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Deady C, McCarthy FP, Barron A, McCarthy CM, O’Keeffe GW, O’Mahony SM. An altered gut microbiome in pre-eclampsia: cause or consequence. Front Cell Infect Microbiol 2024; 14:1352267. [PMID: 38774629 PMCID: PMC11106424 DOI: 10.3389/fcimb.2024.1352267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Hypertensive disorders of pregnancy, including pre-eclampsia, are a leading cause of serious and debilitating complications that affect both the mother and the fetus. Despite the occurrence and the health implications of these disorders there is still relatively limited evidence on the molecular underpinnings of the pathophysiology. An area that has come to the fore with regard to its influence on health and disease is the microbiome. While there are several microbiome niches on and within the body, the distal end of the gut harbors the largest of these impacting on many different systems of the body including the central nervous system, the immune system, and the reproductive system. While the role of the microbiome in hypertensive disorders, including pre-eclampsia, has not been fully elucidated some studies have indicated that several of the symptoms of these disorders are linked to an altered gut microbiome. In this review, we examine both pre-eclampsia and microbiome literature to summarize the current knowledge on whether the microbiome drives the symptoms of pre-eclampsia or if the aberrant microbiome is a consequence of this condition. Despite the paucity of studies, obvious gut microbiome changes have been noted in women with pre-eclampsia and the individual symptoms associated with the condition. Yet further research is required to fully elucidate the role of the microbiome and the significance it plays in the development of the symptoms. Regardless of this, the literature highlights the potential for a microbiome targeted intervention such as dietary changes or prebiotic and probiotics to reduce the impact of some aspects of these disorders.
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Affiliation(s)
- Clara Deady
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Fergus P. McCarthy
- Department of Obstetrics and Gynecology, University College Cork, Cork, Ireland
- The Infant Research Centre, University College Cork, Cork, Ireland
| | - Aaron Barron
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Cathal M. McCarthy
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | - Gerard W. O’Keeffe
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Cork Neuroscience Centre, University College Cork, Cork, Ireland
| | - Siobhain M. O’Mahony
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Yu SY, Oh BS, Ryu SW, Bak JE, Heo ES, Moon JC, Jeong JH, Lee JH. Novel microbiota Mesosutterella faecium sp. nov. has a protective effect against inflammatory bowel disease. Front Microbiol 2024; 15:1342098. [PMID: 38633706 PMCID: PMC11022602 DOI: 10.3389/fmicb.2024.1342098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
A novel Gram-negative, obligate anaerobe, non-motile, flagella-lacking, catalase- and oxidase-negative, coccobacilli-shaped bacterial strain designated AGMB02718T was isolated from swine feces. The 16S rRNA gene analysis indicated that strain AGMB02718T belonged to the genus Mesosutterella with the highest similarity to M. multiformis 4NBBH2T (= DSM 106860T) (sequence similarity of 96.2%), forming a distinct phylogenetic lineage. Its growth occurred at 25-45°C (optimal 37°C) and in 0.5-1% NaCl (optimal 0.5%). Strain AGMB02718T was asaccharolytic and contained menaquinone 6 (MK-6) and methylmenaquinone 6 (MMK-6) as the predominant respiratory quinones. The major cellular fatty acids in the isolate were C18:1ω9c and C16:0. Based on the whole-genome sequencing analysis, strain AGMB02718T had a 2,606,253 bp circular chromosome with a G + C content of 62.2%. The average nucleotide identity value between strain AGMB02718T and M. multiformis 4NBBH2T was 72.1%, while the digital DNA-DNA hybridization value was 20.9%. Interestingly, genome analysis suggested that strain AGMB02718T possessed a low-toxicity lipopolysaccharide (LPS) because the genome of the isolate does not include lpxJ and lpxM genes for Kdo2-Lipid A (KLA) assembly, which confers high toxicity to LPS. Moreover, in vitro macrophage stimulation assay confirmed that AGMB02718T produced LPS with low toxicity. Because the low-toxicity LPS produced by the Sutterellaceae family is involved in regulating host immunity and low-toxicity LPS-producing strains can help maintain host immune homeostasis, we evaluated the anti-inflammatory activity of strain AGMB02718T against inflammatory bowel disease (IBD). As a result, strain AGMB02718T was able to prevent the inflammatory response in a dextran sulfate sodium (DSS)-induced colitis model. Therefore, this strain represents a novel species of Mesosutterella that has a protective effect against DSS-induced colitis, and the proposed name is Mesosutterella faecium sp. nov. The type strain is AGMB02718T (=GDMCC 1.2717T = KCTC 25541T).
