1
|
Spigaglia P. Clostridioides difficile and Gut Microbiota: From Colonization to Infection and Treatment. Pathogens 2024; 13:646. [PMID: 39204246 PMCID: PMC11357127 DOI: 10.3390/pathogens13080646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
Clostridioides difficile is the main causative agent of antibiotic-associated diarrhea (AAD) in hospitals in the developed world. Both infected patients and asymptomatic colonized individuals represent important transmission sources of C. difficile. C. difficile infection (CDI) shows a large range of symptoms, from mild diarrhea to severe manifestations such as pseudomembranous colitis. Epidemiological changes in CDIs have been observed in the last two decades, with the emergence of highly virulent types and more numerous and severe CDI cases in the community. C. difficile interacts with the gut microbiota throughout its entire life cycle, and the C. difficile's role as colonizer or invader largely depends on alterations in the gut microbiota, which C. difficile itself can promote and maintain. The restoration of the gut microbiota to a healthy state is considered potentially effective for the prevention and treatment of CDI. Besides a fecal microbiota transplantation (FMT), many other approaches to re-establishing intestinal eubiosis are currently under investigation. This review aims to explore current data on C. difficile and gut microbiota changes in colonized individuals and infected patients with a consideration of the recent emergence of highly virulent C. difficile types, with an overview of the microbial interventions used to restore the human gut microbiota.
Collapse
Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Roma, Italy
| |
Collapse
|
2
|
Pensinger DA, Dobrila HA, Stevenson DM, Hryckowian ND, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters virulence phenotypes in Clostridioides difficile. mBio 2024; 15:e0253523. [PMID: 38289141 PMCID: PMC10936429 DOI: 10.1128/mbio.02535-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/20/2023] [Indexed: 02/13/2024] Open
Abstract
The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short-chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells and is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of a butyrogenic pathway(s) in C. difficile coincides with alterations in toxin release and sporulation. Together, this work highlights butyrate as a marker of a C. difficile-inhospitable environment to which C. difficile responds by releasing its diarrheagenic toxins and producing environmentally resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate alters C. difficile virulence in the face of a highly competitive and dynamic gut environment.IMPORTANCEThe gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile, but the molecular basis of this colonization resistance is incompletely understood, which hinders the development of novel therapeutic interventions for C. difficile infection (CDI). We investigated how C. difficile responds to butyrate, an end-product of gut microbiome community metabolism which inhibits C. difficile growth. We show that exogenously produced butyrate is internalized into C. difficile, which inhibits C. difficile growth by interfering with its own butyrate production. This growth inhibition coincides with increased toxin release from C. difficile cells and the production of environmentally resistant spores necessary for transmission between hosts. Future work to disentangle the molecular mechanisms underlying these growth and virulence phenotypes will likely lead to new strategies to restrict C. difficile growth in the gut and minimize its pathogenesis during CDI.
Collapse
Affiliation(s)
- Daniel A. Pensinger
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Horia A. Dobrila
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicole D. Hryckowian
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| |
Collapse
|
3
|
Jernfors T, Lavrinienko A, Vareniuk I, Landberg R, Fristedt R, Tkachenko O, Taskinen S, Tukalenko E, Mappes T, Watts PC. Association between gut health and gut microbiota in a polluted environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169804. [PMID: 38184263 DOI: 10.1016/j.scitotenv.2023.169804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/28/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, digestion of otherwise undigestible foodstuffs, and impacts on host behaviour. Exposure to stressors, such as environmental pollution, parasites, and/or predators, can alter the composition of the gut microbiome, potentially affecting host-microbiome interactions that can be manifest in the host as, for example, metabolic dysfunction or inflammation. However, whether a change in gut microbiota in wild animals associates with a change in host condition is seldom examined. Thus, we quantified whether wild bank voles inhabiting a polluted environment, areas where there are environmental radionuclides, exhibited a change in gut microbiota (using 16S amplicon sequencing) and concomitant change in host health using a combined approach of transcriptomics, histological staining analyses of colon tissue, and quantification of short-chain fatty acids in faeces and blood. Concomitant with a change in gut microbiota in animals inhabiting contaminated areas, we found evidence of poor gut health in the host, such as hypotrophy of goblet cells and likely weakened mucus layer and related changes in Clca1 and Agr2 gene expression, but no visible inflammation in colon tissue. Through this case study we show that inhabiting a polluted environment can have wide reaching effects on the gut health of affected animals, and that gut health and other host health parameters should be examined together with gut microbiota in ecotoxicological studies.
Collapse
Affiliation(s)
- Toni Jernfors
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland.
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland; Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Igor Vareniuk
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Rikard Fristedt
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Olena Tkachenko
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Sara Taskinen
- Department of Mathematics and Statistics, University of Jyväskylä, FI-40014, Finland
| | - Eugene Tukalenko
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, 020000, Ukraine
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
| |
Collapse
|
4
|
Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell Host Microbe 2024; 32:209-226.e7. [PMID: 38215740 PMCID: PMC10923022 DOI: 10.1016/j.chom.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/14/2024]
Abstract
Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.
Collapse
Affiliation(s)
- Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Martin Stražar
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Eric M Brown
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Temple
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amy Deik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bullock
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Jeanfavre
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kerry Pierce
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shen Jin
- Translational Microbiome Data Integration, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | - Marie-Madlen Pust
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Zach Costliow
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R Mack
- Division of Gastroenterology, Hepatology & Nutrition, Children's Hospital of Eastern Ontario and University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Anne M Griffiths
- Division of Gastroenterology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thomas Walters
- Division of Gastroenterology, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Brendan M Boyle
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Hera Vlamakis
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeffrey Hyams
- Connecticut Children's Medical Center, Division of Digestive Diseases, Hartford, CT 06106, USA
| | - Lee Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Clary B Clish
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
5
|
Pensinger DA, Dobrila HA, Stevenson DM, Davis NM, Amador-Noguez D, Hryckowian AJ. Exogenous butyrate inhibits butyrogenic metabolism and alters expression of virulence genes in Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548018. [PMID: 37461482 PMCID: PMC10350080 DOI: 10.1101/2023.07.06.548018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
The gut microbiome engenders colonization resistance against the diarrheal pathogen Clostridioides difficile but the molecular basis of this colonization resistance is incompletely understood. A prominent class of gut microbiome-produced metabolites important for colonization resistance against C. difficile is short chain fatty acids (SCFAs). In particular, one SCFA (butyrate) decreases the fitness of C. difficile in vitro and is correlated with C. difficile-inhospitable gut environments, both in mice and in humans. Here, we demonstrate that butyrate-dependent growth inhibition in C. difficile occurs under conditions where C. difficile also produces butyrate as a metabolic end product. Furthermore, we show that exogenous butyrate is internalized into C. difficile cells, is incorporated into intracellular CoA pools where it is metabolized in a reverse (energetically unfavorable) direction to crotonyl-CoA and (S)-3-hydroxybutyryl-CoA and/or 4-hydroxybutyryl-CoA. This internalization of butyrate and reverse metabolic flow of butyrogenic pathway(s) in C. difficile coincides with alterations in toxin production and sporulation. Together, this work highlights butyrate as a signal of a C. difficile inhospitable environment to which C. difficile responds by producing its diarrheagenic toxins and producing environmentally-resistant spores necessary for transmission between hosts. These findings provide foundational data for understanding the molecular and genetic basis of how C. difficile growth is inhibited by butyrate and how butyrate serves as a signal to alter C. difficile virulence in the face of a highly competitive and dynamic gut environment.
