrate them with other data constructs remains nascent. This emergent analytical toolset frequently ports over techniques developed in other multi-omics investigations, especially the growing array of statistical and computational techniques for integrating and representing data through networks. While network analysis has emerged as a powerful approach to modeling microbiome data, oftentimes by integrating these data with other types of omics data to discern their functional linkages, it is not always evident if the statistical details of the approach being applied are consistent with the assumptions of microbiome data or how they impact data interpretation. In this review, we overview some of the most important network methods for integrative analysis, with an emphasis on methods that have been applied or have great potential to be applied to the analysis of multi-omics integration of microbiome data. We compare advantages and disadvantages of various statistical tools, assess their applicability to microbiome data, and discuss their biological interpretability. We also highlight on-going statistical challenges and opportunities for integrative network analysis of microbiome data.
Collapse
Affiliation(s)
- Duo Jiang
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Courtney R Armour
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Chenxiao Hu
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Meng Mei
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Chuan Tian
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Statistics, Oregon State University, Corvallis, OR, United States
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, OR, United States
| |
Collapse
|
218
|
Buchta V, Bolehovská R, Hovorková E, Cornely OA, Seidel D, Žák P. Saprochaete clavata Invasive Infections - A New Threat to Hematological-Oncological Patients. Front Microbiol 2019; 10:2196. [PMID: 31736883 PMCID: PMC6830389 DOI: 10.3389/fmicb.2019.02196] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022] Open
Abstract
Background Saprochaete clavata (formerly Geotrichum clavatum, now proposed as Magnusiomyces clavatus) is a filamentous yeast-like fungus that has recently been described as an emerging pathogen mostly in patients with acute leukemia. Methods This is a retrospective study of patients diagnosed with proven and probable S. clavata infection at the University Hospital, Hradec Králové, Czechia between March 2005 and December 2017. Previous cases were identified from the literature and FungiScope® database. Results Six new cases (5 females, 1 male) of blood-stream S. clavata infections at the hemato-oncological department were described including epidemiological data of additional 48 patients colonized with the species. Overall, 116 strains of S. clavata were isolated from different clinical specimens of 54 patients; most of them belonged to the respiratory tract (60.3%). S. clavata was the most frequent species among arthroconidial yeasts (Trichosporon, Galactomyces, Magnusiomyces) recovered from the blood. All our patients with S. clavata infection had profound neutropenia, a central venous catheter, broad-spectrum antibiotics and antifungal prophylaxis; four had a history of a biliary tract system disease. The diagnosis was based on a positive blood culture in all patients. Four patients died of multiorgan failure and sepsis despite treatment with lipid-based amphotericin B and/or voriconazole. From the literature and FungiScope database, 67 previous cases of S. clavata infections were evaluated in context of our cases. Conclusion Saprochaete clavata infection represents a life-threatening mycosis in severely immunocompromised patients. The successful outcome of treatment seems to be critically dependent on the early diagnosis and the recovery of underlying conditions associated with immune dysfunction or deficiency.
Collapse
Affiliation(s)
- Vladimir Buchta
- Department of Clinical Microbiology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Radka Bolehovská
- Department of Clinical Biochemistry and Diagnostics, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Eva Hovorková
- The Fingerland Department of Pathology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Department I of Internal Medicine, ECMM Diamond Center of Excellence in Medical Mycology, German Centre for Infection Research (DZIF), University of Cologne, Cologne, Germany.,Clinical Trials Centre Cologne (ZKS Köln), University of Cologne, Cologne, Germany
| | - Danila Seidel
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Department of Internal Medicine, ECMM Diamond Center of Excellence in Medical Mycology, University of Cologne, Cologne, Germany
| | - Pavel Žák
- 4th Department of Internal Medicine - Division of Hematology, Faculty of Medicine in Hradec Králové, Faculty Hospital in Hradec Králové, Charles University in Prague, Hradec Králové, Czechia
| |
Collapse
|
219
|
Savidge T, Sorg JA. Role of Bile in Infectious Disease: the Gall of 7α-Dehydroxylating Gut Bacteria. Cell Chem Biol 2019; 26:1-3. [PMID: 30658109 DOI: 10.1016/j.chembiol.2018.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Local antibiotics and quorum sensors produced by gut bacteria regulate microbiota community structure and guard against pathogens. In this issue of Cell Chemical Biology, Kang et al. (2019) guide us through a reciprocal host-antimicrobial interplay that redefines our understanding of Clostridioides (Clostridium) difficile pathogenesis.
Collapse
Affiliation(s)
- Tor Savidge
- Department of Pathology & Immunology, Baylor College of Medicine, Houston TX, 77030, USA; Texas Children's Microbiome Center, Texas Children's Hospital, Houston TX, 77030, USA.
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station TX, 77843, USA
| |
Collapse
|
220
|
Battaglioli EJ, Hale VL, Chen J, Jeraldo P, Ruiz-Mojica C, Schmidt BA, Rekdal VM, Till LM, Huq L, Smits SA, Moor WJ, Jones-Hall Y, Smyrk T, Khanna S, Pardi DS, Grover M, Patel R, Chia N, Nelson H, Sonnenburg JL, Farrugia G, Kashyap PC. Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea. Sci Transl Med 2019; 10:10/464/eaam7019. [PMID: 30355801 DOI: 10.1126/scitranslmed.aam7019] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 11/17/2017] [Accepted: 03/22/2018] [Indexed: 12/16/2022]
Abstract
The gut microbiota plays a critical role in pathogen defense. Studies using antibiotic-treated mice reveal mechanisms that increase susceptibility to Clostridioides difficile infection (CDI), but risk factors associated with CDI in humans extend beyond antibiotic use. Here, we studied the dysbiotic gut microbiota of a subset of patients with diarrhea and modeled the gut microbiota of these patients by fecal transplantation into germ-free mice. When challenged with C. difficile, the germ-free mice transplanted with fecal samples from patients with dysbiotic microbial communities showed increased gut amino acid concentrations and greater susceptibility to CDI. A C. difficile mutant that was unable to use proline as an energy source was unable to robustly infect germ-free mice transplanted with a dysbiotic or healthy human gut microbiota. Prophylactic dietary intervention using a low-proline or low-protein diet in germ-free mice colonized by a dysbiotic human gut microbiota resulted in decreased expansion of wild-type C. difficile after challenge, suggesting that amino acid availability might be important for CDI. Furthermore, a prophylactic fecal microbiota transplant in mice with dysbiosis reduced proline availability and protected the mice from CDI. Last, we identified clinical risk factors that could potentially predict gut microbial dysbiosis and thus greater susceptibility to CDI in a retrospective cohort of patients with diarrhea. Identifying at-risk individuals and reducing their susceptibility to CDI through gut microbiota-targeted therapies could be a new approach to preventing C. difficile infection in susceptible patients.
Collapse
Affiliation(s)
- Eric J Battaglioli
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Vanessa L Hale
- Department of Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Veterinary Preventive Medicine, Ohio State University, Columbus, OH, USA
| | - Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Coral Ruiz-Mojica
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Bradley A Schmidt
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Vayu M Rekdal
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lisa M Till
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lutfi Huq
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Samuel A Smits
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - William J Moor
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Yava Jones-Hall
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Thomas Smyrk
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sahil Khanna
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Darrell S Pardi
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Madhusudan Grover
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Robin Patel
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | - Purna C Kashyap
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. .,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
221
|
Battaglioli EJ, Hale VL, Chen J, Jeraldo P, Ruiz-Mojica C, Schmidt BA, Rekdal VM, Till LM, Huq L, Smits SA, Moor WJ, Jones-Hall Y, Smyrk T, Khanna S, Pardi DS, Grover M, Patel R, Chia N, Nelson H, Sonnenburg JL, Farrugia G, Kashyap PC. Clostridioides difficile uses amino acids associated with gut microbial dysbiosis in a subset of patients with diarrhea. Sci Transl Med 2019. [PMID: 30355801 DOI: 10.1126/scitranslmed.aam7019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The gut microbiota plays a critical role in pathogen defense. Studies using antibiotic-treated mice reveal mechanisms that increase susceptibility to Clostridioides difficile infection (CDI), but risk factors associated with CDI in humans extend beyond antibiotic use. Here, we studied the dysbiotic gut microbiota of a subset of patients with diarrhea and modeled the gut microbiota of these patients by fecal transplantation into germ-free mice. When challenged with C. difficile, the germ-free mice transplanted with fecal samples from patients with dysbiotic microbial communities showed increased gut amino acid concentrations and greater susceptibility to CDI. A C. difficile mutant that was unable to use proline as an energy source was unable to robustly infect germ-free mice transplanted with a dysbiotic or healthy human gut microbiota. Prophylactic dietary intervention using a low-proline or low-protein diet in germ-free mice colonized by a dysbiotic human gut microbiota resulted in decreased expansion of wild-type C. difficile after challenge, suggesting that amino acid availability might be important for CDI. Furthermore, a prophylactic fecal microbiota transplant in mice with dysbiosis reduced proline availability and protected the mice from CDI. Last, we identified clinical risk factors that could potentially predict gut microbial dysbiosis and thus greater susceptibility to CDI in a retrospective cohort of patients with diarrhea. Identifying at-risk individuals and reducing their susceptibility to CDI through gut microbiota-targeted therapies could be a new approach to preventing C. difficile infection in susceptible patients.
