1
|
Mishra S, Tejesvi MV, Hekkala J, Turunen J, Kandikanti N, Kaisanlahti A, Suokas M, Leppä S, Vihinen P, Kuitunen H, Sunela K, Koivunen J, Jukkola A, Kalashnikov I, Auvinen P, Kääriäinen OS, Peñate Medina T, Peñate Medina O, Saarnio J, Meriläinen S, Rautio T, Aro R, Häivälä R, Suojanen J, Laine M, Erawijattari PP, Lahti L, Karihtala P, Ruuska TS, Reunanen J. Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours. J Adv Res 2024:S2090-1232(24)00090-0. [PMID: 38458256 DOI: 10.1016/j.jare.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/17/2024] [Accepted: 03/06/2024] [Indexed: 03/10/2024] Open
Abstract
INTRODUCTION Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnered interest as promising tools for studying the link between the gut microbiome and human health. The diverse composition of bEVs, including their proteins, mRNAs, metabolites, and lipids, makes them useful for investigating diseases such as cancer. However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbiome communication. In clinical microbiome research, there is a gap in the knowledge on the role of bEVs in solid tumor patients. OBJECTIVES Analyzing the functionality of bEVs using (meta)genomics and proteomics could highlight the unique aspects of host-gut microbiome interactions in solid tumor patients. Therefore, we performed a comparative analysis of the proteome and microbiota composition of gut microbiome-derived bEVs isolated from patients with solid tumors and healthy controls. METHODS After isolating bEVs from the feces of solid tumor patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of feces from patients and controls using 16S sequencing and used machine learning to classify the samples into patients and controls based on their bEVs and fecal microbiomes. RESULTS Solid tumor patients showed decreased microbiota richness and diversity in both the bEVs and feces. However, the bEV proteomes were more diverse in patients than in the controls and were enriched with proteins associated with the metabolism of amino acids and carbohydrates, nucleotide binding, and oxidoreductase activity. Metadata classification of samples was more accurate using fecal bEVs (100%) compared with fecal samples (93%). CONCLUSION Our findings suggest that bEVs are unique functional entities. There is a need to explore bEVs together with conventional gut microbiome analysis in functional cancer research to decipher the potential of bEVs as cancer diagnostic or therapeutic biomarkers.
Collapse
Affiliation(s)
- Surbhi Mishra
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Mysore Vishakantegowda Tejesvi
- Biocenter Oulu, University of Oulu, Oulu, Finland; Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Jenni Hekkala
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Jenni Turunen
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Niyati Kandikanti
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
| | - Anna Kaisanlahti
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marko Suokas
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Sirpa Leppä
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Pia Vihinen
- FICAN West Cancer Centre and Department of Oncology, Turku University Hospital and University of Turku, 20521 Turku, Finland
| | - Hanne Kuitunen
- Department of Oncology, Oulu University Hospital, Oulu, Finland
| | | | - Jussi Koivunen
- Department of Medical Oncology and Radiotherapy and Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Arja Jukkola
- Tampere Cancer Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ilja Kalashnikov
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland; Research Program Unit, Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Päivi Auvinen
- Cancer Center, Kuopio University Hospital, Northern Savonia Healthcare Municipality, Kuopio, Finland
| | - Okko-Sakari Kääriäinen
- Cancer Center, Kuopio University Hospital, Northern Savonia Healthcare Municipality, Kuopio, Finland
| | - T Peñate Medina
- Section Biomedical Imaging, Department of Radiology and Neuroradiology and Institute for Experimental Cancer Research, Kiel University, 24105 Kiel, Germany
| | - O Peñate Medina
- Section Biomedical Imaging, Department of Radiology and Neuroradiology and Institute for Experimental Cancer Research, Kiel University, 24105 Kiel, Germany; Lonza Netherlands B.V., 6167 RB Geleen, the Netherlands
| | - Juha Saarnio
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Sanna Meriläinen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Tero Rautio
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Raila Aro
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Reetta Häivälä
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Juho Suojanen
- Päijät-Häme Joint Authority for Health and Wellbeing, Department of Oral and Maxillofacial Surgery, Lahti Central Hospital, 15850 Lahti, Finland; Cleft Palate and Craniofacial Centre, Department of Plastic Surgery, Helsinki University Hospital, 00029 Helsinki, Finland; Clinicum, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Mikael Laine
- Department of Abdominal Surgery, Porvoo Hospital, Hospital District of Helsinki and Uusimaa, Porvoo, Finland
| | | | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Peeter Karihtala
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland; Department of Oncology, Oulu University Hospital, Oulu, Finland
| | - Terhi S Ruuska
- Biocenter Oulu, University of Oulu, Oulu, Finland; Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland; Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Justus Reunanen
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| |
Collapse
|
2
|
Acquasaliente L, De Filippis V. The Role of Proteolysis in Amyloidosis. Int J Mol Sci 2022; 24:ijms24010699. [PMID: 36614141 PMCID: PMC9820691 DOI: 10.3390/ijms24010699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
Amyloidoses are a group of diseases associated with deposits of amyloid fibrils in different tissues. So far, 36 different types of amyloidosis are known, each due to the misfolding and accumulation of a specific protein. Amyloid deposits can be found in several organs, including the heart, brain, kidneys, and spleen, and can affect single or multiple organs. Generally, amyloid-forming proteins become prone to aggregate due to genetic mutations, acquired environmental factors, excessive concentration, or post-translational modifications. Interestingly, amyloid aggregates are often composed of proteolytic fragments, derived from the degradation of precursor proteins by yet unidentified proteases, which display higher amyloidogenic tendency compared to precursor proteins, thus representing an important mechanism in the onset of amyloid-based diseases. In the present review, we summarize the current knowledge on the proteolytic susceptibility of three of the main human amyloidogenic proteins, i.e., transthyretin, β-amyloid precursor protein, and α-synuclein, in the onset of amyloidosis. We also highlight the role that proteolytic enzymes can play in the crosstalk between intestinal inflammation and amyloid-based diseases.
Collapse
Affiliation(s)
- Laura Acquasaliente
- Correspondence: (L.A.); (V.D.F.); Tel.: +39-0498275703 (L.A.); +39-0498275698 (V.D.F.)
| | - Vincenzo De Filippis
- Correspondence: (L.A.); (V.D.F.); Tel.: +39-0498275703 (L.A.); +39-0498275698 (V.D.F.)
| |
Collapse
|
3
|
Affiliation(s)
- Suprabhat Giri
- Department of Gastroenterology, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Sumaswi Angadi
- Department of Gastroenterology, Nizam's Institute of Medical Sciences, Hyderabad, India
| | - Vaneet Jearth
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
4
|
Li Y, Watanabe E, Kawashima Y, Plichta DR, Wang Z, Ujike M, Ang QY, Wu R, Furuichi M, Takeshita K, Yoshida K, Nishiyama K, Kearney SM, Suda W, Hattori M, Sasajima S, Matsunaga T, Zhang X, Watanabe K, Fujishiro J, Norman JM, Olle B, Matsuyama S, Namkoong H, Uwamino Y, Ishii M, Fukunaga K, Hasegawa N, Ohara O, Xavier RJ, Atarashi K, Honda K. Identification of trypsin-degrading commensals in the large intestine. Nature 2022. [PMID: 36071157 DOI: 10.1038/s41586-022-05181-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 08/02/2022] [Indexed: 11/23/2022]
Abstract
Increased levels of proteases, such as trypsin, in the distal intestine have been implicated in intestinal pathological conditions1–3. However, the players and mechanisms that underlie protease regulation in the intestinal lumen have remained unclear. Here we show that Paraprevotella strains isolated from the faecal microbiome of healthy human donors are potent trypsin-degrading commensals. Mechanistically, Paraprevotella recruit trypsin to the bacterial surface through type IX secretion system-dependent polysaccharide-anchoring proteins to promote trypsin autolysis. Paraprevotella colonization protects IgA from trypsin degradation and enhances the effectiveness of oral vaccines against Citrobacter rodentium. Moreover, Paraprevotella colonization inhibits lethal infection with murine hepatitis virus-2, a mouse coronavirus that is dependent on trypsin and trypsin-like proteases for entry into host cells4,5. Consistently, carriage of putative genes involved in trypsin degradation in the gut microbiome was associated with reduced severity of diarrhoea in patients with SARS-CoV-2 infection. Thus, trypsin-degrading commensal colonization may contribute to the maintenance of intestinal homeostasis and protection from pathogen infection. Colonization of trypsin-degrading commensal bacteria may contribute to the maintenance of intestinal homeostasis and protection against pathogen infection in humans and mice.