Collapse
Affiliation(s)
- Daniel A. Pensinger
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Horia A. Dobrila
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Nicole M. Davis
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Andrew J. Hryckowian
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| |
Collapse
|
6
|
Butyrate Differentiates Permissiveness to Clostridioides difficile Infection and Influences Growth of Diverse C. difficile Isolates. Infect Immun 2023; 91:e0057022. [PMID: 36692308 PMCID: PMC9933713 DOI: 10.1128/iai.00570-22] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
A disrupted "dysbiotic" gut microbiome engenders susceptibility to the diarrheal pathogen Clostridioides difficile by impacting the metabolic milieu of the gut. Diet, in particular the microbiota-accessible carbohydrates (MACs) found in dietary fiber, is one of the most powerful ways to affect the composition and metabolic output of the gut microbiome. As such, diet is a powerful tool for understanding the biology of C. difficile and for developing alternative approaches for coping with this pathogen. One prominent class of metabolites produced by the gut microbiome is short-chain fatty acids (SCFAs), the major metabolic end products of MAC metabolism. SCFAs are known to decrease the fitness of C. difficile in vitro, and high intestinal SCFA concentrations are associated with reduced fitness of C. difficile in animal models of C. difficile infection (CDI). Here, we use controlled dietary conditions (8 diets that differ only by MAC composition) to show that C. difficile fitness is most consistently impacted by butyrate, rather than the other two prominent SCFAs (acetate and propionate), during murine model CDI. We similarly show that butyrate concentrations are lower in fecal samples from humans with CDI than in those from healthy controls. Finally, we demonstrate that butyrate impacts growth in diverse C. difficile isolates. These findings provide a foundation for future work which will dissect how butyrate directly impacts C. difficile fitness and will lead to the development of diverse approaches distinct from antibiotics or fecal transplant, such as dietary interventions, for mitigating CDI in at-risk human populations. IMPORTANCE Clostridioides difficile is a leading cause of infectious diarrhea in humans, and it imposes a tremendous burden on the health care system. Current treatments for C. difficile infection (CDI) include antibiotics and fecal microbiota transplant, which contribute to recurrent CDIs and face major regulatory hurdles, respectively. Therefore, there is an ongoing need to develop new ways to cope with CDI. Notably, a disrupted "dysbiotic" gut microbiota is the primary risk factor for CDI, but we incompletely understand how a healthy microbiota resists CDI. Here, we show that a specific molecule produced by the gut microbiota, butyrate, is negatively associated with C. difficile burdens in humans and in a mouse model of CDI and that butyrate impedes the growth of diverse C. difficile strains in pure culture. These findings help to build a foundation for designing alternative, possibly diet-based, strategies for mitigating CDI in humans.
Collapse
|
7
|
Chen YY, Tun HM, Field CJ, Mandhane PJ, Moraes TJ, Simons E, Turvey SE, Subbarao P, Scott JA, Kozyrskyj AL. Impact of Cesarean Delivery and Breastfeeding on Secretory Immunoglobulin A in the Infant Gut Is Mediated by Gut Microbiota and Metabolites. Metabolites 2023; 13:metabo13020148. [PMID: 36837767 PMCID: PMC9959734 DOI: 10.3390/metabo13020148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/19/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
How gut immunity in early life is shaped by birth in relation to delivery mode, intrapartum antibiotic prophylaxis (IAP) and labor remains undetermined. We aimed to address this gap with a study of secretory Immunoglobulin A (SIgA) in the infant gut that also tested SIgA-stimulating pathways mediated by gut microbiota and metabolites. Among 1017 Canadian full-term infants, gut microbiota of fecal samples collected at 3 and 12 months were profiled using 16S rRNA sequencing; C. difficile was quantified by qPCR; fecal metabolites and SIgA levels were measured by NMR and SIgA enzyme-linked immunosorbent assay, respectively. We assessed the putative causal relationships from birth events to gut microbiota and metabolites, and ultimately to SIgA, in statistical sequential mediation models, adjusted for maternal gravida status in 551 infants. As birth mode influences the ability to breastfeed, the statistical mediating role of breastfeeding status and milk metabolites was also evaluated. Relative to vaginal birth without maternal IAP, cesarean section (CS) after labor was associated with reduced infant gut SIgA levels at 3 months (6.27 vs. 4.85 mg/g feces, p < 0.05); this association was sequentially mediated through gut microbiota and metabolites of microbial or milk origin. Mediating gut microbiota included Enterobacteriaceae, C. difficile, and Streptococcus. The milk or microbial metabolites in CS-SIgA mediating pathways were galactose, fucose, GABA, choline, lactate, pyruvate and 1,2-propanediol. This cohort study documented the impact of birth on infant gut mucosal SIgA. It is the first to characterize gut microbe-metabolite mediated pathways for early-life SIgA maturation, pathways that require experimental verification.
Collapse
Affiliation(s)
- Yuan Yao Chen
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Hein M. Tun
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1C9, Canada
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Catherine J. Field
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Piushkumar J. Mandhane
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Theo J. Moraes
- Department of Pediatrics and Physiology, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Elinor Simons
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB R3A 1S1, Canada
| | - Stuart E. Turvey
- Department of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, BC V6H 0B3, Canada
| | - Padmaja Subbarao
- Department of Pediatrics and Physiology, Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - James A. Scott
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Anita L. Kozyrskyj
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Correspondence: ; Tel.: +1-780-248-5508
| |
Collapse
|
8
|
Horvat S, Mahnic A, Makuc D, Pečnik K, Plavec J, Rupnik M. Children gut microbiota exhibits a different composition and metabolic profile after in vitro exposure to Clostridioides difficile and increases its sporulation. Front Microbiol 2022; 13:1042526. [PMID: 36569098 PMCID: PMC9780542 DOI: 10.3389/fmicb.2022.1042526] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile (Clostridium difficile) infection (CDI) is one of the main public health concerns in adults, while children under 2 years of age are often colonized asymptomatically. In both adults and children, CDI is strongly associated with disturbances in gut microbiota. In this study, an in-vitro model of children gut microbiota was challenged with vegetative cells or a conditioned media of six different toxigenic C. difficile strains belonging to the ribotypes 027, 078, and 176. In the presence of C. difficile or conditioned medium the children gut microbiota diversity decreased and all main phyla (Bacteroidetes, Firmicutes, and Proteobacteria) were affected. The NMR metabolic spectra divided C. difficile exposed children gut microbiota into three clusters. The grouping correlated with nine metabolites (short chain fatty acids, ethanol, phenolic acids and tyramine). All strains were able to grow in the presence of children gut microbiota and showed a high sporulation rate of up to 57%. This high sporulation rate in combination with high asymptomatic carriage in children could contribute to the understanding of the reported role of children in C. difficile transmissions.
Collapse
Affiliation(s)
- Sabina Horvat
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Aleksander Mahnic
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia,Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia
| | - Damjan Makuc
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Klemen Pečnik
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Ljubljana, Slovenia
| | - Maja Rupnik
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia,Centre for Medical Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia,*Correspondence: Maja Rupnik,
| |
Collapse
|
9
|
Gut Microbiota Composition Associated with Clostridioides difficile Colonization and Infection. Pathogens 2022; 11:pathogens11070781. [PMID: 35890026 PMCID: PMC9322938 DOI: 10.3390/pathogens11070781] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 12/12/2022] Open
Abstract
Clostridioides difficile is an anaerobic Gram-positive and spore-forming bacterium. The majority of C. difficile strains produce two toxins, A and B, associated with the development of acute diarrhea and/or colitis. In this review, two situations are distinguished: C. difficile infection (CDI) and asymptomatic colonization (AC). The main objective of this review is to explore the available data related to the link between the gut microbiota and the development of CDI. The secondary aim is to provide more information on why some people colonized with toxigenic C. difficile develop an infection while others show no signs of disease. Several factors, such as the use of antibiotics and proton pump inhibitors, hospitalization, and age, predispose individuals to C. difficile colonization and/or C. difficile infection. The gut microbiota of people with AC showed decreased abundances of Prevotella, Alistipes, Bacteroides, Bifidobacterium, Dorea, Coprococcus, and Roseburia. The gut microbiota of people suffering from CDI showed reductions in the abundances of Lachnospiraceae, Ruminococcaceae, Blautia spp., Prevotella spp., Dialister spp., Bifidobacterium spp., Roseburia spp., Anaerostipes spp., Faecalibacterium spp. and Coprococcus spp., in comparison with healthy people. Furthermore, increases in the abundances of Enterococcaceae and Enterococcus were associated with C. difficile infection.
Collapse
|
10
|
Jenior ML, Papin JA. Computational approaches to understanding Clostridioides difficile metabolism and virulence. Curr Opin Microbiol 2022; 65:108-115. [PMID: 34839237 PMCID: PMC8792252 DOI: 10.1016/j.mib.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 02/03/2023]
Abstract
The progress of infection by Clostridioides difficile is strongly influenced by metabolic cues it encounters as it colonizes the gastrointestinal tract. Both colonization and regulation of virulence have a multi-factorial interaction between host, microbiome, and gene expression cascades. While these connections with metabolism have been understood for some time, many mechanisms of control have remained difficult to directly assay due to high metabolic variability among C. difficile isolates and difficult genetic systems. Computational systems offer a means to interrogate structure of complex or noisy datasets and generate useful, tractable hypotheses to be tested in the laboratory. Recently, in silico techniques have provided powerful insights into metabolic elements of C. difficile infection ranging from virulence regulation to interactions with the gut microbiota. In this review, we introduce and provide context to the methods of computational modeling that have been applied to C. difficile metabolism and virulence thus far. The techniques discussed here have laid the foundation for future multi-scale efforts aimed at understanding the complex interplay of metabolic activity between pathogen, host, and surrounding microbial community in the regulation of C. difficile pathogenesis.