Collapse
Affiliation(s)
- Eric J Battaglioli
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Vanessa L Hale
- Department of Surgery, Mayo Clinic, Rochester, MN, USA.,Department of Veterinary Preventive Medicine, Ohio State University, Columbus, OH, USA
| | - Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Coral Ruiz-Mojica
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Bradley A Schmidt
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Vayu M Rekdal
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lisa M Till
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lutfi Huq
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Samuel A Smits
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - William J Moor
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Yava Jones-Hall
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Thomas Smyrk
- Department of Laboratory Medicine and Pathology, Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sahil Khanna
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Darrell S Pardi
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Madhusudan Grover
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Robin Patel
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | - Purna C Kashyap
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA. .,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
222
|
Cabral DJ, Penumutchu S, Reinhart EM, Zhang C, Korry BJ, Wurster JI, Nilson R, Guang A, Sano WH, Rowan-Nash AD, Li H, Belenky P. Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. Cell Metab 2019; 30:800-823.e7. [PMID: 31523007 PMCID: PMC6948150 DOI: 10.1016/j.cmet.2019.08.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/24/2019] [Accepted: 08/20/2019] [Indexed: 12/22/2022]
Abstract
Although antibiotics disturb the structure of the gut microbiota, factors that modulate these perturbations are poorly understood. Bacterial metabolism is an important regulator of susceptibility in vitro and likely plays a large role within the host. We applied a metagenomic and metatranscriptomic approach to link antibiotic-induced taxonomic and transcriptional responses within the murine microbiome. We found that antibiotics significantly alter the expression of key metabolic pathways at the whole-community and single-species levels. Notably, Bacteroides thetaiotaomicron, which blooms in response to amoxicillin, upregulated polysaccharide utilization. In vitro, we found that the sensitivity of this bacterium to amoxicillin was elevated by glucose and reduced by polysaccharides. Accordingly, we observed that dietary composition affected the abundance and expansion of B. thetaiotaomicron, as well as the extent of microbiome disruption with amoxicillin. Our work indicates that the metabolic environment of the microbiome plays a role in the response of this community to antibiotics.
Collapse
Affiliation(s)
- Damien J Cabral
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Swathi Penumutchu
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Elizabeth M Reinhart
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Cheng Zhang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Rachael Nilson
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - August Guang
- Center for Computation & Visualization, Brown University, Brown University, Providence, RI 02906, USA; Center for Computational Biology of Human Disease, Brown University, Providence, RI 02906, USA
| | - William H Sano
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55904, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02906, USA.
| |
Collapse
|
223
|
Mullish BH, McDonald JAK, Pechlivanis A, Allegretti JR, Kao D, Barker GF, Kapila D, Petrof EO, Joyce SA, Gahan CGM, Glegola-Madejska I, Williams HRT, Holmes E, Clarke TB, Thursz MR, Marchesi JR. Microbial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent Clostridioides difficile infection. Gut 2019; 68:1791-1800. [PMID: 30816855 PMCID: PMC6839797 DOI: 10.1136/gutjnl-2018-317842] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/26/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Faecal microbiota transplant (FMT) effectively treats recurrent Clostridioides difficile infection (rCDI), but its mechanisms of action remain poorly defined. Certain bile acids affect C. difficile germination or vegetative growth. We hypothesised that loss of gut microbiota-derived bile salt hydrolases (BSHs) predisposes to CDI by perturbing gut bile metabolism, and that BSH restitution is a key mediator of FMT's efficacy in treating the condition. DESIGN Using stool collected from patients and donors pre-FMT/post-FMT for rCDI, we performed 16S rRNA gene sequencing, ultra performance liquid chromatography mass spectrometry (UPLC-MS) bile acid profiling, BSH activity measurement, and qPCR of bsh/baiCD genes involved in bile metabolism. Human data were validated in C. difficile batch cultures and a C57BL/6 mouse model of rCDI. RESULTS From metataxonomics, pre-FMT stool demonstrated a reduced proportion of BSH-producing bacterial species compared with donors/post-FMT. Pre-FMT stool was enriched in taurocholic acid (TCA, a potent C. difficile germinant); TCA levels negatively correlated with key bacterial genera containing BSH-producing organisms. Post-FMT samples demonstrated recovered BSH activity and bsh/baiCD gene copy number compared with pretreatment (p<0.05). In batch cultures, supernatant from engineered bsh-expressing E. coli and naturally BSH-producing organisms (Bacteroides ovatus, Collinsella aerofaciens, Bacteroides vulgatus and Blautia obeum) reduced TCA-mediated C. difficile germination relative to culture supernatant of wild-type (BSH-negative) E. coli. C. difficile total viable counts were ~70% reduced in an rCDI mouse model after administration of E. coli expressing highly active BSH relative to mice administered BSH-negative E. coli (p<0.05). CONCLUSION Restoration of gut BSH functionality contributes to the efficacy of FMT in treating rCDI.
Collapse
Affiliation(s)
- Benjamin H Mullish
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Julie A K McDonald
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Alexandros Pechlivanis
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Jessica R Allegretti
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women’s Hospital, Boston, Massachusetts, USA,Harvard Medical School, Harvard University, Boston, Massachusetts, USA
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Grace F Barker
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Diya Kapila
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Elaine O Petrof
- Division of Infectious Diseases/ GI Diseases Research Unit Wing, Department of Medicine, Kingston General Hospital, Queen’s University, Kingston, Ontario, Canada
| | - Susan A Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Institute, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | | | - Horace R T Williams
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Elaine Holmes
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Thomas B Clarke
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Mark R Thursz
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Integrative Systems Medicine and Digestive Disease, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK,School of Biosciences, Cardiff University, Cardiff, UK
| |
Collapse
|
224
|
Ciftci Y, Girinathan BP, Dhungel BA, Hasan MK, Govind R. Clostridioides difficile SinR' regulates toxin, sporulation and motility through protein-protein interaction with SinR. Anaerobe 2019; 59:1-7. [PMID: 31077800 PMCID: PMC6785386 DOI: 10.1016/j.anaerobe.2019.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/10/2019] [Accepted: 05/07/2019] [Indexed: 12/18/2022]
Abstract
Clostridioides difficile is a Gram-positive, anaerobic bacterium. It is known that C. difficile is one of the major causes of antibiotic associated diarrhea. The enhanced antibiotic resistance observed in C. difficile is the result of highly resistant spores produced by the bacterium. In Bacillus subtilis, the sin operon is involved in sporulation inhibition. Two proteins coded within this operon, SinR and SinI, have an antagonistic relationship; SinR acts as an inhibitor to sporulation whereas SinI represses the activity of SinR, thus allowing the bacterium to sporulate. In a previous study, we examined the sin locus in C. difficile and named the two genes associated with this operon sinR and sinR', analogous to sinR and sinI in B. subtilis, respectively. We have shown that SinR and SinR' have pleiotropic roles in pathogenesis pathways and interact antagonistically with each other. Unlike B. subtilis SinI, SinR' in C. difficile carries two domains: the HTH domain and the Multimerization Domain (MD). In this study, we first performed a GST Pull-down experiment to determine the domain within SinR' that interacts with SinR. Second, the effect of these two domains on three phenotypes; sporulation, motility, and toxin production was examined. The findings of this study confirmed the prediction that the Multimerization Domain (MD) of SinR' is responsible for the interaction between SinR and SinR'. It was also discovered that SinR' regulates sporulation, toxin production and motility primarily by inhibiting SinR activity through the Multimerization Domain (MD).