Collapse
|
5
|
Song X, Wang W, Ding S, Wang Y, Ye L, Chen X, Ma H. Exploring the potential antidepressant mechanisms of puerarin: Anti-inflammatory response via the gut-brain axis. J Affect Disord 2022; 310:459-471. [PMID: 35568321 DOI: 10.1016/j.jad.2022.05.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Puerarin has been shown to have a good antidepressant effect, and our previous study found that it can remedy stress-induced dysbiosis. However, its gut microbiota-related mechanism has not been fully elucidated. Therefore, this study aimed to investigate the potential link between puerarin on gut microbiota and inflammatory responses in depressed rats. METHODS A chronic unpredictable mild stress (CUMS) rat model of depression was established, open field test (OFT), sucrose preference test (SPT) and forced swimming test (FST) were used to evaluate its antidepressant effect. 16S rRNA sequencing was performed to identify the rat fecal microflora. At the same time, inflammatory cytokines, colonic histopathological changes, and brain-derived neurotrophic factor (BDNF), nuclear factor kappa-B (NF-κB), inhibitor a of NF-κB (IκB-α) protein expression were detected. RESULTS Puerarin attenuated CUMS-induced depressive-like behavior and gut microbiota dysregulation in rats, significantly reducing the abundance of harmful bacteria such as Desulfovibrio, Verrucomicrobiae, and Verrucomicrobia. In addition, puerarin can also reduce the pro-inflammatory factors and increase the level of anti-inflammatory factors in depressed rats, improve the damaged colon tissue, enhance the expression of BDNF and IκB-α in the hippocampus and inhibit the expression of NF-κB. LIMITATIONS Direct evidence that puerarin improves depressive-like behaviors via gut microbiota is lacking. CONCLUSION The underlying mechanism of puerarin's antidepressant-like effect is closely related to the bidirectional communication of the microbiota-gut-brain axis by regulating the inflammatory response.
Collapse
Affiliation(s)
- Xujiao Song
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Weihao Wang
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Shanshan Ding
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Yan Wang
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Lufen Ye
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Xin Chen
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Hao Ma
- School of Aesthetic Medicine, Yichun University, Yichun 336000, China.
| |
Collapse
|
6
|
Zhang XS, Yin YS, Wang J, Battaglia T, Krautkramer K, Li WV, Li J, Brown M, Zhang M, Badri MH, Armstrong AJS, Strauch CM, Wang Z, Nemet I, Altomare N, Devlin JC, He L, Morton JT, Chalk JA, Needles K, Liao V, Mount J, Li H, Ruggles KV, Bonneau RA, Dominguez-Bello MG, Bäckhed F, Hazen SL, Blaser MJ. Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice. Cell Host Microbe 2021; 29:1249-1265.e9. [PMID: 34289377 PMCID: PMC8370265 DOI: 10.1016/j.chom.2021.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/27/2021] [Accepted: 06/18/2021] [Indexed: 01/04/2023]
Abstract
Early-life antibiotic exposure perturbs the intestinal microbiota and accelerates type 1 diabetes (T1D) development in the NOD mouse model. Here, we found that maternal cecal microbiota transfer (CMT) to NOD mice after early-life antibiotic perturbation largely rescued the induced T1D enhancement. Restoration of the intestinal microbiome was significant and persistent, remediating the antibiotic-depleted diversity, relative abundance of particular taxa, and metabolic pathways. CMT also protected against perturbed metabolites and normalized innate and adaptive immune effectors. CMT restored major patterns of ileal microRNA and histone regulation of gene expression. Further experiments suggest a gut-microbiota-regulated T1D protection mechanism centered on Reg3γ, in an innate intestinal immune network involving CD44, TLR2, and Reg3γ. This regulation affects downstream immunological tone, which may lead to protection against tissue-specific T1D injury.
Collapse
Affiliation(s)
- Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA; Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA.
| | - Yue Sandra Yin
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA; Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Jincheng Wang
- Department of Biochemistry and Microbiology, Rutgers University - New Brunswick, New Brunswick, NJ, USA
| | - Thomas Battaglia
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Kimberly Krautkramer
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Göteborg 41345, Sweden
| | - Wei Vivian Li
- Department of Biostatistics and Epidemiology, Rutgers University School of Public Health, Piscataway, NJ, USA
| | - Jackie Li
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Mark Brown
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Meifan Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA; Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Michelle H Badri
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA; New York University, Center for Data Science, New York, NY, USA
| | - Abigail J S Armstrong
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Christopher M Strauch
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
| | - Zeneng Wang
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
| | - Ina Nemet
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
| | - Nicole Altomare
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Joseph C Devlin
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Linchen He
- Department of Population Health, New York University Langone Medical Center, New York, NY, USA
| | - Jamie T Morton
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - John Alex Chalk
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Kelly Needles
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Viviane Liao
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Julia Mount
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Huilin Li
- Department of Population Health, New York University Langone Medical Center, New York, NY, USA
| | - Kelly V Ruggles
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA
| | - Richard A Bonneau
- Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA; New York University, Center for Data Science, New York, NY, USA; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University - New Brunswick, New Brunswick, NJ, USA; Institute for Food, Nutrition and Health, Rutgers University - New Brunswick, New Brunswick, NJ, USA
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Göteborg 41345, Sweden; Region västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stanley L Hazen
- Cardiovascular & Metabolic Sciences, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA; Heart, Vascular & Thoracic Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA; Human Microbiome Program, New York University Langone Medical Center, New York, NY, USA.
| |
Collapse
|
7
|
Song X, Wang W, Ding S, Liu X, Wang Y, Ma H. Puerarin ameliorates depression-like behaviors of with chronic unpredictable mild stress mice by remodeling their gut microbiota. J Affect Disord 2021; 290:353-363. [PMID: 34049088 DOI: 10.1016/j.jad.2021.04.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/19/2021] [Accepted: 04/21/2021] [Indexed: 12/28/2022]
Abstract
BACKGROUND Puerarin is an isoflavone derivative isolated from the traditional Chinese medicine Pueraria Lobelia, which has proven to relieve depression-like behavior. However, its underlying antidepressant mechanisms have been poorly characterized. Herein, we explored whether Puerarin's antidepressant effect is associated with changes in the gut microbiota (GM). METHODS The model of depression in mice featuring chronic unpredictable mild stress (CUMS) was eastablished, and its antidepressant effect was estimated by sugar water preference and forced swimming test. Genomic DNA extracted from fecal samples was employed to sequence the 16S rRNA gene for gut microbiota identification. RESULTS Puerarin (100 mg/kg) treatment was found to alleviate the CUMS-induced depression-like behaviors. Furthermore, chronic stress led to pathological microbial flora, which was principally marked by the increased abundance of pathogenic bacteria (Proteobacteria, Flexispira, Desulfovibrio) and the decreased abundance of beneficial bacteria (Firmicutes, Bacillales, Lactobacillus). Intriguingly, puerarin treatment reversed these changes. LIMITATIONS The specific role and anti-depression mechanism of characteristic gut microflora were not confirmed. CONCLUSION Puerarin can remedy stress-induced disruptions of normal gut microflora. It is suggested that the antidepressant mechanism of puerarin may closely interact with restoring beneficial microflora.
Collapse
Affiliation(s)
- Xujiao Song
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Weihao Wang
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Shanshan Ding
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Xingyue Liu
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Yan Wang
- School of Chemical and Biological Engineering, Yichun University, Yichun 336000, China
| | - Hao Ma
- School of Aesthetic Medicine, Yichun University, Yichun 336000, China.
| |
Collapse
|
8
|
Aldars-García L, Chaparro M, Gisbert JP. Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease. Microorganisms 2021; 9:microorganisms9050977. [PMID: 33946482 PMCID: PMC8147118 DOI: 10.3390/microorganisms9050977] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing-remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.