Collapse
Affiliation(s)
- Matthew L Jenior
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA,denotes co-corresponding author
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, Department of Medicine, Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA, Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA,denotes co-corresponding author
| |
Collapse
|
11
|
Munneke MJ, Skaar EP. Ornithine supports C. difficile gut carriage. Nat Metab 2022; 4:7-8. [PMID: 34992298 DOI: 10.1038/s42255-021-00510-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew J Munneke
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
| |
Collapse
|
12
|
Pruss KM, Enam F, Battaglioli E, DeFeo M, Diaz OR, Higginbottom SK, Fischer CR, Hryckowian AJ, Van Treuren W, Dodd D, Kashyap P, Sonnenburg JL. Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization. Nat Metab 2022; 4:19-28. [PMID: 34992297 PMCID: PMC8803604 DOI: 10.1038/s42255-021-00506-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 11/12/2021] [Indexed: 01/08/2023]
Abstract
The enteric pathogen Clostridioides difficile (Cd) is responsible for a toxin-mediated infection that causes more than 200,000 recorded hospitalizations and 13,000 deaths in the United States every year1. However, Cd can colonize the gut in the absence of disease symptoms. Prevalence of asymptomatic colonization by toxigenic Cd in healthy populations is high; asymptomatic carriers are at increased risk of infection compared to noncolonized individuals and may be a reservoir for transmission of Cd infection2,3. Elucidating the molecular mechanisms by which Cd persists in the absence of disease is necessary for understanding pathogenesis and developing refined therapeutic strategies. Here, we show with gut microbiome metatranscriptomic analysis that mice recalcitrant to Cd infection and inflammation exhibit increased community-wide expression of arginine and ornithine metabolic pathways. To query Cd metabolism specifically, we leverage RNA sequencing in gnotobiotic mice infected with two wild-type strains (630 and R20291) and isogenic toxin-deficient mutants of these strains to differentiate inflammation-dependent versus -independent transcriptional states. A single operon encoding oxidative ornithine degradation is consistently upregulated across non-toxigenic Cd strains. Combining untargeted and targeted metabolomics with bacterial and host genetics, we demonstrate that both diet- and host-derived sources of ornithine provide a competitive advantage to Cd, suggesting a mechanism for Cd persistence within a non-inflammatory, healthy gut.
Collapse
Affiliation(s)
- Kali M Pruss
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fatima Enam
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric Battaglioli
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Mary DeFeo
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Oscar R Diaz
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Curt R Fischer
- ChEM-H, Stanford University, Stanford, CA, USA
- Octant Bio, Emeryville, CA, USA
| | - Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dylan Dodd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Purna 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
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Human Microbiome Studies, Stanford, CA, USA.
| |
Collapse
|
13
|
Kubacka A, Rojo D, Muñoz-Batista MJ, Barbas C, Fernández-García M, Ferrer M. Metabolomics reveals synergy between Ag and g-C 3N 4 in Ag/g-C 3N 4 composite photocatalysts: a unique feature among Ag-doped biocidal materials. Metabolomics 2021; 17:53. [PMID: 34061256 DOI: 10.1007/s11306-021-01804-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION The silver/graphitic carbon nitride (Ag/g-C3N4) composite system exerts biocidal activity against the pathogenic bacterium Escherichia coli 1337-H that is stronger than that of well-known silver and titanium oxide (TiO2)-based composites. However, whether the Ag/g-C3N4 composite system has biocidal properties that the parent components do or do not have as separate chemical entities and whether they differ from those in Ag/TiO2 composite photocatalysts have not been clarified. OBJECTIVE We investigated the chemical (cooperative charge handling and electronic properties) and biological (metabolic) effects exerted by the addition of Ag to g-C3N4 and to TiO2. METHODS In this work, we undertook metabolome-wide analysis by liquid chromatography-electrospray ionization-quadrupole-time of flight-mass spectrometry to compare the metabolite profiles of untreated E. coli 1337-H cells or those subjected to disinfection with Ag, g-C3N4, 2Ag/g-C3N4, TiO2 and 2Ag/TiO2. RESULTS While Ag or g-C3N4 moderately affected microbial metabolism according to the mean of the altered metabolites, multiple cell systems contributing to rapid cell death were immediately affected by the light-triggered radical species produced when Ag and g-C3N4 were as xAg/g-C3N4. The effects include drastically reduced production of small metabolites essential for detoxifying reactive oxygen species and those that regulate DNA replication fidelity, cell morphology and energy status. These biological consequences were different from those caused by Ag/TiO2-based biocides, demonstrating the uniqueness of the Ag/g-C3N4 system. CONCLUSIONS Our results support the idea that the unique Ag/g-C3N4 biocidal properties are based on synergistic action and reveal new directions for designing future photocatalysts for use in disinfection and microbial control.
Collapse
Affiliation(s)
- Anna Kubacka
- Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, c/Marie Curie 2, 28049, Madrid, Spain
| | - David Rojo
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Centre for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Mario J Muñoz-Batista
- Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, c/Marie Curie 2, 28049, Madrid, Spain
- Department of Chemical Engineering, University of Granada, Av. de La Fuente Nueva S/N, 18071, Granada, Spain
| | - Coral Barbas
- Department of Chemistry and Biochemistry, Facultad de Farmacia, Centre for Metabolomics and Bioanalysis (CEMBIO), Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Marcos Fernández-García
- Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, c/Marie Curie 2, 28049, Madrid, Spain.
| | - Manuel Ferrer
- Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, c/Marie Curie 2, 28049, Madrid, Spain.
| |
Collapse
|
14
|
Vieira KCDO, Silva HRAD, Rocha IPM, Barboza E, Eller LKW. Foodborne pathogens in the omics era. Crit Rev Food Sci Nutr 2021; 62:6726-6741. [PMID: 33783282 DOI: 10.1080/10408398.2021.1905603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.
Collapse
Affiliation(s)
| | | | | | - Emmanuel Barboza
- Health Sciences Faculty, University of Western Sao Paulo, Presidente Prudente, Sao Paulo, Brazil
| | | |
Collapse
|
15
|
Zubeldia-Varela E, Barber D, Barbas C, Perez-Gordo M, Rojo D. Sample pre-treatment procedures for the omics analysis of human gut microbiota: Turning points, tips and tricks for gene sequencing and metabolomics. J Pharm Biomed Anal 2020; 191:113592. [PMID: 32947167 DOI: 10.1016/j.jpba.2020.113592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/29/2020] [Accepted: 08/23/2020] [Indexed: 02/06/2023]
Abstract
The connection between gut microbiota and human health is becoming increasingly relevant and the number of groups working in this field is constantly growing. In this context, from high-throughput gene sequencing to metabolomics analysis, the omics technologies have contributed enormously to unveil the secret crosstalk between us and our microbes. All the omics technologies produce a great amount of information, and processing this information is time-consuming and expensive. For this reason, a correct experimental design and a careful pre-analytical planning are crucial. To study the human gut microbiota, faeces are the sample of choice. Faecal material is complex, and procedures for collecting and preserving faeces are not well-established. Furthermore, increasing evidence suggests that multiple confounding factors, such as antibiotics consumption, mode of delivery, diet, aging and several diseases and disorders can alter the composition and functionality of the microbiota. This review is focused on the discussion of critical general issues during the pre-analytical planning, from patient handling to faeces sampling, including collection procedures, transport, storage conditions and possible pre-treatments, which are critical for a successful research in omics with a special attention to metabolomics and gene sequencing. We also point out that the adoption of standard operating procedures in the field is needed to guarantee accuracy and reproducibility of results.
Collapse
Affiliation(s)
- Elisa Zubeldia-Varela
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Domingo Barber
- Institute of Applied and Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Marina Perez-Gordo
- Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Institute of Applied and Molecular Medicine (IMMA), Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, ARADyAL, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - David Rojo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain.
| |
Collapse
|
16
|
Insects' potential: Understanding the functional role of their gut microbiome. J Pharm Biomed Anal 2020; 194:113787. [PMID: 33272789 DOI: 10.1016/j.jpba.2020.113787] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022]
Abstract
The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.