Collapse
Affiliation(s)
- Yusuf Ciftci
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Brintha Parasumanna Girinathan
- Division of Biology, Kansas State University, Manhattan, KS, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA
| | | | - Md Kamrul Hasan
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Revathi Govind
- Division of Biology, Kansas State University, Manhattan, KS, USA.
| |
Collapse
|
225
|
Guinan J, Thangamani S. Antibiotic-induced alterations in taurocholic acid levels promote gastrointestinal colonization of Candida albicans. FEMS Microbiol Lett 2019; 365:5066169. [PMID: 30137306 DOI: 10.1093/femsle/fny196] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/02/2018] [Indexed: 12/12/2022] Open
Abstract
Candida albicans is a fungal pathogen that poses a significant public health risk due to high incidence and mortality rates among immunocompromised patients. Candida albicans infections begin with successful gastrointestinal (GI) colonization; however, the mechanisms behind this colonization remain to be elucidated. In this study, we investigated the role of taurocholic acid (TCA) on growth and GI colonization of C. albicans. Our results indicate that cefoperazone-treated mice susceptible to C. albicans infection had significantly increased levels of TCA in the gut contents. In addition, an increase in TCA levels directly correlates with higher C. albicans load in the fecal and gut contents of antibiotic-treated infected mice. Using in vitro assays, we also demonstrated that TCA enhances the growth of C. albicans and its ability to develop filamentous hyphae. Furthermore, TCA significantly increased the ability of C. albicans to attach to mammalian cells. These results demonstrate that antibiotic treatment alters TCA levels in the gut and potentially enhances GI colonization of C. albicans.
Collapse
Affiliation(s)
- Jack Guinan
- Department of Pathology and Population Medicine, College of Veterinary Medicine, Midwestern University, 19555 N. 59th Ave. Glendale, AZ 85308, USA
| | - Shankar Thangamani
- Department of Pathology and Population Medicine, College of Veterinary Medicine, Midwestern University, 19555 N. 59th Ave. Glendale, AZ 85308, USA
| |
Collapse
|
226
|
Chi L, Lai Y, Tu P, Liu CW, Xue J, Ru H, Lu K. Lipid and Cholesterol Homeostasis after Arsenic Exposure and Antibiotic Treatment in Mice: Potential Role of the Microbiota. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:97002. [PMID: 31532247 PMCID: PMC6792374 DOI: 10.1289/ehp4415] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 08/05/2019] [Accepted: 08/13/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Arsenic-induced liver X receptor/retinoid X receptor (LXR/RXR) signaling inhibition is a potential mechanism underlying the cardiovascular effects caused by arsenic. The gut microbiota can influence arsenic toxic effects. OBJECTIVE We aimed to explore whether gut microbiota play a role in arsenic-induced LXR/RXR signaling inhibition and the subsequent lipid and cholesterol dysbiosis. METHODS Conventional and antibiotic-treated mice (AB-treated mice) were exposed to 0.25 ppm and 1 ppm arsenic for 2 wk. Hepatic mRNAs were extracted and sequenced. The expression levels of genes associated with LXR/RXR signaling were quantified by quantitative real-time polymerase chain reaction (qPCR), and serum and hepatic cholesterol levels were measured. Liquid chromatography-mass spectrometry (LC-MS)-based lipidomics were used to examine serum and hepatic lipids. RESULTS Pathway analysis indicated that arsenic exposure differentially influenced the hepatic signaling pathways in conventional and AB-treated mice. The expression of sterol regulatory element-binding protein 1 (Srebp1c), 3-hydroxy-3-methylglutaryl-CoA reductase (Hmgcr), and cytochrome P450 family 7 subfamily A member 1 (Cyp7a1), as well as cholesterol efflux genes, including ATP binding cassette subfamily G member 5/8 (Abcg5/8) and cluster of differentiation 36 (Cd36), was lower in arsenic-exposed conventional mice but not in AB-treated mice. Similarly, under arsenic exposure, the hepatic expression of scavenger receptor class B member 1 (Scarb1), which is involved in reverse cholesterol transport (RCT), was lower in conventional mice, but was higher in AB-treated animals compared with controls. Correspondingly, arsenic exposure exerted opposite effects on the serum cholesterol levels in conventional and AB-treated mice, i.e., higher serum cholesterol levels in conventional mice but lower levels in AB-treated mice than in respective controls. Serum lipid levels, especially triglyceride (TG) levels, were higher in conventional mice exposed to 1 ppm arsenic, while arsenic exposure did not significantly affect the serum lipids in AB-treated mice. Liver lipid patterns were also differentially perturbed in a microbiota-dependent manner. CONCLUSIONS Our results suggest that in mice, the gut microbiota may be a critical factor regulating arsenic-induced LXR/RXR signaling perturbation, suggesting that modulation of the gut microbiota might be an intervention strategy to reduce the toxic effects of arsenic on lipid and cholesterol homeostasis. https://doi.org/10.1289/EHP4415.
Collapse
Affiliation(s)
- Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Yunjia Lai
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Jingchuan Xue
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, North Carolina, USA
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, North Carolina, USA
| |
Collapse
|
227
|
Wang S, Martins R, Sullivan MC, Friedman ES, Misic AM, El-Fahmawi A, De Martinis ECP, O'Brien K, Chen Y, Bradley C, Zhang G, Berry ASF, Hunter CA, Baldassano RN, Rondeau MP, Beiting DP. Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids. MICROBIOME 2019; 7:126. [PMID: 31472697 PMCID: PMC6717631 DOI: 10.1186/s40168-019-0740-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/19/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND The microbiome has been implicated in the initiation and persistence of inflammatory bowel disease. Despite the fact that diet is one of the most potent modulators of microbiome composition and function and that dietary intervention is the first-line therapy for treating pediatric Crohn's disease, the relationships between diet-induced remission, enteropathy, and microbiome are poorly understood. Here, we leverage a naturally-occurring canine model of chronic inflammatory enteropathy that exhibits robust remission following nutritional therapy, to perform a longitudinal study that integrates clinical monitoring, 16S rRNA gene amplicon sequencing, metagenomic sequencing, metabolomic profiling, and whole genome sequencing to investigate the relationship between therapeutic diet, microbiome, and disease. RESULTS We show that remission induced by a hydrolyzed protein diet is accompanied by alterations in microbial community structure marked by decreased abundance of pathobionts (e.g., Escherichia coli and Clostridium perfringens), reduced severity of dysbiosis, and increased levels of the secondary bile acids, lithocholic and deoxycholic acid. Physiologic levels of these bile acids inhibited the growth of E. coli and C. perfringens isolates, in vitro. Metagenomic analysis and whole genome sequencing identified the bile acid producer Clostridium hiranonis as elevated after dietary therapy and a likely source of secondary bile acids during remission. When C. hiranonis was administered to mice, levels of deoxycholic acid were preserved and pathology associated with DSS colitis was ameliorated. Finally, a closely related bile acid producer, Clostridium scindens, was associated with diet-induced remission in human pediatric Crohn's disease. CONCLUSIONS These data highlight that remission induced by a hydrolyzed protein diet is associated with improved microbiota structure, an expansion of bile acid-producing clostridia, and increased levels of secondary bile acids. Our observations from clinical studies of exclusive enteral nutrition in human Crohn's disease, along with our in vitro inhibition assays and in vivo studies in mice, suggest that this may be a conserved response to diet therapy with the potential to ameliorate disease. These findings provide insight into diet-induced remission of gastrointestinal disease and could help guide the rational design of more effective therapeutic diets.
Collapse
Affiliation(s)
- Shuai Wang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rene Martins
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Megan C Sullivan
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elliot S Friedman
- Division of Gastroenterology, School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ana M Misic
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ayah El-Fahmawi
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | - Kevin O'Brien
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ying Chen
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Charles Bradley
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Grace Zhang
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexander S F Berry
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Christopher A Hunter
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Robert N Baldassano
- Department of Pediatric Gastroenterology Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mark P Rondeau
- Department of Clinical Sciences and Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
228
|
Robinson JI, Weir WH, Crowley JR, Hink T, Reske KA, Kwon JH, Burnham CAD, Dubberke ER, Mucha PJ, Henderson JP. Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections. J Clin Invest 2019; 129:3792-3806. [PMID: 31403473 DOI: 10.1172/jci126905] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile infection (CDI) accounts for a substantial proportion of deaths attributable to antibiotic-resistant bacteria in the United States. Although C. difficile can be an asymptomatic colonizer, its pathogenic potential is most commonly manifested in patients with antibiotic-modified intestinal microbiomes. In a cohort of 186 hospitalized patients, we showed that host and microbe-associated shifts in fecal metabolomes had the potential to distinguish patients with CDI from those with non-C. difficile diarrhea and C. difficile colonization. Patients with CDI exhibited a chemical signature of Stickland amino acid fermentation that was distinct from those of uncolonized controls. This signature suggested that C. difficile preferentially catabolizes branched chain amino acids during CDI. Unexpectedly, we also identified a series of noncanonical, unsaturated bile acids that were depleted in patients with CDI. These bile acids may derive from an extended host-microbiome dehydroxylation network in uninfected patients. Bile acid composition and leucine fermentation defined a prototype metabolomic model with potential to distinguish clinical CDI from asymptomatic C. difficile colonization.
