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Stange EF. Dysbiosis in inflammatory bowel diseases: egg, not chicken. Front Med (Lausanne) 2024; 11:1395861. [PMID: 38846142 PMCID: PMC11153678 DOI: 10.3389/fmed.2024.1395861] [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: 03/04/2024] [Accepted: 05/06/2024] [Indexed: 06/09/2024] Open
Abstract
There is agreement that inflammatory bowel diseases are, both in terms of species composition and function, associated with an altered intestinal microbiome. This is usually described by the term "dysbiosis," but this is a vague definition lacking quantitative precision. In this brief narrative review, the evidence concerning the primary or secondary role of this dysbiotic state is critically evaluated. Among others, the following facts argue against a primary etiological impact: 1) There is no specific dysbiotic microbiome in IBD, 2) the presence or absence of mucosal inflammation has a profound impact on the composition of the microbiome, 3) dysbiosis is not specific for IBD but linked to many unrelated diseases, 4) antibiotics, probiotics, and microbiome transfer have a very limited therapeutic effect, 5) the microbiome in concordant twins is similar to disease-discordant twins, and 6) the microbiome in relatives of IBD patients later developing IBD is altered, but these individuals already display subclinical inflammation.
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Affiliation(s)
- Eduard F. Stange
- Klinik für Innere Medizin I, Universitätsklinik Tübingen, Tübingen, Germany
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2
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Camilleri M, Boeckxstaens G. Irritable bowel syndrome: treatment based on pathophysiology and biomarkers. Gut 2023; 72:590-599. [PMID: 36307180 PMCID: PMC9990119 DOI: 10.1136/gutjnl-2022-328515] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/16/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To appraise the evidence that pathophysiological mechanisms and individualised treatment directed at those mechanisms provide an alternative approach to the treatment of patients with irritable bowel syndrome (IBS). DESIGN A PubMED-based literature review of mechanisms and treatment of IBS was conducted independently by the two authors, and any differences of perspective or interpretation of the literature were resolved following discussion. RESULTS The availability of several noninvasive clinical tests can appraise the mechanisms responsible for symptom generation in IBS, including rectal evacuation disorders, abnormal transit, visceral hypersensitivity or hypervigilance, bile acid diarrhoea, sugar intolerances, barrier dysfunction, the microbiome, immune activation and chemicals released by the latter mechanism. The basic molecular mechanisms contributing to these pathophysiologies are increasingly recognised, offering opportunities to intervene with medications directed specifically to food components, receptors and potentially the microbiome. Although the evidence supporting interventions for each mechanism is not at the same level of proof, the current state-of-the-art provides the opportunity to advance the practice from treatment based on symptoms to individualisation of treatment guided by pathophysiology and clinically identified biomarkers. CONCLUSION These advances augur well for the implementation of evidence-based individualised treatment for patients with IBS based on actionable biomarkers or psychological disturbances.
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Affiliation(s)
- Michael Camilleri
- Clinical Enteric Neuroscience Translational and Epidemiological Research (CENTER), Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Guy Boeckxstaens
- Center of Intestinal Neuroimmune Interaction, Division of Gastroenterology, Translational Research Center for GI Disorders (TARGID), Leuven University, Leuven, Belgium
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3
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Iribarren C, Nordlander S, Sundin J, Isaksson S, Savolainen O, Törnblom H, Magnusson MK, Simrén M, Öhman L. Fecal luminal factors from patients with irritable bowel syndrome induce distinct gene expression of colonoids. Neurogastroenterol Motil 2022; 34:e14390. [PMID: 35485994 PMCID: PMC9786662 DOI: 10.1111/nmo.14390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/24/2022] [Accepted: 04/11/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Alteration of the host-microbiota cross talk at the intestinal barrier may participate in the pathophysiology of irritable bowel syndrome (IBS). Therefore, we aimed to determine effects of fecal luminal factors from IBS patients on the colonic epithelium using colonoids. METHODS Colon-derived organoid monolayers, colonoids, generated from a healthy subject, underwent stimulation with fecal supernatants from healthy subjects and IBS patients with predominant diarrhea, phosphate-buffered saline (PBS), or lipopolysaccharide (LPS). Cytokines in cell cultures and fecal LPS were measured by ELISA and mRNA gene expression of monolayers was analyzed using Qiagen RT2 Profiler PCR Arrays. The fecal microbiota profile was determined by the GA-map™ dysbiosis test and the fecal metabolite profile was analyzed by untargeted liquid chromatography/mass spectrometry. KEY RESULTS Colonoid monolayers stimulated with fecal supernatants from healthy subjects (n = 7), PBS (n = 4) or LPS (n = 3) presented distinct gene expression profiles, with some overlap (R2 Y = 0.70, Q2 = 0.43). Addition of fecal supernatants from healthy subjects and IBS patients (n = 9) gave rise to different gene expression profiles of the colonoid monolayers (R2 Y = 0.79, Q2 = 0.64). Genes (n = 22) related to immune response (CD1D, TLR5) and barrier integrity (CLDN15, DSC2) contributed to the separation. Levels of proinflammatory cytokines in colonoid monolayer cultures were comparable when stimulated with fecal supernatants from either donor types. Fecal microbiota and metabolite profiles, but not LPS content, differed between the study groups. CONCLUSIONS Fecal luminal factors from IBS patients induce a distinct colonic epithelial gene expression, potentially reflecting the disease pathophysiology. The culture of colonoids from healthy subjects with fecal supernatants from IBS patients may facilitate the exploration of IBS related intestinal micro-environmental and barrier interactions.