Collapse
Affiliation(s)
- Laila Aldars-García
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - María Chaparro
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
| | - Javier P. Gisbert
- Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, 28006 Madrid, Spain; (L.A.-G.); (M.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 28006 Madrid, Spain
- Correspondence: ; Tel.: +34-913-093-911; Fax: +34-915-204-013
| |
Collapse
|
9
|
Yan Z, He F, Xiao F, He H, Li D, Cong L, Lin L, Zhu H, Wu Y, Yan R, Li X, Shan H. A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis. Microbiome 2021; 9:12. [PMID: 33436102 PMCID: PMC7805185 DOI: 10.1186/s40168-020-00967-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut microbial proteolytic signatures under complex disease status such as inflammatory bowel disease (IBD, including Crohn's disease (CD) and ulcerative colitis (UC)), have not been investigated. Metaproteomics holds the potential to investigate gut microbial proteolysis because semi-tryptic peptides mainly derive from endogenous proteolysis. RESULTS We have developed a semi-tryptic peptide centric metaproteomic mining approach to obtain a snapshot of human gut microbial proteolysis signatures. This approach employed a comprehensive meta-database, two-step multiengine database search, and datasets with high-resolution fragmentation spectra to increase the confidence of semi-tryptic peptide identification. The approach was validated by discovering altered proteolysis signatures of Escherichia coli heat shock response. Utilizing two published large-scale metaproteomics datasets containing 623 metaproteomes from 447 fecal and 176 mucosal luminal interface (MLI) samples from IBD patients and healthy individuals, we obtain potential signatures of altered gut microbial proteolysis at taxonomic, functional, and cleavage site motif levels. The functional alterations mainly involved microbial carbohydrate transport and metabolism, oxidative stress, cell motility, protein synthesis, and maturation. Altered microbial proteolysis signatures of CD and UC mainly occurred in terminal ileum and descending colon, respectively. Microbial proteolysis patterns exhibited low correlations with β-diversity and moderate correlations with microbial protease and chaperones levels, respectively. Human protease inhibitors and immunoglobulins were mainly negatively associated with microbial proteolysis patterns, probably because of the inhibitory effects of these host factors on gut microbial proteolysis events. CONCLUSIONS This semi-tryptic peptide centric mining strategy offers a label-free approach to discover signatures of in vivo gut microbial proteolysis events if experimental conditions are well controlled. It can also capture in vitro proteolysis signatures to facilitate the evaluation and optimization of experimental conditions. Our findings highlight the complex and diverse proteolytic events of gut microbiome, providing a unique layer of information beyond taxonomic and proteomic abundance. Video abstract.
Collapse
Affiliation(s)
- Zhixiang Yan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.
| | - Feixiang He
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Fei Xiao
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Huanhuan He
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Dan Li
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Li Cong
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Lu Lin
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Huijin Zhu
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Yanyan Wu
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China
| | - Ru Yan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China.
| | - Xiaofeng Li
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.
| | - Hong Shan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.
- Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, Guangdong Province, China.
| |
Collapse
|
10
|
Peterle D, Pontarollo G, Spada S, Brun P, Palazzi L, Sokolov AV, Spolaore B, Polverino de Laureto P, Vasilyev VB, Castagliuolo I, De Filippis V. A serine protease secreted from Bacillus subtilis cleaves human plasma transthyretin to generate an amyloidogenic fragment. Commun Biol 2020; 3:764. [PMID: 33311636 DOI: 10.1038/s42003-020-01493-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
Aggregation of human wild-type transthyretin (hTTR), a homo-tetrameric plasma protein, leads to acquired senile systemic amyloidosis (SSA), recently recognised as a major cause of cardiomyopathies in 1-3% older adults. Fragmented hTTR is the standard composition of amyloid deposits in SSA, but the protease(s) responsible for amyloidogenic fragments generation in vivo is(are) still elusive. Here, we show that subtilisin secreted from Bacillus subtilis, a gut microbiota commensal bacterium, translocates across a simulated intestinal epithelium and cleaves hTTR both in solution and human plasma, generating the amyloidogenic fragment hTTR(59-127), which is also found in SSA amyloids in vivo. To the best of our knowledge, these findings highlight a novel pathogenic mechanism for SSA whereby increased permeability of the gut mucosa, as often occurs in elderly people, allows subtilisin (and perhaps other yet unidentified bacterial proteases) to reach the bloodstream and trigger generation of hTTR fragments, acting as seeding nuclei for preferential amyloid fibrils deposition in the heart.
Collapse
|
11
|
Liu RT, Rowan-Nash AD, Sheehan AE, Walsh RFL, Sanzari CM, Korry BJ, Belenky P. Reductions in anti-inflammatory gut bacteria are associated with depression in a sample of young adults. Brain Behav Immun 2020; 88:308-324. [PMID: 32229219 PMCID: PMC7415740 DOI: 10.1016/j.bbi.2020.03.026] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/07/2020] [Accepted: 03/25/2020] [Indexed: 12/15/2022] Open
Abstract
We assessed the gut microbiota of 90 American young adults, comparing 43 participants with major depressive disorder (MDD) and 47 healthy controls, and found that the MDD subjects had significantly different gut microbiota compared to the healthy controls at multiple taxonomic levels. At the phylum level, participants with MDD had lower levels of Firmicutes and higher levels of Bacteroidetes, with similar trends in the at the class (Clostridia and Bacteroidia) and order (Clostridiales and Bacteroidales) levels. At the genus level, the MDD group had lower levels of Faecalibacterium and other related members of the family Ruminococcaceae, which was also reduced relative to healthy controls. Additionally, the class Gammaproteobacteria and genus Flavonifractor were enriched in participants with MDD. Accordingly, predicted functional differences between the two groups include a reduced abundance of short-chain fatty acid production pathways in the MDD group. We also demonstrated that the magnitude of taxonomic changes was associated with the severity of depressive symptoms in many cases, and that most changes were present regardless of whether depressed participants were taking psychotropic medications. Overall, our results support a link between MDD and lower levels of anti-inflammatory, butyrate-producing bacteria, and may support a connection between the gut microbiota and the chronic, low-grade inflammation often observed in MDD patients.
Collapse
Affiliation(s)
- Richard T Liu
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA.
| | - Aislinn D Rowan-Nash
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Ana E Sheehan
- Department of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Rachel F L Walsh
- Department of Psychology, Temple University, Philadelphia, PA, USA
| | - Christina M Sanzari
- Department of Psychiatry and Human Behavior, Alpert Medical School of Brown University, Providence, RI, USA
| | - Benjamin J Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, USA
| |
Collapse
|
12
|
Kriaa A, Jablaoui A, Mkaouar H, Akermi N, Maguin E, Rhimi M. Serine proteases at the cutting edge of IBD: Focus on gastrointestinal inflammation. FASEB J 2020; 34:7270-7282. [PMID: 32307770 DOI: 10.1096/fj.202000031rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/15/2022]
Abstract
Serine proteases have been long recognized to coordinate many physiological processes and play key roles in regulating the inflammatory response. Accordingly, their dysregulation has been regularly associated with several inflammatory disorders and suggested as a central mechanism in the pathophysiology of digestive inflammation. So far, studies addressing the proteolytic homeostasis in the gut have mainly focused on host serine proteases as candidates of interest, while largely ignoring the potential contribution of their bacterial counterparts. The human gut microbiota comprises a complex ecosystem that contributes to host health and disease. Yet, our understanding of microbially produced serine proteases and investigation of whether they are causally linked to IBD is still in its infancy. In this review, we highlight recent advances in the emerging roles of host and bacterial serine proteases in digestive inflammation. We also discuss the application of available tools in the gut to monitor disease-related serine proteases. An exhaustive representation and understanding of such functional potential would help in closing existing gaps in mechanistic knowledge.
Collapse
Affiliation(s)
- Aicha Kriaa
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Amin Jablaoui
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Héla Mkaouar
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Nizar Akermi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Emmanuelle Maguin
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| | - Moez Rhimi
- Microbiota Interaction with Human and Animal Team (MIHA), Micalis Institute, AgroParisTech, Université Paris-Saclay, INRAE, Jouy-en-Josas, France
| |
Collapse
|
13
|
Jablaoui A, Kriaa A, Mkaouar H, Akermi N, Soussou S, Wysocka M, Wołoszyn D, Amouri A, Gargouri A, Maguin E, Lesner A, Rhimi M. Fecal Serine Protease Profiling in Inflammatory Bowel Diseases. Front Cell Infect Microbiol 2020; 10:21. [PMID: 32117798 PMCID: PMC7011180 DOI: 10.3389/fcimb.2020.00021] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
Serine proteases are extensively known to play key roles in many physiological processes. However, their dysregulation is often associated to several diseases including inflammatory bowel diseases (IBD). Here, we used specific substrates to monitor fecal protease activities in a large cohort of healthy and IBD patients. Of interest, serine protease activity was 10-fold higher in IBD fecal samples compared to healthy controls. Moreover, functional analysis of these fecal proteolytic activities revealed that the most increased activities are trypsin-like, elastase-like and cathepsin G-like. We also show for the first time, an increase of proteinase 3-like activity in these samples compared to controls. Results presented here will guide further investigations to better understand the relevance of these peptidases in IBD.