Collapse
Affiliation(s)
- John I Robinson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - William H Weir
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jan R Crowley
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A Reske
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennie H Kwon
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Erik R Dubberke
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Peter J Mucha
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
229
|
Kemis JH, Linke V, Barrett KL, Boehm FJ, Traeger LL, Keller MP, Rabaglia ME, Schueler KL, Stapleton DS, Gatti DM, Churchill GA, Amador-Noguez D, Russell JD, Yandell BS, Broman KW, Coon JJ, Attie AD, Rey FE. Genetic determinants of gut microbiota composition and bile acid profiles in mice. PLoS Genet 2019; 15:e1008073. [PMID: 31465442 PMCID: PMC6715156 DOI: 10.1371/journal.pgen.1008073] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/14/2019] [Indexed: 02/03/2023] Open
Abstract
The microbial communities that inhabit the distal gut of humans and other mammals exhibit large inter-individual variation. While host genetics is a known factor that influences gut microbiota composition, the mechanisms underlying this variation remain largely unknown. Bile acids (BAs) are hormones that are produced by the host and chemically modified by gut bacteria. BAs serve as environmental cues and nutrients to microbes, but they can also have antibacterial effects. We hypothesized that host genetic variation in BA metabolism and homeostasis influence gut microbiota composition. To address this, we used the Diversity Outbred (DO) stock, a population of genetically distinct mice derived from eight founder strains. We characterized the fecal microbiota composition and plasma and cecal BA profiles from 400 DO mice maintained on a high-fat high-sucrose diet for ~22 weeks. Using quantitative trait locus (QTL) analysis, we identified several genomic regions associated with variations in both bacterial and BA profiles. Notably, we found overlapping QTL for Turicibacter sp. and plasma cholic acid, which mapped to a locus containing the gene for the ileal bile acid transporter, Slc10a2. Mediation analysis and subsequent follow-up validation experiments suggest that differences in Slc10a2 gene expression associated with the different strains influences levels of both traits and revealed novel interactions between Turicibacter and BAs. This work illustrates how systems genetics can be utilized to generate testable hypotheses and provide insight into host-microbe interactions.
Collapse
Affiliation(s)
- Julia H. Kemis
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Vanessa Linke
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Kelsey L. Barrett
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Frederick J. Boehm
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Lindsay L. Traeger
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mary E. Rabaglia
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Kathryn L. Schueler
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Donald S. Stapleton
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Daniel M. Gatti
- Jackson Laboratory, Bar Harbor, Maine, United States of America
| | | | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jason D. Russell
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Brian S. Yandell
- Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Karl W. Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
230
|
Guinan J, Wang S, Hazbun TR, Yadav H, Thangamani S. Antibiotic-induced decreases in the levels of microbial-derived short-chain fatty acids correlate with increased gastrointestinal colonization of Candida albicans. Sci Rep 2019; 9:8872. [PMID: 31222159 PMCID: PMC6586901 DOI: 10.1038/s41598-019-45467-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 06/05/2019] [Indexed: 02/07/2023] Open
Abstract
Candida albicans is the fourth most common cause of systemic nosocomial infections, posing a significant risk in immunocompromised individuals. As the majority of systemic C. albicans infections stem from endogenous gastrointestinal (GI) colonization, understanding the mechanisms associated with GI colonization is essential in the development of novel methods to prevent C. albicans-related mortality. In this study, we investigated the role of microbial-derived short-chain fatty acids (SCFAs) including acetate, butyrate, and propionate on growth, morphogenesis, and GI colonization of C. albicans. Our results indicate that cefoperazone-treated mice susceptible to C. albicans infection had significantly decreased levels of SCFAs in the cecal contents that correlate with a higher fungal load in the feces. Further, using in vivo concentration of SCFAs, we demonstrated that SCFAs inhibit the growth, germ tube, hyphae and biofilm development of C. albicans in vitro. Collectively, results from this study suggest that antibiotic-induced decreases in the levels of SCFAs in the cecum enhances the growth and GI colonization of C. albicans.
Collapse
Affiliation(s)
- Jack Guinan
- College of Veterinary Medicine, Midwestern University, 19555N. 59th Ave, Glendale, AZ, 85308, USA
| | - Shaohua Wang
- Department of Internal Medicine-Molecular Medicine, Wake Forest School of Medicine, 575 North Patterson Ave, Winston-Salem, NC, 27101, USA
| | - Tony R Hazbun
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47906, USA.,Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, 47906, USA
| | - Hariom Yadav
- Department of Internal Medicine-Molecular Medicine, Wake Forest School of Medicine, 575 North Patterson Ave, Winston-Salem, NC, 27101, USA
| | - Shankar Thangamani
- Department of Pathology and Population Medicine, College of Veterinary Medicine, Midwestern University, 19555N. 59th Ave, Glendale, AZ, 85308, USA.
| |
Collapse
|
231
|
Reese AT, Carmody RN. Thinking Outside the Cereal Box: Noncarbohydrate Routes for Dietary Manipulation of the Gut Microbiota. Appl Environ Microbiol 2019; 85:e02246-18. [PMID: 30504210 PMCID: PMC6498178 DOI: 10.1128/aem.02246-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gut microbiota is a diverse and dynamic ecological community that is increasingly recognized to play important roles in host metabolic, immunological, and behavioral functioning. As such, identifying new routes for manipulating the microbiota may provide valuable additional methods for improving host health. Dietary manipulations and prebiotic supplementation are active targets of research for altering the microbiota, but to date, this work has disproportionately focused on carbohydrates. However, many other resources can limit or shape microbial growth. Here, we provide a brief overview of the resource landscape in the mammalian gut and review relevant literature documenting associations between noncarbohydrate nutrients and the composition of the gut microbiota. To spur future work and accelerate translational applications, we propose that researchers take new approaches for studying the effects of diet on gut microbial communities, including more-careful consideration of media for in vitro experiments, measurement of absolute as well as relative abundances, concerted efforts to articulate how physiology may differ between humans and the animal models used in translational studies, and leveraging natural variation for additional insights. Finally, we close with a discussion of how to determine when or where to employ these potential dietary levers for manipulating the microbiota.
Collapse
Affiliation(s)
- Aspen T Reese
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Society of Fellows, Harvard University, Cambridge, Massachusetts, USA
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
232
|
Pathogen Colonization Resistance in the Gut and Its Manipulation for Improved Health. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1300-1310. [PMID: 31100210 DOI: 10.1016/j.ajpath.2019.03.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/15/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
Mammals have coevolved with a large community of symbiotic, commensal, and some potentially pathogenic microbes. The trillions of bacteria and hundreds of species in our guts form a relatively stable community that resists invasion by outsiders, including pathogens. This powerful protective force is referred to as colonization resistance. We discuss the variety of proposed or demonstrated mechanisms that can mediate colonization resistance and some potential ways to manipulate them for improved human health. Instances in which certain bacterial pathogens can overcome colonization resistance are also discussed.
Collapse
|
233
|
Ünal CM, Karagöz MS, Berges M, Priebe C, Borrero de Acuña JM, Wissing J, Jänsch L, Jahn D, Steinert M. Pleiotropic Clostridioides difficile Cyclophilin PpiB Controls Cysteine-Tolerance, Toxin Production, the Central Metabolism and Multiple Stress Responses. Front Pharmacol 2019; 10:340. [PMID: 31024308 PMCID: PMC6459899 DOI: 10.3389/fphar.2019.00340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/19/2019] [Indexed: 01/05/2023] Open
Abstract
The Gram-positive pathogen Clostridioides difficile is the main bacterial agent of nosocomial antibiotic associated diarrhea. Bacterial peptidyl-prolyl-cis/trans-isomerases (PPIases) are well established modulators of virulence that influence the outcome of human pathologies during infections. Here, we present the first interactomic network of the sole cyclophilin-type PPIase of C. difficile (CdPpiB) and show that it has diverse interaction partners including major enzymes of the amino acid-dependent energy (LdhA, EtfAB, Had, Acd) and the glucose-derived (Fba, GapA, Pfo, Pyk, Pyc) central metabolism. Proteins of the general (UspA), oxidative (Rbr1,2,3, Dsr), alkaline (YloU, YphY) and cold shock (CspB) response were found bound to CdPpiB. The transcriptional (Lrp), translational (InfC, RFF) and folding (GroS, DnaK) control proteins were also found attached. For a crucial enzyme of cysteine metabolism, O-acetylserine sulfhydrylase (CysK), the global transcription regulator Lrp and the flagellar subunit FliC, these interactions were independently confirmed using a bacterial two hybrid system. The active site residues F50, F109, and F110 of CdPpiB were shown to be important for the interaction with the residue P87 of Lrp. CysK activity after heat denaturation was restored by interaction with CdPpiB. In accordance, tolerance toward cell wall stress caused by the exposure to amoxicillin was reduced. In the absence of CdPpiB, C. difficile was more susceptible toward L-cysteine. At the same time, the cysteine-mediated suppression of toxin production ceased resulting in higher cytotoxicity. In summary, the cyclophilin-type PPIase of C. difficile (CdPpiB) coordinates major cellular processes via its interaction with major regulators of transcription, translation, protein folding, stress response and the central metabolism.