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Affiliation(s)
- Cristina Iribarren
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Sofia Nordlander
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Johanna Sundin
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Stefan Isaksson
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Otto Savolainen
- Chalmers Mass Spectrometry InfrastructureDepartment of Biology and Biological EngineeringChalmers University of TechnologyGothenburgSweden
| | - Hans Törnblom
- Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Maria K. Magnusson
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Magnus Simrén
- Department of Molecular and Clinical MedicineInstitute of MedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden,Center for Functional GI and Motility DisordersUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Lena Öhman
- Department of Microbiology and ImmunologyInstitute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
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4
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Chikhaoui A, Jones M, Režen T, Ben Ahmed M, Naouali C, Komel R, Zghal M, Boubaker S, Abdelhak S, Yacoub-Youssef H. Inflammatory landscape in Xeroderma pigmentosum patients with cutaneous melanoma. Sci Rep 2022; 12:13854. [PMID: 35974070 PMCID: PMC9381529 DOI: 10.1038/s41598-022-17928-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022] Open
Abstract
Xeroderma pigmentosum (XP) is a DNA repair disease that predisposes to early skin cancers as cutaneous melanoma. Melanoma microenvironment contains inflammatory mediators, which would be interesting biomarkers for the prognosis or for the identification of novel therapeutic targets. We used a PCR array to evaluate the transcriptional pattern of 84 inflammatory genes in melanoma tumors obtained from XP patients (XP-Mel) and in sporadic melanoma (SP-Mel) compared to healthy skin. Commonly expressed inflammatory genes were further explored via GTEx and GEPIA databases. The differentially expressed inflammatory genes in XP were compared to their expression in skin exposed to UVs, and evaluated on the basis of the overall survival outcomes of patients with melanoma. Monocyte subsets of patients with SP-Mel, XP and healthy donors were also assessed. PCR array data revealed that 34 inflammatory genes were under-expressed in XP-Mel compared to SP-Mel. Differentially expressed genes that were common in XP-Mel and SP-Mel were correlated with the transcriptomic datasets from GEPIA and GTEx and highlighted the implication of KLK1 and IL8 in the tumorigenesis. We showed also that in XP-Mel tumors, there was an overexpression of KLK6 and KLK10 genes, which seems to be associated with a bad survival rate. As for the innate immunity, we observed a decrease of intermediate monocytes in patients with SP-Mel and in XP. We highlight an alteration in the immune response in XP patients. We identified candidate biomarkers involved in the tumorigenesis, and in the survival of patients with melanoma. Intermediate monocyte's in patients at risk could be a prognostic biomarker for melanoma outcome.