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Affiliation(s)
- Seung Yeob Yu
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Republic of Korea
| | - Byeong Seob Oh
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
| | - Seoung Woo Ryu
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Republic of Korea
| | - Jeong Eun Bak
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Republic of Korea
| | - Eun Seo Heo
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
- University of Science and Technology (UST), Daejeon, Republic of Korea
| | | | - Jae-Ho Jeong
- BioMedical Sciences Graduate Program (BMSGP), Chonnam National University, Hwasun, Republic of Korea
| | - Ju Huck Lee
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Republic of Korea
- University of Science and Technology (UST), Daejeon, Republic of Korea
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3
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Acciarino A, Diwakarla S, Handreck J, Bergola C, Sahakian L, McQuade RM. The role of the gastrointestinal barrier in obesity-associated systemic inflammation. Obes Rev 2024; 25:e13673. [PMID: 38111141 DOI: 10.1111/obr.13673] [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: 01/26/2023] [Revised: 10/05/2023] [Accepted: 10/27/2023] [Indexed: 12/20/2023]
Abstract
Systemic inflammation is a key contributor to the onset and progression of several obesity-associated diseases and is thought to predominantly arise from the hyperplasia and hypertrophy of white adipose tissue. However, a growing body of works suggests that early changes in the gastrointestinal (GI) barrier may contribute to both local, within the GI lining, and systemic inflammation in obesity. Intestinal barrier dysfunction is well-characterized in inflammatory GI disorders such as inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) and is known to contribute to systemic inflammation. Thus, drawing parallels between GI disorders, where intestinal permeability and systemic inflammation are prominent features, and obesity-induced GI manifestations may provide insights into the potential role of the intestinal barrier in systemic inflammation in obesity. This review summarizes the current literature surrounding intestinal barrier dysfunction in obesity and explores the potential role of intestinal hyperpermeability and intestinal barrier dysfunction in the development of systemic inflammation and GI dysfunction in obesity.
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Affiliation(s)
- Adriana Acciarino
- Gut Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Western Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shanti Diwakarla
- Gut Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Western Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jessica Handreck
- Gut Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Western Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Cedrick Bergola
- Gut Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lauren Sahakian
- Gut Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rachel M McQuade
- Gut Barrier and Disease Laboratory, Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine, Western Health, The University of Melbourne, Melbourne, Victoria, Australia
- Australian Institute for Musculoskeletal Science (AIMSS), Melbourne University, Melbourne, Victoria, Australia
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4
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Qu H, Zhang W, Li J, Fu Q, Li X, Wang M, Fu G, Cui J. A rapid and sensitive CRISPR-Cas12a for the detection of Fusobacterium nucleatum. Microbiol Spectr 2024; 12:e0362923. [PMID: 38197659 PMCID: PMC10845955 DOI: 10.1128/spectrum.03629-23] [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: 10/10/2023] [Accepted: 12/04/2023] [Indexed: 01/11/2024] Open
Abstract
Fusobacterium nucleatum (Fn), as a conditional pathogen, can cause a range of oral and gastrointestinal diseases. However, existing clinical detection methods require expensive equipment and complex procedures, which are inconvenient for large-scale screening in epidemiological research. The purpose of this study was to establish a reliable, rapid, and inexpensive detection method based on CRISPR/Cas12a technology for the detection of Fn. Specific recombinase polymerase amplification (RPA) primer sequences and crRNA sequences were designed based on the nusG gene of Fn. Subsequently, a fluorescence assay and a lateral flow immunoassay were established using the RPA and CRISPR-Cas12a system (RPA-CRISPR-Cas12a). Sensitivity validation revealed a limit of detection of 5 copies/µL. This method could distinguish Fn from other pathogens with excellent specificity. Furthermore, the RPA-CRISPR-Cas12a assay was highly consistent with the classical quantitative real-time PCR method when testing periodontal pocket samples. This makes it a promising method for the detection of Fn and has the potential to play an increasingly important role in infectious disease testing.IMPORTANCEFusobacterium nucleatum (Fn) naturally exists in the microbial communities of the oral and gastrointestinal tracts of healthy individuals and can cause inflammatory diseases in the oral and gastrointestinal tracts. Recent studies have shown that Fn is closely associated with the occurrence and development of gastrointestinal cancer. Therefore, the detection of Fn is very important. Unlike the existing clinical detection methods, this study established a fluorescence-based assay and lateral flow immunoassay based on the RPA and CRISPR-Cas12a system (RPA-CRISPR-Cas12a), which is fast, reliable, and inexpensive and can complete the detection within 30-40 minutes. This makes it a promising method for the detection of Fn and has the potential to play an increasingly important role in infectious disease testing.