Collapse
Affiliation(s)
- Can Murat Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Moleküler Biyoteknoloji Bölümü, Türk-Alman Üniversitesi, Istanbul, Turkey
| | | | - Mareike Berges
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
| | - Christina Priebe
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Josef Wissing
- Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.,Cellular Proteomics Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Lothar Jänsch
- Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.,Cellular Proteomics Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
| |
Collapse
|
234
|
Clostridium scindens ATCC 35704: Integration of Nutritional Requirements, the Complete Genome Sequence, and Global Transcriptional Responses to Bile Acids. Appl Environ Microbiol 2019; 85:AEM.00052-19. [PMID: 30737348 DOI: 10.1128/aem.00052-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 01/30/2019] [Indexed: 01/13/2023] Open
Abstract
In the human gut, Clostridium scindens ATCC 35704 is a predominant bacterium and one of the major bile acid 7α-dehydroxylating anaerobes. While this organism is well-studied relative to bile acid metabolism, little is known about the basic nutrition and physiology of C. scindens ATCC 35704. To determine the amino acid and vitamin requirements of C. scindens, the leave-one-out (one amino acid group or vitamin) technique was used to eliminate the nonessential amino acids and vitamins. With this approach, the amino acid tryptophan and three vitamins (riboflavin, pantothenate, and pyridoxal) were found to be required for the growth of C. scindens In the newly developed defined medium, C. scindens fermented glucose mainly to ethanol, acetate, formate, and H2. The genome of C. scindens ATCC 35704 was completed through PacBio sequencing. Pathway analysis of the genome sequence coupled with transcriptome sequencing (RNA-Seq) under defined culture conditions revealed consistency with the growth requirements and end products of glucose metabolism. Induction with bile acids revealed complex and differential responses to cholic acid and deoxycholic acid, including the expression of potentially novel bile acid-inducible genes involved in cholic acid metabolism. Responses to toxic deoxycholic acid included expression of genes predicted to be involved in DNA repair, oxidative stress, cell wall maintenance/metabolism, chaperone synthesis, and downregulation of one-third of the genome. These analyses provide valuable insight into the overall biology of C. scindens which may be important in treatment of disease associated with increased colonic secondary bile acids.IMPORTANCE C. scindens is one of a few identified gut bacterial species capable of converting host cholic acid into disease-associated secondary bile acids such as deoxycholic acid. The current work represents an important advance in understanding the nutritional requirements and response to bile acids of the medically important human gut bacterium, C. scindens ATCC 35704. A defined medium has been developed which will further the understanding of bile acid metabolism in the context of growth substrates, cofactors, and other metabolites in the vertebrate gut. Analysis of the complete genome supports the nutritional requirements reported here. Genome-wide transcriptomic analysis of gene expression in the presence of cholic acid and deoxycholic acid provides a unique insight into the complex response of C. scindens ATCC 35704 to primary and secondary bile acids. Also revealed are genes with the potential to function in bile acid transport and metabolism.
Collapse
|
235
|
Sievers S, Metzendorf NG, Dittmann S, Troitzsch D, Gast V, Tröger SM, Wolff C, Zühlke D, Hirschfeld C, Schlüter R, Riedel K. Differential View on the Bile Acid Stress Response of Clostridioides difficile. Front Microbiol 2019; 10:258. [PMID: 30833939 PMCID: PMC6387971 DOI: 10.3389/fmicb.2019.00258] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/31/2019] [Indexed: 12/16/2022] Open
Abstract
Clostridioides difficile is an intestinal human pathogen that uses the opportunity of a depleted microbiota to cause an infection. It is known, that the composition of the intestinal bile acid cocktail has a great impact on the susceptibility toward a C. difficile infection. However, the specific response of growing C. difficile cells to diverse bile acids on the molecular level has not been described yet. In this study, we recorded proteome signatures of shock and long-term (LT) stress with the four main bile acids cholic acid (CA), chenodeoxycholic acid (CDCA), deoxycholic acid (DCA), and lithocholic acid (LCA). A general overlapping response to all tested bile acids could be determined particularly in shock experiments which appears plausible in the light of their common steroid structure. However, during LT stress several proteins showed an altered abundance in the presence of only a single or a few of the bile acids indicating the existence of specific adaptation mechanisms. Our results point at a differential induction of the groEL and dnaKJgrpE chaperone systems, both belonging to the class I heat shock genes. Additionally, central metabolic pathways involving butyrate fermentation and the reductive Stickland fermentation of leucine were effected, although CA caused a proteome signature different from the other three bile acids. Furthermore, quantitative proteomics revealed a loss of flagellar proteins in LT stress with LCA. The absence of flagella could be substantiated by electron microscopy which also indicated less flagellated cells in the presence of DCA and CDCA and no influence on flagella formation by CA. Our data break down the bile acid stress response of C. difficile into a general and a specific adaptation. The latter cannot simply be divided into a response to primary and secondary bile acids, but rather reflects a complex and variable adaptation process enabling C. difficile to survive and to cause an infection in the intestinal tract.
Collapse
Affiliation(s)
- Susanne Sievers
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Nicole G Metzendorf
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Silvia Dittmann
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Daniel Troitzsch
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Viola Gast
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Sophie Marlen Tröger
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Christian Wolff
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Claudia Hirschfeld
- Department of Microbial Proteomics, Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany
| |
Collapse
|
236
|
Metabolic Modeling of Clostridium difficile Associated Dysbiosis of the Gut Microbiota. Processes (Basel) 2019. [DOI: 10.3390/pr7020097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Recent in vitro experiments have demonstrated the ability of the pathogen Clostridium difficile and commensal gut bacteria to form biofilms on surfaces, and biofilm development in vivo is likely. Various studies have reported that 3%–15% of healthy adults are asymptomatically colonized with C. difficile, with commensal species providing resistance against C. difficile pathogenic colonization. C. difficile infection (CDI) is observed at a higher rate in immunocompromised patients previously treated with broad spectrum antibiotics that disrupt the commensal microbiota and reduce competition for available nutrients, resulting in imbalance among commensal species and dysbiosis conducive to C. difficile propagation. To investigate the metabolic interactions of C. difficile with commensal species from the three dominant phyla in the human gut, we developed a multispecies biofilm model by combining genome-scale metabolic reconstructions of C. difficile, Bacteroides thetaiotaomicron from the phylum Bacteroidetes, Faecalibacterium prausnitzii from the phylum Firmicutes, and Escherichia coli from the phylum Proteobacteria. The biofilm model was used to identify gut nutrient conditions that resulted in C. difficile-associated dysbiosis characterized by large increases in C. difficile and E. coli abundances and large decreases in F. prausnitzii abundance. We tuned the model to produce species abundances and short-chain fatty acid levels consistent with available data for healthy individuals. The model predicted that experimentally-observed host-microbiota perturbations resulting in decreased carbohydrate/increased amino acid levels and/or increased primary bile acid levels would induce large increases in C. difficile abundance and decreases in F. prausnitzii abundance. By adding the experimentally-observed perturbation of increased host nitrate secretion, the model also was able to predict increased E. coli abundance associated with C. difficile dysbiosis. In addition to rationalizing known connections between nutrient levels and disease progression, the model generated hypotheses for future testing and has the capability to support the development of new treatment strategies for C. difficile gut infections.
Collapse
|
237
|
Zong E, Yan S, Wang M, Yin L, Wang Q, Yin J, Li J, Li Y, Ding X, Huang P, He S, Yang H, Yin Y. The effects of dietary supplementation with hyodeoxycholic acid on the differentiation and function of enteroendocrine cells and the serum biochemical indices in weaned piglets. J Anim Sci 2019; 97:5315629. [PMID: 30753616 PMCID: PMC6447273 DOI: 10.1093/jas/skz059] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 02/09/2019] [Indexed: 08/03/2023] Open
Abstract
Bile acid, a cholesterol metabolite, promotes gastrointestinal tract digestion and absorption of cholesterol, lipids, and fat-soluble vitamins. It is a signaling regulatory molecule that influences a variety of endocrinal and metabolic activities. This study investigated the effects hyodeoxycholic acid (HDCA) as a dietary supplement on endocrine cell differentiation and function and weaned piglet serum biochemical indices. Sixteen piglets (Duroc × [Landrace × Yorkshire]) were individually housed and weaned at 21 days of age (body weight of 6.14 ± 0.22 kg). Uniform weight animals were randomly assigned to one of two treatments (eight replicate pens per treatment and one piglet per pen). The treatments were 1) base diet (control); and 2) base diet supplemented with 2 g/kg of HDCA. Control and HDCA piglet numbers of CgA-positive cells per crypt did not differ. HDCA CgA-positive cells numbers decreased (P < 0.05) in the jejunal villi, showed a tendency to decrease (P < 0.10) in the ileal villi, and showed tendency toward an increase (P < 0.10) in the duodenal villi compared to the controls. The HDCA diet led to a decline in GLP-2 (P < 0.01) concentrations, but did not affect plasma GLP-1. HDCA supplementation increased (P < 0.05) the mRNA expression of jejunal Insm1, Sst, PG, and Gast, but decreased (P < 0.05) duodenal expression of Insm1, jejunal Pdx1, and ileal NeuroD1. HDCA elevated GLO and IgA (P < 0.05) serum concentrations and decreased the A/G ratio (P < 0.05). TP and IgG serum levels tended to increase compared to the control group. These results indicate that dietary HDCA at 2 g/kg may regulate enteroendocrine cell differentiation and play a role in increasing weaned piglet humoral immunity.