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Affiliation(s)
- Asma Chikhaoui
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Meriem Jones
- Département de Dermatologie, Hôpital Charles Nicolle de Tunis, Tunis, Tunisia
| | - Tadeja Režen
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips and Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Melika Ben Ahmed
- Laboratoire de Transmission, Contrôle Et Immunobiologie de L'infection, LR16IPT02, Institut Pasteur de Tunis Université de Tunis El Manar I, 2092, Tunis, Tunisia
| | - Chokri Naouali
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Radovan Komel
- Faculty of Medicine, Centre for Functional Genomics and Bio-Chips and Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, University of Ljubljana, Ljubljana, Slovenia
| | - Mohamed Zghal
- Département de Dermatologie, Hôpital Charles Nicolle de Tunis, Tunis, Tunisia
| | - Samir Boubaker
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.,Université Tunis El Manar, Tunis, Tunisia
| | - Houda Yacoub-Youssef
- Laboratoire de Génomique Biomédicale Et Oncogénétique (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia. .,Université Tunis El Manar, Tunis, Tunisia.
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5
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Choo C, Mahurkar-Joshi S, Dong TS, Lenhart A, Lagishetty V, Jacobs JP, Labus JS, Jaffe N, Mayer EA, Chang L. Colonic mucosal microbiota is associated with bowel habit subtype and abdominal pain in patients with irritable bowel syndrome. Am J Physiol Gastrointest Liver Physiol 2022; 323:G134-G143. [PMID: 35726867 PMCID: PMC9359639 DOI: 10.1152/ajpgi.00352.2021] [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] [Indexed: 01/31/2023]
Abstract
Mucosal microbiota differ significantly from fecal microbiota and may play a different role in the pathophysiology of irritable bowel syndrome (IBS). The aims of this study were to determine if the composition of mucosal microbiota differed between IBS, or IBS bowel habit (BH) subtypes, and healthy controls (HCs). Sigmoid colon mucosal biopsies were obtained from 97 Rome-positive patients with IBS (28% IBS-constipation, 38% IBS-diarrhea, 24% IBS-mixed, and 10% IBS-unsubtyped) and 54 HCs, from which DNA was extracted. 16S rRNA gene sequencing and microbial composition analysis were performed. Group differences in α and β diversity and taxonomic level differences were determined using linear regression while controlling for confounding variables. IBS BH subtype was associated with microbial α diversity (P = 0.0003) with significant differences seen in the mucosal microbiota of IBS-constipation versus IBS-diarrhea (P = 0.046). There were no significant differences in α or β diversity in the mucosal microbiota of IBS versus HCs (P = 0.29 and 0.93, respectively), but metagenomic profiling suggested functional differences. The relative abundance of Prevotella_9 copri within IBS was significantly correlated with increased abdominal pain (r = 0.36, P = 0.0003), which has not been previously reported in IBS. Significant differences in the mucosal microbiota were present within IBS BH subtypes but not between IBS and HCs, supporting the possibility of IBS BH subtype-specific pathogenesis. Increased Prevotella copri may contribute to symptoms in patients with IBS.NEW & NOTEWORTHY Gut mucosal microbiota differs significantly from fecal microbiota in irritable bowel syndrome (IBS) and may play a different role in its pathophysiology. Investigation of colonic mucosal microbiota in the largest cohort of patients with IBS and healthy controls accounting for confounding variables, including diet demonstrated significant differences in mucosal microbiota between IBS bowel habit subtypes but not between IBS and healthy controls. In addition, the study reported gut microbiota is associated with abdominal pain in patients with IBS.
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Affiliation(s)
- Charlene Choo
- 1David Geffen School of Medicine, University of
California, Los Angeles, California
| | - Swapna Mahurkar-Joshi
- 2G. Oppenheimer Center for Neurobiology of Stress and Resilience,
Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, California
| | - Tien S. Dong
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California
| | - Adrienne Lenhart
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California
| | - Venu Lagishetty
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California
| | - Jonathan P. Jacobs
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California,4Division of Gastroenterology, Hepatology and Parenteral Nutrition,
Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, California
| | - Jennifer S. Labus
- 2G. Oppenheimer Center for Neurobiology of Stress and Resilience,
Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, California
| | - Nancee Jaffe
- 3Vatche and Tamar Manoukian Division of Digestive Diseases,
University of California, Los Angeles, California
| | - Emeran A. Mayer
- 2G. Oppenheimer Center for Neurobiology of Stress and Resilience,
Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, California
| | - Lin Chang
- 2G. Oppenheimer Center for Neurobiology of Stress and Resilience,
Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, California
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6
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Priya S, Burns MB, Ward T, Mars RAT, Adamowicz B, Lock EF, Kashyap PC, Knights D, Blekhman R. Identification of shared and disease-specific host gene-microbiome associations across human diseases using multi-omic integration. Nat Microbiol 2022; 7:780-795. [PMID: 35577971 PMCID: PMC9159953 DOI: 10.1038/s41564-022-01121-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/06/2022] [Indexed: 12/19/2022]
Abstract
While gut microbiome and host gene regulation independently contribute to gastrointestinal disorders, it is unclear how the two may interact to influence host pathophysiology. Here we developed a machine learning-based framework to jointly analyse paired host transcriptomic (n = 208) and gut microbiome (n = 208) profiles from colonic mucosal samples of patients with colorectal cancer, inflammatory bowel disease and irritable bowel syndrome. We identified associations between gut microbes and host genes that depict shared as well as disease-specific patterns. We found that a common set of host genes and pathways implicated in gastrointestinal inflammation, gut barrier protection and energy metabolism are associated with disease-specific gut microbes. Additionally, we also found that mucosal gut microbes that have been implicated in all three diseases, such as Streptococcus, are associated with different host pathways in each disease, suggesting that similar microbes can affect host pathophysiology in a disease-specific manner through regulation of different host genes. Our framework can be applied to other diseases for the identification of host gene-microbiome associations that may influence disease outcomes.