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Affiliation(s)
- Hai Qu
- Department of Pathogens, Medical College, Zhengzhou University, Zhengzhou, China
| | - Wenjing Zhang
- Medical College, Henan University of Traditional Chinese Medicine, Zhengzhou, China
| | - Jianghao Li
- Autobio Diagnostics Co., Ltd, Zhengzhou, China
| | - Qingshan Fu
- Autobio Diagnostics Co., Ltd, Zhengzhou, China
| | - Xiaoxia Li
- Autobio Diagnostics Co., Ltd, Zhengzhou, China
| | | | - Guangyu Fu
- Autobio Diagnostics Co., Ltd, Zhengzhou, China
| | - Jing Cui
- Department of Pathogens, Medical College, Zhengzhou University, Zhengzhou, China
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Metwaly A, Haller D. The TNF∆ARE Model of Crohn's Disease-like Ileitis. Inflamm Bowel Dis 2024; 30:132-145. [PMID: 37756666 DOI: 10.1093/ibd/izad205] [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: 04/08/2023] [Indexed: 09/29/2023]
Abstract
Crohn's disease (CD) is one of the 2 main phenotypes of inflammatory bowel diseases (IBDs); CD ischaracterized by a discontinuous, spontaneously recurring, transmural immunopathology that largely affects the terminal ileum. Crohn's disease exhibits both a relapsing and progressive course, and its prevalence is on the rise globally, mirroring the trends of industrialization. While the precise pathogenesis of CD remains unknown, various factors including immune cell dysregulation, microbial dysbiosis, genetic susceptibility, and environmental factors have been implicated in disease etiology. Animal models, particularly ileitis mouse models, have provided valuable tools for studying the specific mechanisms underlying CD, allowing longitudinal assessment and sampling in interventional preclinical studies. Furthermore, animal models assess to evaluate the distinct role that bacterial and dietary antigens play in causing inflammation, using germ-free animals, involving the introduction of individual bacteria (monoassociation studies), and experimenting with well-defined dietary components. An ideal animal model for studying IBD, specifically CD, should exhibit an inherent intestinal condition that arises spontaneously and closely mimics the distinct transmural inflammation observed in the human disease, particularly in the terminal ileum. We have recently characterized the impact of disease-relevant, noninfectious microbiota and specific bacteria in a mouse model that replicates CD-like ileitis, capturing the intricate nature of human CD, namely the TNF∆ARE mouse model. Using germ-free mice, we studied the impact of different diets on the expansion of disease-relevant pathobionts and on the severity of inflammation. In this review article, we review some of the currently available ileitis mouse models and discuss in detail the TNF∆ARE model of CD-like Ileitis.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
- ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
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Bacsur P, Rutka M, Asbóth A, Resál T, Szántó K, Jójárt B, Bálint A, Ari E, Ajibola W, Kintses B, Fehér T, Pigniczki D, Bor R, Fábián A, Maléth J, Szepes Z, Farkas K, Molnár T. Effects of bowel cleansing on the composition of the gut microbiota in inflammatory bowel disease patients and healthy controls. Therap Adv Gastroenterol 2023; 16:17562848231174298. [PMID: 37324319 PMCID: PMC10265323 DOI: 10.1177/17562848231174298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/20/2023] [Indexed: 06/17/2023] Open
Abstract
Background In patients with inflammatory bowel disease (IBD), Crohn's disease (CD), and ulcerative colitis (UC), numerous cases of exacerbations could be observed after colonoscopy, raising the possible pathogenetic effect of colonic microbiota alterations in IBD flare. Objectives We aimed to investigate the changes in the fecal microbiota composition in IBD patients influenced by the bowel preparation with sodium picosulfate. Design We enrolled patients with IBD undergoing bowel preparation for colonoscopy in the prospective cohort study. The control group (Con) comprised non-IBD patients who underwent colonoscopy. Clinical data, blood, and stool samples were collected before colonoscopy (timepoint A), 3 days later (timepoint B), and 4 weeks later (timepoint C). Methods Disease activity and gut microbiota changes were assessed at each timepoint. Fecal microbiota structure - at family level - was determined by sequencing the V4 region of the 16S rRNA gene. Statistical analysis included differential abundance analysis and Mann-Whitney tests. Results Forty-one patients (9 CD, 13 UC, and 19 Con) were included. After bowel preparation, alpha diversity was lower in the CD group than in the UC (p = 0.01) and Con (p = 0.02) groups at timepoint B. Alpha diversity was significantly higher in the UC group than in the CD and Con (p = 0.03) groups at timepoint C. Beta diversity difference differed between the IBD and Con (p = 0.001) groups. Based on the differential abundance analysis, the Clostridiales family was increased, whereas the Bifidobacteriaceae family was decreased in CD patients compared to the Con at timepoint B. Conclusions Bowel preparation may change the fecal microbial composition in IBD patients, which may have a potential role in disease exacerbation after bowel cleansing.