Collapse
Affiliation(s)
- Amin Jablaoui
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Microbiota Interaction with Human and Animal Team (MIHA), Jouy-en-Josas, France
| | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Microbiota Interaction with Human and Animal Team (MIHA), Jouy-en-Josas, France
| | - Héla Mkaouar
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Microbiota Interaction with Human and Animal Team (MIHA), Jouy-en-Josas, France
| | - Nizar Akermi
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Microbiota Interaction with Human and Animal Team (MIHA), Jouy-en-Josas, France
| | - Souha Soussou
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Microbiota Interaction with Human and Animal Team (MIHA), Jouy-en-Josas, France
| | | | | | - Ali Amouri
- Department of Gastroenterology, Hedi Chaker University Hospital, Sfax, Tunisia
| | - Ali Gargouri
- Laboratory of Molecular Biology of Eukaryotes, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Microbiota Interaction with Human and Animal Team (MIHA), Jouy-en-Josas, France
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Moez Rhimi
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Microbiota Interaction with Human and Animal Team (MIHA), Jouy-en-Josas, France
| |
Collapse
|
14
|
Tamura Y, Ohta H, Kagawa Y, Osuga T, Morishita K, Sasaki N, Takiguchi M. Plasma amino acid profiles in dogs with inflammatory bowel disease. J Vet Intern Med 2019; 33:1602-1607. [PMID: 31111561 PMCID: PMC6639477 DOI: 10.1111/jvim.15525] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/08/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Lymphocytic-plasmacytic enteritis is the common form of idiopathic inflammatory bowel disease (IBD) in dogs. In human IBD, disturbances of amino acid metabolism have been demonstrated to be involved in the pathophysiology of IBD. Therefore, plasma amino acid profile might represent a novel marker of human IBD. OBJECTIVES To determine the plasma amino acid profiles of dogs with IBD and its usefulness as a novel marker of IBD in dogs. ANIMALS Fasting blood plasma was obtained from 10 dogs with IBD and 12 healthy dogs. METHODS All IBD dogs were prospectively included in this study, and heparinized blood samples were collected. The plasma concentrations of 21 amino acids were determined using the ninhydrin method. The relationships among the plasma amino acid concentrations and plasma C-reactive protein (CRP) concentration, canine chronic enteropathy clinical activity index (CCECAI), and overall World Small Animal Veterinary Association (WSAVA) score were investigated. RESULTS Median concentration (nmol/mL) of methionine [46.2; range, 30.0-59.3], proline [119.4; range, 76.7-189.2], serine [115.1; range, 61.4-155.9], and tryptophan [17.4; range, 11.9-56.3]) were significantly lower than in control dogs [62.6; range, 51.0-83.6, 199.1; range, 132.5-376.7, 164.3; range, 124.7-222.9, and 68.3; range, 35.7-94.8, respectively]. A negative correlation was identified between the plasma serine concentration and CCECAI (r s = -.67, P = .03), but there were no correlations between plasma amino acid concentrations and CRP concentration or overall WSAVA score. CONCLUSIONS AND CLINICAL IMPORTANCE Plasma serine concentration might represent a novel maker of IBD in dogs.
Collapse
Affiliation(s)
- Yu Tamura
- Laboratory of Veterinary Internal Medicine, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroshi Ohta
- Laboratory of Veterinary Internal Medicine, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yumiko Kagawa
- Diagnostic Pathology, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Tatsuyuki Osuga
- Veterinary Teaching Hospital, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Keitaro Morishita
- Veterinary Teaching Hospital, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Noboru Sasaki
- Laboratory of Veterinary Internal Medicine, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mitsuyoshi Takiguchi
- Laboratory of Veterinary Internal Medicine, Department of Veterinary Clinical Sciences, Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| |
Collapse
|
15
|
Sundqvist T, Stenhammar L, Tjellström B, Magnusson KE, Midtvedt T, Norin E, Högberg L. Evidence of Disturbed Gut Microbial Metabolic Activity in Pediatric Crohn’s Disease. Crohn's & Colitis 360 2019. [DOI: 10.1093/crocol/otz010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Abstract
Background
Dysbiosis, that is, disturbed gut microbial balance, is well documented in Crohn’s disease (CD). We aimed at studying CD-linked dysbiosis in children by analyzing fecal microbe-associated characteristics, previously not reported in children.
Methods
This observational study included 28 children with active CD and healthy controls. We assessed the following three indicators of gut microbiota metabolism in the feces: the presence of tryptic activity, the conversion of cholesterol to coprostanol, and the conversion of bilirubin to urobilinogen.
Results
The fecal tryptic activity was significantly higher in children with active CD compared to the control group (P < 0.01). The fecal coprostanol of the CD children was close to zero and differed significantly from the controls (P < 0.001). Furthermore, the children with CD had very low fecal urobilinogen, differing significantly from the control group (P < 0.001).
Conclusions
The significant differences in levels of fecal bacterial metabolites in patients with active CD compared to healthy controls reflect major perturbation of gut microbial functions and have not previously been reported in children. This fits well with the prevailing concept of a dysbiotic gut microbiota in CD and may have important clinical implications by bringing the dysbiosis back into balance.
Collapse
Affiliation(s)
- Tommy Sundqvist
- Division of Microbiology, Infection and Inflammation Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Lars Stenhammar
- Department of Paediatrics and Department of Clinical and Experimental Medicine, Linköping University, Norrköping, Sweden
| | - Bo Tjellström
- Department of Paediatrics and Department of Clinical and Experimental Medicine, Linköping University, Norrköping, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karl-Eric Magnusson
- Division of Microbiology, Infection and Inflammation Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Tore Midtvedt
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Elisabeth Norin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Lotta Högberg
- Department of Paediatrics and Department of Clinical and Experimental Medicine, Linköping University, Norrköping, Sweden
| |
Collapse
|
16
|
Roncase EJ, González-Páez GE, Wolan DW. X-ray Structures of Two Bacteroides thetaiotaomicron C11 Proteases in Complex with Peptide-Based Inhibitors. Biochemistry 2019; 58:1728-1737. [PMID: 30835452 DOI: 10.1021/acs.biochem.9b00098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Commensal bacteria secrete proteins and metabolites to influence host intestinal homeostasis, and proteases represent a significant constituent of the components at the host:microbiome interface. Here, we determined the structures of the two secreted C11 cysteine proteases encoded by the established gut commensal Bacteroides thetaiotaomicron. We employed mutational analysis to demonstrate the two proteases, termed "thetapain" and "iotapain", undergo in trans autoactivation after lysine and/or arginine residues, as observed for other C11 proteases. We determined the structures of the active forms of thetapain and iotapain in complex with irreversible peptide inhibitors, Ac-VLTK-AOMK and biotin-VLTK-AOMK, respectively. Structural comparisons revealed key active-site interactions important for peptide recognition are more extensive for thetapain; however, both proteases employ a glutamate residue to preferentially bind small polar residues at the P2 position. Our results will aid in the design of protease-specific probes to ultimately understand the biological role of C11 proteases in bacterial fitness, elucidate their host and/or microbial substrates, and interrogate their involvement in microbiome-related diseases.
Collapse
Affiliation(s)
- Emily J Roncase
- Departments of Molecular Medicine and Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Gonzalo E González-Páez
- Departments of Molecular Medicine and Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Dennis W Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| |
Collapse
|
17
|
Yoon H, Schaubeck M, Lagkouvardos I, Blesl A, Heinzlmeir S, Hahne H, Clavel T, Panda S, Ludwig C, Kuster B, Manichanh C, Kump P, Haller D, Hörmannsperger G. Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers Colitis. Cell Mol Gastroenterol Hepatol 2018; 6:370-388.e3. [PMID: 30182050 PMCID: PMC6121113 DOI: 10.1016/j.jcmgh.2018.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/15/2018] [Indexed: 12/19/2022]
Abstract
Background & Aims Antibiotic (ABx) therapy is associated with increased risk for Crohn's disease but underlying mechanisms are unknown. We observed high fecal serine protease activity (PA) to be a frequent side effect of ABx therapy. The aim of the present study was to unravel whether this rise in large intestinal PA may promote colitis development via detrimental effects on the large intestinal barrier. Methods Transwell experiments were used to assess the impact of high PA in ABx-treated patients or vancomycin/metronidazole-treated mice on the epithelial barrier. Serine protease profiling was performed using liquid chromatography-mass spectrometry/mass spectrometry analysis. The impact of high large intestinal PA on the intestinal barrier in wild-type and interleukin (IL)10-/- mice and on colitis development in IL10-/- mice was investigated using vancomycin/metronidazole with or without oral serine protease inhibitor (AEBSF) treatment. Results The ABx-induced, high large intestinal PA was caused by significantly increased levels of pancreatic proteases and impaired epithelial barrier integrity. In wild-type mice, the rise in PA caused a transient increase in intestinal permeability but did not affect susceptibility to chemically induced acute colitis. In IL10-/- mice, increased PA caused a consistent impairment of the intestinal barrier associated with inflammatory activation in the large intestinal tissue. In the long term, the vancomycin/metronidazole-induced lasting increase in PA aggravated colitis development in IL10-/- mice. Conclusions High large intestinal PA is a frequent adverse effect of ABx therapy, which is detrimental to the large intestinal barrier and may contribute to the development of chronic intestinal inflammation in susceptible individuals.
