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Thumann TA, Pferschy-Wenzig EM, Kumpitsch C, Duller S, Högenauer C, Kump P, Aziz-Kalbhenn H, Ammar RM, Rabini S, Moissl-Eichinger C, Bauer R. Rapid biotransformation of STW 5 constituents by human gut microbiome from IBS- and non-IBS donors. Microbiol Spectr 2024; 12:e0403123. [PMID: 38738925 DOI: 10.1128/spectrum.04031-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/03/2024] [Indexed: 05/14/2024] Open
Abstract
STW 5, a blend of nine medicinal plant extracts, exhibits promising efficacy in treating functional gastrointestinal disorders, notably irritable bowel syndrome (IBS). Nonetheless, its effects on the gastrointestinal microbiome and the role of microbiota on the conversion of its constituents are still largely unexplored. This study employed an experimental ex vivo model to investigate STW 5's differential effects on fecal microbial communities and metabolite production in samples from individuals with and without IBS. Using 560 fecal microcosms (IBS patients, n = 6; healthy controls, n = 10), we evaluated the influence of pre-digested STW 5 and controls on microbial and metabolite composition at time points 0, 0.5, 4, and 24 h. Our findings demonstrate the potential of this ex vivo platform to analyze herbal medicine turnover within 4 h with minimal microbiome shifts due to abiotic factors. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products, such as 18β-glycyrrhetinic acid, davidigenin, herniarin, 3-(3-hydroxyphenyl)propanoic acid, and 3-(2-hydroxy-4-methoxyphenyl)propanoic acid occurred. For davidigenin, 3-(3-hydroxyphenyl)propanoic acid and 18β-glycyrrhetinic acid, anti-inflammatory, cytoprotective, or spasmolytic activities have been previously described. Notably, the microbiome-driven metabolic transformation did not induce a global microbiome shift, and the detected metabolites were minimally linked to specific taxa. Observed biotransformations were independent of IBS diagnosis, suggesting potential benefits for IBS patients from biotransformation products of STW 5. IMPORTANCE STW 5 is an herbal medicinal product with proven clinical efficacy in the treatment of functional gastrointestinal disorders, like functional dyspepsia and irritable bowel syndrome (IBS). The effects of STW 5 on fecal microbial communities and metabolite production effects have been studied in an experimental model with fecal samples from individuals with and without IBS. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products with reported anti-inflammatory, cytoprotective, or spasmolytic activities was observed, which may be relevant for the pharmacological activity of STW 5.
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Affiliation(s)
- Timo A Thumann
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Eva-Maria Pferschy-Wenzig
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Stefanie Duller
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | | | - Patrizia Kump
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Heba Aziz-Kalbhenn
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
| | - Ramy M Ammar
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
- Department of Pharmacology, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Sabine Rabini
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
| | - Christine Moissl-Eichinger
- BioTechMed, Graz, Austria
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Rudolf Bauer
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
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Marasco G, Cremon C, Barbaro MR, Bianco F, Stanghellini V, Barbara G. Microbiota modulation in disorders of gut-brain interaction. Dig Liver Dis 2024:S1590-8658(24)00742-4. [PMID: 38772789 DOI: 10.1016/j.dld.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Disorders of gut-brain interaction (DGBI) are common chronic conditions characterized by persistent and recurring gastrointestinal symptoms triggered by several pathophysiological factors, including an altered gut microbiota. The most common DGBI are irritable bowel syndrome (IBS), functional constipation (FC) and functional dyspepsia (FD). Recently, a deep understanding of the role of the gut microbiota in these diseases was possible due to multi-omics methods capable to provide a comprehensive assessment. Most of the therapies recommended for these patients, can modulate the gut microbiota such as diet, prebiotics, probiotics and non-absorbable antibiotics, which were shown to be safe and effective. Since patients complain symptoms after food ingestion, diet represents the first line therapeutic approach. Avoiding dietary fat and fermentable oligosaccharides, disaccharides, monosaccharides, and polyols, and increasing the number of soluble fibers represent the therapeutic choices for FD, IBS and FC respectively. Probiotics, as a category, have been employed with good results in all the abovementioned DGBI. Rifaximin has been shown to be useful in the context of bowel related disorders, although a recent trial showed positive results for FD. Fecal microbiota transplantation has been tested for IBS and FC with promising results. In this review, we will briefly summarize the current understanding on dysbiosis and discuss microbiota modulation strategies to treat patients with DGBI.
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Affiliation(s)
- Giovanni Marasco
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Italy
| | - Cesare Cremon
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Italy
| | | | - Francesca Bianco
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy
| | - Vincenzo Stanghellini
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Italy
| | - Giovanni Barbara
- IRCCS Azienda Ospedaliero Universitaria di Bologna, Bologna, Italy; Department of Medical and Surgical Sciences, University of Bologna, Italy.
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O'Toole PW. Ageing, microbes and health. Microb Biotechnol 2024; 17:e14477. [PMID: 38801344 PMCID: PMC11129672 DOI: 10.1111/1751-7915.14477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
The human gut microbiome is a modifier of the risk for many non-communicable diseases throughout the lifespan. In ageing, the effect of the microbiome appears to be more pronounced because of the lower physiological reserve. Microbial metabolites and other bioactive products act upon some of the key physiological processes involved in the Hallmarks of Ageing. Dietary interventions that delay age-related change in the microbiome have also led to delayed onset of ageing-related health loss, and improved levels of cognitive function, inflammatory status and frailty. Cross-sectional analysis of thousands of gut microbiome datasets from around the world has identified key taxa that are depleted during accelerated health loss, and other taxa that become more abundant, but these signatures differ in some geographical regions. The key challenges for research in this area are to experimentally prove that particular species or strains directly contribute to health-related ageing outcomes, and to develop practical ways of retaining or re-administering them on a population basis. The promotion of a health-associated gut microbiome in ageing mirrors the challenge of maintaining planetary microbial ecosystems in the face of anthropogenic effects and climate change. Lessons learned from acting at the individual level can inform microbiome-targeting strategies for achieving Sustainable Development Goals at a global level.
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Affiliation(s)
- Paul W. O'Toole
- School of MicrobiologyUniversity College CorkCorkIreland
- APC Microbiome IrelandUniversity College CorkCorkIreland
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Nyboe Andersen N, Wildt S, Iversen AT, Poulsen G, Jess T, Munck LK, Borup C. Risk of cancer in patients with bile acid diarrhoea: a Danish nationwide matched cohort study. BMJ Open Gastroenterol 2024; 11:e001340. [PMID: 38688717 PMCID: PMC11085898 DOI: 10.1136/bmjgast-2023-001340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
OBJECTIVE Bile acid diarrhoea is a common cause of chronic diarrhoea. Increased levels of potentially carcinogenic bile acids in faeces, theoretically, may increase the risk of colorectal cancer in particular, but the long-term disease course is unknown. We aimed to investigate the overall and site-specific cancer risk in bile acid diarrhoea. DESIGN Adult patients with bile acid diarrhoea were identified using nationwide Danish registries from 2003 to 2020 by a diagnostic gold-standard 75-selenium tauroselcholic acid procedure followed within 6 months by sequestrant prescription. The risk of overall and site-specific cancers in cases with bile acid diarrhoea was compared with sex, age and comorbidity-adjusted matched controls. A competing risk model estimated cumulative incidence functions and cause-specific HRs. RESULTS We identified 2260 patients with bile acid diarrhoea with a mean follow-up of 5.5 years (SD 4.2). The overall cancer risk was increased by an HR of 1.32 (95% CI 1.12 to 1.54). The risk of site-specific cancer was increased in 3 of 10 cancer groups: haematological, HR 2.41 (1.36 to 4.02); skin, HR 1.33 (1.01 to 1.71); and male genital cancers, HR 1.85 (1.11 to 2.92). No increased risk of colorectal cancer was detected in patients with bile acid diarrhoea, HR 0.73 (0.34 to 1.63). CONCLUSIONS Bile acid diarrhoea was associated with an increased overall risk of cancer, especially haematological cancers, but the risk of colorectal cancer was not increased. The lack of a diagnostic code for bile acid diarrhoea and potential residual confounding are limitations, and the findings should be replicated in other cohorts.
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Affiliation(s)
| | - Signe Wildt
- Department of Gastroenterology and Hepatology, Hvidovre Hospital, Hvidovre, Denmark
| | - Aske Thorn Iversen
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, The Faculty of Medicine, Aalborg University, Copenhagen, Denmark
| | - Gry Poulsen
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, The Faculty of Medicine, Aalborg University, Copenhagen, Denmark
| | - Tine Jess
- Center for Molecular Prediction of Inflammatory Bowel Disease, Department of Clinical Medicine, The Faculty of Medicine, Aalborg University, Copenhagen, Denmark
| | - Lars Kristian Munck
- Department of Gastroenterology, Zealand University Hospital Koge, Koge, Denmark
| | - Christian Borup
- Department of Gastroenterology, Zealand University Hospital Koge, Koge, Denmark
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5
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Wang KY, Zhong XQ. Overview of relationship between intestinal flora imbalance and diseases. WORLD CHINESE JOURNAL OF DIGESTOLOGY 2024; 32:280-284. [DOI: 10.11569/wcjd.v32.i4.280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
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6
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Alagiakrishnan K, Morgadinho J, Halverson T. Approach to the diagnosis and management of dysbiosis. Front Nutr 2024; 11:1330903. [PMID: 38706561 PMCID: PMC11069313 DOI: 10.3389/fnut.2024.1330903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/12/2024] [Indexed: 05/07/2024] Open
Abstract
All microorganisms like bacteria, viruses and fungi that reside within a host environment are considered a microbiome. The number of bacteria almost equal that of human cells, however, the genome of these bacteria may be almost 100 times larger than the human genome. Every aspect of the physiology and health can be influenced by the microbiome living in various parts of our body. Any imbalance in the microbiome composition or function is seen as dysbiosis. Different types of dysbiosis are seen and the corresponding symptoms depend on the site of microbial imbalance. The contribution of the intestinal and extra-intestinal microbiota to influence systemic activities is through interplay between different axes. Whole body dysbiosis is a complex process involving gut microbiome and non-gut related microbiome. It is still at the stage of infancy and has not yet been fully understood. Dysbiosis can be influenced by genetic factors, lifestyle habits, diet including ultra-processed foods and food additives, as well as medications. Dysbiosis has been associated with many systemic diseases and cannot be diagnosed through standard blood tests or investigations. Microbiota derived metabolites can be analyzed and can be useful in the management of dysbiosis. Whole body dysbiosis can be addressed by altering lifestyle factors, proper diet and microbial modulation. The effect of these interventions in humans depends on the beneficial microbiome alteration mostly based on animal studies with evolving evidence from human studies. There is tremendous potential for the human microbiome in the diagnosis, treatment, and prognosis of diseases, as well as, for the monitoring of health and disease in humans. Whole body system-based approach to the diagnosis of dysbiosis is better than a pure taxonomic approach. Whole body dysbiosis could be a new therapeutic target in the management of various health conditions.
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Affiliation(s)
| | - Joao Morgadinho
- Kaye Edmonton Clinic, Alberta Health Services, Edmonton, AB, Canada
| | - Tyler Halverson
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
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Iribarren C, Savolainen O, Sapnara M, Törnblom H, Simrén M, Magnusson MK, Öhman L. Temporal stability of fecal metabolomic profiles in irritable bowel syndrome. Neurogastroenterol Motil 2024; 36:e14741. [PMID: 38243381 DOI: 10.1111/nmo.14741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/15/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024]
Abstract
BACKGROUND The potential of the fecal metabolome to serve as a biomarker for irritable bowel syndrome (IBS) depends on its stability over time. Therefore, this study aimed to determine the temporal dynamics of the fecal metabolome, and the potential relationship with stool consistency, in patients with IBS and healthy subjects. METHODS Fecal samples were collected in two cohorts comprising patients with IBS and healthy subjects. For Cohort A, fecal samples collected during 5 consecutive days were analyzed by gas chromatography-tandem mass spectrometry (GC-MS/MS). For Cohort B, liquid chromatography-MS (LC-MS) was used to analyze fecal samples collected at week 0 (healthy and IBS) and at week 4 (patients only). Stool consistency was determined by the Bristol Stool Form scale. KEY RESULTS Fecal samples were collected from Cohort A (seven healthy subjects and eight IBS patients), and Cohort B (seven healthy subjects and 11 IBS patients). The fecal metabolome of IBS patients was stable short-term (Cohort A, 5 days and within the same day) and long-term (Cohort B, 4 weeks). A similar trend was observed over 5 days in the healthy subjects of Cohort A. The metabolome dissimilarity was larger between than within participants over time in both healthy subjects and IBS patients. Further analyses showed that patients had greater range of stool forms (types) than healthy subjects, with no apparent influence on metabolomic dynamics. CONCLUSION & INFERENCES The fecal metabolome is stable over time within IBS patients as well as healthy subjects. This supports the concept of a stable fecal metabolome in IBS despite fluctuations in stool consistency, and the use of single timepoint sampling to further explore how the fecal metabolome is related to IBS pathogenesis.