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Affiliation(s)
- Péter Bacsur
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - Mariann Rutka
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - András Asbóth
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Tamás Resál
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - Kata Szántó
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - Boldizsár Jójárt
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
- Hungarian Academy of Science – University of Szeged Momentum Epithelial Cell Signaling and Secretion Research Group, Szeged, Hungary
- HCEMM-USZ Molecular Gastroenterology Research Group, Szeged, Hungary
| | - Anita Bálint
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - Eszter Ari
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Department of Genetics, ELTE Eötvös Loránd University, Budapest, Hungary
- HCEMM-BRC Metabolic Systems Biology Research Group, Szeged, Hungary
| | - Walliyulahi Ajibola
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Bálint Kintses
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
- Department of Biochemistry and Molecular Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
- HCEMM-BRC Translational Microbiology Research Group, Szeged, Hungary
- National Laboratory of Biotechnology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Tamás Fehér
- Synthetic and System Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Daniella Pigniczki
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - Renáta Bor
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - Anna Fábián
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - József Maléth
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
- Hungarian Academy of Science – University of Szeged Momentum Epithelial Cell Signaling and Secretion Research Group, Szeged, Hungary
- HCEMM-USZ Molecular Gastroenterology Research Group, Szeged, Hungary
| | - Zoltán Szepes
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - Klaudia Farkas
- Department of Medicine, Szent-Györgyi Albert Medical School, University of Szeged, Szeged, Hungary
| | - Tamás Molnár
- Department of Medicine, Albert Szent-Györgyi Medical School, University of Szeged, Kálvária Avenue 57, H-6720 Szeged, Hungary
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Watson AR, Füssel J, Veseli I, DeLongchamp JZ, Silva M, Trigodet F, Lolans K, Shaiber A, Fogarty E, Runde JM, Quince C, Yu MK, Söylev A, Morrison HG, Lee STM, Kao D, Rubin DT, Jabri B, Louie T, Eren AM. Metabolic independence drives gut microbial colonization and resilience in health and disease. Genome Biol 2023; 24:78. [PMID: 37069665 PMCID: PMC10108530 DOI: 10.1186/s13059-023-02924-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 04/07/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. RESULTS Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. CONCLUSIONS These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
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Affiliation(s)
- Andrea R Watson
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jessika Füssel
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany
| | - Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Marisela Silva
- Department of Medicine, The University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Karen Lolans
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Alon Shaiber
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Emily Fogarty
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph M Runde
- Department of Pediatrics, Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA
| | - Arda Söylev
- Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
| | - Hilary G Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Falmouth, MA, 02543, USA
| | - Sonny T M Lee
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Dina Kao
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - David T Rubin
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Thomas Louie
- Department of Medicine, The University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - A Murat Eren
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany.