Collapse
|
17
|
Abbas A, Zackular JP. Microbe-microbe interactions during Clostridioides difficile infection. Curr Opin Microbiol 2020; 53:19-25. [PMID: 32088581 DOI: 10.1016/j.mib.2020.01.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
Clostridioides difficile is the leading cause of hospital-acquired gastrointestinal infections and a major public health burden in the United States. C. difficile infection causes a spectrum of disease from mild diarrhea to severe complications such as pseudomembranous colitis, toxic megacolon and death. This broad range of disease is only partially explained by bacterial genetic factors, host genetics, comorbidities and previous drug exposures. Another important factor is the gut microbiome, the disruption of which results in a loss of colonization resistance to C. difficile. Here, we review how gut microbiota and their metabolites impact C. difficile virulence and influence disease.
Collapse
Affiliation(s)
- Arwa Abbas
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| |
Collapse
|
18
|
Zhai SS, Ruan D, Zhu YW, Li MC, Ye H, Wang WC, Yang L. Protective effect of curcumin on ochratoxin A-induced liver oxidative injury in duck is mediated by modulating lipid metabolism and the intestinal microbiota. Poult Sci 2020; 99:1124-1134. [PMID: 32036964 PMCID: PMC7587726 DOI: 10.1016/j.psj.2019.10.041] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022] Open
Abstract
Curcumin has antioxidant functions, regulates the intestinal microbial composition, and alleviates mycotoxin toxicity. The present study aimed to explore whether curcumin could alleviate ochratoxin A (OTA)-induced liver injury via the intestinal microbiota. A total of 720 mixed-sex 1-day-old White Pekin ducklings were randomly assigned into 4 groups: CON (control group, without OTA), OTA (fed a diet with 2 mg/kg OTA), CUR (ducks fed a diet with 400 mg/kg curcumin), and OTA + CUR (2 mg/kg OTA plus 400 mg/kg curcumin). Each treatment consisted of 6 replicates and 30 ducklings per replicate. Treatment lasted for 21 D. Results were analyzed by a two-tailed Student t test between 2 groups. Our results demonstrated that OTA treatment had the highest serum low-density lipoprotein (LDL) level among 4 groups. Compared with OTA group, OTA + CUR decreased serum LDL level (P < 0.05). OTA decreased liver catalase (CAT) activity in ducks (P < 0.05), while addition of curcumin in OTA group increased liver CAT activity (P < 0.05). 16S ribosomal RNA sequencing suggested that curcumin increased the richness indices (ACE index) and diversity indices (Simpson index) compared with OTA group (P < 0.05) and recovered the OTA-induced alterations in composition of the intestinal microbiota. Curcumin supplementation relieved the decreased abundance of butyric acid producing bacteria, including blautia, butyricicoccus, and butyricimonas, induced by OTA (P < 0.05). OTA also significantly influenced the metabolism of the intestinal microbiota, such as tryptophan metabolism and glyceropholipid metabolism. Curcumin could alleviate the upregulation of oxidative stress pathways induced by OTA. OTA treatment also increased SREBP-1c expression (P < 0.05). The curcumin group had the lowest expression of FAS and PPARG mRNA (P < 0.05) and the highest expression of NRF2 and HMOX1 mRNA. These results indicated that curcumin could alleviate OTA-induced oxidative injury and lipid metabolism disruption by modulating the cecum microbiota.
Collapse
Affiliation(s)
- S S Zhai
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - D Ruan
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Y W Zhu
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - M C Li
- Dayitongchuang Biotech Co., Ltd., Tianjin 300000, China
| | - H Ye
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - W C Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| | - L Yang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
19
|
Mayneris-Perxachs J, Fernández-Real JM. Exploration of the microbiota and metabolites within body fluids could pinpoint novel disease mechanisms. FEBS J 2019; 287:856-865. [PMID: 31709683 DOI: 10.1111/febs.15130] [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: 06/18/2019] [Revised: 09/24/2019] [Accepted: 11/08/2019] [Indexed: 12/25/2022]
Abstract
Thanks to the emergence and recent advances in high-throughput sequencing technologies, it is becoming more evident every day that changes in the microbiome composition are linked to a myriad of health conditions. Despite this, the mechanisms of host-microbiota signalling remain largely unknown. The microbiome has an extensive metabolic activity that leads to the generation of a large number of compounds that are likely to influence host health. Therefore, the microbiome-host cross-talk is in part mediated by microbial-derived metabolites. Unlike metagenomics, which only provides information about microbial genes and thus the microbiome functional potential, metabolic phenotyping is well suited to capture their actual metabolic activity. Here, we provide an overview of these approaches and propose an integration of metagenomics, as a microbiome compositional readout, with faecal and plasma/urine metabolomics, as a functional readout, to unravel novel mechanisms linking the microbiome to host health and disease.
Collapse
Affiliation(s)
- Jordi Mayneris-Perxachs
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona 'Dr Josep Trueta', University of Girona, Girona Biomedical Research Institute (IdibGi), Spain.,CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
| | - José-Manuel Fernández-Real
- Department of Endocrinology, Diabetes and Nutrition, Hospital of Girona 'Dr Josep Trueta', University of Girona, Girona Biomedical Research Institute (IdibGi), Spain.,CIBERobn Pathophysiology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
20
|
González-Riano C, Dudzik D, Garcia A, Gil-de-la-Fuente A, Gradillas A, Godzien J, López-Gonzálvez Á, Rey-Stolle F, Rojo D, Ruperez FJ, Saiz J, Barbas C. Recent Developments along the Analytical Process for Metabolomics Workflows. Anal Chem 2019; 92:203-226. [PMID: 31625723 DOI: 10.1021/acs.analchem.9b04553] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Carolina González-Riano
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Danuta Dudzik
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain.,Department of Biopharmaceutics and Pharmacodynamics, Faculty of Pharmacy , Medical University of Gdańsk , 80-210 Gdańsk , Poland
| | - Antonia Garcia
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Alberto Gil-de-la-Fuente
- Department of Information Technology, Escuela Politécnica Superior , Universidad San Pablo-CEU , 28003 Madrid , Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain.,Clinical Research Centre , Medical University of Bialystok , 15-089 Bialystok , Poland
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - David Rojo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Francisco J Ruperez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Jorge Saiz
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| |
Collapse
|
21
|
Modified Mouse Model of Clostridioides difficile Infection as a Platform for Probiotic Efficacy Studies. Antimicrob Agents Chemother 2019; 63:AAC.00111-19. [PMID: 30988143 DOI: 10.1128/aac.00111-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
Probiotics may represent a promising approach for reducing Clostridioides (Clostridium) difficile infections (CDIs). A clinical trial conducted by our group demonstrated that CDI patients undergoing adjunctive treatment with Lactobacillus and Bifidobacterium probiotics had a reduction in diarrheal duration and compositional changes in their stool microbiomes. Here, we modified a CDI mouse model to represent clinical outcomes observed in patients and employed this model to identify evidence for the prevention of primary CDI and relapse with the same probiotic. Mice (n = 80) were administered 0.25 mg/ml cefoperazone over 5 days and subsequently challenged with 102 C. difficile VPI 10463 spores. A subset of mice (n = 40) were administered 108 CFU of probiotics daily alongside cefoperazone pretreatment and until experimental endpoints were reached. Clinical scoring was performed daily on mice and used to evaluate CDI onset and severity. Moderate CDI in mice was defined by survival beyond day 3 postinfection, while mice with severe CDI were those who succumbed to infection prior to day 3 postinfection. Sequencing and analysis of 16S rRNA from stool content were performed to determine compositional alterations to the microbiota. Using total clinical scores, we identified an association between probiotic treatment and delayed onset of primary CDI and relapse by approximately 12 to 24 h (P < 0.001). The stool microbiome of mice with moderate CDI receiving probiotic treatment was significantly enriched with Lachnospiraceae during primary CDI (P < 0.05). The outcomes observed present an opportunity to use this modified CDI mouse model to examine the efficacy of nonantibiotic options for CDI management.
Collapse
|
22
|
Silvestre R, Torrado E. Metabolomic-Based Methods in Diagnosis and Monitoring Infection Progression. EXPERIENTIA SUPPLEMENTUM (2012) 2019; 109:283-315. [PMID: 30535603 PMCID: PMC7124096 DOI: 10.1007/978-3-319-74932-7_7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A robust biomarker screening and validation is crucial for overcoming the current limits in the clinical management of infectious diseases. In this chapter, a general workflow for metabolomics is summarized. Subsequently, an overview of the major contributions of this omics science to the field of biomarkers of infectious diseases is discussed. Different approaches using a variety of analytical platforms can be distinguished to unveil the key metabolites for the diagnosis, prognosis, response to treatment and susceptibility for infectious diseases. To allow the implementation of such biomarkers into the clinics, the performance of large-scale studies employing solid validation criteria becomes essential. Focusing on the etiological agents and after an extensive review of the field, we present a comprehensive revision of the main metabolic biomarkers of viral, bacterial, fungal, and parasitic diseases. Finally, we discussed several articles which show the strongest validation criteria. Following these research avenues, precious clinical resources will be revealed, allowing for reduced misdiagnosis, more efficient therapies, and affordable costs, ultimately leading to a better patient management.