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Affiliation(s)
- Sambhawa Priya
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, USA
| | - Michael B Burns
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Tonya Ward
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Beth Adamowicz
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Ran Blekhman
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN, USA.
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7
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Brock C. Are measures of enteric and autonomic nervous system associated? J Intern Med 2021; 290:1105-1107. [PMID: 34255391 DOI: 10.1111/joim.13360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christina Brock
- Mech-Sense, Aalborg University Hospital and Clinical Institute, Aalborg, Denmark
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8
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Iribarren C, Magnusson MK, Vigsnæs LK, Aziz I, Amundsen ID, Šuligoj T, Juge N, Patel P, Sapnara M, Johnsen L, Sørensen N, Sundin J, Törnblom H, Simrén M, Öhman L. The Effects of Human Milk Oligosaccharides on Gut Microbiota, Metabolite Profiles and Host Mucosal Response in Patients with Irritable Bowel Syndrome. Nutrients 2021; 13:nu13113836. [PMID: 34836092 PMCID: PMC8622683 DOI: 10.3390/nu13113836] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Human milk oligosaccharide supplementation safely modulates fecal bifidobacteria abundance and holds the potential to manage symptoms in irritable bowel syndrome (IBS). Here, we aimed to determine the role of a 4:1 mix of 2′-O-fucosyllactose and lacto-N-neotetraose (2′FL/LNnT) on the modulation of the gut microbiota composition and host mucosal response, as well as the link between the bifidobacteria abundance and metabolite modulation, in IBS patients. Methods: Biological samples were collected from IBS patients (n = 58) at baseline and week 4 post-supplementation with placebo, 5 g or 10 g doses of 2′FL/LNnT. The gut microbiota composition, metabolite profiles and expression of genes related to host mucosal response were determined. Results: Moderate changes in fecal, but not mucosal, microbial composition (β-diversity) was observed during the intervention with higher dissimilarity observed within individuals receiving 10g 2′FL/LNnT compared to placebo. Both fecal and mucosal Bifidobacterium spp. increased after 2′FL/LNnT intake, with increased proportions of Bifidobacterium adolescentis and Bifidobacterium longum. Moreover, the intervention modulated the fecal and plasma metabolite profiles, but not the urine metabolite profile or the host mucosal response. Changes in the metabolite profiles were associated to changes in bifidobacteria abundance. Conclusion: Supplementation with 2′FL/LNnT modulated the gut microbiota, fecal and plasma metabolite profiles, but not the host mucosal response in IBS. Furthermore, the bifidogenic effect was associated with metabolite modulation. Overall, these findings support the assertion that 2′FL/LNnT supplementation modulate the intestinal microenvironment of patients with IBS, potentially related to health.
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Affiliation(s)
- Cristina Iribarren
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (C.I.); (M.K.M.); (M.S.); (J.S.)
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (I.A.); (P.P.); (H.T.); (M.S.)
| | - Maria K. Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (C.I.); (M.K.M.); (M.S.); (J.S.)
| | - Louise K. Vigsnæs
- DSM, Kogle Alle 4, 2970 Hørsholm, Denmark; (L.K.V.); (I.D.A.)