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Falmouth, MA, 02543, USA.
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany.
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8
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Assessing the Relationship between the Gut Microbiota and Inflammatory Bowel Disease Therapeutics: A Systematic Review. Pathogens 2023; 12:pathogens12020262. [PMID: 36839534 PMCID: PMC9965214 DOI: 10.3390/pathogens12020262] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
Current inflammatory bowel disease (IBD) treatments including non-biological, biological, and nutritional therapies aim to achieve remission and mucosal healing. Treatment efficacy, however, is highly variable, and there is growing evidence that the gut microbiota influences therapeutic efficacy. The aim of this study was to conduct a systematic review and meta-analysis to define changes in the gut microbiota following IBD treatment and to identify microbial predictors of treatment response. A systematic search using MEDLINE/Embase and PubMed was performed in July 2022. The review was conducted based on the Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Studies were included if they reported longitudinal microbiota analysis (>2 weeks) using next-generation sequencing or high-throughput sequencing of faecal/mucosal samples from IBD patients commencing treatment. Meta-analysis on alpha-diversity changes following infliximab treatment was conducted. Thirty-nine studies met the inclusion criteria, and four studies were included in the meta-analysis. An increase in alpha diversity was observed following treatment with 5-aminosalicylates, corticosteroids, and biological therapies in most studies. Characteristic signatures involving the enrichment of short-chain-fatty-acid-producing bacteria including Faecalibacterium prausnitzii and a reduction of pathogenic bacteria including various Proteobacteria were demonstrated following treatment with specific signatures identified based on treatment outcome. The meta-analysis demonstrated a statistically significant increase in bacterial richness following infliximab treatment (standardised mean difference -1.16 (-1.50, -0.83), p < 0.00001). Conclusion: Distinct microbial signatures are seen following treatment and are associated with treatment response. The interrogation of large longitudinal studies is needed to establish the link between the gut microbiota and IBD therapeutic outcomes.
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Al-Amrah H, Saadah OI, Mosli M, Annese V, Al-Hindi R, Edris S, Alshehri D, Alatawi H, Alatawy M, Bahieldin A. Composition of the gut microbiota in patients with inflammatory bowel disease in Saudi Arabia: A pilot study. Saudi J Gastroenterol 2023; 29:102-110. [PMID: 36695274 DOI: 10.4103/sjg.sjg_368_22] [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: 01/25/2023] Open
Abstract
CONCLUSIONS The results of this study provide an overview of the variations in microbiota diversity present in Saudi IBD patients compared to healthy controls. RESULTS The key finding was three negative bacterial biomarkers, Paraprevotellaceae, the Muribaculaceae families of Bacteroidetes phylum, and the Leuconostocaceae family of Firmicutes phylum, which had a higher relative abundance in healthy individuals compared to IBD patients. It was also found that primary microbiota signatures at certain genera and species levels, including Prevotella copri, Bifidobacterium adolescentis, Ruminococcus callidus, Coprococcus sp., Ruminococcus gnavus, Dorea formicigenerans, Leuconostoc, Dialister, Catenibacterium, Eubacterium biforme, and Lactobacillus mucosae, were absent in almost all IBD patients, while Veillonella dispar was absent in all healthy individuals. METHODS After obtaining an informed consent, fecal samples were collected from 11 participants with IBD (patients) and 10 healthy individuals (controls). The bacterial components of the microbial population were identified by next-generation sequencing of partial 16S rRNA. Statistically significant dissimilarities were observed between samples for all metrics. BACKGROUND Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory condition attributed to a complex interaction between imbalances in the gut microbiome, environmental conditions, and a deregulated immune response. The aim of the study was to investigate the composition of the gut microbiome of Saudi patients with IBD.