Collapse
Affiliation(s)
- Enyan Zong
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shanling Yan
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Meiwei Wang
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Lanmei Yin
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Qiye Wang
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Jia Yin
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Jianzhong Li
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Yali Li
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Xueqin Ding
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Pengfei Huang
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Shanping He
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
| | - Huansheng Yang
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
- Chinese Academy of Science, Institute of Subtropical Agriculture, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, Hunan, China
| | - Yulong Yin
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, Hunan, China
- Chinese Academy of Science, Institute of Subtropical Agriculture, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha, Hunan, China
| |
Collapse
|
238
|
Leslie JL, Vendrov KC, Jenior ML, Young VB. The Gut Microbiota Is Associated with Clearance of Clostridium difficile Infection Independent of Adaptive Immunity. mSphere 2019; 4:e00698-18. [PMID: 30700514 PMCID: PMC6354811 DOI: 10.1128/mspheredirect.00698-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 01/05/2019] [Indexed: 12/26/2022] Open
Abstract
Clostridium (Clostridioides) difficile, a Gram-positive, anaerobic bacterium, is the leading single cause of nosocomial infections in the United States. A major risk factor for Clostridium difficile infection (CDI) is prior exposure to antibiotics, as they increase susceptibility to CDI by altering the membership of the microbial community enabling colonization. The importance of the gut microbiota in providing protection from CDI is underscored by the reported 80 to 90% success rate of fecal microbial transplants in treating recurrent infections. Adaptive immunity, specifically humoral immunity, is also sufficient to protect from both acute and recurrent CDI. However, the role of the adaptive immune system in mediating clearance of C. difficile has yet to be resolved. Using murine models of CDI, we found that adaptive immunity is dispensable for clearance of C. difficile However, random forest analysis using only two members of the resident bacterial community correctly identified animals that would go on to clear the infection with 66.7% accuracy. These findings indicate that the indigenous gut microbiota independent of adaptive immunity facilitates clearance of C. difficile from the murine gastrointestinal tract.IMPORTANCEClostridium difficile infection is a major cause of morbidity and mortality in hospitalized patients in the United States. Currently, the role of the adaptive immune response in modulating levels of C. difficile colonization is unresolved. This work suggests that the indigenous gut microbiota is a main factor that promotes clearance of C. difficile from the GI tract. Our results show that clearance of C. difficile can occur without contributions from the adaptive immune response. This study also has implications for the design of preclinical studies testing the efficacy of vaccines on clearance of bacterial pathogens, as inherent differences in the baseline community structure of animals may bias findings.
Collapse
Affiliation(s)
- Jhansi L Leslie
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kimberly C Vendrov
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Matthew L Jenior
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| |
Collapse
|
239
|
Carlucci C, Jones CS, Oliphant K, Yen S, Daigneault M, Carriero C, Robinson A, Petrof EO, Weese JS, Allen-Vercoe E. Effects of defined gut microbial ecosystem components on virulence determinants of Clostridioides difficile. Sci Rep 2019; 9:885. [PMID: 30696914 PMCID: PMC6351598 DOI: 10.1038/s41598-018-37547-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022] Open
Abstract
Many cases of Clostridioides difficile infection (CDI) are poorly responsive to standard antibiotic treatment strategies, and often patients suffer from recurrent infections characterized by severe diarrhea. Our group previously reported the successful cure of two patients with recurrent CDI using a standardized stool-derived microbial ecosystem therapeutic (MET-1). Using an in vitro model of the distal gut to support bacterial communities, we characterized the metabolite profiles of two defined microbial ecosystems derived from healthy donor stool (DEC58, and a subset community, MET-1), as well as an ecosystem representative of a dysbiotic state (ciprofloxacin-treated DEC58). The growth and virulence determinants of two C. difficile strains were then assessed in response to components derived from the ecosystems. CD186 (ribotype 027) and CD973 (ribotype 078) growth was decreased upon treatment with DEC58 metabolites compared to ciprofloxacin-treated DEC58 metabolites. Furthermore, CD186 TcdA and TcdB secretion was increased following treatment with ciprofloxacin-treated DEC58 spent medium compared to DEC58 spent medium alone. The net metabolic output of C. difficile was also modulated in response to spent media from defined microbial ecosystems, although several metabolite levels were divergent across the two strains examined. Further investigation of these antagonistic properties will guide the development of microbiota-based therapeutics for CDI.
Collapse
Affiliation(s)
- Christian Carlucci
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.
| | - Carys S Jones
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Sandi Yen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Michelle Daigneault
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Charley Carriero
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Avery Robinson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Elaine O Petrof
- Division of Infectious Diseases/Gastrointestinal Diseases Research Unit, Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| |
Collapse
|
240
|
The Impact of Cholecystectomy on the Gut Microbiota: A Case-Control Study. J Clin Med 2019; 8:jcm8010079. [PMID: 30641967 PMCID: PMC6352247 DOI: 10.3390/jcm8010079] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 12/21/2022] Open
Abstract
Cholecystectomy alters the bile flow into the intestine and the enterohepatic circulation of the bile acids; this may affect the gut microbiota. We assessed the gut microbiota composition of patients who had undergone cholecystectomy and compared with those who had not. From a cohort of 1463 adult participants who underwent comprehensive health screening examinations, 27 subjects who had undergone cholecystectomy (cholecystectomy group) and 81 age- and sex-matched subjects who had not (control group) were selected. Clinical parameters were collected and compared. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from fecal samples. We evaluated differences in the overall microbial composition and in the abundance of taxa. The two groups were comparable with respect to clinical characteristics and laboratory results. The actual number of taxa observed in a sample (observed features) was significantly lower in the cholecystectomy group than in the control group (p = 0.042). The beta diversity of Jaccard distance index was significantly different between the two groups (p = 0.027). Blautia obeum and Veillonella parvula were more abundant in the cholecystectomy group. The difference in the diversity of the gut microbiota between the cholecystectomy and control groups was subtle. However, B. obeum and V. parvula, which have azoreductase activity, were more abundant in the cholecystectomy group. The impact of such changes in the gut microbiota on health remains to be determined.
Collapse
|
241
|
Dieterle MG, Rao K, Young VB. Novel therapies and preventative strategies for primary and recurrent Clostridium difficile infections. Ann N Y Acad Sci 2019; 1435:110-138. [PMID: 30238983 PMCID: PMC6312459 DOI: 10.1111/nyas.13958] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 12/15/2022]
Abstract
Clostridium difficile is the leading infectious cause of antibiotic-associated diarrhea and colitis. C. difficile infection (CDI) places a heavy burden on the healthcare system, with nearly half a million infections yearly and an approximate 20% recurrence risk after successful initial therapy. The high incidence has driven new research on improved prevention such as the emerging use of probiotics, intestinal microbiome manipulation during antibiotic therapies, vaccinations, and newer antibiotics that reduce the disruption of the intestinal microbiome. While the treatment of acute C. difficile is effective in most patients, it can be further optimized by adjuvant therapies that improve the initial treatment success and decrease the risk of subsequent recurrence. Finally, the high risk of recurrence has led to multiple emerging therapies that target toxin activity, recovery of the intestinal microbial community, and elimination of latent C. difficile in the intestine. In summary, CDIs illustrate the complex interaction among host physiology, microbial community, and pathogen that requires specific therapies to address each of the factors leading to primary infection and recurrence.