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Affiliation(s)
- Cristina Iribarren
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry Infrastructure, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Maria Sapnara
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Maria K Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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8
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Yang D, Lyu C, He K, Pang K, Guo Z, Wu D. Bile Acid Diarrhea: From Molecular Mechanisms to Clinical Diagnosis and Treatment in the Era of Precision Medicine. Int J Mol Sci 2024; 25:1544. [PMID: 38338820 PMCID: PMC10855108 DOI: 10.3390/ijms25031544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/18/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Bile acid diarrhea (BAD) is a multifaceted intestinal disorder involving intricate molecular mechanisms, including farnesoid X receptor (FXR), fibroblast growth factor receptor 4 (FGFR4), and Takeda G protein-coupled receptor 5 (TGR5). Current diagnostic methods encompass bile acid sequestrants (BAS), 48-h fecal bile acid tests, serum 7α-hydroxy-4-cholesten-3-one (C4), fibroblast growth factor 19 (FGF19) testing, and 75Selenium HomotauroCholic acid test (75SeHCAT). Treatment primarily involves BAS and FXR agonists. However, due to the limited sensitivity and specificity of current diagnostic methods, as well as suboptimal treatment efficacy and the presence of side effects, there is an urgent need to establish new diagnostic and treatment methods. While prior literature has summarized various diagnostic and treatment methods and the pathogenesis of BAD, no previous work has linked the two. This review offers a molecular perspective on the clinical diagnosis and treatment of BAD, with a focus on FXR, FGFR4, and TGR5, emphasizing the potential for identifying additional molecular mechanisms as treatment targets and bridging the gap between diagnostic and treatment methods and molecular mechanisms for a novel approach to the clinical management of BAD.
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Affiliation(s)
- Daiyu Yang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (D.Y.); (K.P.); (Z.G.)
| | - Chengzhen Lyu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (C.L.); (K.H.)
| | - Kun He
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (C.L.); (K.H.)
| | - Ke Pang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (D.Y.); (K.P.); (Z.G.)
| | - Ziqi Guo
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (D.Y.); (K.P.); (Z.G.)
| | - Dong Wu
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; (C.L.); (K.H.)
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9
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Wu Q, Badu S, So SY, Treangen TJ, Savidge TC. The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease. J Clin Invest 2024; 134:e170859. [PMID: 37962956 PMCID: PMC10786686 DOI: 10.1172/jci170859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Targeted metagenomic sequencing is an emerging strategy to survey disease-specific microbiome biomarkers for clinical diagnosis and prognosis. However, this approach often yields inconsistent or conflicting results owing to inadequate study power and sequencing bias. We introduce Taxa4Meta, a bioinformatics pipeline explicitly designed to compensate for technical and demographic bias. We designed and validated Taxa4Meta for accurate taxonomic profiling of 16S rRNA amplicon data acquired from different sequencing strategies. Taxa4Meta offers significant potential in identifying clinical dysbiotic features that can reliably predict human disease, validated comprehensively via reanalysis of individual patient 16S data sets. We leveraged the power of Taxa4Meta's pan-microbiome profiling to generate 16S-based classifiers that exhibited excellent utility for stratification of diarrheal patients with Clostridioides difficile infection, irritable bowel syndrome, or inflammatory bowel diseases, which represent common misdiagnoses and pose significant challenges for clinical management. We believe that Taxa4Meta represents a new "best practices" approach to individual microbiome surveys that can be used to define gut dysbiosis at a population-scale level.
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Affiliation(s)
- Qinglong Wu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Shyam Badu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Sik Yu So
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
| | - Todd J. Treangen
- Department of Computer Science, Rice University, Houston, Texas, USA
| | - Tor C. Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Microbiome Center, Department of Pathology, Texas Children’s Hospital, Houston, Texas, USA
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10
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Sung CH, Marsilio S, Pilla R, Wu YA, Cavasin JP, Hong MP, Suchodolski JS. Temporal Variability of the Dominant Fecal Microbiota in Healthy Adult Cats. Vet Sci 2024; 11:31. [PMID: 38250937 PMCID: PMC10819787 DOI: 10.3390/vetsci11010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
While shifts in gut microbiota have been studied in diseased states, the temporal variability of the microbiome in cats has not been widely studied. This study investigated the temporal variability of the feline dysbiosis index (DI) and the abundance of core bacterial groups in healthy adult cats. The secondary aim was to evaluate the relationship between the fecal abundance of Clostridium hiranonis and the fecal concentrations of unconjugated bile acids. A total of 142 fecal samples collected from 17 healthy cats were prospectively included: nine cats with weekly collection over 3 weeks (at least four time points), five cats with monthly collection over 2 months (three time points), and three cats with additional collections for up to 10 months. The DI remained stable within the reference intervals over two months for all cats (Friedman test, p > 0.2), and 100% of the DI values (n = 142) collected throughout the study period remained within the RI. While some temporal individual variation was observed for individual taxa, the magnitude was minimal compared to cats with chronic enteropathy and antibiotic exposure. Additionally, the abundance of Clostridium hiranonis was significantly correlated with the percentage of fecal primary bile acids, supporting its role as a bile acid converter in cats.
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Affiliation(s)
- Chi-Hsuan Sung
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Sina Marsilio
- UC Davis School of Veterinary Medicine, Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA 95616, USA
| | - Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Yu-An Wu
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Joao Pedro Cavasin
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Min-Pyo Hong
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
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11
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Lehmann CJ, Dylla NP, Odenwald M, Nayak R, Khalid M, Boissiere J, Cantoral J, Adler E, Stutz MR, Dela Cruz M, Moran A, Lin H, Ramaswamy R, Sundararajan A, Sidebottom AM, Little J, Pamer EG, Aronsohn A, Fung J, Baker TB, Kacha A. Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection. Cell Host Microbe 2024; 32:117-130.e4. [PMID: 38103544 DOI: 10.1016/j.chom.2023.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/06/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
Metabolites produced by the intestinal microbiome modulate mucosal immune defenses and optimize epithelial barrier function. Intestinal dysbiosis, including loss of intestinal microbiome diversity and expansion of antibiotic-resistant pathobionts, is accompanied by changes in fecal metabolite concentrations and increased incidence of systemic infection. Laboratory tests that quantify intestinal dysbiosis, however, have yet to be incorporated into clinical practice. We quantified fecal metabolites in 107 patients undergoing liver transplantation (LT) and correlated these with fecal microbiome compositions, pathobiont expansion, and postoperative infections. Consistent with experimental studies implicating microbiome-derived metabolites with host-mediated antimicrobial defenses, reduced fecal concentrations of short- and branched-chain fatty acids, secondary bile acids, and tryptophan metabolites correlate with compositional microbiome dysbiosis in LT patients and the relative risk of postoperative infection. Our findings demonstrate that fecal metabolite profiling can identify LT patients at increased risk of postoperative infection and may provide guideposts for microbiome-targeted therapies.
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Affiliation(s)
- Christopher J Lehmann
- Department of Medicine, Section of Infectious Disease and Global Health, University of Chicago Medicine, 5841 S. Maryland Ave., Chicago, IL 60637, USA; Department of Pediatrics, Section of Pediatric Infectious Diseases, University of Chicago Medicine, 5841 S. Maryland Ave., Chicago, IL 60637, USA.
| | - Nicholas P Dylla
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Matthew Odenwald
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA; Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA
| | - Ravi Nayak
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Maryam Khalid
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Jaye Boissiere
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Jackelyn Cantoral
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Emerald Adler
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Matthew R Stutz
- Department of Pulmonary and Critical Care Medicine, Cook County Health, 1950 W. Polk St, Chicago, IL 60612, USA
| | - Mark Dela Cruz
- Department of Cardiology, Advocate Health Care Systems, 4400 W. 95(th) St, Oak Lawn, IL 60453, USA
| | - Angelica Moran
- Department of Pathology, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA
| | - Huaiying Lin
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Ramanujam Ramaswamy
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Anitha Sundararajan
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Jessica Little
- Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA
| | - Eric G Pamer
- Department of Medicine, Section of Infectious Disease and Global Health, University of Chicago Medicine, 5841 S. Maryland Ave., Chicago, IL 60637, USA; Duchossois Family Institute, Biological Sciences Division, University of Chicago, 900 E. 57th St, Chicago, IL 60637, USA.
| | - Andrew Aronsohn
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA
| | - John Fung
- Department of Surgery, Section of Transplant Surgery, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA
| | - Talia B Baker
- Department of Surgery, Division of Transplantation and Advanced Hepatobiliary Surgery, University of Utah Health, 30 N. 1900 East, Salt Lake City, UT 84132, USA
| | - Aalok Kacha
- Department of Anesthesia and Critical Care, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL 60637, USA.
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12
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Martin FP, Cominetti O, Berger B, Combremont S, Marquis J, Xie G, Jia W, Pinto-Sanchez MI, Bercik P, Bergonzelli G. Metabolome-associated psychological comorbidities improvement in irritable bowel syndrome patients receiving a probiotic. Gut Microbes 2024; 16:2347715. [PMID: 38717445 PMCID: PMC11085950 DOI: 10.1080/19490976.2024.2347715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Our recent randomized, placebo-controlled study in Irritable Bowel Syndrome (IBS) patients with diarrhea or alternating bowel habits showed that the probiotic Bifidobacterium longum (BL) NCC3001 improves depression scores and decreases brain emotional reactivity. However, the involved metabolic pathways remain unclear. This analysis aimed to investigate the biochemical pathways underlying the beneficial effects of BL NCC3001 using metabolomic profiling. Patients received probiotic (1x 1010CFU, n=16) or placebo (n=19) daily for 6 weeks. Anxiety and depression were measured using the Hospital Anxiety and Depression Scale. Brain activity in response to negative emotional stimuli was assessed by functional Magnetic Resonance Imaging. Probiotic fecal abundance was quantified by qPCR. Quantitative measurement of specific panels of plasma host-microbial metabolites was performed by mass spectrometry-based metabolomics. Probiotic abundance in feces was associated with improvements in anxiety and depression scores, and a decrease in amygdala activation. The probiotic treatment increased the levels of butyric acid, tryptophan, N-acetyl tryptophan, glycine-conjugated bile acids, and free fatty acids. Butyric acid concentration correlated with lower anxiety and depression scores, and decreased amygdala activation. Furthermore, butyric acid concentration correlated with the probiotic abundance in feces. In patients with non-constipation IBS, improvements in psychological comorbidities and brain emotional reactivity were associated with an increased abundance of BL NCC3001 in feces and specific plasma metabolites, mainly butyric acid. These findings suggest the importance of a probiotic to thrive in the gut and highlight butyric acid as a potential biochemical marker linking microbial metabolism with beneficial effects on the gut-brain axis.
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Affiliation(s)
- Francois-Pierre Martin
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Ornella Cominetti
- Nestlé Institute of Food Safety and Analytical Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Bernard Berger
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Séverine Combremont
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Julien Marquis
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
| | - Guoxiang Xie
- University of Hawaii Cancer Center (UHCC), Honolulu, HI, USA
- Human Metabolomics Institute, Inc, Shenzhen, Guangdong, China
| | - Wei Jia
- University of Hawaii Cancer Center (UHCC), Honolulu, HI, USA
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Maria Inés Pinto-Sanchez
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Premysl Bercik
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Gabriela Bergonzelli
- Nestlé Institute of Health Sciences, Société des Produits Nestlé S.A, Lausanne, Switzerland
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13
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Lee BL, Rout M, Mandal R, Wishart DS. Automated identification and quantification of metabolites in human fecal extracts by nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:705-717. [PMID: 37265043 DOI: 10.1002/mrc.5372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/03/2023]
Abstract
We report the development of a software program, called MagMet-F, that automates the processing and quantification of 1D 1 H NMR of human fecal extracts. To optimize the program, we identified 82 potential fecal metabolites using 1D 1 H NMR of six human fecal extracts using manual profiling and a literature review of known fecal metabolites. We acquired pure versions of those metabolites and then acquired their 1D 1 H NMR spectra at 700 MHz to generate a fecal metabolite spectral library for MagMet-F. The fitting of these metabolites by MagMet-F was iteratively optimized to replicate manual profiling. We validated MagMet-F's automated profiling using a test set of six fecal extracts. It correctly identified 80% of the compounds and quantified those within <20% of the values determined by manual profiling using Chenomx. We also compared MagMet-F's profiling performance to two other open-access NMR profiling tools, Bayesil and Batman. MagMet-F outperformed both. Bayesil repeatedly overestimated metabolite concentrations by 10% to 40% while Batman was unable to properly quantify any compounds and took 10-20× longer. We have implemented MagMet-F as a freely accessible web server to enable automated, fast and convenient 1D 1 H NMR spectral profiling of fecal samples. MagMet-F is available at https://www.magmet.ca.