- Department of Technology, Faculty of Health, University College Copenhagen, 1799 Copenhagen, Denmark
| | - Imran Aziz
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (I.A.); (P.P.); (H.T.); (M.S.)
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2JF, UK
| | | | - Tanja Šuligoj
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (T.Š.); (N.J.)
| | - Nathalie Juge
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (T.Š.); (N.J.)
| | - Piyush Patel
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (I.A.); (P.P.); (H.T.); (M.S.)
| | - Maria Sapnara
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (C.I.); (M.K.M.); (M.S.); (J.S.)
| | | | | | - Johanna Sundin
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (C.I.); (M.K.M.); (M.S.); (J.S.)
| | - Hans Törnblom
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (I.A.); (P.P.); (H.T.); (M.S.)
| | - Magnus Simrén
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (I.A.); (P.P.); (H.T.); (M.S.)
- Center for Functional GI and Motility Disorders, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 40530 Gothenburg, Sweden; (C.I.); (M.K.M.); (M.S.); (J.S.)
- Correspondence: ; Tel.: +46-317-866-214
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9
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Wauters L, Ceulemans M, Vanuytsel T. Duodenum at a crossroads: Key integrator of overlapping and psychological symptoms in functional dyspepsia? Neurogastroenterol Motil 2021; 33:e14262. [PMID: 34561921 DOI: 10.1111/nmo.14262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/20/2022]
Abstract
The study of the interaction between gastrointestinal (GI) function and psychological features is a complex and developing field. The bidirectional communication between the gut and the brain or gut-brain axis is considered as a pivotal player in the pathogenesis of the highly prevalent functional GI disorders, including irritable bowel syndrome and functional dyspepsia (FD), which have been redefined as disorders of gut-brain interaction. However, the mechanisms through which changes in the gut alter brain functioning, feelings, and behavior remain unclear. Based on the presence of duodenal pathology in adult FD patients, Ronkainen et al. provide the first prospective evidence for duodenal eosinophils potentially driving anxiety. Also in this edition, associations between gastroduodenal pathology and rumination syndrome, which may coexist with FD, have now been confirmed in children by Friesen et al. Together these findings confirm not only the potential role of duodenal alterations in determining overlapping upper GI but also psychological symptoms, which result from bidirectional and complex interactions. In this review, we provide an overview of the recent advances in this field and highlight the novel contributions of the original studies of Ronkainen et al. and Friesen et al. to this topic.
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Affiliation(s)
- Lucas Wauters
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium.,Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Matthias Ceulemans
- Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Tim Vanuytsel
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium.,Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
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10
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Nichols RG, Davenport ER. The relationship between the gut microbiome and host gene expression: a review. Hum Genet 2021; 140:747-760. [PMID: 33221945 PMCID: PMC7680557 DOI: 10.1007/s00439-020-02237-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022]
Abstract
Despite the growing knowledge surrounding host-microbiome interactions, we are just beginning to understand how the gut microbiome influences-and is influenced by-host gene expression. Here, we review recent literature that intersects these two fields, summarizing themes across studies. Work in model organisms, human biopsies, and cell culture demonstrate that the gut microbiome is an important regulator of several host pathways relevant for disease, including immune development and energy metabolism, and vice versa. The gut microbiome remodels host chromatin, causes differential splicing, alters the epigenetic landscape, and directly interrupts host signaling cascades. Emerging techniques like single-cell RNA sequencing and organoid generation have the potential to refine our understanding of the relationship between the gut microbiome and host gene expression in the future. By intersecting microbiome and host gene expression, we gain a window into the physiological processes important for fostering the extensive cross-kingdom interactions and ultimately our health.