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Affiliation(s)
- Hadba Al-Amrah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Omar I Saadah
- Department of Pediatrics, Faculty of Medicine; Department of Inflammatory Bowel Disease Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmoud Mosli
- Department of Inflammatory Bowel Disease Research Group; Department of Internal Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vito Annese
- Fakeeh University Hospital, Dubai, United Arab Emirates
| | - Rashad Al-Hindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University; Princess Al Jawhara Albrahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Ain Shams University, Cairo, Egypt; Al Borg Medical Laboratories, Al Borg Diagnostics, Jeddah, Saudi Arabia
| | - Dikhnah Alshehri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah; Department of Biological Sciences, College of Science, Univesity of Tabuk, Tabuk, Saudi Arabia
| | - Hanan Alatawi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah; Department of Biological Sciences, College of Science, Univesity of Tabuk, Tabuk, Saudi Arabia
| | - Marfat Alatawy
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah; Department of Biological Sciences, College of Science, Univesity of Tabuk, Tabuk, Saudi Arabia
| | - Ahmad Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Ain Shams University, Cairo, Egypt
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10
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Luo Y, Cui X, Cheruba E, Chua YK, Ng C, Tan RZ, Tan KK, Cheow LF. SAMBA: A Multicolor Digital Melting PCR Platform for Rapid Microbiome Profiling. SMALL METHODS 2022; 6:e2200185. [PMID: 35652511 DOI: 10.1002/smtd.202200185] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/27/2022] [Indexed: 06/15/2023]
Abstract
During the past decade, breakthroughs in sequencing technology have provided the basis for studies of the myriad ways in which microbial communities in and on the human body influence human health and disease. In almost every medical specialty, there is now a growing interest in accurate and quantitative profiling of the microbiota for use in diagnostic and therapeutic applications. However, the current next-generation sequencing approach for microbiome profiling is costly, requires laborious library preparation, and is challenging to scale up for routine diagnostics. Split, Amplify, and Melt analysis of BActeria-community (SAMBA), a novel multicolor digital melting polymerase chain reaction platform with unprecedented multiplexing capability is presented, and the capability to distinguish and quantify 16 bacteria species in mixtures is demonstrated. Subsequently, SAMBA is applied to measure the compositions of bacteria in the gut microbiome to identify microbial dysbiosis related to colorectal cancer. This rapid, low cost, and high-throughput approach will enable the implementation of microbiome diagnostics in clinical laboratories and routine medical practice.
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Affiliation(s)
- Yongqiang Luo
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Xu Cui
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
| | - Yong Kang Chua
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Charmaine Ng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Rui Zhen Tan
- Engineering Cluster, Singapore Institute of Technology, Singapore, 138683, Singapore
| | - Ker-Kan Tan
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Division of Colorectal Surgery, National University Hospital, Singapore, 119074, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering & Institute for Health Innovation and Technology, National University of Singapore, Singapore, 119077, Singapore
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11
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Hong ZS, Xie J, Wang XF, Dai JJ, Mao JY, Bai YY, Sheng J, Tian Y. Moringa oleifera Lam. Peptide Remodels Intestinal Mucosal Barrier by Inhibiting JAK-STAT Activation and Modulating Gut Microbiota in Colitis. Front Immunol 2022; 13:924178. [PMID: 35911761 PMCID: PMC9336532 DOI: 10.3389/fimmu.2022.924178] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/20/2022] [Indexed: 12/11/2022] Open
Abstract
Ulcerative colitis is a chronic inflammatory bowel disease (IBD), but progress in exploring its pathogenesis and finding effective drugs for its prevention and treatment has stalled in recent years. The seeds of Moringa oleifera Lam. are rich in proteins known to have multiple physiological activities. In our earlier work, we had isolated and purified a peptide (MOP) having the sequence KETTTIVR, from M. oleifera seeds; however, its anti-inflammatory activity and mechanism in vivo were unclear. Here we used the dextran sulfate sodium (DSS)-induced colitis model to study the anti-inflammatory activity and mechanism of this MOP. Our results are the first to show that MOP can ameliorate the pathological phenotype, inflammation, and intestinal barrier disruption in mice with colitis. Furthermore, RNA sequencing revealed that MOP inhibits the Janus kinase/signal transducer and activator of transcription (JAK-STAT) pathway activation. Next, by using 16s rRNA gene sequencing, we found that MOP can ameliorate DSS-induced gut microbiota dysbiosis. In addition, an untargeted metabolomics analysis suggested that MOP is able to modulate the level of lipid and amino acid metabolites in IBD-stricken mice. Altogether, these results indicate that MOP ameliorates colitis by remodeling intestinal mucosal barrier by inhibiting JAK-STAT pathway’s activation and regulating gut microbiota and its metabolites, thus providing a basis for further processing and design of bioactive foods from M. oleifera seeds.