Collapse
Affiliation(s)
- Ricardo Silvestre
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
| | - Egídio Torrado
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
| |
Collapse
|
23
|
The functional consequences of the microbiome in HIV: insights from metabolomic studies. Curr Opin HIV AIDS 2018; 13:88-94. [PMID: 29035945 DOI: 10.1097/coh.0000000000000430] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
PURPOSE OF REVIEW It is critical to gain insight into the metabolic pathways by which the microbiota might influence HIV immunopathogenesis to exploit host-microbiota interactions. The aim of this review is to sketch a very broad picture of recent advances in our knowledge of how HIV might affect the microbiota, with a focus on specific gene products, particularly, metabolites produced by the microbiota that may affect HIV immunopathogenesis. RECENT FINDINGS First, we describe the different approaches used to explore imbalances in effector microbial products during HIV infection. Then, we review the mechanisms by which the microbiota might affect HIV immunopathogenesis. We cover several aspects of HIV immunopathogenesis, including systemic inflammation, mucosal immunity, enterocyte barrier integrity, HIV persistence and effects on HIV-specific humoral and cytotoxic responses. The altered interplay between mucosal immunity and dysbiotic bacteria helps to explain poorly understood observations in HIV infection, including susceptibility to HIV acquisition or the risk of HPV-related cancers, lung infections and cardiovascular disease. SUMMARY Although there is an urgent need to standardize the methods used for assessing the functional level of the microbiota, it is recognized that functional modulation of the microbiota for therapeutic purposes should be evaluated to improve HIV care.
Collapse
|
24
|
Jenior ML, Leslie JL, Young VB, Schloss PD. Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization. mSphere 2018; 3:e00261-18. [PMID: 29950381 PMCID: PMC6021602 DOI: 10.1128/msphere.00261-18] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/04/2018] [Indexed: 01/07/2023] Open
Abstract
Susceptibility to Clostridium difficile infection (CDI) is primarily associated with previous exposure to antibiotics, which compromise the structure and function of the gut bacterial community. Specific antibiotic classes correlate more strongly with recurrent or persistent C. difficile infection. As such, we utilized a mouse model of infection to explore the effect of distinct antibiotic classes on the impact that infection has on community-level transcription and metabolic signatures shortly following pathogen colonization and how those changes may associate with persistence of C. difficile Untargeted metabolomic analysis revealed that C. difficile infection had significantly larger impacts on the metabolic environment across cefoperazone- and streptomycin-pretreated mice, which became persistently colonized compared to clindamycin-pretreated mice, where infection quickly became undetectable. Through metagenome-enabled metatranscriptomics, we observed that transcripts for genes associated with carbon and energy acquisition were greatly reduced in infected animals, suggesting that those niches were instead occupied by C. difficile Furthermore, the largest changes in transcription were seen in the least abundant species, indicating that C. difficile may "attack the loser" in gut environments where sustained infection occurs more readily. Overall, our results suggest that C. difficile is able to restructure the nutrient-niche landscape in the gut to promote persistent infection.IMPORTANCEClostridium difficile has become the most common single cause of hospital-acquired infection over the last decade in the United States. Colonization resistance to the nosocomial pathogen is primarily provided by the gut microbiota, which is also involved in clearing the infection as the community recovers from perturbation. As distinct antibiotics are associated with different risk levels for CDI, we utilized a mouse model of infection with 3 separate antibiotic pretreatment regimens to generate alternative gut microbiomes that each allowed for C. difficile colonization but varied in clearance rate. To assess community-level dynamics, we implemented an integrative multi-omics approach that revealed that infection significantly changed many aspects of the gut community. The degree to which the community changed was inversely correlated with clearance during the first 6 days of infection, suggesting that C. difficile differentially modifies the gut environment to promote persistence. This is the first time that metagenome-enabled metatranscriptomics have been employed to study the behavior of a host-associated microbiota in response to an infection. Our results allow for a previously unseen understanding of the ecology associated with C. difficile infection and provide the groundwork for identification of context-specific probiotic therapies.
Collapse
Affiliation(s)
- Matthew L Jenior
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jhansi L Leslie
- 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/Infectious Diseases Division, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Patrick D Schloss
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
25
|
Hryckowian AJ, Van Treuren W, Smits SA, Davis NM, Gardner JO, Bouley DM, Sonnenburg JL. Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model. Nat Microbiol 2018; 3:662-669. [PMID: 29686297 PMCID: PMC6126909 DOI: 10.1038/s41564-018-0150-6] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/21/2018] [Indexed: 12/18/2022]
Abstract
Clostridium difficile is an opportunistic diarrhoeal pathogen, and C. difficile infection (CDI) represents a major health care concern, causing an estimated 15,000 deaths per year in the United States alone 1 . Several enteric pathogens, including C. difficile, leverage inflammation and the accompanying microbial dysbiosis to thrive in the distal gut 2 . Although diet is among the most powerful available tools for affecting the health of humans and their relationship with their microbiota, investigation into the effects of diet on CDI has been limited. Here, we show in mice that the consumption of microbiota-accessible carbohydrates (MACs) found in dietary plant polysaccharides has a significant effect on CDI. Specifically, using a model of antibiotic-induced CDI that typically resolves within 12 days of infection, we demonstrate that MAC-deficient diets perpetuate CDI. We show that C. difficile burdens are suppressed through the addition of either a diet containing a complex mixture of MACs or a simplified diet containing inulin as the sole MAC source. We show that switches between these dietary conditions are coincident with changes to microbiota membership, its metabolic output and C. difficile-mediated inflammation. Together, our data demonstrate the outgrowth of MAC-utilizing taxa and the associated end products of MAC metabolism, namely, the short-chain fatty acids acetate, propionate and butyrate, are associated with decreased C. difficile fitness despite increased C. difficile toxin expression in the gut. Our findings, when placed into the context of the known fibre deficiencies of a human Western diet, provide rationale for pursuing MAC-centric dietary strategies as an alternate line of investigation for mitigating CDI.
Collapse
Affiliation(s)
- Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - William Van Treuren
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Samuel A Smits
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jackson O Gardner
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Donna M Bouley
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
26
|
Mancabelli L, Milani C, Lugli GA, Turroni F, Cocconi D, van Sinderen D, Ventura M. Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis. FEMS Microbiol Ecol 2018; 93:4604777. [PMID: 29126267 DOI: 10.1093/femsec/fix153] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/07/2017] [Indexed: 12/28/2022] Open
Abstract
Intestinal diseases, such as Crohn's disease (CD), ulcerative colitis (UC) and pseudomembranous colitis (CDI), are among the most common diseases in humans and may lead to more serious pathologies, e.g. colorectal cancer (CRC). Next generation sequencing has in recent years allowed the identification of correlations between intestinal bacteria and diseases, although the formulation of universal gut microbial biomarkers for such diseases is only in its infancy. In the current study, we selected and reanalyzed a total of 3048 public datasets obtained from 16S rRNA profiling of individuals affected by CD, UC, CDI and CRC. This meta-analysis revealed possible biases in the reconstruction of the gut microbiota composition due to the use of different primer pairs employed for PCR of 16S rRNA gene fragments. Notably, this approach also identified common features of individuals affected by gut diseases (DS), including lower biodiversity compared to control subjects. Moreover, potential universal intestinal disease microbial biomarkers were identified through cross-disease comparisons. In detail, CTRL showed high abundance of the genera Barnesiella, Ruminococcaceae UCG-005, Alistipes, Christensenellaceae R-7 group and unclassified member of Lachnospiraceae family, while DS exhibited high abundance of Lactobacillus, unclassified member of Erysipelotrichaceae family and Streptococcus genera.