Collapse
Key Words
- ABx, antibiotics
- AEBSF, 4-(2-aminoethyl) benzenesulfonyl fluoride hydrochloride
- DSS, dextran sulfate sodium
- Epithelial Barrier
- GF, germ-free
- Gut Microbiota
- IBD, inflammatory bowel diseases
- IL, interleukin
- Inflammatory Bowel Diseases
- LC-MS/MS, liquid chromatography–mass spectrometry/mass spectrometry
- PA, protease activity
- PBS, phosphate-buffered saline
- PMSF, phenylmethane-sulfonylfluoride
- SPF, specific pathogen-free
- Serine Proteases
- TEER, transepithelial electrical resistance
- V/M, vancomycin/metronidazole
- WT, wild-type
- cecal-sup, cecal-supernatants
- ctr, control
- stool-sup, stool-supernatants
Collapse
Affiliation(s)
- Hongsup Yoon
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
| | - Monika Schaubeck
- Max Planck Institute of Neurobiology, Department of Neuroimmunology, Martinsried, Germany
| | - Ilias Lagkouvardos
- Technische Universität München, Junior Research Group Microbial Bioinformatics, ZIEL – Institute for Food and Health, Freising-Weihenstephan, Germany
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Andreas Blesl
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Stephanie Heinzlmeir
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | - Hannes Hahne
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- OmicScouts GmbH, Freising, Germany
| | - Thomas Clavel
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
- RWTH University Hospital, Institute of Medical Microbiology, Functional Microbiome Research Group, Aachen, Germany
| | - Suchita Panda
- Vall d'Hebron Research Institute, Digestive Research Unit, Barcelona, Spain
| | - Christina Ludwig
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | - Bernhard Kuster
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | | | - Patrizia Kump
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Dirk Haller
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Gabriele Hörmannsperger
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
| |
Collapse
|
18
|
Santoru ML, Piras C, Murgia A, Palmas V, Camboni T, Liggi S, Ibba I, Lai MA, Orrù S, Blois S, Loizedda AL, Griffin JL, Usai P, Caboni P, Atzori L, Manzin A. Cross sectional evaluation of the gut-microbiome metabolome axis in an Italian cohort of IBD patients. Sci Rep 2017; 7:9523. [PMID: 28842640 DOI: 10.1038/s41598-017-10034-5] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract of uncertain origin, which includes ulcerative colitis (UC) and Crohn’s disease (CD). The composition of gut microbiota may change in IBD affected individuals, but whether dysbiosis is the cause or the consequence of inflammatory processes in the intestinal tissue is still unclear. Here, the composition of the microbiota and the metabolites in stool of 183 subjects (82 UC, 50 CD, and 51 healthy controls) were determined. The metabolites content and the microbiological profiles were significantly different between IBD and healthy subjects. In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia, and Fusobacteria were significantly increased, whereas Bacteroidetes and Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium, Streptococcus, Sutterella and Veillonella were increased, whereas Bacteroides, Flavobacterium, and Oscillospira decreased. Various metabolites including biogenic amines, amino acids, lipids, were significantly increased in IBD, while others, such as two B group vitamins, were decreased in IBD compared to healthy subjects. This study underlines the potential role of an inter-omics approach in understanding the metabolic pathways involved in IBD. The combined evaluation of metabolites and fecal microbiome can be useful to discriminate between healthy subjects and patients with IBD.
Collapse
|
19
|
Zhou JA, Jiang M, Yang X, Liu Y, Guo J, Zheng J, Qu Y, Song Y, Li R, Qin X, Wang X. Unconjugated bilirubin ameliorates the inflammation and digestive protease increase in TNBS-induced colitis. Mol Med Rep 2017; 16:1779-1784. [PMID: 28656252 PMCID: PMC5562003 DOI: 10.3892/mmr.2017.6825] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/31/2017] [Indexed: 12/12/2022] Open
Abstract
The authors previously demonstrated that unconjugated bilirubin (UCB) may inhibit the activities of various digestive proteases, including trypsin and chymotrypsin. The digestive proteases in the lower gut are important in the pathogenesis of inflammatory bowel diseases. The effects of UCB on the inflammation and levels of digestive proteases in feces of rats with colitis have not yet been revealed. The present study investigated the effect of UCB on the inflammatory status and levels of trypsin and chymotrypsin in the feces of rats with trinitrobenzenesulfonic acid (TNBS)-induced colitis. The data indicated that treatment with TNBS resulted in a marked reduction in weight gain, which was significantly alleviated in UCB-treated rats. Furthermore, UCB treatment alleviated the inflammation induced by TNBS, detected via macroscopic damage and microscopic inflammation scores, and pro-inflammatory markers including myeloperoxidase (MPO), tumor necrosis factor (TNF)-α and interleukin (IL)-1β. Furthermore, rats with colitis demonstrated significant increases in fecal trypsin and chymotrypsin levels, whereas UCB treatment significantly alleviated these increases. A significant positive correlation was additionally revealed among the pro-inflammatory markers (MPO, TNF-α and IL-1β) and fecal digestive proteases (trypsin and chymotrypsin) in colitis. The results of the present study demonstrated that UCB ameliorated the inflammation and digestive protease increase in TNBS-induced colitis.
Collapse
Affiliation(s)
- Jin-An Zhou
- Department of Biochemistry and Molecular Biology, Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Mingshan Jiang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Xinguang Yang
- Department of Biochemistry and Molecular Biology, Daqing Branch of Harbin Medical University, Daqing, Heilongjiang 163319, P.R. China
| | - Yuanli Liu
- Department of Biochemistry and Molecular Biology, Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Junyu Guo
- Department of Biochemistry and Molecular Biology, Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Jiadong Zheng
- Department of Biochemistry and Molecular Biology, Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Yilin Qu
- Department of Biochemistry and Molecular Biology, Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Yu Song
- Department of Biochemistry and Molecular Biology, Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Rongyan Li
- Department of Biochemistry and Molecular Biology, Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| | - Xiaofa Qin
- GI Biopharma Inc., Westfield, NJ 07090, USA
| | - Xiuhong Wang
- Department of Biochemistry and Molecular Biology, Heilongjiang Provincial Science and Technology Innovation Team in Higher Education Institutes for Infection and Immunity, Harbin Medical University, Harbin, Heilongjiang 150086, P.R. China
| |
Collapse
|
20
|
Roncase EJ, Moon C, Chatterjee S, González-Páez GE, Craik CS, O’Donoghue AJ, Wolan DW. Substrate Profiling and High Resolution Co-complex Crystal Structure of a Secreted C11 Protease Conserved across Commensal Bacteria. ACS Chem Biol 2017; 12:1556-1565. [PMID: 28414448 PMCID: PMC5575927 DOI: 10.1021/acschembio.7b00143] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cysteine proteases are among the most abundant hydrolytic enzymes produced by bacteria, and this diverse family of proteins have significant biological roles in bacterial viability and environmental interactions. Members of the clostripain-like (C11) family of cysteine proteases from commensal gut bacterial strains have recently been shown to mediate immune responses by inducing neutrophil phagocytosis and activating bacterial pathogenic toxins. Development of substrates, inhibitors, and probes that target C11 proteases from enteric bacteria will help to establish the role of these proteins at the interface of the host and microbiome in health and disease. We employed a mass spectrometry-based substrate profiling method to identify an optimal peptide substrate of PmC11, a C11 protease secreted by the commensal bacterium Parabacteroides merdae. Using this substrate sequence information, we synthesized a panel of fluorogenic substrates to calculate kcat and KM and to evaluate the importance of the P2 amino acid for substrate turnover. A potent and irreversible tetrapeptide inhibitor with a C-terminal acyloxymethyl ketone warhead, Ac-VLTK-AOMK, was then synthesized. We determined the crystal structure of PmC11 in complex with this inhibitor and uncovered key active-site interactions that govern PmC11 substrate recognition and specificity. This is the first C11 protease structure in complex with a substrate mimetic and is also the highest resolution crystal structure of a C11 protease to date at 1.12 Å resolution. Importantly, subjecting human epithelial cell lysates to PmC11 hydrolysis in combination with subtiligase-based N-terminal labeling and tandem mass spectrometry proteomics complemented the stringent substrate specificity observed in the in vitro substrate profiling experiment. The combination of chemical biological, biophysical, and biochemical techniques presented here to elucidate and characterize PmC11 substrate selectivity can be expanded to other proteases and the development of chemical tools to study these essential proteins in biologically relevant samples, such as the highly complex distal gut microbiome.