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Affiliation(s)
- Zi-Shan Hong
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- National Research and Development Professional Center for Moringa Processing Technology, Yunnan Agricultural University, Kunming, China
| | - Jing Xie
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- National Research and Development Professional Center for Moringa Processing Technology, Yunnan Agricultural University, Kunming, China
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Xue-Feng Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, China
| | - Jing-Jing Dai
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- National Research and Development Professional Center for Moringa Processing Technology, Yunnan Agricultural University, Kunming, China
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming, China
| | - Jia-Ying Mao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- National Research and Development Professional Center for Moringa Processing Technology, Yunnan Agricultural University, Kunming, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, China
| | - Yu-Ying Bai
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming, China
- Yunnan Provincial Engineering Research Center for Edible and Medicinal Homologous Functional Food, Yunnan Agricultural University, Kunming, China
| | - Jun Sheng
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Pu-er Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming, China
- *Correspondence: Jun Sheng, ; Yang Tian,
| | - Yang Tian
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
- Engineering Research Center of Development and Utilization of Food and Drug Homologous Resources, Ministry of Education, Yunnan Agricultural University, Kunming, China
- *Correspondence: Jun Sheng, ; Yang Tian,
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12
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Xue J, Dominguez Rieg JA, Thomas L, White JR, Rieg T. Intestine-Specific NHE3 Deletion in Adulthood Causes Microbial Dysbiosis. Front Cell Infect Microbiol 2022; 12:896309. [PMID: 35719363 PMCID: PMC9204535 DOI: 10.3389/fcimb.2022.896309] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
In the intestine, the Na+/H+ exchanger 3 (NHE3) plays a critical role for Na+ and fluid absorption. NHE3 deficiency predisposes patients to inflammatory bowel disease (IBD). In mice, selective deletion of intestinal NHE3 causes various local and systemic pathologies due to dramatic changes in the intestinal environment, which can influence microbiota colonization. By using metagenome shotgun sequencing, we determined the effect of inducible intestinal epithelial cell-specific deletion of NHE3 (NHE3IEC-KO) in adulthood on the gut microbiome in mice. Compared with control mice, NHE3IEC-KO mice show a significantly different gut microbiome signature, with an unexpected greater diversity. At the phylum level, NHE3IEC-KO mice showed a significant expansion in Proteobacteria and a tendency for lower Firmicutes/Bacteroidetes (F/B) ratio, an indicator of dysbiosis. At the family level, NHE3IEC-KO mice showed significant expansions in Bacteroidaceae, Rikenellaceae, Tannerellaceae, Flavobacteriaceae and Erysipelotrichaceae, but had contractions in Lachnospiraceae, Prevotellaceae and Eubacteriaceae. At the species level, after removing those with lowest occurrence and abundance, we identified 23 species that were significantly expanded (several of which are established pro-inflammatory pathobionts); whereas another 23 species were found to be contracted (some of which are potential anti-inflammatory probiotics) in NHE3IEC-KO mice. These results reveal that intestinal NHE3 deletion creates an intestinal environment favoring the competitive advantage of inflammophilic over anti-inflammatory species, which is commonly featured in conventional NHE3 knockout mice and patients with IBD. In conclusion, our study emphasizes the importance of intestinal NHE3 for gut microbiota homeostasis, and provides a deeper understanding regarding interactions between NHE3, dysbiosis, and IBD.