Collapse
Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Deborah Cocconi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| |
Collapse
|
27
|
Complementary Methodologies To Investigate Human Gut Microbiota in Host Health, Working towards Integrative Systems Biology. J Bacteriol 2018; 200:JB.00376-17. [PMID: 28874411 DOI: 10.1128/jb.00376-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In 1680, Antonie van Leeuwenhoek noted compositional differences in his oral and fecal microbiota, pioneering the study of the diversity of the human microbiome. From Leeuwenhoek's time to successful modern attempts at changing the gut microbial landscape to cure disease, there has been an exponential increase in the recognition of our resident microbes as part of ourselves. Thus, the human host and microbiome have evolved in parallel to configure a balanced system in which microbes survive in homeostasis with our innate and acquired immune systems, unless disease occurs. A growing number of studies have demonstrated a correlation between the presence/absence of microbial taxa and some of their functional molecules (i.e., genes, proteins, and metabolites) with health and disease states. Nevertheless, misleading experimental design on human subjects and the cost and lack of standardized animal models pose challenges to answering the question of whether changes in microbiome composition are cause or consequence of a certain biological state. In this review, we evaluate the state of the art of methodologies that enable the study of the gut microbiome, encouraging a change in broadly used analytic strategies by choosing effector molecules (proteins and metabolites) in combination with coding nucleic acids. We further explore microbial and effector microbial product imbalances that relate to disease and health.
Collapse
|
28
|
Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure. Sci Rep 2017; 7:16448. [PMID: 29180685 PMCID: PMC5703886 DOI: 10.1038/s41598-017-15434-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 10/26/2017] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile infection (CDI) is typically associated with disturbed gut microbiota and changes related to decreased colonization resistance against C. difficile are well described. However, nothing is known about possible effects of C. difficile on gut microbiota restoration during or after CDI. In this study, we have mimicked such a situation by using C. difficile conditioned medium of six different C. difficile strains belonging to PCR ribotypes 027 and 014/020 for cultivation of fecal microbiota. A marked decrease of microbial diversity was observed in conditioned medium of both tested ribotypes. The majority of differences occurred within the phylum Firmicutes, with a general decrease of gut commensals with putative protective functions (i.e. Lactobacillus, Clostridium_XIVa) and an increase in opportunistic pathogens (i.e. Enterococcus). Bacterial populations in conditioned medium differed between the two C. difficile ribotypes, 027 and 014/020 and are likely associated with nutrient availability. Fecal microbiota cultivated in medium conditioned by E. coli, Salmonella Enteritidis or Staphylococcus epidermidis grouped together and was clearly different from microbiota cultivated in C. difficile conditioned medium suggesting that C. difficile effects are specific. Our results show that the changes observed in microbiota of CDI patients are partially directly influenced by C. difficile.
Collapse
|
29
|
Mancabelli L, Milani C, Lugli GA, Turroni F, Mangifesta M, Viappiani A, Ticinesi A, Nouvenne A, Meschi T, van Sinderen D, Ventura M. Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses. Sci Rep 2017; 7:9879. [PMID: 28852182 PMCID: PMC5575163 DOI: 10.1038/s41598-017-10663-w] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022] Open
Abstract
Functional constipation (FC) is a gastrointestinal disorder with a high prevalence among the general population. The precise causes of FC are still unknown and are most likely multifactorial. Growing evidence indicates that alterations of gut microbiota composition contribute to constipation symptoms. Nevertheless, many discrepancies exist in literature and no clear link between FC and gut microbiota composition has as yet been identified. In this study, we performed 16 S rRNA-based microbial profiling analysis of 147 stool samples from 68 FC individuals and compared their microbial profiles with those of 79 healthy subjects (HS). Notably, the gut microbiota of FC individuals was shown to be depleted of members belonging to Bacteroides, Roseburia and Coprococcus 3. Furthermore, the metabolic capabilities of the gut microbiomes of five FC and five HS individuals were evaluated through shotgun metagenomics using a MiSeq platform, indicating that HS are enriched in pathways involved in carbohydrate, fatty acid and lipid metabolism as compared to FC. In contrast, the microbiomes corresponding to FC were shown to exhibit high abundance of genes involved in hydrogen production, methanogenesis and glycerol degradation. The identified differences in bacterial composition and metabolic capabilities may play an important role in development of FC symptoms.
Collapse
Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio srl, Parma, Italy
| | | | - Andrea Ticinesi
- Department of Medicine and Surgery, University of Parma, Italy; Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Antonio Nouvenne
- Department of Medicine and Surgery, University of Parma, Italy; Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, University of Parma, Italy; Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.
| |
Collapse
|
30
|
Ferrer M, Raczkowska BA, Martínez-Martínez M, Barbas C, Rojo D. Phenotyping of gut microbiota: Focus on capillary electrophoresis. Electrophoresis 2017; 38:2275-2286. [DOI: 10.1002/elps.201700056] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/04/2017] [Accepted: 06/01/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis; Consejo Superior de Investigaciones Científicas (CSIC); Madrid Spain
| | - Beata Anna Raczkowska
- Department of Endocrinology; Diabetology and Internal Medicine, Medical University of Bialystok; Bialystok Poland
| | | | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO); Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe; Madrid Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO); Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe; Madrid Spain
| |
Collapse
|
31
|
Rojo D, Méndez-García C, Raczkowska BA, Bargiela R, Moya A, Ferrer M, Barbas C. Exploring the human microbiome from multiple perspectives: factors altering its composition and function. FEMS Microbiol Rev 2017; 41:453-478. [PMID: 28333226 PMCID: PMC5812509 DOI: 10.1093/femsre/fuw046] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Our microbiota presents peculiarities and characteristics that may be altered by multiple factors. The degree and consequences of these alterations depend on the nature, strength and duration of the perturbations as well as the structure and stability of each microbiota. The aim of this review is to sketch a very broad picture of the factors commonly influencing different body sites, and which have been associated with alterations in the human microbiota in terms of composition and function. To do so, first, a graphical representation of bacterial, fungal and archaeal genera reveals possible associations among genera affected by different factors. Then, the revision of sequence-based predictions provides associations with functions that become part of the active metabolism. Finally, examination of microbial metabolite contents and fluxes reveals whether metabolic alterations are a reflection of the differences observed at the level of population structure, and in the last step, link microorganisms to functions under perturbations that differ in nature and aetiology. The utilisation of complementary technologies and methods, with a special focus on metabolomics research, is thoroughly discussed to obtain a global picture of microbiota composition and microbiome function and to convey the urgent need for the standardisation of protocols.
Collapse
Affiliation(s)
- David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
| | | | - Beata Anna Raczkowska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), 46020 Valencia, Spain
- Network Research Center for Epidemiology and Public Health (CIBER-ESP), 28029 Madrid, Spain
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Paterna, 46980 Valencia, Spain
- These authors contributed equally to this work
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
- Corresponding author: Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain. Tel: (+34) 915854872; E-mail:
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, 28668 Madrid, Spain
- These authors contributed equally to this work
| |
Collapse
|
32
|
Ferrer M, Méndez-García C, Rojo D, Barbas C, Moya A. Antibiotic use and microbiome function. Biochem Pharmacol 2017; 134:114-126. [PMID: 27641814 DOI: 10.1016/j.bcp.2016.09.007] [Citation(s) in RCA: 191] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/12/2016] [Indexed: 02/06/2023]
Abstract
Our microbiome should be understood as one of the most complex components of the human body. The use of β-lactam antibiotics is one of the microbiome covariates that influence its composition. The extent to which our microbiota changes after an antibiotic intervention depends not only on the chemical nature of the antibiotic or cocktail of antibiotics used to treat specific infections, but also on the type of administration, duration and dose, as well as the level of resistance that each microbiota develops. We have begun to appreciate that not all bacteria within our microbiota are vulnerable or reactive to different antibiotic interventions, and that their influence on both microbial composition and metabolism may differ. Antibiotics are being used worldwide on a huge scale and the prescription of antibiotics is continuing to rise; however, their effects on our microbiota have been reported for only a limited number of them. This article presents a critical review of the antibiotics or antibiotic cocktails whose use in humans has been linked to changes in the composition of our microbial communities, with a particular focus on the gut, oral, respiratory, skin and vaginal microbiota, and on their molecular agents (genes, proteins and metabolites). We review the state of the art as of June 2016, and cover a total of circa 68 different antibiotics. The data herein are the first to compile information about the bacteria, fungi, archaea and viruses most influenced by the main antibiotic treatments prescribed nowadays.