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Affiliation(s)
- Brian L Lee
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Manoj Rout
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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14
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Wang Y, Ma W, Mehta R, Nguyen LH, Song M, Drew DA, Asnicar F, Huttenhower C, Segata N, Wolf J, Spector T, Berry S, Staller K, Chan AT. Diet and gut microbial associations in irritable bowel syndrome according to disease subtype. Gut Microbes 2023; 15:2262130. [PMID: 37786251 PMCID: PMC10549191 DOI: 10.1080/19490976.2023.2262130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/15/2023] [Indexed: 10/04/2023] Open
Abstract
The role of diet and the gut microbiome in the etiopathogenesis of irritable bowel syndrome (IBS) is not fully understood. Therefore, we investigated the interplay between dietary risk factors and gut microbiota in IBS subtypes using a food frequency questionnaire and stool metagenome data from 969 participants aged 18-65 years in the ZOE PREDICT 1 study, an intervention study designed to predict postprandial metabolic responses. We identified individuals with IBS subtype according to the Rome III criteria based on predominant bowel habits during symptom onset: diarrhea (i.e. looser), constipation (i.e. harder), and mixed. Participants with IBS-D (n = 59) consumed more healthy plant-based foods (e.g. whole grains, leafy vegetables) and fiber, while those with IBS-C (n = 49) tended to consume more unhealthy plant-based foods (e.g. refined grains, fruit juice) than participants without IBS (n = 797). Microbial diversity was nominally lower in patients with IBS-D than in participants without IBS or with IBS-C. Using multivariable-adjusted linear regression, we identified specific microbiota variations in IBS subtypes, including slight increases in pro-inflammatory taxa in IBS-C (e.g. Escherichia coli) and loss of strict anaerobes in IBS-D (e.g. Faecalibacterium prausnitzii). Our analysis also revealed intriguing evidence of interactions between diet and Faecalibacterium prausnitzii. The positive associations between fiber and iron intake and IBS-diarrhea were stronger among individuals with a higher relative abundance of Faecalibacterium prausnitzii, potentially driven by carbohydrate metabolic pathways, including the superpathway of β-D-glucuronide and D-glucuronate degradation. In conclusion, our findings suggest subtype-specific variations in dietary habits, gut microbial composition and function, and diet-microbiota interactions in IBS, providing insights into potential microbiome-informed dietary interventions.
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Affiliation(s)
- Yiqing Wang
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wenjie Ma
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raaj Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Long H. Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
| | - David A. Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
- European Institute of Oncology Scientific Institute for Research, Hospitalization and Healthcare, Milan, Italy
| | | | - Tim Spector
- Department of Twin Research, King’s College London, London, UK
| | - Sarah Berry
- Department of Nutritional Sciences, King’s College London, London, UK
| | - Kyle Staller
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, USA
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15
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Diwan B, Yadav R, Singh A, Kumar D, Sharma R. Murine sterile fecal filtrate is a potent pharmacological agent that exerts age-independent immunomodulatory effects in RAW264.7 macrophages. BMC Complement Med Ther 2023; 23:362. [PMID: 37833682 PMCID: PMC10576334 DOI: 10.1186/s12906-023-04193-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Sterile fecal filtrate (SFF) is being considered a safer alternative to fecal microbiota transplantation (FMT) therapy; however, its bioactive potency is very little understood. The present study thus assessed the age-dependent immunostimulatory and immunomodulatory attributes of murine SFF in vitro. METHODS SFF from young (Y-SFF) and old (O-SFF) Swiss albino mice were prepared. Immunostimulatory and immunomodulatory effects of SFF were evaluated in resting and lipopolysaccharide (LPS) stimulated macrophage cells by measuring intracellular reactive oxygen species (ROS), nitric oxide (NO) production, inflammatory cytokines profile, as well as gene expression of oxidative and inflammatory transcription factors. SFF were also evaluated for native antioxidant capacity by measuring DPPH and ABTS free radical scavenging activity. Bioactive components present in SFF were also determined by GC/MS analysis. RESULTS Both Y-SFF and O-SFF induced potent immunostimulatory effects characterized by changes in cell morphology, a significant increase in NO production, ROS levels, and an increased ratio of pro-inflammatory (IL-6, TNF-α, IL-1β) to anti-inflammatory (IL-10) secretory proteins although no significant aggravation in the transcription of NF-κB and Nrf-2 could be observed. Application of LPS to cells significantly augmented a pro-oxidative and pro-inflammatory response which was much higher in comparison to Y-SFF or O-SFF application alone and mediated by strong suppression of Nrf-2 gene expression. Pre-treatment of macrophages with both Y-SFF and O-SFF robustly attenuated cellular hyperresponsiveness to LPS characterized by significantly decreased levels of NO, ROS, and inflammatory cytokines while a concomitant increase in anti-inflammatory protein (IL-10) was observed. Further, both Y-SFF and O-SFF strongly resisted LPS-induced downregulation of Nrf-2 expression although O-SFF appeared to protect cells slightly better from the overall LPS threat. Neat SFF samples exhibited moderate antioxidant capacity and GC/MS analysis of SFF revealed diverse volatile organic compounds characterized by alkanes, organosulphur compounds, furans, amides, amino acids, and antimicrobial elements. CONCLUSION Our results indicate that SFF is a potent stimulant of macrophages and confers strong anti-inflammatory effects regardless of donor age thereby suggesting its therapeutic efficacy in lieu of FMT therapy.
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Affiliation(s)
- Bhawna Diwan
- Faculty of Applied Sciences & Biotechnology, Shoolini University, Solan, 173229, India
| | - Rahul Yadav
- Faculty of Applied Sciences & Biotechnology, Shoolini University, Solan, 173229, India
| | - Anamika Singh
- Faculty of Applied Sciences & Biotechnology, Shoolini University, Solan, 173229, India
| | - Dinesh Kumar
- Faculty of Applied Sciences & Biotechnology, Shoolini University, Solan, 173229, India
| | - Rohit Sharma
- Faculty of Applied Sciences & Biotechnology, Shoolini University, Solan, 173229, India.
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16
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Napolitano M, Fasulo E, Ungaro F, Massimino L, Sinagra E, Danese S, Mandarino FV. Gut Dysbiosis in Irritable Bowel Syndrome: A Narrative Review on Correlation with Disease Subtypes and Novel Therapeutic Implications. Microorganisms 2023; 11:2369. [PMID: 37894027 PMCID: PMC10609453 DOI: 10.3390/microorganisms11102369] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a prevalent functional gastrointestinal disorder characterized by chronic abdominal pain and altered bowel habits. It can be subclassified in different subtypes according to the main clinical manifestation: constipation, diarrhea, mixed, and unclassified. Over the past decade, the role of gut microbiota in IBS has garnered significant attention in the scientific community. Emerging research spotlights the intricate involvement of microbiota dysbiosis in IBS pathogenesis. Studies have demonstrated reduced microbial diversity and stability and specific microbial alterations for each disease subgroup. Microbiota-targeted treatments, such as antibiotics, probiotics, prebiotics, synbiotics, fecal microbiota transplantation, and even diet, offer exciting prospects for managing IBS. However, definitive conclusions are hindered by the heterogeneity of these studies. Further research should focus on elucidating the mechanisms, developing microbiome-based diagnostics, and enabling personalized therapies tailored to an individual's microbiome profile. This review takes a deep dive into the microscopic world inhabiting our guts, and its implications for IBS. Our aim is to elucidate the complex interplay between gut microbiota and each IBS subtype, exploring novel microbiota-targeted treatments and providing a comprehensive overview of the current state of knowledge.
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Affiliation(s)
- Maria Napolitano
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Ernesto Fasulo
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Federica Ungaro
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Luca Massimino
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - Emanuele Sinagra
- Gastroenterology & Endoscopy Unit, Fondazione Istituto G. Giglio, Contrada Pietra Pollastra Pisciotto, 90015 Cefalù, Italy;
| | - Silvio Danese
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
- Gastroenterology and Endoscopy, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Francesco Vito Mandarino
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, 20132 Milan, Italy; (E.F.); (F.U.); (L.M.); (S.D.); (F.V.M.)
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17
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Sung CH, Pilla R, Marsilio S, Chow B, Zornow KA, Slovak JE, Lidbury JA, Steiner JM, Hill SL, Suchodolski JS. Fecal Concentrations of Long-Chain Fatty Acids, Sterols, and Unconjugated Bile Acids in Cats with Chronic Enteropathy. Animals (Basel) 2023; 13:2753. [PMID: 37685017 PMCID: PMC10486672 DOI: 10.3390/ani13172753] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Chronic enteropathy (CE) in cats encompasses food-responsive enteropathy, chronic inflammatory enteropathy (or inflammatory bowel disease), and low-grade intestinal T-cell lymphoma. While alterations in the gut metabolome have been extensively studied in humans and dogs with gastrointestinal disorders, little is known about the specific metabolic profile of cats with CE. As lipids take part in energy storage, inflammation, and cellular structure, investigating the lipid profile in cats with CE is crucial. This study aimed to measure fecal concentrations of various fatty acids, sterols, and bile acids. Fecal samples from 56 cats with CE and 77 healthy control cats were analyzed using gas chromatography-mass spectrometry, targeting 12 fatty acids, 10 sterols, and 5 unconjugated bile acids. Fecal concentrations of nine targeted fatty acids and animal-derived sterols were significantly increased in cats with CE. However, fecal concentrations of plant-derived sterols were significantly decreased in cats with CE. Additionally, an increased percentage of primary bile acids was observed in a subset of cats with CE. These findings suggest the presence of lipid maldigestion, malabsorption, and inflammation in the gastrointestinal tract of cats with CE. Understanding the lipid alterations in cats with CE can provide insights into the disease mechanisms and potential future therapeutic strategies.
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Affiliation(s)
- Chi-Hsuan Sung
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Sina Marsilio
- UC Davis School of Veterinary Medicine, Department of Veterinary Medicine and Epidemiology, University of California, Davis, CA 95616, USA
| | - Betty Chow
- Veterinary Specialty Hospital, San Diego, CA 92121, USA
- VCA Animal Specialty and Emergency Center, Los Angeles, CA 90025, USA
| | | | | | - Jonathan A. Lidbury
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Joerg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
| | - Steve L. Hill
- Veterinary Specialty Hospital, San Diego, CA 92121, USA
- Flagstaff Veterinary Internal Medicine Consulting, Flagstaff, AZ 86004, USA
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX 77843, USA; (C.-H.S.)
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18
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Salmeri N, Sinagra E, Dolci C, Buzzaccarini G, Sozzi G, Sutera M, Candiani M, Ungaro F, Massimino L, Danese S, Mandarino FV. Microbiota in Irritable Bowel Syndrome and Endometriosis: Birds of a Feather Flock Together-A Review. Microorganisms 2023; 11:2089. [PMID: 37630649 PMCID: PMC10458414 DOI: 10.3390/microorganisms11082089] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Endometriosis and irritable bowel syndrome (IBS) are chronic conditions affecting up to 10% of the global population, imposing significant burdens on healthcare systems and patient quality of life. Interestingly, around 20% of endometriosis patients also present with symptoms indicative of IBS. The pathogenesis of both these multifactorial conditions remains to be fully elucidated, but connections to gut microbiota are becoming more apparent. Emerging research underscores significant differences in the gut microbiota composition between healthy individuals and those suffering from either endometriosis or IBS. Intestinal dysbiosis appears pivotal in both conditions, exerting an influence via similar mechanisms. It impacts intestinal permeability, triggers inflammatory reactions, and initiates immune responses. Furthermore, it is entwined in a bidirectional relationship with the brain, as part of the gut-brain axis, whereby dysbiosis influences and is influenced by mental health and pain perception. Recent years have witnessed the development of microbiota-focused therapies, such as low FODMAP diets, prebiotics, probiotics, antibiotics, and fecal microbiota transplantation, designed to tackle dysbiosis and relieve symptoms. While promising, these treatments present inconsistent data, highlighting the need for further research. This review explores the evidence of gut dysbiosis in IBS and endometriosis, underscoring the similar role of microbiota in both conditions. A deeper understanding of this common mechanism may enable enhanced diagnostics and therapeutic advancements.