Collapse
Affiliation(s)
- Emily J. Roncase
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Clara Moon
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Sandip Chatterjee
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Gonzalo E. González-Páez
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Charles S. Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Dennis W. Wolan
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037,Corresponding Author:
| |
Collapse
|
21
|
Chen SY, Tsai CN, Lee YS, Lin CY, Huang KY, Chao HC, Lai MW, Chiu CH. Intestinal microbiome in children with severe and complicated acute viral gastroenteritis. Sci Rep 2017; 7:46130. [PMID: 28397879 PMCID: PMC5387401 DOI: 10.1038/srep46130] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 03/13/2017] [Indexed: 12/17/2022] Open
Abstract
The aim of the present study was to evaluate the microbiota of children with severe or complicated acute viral gastroenteritis (AGE). To that end, next-generation sequencing (NGS) technology was used to sequence the 16S ribosomal RNA (16S rRNA) gene in 20 hospitalized pediatric patients with severe or complicated AGE and a further 20 otherwise healthy children; the fecal microbiome was then assessed. Comparative metagenomics data were analyzed by a Wilcoxon rank–sum test and hierarchical clustering analysis of bacterial reads. The statistical analyses showed a significantly decreased Shannon diversity index (entropy score) of the intestinal microbiota in patients with severe AGE compared with normal controls (P = 0.017) and patients with mild-to-moderate AGE (P = 0.011). The intestinal microbiota score of the 5 patients with rotavirus AGE was significantly lower than that of those with norovirus infection (P = 0.048). Greater richness in Campylobacteraceae (P = 0.0003), Neisseriaceae (P = 0.0115), Methylobacteriaceae (P = 0.0004), Sphingomonadaceae (P = 0.0221), and Enterobacteriaceae (P = 0.0451) was found in patients with complicated AGE compared with normal controls. The data suggest a significant reduction in intestinal microbial diversity in patients with severe AGE, particularly those with rotavirus infection.
Collapse
Affiliation(s)
- Shih-Yen Chen
- Division of Pediatric Gastroenterology, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Chi-Neu Tsai
- Division of Pediatric Gastroenterology, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan.,Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yun-Shien Lee
- Department of Biotechnology, Min-Chuan University, Taoyuan, Taiwan
| | - Chun-Yuan Lin
- Department of Computer Science and Information Engineering, Chang Gung University College of Engineering, Taoyuan, Taiwan
| | - Kuan-Yeh Huang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hsun-Ching Chao
- Division of Pediatric Gastroenterology, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ming-Wei Lai
- Division of Pediatric Gastroenterology, Chang Gung Children's Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| |
Collapse
|
22
|
Primec M, Mičetić-Turk D, Langerholc T. Analysis of short-chain fatty acids in human feces: A scoping review. Anal Biochem 2017; 526:9-21. [PMID: 28300535 DOI: 10.1016/j.ab.2017.03.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/18/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Short-chain fatty acids (SCFAs) play a crucial role in maintaining homeostasis in humans, therefore the importance of a good and reliable SCFAs analytical detection has raised a lot in the past few years. The aim of this scoping review is to show the trends in the development of different methods of SCFAs analysis in feces, based on the literature published in the last eleven years in all major indexing databases. The search criteria included analytical quantification techniques of SCFAs in different human clinical and in vivo studies. SCFAs analysis is still predominantly performed using gas chromatography (GC), followed by high performance liquid chromatography (HPLC), nuclear magnetic resonance (NMR) and capillary electrophoresis (CE). Performances, drawbacks and advantages of these methods are discussed, especially in the light of choosing a proper pretreatment, as feces is a complex biological material. Further optimization to develop a simple, cost effective and robust method for routine use is needed.
Collapse
Affiliation(s)
- Maša Primec
- Department of Microbiology, Biochemistry, Molecular Biology and Biotechnology, Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, 2311 Hoče, Slovenia.
| | - Dušanka Mičetić-Turk
- Department of Pediatrics, Faculty of Medicine, University of Maribor, Taborska Ulica 8, 2000 Maribor, Slovenia
| | - Tomaž Langerholc
- Department of Microbiology, Biochemistry, Molecular Biology and Biotechnology, Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, 2311 Hoče, Slovenia
| |
Collapse
|
23
|
Yadav V, Varum F, Bravo R, Furrer E, Bojic D, Basit AW. Inflammatory bowel disease: exploring gut pathophysiology for novel therapeutic targets. Transl Res 2016; 176:38-68. [PMID: 27220087 DOI: 10.1016/j.trsl.2016.04.009] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 03/17/2016] [Accepted: 04/28/2016] [Indexed: 12/14/2022]
Abstract
Ulcerative colitis and Crohn's disease are the 2 major phenotypes of inflammatory bowel disease (IBD), which are influenced by a complex interplay of immunological and genetic elements, though the precise etiology still remains unknown. With IBD developing into a globally prevailing disease, there is a need to explore new targets and a thorough understanding of the pathophysiological differences between the healthy and diseased gut could unearth new therapeutic opportunities. In this review, we provide an overview of the major aspects of IBD pathogenesis and thereafter present a comprehensive analysis of the gut pathophysiology leading to a discussion on some of the most promising targets and biologic therapies currently being explored. These include various gut proteins (CXCL-10, GATA-3, NKG2D, CD98, microRNAs), immune cells recruited to the gut (mast cells, eosinophils, toll-like receptors 2, 4), dysregulated proinflammatory cytokines (interleukin-6, -13, -18, -21), and commensal microbiota (probiotics and fecal microbiota transplantation). We also evaluate some of the emerging nonconventional therapies being explored in IBD treatment focusing on the latest developments in stem cell research, oral targeting of the gut-associated lymphoid tissue, novel anti-inflammatory signaling pathway targeting, adenosine deaminase inhibition, and the beneficial effects of antioxidant and nutraceutical therapies. In addition, we highlight the growth of biologics and their targets in IBD by providing information on the preclinical and clinical development of over 60 biopharmaceuticals representing the state of the art in ulcerative colitis and Crohn's disease drug development.
Collapse
|
24
|
Li R, Zheng J, Jiang M, Liu Y, Qin X, Wang X. Increased Digestive Proteases and Decreased β-Glucuronidase in Feces of Rats Treated with Sucralose and Saccharin-Another Critical Evidence That These Dietary Chemicals May Be Important Causative Factors for Inflammatory Bowel Disease. Inflamm Bowel Dis 2016; 22:E29-30. [PMID: 27416049 DOI: 10.1097/MIB.0000000000000859] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
|
25
|
Kolmeder CA, Salojärvi J, Ritari J, de Been M, Raes J, Falony G, Vieira-Silva S, Kekkonen RA, Corthals GL, Palva A, Salonen A, de Vos WM. Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults. PLoS One 2016; 11:e0153294. [PMID: 27070903 PMCID: PMC4829149 DOI: 10.1371/journal.pone.0153294] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 03/28/2016] [Indexed: 12/31/2022] Open
Abstract
Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (1010 cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.
Collapse
Affiliation(s)
- Carolin A. Kolmeder
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Jarkko Salojärvi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Jarmo Ritari
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mark de Been
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium
- VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium
- VIB, Center for the Biology of Disease, Leuven, Belgium
| | - Sara Vieira-Silva
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Leuven, Belgium
- VIB, Center for the Biology of Disease, Leuven, Belgium
| | | | - Garry L. Corthals
- Translational Proteomics, Turku Center for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Anne Salonen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
| | - Willem M. de Vos
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, Immunobiology Research Program, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| |
Collapse
|
26
|
Nitzan O, Elias M, Peretz A, Saliba W. Role of antibiotics for treatment of inflammatory bowel disease. World J Gastroenterol 2016; 22:1078-1087. [PMID: 26811648 PMCID: PMC4716021 DOI: 10.3748/wjg.v22.i3.1078] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/06/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease is thought to be caused by an aberrant immune response to gut bacteria in a genetically susceptible host. The gut microbiota plays an important role in the pathogenesis and complications of the two main inflammatory bowel diseases: Crohn’s disease (CD) and ulcerative colitis. Alterations in gut microbiota, and specifically reduced intestinal microbial diversity, have been found to be associated with chronic gut inflammation in these disorders. Specific bacterial pathogens, such as virulent Escherichia coli strains, Bacteroides spp, and Mycobacterium avium subspecies paratuberculosis, have been linked to the pathogenesis of inflammatory bowel disease. Antibiotics may influence the course of these diseases by decreasing concentrations of bacteria in the gut lumen and altering the composition of intestinal microbiota. Different antibiotics, including ciprofloxacin, metronidazole, the combination of both, rifaximin, and anti-tuberculous regimens have been evaluated in clinical trials for the treatment of inflammatory bowel disease. For the treatment of active luminal CD, antibiotics may have a modest effect in decreasing disease activity and achieving remission, and are more effective in patients with disease involving the colon. Rifamixin, a non absorbable rifamycin has shown promising results. Treatment of suppurative complications of CD such as abscesses and fistulas, includes drainage and antibiotic therapy, most often ciprofloxacin, metronidazole, or a combination of both. Antibiotics might also play a role in maintenance of remission and prevention of post operative recurrence of CD. Data is more sparse for ulcerative colitis, and mostly consists of small trials evaluating ciprofloxacin, metronidazole and rifaximin. Most trials did not show a benefit for the treatment of active ulcerative colitis with antibiotics, though 2 meta-analyses concluded that antibiotic therapy is associated with a modest improvement in clinical symptoms. Antibiotics show a clinical benefit when used for the treatment of pouchitis. The downsides of antibiotic treatment, especially with recurrent or prolonged courses such as used in inflammatory bowel disease, are significant side effects that often cause intolerance to treatment, Clostridium dificile infection, and increasing antibiotic resistance. More studies are needed to define the exact role of antibiotics in inflammatory bowel diseases.