Collapse
Affiliation(s)
- Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| | | | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community Public Health (FISABIO), Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain.
| |
Collapse
|
33
|
Hryckowian AJ, Pruss KM, Sonnenburg JL. The emerging metabolic view of Clostridium difficile pathogenesis. Curr Opin Microbiol 2017; 35:42-47. [PMID: 27997854 PMCID: PMC5474191 DOI: 10.1016/j.mib.2016.11.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/20/2022]
Abstract
It is widely accepted that Clostridium difficile exploits dysbiosis and leverages inflammation to thrive in the gut environment, where it can asymptomatically colonize humans or cause a toxin-mediated disease ranging in severity from frequent watery diarrhea to pseudomembranous colitis or toxic megacolon. Here, we synthesize recent findings from the gut microbiota and enteric pathogenesis fields to inform the next steps toward a better understanding of C. difficile infection (CDI). In this review, we present a model in which the lifestyle of C. difficile is dictated by the metabolic state of the distal gut ecosystem. Contributions by C. difficile (specifically the production and action of the large glycosylating toxins TcdA and TcdB), the microbiota, and the host dictate whether the gut environment is supportive to the pathogen. Mechanistic, metabolic pathway-focused approaches encompassing the roles of all of these players are helping to elucidate the molecular ecology of the distal gut underlying a diseased or healthy ecosystem. A new generation of therapeutic strategies that are more targeted (and palatable) than fecal microbiota transplants or broad-spectrum antibiotics will be fueled by insight into the interspecies (host-microbe and microbe-microbe) interactions that differentiate healthy from pathogen-infested microbiotas.
Collapse
Affiliation(s)
- Andrew J Hryckowian
- Department of Microbiology and Immunology, Stanford University, CA, United States
| | - Kali M Pruss
- Department of Microbiology and Immunology, Stanford University, CA, United States
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, CA, United States.
| |
Collapse
|
34
|
Capillary electrophoresis mass spectrometry as a tool for untargeted metabolomics. Bioanalysis 2017; 9:99-130. [PMID: 27921456 DOI: 10.4155/bio-2016-0216] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Highly polar and ionic metabolites, such as sugars, most amino acids, organic acids or nucleotides are not retained by conventional reversed-phase LC columns and polar stationary phases and hydrophilic-interaction LC lacks of robustness, which is still limiting their applications for untargeted metabolomics where reproducibility is a must. Biological samples such as blood, urine or even tissues include many hydrophilic compounds secreted from cells, their analysis is essential for biomarker discovery, disease progression or treatment effects. This review focuses on CE coupled to MS as a mature technique for untargeted metabolomics including sample pretreatment, types of matrices, analytical methods, applications and data treatment strategies for polar compound analysis in biological matrices. The main applications and results of CE-MS in untargeted metabolomics are discussed and presented in a tabulated format.
Collapse
|
35
|
The metabolomic signature of hematologic malignancies. Leuk Res 2016; 49:22-35. [PMID: 27526405 DOI: 10.1016/j.leukres.2016.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 12/17/2022]
Abstract
The ongoing accumulation of knowledge raises hopes that understanding tumor metabolism will provide new ways for predicting, diagnosing, and even treating cancers. Some metabolic biomarkers are at present routinely utilized to diagnose cancer and metabolic alterations of tumors are being confirmed as therapeutic targets. The growing utilization of metabolomics in clinical research may rapidly turn it into one of the most potent instruments used to detect and fight tumor. In fact, while the current state and trends of high throughput metabolomics profiling focus on the purpose of discovering biomarkers and hunting for metabolic mechanism, a prospective direction, namely reprogramming metabolomics, highlights the way to use metabolomics approach for the aim of treatment of disease by way of reconstruction of disturbed metabolic pathways. In this review, we present an ample summary of the current clinical appliances of metabolomics in hematological malignancies.
Collapse
|
36
|
Serrano-Villar S, Rojo D, Martínez-Martínez M, Deusch S, Vázquez-Castellanos JF, Bargiela R, Sainz T, Vera M, Moreno S, Estrada V, Gosalbes MJ, Latorre A, Seifert J, Barbas C, Moya A, Ferrer M. Gut Bacteria Metabolism Impacts Immune Recovery in HIV-infected Individuals. EBioMedicine 2016; 8:203-216. [PMID: 27428431 PMCID: PMC4919658 DOI: 10.1016/j.ebiom.2016.04.033] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/01/2016] [Accepted: 04/25/2016] [Indexed: 02/07/2023] Open
Abstract
While changes in gut microbial populations have been described in human immuno-deficiency virus (HIV)-infected patients undergoing antiretroviral therapy (ART), the mechanisms underlying the contributions of gut bacteria and their molecular agents (metabolites and proteins) to immune recovery remain unexplored. To study this, we examined the active fraction of the gut microbiome, through examining protein synthesis and accumulation of metabolites inside gut bacteria and in the bloodstream, in 8 healthy controls and 29 HIV-infected individuals (6 being longitudinally studied). We found that HIV infection is associated to dramatic changes in the active set of gut bacteria simultaneously altering the metabolic outcomes. Effects were accentuated among immunological ART responders, regardless diet, subject characteristics, clinical variables other than immune recovery, the duration and type of ART and sexual preferences. The effect was found at quantitative levels of several molecular agents and active bacteria which were herein identified and whose abundance correlated with HIV immune pathogenesis markers. Although, we cannot rule out the possibility that some changes are partially a random consequence of the disease status, our data suggest that most likely reduced inflammation and immune recovery is a joint solution orchestrated by both the active fraction of the gut microbiota and the host.
Collapse
Affiliation(s)
- Sergio Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | | | - Simon Deusch
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Jorge F Vázquez-Castellanos
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Talía Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute (IdiPAZ), Madrid, Spain
| | - Mar Vera
- Centro Sanitario Sandoval, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Vicente Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - María José Gosalbes
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Amparo Latorre
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
| | - Jana Seifert
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain.
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain; Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain.
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.
| |
Collapse
|
37
|
Active and Secretory IgA-Coated Bacterial Fractions Elucidate Dysbiosis in Clostridium difficile Infection. mSphere 2016; 1:mSphere00101-16. [PMID: 27303742 PMCID: PMC4888886 DOI: 10.1128/msphere.00101-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/03/2016] [Indexed: 12/18/2022] Open
Abstract
C. difficile is a major enteric pathogen with worldwide distribution. Its expansion is associated with broad-spectrum antibiotics which disturb the normal gut microbiome. In this study, the DNA sequencing of highly active bacteria and bacteria opsonized by intestinal secretory immunoglobulin A (SIgA) separated from the whole bacterial community by FACS elucidated how the gut dysbiosis promotes C. difficile infection (CDI). Bacterial groups with inhibitory effects on C. difficile growth, such as Lactobacillales, were mostly inactive in the CDI patients. C. difficile was typical for the bacterial fraction opsonized by SIgA in patients with CDI, while Fusobacterium was characteristic for the SIgA-opsonized fraction of the controls. The study demonstrates that sequencing of specific bacterial fractions provides additional information about dysbiotic processes in the gut. The detected patterns have been confirmed with the whole patient cohort independently of the taxonomic differences detected in the nonfractionated microbiomes. The onset of Clostridium difficile infection (CDI) has been associated with treatment with wide-spectrum antibiotics. Antibiotic treatment alters the activity of gut commensals and may result in modified patterns of immune responses to pathogens. To study these mechanisms during CDI, we separated bacteria with high cellular RNA content (the active bacteria) and their inactive counterparts by fluorescence-activated cell sorting (FACS) of the fecal bacterial suspension. The gut dysbiosis due to the antibiotic treatment may result in modification of immune recognition of intestinal bacteria. The immune recognition patterns were assessed by FACS of bacterial fractions either coated or not with intestinal secretory immunoglobulin A (SIgA). We described the taxonomic distributions of these four bacterial fractions (active versus inactive and SIgA coated versus non-SIgA coated) by massive 16S rRNA gene amplicon sequencing and quantified the proportion of C. difficile toxin genes in the samples. The overall gut microbiome composition was more robustly influenced by antibiotics than by the C. difficile toxins. Bayesian networks revealed that the C. difficile cluster was preferentially SIgA coated during CDI. In contrast, in the CDI-negative group Fusobacterium was the characteristic genus of the SIgA-opsonized fraction. Lactobacillales and Clostridium cluster IV were mostly inactive in CDI-positive patients. In conclusion, although the proportion of C. difficile in the gut is very low, it is able to initiate infection during the gut dysbiosis caused by environmental stress (antibiotic treatment) as a consequence of decreased activity of the protective bacteria. IMPORTANCEC. difficile is a major enteric pathogen with worldwide distribution. Its expansion is associated with broad-spectrum antibiotics which disturb the normal gut microbiome. In this study, the DNA sequencing of highly active bacteria and bacteria opsonized by intestinal secretory immunoglobulin A (SIgA) separated from the whole bacterial community by FACS elucidated how the gut dysbiosis promotes C. difficile infection (CDI). Bacterial groups with inhibitory effects on C. difficile growth, such as Lactobacillales, were mostly inactive in the CDI patients. C. difficile was typical for the bacterial fraction opsonized by SIgA in patients with CDI, while Fusobacterium was characteristic for the SIgA-opsonized fraction of the controls. The study demonstrates that sequencing of specific bacterial fractions provides additional information about dysbiotic processes in the gut. The detected patterns have been confirmed with the whole patient cohort independently of the taxonomic differences detected in the nonfractionated microbiomes.