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Affiliation(s)
- Noemi Salmeri
- Gynecology/Obstetrics Unit, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, 20132 Milan, Italy; (C.D.); (G.B.); (M.C.)
| | - Emanuele Sinagra
- Gastroenterology & Endoscopy Unit, Fondazione Istituto G. Giglio, Contrada Pietra Pollastra Pisciotto, 90015 Cefalù, Italy;
| | - Carolina Dolci
- Gynecology/Obstetrics Unit, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, 20132 Milan, Italy; (C.D.); (G.B.); (M.C.)
| | - Giovanni Buzzaccarini
- Gynecology/Obstetrics Unit, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, 20132 Milan, Italy; (C.D.); (G.B.); (M.C.)
| | - Giulio Sozzi
- Gynecology/Obstetrics Unit, Fondazione Istituto G. Giglio, Contrada Pietra Pollastra Pisciotto, 90015 Cefalù, Italy; (G.S.); (M.S.)
| | - Miriam Sutera
- Gynecology/Obstetrics Unit, Fondazione Istituto G. Giglio, Contrada Pietra Pollastra Pisciotto, 90015 Cefalù, Italy; (G.S.); (M.S.)
| | - Massimo Candiani
- Gynecology/Obstetrics Unit, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, 20132 Milan, Italy; (C.D.); (G.B.); (M.C.)
| | - Federica Ungaro
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Luca Massimino
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Silvio Danese
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.U.); (L.M.); (S.D.); (F.V.M.)
| | - Francesco Vito Mandarino
- Department of Gastroenterology and Gastrointestinal Endoscopy, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, 20132 Milan, Italy; (F.U.); (L.M.); (S.D.); (F.V.M.)
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19
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Tanaka K, Tanigawa N, Song I, Komatsu T, Kuriki Y, Tanaka Y, Fukudo S, Urano Y, Fukuda S. A protease activity-based machine-learning approach as a complementary tool for conventional diagnosis of diarrhea-predominant irritable bowel syndrome. Front Microbiol 2023; 14:1179534. [PMID: 37485510 PMCID: PMC10361618 DOI: 10.3389/fmicb.2023.1179534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Irritable bowel syndrome (IBS) has no clinically accepted biomarkers even though it affects a large number of individuals worldwide. To address this lack of understanding, we evaluated peptidase activity in fecal samples from 35 patients with diarrheal IBS without symptom exacerbation (IBS-n) and 35 healthy subjects using a library of 384 fluorescent enzymatic substrate probes. IBS-n patients had high trypsin-like peptidase activity for cleavage of C-terminal lysine and arginine residues and low elastase-like activity for cleavage of C-terminal serine and glycine residues. These fluorescent probe library data, together with diagnostic machine-learning techniques, were able to accurately predict IBS-n. This approach can be used to diagnose diseases where no clinically accepted biomarkers exist, in which fecal enzyme activity is altered and also suggests that the development of new therapies targeting enzyme activities is possible.
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Affiliation(s)
- Kazuki Tanaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
| | - Naoki Tanigawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, Japan
| | - Yugo Kuriki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, Japan
| | - Yukari Tanaka
- Department of Gastroenterology, Sendai Kousei Hospital, Sendai, Miyagi, Japan
- Department of Behavioral Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shin Fukudo
- Department of Behavioral Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Hongo, Tokyo, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Hongo, Tokyo, Japan
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20
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Endres K, Friedland K. Talk to Me-Interplay between Mitochondria and Microbiota in Aging. Int J Mol Sci 2023; 24:10818. [PMID: 37445995 DOI: 10.3390/ijms241310818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
The existence of mitochondria in eukaryotic host cells as a remnant of former microbial organisms has been widely accepted, as has their fundamental role in several diseases and physiological aging. In recent years, it has become clear that the health, aging, and life span of multicellular hosts are also highly dependent on the still-residing microbiota, e.g., those within the intestinal system. Due to the common evolutionary origin of mitochondria and these microbial commensals, it is intriguing to investigate if there might be a crosstalk based on preserved common properties. In the light of rising knowledge on the gut-brain axis, such crosstalk might severely affect brain homeostasis in aging, as neuronal tissue has a high energy demand and low tolerance for according functional decline. In this review, we summarize what is known about the impact of both mitochondria and the microbiome on the host's aging process and what is known about the aging of both entities. For a long time, bacteria were assumed to be immortal; however, recent evidence indicates their aging and similar observations have been made for mitochondria. Finally, we present pathways by which mitochondria are affected by microbiota and give information about therapeutic anti-aging approaches that are based on current knowledge.
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Affiliation(s)
- Kristina Endres
- Department of Psychiatry and Psychotherapy, University Medical Center of the Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Kristina Friedland
- Department of Pharmacology and Toxicology, Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, 55128 Mainz, Germany
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21
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Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R. The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases. Gastroenterology 2023; 164:1069-1085. [PMID: 36841488 PMCID: PMC10205675 DOI: 10.1053/j.gastro.2023.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 02/27/2023]
Abstract
The human gut microbiome has been linked to numerous digestive disorders, but its metabolic products have been much less well characterized, in part due to the expense of untargeted metabolomics and lack of ability to process the data. In this review, we focused on the rapidly expanding information about the bile acid repertoire produced by the gut microbiome, including the impacts of bile acids on a wide range of host physiological processes and diseases, and discussed the role of short-chain fatty acids and other important gut microbiome-derived metabolites. Of particular note is the action of gut microbiome-derived metabolites throughout the body, which impact processes ranging from obesity to aging to disorders traditionally thought of as diseases of the nervous system, but that are now recognized as being strongly influenced by the gut microbiome and the metabolites it produces. We also highlighted the emerging role for modifying the gut microbiome to improve health or to treat disease, including the "engineered native bacteria'' approach that takes bacterial strains from a patient, modifies them to alter metabolism, and reintroduces them. Taken together, study of the metabolites derived from the gut microbiome provided insights into a wide range of physiological and pathophysiological processes, and has substantial potential for new approaches to diagnostics and therapeutics of disease of, or involving, the gastrointestinal tract.
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Affiliation(s)
- Kelly A Fogelson
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California; Department of Pediatrics, University of California San Diego, San Diego, California; Center for Microbiome Innovation, University of California San Diego, San Diego, California.
| | - Amir Zarrinpar
- Center for Microbiome Innovation, University of California San Diego, San Diego, California; Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, San Diego, California; Division of Gastroenterology, University of California San Diego, San Diego, California; Institute of Diabetes and Metabolic Health, University of California San Diego, San Diego, California.
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California; Center for Microbiome Innovation, University of California San Diego, San Diego, California; Department of Bioengineering, University of California San Diego, San Diego, California; Department of Computer Science and Engineering, University of California San Diego, San Diego, California.
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22
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Chen X, Hu C, Yan C, Tao E, Zhu Z, Shu X, Guo R, Jiang M. Maternal separation leads to dynamic changes of visceral hypersensitivity and fecal metabolomics from childhood to adulthood. Sci Rep 2023; 13:7670. [PMID: 37169847 PMCID: PMC10175246 DOI: 10.1038/s41598-023-34792-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
We assessed dynamic changes in visceral hypersensitivity and fecal metabolomics through a mouse model of irritable bowel syndrome (IBS) from childhood to adulthood. A mouse model of IBS was constructed with maternal separation (MS) in early life. Male mice aged 25, 40, and 70 days were used. Visceral sensitivity was assessed by recording the reaction between the abdominal withdrawal reflex and colorectal distension. Metabolomics was identified and quantified by liquid chromatography-tandem mass spectrometry. The visceral sensitivity of the MS group was significantly higher than that of the non-separation (NS) group in the three age groups. The top four fecal differential metabolites in the different age groups were lipids, lipid molecules, organic heterocyclic compounds, organic acids and derivatives, and benzenoids. Five identical differential metabolites were detected in the feces and ileal contents of the MS and NS groups at different ages, namely, benzamide, taurine, acetyl-L-carnitine, indole, and ethylbenzene. Taurine and hypotaurine metabolism were the most relevant pathways at P25, whereas histidine metabolism was the most relevant pathway at P40 and P70. Visceral hypersensitivity in the MS group lasted from childhood to adulthood. The different metabolites and metabolic pathways detected in MS groups of different ages provide a theoretical basis for IBS pathogenesis.
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Affiliation(s)
- Xiaolong Chen
- Pediatric Endoscopy Center and Gastrointestinal Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
- Department of Pediatrics, The First People's Hospital of Jiashan, Jiashan, 314100, China
| | - Chenmin Hu
- Pediatric Endoscopy Center and Gastrointestinal Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Chenxi Yan
- Pediatric Endoscopy Center and Gastrointestinal Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Enfu Tao
- Pediatric Endoscopy Center and Gastrointestinal Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Zhenya Zhu
- Pediatric Endoscopy Center and Gastrointestinal Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Xiaoli Shu
- Pediatric Endoscopy Center and Gastrointestinal Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Rui Guo
- Pediatric Endoscopy Center and Gastrointestinal Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China
| | - Mizu Jiang
- Pediatric Endoscopy Center and Gastrointestinal Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China.
- Department of Gastroenterology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, Hangzhou, 310052, China.
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23
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Wang L, Lv WQ, Yang JT, Lin X, Liu HM, Tan HJ, Quan RP, Long PP, Shen H, Shen J, Deng HW, Xiao HM. Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation. Front Microbiol 2023; 14:1117905. [PMID: 37228368 PMCID: PMC10203953 DOI: 10.3389/fmicb.2023.1117905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Functional constipation (FC) is a high morbidity gastrointestinal disease for which dysfunction in the enteric nervous system is a major pathogenesis mechanism. To enhance our understanding of the involvement of intestinal microbiota and its metabolites in the pathogenesis of FC, we conducted a shotgun metagenomic sequencing analysis of gut microbiota and serum short-chain fatty acids (SCFAs) analysis in 460 Chinese women with different defecation frequencies. We observed that the abundance ofFusobacterium_varium, a butyric acid-producing bacterium, was positively correlated (P = 0.0096) with the frequency of defecation; however, the concentrations of serum butyric acid was negatively correlated (P = 3.51E-05) with defecation frequency. These results were verified in an independent cohort (6 patients with FC and 6 controls). To further study the effects of butyric acid on intestinal nerve cells, we treated mouse intestinal neurons in vitro with various concentrations of butyrate (0.1, 0.5, 1, and 2.5 mM). We found that intestinal neurons treated with 0.5 mM butyrate proliferated better than those in the other treatment groups, with significant differences in cell cycle and oxidative phosphorylation signal pathways. We suggest that the decreased butyrate production resulting from the reduced abundance of Fusobacterium in gut microbiota affects the proliferation of intestinal neurons and the energy supply of intestinal cells. However, with FC disease advancing, the consumption and excretion of butyric acid reduce, leading to its accumulation in the intestine. Moreover, the accumulation of an excessively high amount of butyric acid inhibits the proliferation of nerve cells and subsequently exacerbates the disease.
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Affiliation(s)
- Le Wang
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- School of Basic Medical Science, Hunan University of Medicine, Huaihua, Hunan, China
| | - Wan-Qiang Lv
- Center of Safety Evaluation and Research, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Key Laboratory of Drug Safety Evaluation and Research of Zhejiang Province, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jun-Ting Yang
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xu Lin
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hui-Min Liu
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Hang-Jing Tan
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Ru-Ping Quan
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Pan-Pan Long
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Hui Shen
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Jie Shen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hong-Wen Deng
- Tulane Center of Biomedical Informatics and Genomics, Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, United States
| | - Hong-Mei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha, Hunan, China
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24
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Strauss JC, Haskey N, Ramay HR, Ghosh TS, Taylor LM, Yousuf M, Ohland C, McCoy KD, Ingram RJM, Ghosh S, Panaccione R, Raman M. Weighted Gene Co-Expression Network Analysis Identifies a Functional Guild and Metabolite Cluster Mediating the Relationship between Mucosal Inflammation and Adherence to the Mediterranean Diet in Ulcerative Colitis. Int J Mol Sci 2023; 24:ijms24087323. [PMID: 37108484 PMCID: PMC10138710 DOI: 10.3390/ijms24087323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/09/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Diet influences the pathogenesis and clinical course of inflammatory bowel disease (IBD). The Mediterranean diet (MD) is linked to reductions in inflammatory biomarkers and alterations in microbial taxa and metabolites associated with health. We aimed to identify features of the gut microbiome that mediate the relationship between the MD and fecal calprotectin (FCP) in ulcerative colitis (UC). Weighted gene co-expression network analysis (WGCNA) was used to identify modules of co-abundant microbial taxa and metabolites correlated with the MD and FCP. The features considered were gut microbial taxa, serum metabolites, dietary components, short-chain fatty acid and bile acid profiles in participants that experienced an increase (n = 13) or decrease in FCP (n = 16) over eight weeks. WGCNA revealed ten modules containing sixteen key features that acted as key mediators between the MD and FCP. Three taxa (Faecalibacterium prausnitzii, Dorea longicatena, Roseburia inulinivorans) and a cluster of four metabolites (benzyl alcohol, 3-hydroxyphenylacetate, 3-4-hydroxyphenylacetate and phenylacetate) demonstrated a strong mediating effect (ACME: -1.23, p = 0.004). This study identified a novel association between diet, inflammation and the gut microbiome, providing new insights into the underlying mechanisms of how a MD may influence IBD. See clinicaltrials.gov (NCT04474561).