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Affiliation(s)
- Robert G. Nichols
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
| | - Emily R. Davenport
- Department of Biology, The Pennsylvania State University, University Park, PA 16802 USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802 USA
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11
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Moraes L, Magnusson MK, Mavroudis G, Polster A, Jonefjäll B, Törnblom H, Sundin J, Simrén M, Strid H, Öhman L. Systemic Inflammatory Protein Profiles Distinguish Irritable Bowel Syndrome (IBS) and Ulcerative Colitis, Irrespective of Inflammation or IBS-Like Symptoms. Inflamm Bowel Dis 2020; 26:874-884. [PMID: 31901089 PMCID: PMC7216771 DOI: 10.1093/ibd/izz322] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Inflammatory mechanisms of ulcerative colitis (UC) and irritable bowel syndrome (IBS) may overlap or are part of different spectrums. However, potential links between inflammation and IBS-like symptoms in these patient groups are still unclear. The aim of this study was to determine if the systemic inflammatory protein (SIP) profiles differ between UC patients, with presence of inflammation or in remission with or without IBS-like symptoms, and IBS patients. METHODS Serum from patients with active UC (UCA), UC patients in remission with or without IBS-like symptoms (UCR + IBS, UCR-IBS), IBS patients (IBS), and healthy subjects (HS) was analyzed using the ProSeek Multiplex Inflammation kit, which detects 92 proteins. RESULTS The exploratory cohort consisted of 166 subjects (UCA, n = 40; UCR-IBS, n = 45; UCR + IBS, n = 20; IBS, n = 40; HS, n = 21). Systemic inflammatory protein profiles separated UC from non-UC (HS and IBS) patients in multivariate analysis, revealing caspase 8, axin 1, sulfotransferase 1A1, and tumor necrosis factor superfamily member 14 as the variables most important to clustering. Although minor differences were detected between UCR + IBS and UCR-IBS, SIP profiles discriminated UCA from UCR, and interleukin (IL) 17C, IL17A, chemokine ligand 9, and transforming growth factor-α characterized active inflammation. SIP profiles weakly discriminated HS from IBS, although fibroblast growth factor 21 and IL6 serum levels were higher in IBS. Results were confirmed in a validation cohort (UCA, n = 15; UCR + IBS, n = 9; IBS, n = 14). CONCLUSIONS SIP profiles distinguish UC patients from IBS patients, irrespective of inflammation or IBS-like symptoms, suggesting that inflammatory mechanisms of the diseases are part of different spectrums.
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Affiliation(s)
- Luiza Moraes
- Department of Microbiology & Immunology, Institute of Biomedicine University of Gothenburg, Gothenburg, Sweden
| | - Maria K Magnusson
- Department of Microbiology & Immunology, Institute of Biomedicine University of Gothenburg, Gothenburg, Sweden
| | | | - Annikka Polster
- Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, Gothenburg, Sweden
| | - Börje Jonefjäll
- Department of Internal Medicine, Kungälv Hospital, Kungälv, Sweden
| | - Hans Törnblom
- Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, Gothenburg, Sweden
| | - Johanna Sundin
- Department of Microbiology & Immunology, Institute of Biomedicine University of Gothenburg, Gothenburg, Sweden,Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, Gothenburg, Sweden,Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Lena Öhman
- Department of Microbiology & Immunology, Institute of Biomedicine University of Gothenburg, Gothenburg, Sweden,Department of Internal Medicine & Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, Gothenburg, Sweden,Address correspondence to: Lena Öhman, PhD, Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Box 435, S-405 30 Gothenburg, Sweden ()
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12
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Xiao QY, Fang XC, Li XQ, Fei GJ. Ethnic differences in genetic polymorphism associated with irritable bowel syndrome. World J Gastroenterol 2020; 26:2049-2063. [PMID: 32536774 PMCID: PMC7267697 DOI: 10.3748/wjg.v26.i17.2049] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/25/2020] [Accepted: 04/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic polymorphism is associated with irritable bowel syndrome (IBS) in terms of susceptibility and clinical manifestations. Previous studies have shown that genetic polymorphism might play a key role in the onset and progression of IBS by modulating components of its pathogenesis such as the gut-brain axis, gastrointestinal motility, inflammatory activity, and immune status. Although underlying pathophysiological mechanisms have not been fully clarified, the potential ethnic differences that are present in worldwide genetic studies of IBS deserve attention. This review surveyed numerous studies focusing on IBS-associated single nucleotide polymorphisms, and investigated the ethnic disparities revealed by them. The results demonstrate the need for more attention on ethnic factors in IBS-related genetic studies. Taking ethnic backgrounds into accounts and placing emphasis on disparities potentially ascribed to ethnicity could help lay a solid and generalized foundation for transcultural, multi-ethnic, or secondary analyses in IBS, for example, a meta-analysis. Broader genetic studies considering ethnic factors are greatly needed to obtain a better understanding of the pathophysiological mechanisms of IBS and to improve the prevention, intervention, and treatment of this disease.