Collapse
Affiliation(s)
- Michael G. Dieterle
- University of Michigan Medical School, Medical Scientist Training Program (MSTP), Ann Arbor, Michigan
- University of Michigan Department of Microbiology and Immunology, Ann Arbor, Michigan
| | - Krishna Rao
- University of Michigan Department of Internal Medicine, Infectious Diseases Division, Ann Arbor, Michigan
| | - Vincent B. Young
- University of Michigan Department of Microbiology and Immunology, Ann Arbor, Michigan
- University of Michigan Department of Internal Medicine, Infectious Diseases Division, Ann Arbor, Michigan
| |
Collapse
|
242
|
Sorbara MT, Pamer EG. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them. Mucosal Immunol 2019; 12:1-9. [PMID: 29988120 PMCID: PMC6312114 DOI: 10.1038/s41385-018-0053-0] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/15/2018] [Accepted: 05/27/2018] [Indexed: 02/08/2023]
Abstract
The communities of bacteria that reside in the intestinal tract are in constant competition within this dynamic and densely colonized environment. At homeostasis, the equilibrium that exists between these species and strains is shaped by their metabolism and also by pathways of active antagonism, which drive competition with related and unrelated strains. Importantly, these normal activities contribute to colonization resistance by the healthy microbiota, which includes the ability to prevent the expansion of potential pathogens. Disruption of the microbiota, resulting from, for example, inflammation or antibiotic use, can reduce colonization resistance. Pathogens that engraft following disruption of the microbiota are often adapted to expand into newly created niches and compete in an altered gut environment. In this review, we examine both the interbacterial mechanisms of colonization resistance and the strategies of pathogenic strains to exploit gaps in colonization resistance.
Collapse
Affiliation(s)
- Matthew T. Sorbara
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G. Pamer
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
- Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
243
|
Libertucci J, Young VB. The role of the microbiota in infectious diseases. Nat Microbiol 2018; 4:35-45. [PMID: 30546094 DOI: 10.1038/s41564-018-0278-4] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 09/28/2018] [Indexed: 02/07/2023]
Abstract
The human body is colonized by a diverse community of microorganisms collectively referred to as the microbiota. Here, we describe how the human microbiota influences susceptibility to infectious diseases using examples from the respiratory, gastrointestinal and female reproductive tract. We will discuss how interactions between the host, the indigenous microbiota and non-native microorganisms, including bacteria, viruses and fungi, can alter the outcome of infections. This Review Article will highlight the complex mechanisms by which the microbiota mediates colonization resistance, both directly and indirectly, against infectious agents. Strategies for the therapeutic modulation of the microbiota to prevent or treat infectious diseases will be discussed, and we will review potential therapies that directly target the microbiota, including prebiotics, probiotics, synbiotics and faecal microbiota transplantation.
Collapse
Affiliation(s)
- Josie Libertucci
- Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
| |
Collapse
|
244
|
Tam J, Hamza T, Ma B, Chen K, Beilhartz GL, Ravel J, Feng H, Melnyk RA. Host-targeted niclosamide inhibits C. difficile virulence and prevents disease in mice without disrupting the gut microbiota. Nat Commun 2018; 9:5233. [PMID: 30531960 PMCID: PMC6286312 DOI: 10.1038/s41467-018-07705-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/19/2018] [Indexed: 12/13/2022] Open
Abstract
Clostridium difficile is the leading cause of nosocomial diarrhea and colitis in the industrialized world. Disruption of the protective gut microbiota by antibiotics enables colonization by multidrug-resistant C. difficile, which secrete up to three different protein toxins that are responsible for the gastrointestinal sequelae. Oral agents that inhibit the damage induced by toxins, without altering the gut microbiota, are urgently needed to prevent primary disease and break the cycle of antibiotic-induced disease recurrence. Here, we show that the anthelmintic drug, niclosamide, inhibits the pathogenesis of all three toxins by targeting a host process required for entry into colonocytes by each toxin. In mice infected with an epidemic strain of C. difficile, expressing all three toxins, niclosamide reduced both primary disease and recurrence, without disrupting the diversity or composition of the gut microbiota. Given its excellent safety profile, niclosamide may address an important unmet need in preventing C. difficile primary and recurrent diseases. Clostridium difficile causes diarrhea and colitis by producing up to three different protein toxins. Here, Tam et al. show that an anthelmintic drug, niclosamide, inhibits the pathogenesis of all three toxins by targeting a host process required for toxin entry into host cells, without disrupting the gut microbiota.
Collapse
Affiliation(s)
- John Tam
- Molecular Medicine, Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Therwa Hamza
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD, 21201, USA
| | - Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kevin Chen
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD, 21201, USA
| | - Greg L Beilhartz
- Molecular Medicine, Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hanping Feng
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, MD, 21201, USA
| | - Roman A Melnyk
- Molecular Medicine, Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| |
Collapse
|
245
|
Ünal CM, Berges M, Smit N, Schiene-Fischer C, Priebe C, Strowig T, Jahn D, Steinert M. PrsA2 (CD630_35000) of Clostridioides difficile Is an Active Parvulin-Type PPIase and a Virulence Modulator. Front Microbiol 2018; 9:2913. [PMID: 30564207 PMCID: PMC6288519 DOI: 10.3389/fmicb.2018.02913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/13/2018] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is the main cause for nosocomial antibiotic associated diarrhea and has become a major burden for the health care systems of industrial countries. Its main virulence factors, the small GTPase glycosylating toxins TcdA and TcdB, are extensively studied. In contrast, the contribution of other factors to development and progression of C. difficile infection (CDI) are only insufficiently understood. Many bacterial peptidyl-prolyl-cis/trans-isomerases (PPIases) have been described in the context of virulence. Among them are the parvulin-type PrsA-like PPIases of Gram-positive bacteria. On this basis, we identified CD630_35000 as the PrsA2 homolog in C. difficile and conducted its enzymatic and phenotypic characterization in order to assess its involvement during C. difficile infection. For this purpose, wild type CdPrsA2 and mutant variants carrying amino acid exchanges mainly in the PPIase domain were recombinantly produced. Recombinant CdPrsA2 showed PPIase activity toward the substrate peptide Ala-Xaa-Pro-Phe with a preference for positively charged amino acids preceding the proline residue. Mutation of conserved residues in its active site pocket impaired the enzymatic activity. A PrsA2 deficient mutant was generated in the C. difficile 630Δerm background using the ClosTron technology. Inactivation of prsA2 resulted in a reduced germination rate in response to taurocholic acid, and in a slight increase in resistance to the secondary bile acids LCA and DCA. Interestingly, in the absence of PrsA2 colonization of mice by C. difficile 630 was significantly reduced. We concluded that CdPrsA2 is an active PPIase that acts as a virulence modulator by influencing crucial processes like sporulation, germination and bile acid resistance resulting in attenuated mice colonization.
Collapse
Affiliation(s)
- Can Murat Ünal
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Türk-Alman Üniversitesi, Moleküler Biyoteknoloji Bölümü, Istanbul, Turkey
| | - Mareike Berges
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nathiana Smit
- Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Cordelia Schiene-Fischer
- Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Christina Priebe
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Till Strowig
- Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Braunschweig, Germany.,Helmholtz-Zentrum für Infektionsforschung, Braunschweig, Germany.,Braunschweig Integrated Centre of Systems Biology, Braunschweig, Germany
| |
Collapse
|
246
|
Palmieri LJ, Rainteau D, Sokol H, Beaugerie L, Dior M, Coffin B, Humbert L, Eguether T, Bado A, Hoys S, Janoir C, Duboc H. Inhibitory Effect of Ursodeoxycholic Acid on Clostridium difficile Germination Is Insufficient to Prevent Colitis: A Study in Hamsters and Humans. Front Microbiol 2018; 9:2849. [PMID: 30524414 PMCID: PMC6262072 DOI: 10.3389/fmicb.2018.02849] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/06/2018] [Indexed: 12/12/2022] Open
Abstract
Introduction: Bile acids (BA) influence germination and growth of Clostridium difficile. Ursodeoxycholic acid (UDCA), a BA minor in human, used for cholestatic liver diseases, inhibits germination and growth of C. difficile in vitro, but was never tested in vivo with an infectious challenge versus control. We hypothesized that UDCA could prevent CDI. We evaluated the effects of UDCA on C. difficile in vitro and in hamsters, with pharmacokinetics study and with an infectious challenge. Then, we studied CDI incidence in UDCA–treated patients. Methods: We evaluated germination and growth of C. difficile, with 0.01, 0.05, and 0.1% UDCA. We analyzed fecal BA of hamsters receiving antibiotics and UDCA (50 mg/kg/day), antibiotics, or UDCA alone. Then, we challenged with spores of C. difficile at D6 hamsters treated with UDCA (50 mg/kg/day) from D1 to D13, versus control. In human, we analyzed the database of a cohort on CDI in acute flares of inflammatory bowel disease (IBD). As PSC-IBD patients were under UDCA treatment, we compared PSC-IBD patients to IBD patients without PSC. Results:In vitro, UDCA inhibited germination and growth of C. difficile at 0.05 and 0.1%, competing with 0.1% TCA (with 0.1%: 0.05% ± 0.05% colony forming unit versus 100% ± 0%, P < 0.0001). In hamsters, UDCA reached high levels only when administered with antibiotics (43.5% UDCA at D5). Without antibiotics, UDCA was in small amount in feces (max. 4.28%), probably because of UDCA transformation into LCA by gut microbiota. During infectious challenge, mortality was similar in animals treated or not with UDCA (62.5%, n = 5/8, P = 0.78). UDCA percentage was high, similar and with the same kinetics in dead and surviving hamsters. However, dead hamsters had a higher ratio of primary over secondary BA compared to surviving hamsters. 9% (n = 41/404) of IBD patients without PSC had a CDI, versus 25% (n = 4/12) of PSC-IBD patients treated with UDCA. Conclusion: We confirmed the inhibitory effect of UDCA on growth and germination of C. difficile in vitro, with 0.05 or 0.1% UDCA. However, in our hamster model, UDCA was inefficient to prevent CDI, despite high levels of UDCA in feces. Patients with PSC-IBD treated with UDCA did not have less CDI than IBD patients.