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Affiliation(s)
- Jaclyn C Strauss
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Natasha Haskey
- Department of Biology, Irving K Barber Faculty of Science, University of British Columbia-Okanagan, 3137 University Way, Kelowna, BC V1V 1V7, Canada
| | - Hena R Ramay
- International Microbiome Centre, HRIC 4AA08 Foothills Campus, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Tarini Shankar Ghosh
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, College Road, National University of Ireland, T12 K8AF Cork, Ireland
| | - Lorian M Taylor
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Munazza Yousuf
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Christina Ohland
- International Microbiome Centre, HRIC 4AA08 Foothills Campus, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Kathy D McCoy
- International Microbiome Centre, HRIC 4AA08 Foothills Campus, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Richard J M Ingram
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Subrata Ghosh
- APC Microbiome Ireland, College of Medicine and Health, University College Cork, College Road, National University of Ireland, T12 K8AF Cork, Ireland
| | - Remo Panaccione
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Maitreyi Raman
- Department of Medicine, Cumming School of Medicine, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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25
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Vanuytsel T, Bercik P, Boeckxstaens G. Understanding neuroimmune interactions in disorders of gut-brain interaction: from functional to immune-mediated disorders. Gut 2023; 72:787-798. [PMID: 36657961 PMCID: PMC10086308 DOI: 10.1136/gutjnl-2020-320633] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/08/2022] [Indexed: 01/21/2023]
Abstract
Functional gastrointestinal disorders-recently renamed into disorders of gut-brain interaction-such as irritable bowel syndrome and functional dyspepsia are highly prevalent conditions with bothersome abdominal symptoms in the absence of structural abnormalities. While traditionally considered as motility disorders or even psychosomatic conditions, our understanding of the pathophysiology has evolved significantly over the last two decades. Initial observations of subtle mucosal infiltration with immune cells, especially mast cells and eosinophils, are since recently being backed up by mechanistic evidence demonstrating increased release of nociceptive mediators by immune cells and the intestinal epithelium. These mediators can activate sensitised neurons leading to visceral hypersensitivity with bothersome symptoms. The interaction between immune activation and an impaired barrier function of the gut is most likely a bidirectional one with alterations in the microbiota, psychological stress and food components as upstream players in the pathophysiology. Only few immune-targeting treatments are currently available, but an improved understanding through a multidisciplinary scientific approach will hopefully identify novel, more precise treatment targets with ultimately better outcomes.
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Affiliation(s)
- Tim Vanuytsel
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism (ChroMeta), KU Leuven, Leuven, Belgium.,Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| | - Premysl Bercik
- Faculty of Health Sciences, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Guy Boeckxstaens
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases and Metabolism (ChroMeta), KU Leuven, Leuven, Belgium .,Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
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26
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Hong G, Li Y, Yang M, Li G, Jin Y, Xiong H, Qian W, Hou X. Baseline gut microbial profiles are associated with the efficacy of Bacillus subtilis and Enterococcus faecium in IBS-D. Scand J Gastroenterol 2023; 58:339-348. [PMID: 36281578 DOI: 10.1080/00365521.2022.2136013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Little is known about association between the efficacy of probiotics and baseline gut microbiota in irritable bowel syndrome (IBS). We aimed to explore gut microbiota in diarrhea-predominant IBS (IBS-D) and whether baseline gut microbiota was related to the efficacy of Bacillus subtilis and Enterococcus faecium (BE). METHODS This study recruited 19 healthy controls (HC) and 50 IBS-D patients, among whom 19 patients were administrated 500 mg BE orally three times daily for 2 weeks. Clinical data and fecal samples were collected from patients before and after treatment. 16S rRNA sequencing was performed to obtain fecal bacterial data. RESULTS There was no significant difference of alpha diversity, beta diversity, profiles of microbial phyla and genera between HC and IBS. BE improved IBS-SSS (IBS severity scoring system) and stool consistency, and altered Enterococcus, Blautia, Lachnoclostridium and Fusobacterium without significant impact on microbial structure in IBS-D. Notably, baseline fecal bacterial composition differed between non-responders and responders to BE concerning abdominal pain and bloating, with Atopobium, Pyramidobacter, Ruminococcus gnavus and Peptostreptococcus enriched in responders in terms of abdominal pain. There was reduced abundance of Prevotella, Ruminococcaceae UCG, Eubacterium eligens, Faecalibacterium and Eubacterium coprostanoligenes in responders compared with non-responders. Furthermore, BE increased beneficial bacteria including Faecalibacterium, Blautia and Butyricicoccus, decreased Lachnoclostridium and Bilophila, and influenced some microbial metabolic pathways in responders, such as mineral absorption, metabolism of arachidonic acid, d-arginine, D-ornithine, phenylalanine and vitamin B6. CONCLUSION Baseline fecal microbiome is associated with the efficacy of BE in attenuating abdominal pain and bloating in IBS-D.
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Affiliation(s)
- Gaichao Hong
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Yang
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gangping Li
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Jin
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hanhua Xiong
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Qian
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohua Hou
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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27
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Shaikh SD, Sun N, Canakis A, Park WY, Weber HC. Irritable Bowel Syndrome and the Gut Microbiome: A Comprehensive Review. J Clin Med 2023; 12:jcm12072558. [PMID: 37048642 PMCID: PMC10095554 DOI: 10.3390/jcm12072558] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 03/31/2023] Open
Abstract
Irritable Bowel Syndrome (IBS) is a functional disorder of the gastrointestinal tract characterized by abdominal pain and altered bowel habits. It has a prevalence of 10 to 25% in the United States and has a high disease burden, as evidenced by reduced quality of life, decreased work productivity and increased healthcare utilization and costs. IBS has been associated with several intra-intestinal and extra-intestinal conditions, including psychiatric comorbidities. Although the pathophysiology of IBS has not been fully elucidated, it involves dysregulation of communication between the brain and gut (brain–gut axis) which is associated with alterations in intestinal motility, gut permeability, visceral hypersensitivity and gut microbiota composition. The purpose of this article is to review the role the gut microbiota plays in the pathophysiology of IBS, understand factors that affect the gut microbiome and explore the microbiome as a target of treatment.
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28
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Kumar A, Quraishi MN, Al-Hassi HO, El-Asrag ME, Segal JP, Jain M, Steed H, Butterworth J, Farmer A, Mclaughlin J, Beggs A, Brookes MJ. The analysis of gut microbiota in patients with bile acid diarrhoea treated with colesevelam. Front Microbiol 2023; 14:1134105. [PMID: 37007510 PMCID: PMC10063896 DOI: 10.3389/fmicb.2023.1134105] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/14/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionBile acid diarrhoea (BAD) is a common disorder that results from an increased loss of primary bile acids and can result in a change in microbiome. The aims of this study were to characterise the microbiome in different cohorts of patients with BAD and to determine if treatment with a bile acid sequestrant, colesevelam, can alter the microbiome and improve microbial diversity.Materials and methodsPatients with symptoms of diarrhoea underwent 75-selenium homocholic acid (75SeHCAT) testing and were categorised into four cohorts: idiopathic BAD, post-cholecystectomy BAD, post-operative Crohn’s disease BAD and 75SeHCAT negative control group. Patients with a positive 75SeHCAT (<15%) were given a trial of treatment with colesevelam. Stool samples were collected pre-treatment, 4-weeks, 8-weeks and 6–12 months post-treatment. Faecal 16S ribosomal RNA gene analysis was undertaken.ResultsA total of 257 samples were analysed from 134 patients. α-diversity was significantly reduced in patients with BAD and more specifically, in the idiopathic BAD cohort and in patients with severe disease (SeHCAT <5%); p < 0.05. Colesevelam did not alter bacterial α/β-diversity but patients who clinically responded to treatment had a significantly greater abundance of Fusobacteria and Ruminococcus, both of which aid in the conversion of primary to secondary bile acids.ConclusionThis is the first study to examine treatment effects on the microbiome in BAD, which demonstrated a possible association with colesevelam on the microbiome through bile acid modulation in clinical responders. Larger studies are now needed to establish a causal relationship with colesevelam and the inter-crosstalk between bile acids and the microbiome.
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Affiliation(s)
- Aditi Kumar
- Department of Gastroenterology, The Royal Wolverhampton NHS Trust, Wolverhampton, United Kingdom
- *Correspondence: Aditi Kumar,
| | - Mohammed Nabil Quraishi
- Microbiome Treatment Centre, University of Birmingham Microbiome Treatment Centre, Birmingham, United Kingdom
- Department of Gastroenterology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Hafid O. Al-Hassi
- Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom
| | - Mohammed E. El-Asrag
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Faculty of Science, Benha University, Benha, Egypt
| | - Jonathan P. Segal
- Department of Gastroenterology, Northern Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Manushri Jain
- Department of Gastroenterology, The Royal Wolverhampton NHS Trust, Wolverhampton, United Kingdom
| | - Helen Steed
- Department of Gastroenterology, The Royal Wolverhampton NHS Trust, Wolverhampton, United Kingdom
- School of Medicine and Clinical Practice, Faculty of Sciences and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom
| | - Jeffrey Butterworth
- Department of Gastroenterology, Shrewsbury and Telford Hospital NHS Trust, Shrewsbury, United Kingdom
| | - Adam Farmer
- Department of Gastroenterology, University Hospitals of North Midlands, Stoke-on-Trent, United Kingdom
| | - John Mclaughlin
- Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Department of Gastroenterology, Salford Royal Foundation Trust, Salford, United Kingdom
| | - Andrew Beggs
- Microbiome Treatment Centre, University of Birmingham Microbiome Treatment Centre, Birmingham, United Kingdom
- Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom
| | - Matthew J. Brookes
- Department of Gastroenterology, The Royal Wolverhampton NHS Trust, Wolverhampton, United Kingdom
- School of Medicine and Clinical Practice, Faculty of Sciences and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom
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29
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Crost EH, Coletto E, Bell A, Juge N. Ruminococcus gnavus: friend or foe for human health. FEMS Microbiol Rev 2023; 47:fuad014. [PMID: 37015876 PMCID: PMC10112845 DOI: 10.1093/femsre/fuad014] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/06/2023] [Accepted: 04/03/2023] [Indexed: 04/06/2023] Open
Abstract
Ruminococcus gnavus was first identified in 1974 as a strict anaerobe in the gut of healthy individuals, and for several decades, its study has been limited to specific enzymes or bacteriocins. With the advent of metagenomics, R. gnavus has been associated both positively and negatively with an increasing number of intestinal and extraintestinal diseases from inflammatory bowel diseases to neurological disorders. This prompted renewed interest in understanding the adaptation mechanisms of R. gnavus to the gut, and the molecular mediators affecting its association with health and disease. From ca. 250 publications citing R. gnavus since 1990, 94% were published in the last 10 years. In this review, we describe the biological characterization of R. gnavus, its occurrence in the infant and adult gut microbiota and the factors influencing its colonization of the gastrointestinal tract; we also discuss the current state of our knowledge on its role in host health and disease. We highlight gaps in knowledge and discuss the hypothesis that differential health outcomes associated with R. gnavus in the gut are strain and niche specific.