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Affiliation(s)
- Qi-Yun Xiao
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiu-Cai Fang
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiao-Qing Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Gui-Jun Fei
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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13
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Chey WD, Shah ED, DuPont HL. Mechanism of action and therapeutic benefit of rifaximin in patients with irritable bowel syndrome: a narrative review. Therap Adv Gastroenterol 2020; 13:1756284819897531. [PMID: 32047534 PMCID: PMC6984424 DOI: 10.1177/1756284819897531] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/02/2019] [Indexed: 02/04/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder with a multifactorial pathophysiology. The gut microbiota differs between patients with IBS and healthy individuals. After a bout of acute gastroenteritis, postinfection IBS may result in up to approximately 10% of those affected. Small intestinal bacterial overgrowth (SIBO) is more common in patients with IBS than in healthy individuals, and eradication of SIBO with systemic antibiotics has decreased symptoms of IBS in some patients with IBS and SIBO. The nonsystemic (i.e. low oral bioavailability) antibiotic rifaximin is indicated in the United States and Canada for the treatment of adults with IBS with diarrhea (IBS-D). The efficacy and safety of 2-week single and repeat courses of rifaximin have been demonstrated in randomized, placebo-controlled studies of adults with IBS. Rifaximin is widely thought to exert its beneficial clinical effects in IBS-D through manipulation of the gut microbiota. However, current studies indicate that rifaximin induces only modest effects on the gut microbiota of patients with IBS-D, suggesting that the efficacy of rifaximin may involve other mechanisms. Indeed, preclinical data reveal a potential role for rifaximin in the modulation of inflammatory cytokines and intestinal permeability, but these two findings have not yet been examined in the context of clinical studies. The mechanism of action of rifaximin in IBS is likely multifactorial, and further study is needed.
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Affiliation(s)
- William D. Chey
- Department of Nutrition Sciences, Division of Gastroenterology, Michigan Medicine, 3912 Taubman Center, SPC 5362, Ann Arbor, MI 48109-5362, USA
| | - Eric D. Shah
- Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Herbert L. DuPont
- Division of Epidemiology, Human Genetics and Environmental Sciences and Center for Infectious Diseases, University of Texas School of Public Health, Houston, TX, USA
- Mary W. Kelsey Chair in Medical Sciences, Division of Internal Medicine, University of Texas McGovern Medical School Houston, TX, USA
- Kelsey Research Foundation, Houston, TX, USA
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14
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Sundin J, Aziz I, Nordlander S, Polster A, Hu YOO, Hugerth LW, Pennhag AAL, Engstrand L, Törnblom H, Simrén M, Öhman L. Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome. Sci Rep 2020; 10:593. [PMID: 31953505 PMCID: PMC6969101 DOI: 10.1038/s41598-020-57468-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/30/2019] [Indexed: 12/14/2022] Open
Abstract
Altered bacterial composition and small intestinal bacterial overgrowth (SIBO) may be associated with irritable bowel syndrome (IBS). This study aimed to determine the fecal and mucosa-associated bacterial composition along the gastrointestinal (GI) tract and to assess SIBO in IBS. Bacterial composition of feces, and mucosa of the duodenum and sigmoid colon was determined by 16S rRNA-amplicon-sequencing. SIBO was evaluated by bacterial culture of duodenal aspirate, glucose and lactulose breath tests. Mucosal antibacterial gene expression was assessed by PCR Array. The bacterial profiles of feces and the mucosa of sigmoid colon, but not duodenum, differed between IBS patients (n = 17) and HS (n = 20). The IBS specific bacterial profiles were linked to the colonic antibacterial gene expression. Fecal bacterial profile differed between IBS subtypes, while the mucosa-associated bacterial profile was associated with IBS symptom severity and breath tests results at baseline (H2 and/or CH4 ≥ 15 ppm). The prevalence of SIBO was similar between IBS patients and HS. This study demonstrates that alterations in the bacterial composition of the sigmoid colon of IBS patients were linked to symptoms and immune activation. While breath tests reflected the mucosa-associated bacterial composition, there was no evidence for high prevalence of SIBO or small intestinal bacterial alterations in IBS.
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Affiliation(s)
- Johanna Sundin
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Imran Aziz
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Sofia Nordlander
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Annikka Polster
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Yue O O Hu
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Luisa W Hugerth
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Alexandra A L Pennhag
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Hans Törnblom
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Centre for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lena Öhman
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden. .,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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