Collapse
|
27
|
Caminero A, Nistal E, Herrán AR, Pérez-Andrés J, Ferrero MA, Vaquero Ayala L, Vivas S, Ruiz de Morales JM, Albillos SM, Casqueiro FJ. Differences in gluten metabolism among healthy volunteers, coeliac disease patients and first-degree relatives. Br J Nutr 2015; 114:1157-67. [PMID: 26428276 DOI: 10.1017/S0007114515002767] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Coeliac disease (CD) is an immune-mediated enteropathy resulting from exposure to gluten in genetically predisposed individuals. Gluten proteins are partially digested by human proteases generating immunogenic peptides that cause inflammation in patients carrying HLA-DQ2 and DQ8 genes. Although intestinal dysbiosis has been associated with patients with CD, bacterial metabolism of gluten has not been studied in depth thus far. The aim of this study was to analyse the metabolic activity of intestinal bacteria associated with gluten intake in healthy individuals, CD patients and first-degree relatives of CD patients. Faecal samples belonging to twenty-two untreated CD patients, twenty treated CD patients, sixteen healthy volunteers on normal diet, eleven healthy volunteers on gluten-free diet (GFD), seventy-one relatives of CD patients on normal diet and sixty-nine relatives on GFD were tested for several proteolytic activities, cultivable bacteria involved in gluten metabolism, SCFA and the amount of gluten in faeces. We detected faecal peptidasic activity against the gluten-derived peptide 33-mer. CD patients showed differences in faecal glutenasic activity (FGA), faecal tryptic activity (FTA), SCFA and faecal gluten content with respect to healthy volunteers. Alterations in specific bacterial groups metabolising gluten such as Clostridium or Lactobacillus were reported in CD patients. Relatives showed similar parameters to CD patients (SCFA) and healthy volunteers (FTA and FGA). Our data support the fact that commensal microbial activity is an important factor in the metabolism of gluten proteins and that this activity is altered in CD patients.
Collapse
|
28
|
De Palma G, Blennerhassett P, Lu J, Deng Y, Park AJ, Green W, Denou E, Silva MA, Santacruz A, Sanz Y, Surette MG, Verdu EF, Collins SM, Bercik P. Microbiota and host determinants of behavioural phenotype in maternally separated mice. Nat Commun 2015. [DOI: 10.1038/ncomms8735] [Citation(s) in RCA: 299] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
29
|
Wright EK, Kamm MA, Teo SM, Inouye M, Wagner J, Kirkwood CD. Recent advances in characterizing the gastrointestinal microbiome in Crohn's disease: a systematic review. Inflamm Bowel Dis 2015; 21:1219-28. [PMID: 25844959 PMCID: PMC4450900 DOI: 10.1097/mib.0000000000000382] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 02/03/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND The intestinal microbiota is involved in the pathogenesis of inflammatory bowel disease. A reduction in the diversity of the intestinal microbiota as well as specific taxonomic and functional shifts have been reported in Crohn's disease and may play a central role in the inflammatory process. The aim was to systematically review recent developments in the structural and functional changes observed in the gastrointestinal microbiome in patients with Crohn's Disease. RESULTS Seventy-two abstracts were included in this review. The effects of host genetics, disease phenotype, and inflammatory bowel disease treatment on the gastrointestinal microbiome in Crohn's disease were reviewed, and taxonomic shifts in patients with early and established disease were described. The relative abundance of Bacteroidetes is increased and Firmicutes decreased in Crohn's disease compared with healthy controls. Enterobacteriaceae, specifically Eschericia coli, is enriched in Crohn's disease. Faecalibacterium prausnitzii is found at lower abundance in Crohn's disease and in those with postoperative recurrence. Observed functional changes include major shifts in oxidative stress pathways, a decrease in butanoate and propanoate metabolism gene expression, lower levels of butyrate, and other short-chain fatty acids, decreased carbohydrate metabolism, and decreased amino acid biosynthesis. CONCLUSIONS Changes in microbial composition and function have been described, although a causative role remains to be established. Larger, prospective, and longitudinal studies are required with deep interrogation of the microbiome if causality is to be determined, and refined microbial manipulation is to emerge as a focused therapy.
Collapse
Affiliation(s)
- Emily K. Wright
- Department of Gastroenterology, St Vincent's Hospital Melbourne, Australia
- Department of Pathology, University of Melbourne, Australia
| | - Michael A. Kamm
- Department of Gastroenterology, St Vincent's Hospital Melbourne, Australia
- Department of Pathology, University of Melbourne, Australia
- Imperial College, London, United Kingdom; and
| | - Shu Mei Teo
- Department of Pathology, University of Melbourne, Australia
| | - Michael Inouye
- Department of Pathology, University of Melbourne, Australia
| | - Josef Wagner
- Enteric Virus Group, Murdoch Children's Research Institute, Melbourne, Australia
| | - Carl D. Kirkwood
- Enteric Virus Group, Murdoch Children's Research Institute, Melbourne, Australia
| |
Collapse
|
30
|
Benno P, Befrits R, Norin E, Berstad A, Dahlgren AL, Midtvedt T, Hellström PM. Is irritable bowel syndrome a dysbiotic bowel syndrome? Microbial Ecology in Health & Disease 2015; 26:27637. [PMID: 26031675 PMCID: PMC4451089 DOI: 10.3402/mehd.v26.27637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Peter Benno
- Gastroenterology and Endoscopy Unit, Läkarhuset Hötorgscity, Stockholm, Sweden
- Department of Microbiology, Tumorbiology and Cellbiology, Karolinska Institutet, Stockholm, Sweden;
| | - Ragnar Befrits
- Gastroenterology and Endoscopy Unit, Läkarhuset Hötorgscity, Stockholm, Sweden
| | - Elisabeth Norin
- Department of Microbiology, Tumorbiology and Cellbiology, Karolinska Institutet, Stockholm, Sweden
| | - Arnold Berstad
- Unger-Vetlesens Institutt, Lovisenberg Diakonale Sykehus, Oslo, Norway
| | - Atti-La Dahlgren
- Department of Microbiology, Tumorbiology and Cellbiology, Karolinska Institutet, Stockholm, Sweden
- Division of International and Humanitarian Medicine, Geneva University Hospital, Geneva, Switzerland
| | - Tore Midtvedt
- Department of Microbiology, Tumorbiology and Cellbiology, Karolinska Institutet, Stockholm, Sweden
| | - Per M Hellström
- Gastroenterology Unit, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| |
Collapse
|
31
|
GUT in FOCUS Symposium NOBEL FORUM, Karolinska Institutet, February 2nd 2015. Microb Ecol Health Dis 2015; 26:28480. [PMID: 26031687 DOI: 10.3402/mehd.v26.28480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
32
|
Abstract
BACKGROUND The intestinal microbiota composition varies between healthy and diseased individuals for numerous diseases. Although any cause or effect relationship between the alterations in the gut microbiota and disease is not always clear, targeting the intestinal microbiota might offer new possibilities for prevention and/or treatment of disease. OBJECTIVE Here we review some examples of manipulating the intestinal microbiota by prebiotics, probiotics, and fecal microbial transplants. RESULTS Prebiotics are best known for their ability to increase the number of bifidobacteria. However, specific prebiotics could potentially also stimulate other species they can also stimulate other species associated with health, like Akkermansia muciniphila, Ruminococcus bromii, the Roseburia/Enterococcus rectale group, and Faecalibacterium prausnitzii. Probiotics have beneficial health effects for different diseases and digestive symptoms. These effects can be due to the direct effect of the probiotic bacterium or its products itself, as well as effects of the probiotic on the resident microbiota. Probiotics can influence the microbiota composition as well as the activity of the resident microbiota. Fecal microbial transplants are a drastic intervention in the gut microbiota, aiming for total replacement of one microbiota by another. With numerous successful studies related to antibiotic-associated diarrhea and Clostridium difficile infection, the potential of fecal microbial transplants to treat other diseases like inflammatory bowel disease, irritable bowel syndrome, and metabolic and cardiovascular disorders is under investigation. CONCLUSIONS Improved knowledge on the specific role of gut microbiota in prevention and treatment of disease will help more targeted manipulation of the intestinal microbiota. Further studies are necessary to see the (long term) effects for health of these interventions.