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Affiliation(s)
- Emmanuelle H Crost
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Erika Coletto
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Andrew Bell
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Nathalie Juge
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
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30
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Deng X, Xiao L, Luo M, Xie P, Xiong L. Intestinal crosstalk between bile acids and microbiota in irritable bowel syndrome. J Gastroenterol Hepatol 2023. [PMID: 36869260 DOI: 10.1111/jgh.16159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/18/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023]
Abstract
Irritable bowel syndrome (IBS) is a relatively common functional gastrointestinal disease with a disturbance of intestinal bacteria. Bile acids, gut microbiota, and the host have close and complex interactions, which play a central role in modulating host immune and metabolic homeostasis. Recent studies suggested that the bile acid-gut microbiota axis played a key role in the development of IBS patients. In order to investigate the role of bile acids in the pathogenesis of IBS and present potentially relevant clinical implications, we conducted a literature search on intestinal interactions between bile acid and gut microbiota. The intestinal crosstalk between bile acids and gut microbiota shapes the compositional and functional alterations in IBS, manifesting as gut microbial dysbiosis, disturbed bile acid pathway, and alteration of the microbial metabolites. Collaboratively, bile acid conducts the pathogenesis of IBS through the alterations of the farnesoid-X receptor and G protein-coupled receptor. Diagnostic markers and treatments targeting the bile acids and its receptor showed promising potential in the management of IBS. Bile acids and gut microbiota play a key role in the development of IBS and make attractive biomarkers for treatments. Individualized therapy aiming at bile acids and its receptor may provide significant diagnostic and requires further investigation.
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Affiliation(s)
- Xuehong Deng
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lin Xiao
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mei Luo
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Peiwei Xie
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lishou Xiong
- Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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31
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Kim GH, Lee K, Shim JO. Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets. Microbiol Spectr 2023; 11:e0212522. [PMID: 36652592 PMCID: PMC9927514 DOI: 10.1128/spectrum.02125-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Research on the gut microbiota in irritable bowel syndrome (IBS) shows discordant results due to inconsistent study designs or small sample sizes. This study aimed to characterize how gut microbiota in IBS patients differs from that in healthy controls by performing a case-control study and cross- and mega-cohort analysis. Multiple publicly shared data sets were examined by using a unified analytical approach. We performed 16S rRNA gene (V3-4) sequencing and taxonomic profiling of the gut bacterial communities. Fecal samples from children with IBS (n = 19) and age-matched healthy controls (n = 24) were used. Next, we analyzed 10 separate data sets using a unified data-processing and analytical approach. In total, 567 IBS patients and 487 healthy controls were examined. In our data sets, no significant differences existed in stool α-diversity between IBS patients and healthy controls. After combining all the data sets using a unified data-processing method, we found significantly lower α-diversity in IBS patients than in healthy controls. In addition, the relative abundance of 21 bacterial species differed between the IBS patients and healthy participants. Although the causal relationship is uncertain, gut bacterial dysbiosis is associated with IBS. Further functional studies are needed to assess whether the change in gut microorganisms contributes to the development of IBS. IMPORTANCE Research on the gut bacteria in irritable bowel syndrome (IBS) shows discordant results due to inconsistent study designs or small sample sizes. To overcome these issues, we analyzed microbiota of 567 IBS patients and 487 healthy people from 10 shared data sets using a unified method. We demonstrated that gut bacteria are less diverse in IBS patients than in healthy people. In addition, the abundance of 21 bacterial species is different between the two groups. Altered bacterial balance, called dysbiosis, has been reported in several disease states. Although the causal relationship is uncertain, gut bacterial dysbiosis also seems to be associated with IBS.
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Affiliation(s)
- Gun-Ha Kim
- Division of Pediatric Neurology, Department of Pediatrics, Korea Cancer Center Hospital, Korea Institute of Radiological & Medical Sciences, Seoul, South Korea
| | | | - Jung Ok Shim
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Korea University College of Medicine, Seoul, South Korea
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32
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Guo C, Che X, Briese T, Ranjan A, Allicock O, Yates RA, Cheng A, March D, Hornig M, Komaroff AL, Levine S, Bateman L, Vernon SD, Klimas NG, Montoya JG, Peterson DL, Lipkin WI, Williams BL. Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS. Cell Host Microbe 2023; 31:288-304.e8. [PMID: 36758522 PMCID: PMC10183837 DOI: 10.1016/j.chom.2023.01.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/10/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained debilitating fatigue, cognitive dysfunction, gastrointestinal disturbances, and orthostatic intolerance. Here, we report a multi-omic analysis of a geographically diverse cohort of 106 cases and 91 healthy controls that revealed differences in gut microbiome diversity, abundances, functional pathways, and interactions. Faecalibacterium prausnitzii and Eubacterium rectale, which are both recognized as abundant, health-promoting butyrate producers in the human gut, were reduced in ME/CFS. Functional metagenomics, qPCR, and metabolomics of fecal short-chain fatty acids confirmed a deficient microbial capacity for butyrate synthesis. Microbiome-based machine learning classifier models were robust to geographic variation and generalizable in a validation cohort. The abundance of Faecalibacterium prausnitzii was inversely associated with fatigue severity. These findings demonstrate the functional nature of gut dysbiosis and the underlying microbial network disturbance in ME/CFS, providing possible targets for disease classification and therapeutic trials.
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Affiliation(s)
- Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Xiaoyu Che
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Thomas Briese
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Amit Ranjan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Orchid Allicock
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Rachel A Yates
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Aaron Cheng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Dana March
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Mady Hornig
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Anthony L Komaroff
- Division of General Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Nancy G Klimas
- Institute for Neuro-Immune Medicine, College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA; Miami VA Medical Center, Miami, FL 33125, USA
| | - Jose G Montoya
- Palo Alto Medical Foundation, Jack S. Remington Laboratory for Specialty Diagnostics of Toxoplasmosis, Palo Alto, CA 94301, USA
| | - Daniel L Peterson
- Sierra Internal Medicine at Incline Village, Incline Village, NV 89451, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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Ohkusa T, Nishikawa Y, Sato N. Gastrointestinal disorders and intestinal bacteria: Advances in research and applications in therapy. Front Med (Lausanne) 2023; 9:935676. [PMID: 36825261 PMCID: PMC9941163 DOI: 10.3389/fmed.2022.935676] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 12/27/2022] [Indexed: 02/09/2023] Open
Abstract
Intestinal bacteria coexist with humans and play a role in suppressing the invasion of pathogens, producing short-chain fatty acids, producing vitamins, and controlling the immune system. Studies have been carried out on culturable bacterial species using bacterial culture methods for many years. However, as metagenomic analysis of bacterial genes has been developed since the 1990s, it has recently revealed that many bacteria in the intestine cannot be cultured and that approximately 1,000 species and 40 trillion bacteria are present in the gut microbiota. Furthermore, the composition of the microbiota is different in each disease state compared with the healthy state, and dysbiosis has received much attention as a cause of various diseases. Regarding gastrointestinal diseases, dysbiosis has been reported to be involved in inflammatory bowel disease, irritable bowel syndrome, and non-alcoholic steatohepatitis. Recent findings have also suggested that dysbiosis is involved in colon cancer, liver cancer, pancreatic cancer, esophageal cancer, and so on. This review focuses on the relationship between the gut microbiota and gastrointestinal/hepatobiliary diseases and also discusses new therapies targeting the gut microbiota.
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Affiliation(s)
| | - Yuriko Nishikawa
- Department of Microbiota Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuhiro Sato
- Department of Microbiota Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Zhai L, Huang C, Ning Z, Zhang Y, Zhuang M, Yang W, Wang X, Wang J, Zhang L, Xiao H, Zhao L, Asthana P, Lam YY, Chow CFW, Huang JD, Yuan S, Chan KM, Yuan CS, Lau JYN, Wong HLX, Bian ZX. Ruminococcus gnavus plays a pathogenic role in diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis. Cell Host Microbe 2023; 31:33-44.e5. [PMID: 36495868 DOI: 10.1016/j.chom.2022.11.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 09/06/2022] [Accepted: 11/15/2022] [Indexed: 12/14/2022]
Abstract
Diarrhea-predominant irritable bowel syndrome (IBS-D), a globally prevalent functional gastrointestinal (GI) disorder, is associated with elevated serotonin that increases gut motility. While anecdotal evidence suggests that the gut microbiota contributes to serotonin biosynthesis, mechanistic insights are limited. We determined that the bacterium Ruminococcus gnavus plays a pathogenic role in IBS-D. Monocolonization of germ-free mice with R. gnavus induced IBS-D-like symptoms, including increased GI transit and colonic secretion, by stimulating the production of peripheral serotonin. R. gnavus-mediated catabolism of dietary phenylalanine and tryptophan generated phenethylamine and tryptamine that directly stimulated serotonin biosynthesis in intestinal enterochromaffin cells via a mechanism involving activation of trace amine-associated receptor 1 (TAAR1). This R. gnavus-driven increase in serotonin levels elevated GI transit and colonic secretion but was abrogated upon TAAR1 inhibition. Collectively, our study provides molecular and pathogenetic insights into how gut microbial metabolites derived from dietary essential amino acids affect serotonin-dependent control of gut motility.
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Affiliation(s)
- Lixiang Zhai
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China
| | - Chunhua Huang
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Ziwan Ning
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yijing Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Min Zhuang
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China
| | - Wei Yang
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China
| | - Xiaolei Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Jingjing Wang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR, China
| | - Lu Zhang
- Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR, China
| | - Haitao Xiao
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Ling Zhao
- Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Pallavi Asthana
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yan Y Lam
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China
| | - Chi Fung Willis Chow
- Center for Systems Biology Dresden, Max Planck Institute for Molecular Cell and Biology, Dresden, Germany
| | - Jian-Dong Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Chun-Su Yuan
- Tang Center for Herbal Medicine Research and Department of Anesthesia and Critical Care, University of Chicago, Chicago, USA
| | - Johnson Yiu-Nam Lau
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | | | - Zhao-Xiang Bian
- Centre for Chinese Herbal Medicine Drug Development Limited, Hong Kong Baptist University, Hong Kong SAR, China; School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China.
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35
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Jacobs JP, Lagishetty V, Hauer MC, Labus JS, Dong TS, Toma R, Vuyisich M, Naliboff BD, Lackner JM, Gupta A, Tillisch K, Mayer EA. Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes. MICROBIOME 2023; 11:5. [PMID: 36624530 PMCID: PMC9830758 DOI: 10.1186/s40168-022-01450-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes. METHODS Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing (n = 486), metatranscriptomics (n = 327), and untargeted metabolomics (n = 368). Differentially abundant microbes, predicted genes, transcripts, and metabolites in IBS were identified by multivariate models incorporating age, sex, race/ethnicity, BMI, diet, and HAD-Anxiety. Inter-omic functional relationships were assessed by transcript/gene ratios and microbial metabolic modeling. Differential features were used to construct random forests classifiers. RESULTS IBS was associated with global alterations in microbiome composition by 16S rRNA sequencing and metatranscriptomics, and in microbiome function by predicted metagenomics, metatranscriptomics, and metabolomics. After adjusting for age, sex, race/ethnicity, BMI, diet, and anxiety, IBS was associated with differential abundance of bacterial taxa such as Bacteroides dorei; metabolites including increased tyramine and decreased gentisate and hydrocinnamate; and transcripts related to fructooligosaccharide and polyol utilization. IBS further showed transcriptional upregulation of enzymes involved in fructose and glucan metabolism as well as the succinate pathway of carbohydrate fermentation. A multi-omics classifier for IBS had significantly higher accuracy (AUC 0.82) than classifiers using individual datasets. Diarrhea-predominant IBS (IBS-D) demonstrated shifts in the metatranscriptome and metabolome including increased bile acids, polyamines, succinate pathway intermediates (malate, fumarate), and transcripts involved in fructose, mannose, and polyol metabolism compared to constipation-predominant IBS (IBS-C). A classifier incorporating metabolites and gene-normalized transcripts differentiated IBS-D from IBS-C with high accuracy (AUC 0.86). CONCLUSIONS IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates-consistent with the clinical benefit of diets restricting this energy source-that also includes multiple previously unrecognized metabolites and metabolic pathways. These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. Video Abstract.