Collapse
Affiliation(s)
- Lola-Jade Palmieri
- ERL INSERM U1157/UMR7203, PM2, Assistance Publique-Hôpitaux de Paris (AP-HP), Faculté de Médecine Saint-Antoine, Sorbonne Université, Paris, France.,EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France.,INSERM U1149, Centre de Recherche sur l'Inflammation, Faculté de Médecine Paris Diderot, Université Paris Diderot, Paris, France
| | - Dominique Rainteau
- ERL INSERM U1157/UMR7203, PM2, Assistance Publique-Hôpitaux de Paris (AP-HP), Faculté de Médecine Saint-Antoine, Sorbonne Université, Paris, France
| | - Harry Sokol
- ERL INSERM U1157/UMR7203, PM2, Assistance Publique-Hôpitaux de Paris (AP-HP), Faculté de Médecine Saint-Antoine, Sorbonne Université, Paris, France.,Department of Gastroenterology and Nutrition, Saint Antoine Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Laurent Beaugerie
- ERL INSERM U1157/UMR7203, PM2, Assistance Publique-Hôpitaux de Paris (AP-HP), Faculté de Médecine Saint-Antoine, Sorbonne Université, Paris, France.,Department of Gastroenterology and Nutrition, Saint Antoine Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Marie Dior
- Department of Gastroenterology, Louis Mourier Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Benoit Coffin
- INSERM U1149, Centre de Recherche sur l'Inflammation, Faculté de Médecine Paris Diderot, Université Paris Diderot, Paris, France.,Department of Gastroenterology, Louis Mourier Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Lydie Humbert
- ERL INSERM U1157/UMR7203, PM2, Assistance Publique-Hôpitaux de Paris (AP-HP), Faculté de Médecine Saint-Antoine, Sorbonne Université, Paris, France
| | - Thibaut Eguether
- ERL INSERM U1157/UMR7203, PM2, Assistance Publique-Hôpitaux de Paris (AP-HP), Faculté de Médecine Saint-Antoine, Sorbonne Université, Paris, France
| | - André Bado
- INSERM U1149, Centre de Recherche sur l'Inflammation, Faculté de Médecine Paris Diderot, Université Paris Diderot, Paris, France
| | - Sandra Hoys
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Claire Janoir
- EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Henri Duboc
- INSERM U1149, Centre de Recherche sur l'Inflammation, Faculté de Médecine Paris Diderot, Université Paris Diderot, Paris, France.,Department of Gastroenterology, Louis Mourier Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| |
Collapse
|
247
|
Kennedy EA, King KY, Baldridge MT. Mouse Microbiota Models: Comparing Germ-Free Mice and Antibiotics Treatment as Tools for Modifying Gut Bacteria. Front Physiol 2018; 9:1534. [PMID: 30429801 PMCID: PMC6220354 DOI: 10.3389/fphys.2018.01534] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/11/2018] [Indexed: 12/14/2022] Open
Abstract
As the intestinal microbiota has become better appreciated as necessary for maintenance of physiologic homeostasis and also as a modulator of disease processes, there has been a corresponding increase in manipulation of the microbiota in mouse models. While germ-free mouse models are generally considered to be the gold standard for studies of the microbiota, many investigators turn to antibiotics treatment models as a rapid, inexpensive, and accessible alternative. Here we describe and compare these two approaches, detailing advantages and disadvantages to both. Further, we detail what is known about the effects of antibiotics treatment on cell populations, cytokines, and organs, and clarify how this compares to germ-free models. Finally, we briefly describe recent findings regarding microbiota regulation of infectious diseases and other immunologic challenges by the microbiota, and highlight important future directions and considerations for the use of antibiotics treatment in manipulation of the microbiota.
Collapse
Affiliation(s)
- Elizabeth A. Kennedy
- Division of Infectious Diseases, Department of Medicine, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Katherine Y. King
- Section of Infectious Diseases, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, United States
| |
Collapse
|
248
|
Gut microbiome disruption altered the biotransformation and liver toxicity of arsenic in mice. Arch Toxicol 2018; 93:25-35. [PMID: 30357543 DOI: 10.1007/s00204-018-2332-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022]
Abstract
The mammalian gut microbiome (GM) plays a critical role in xenobiotic biotransformation and can profoundly affect the toxic effects of xenobiotics. Previous in vitro studies have demonstrated that gut bacteria have the capability to metabolize arsenic (As); however, the specific roles of the gut microbiota in As metabolism in vivo and the toxic effects of As are largely unknown. Here, we administered sodium arsenite to conventionally raised mice (with normal microbiomes) and GM-disrupted mice with antibiotics to investigate the role of the gut microbiota in As biotransformation and its toxicity. We found that the urinary total As levels of GM-disrupted mice were much higher, but the fecal total As levels were lower, than the levels in the conventionally raised mice. In vitro experiments, in which the GM was incubated with As, also demonstrated that the gut bacteria could adsorb or take up As and thus reduce the free As levels in the culture medium. With the disruption of the gut microbiota, arsenic biotransformation was significantly perturbed. Of note, the urinary monomethylarsonic acid/dimethylarsinic acid ratio, a biomarker of arsenic metabolism and toxicity, was markedly increased. Meanwhile, the expression of genes of one-carbon metabolism, including folr2, bhmt, and mthfr, was downregulated, and the liver S-adenosylmethionine (SAM) levels were significantly decreased in the As-treated GM-disrupted mice only. Moreover, As exposure altered the expression of genes of the p53 signaling pathway, and the expression of multiple genes associated with hepatocellular carcinoma (HCC) was also changed in the As-treated GM-disrupted mice only. Collectively, disruption of the GM enhances the effect of As on one-carbon metabolism, which could in turn affect As biotransformation. GM disruption also increases the toxic effects of As and may increase the risk of As-induced HCC in mice.
Collapse
|
249
|
Xu Q, Gu S, Chen Y, Quan J, Lv L, Chen D, Zheng B, Xu L, Li L. Protective Effect of Pediococcus pentosaceus LI05 Against Clostridium difficile Infection in a Mouse Model. Front Microbiol 2018; 9:2396. [PMID: 30356740 PMCID: PMC6189400 DOI: 10.3389/fmicb.2018.02396] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/19/2018] [Indexed: 12/26/2022] Open
Abstract
Clostridium difficile infection (CDI) is a major cause of infectious diarrhea among hospitalized patients. Probiotics could be instrumental in restoring the intestinal dysbiosis caused by CDI. Here, we examined the protective effect of Pediococcus pentosaceus LI05 in a mouse CDI model. C57BL/6 mice were administrated P. pentosaceus LI05 (LI05 group) or sterile anaerobic PBS (CDI group) everyday for 14 days. Mice were exposed to antibiotics cocktail for 5 days; then challenged with C. difficile strain VPI10463. Mice were monitored daily for survival and weight loss. Colonic tissue and serum samples were assessed for intestinal histopathology, intestinal barrier function and systemic inflammation. The oral administration of P. pentosaceus LI05 improved the survival rate and alleviated the histopathological impact of C. difficile. Compared to the CDI group, the levels of inflammatory mediators in the colon as well as inflammatory cytokines and chemokines in serum were substantially attenuated in the LI05 group. P. pentosaceus LI05 alleviated the CDI-induced of disruption of ZO-1, occludin and claudin-1. Additionally, fecal microbiome analysis showed an enrichment in the abundance of the Porphyromonadaceae and Rikenellaceae, while, the relative abundance of Enterobacteriaceae were decreased. Our results demonstrated that the preventive effect of P. pentosaceus LI05 against CDI was mediated via improving tight junction proteins and down-regulating the inflammatory response. Therefore, P. pentosaceus LI05 could be a promising probiotic in CDI.
Collapse
Affiliation(s)
- Qiaomai Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Silan Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiazheng Quan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dazhi Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lichen Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| |
Collapse
|
250
|
|