Collapse
|
38
|
Serrano-Villar S, Rojo D, Martínez-Martínez M, Deusch S, Vázquez-Castellanos JF, Sainz T, Vera M, Moreno S, Estrada V, Gosalbes MJ, Latorre A, Margolles A, Seifert J, Barbas C, Moya A, Ferrer M. HIV infection results in metabolic alterations in the gut microbiota different from those induced by other diseases. Sci Rep 2016; 6:26192. [PMID: 27189771 PMCID: PMC4870624 DOI: 10.1038/srep26192] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/28/2016] [Indexed: 12/14/2022] Open
Abstract
Imbalances in gut bacteria have been associated with multiple diseases. However, whether there are disease-specific changes in gut microbial metabolism remains unknown. Here, we demonstrate that human immunodeficiency virus (HIV) infection (n = 33) changes, at quantifiable levels, the metabolism of gut bacteria. These changes are different than those observed in patients with the auto-immune disease systemic lupus erythaematosus (n = 18), and Clostridium difficile-associated diarrhoea (n = 6). Using healthy controls as a baseline (n = 16), we demonstrate that a trend in the nature and directionality of the metabolic changes exists according to the type of the disease. The impact on the gut microbial activity, and thus the metabolite composition and metabolic flux of gut microbes, is therefore disease-dependent. Our data further provide experimental evidence that HIV infection drastically changed the microbial community, and the species responsible for the metabolism of 4 amino acids, in contrast to patients with the other two diseases and healthy controls. The identification in this present work of specific metabolic deficits in HIV-infected patients may define nutritional supplements to improve the health of these patients.
Collapse
Affiliation(s)
- Sergio Serrano-Villar
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | | | - Simon Deusch
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Jorge F Vázquez-Castellanos
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain.,Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Talía Sainz
- Department of Pediatric Infectious Diseases, University Hospital La Paz, and La Paz Research Institute (IdiPAZ), Madrid, Spain
| | - Mar Vera
- Centro Sanitario Sandoval, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, University Hospital Ramón y Cajal and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Vicente Estrada
- HIV Unit, Department of Internal Medicine, University Hospital Clínico San Carlos, Madrid, Spain
| | - María José Gosalbes
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain.,Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Amparo Latorre
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain.,Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute (IPLA), CSIC, Villaviciosa, Asturias, Spain
| | - Jana Seifert
- Institute of Animal Science, Universität Hohenheim, Stuttgart, Germany
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Andrés Moya
- Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) - Public Health, Valencia, Spain.,Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Instituto Cavanilles de Biodiversidad y Biología Evolutiva (Universidad de Valencia), Valencia, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| |
Collapse
|
39
|
Ross CL, Spinler JK, Savidge TC. Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection. Anaerobe 2016; 41:37-43. [PMID: 27180006 DOI: 10.1016/j.anaerobe.2016.05.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/05/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023]
Abstract
Alteration of the gut microbial community structure and function through antibiotic use increases susceptibility to colonization by Clostridium difficile and other enteric pathogens. However, the mechanisms that mediate colonization resistance remain elusive. As the leading definable cause of infectious diarrhea, toxigenic C. difficile represents a burden for patients and health care systems, underscoring the need for better diagnostics and treatment strategies. Next-generation sequence data has increased our understanding of how the gut microbiota is influenced by many factors including diet, disease, aging and drugs. However, a microbial-based biomarker differentiating C. difficile infection from antibiotic-associated diarrhea has not been identified. Metabolomics profiling, which is highly responsive to changes in physiological conditions, have shown promise in differentiating subtle disease phenotypes that exhibit a nearly identical microbiome community structure, suggesting metabolite-based biomarkers may be an ideal diagnostic for identifying patients with CDI. This review focuses on the current understanding of structural and functional changes to the gut microbiota during C. difficile infection obtained from studies assessing the microbiome and metabolome of samples from patients and murine models.
Collapse
Affiliation(s)
- Caná L Ross
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, 1102 Bates Ave., Houston, TX, USA; Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Jennifer K Spinler
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, 1102 Bates Ave., Houston, TX, USA; Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Tor C Savidge
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, 1102 Bates Ave., Houston, TX, USA; Department of Pathology & Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
| |
Collapse
|
40
|
Moya A, Ferrer M. Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance. Trends Microbiol 2016; 24:402-413. [PMID: 26996765 DOI: 10.1016/j.tim.2016.02.002] [Citation(s) in RCA: 324] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/26/2016] [Accepted: 02/01/2016] [Indexed: 02/07/2023]
Abstract
The microbiota should be considered as just another component of the human epigenetic landscape. Thus, health is also a reflection of the diversity and composition of gut microbiota and its metabolic status. In defining host health, it remains unclear whether diversity is paramount, or whether greater weight is held by gut microbiota composition or mono- or multiple-functional capacity of the different taxa and the mechanisms involved. A network-biology approach may shed light on the key gut players acting to protect against, or promote, disorders or diseases. This could be achieved by integrating data on total and active species, proteins and molecules, and their association with host response. In this review, we discuss the utilization of top-down and bottom-up approaches, following a functional hierarchy perspective.
Collapse
Affiliation(s)
- Andrés Moya
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain; Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO), Valencia, Spain; Network Research Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| |
Collapse
|
41
|
Pérez-Cobas AE, Moya A, Gosalbes MJ, Latorre A. Colonization Resistance of the Gut Microbiota against Clostridium difficile. Antibiotics (Basel) 2015; 4:337-57. [PMID: 27025628 PMCID: PMC4790290 DOI: 10.3390/antibiotics4030337] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 08/03/2015] [Indexed: 02/06/2023] Open
Abstract
Antibiotics strongly disrupt the human gut microbiota, which in consequence loses its colonization resistance capacity, allowing infection by opportunistic pathogens such as Clostridium difficile. This bacterium is the main cause of antibiotic-associated diarrhea and a current problem in developed countries, since its incidence and severity have increased during the last years. Furthermore, the emergence of antibiotic resistance strains has reduced the efficiency of the standard treatment with antibiotics, leading to a higher rate of relapses. Here, we review recent efforts focused on the impact of antibiotics in the gut microbiome and their relationship with C. difficile colonization, as well as, in the identification of bacteria and mechanisms involved in the protection against C. difficile infection. Since a healthy gut microbiota is able to avoid pathogen colonization, restoration of the gut microbiota seems to be the most promising approach to face C. difficile infection, especially for recurrent cases. Therefore, it would be possible to design probiotics for patients undergoing antimicrobial therapies in order to prevent or fight the expansion of the pathogen in the gut ecosystem.
Collapse
Affiliation(s)
- Ana Elena Pérez-Cobas
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - Andrés Moya
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - María José Gosalbes
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| | - Amparo Latorre
- Joint Research Unit of Foundation for the Promotion of Health and Biomedical Research of Valencian Region (FISABIO) and the Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE) of the University of Valencia, Valencia 46020, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid 28029, Spain.
| |
Collapse
|
42
|
Functional metabolomics: from biomarker discovery to metabolome reprogramming. Protein Cell 2015; 6:628-37. [PMID: 26135925 PMCID: PMC4537470 DOI: 10.1007/s13238-015-0185-x] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022] Open
Abstract
Metabolomics is emerging as a powerful tool for studying metabolic processes, identifying crucial biomarkers responsible for metabolic characteristics and revealing metabolic mechanisms, which construct the content of discovery metabolomics. The crucial biomarkers can be used to reprogram a metabolome, leading to an aimed metabolic strategy to cope with alteration of internal and external environments, naming reprogramming metabolomics here. The striking feature on the similarity of the basic metabolic pathways and components among vastly different species makes the reprogramming metabolomics possible when the engineered metabolites play biological roles in cellular activity as a substrate of enzymes and a regulator to other molecules including proteins. The reprogramming metabolomics approach can be used to clarify metabolic mechanisms of responding to changed internal and external environmental factors and to establish a framework to develop targeted tools for dealing with the changes such as controlling and/or preventing infection with pathogens and enhancing host immunity against pathogens. This review introduces the current state and trends of discovery metabolomics and reprogramming metabolomics and highlights the importance of reprogramming metabolomics.
Collapse
|