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Affiliation(s)
- Jonathan P Jacobs
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA.
| | - Venu Lagishetty
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Megan C Hauer
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer S Labus
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Tien S Dong
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Ryan Toma
- Viome Life Sciences, Bellevue, WA, USA
| | | | - Bruce D Naliboff
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeffrey M Lackner
- Division of Behavioral Medicine, Department of Medicine, Jacobs School of Medicine, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Arpana Gupta
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kirsten Tillisch
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Integrative Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Emeran A Mayer
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- G. Oppenheimer Center for Neurobiology of Stress and Resilience, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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Li J, Ghosh TS, McCann R, Mallon P, Hill C, Draper L, Schult D, Fanning LJ, Shannon R, Sadlier C, Horgan M, O’Mahony L, O’Toole PW. Robust cross-cohort gut microbiome associations with COVID-19 severity. Gut Microbes 2023; 15:2242615. [PMID: 37550964 PMCID: PMC10411309 DOI: 10.1080/19490976.2023.2242615] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/07/2023] [Accepted: 07/26/2023] [Indexed: 08/09/2023] Open
Abstract
Although many recent studies have examined associations between the gut microbiome and COVID-19 disease severity in individual patient cohorts, questions remain on the robustness across international cohorts of the biomarkers they reported. Here, we performed a meta-analysis of eight shotgun metagenomic studies of COVID-19 patients (comprising 1,023 stool samples) and 23 > 16S rRNA gene amplicon sequencing (16S) cohorts (2,415 total stool samples). We found that disease severity (as defined by the WHO clinical progression scale) was associated with taxonomic and functional microbiome differences. This alteration in gut microbiome configuration peaks at days 7-30 post diagnosis, after which the gut microbiome returns to a configuration that becomes more similar to that of healthy controls over time. Furthermore, we identified a core set of species that were consistently associated with disease severity across shotgun metagenomic and 16S cohorts, and whose abundance can accurately predict disease severity category of SARS-CoV-2 infected subjects, with Actinomyces oris abundance predicting population-level mortality rate of COVID-19. Additionally, we used relational diet-microbiome databases constructed from cohort studies to predict microbiota-targeted diet patterns that would modulate gut microbiota composition toward that of healthy controls. Finally, we demonstrated the association of disease severity with the composition of intestinal archaeal, fungal, viral, and parasitic communities. Collectively, this study has identified robust COVID-19 microbiome biomarkers, established accurate predictive models as a basis for clinical prognostic tests for disease severity, and proposed biomarker-targeted diets for managing COVID-19 infection.
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Affiliation(s)
- Junhui Li
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Tarini Shankar Ghosh
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Rachel McCann
- Centre for Experimental Pathogen Host Research, School of Medicine, University College Dublin, St Vincent’s University Hospital, Dublin, Ireland
| | - Patrick Mallon
- Centre for Experimental Pathogen Host Research, School of Medicine, University College Dublin, St Vincent’s University Hospital, Dublin, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Lorraine Draper
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - David Schult
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technical University of Munich, School of Medicine, Munich, Germany
| | - Liam J. Fanning
- Department of Medicine, University College Cork, Cork, Ireland
| | - Robert Shannon
- Department of Infectious Diseases, Cork University Hospital, Cork, Ireland
| | - Corinna Sadlier
- Department of Medicine, University College Cork, Cork, Ireland
- Department of Infectious Diseases, Cork University Hospital, Cork, Ireland
| | - Mary Horgan
- Department of Medicine, University College Cork, Cork, Ireland
- Department of Infectious Diseases, Cork University Hospital, Cork, Ireland
| | - Liam O’Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Paul W. O’Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Caminero A, Guzman M, Libertucci J, Lomax AE. The emerging roles of bacterial proteases in intestinal diseases. Gut Microbes 2023; 15:2181922. [PMID: 36843008 PMCID: PMC9980614 DOI: 10.1080/19490976.2023.2181922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2023] Open
Abstract
Proteases are an evolutionarily conserved family of enzymes that degrade peptide bonds and have been implicated in several common gastrointestinal (GI) diseases. Although luminal proteolytic activity is important for maintenance of homeostasis and health, the current review describes recent advances in our understanding of how overactivity of luminal proteases contributes to the pathophysiology of celiac disease, irritable bowel syndrome, inflammatory bowel disease and GI infections. Luminal proteases, many of which are produced by the microbiota, can modulate the immunogenicity of dietary antigens, reduce mucosal barrier function and activate pro-inflammatory and pro-nociceptive host signaling. Increased proteolytic activity has been ascribed to both increases in protease production and decreases in inhibitors of luminal proteases. With the identification of strains of bacteria that are important sources of proteases and their inhibitors, the stage is set to develop drug or microbial therapies to restore protease balance and alleviate disease.
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Affiliation(s)
- Alberto Caminero
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Mabel Guzman
- Gastrointestinal Diseases Research Unit, Kingston General Hospital, Queen’s University, Kingston, Ontario, Canada
| | - Josie Libertucci
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Alan E. Lomax
- Gastrointestinal Diseases Research Unit, Kingston General Hospital, Queen’s University, Kingston, Ontario, Canada,CONTACT Alan E. Lomax Gastrointestinal Diseases Research Unit, Kingston General Hospital, Kingston, ON, K7L 2V7, Canada
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Yao C, Li Y, Luo L, Xie F, Xiong Q, Li T, Yang C, Feng PM. Significant Differences in Gut Microbiota Between Irritable Bowel Syndrome with Diarrhea and Healthy Controls in Southwest China. Dig Dis Sci 2023; 68:106-127. [PMID: 35503487 DOI: 10.1007/s10620-022-07500-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/24/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) is a heterogeneous disease, which is closely related to environmental factors and gut microbiota. OBJECTIVE To study gut microbiota in IBS-D of Han nationality in Southwest China and explore its relationship with environmental factors. METHODS One hundred and twenty cases of IBS-D and 63 cases of HCs were recruited; baseline data such as age, height, and weight were collected. HAMA, HAMD, IBS-SSS, IBS-QOL, and laboratory tests were performed. Feces were collected for 16S rDNA sequencing. Then, the differences of gut microbiota were analyzed and looked for biomarkers of each. FAPROTAX was used to predict the functional differences of gut microbiota. Spearman analysis was conducted between the phylum level and environmental factor. RESULTS There were significant differences in daily life between IBS-D and HCs, especially in the spicy taste. The scores of HAMA and HAMD, urea, and transaminase in IBS-D were significantly higher than those of HCs. The richness of gut microbiota in IBS-D was significantly lower than that of HCs, as well as the beta diversity, but not diversity. The biomarkers of IBS-D were Prevotella, Clostridiales, and Roseburia, and the biomarkers of HCs were Veillonellaceae, Bacteroides coprocola, and Bifidobacteriales. The functions of gut microbiota in IBS-D were significantly different from HCs. Correlation analysis showed that multiple gut microbiota were closely related to HAMA, IBS-SSS, IBS-QOL, inflammatory indexes, and liver enzymes. CONCLUSION There are significant differences in richness of gut microbiota, flora structure, and flora function between IBS-D and HCs in Southwest China. These differences may be closely related to environmental factors such as eating habits, living habits, and mental and psychological factors. CLINICAL TRIAL REGISTRATION The trial was registered and approved in China Clinical Trial Registry (Registration No. ChiCTR2100045751).
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Affiliation(s)
- Chengjiao Yao
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610000, Sichuan, China.,Department of Geriatrics of the Affiliated Hospital, North Sichuan Medical College, Nanchong, Sichuan, China
| | - Yilin Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610000, Sichuan, China.,North Sichuan Medical College, Nanchong, Sichuan, China
| | - Lihong Luo
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610000, Sichuan, China
| | - Fengjiao Xie
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610000, Sichuan, China
| | - Qin Xiong
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610000, Sichuan, China
| | - Tinglin Li
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610000, Sichuan, China
| | - Chunrong Yang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610000, Sichuan, China
| | - Pei-Min Feng
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, 610000, Sichuan, China.
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Shin A, Kashyap PC. Multi-omics for biomarker approaches in the diagnostic evaluation and management of abdominal pain and irritable bowel syndrome: what lies ahead. Gut Microbes 2023; 15:2195792. [PMID: 37009874 PMCID: PMC10072066 DOI: 10.1080/19490976.2023.2195792] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/23/2023] [Indexed: 04/04/2023] Open
Abstract
Reliable biomarkers for common disorders of gut-brain interaction characterized by abdominal pain, including irritable bowel syndrome (IBS), are critically needed to enhance care and develop individualized therapies. The dynamic and heterogeneous nature of the pathophysiological mechanisms that underlie visceral hypersensitivity have challenged successful biomarker development. Consequently, effective therapies for pain in IBS are lacking. However, recent advances in modern omics technologies offer new opportunities to acquire deep biological insights into mechanisms of pain and nociception. Newer methods for large-scale data integration of complementary omics approaches have further expanded our ability to build a holistic understanding of complex biological networks and their co-contributions to abdominal pain. Here, we review the mechanisms of visceral hypersensitivity, focusing on IBS. We discuss candidate biomarkers for pain in IBS identified through single omics studies and summarize emerging multi-omics approaches for developing novel biomarkers that may transform clinical care for patients with IBS and abdominal pain.
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Affiliation(s)
- Andrea Shin
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Purna C. Kashyap
- Clinical Enteric Neuroscience Translational and Epidemiological Research Program, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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40
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Beneficial Effects of Limosilactobacillus fermentum in the DCA Experimental Model of Irritable Bowel Syndrome in Rats. Nutrients 2022; 15:nu15010024. [PMID: 36615683 PMCID: PMC9824399 DOI: 10.3390/nu15010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Limosilactobacillus fermentum CECT5716, a probiotic strain isolated from human milk, has reported beneficial effects on different gastrointestinal disorders. Moreover, it has shown its ability to restore altered immune responses, in association with microbiome modulation in different pathological conditions. Therefore, our aim was to assess the effects of a Limosilacbacillus fermentum CECT5716 in a rat experimental model of irritable bowel syndrome (IBS) that resembles human IBS. The experimental IBS was induced by deoxycholic acid (DCA) in rats and then, Limosilactobacillus fermentum CECT5716 (109 CFU/day/rat) was administered. Behavioral studies, hyperalgesia and intestinal hypersensitivity determinations were performed and the impact of the probiotic on the inflammatory and intestinal barrier integrity was evaluated. Additionally, the gut microbiota composition was analyzed. Limosilactobacillus fermentum CECT5716 attenuated the anxiety-like behavior as well as the visceral hypersensitivity and referred pain. Moreover, this probiotic ameliorated the gut inflammatory status, re-establishing the altered intestinal permeability, reducing the mast cell degranulation and re-establishing the gut dysbiosis in experimental IBS. Therefore, our results suggest a potential use of Limosilactobacillus fermentum CECT5716 in clinical practice for the management of IBS patients.
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41
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High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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42
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Xie S, Zhu S, Min L. Mucosal Microbiota: Closer to the Pathology, Closer to the Truth? Dig Dis Sci 2022; 67:5361-5363. [PMID: 35879513 DOI: 10.1007/s10620-022-07595-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2022] [Indexed: 01/05/2023]
Affiliation(s)
- Sian Xie
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China. .,National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China.
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43
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Biofilms and Benign Colonic Diseases. Int J Mol Sci 2022; 23:ijms232214259. [PMID: 36430737 PMCID: PMC9698058 DOI: 10.3390/ijms232214259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/06/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
The colon has a very large surface area that is covered by a dense mucus layer. The biomass in the colon includes 500-1000 bacterial species at concentrations of ~1012 colony-forming units per gram of feces. The intestinal epithelial cells and the commensal bacteria in the colon have a symbiotic relationship that results in nutritional support for the epithelial cells by the bacteria and maintenance of the optimal commensal bacterial population by colonic host defenses. Bacteria can form biofilms in the colon, but the exact frequency is uncertain because routine methods to undertake colonoscopy (i.e., bowel preparation) may dislodge these biofilms. Bacteria in biofilms represent a complex community that includes living and dead bacteria and an extracellular matrix composed of polysaccharides, proteins, DNA, and exogenous debris in the colon. The formation of biofilms occurs in benign colonic diseases, such as inflammatory bowel disease and irritable bowel syndrome. The development of a biofilm might serve as a marker for ongoing colonic inflammation. Alternatively, the development of biofilms could contribute to the pathogenesis of these disorders by providing sanctuaries for pathogenic bacteria and reducing the commensal bacterial population. Therapeutic approaches to patients with benign colonic diseases could include the elimination of biofilms and restoration of normal commensal bacteria populations. However, these studies will be extremely difficult unless investigators can develop noninvasive methods for measuring and identifying biofilms. These methods that might include the measurement of quorum sensing molecules, measurement of bile acids, and identification of bacteria uniquely associated with biofilms in the colon.