Collapse
Affiliation(s)
- Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Tore Midtvedt
- Department of Microbiology, Tumor and Cell Biology (MTC) Karolinska Institute, Stockholm, Sweden
| | | |
Collapse
|
33
|
Serrano IC, Stoica G, Adams AM, Palomares E. Dual core quantum dots for highly quantitative ratiometric detection of trypsin activity in cystic fibrosis patients. Nanoscale 2014; 6:13623-13629. [PMID: 25274267 DOI: 10.1039/c4nr03952a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We present herein two colour encoded silica nanospheres (2nanoSi) for the fluorescence quantitative ratiometric determination of trypsin in humans. Current detection methods for cystic fibrosis diagnosis are slow, costly and suffer from false positives. The 2nanoSi proved to be a highly sensitive, fast (minutes), and single-step approach nanosensor for the screening and diagnosis of cystic fibrosis, allowing the quantification of trypsin concentrations in a wide range relevant for clinical applications (25-350 μg L(-1)). Furthermore, as trypsin is directly related to the development of cystic fibrosis (CF), different human genotypes, i.e. CF homozygotic, CF heterozygotic, and unaffected, respectively, can be determined using our 2nanoSi nanospheres. We anticipate the 2nanoSi system to be a starting point for non-invasive, easy-to-use and cost effective ratiometric fluorescent biomarkers for recessive genetic diseases like human cystic fibrosis. In a screening program in which the goal is to detect disease and also the carrier status, early diagnosis could be of great help.
Collapse
Affiliation(s)
- Iván Castelló Serrano
- Institute of Chemical Research of Catalonia (ICIQ), Avinguda del Països Catalans 16, 43007 Tarragona, Spain.
| | | | | | | |
Collapse
|
34
|
Qin X. May bacterial or pancreatic proteases play a critical role in inflammatory bowel disease? World J Gastroenterol 2014; 20:12709-12710. [PMID: 25253982 PMCID: PMC4168115 DOI: 10.3748/wjg.v20.i35.12709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/22/2014] [Accepted: 04/23/2014] [Indexed: 02/06/2023] Open
Abstract
In a recent review paper, Carroll and Maharshak discussed a critical role of enteric bacterial proteases in the pathogenesis of inflammatory bowel disease (IBD). I take a great interest in this paper as I also suspected proteases, not from the bacteria, but those originated from the pancreas that failed to be inactivated in the lower gut due to a reduction in gut bacteria, may have played a critical role in the pathogenesis of IBD, which was first published more than a decade ago and discussed again in more detail in a recent paper published in this journal. Antibiotics may result in a big reduction in gut bacteria and bacterial proteases, but multiple studies demonstrated dramatic increased of pancreatic proteases like trypsin and chymotrypsin in the feces of animals or patients treated with antibiotics. Multiple large-scale studies also demonstrated use of antibiotics caused an increase but not decrease in the risk of developing IBD, suggesting impaired inactivation and degradation of pancreatic proteases may have played a more critical role in the pathogenesis of IBD.
Collapse
|
35
|
Abstract
Alterations in the bidirectional interactions between the intestine and the nervous system have important roles in the pathogenesis of irritable bowel syndrome (IBS). A body of largely preclinical evidence suggests that the gut microbiota can modulate these interactions. A small and poorly defined role for dysbiosis in the development of IBS symptoms has been established through characterization of altered intestinal microbiota in IBS patients and reported improvement of subjective symptoms after its manipulation with prebiotics, probiotics, or antibiotics. It remains to be determined whether IBS symptoms are caused by alterations in brain signaling from the intestine to the microbiota or primary disruption of the microbiota, and whether they are involved in altered interactions between the brain and intestine during development. We review the potential mechanisms involved in the pathogenesis of IBS in different groups of patients. Studies are needed to better characterize alterations to the intestinal microbiome in large cohorts of well-phenotyped patients, and to correlate intestinal metabolites with specific abnormalities in gut-brain interactions.
Collapse
Affiliation(s)
- Emeran A Mayer
- Oppenheimer Center for Neurobiology of Stress, Division of Digestive Diseases, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, California.
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Department of Pathology, Houston, Texas; Texas Children's Hospital, Houston, Texas
| | - Robert J Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Children's Nutrition Research Center, Houston, Texas; Texas Children's Hospital, Houston, Texas
| |
Collapse
|
36
|
Rogler G, Vavricka S, Schoepfer A, Lakatos PL. Mucosal healing and deep remission: What does it mean? World J Gastroenterol 2013; 19:7552-7560. [PMID: 24282345 PMCID: PMC3837253 DOI: 10.3748/wjg.v19.i43.7552] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/27/2013] [Accepted: 09/29/2013] [Indexed: 02/06/2023] Open
Abstract
The use of specific terms under different meanings and varying definitions has always been a source of confusion in science. When we point our efforts towards an evidence based medicine for inflammatory bowel diseases (IBD) the same is true: Terms such as “mucosal healing” or “deep remission” as endpoints in clinical trials or treatment goals in daily patient care may contribute to misconceptions if meanings change over time or definitions are altered. It appears to be useful to first have a look at the development of terms and their definitions, to assess their intrinsic and context-independent problems and then to analyze the different relevance in present-day clinical studies and trials. The purpose of such an attempt would be to gain clearer insights into the true impact of the clinical findings behind the terms. It may also lead to a better defined use of those terms for future studies. The terms “mucosal healing” and “deep remission” have been introduced in recent years as new therapeutic targets in the treatment of IBD patients. Several clinical trials, cohort studies or inception cohorts provided data that the long term disease course is better, when mucosal healing is achieved. However, it is still unclear whether continued or increased therapeutic measures will aid or improve mucosal healing for patients in clinical remission. Clinical trials are under way to answer this question. Attention should be paid to clearly address what levels of IBD activity are looked at. In the present review article authors aim to summarize the current evidence available on mucosal healing and deep remission and try to highlight their value and position in the everyday decision making for gastroenterologists.
Collapse
|
37
|
Carroll IM, Ringel-Kulka T, Ferrier L, Wu MC, Siddle JP, Bueno L, Ringel Y. Fecal protease activity is associated with compositional alterations in the intestinal microbiota. PLoS One 2013; 8:e78017. [PMID: 24147109 PMCID: PMC3798377 DOI: 10.1371/journal.pone.0078017] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/16/2013] [Indexed: 12/23/2022] Open
Abstract
Objective Intestinal proteases carry out a variety of functions in the gastrointestinal (GI) tract. Studies have reported that elevated enteric proteases in patients with GI disease can alter intestinal physiology, however the origin (human vs. microbial) of elevated proteases in patients with GI disease is unclear. Aim The aim of this study was to investigate the association between protease activity and the microbiota in human fecal samples. Design In order to capture a wide range of fecal protease (FP) activity stool samples were collected from 30 IBS patients and 24 healthy controls. The intestinal microbiota was characterized using 454 high throughput pyro-sequencing of the 16S rRNA gene. The composition and diversity of microbial communities were determined and compared using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline. FP activity levels were determined using an ELISA-based method. FP activity was ranked and top and bottom quartiles (n=13 per quartile) were identified as having high and low FP activity, respectively. Results The overall diversity of the intestinal microbiota displayed significant clustering separation (p = 0.001) between samples with high vs. low FP activity. The Lactobacillales, Lachnospiraceae, and Streptococcaceae groups were positively associated with FP activity across the entire study population, whilst the Ruminococcaceae family and an unclassified Coriobacteriales family were negatively associated with FP activity. Conclusions These data demonstrate significant associations between specific intestinal bacterial groups and fecal protease activity and provide a basis for further causative studies investigating the role of enteric microbes and GI diseases.
Collapse
Affiliation(s)
- Ian M. Carroll
- Division of Gastroenterology and Hepatology, Department of Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tamar Ringel-Kulka
- Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Laurent Ferrier
- INRA, UMR1331 Toxalim, Neuro-Gastroenterology & Nutrition group, Toulouse, France
| | - Michael C. Wu
- Department of Biostatistics, Gillings School of Global Public Health, the University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jennica P. Siddle
- Division of Gastroenterology and Hepatology, Department of Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lionel Bueno
- INRA, UMR1331 Toxalim, Neuro-Gastroenterology & Nutrition group, Toulouse, France
| | - Yehuda Ringel
- Division of Gastroenterology and Hepatology, Department of Medicine, the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|