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Torres-Maravilla E, Holowacz S, Delannoy J, Lenoir L, Jacouton E, Gervason S, Meynier M, Boucard AS, Carvalho FA, Barbut F, Bermúdez-Humarán LG, Langella P, Waligora-Dupriet AJ. Serpin-positive Bifidobacterium breve CNCM I-5644 improves intestinal permeability in two models of irritable bowel syndrome. Sci Rep 2022; 12:19776. [PMID: 36396717 PMCID: PMC9672316 DOI: 10.1038/s41598-022-21746-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/30/2022] [Indexed: 11/19/2022] Open
Abstract
Probiotic supplementation can help to mitigate the pathogenesis of irritable bowel syndrome (IBS) by reinforcing the intestinal barrier, and reducing both inflammation and proteolytic activity. Here, a combination of in vitro tests was performed on 33 Bifidobacterium strains as probiotic candidates for IBS. In addition to the classical tests performed, the detection of the serine protease inhibitor (serpin) enzyme capable of decreasing the high proteolytic activity found in IBS patients was included. Three serpin-positive strains were selected: Bifidobacterium breve CNCM I-5644, Bifidobacterium longum subsp. infantis CNCM I-5645 and B. longum CNCM I-5646 for their immunomodulation properties and protection of intestinal epithelial integrity in vitro. Furthermore, we found that B. breve CNCM I-5644 strain prevented intestinal hyperpermeability by upregulating Cingulin and Tight Junction Protein 1 mRNA levels and reducing pro-inflammatory markers. The ability of CNCM I-5644 strain to restore intestinal hyperpermeability (FITC-dextran) was shown in the murine model of low-grade inflammation induced by dinitrobenzene sulfonic acid (DNBS). This effect of this strain was corroborated in a second model of IBS, the neonatal maternal separation model in mice. Altogether, these data suggest that serpin-positive B. breve CNCM I-5644 may partially prevent disorders associated with increased barrier permeability such as IBS.
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Affiliation(s)
- Edgar Torres-Maravilla
- grid.460789.40000 0004 4910 6535INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France ,grid.7429.80000000121866389Université Paris Cité, INSERM, 3PHM, F-75006 Paris, France
| | - Sophie Holowacz
- PiLeJe Laboratoire, 37 Quai de Grenelle, 75015 Paris Cedex 15, France
| | - Johanne Delannoy
- grid.7429.80000000121866389Université Paris Cité, INSERM, 3PHM, F-75006 Paris, France
| | - Loïc Lenoir
- PiLeJe Laboratoire, 37 Quai de Grenelle, 75015 Paris Cedex 15, France
| | - Elsa Jacouton
- PiLeJe Laboratoire, 37 Quai de Grenelle, 75015 Paris Cedex 15, France
| | - Sandie Gervason
- grid.494717.80000000115480420INSERM UMR 1107 NeuroDol, University of Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Maëva Meynier
- grid.494717.80000000115480420INSERM UMR 1107 NeuroDol, University of Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Anne-Sophie Boucard
- grid.460789.40000 0004 4910 6535INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Frédéric A. Carvalho
- grid.494717.80000000115480420INSERM UMR 1107 NeuroDol, University of Clermont Auvergne, 63001 Clermont-Ferrand, France
| | - Frédéric Barbut
- grid.7429.80000000121866389Université Paris Cité, INSERM, 3PHM, F-75006 Paris, France ,grid.50550.350000 0001 2175 4109National Reference Laboratory for C. Difficile, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de Paris, 75012 Paris, France
| | - Luis G. Bermúdez-Humarán
- grid.460789.40000 0004 4910 6535INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Philippe Langella
- grid.460789.40000 0004 4910 6535INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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45
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Ghosh TS, Shanahan F, O'Toole PW. Toward an improved definition of a healthy microbiome for healthy aging. NATURE AGING 2022; 2:1054-1069. [PMID: 37118093 PMCID: PMC10154212 DOI: 10.1038/s43587-022-00306-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/04/2022] [Indexed: 04/30/2023]
Abstract
The gut microbiome is a modifier of disease risk because it interacts with nutrition, metabolism, immunity and infection. Aging-related health loss has been correlated with transition to different microbiome states. Microbiome summary indices including alpha diversity are apparently useful to describe these states but belie taxonomic differences that determine biological importance. We analyzed 21,000 fecal microbiomes from seven data repositories, across five continents spanning participant ages 18-107 years, revealing that microbiome diversity and uniqueness correlate with aging, but not healthy aging. Among summary statistics tested, only Kendall uniqueness accurately reflects loss of the core microbiome and the abundance and ranking of disease-associated and health-associated taxa. Increased abundance of these disease-associated taxa and depletion of a coabundant subset of health-associated taxa are a generic feature of aging. These alterations are stronger correlates of unhealthy aging than most microbiome summary statistics and thus help identify better targets for therapeutic modulation of the microbiome.
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Affiliation(s)
- Tarini Shankar Ghosh
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
- Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland.
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
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46
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Ahmed E, Hens K. Microbiome in Precision Psychiatry: An Overview of the Ethical Challenges Regarding Microbiome Big Data and Microbiome-Based Interventions. AJOB Neurosci 2022; 13:270-286. [PMID: 34379050 DOI: 10.1080/21507740.2021.1958096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
There has been a spurt in both fundamental and translational research that examines the underlying mechanisms of the human microbiome in psychiatric disorders. The personalized and dynamic features of the human microbiome suggest the potential of its manipulation for precision psychiatry in ways to improve mental health and avoid disease. However, findings in the field of microbiome also raise philosophical and ethical questions. From a philosophical point of view, they may yet be another attempt at providing a biological cause for phenomena that ultimately cannot be so easily localized. From an ethical point of view, it is relevant that the human gut microbiome comprises data on the individual's lifestyle, disease history, previous medications, and mental health. Massive datasets of microbiome sequences are collected to facilitate comparative studies to identify specific links between the microbiome and mental health. Although this emerging research domain may show promise for psychiatric patients, it is surrounded by ethical challenges regarding patient privacy, health risks, effects on personal identity, and concerns about responsibility. This narrative overview displays the roles and advances of microbiome research in psychiatry and discusses the philosophical and ethical implications of microbiome big data and microbiome-based interventions for psychiatric patients. We also investigate whether these issues are really "new," or "old wine in new bottles."
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Affiliation(s)
- Eman Ahmed
- University of Antwerp.,Suez Canal University
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47
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Ma W, Drew DA, Staller K. The Gut Microbiome and Colonic Motility Disorders: A Practical Framework for the Gastroenterologist. Curr Gastroenterol Rep 2022; 24:115-126. [PMID: 35943661 PMCID: PMC10039988 DOI: 10.1007/s11894-022-00847-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2022] [Indexed: 10/15/2022]
Abstract
PURPOSE OF REVIEW Colonic motility disorders may be influenced by the gut microbiota, which plays a role in modulating sensory and motor function. However, existing data are inconsistent, possibly due to complex disease pathophysiology, fluctuation in symptoms, and difficulty characterizing high-resolution taxonomic composition and function of the gut microbiome. RECENT FINDINGS Increasingly, human studies have reported associations between gut microbiome features and colonic motility disorders, such as irritable bowel syndrome and constipation. Several microbial metabolites have been identified as regulators of colonic motility in animal models. Modulation of the gut microbiota via dietary intervention, probiotics, and fecal microbiota transplant is a promising avenue for treatment for these diseases. An integration of longitudinal multi-omics data will facilitate further understanding of the causal effects of dysbiosis on disease. Further understanding of the microbiome-driven mechanisms underlying colonic motility disorders may be leveraged to develop personalized, microbiota-based approaches for disease prevention and treatment.
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Affiliation(s)
- Wenjie Ma
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, 02114-2696, Boston, MA, United States
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, 02114-2696, Boston, MA, United States
| | - Kyle Staller
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States.
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, 02114-2696, Boston, MA, United States.
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48
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Bushyhead D, Quigley EMM. Small Intestinal Bacterial Overgrowth-Pathophysiology and Its Implications for Definition and Management. Gastroenterology 2022; 163:593-607. [PMID: 35398346 DOI: 10.1053/j.gastro.2022.04.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/28/2022] [Accepted: 04/03/2022] [Indexed: 12/19/2022]
Abstract
The concept of small intestinal bacterial overgrowth (SIBO) arose in the context of maldigestion and malabsorption among patients with obvious risk factors that permitted the small bowel to be colonized by potentially injurious colonic microbiota. Such colonization resulted in clinical signs, symptoms, and laboratory abnormalities that were explicable within a coherent pathophysiological framework. Coincident with advances in medical science, diagnostic testing evolved from small bowel culture to breath tests and on to next-generation, culture-independent microbial analytics. The advent and ready availability of breath tests generated a dramatic expansion in both the rate of diagnosis of SIBO and the range of associated gastrointestinal and nongastrointestinal clinical scenarios. However, issues with the specificity of these same breath tests have clouded their interpretation and aroused some skepticism regarding the role of SIBO in this expanded clinical repertoire. Furthermore, the pathophysiological plausibility that underpins SIBO as a cause of maldigestion/malabsorption is lacking in regard to its purported role in irritable bowel syndrome, for example. One hopes that the application of an ever-expanding armamentarium of modern molecular microbiology to the human small intestinal microbiome in both health and disease will ultimately resolve this impasse and provide an objective basis for the diagnosis of SIBO.
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Affiliation(s)
- Daniel Bushyhead
- Lynda K. and David M. Underwood Center for Digestive Disorders, Division of Gastroenterology and Hepatology, Houston Methodist Hospital and Weill Cornell Medical College, Houston, Texas.
| | - Eamonn M M Quigley
- Lynda K. and David M. Underwood Center for Digestive Disorders, Division of Gastroenterology and Hepatology, Houston Methodist Hospital and Weill Cornell Medical College, Houston, Texas
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49
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Vervier K, Moss S, Kumar N, Adoum A, Barne M, Browne H, Kaser A, Kiely CJ, Neville BA, Powell N, Raine T, Stares MD, Zhu A, De La Revilla Negro J, Lawley TD, Parkes M. Two microbiota subtypes identified in irritable bowel syndrome with distinct responses to the low FODMAP diet. Gut 2022; 71:1821-1830. [PMID: 34810234 PMCID: PMC9380505 DOI: 10.1136/gutjnl-2021-325177] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/09/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Reducing FODMAPs (fermentable oligosaccharides, disaccharides, monosaccharides and polyols) can be clinically beneficial in IBS but the mechanism is incompletely understood. We aimed to detect microbial signatures that might predict response to the low FODMAP diet and assess whether microbiota compositional and functional shifts could provide insights into its mode of action. DESIGN We used metagenomics to determine high-resolution taxonomic and functional profiles of the stool microbiota from IBS cases and household controls (n=56 pairs) on their usual diet. Clinical response and microbiota changes were studied in 41 pairs after 4 weeks on a low FODMAP diet. RESULTS Unsupervised analysis of baseline IBS cases pre-diet identified two distinct microbiota profiles, which we refer to as IBSP (pathogenic-like) and IBSH (health-like) subtypes. IBSP microbiomes were enriched in Firmicutes and genes for amino acid and carbohydrate metabolism, but depleted in Bacteroidetes species. IBSH microbiomes were similar to controls. On the low FODMAP diet, IBSH and control microbiota were unaffected, but the IBSP signature shifted towards a health-associated microbiome with an increase in Bacteroidetes (p=0.009), a decrease in Firmicutes species (p=0.004) and normalisation of primary metabolic genes. The clinical response to the low FODMAP diet was greater in IBSP subjects compared with IBSH (p=0.02). CONCLUSION 50% of IBS cases manifested a 'pathogenic' gut microbial signature. This shifted towards the healthy profile on the low FODMAP diet; and IBSP cases showed an enhanced clinical responsiveness to the dietary therapy. The effectiveness of FODMAP reduction in IBSP may result from the alterations in gut microbiota and metabolites produced. Microbiota signatures could be useful as biomarkers to guide IBS treatment; and investigating IBSP species and metabolic pathways might yield insights regarding IBS pathogenic mechanisms.
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Affiliation(s)
- Kevin Vervier
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Stephen Moss
- Department of Gastroenterology, Addenbrookes Hospital, Cambridge, UK
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Anne Adoum
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Meg Barne
- Department of Dietetics, Addenbrookes Hospital, Cambridge, UK
| | - Hilary Browne
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, Cambridgeshire, UK
| | - Christopher J Kiely
- Department of Gastroenterology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - B Anne Neville
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Nina Powell
- Department of Dietetics, Addenbrookes Hospital, Cambridge, UK
| | - Tim Raine
- Department of Gastroenterology, Addenbrookes Hospital, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Mark D Stares
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Ana Zhu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | | | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Miles Parkes
- Department of Gastroenterology, Addenbrookes Hospital, Cambridge, UK
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge, Cambridgeshire, UK
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50
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Abstract
The gut microbiome is a contributory factor in ageing-related health loss and in several non-communicable diseases in all age groups. Some age-linked and disease-linked compositional and functional changes overlap, while others are distinct. In this Review, we explore targeted studies of the gut microbiome of older individuals and general cohort studies across geographically distinct populations. We also address the promise of the targeted restoration of microorganisms associated with healthier ageing.
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Affiliation(s)
- Tarini Shankar Ghosh
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland
- Department of Medicine, University College Cork, National University of Ireland, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, Ireland.
- School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
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