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Affiliation(s)
- Jianxiang Xue
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States
| | - Jessica A Dominguez Rieg
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States.,James A. Haley Veterans' Hospital, Tampa, FL, United States
| | - Linto Thomas
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States
| | - James R White
- Resphera Biosciences LLC, Baltimore, MD, United States
| | - Timo Rieg
- Department of Molecular Pharmacology and Physiology, University of South Florida, Tampa, FL, United States.,James A. Haley Veterans' Hospital, Tampa, FL, United States.,Center for Hypertension and Kidney Research, University of South Florida, Tampa, FL, United States
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13
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3-oxo-C12:2-HSL, quorum sensing molecule from human intestinal microbiota, inhibits pro-inflammatory pathways in immune cells via bitter taste receptors. Sci Rep 2022; 12:9440. [PMID: 35676403 PMCID: PMC9177545 DOI: 10.1038/s41598-022-13451-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/13/2022] [Indexed: 12/26/2022] Open
Abstract
In the gut ecosystem, microorganisms regulate group behaviour and interplay with the host via a molecular system called quorum sensing (QS). The QS molecule 3-oxo-C12:2-HSL, first identified in human gut microbiota, exerts anti-inflammatory effects and could play a role in inflammatory bowel diseases where dysbiosis has been described. Our aim was to identify which signalling pathways are involved in this effect. We observed that 3-oxo-C12:2-HSL decreases expression of pro-inflammatory cytokines such as Interleukine-1β (− 35%) and Tumor Necrosis Factor-α (TNFα) (− 40%) by stimulated immune RAW264.7 cells and decreased TNF secretion by stimulated PBMC in a dose-dependent manner, between 25 to 100 µM. Transcriptomic analysis of RAW264.7 cells exposed to 3-oxo-C12:2-HSL, in a pro-inflammatory context, highlighted JAK-STAT, NF-κB and TFN signalling pathways and we confirmed that 3-oxo-C12:2-HSL inhibited JAK1 and STAT1 phosphorylation. We also showed through a screening assay that 3-oxo-C12:2-HSL interacted with several human bitter taste receptors. Its anti-inflammatory effect involved TAS2R38 as shown by pharmacologic inhibition and led to an increase in intracellular calcium levels. We thus unravelled the involvement of several cellular pathways in the anti-inflammatory effects exerted by the QS molecule 3-oxo-C12:2-HSL.
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14
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Metwaly A, Reitmeier S, Haller D. Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders. Nat Rev Gastroenterol Hepatol 2022; 19:383-397. [PMID: 35190727 DOI: 10.1038/s41575-022-00581-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/12/2022]
Abstract
The intestine harbours a complex array of microorganisms collectively known as the gut microbiota. The past two decades have witnessed increasing interest in studying the gut microbiota in health and disease, largely driven by rapid innovation in high-throughput multi-omics technologies. As a result, microbial dysbiosis has been linked to many human pathologies, including type 2 diabetes mellitus and inflammatory bowel disease. Integrated analyses of multi-omics data, including metagenomics and metabolomics along with measurements of host response and cataloguing of bacterial isolates, have identified many bacteria and bacterial products that are correlated with disease. Nevertheless, insight into the mechanisms through which microbes affect intestinal health requires going beyond correlation to causation. Current understanding of the contribution of the gut microbiota to disease causality remains limited, largely owing to the heterogeneity of microbial community structures, interindividual differences in disease evolution and incomplete understanding of the mechanisms that integrate microbiota-derived signals into host signalling pathways. In this Review, we provide a broad insight into the microbiome signatures linked to inflammatory and metabolic disorders, discuss outstanding challenges in this field and propose applications of multi-omics technologies that could lead to an improved mechanistic understanding of microorganism-host interactions.
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Affiliation(s)
- Amira Metwaly
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany
| | - Sandra Reitmeier
- ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technical University of Munich, Freising, Germany. .,ZIEL Institute for Food & Health, Technical University of Munich, Freising, Germany.
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15
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Ye L, Dong N, Xiong W, Li J, Li R, Heng H, Chan EWC, Chen S. High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly. Front Microbiol 2022; 13:801587. [PMID: 35633679 PMCID: PMC9134245 DOI: 10.3389/fmicb.2022.801587] [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: 10/25/2021] [Accepted: 04/11/2022] [Indexed: 11/15/2022] Open
Abstract
Metagenome assembly is a core yet methodologically challenging step for taxonomic classification and functional annotation of a microbiome. This study aims to generate the high-resolution human gut metagenome using both Illumina and Nanopore platforms. Assembly was achieved using four assemblers, including Flye (Nanopore), metaSPAdes (Illumina), hybridSPAdes (Illumina and Nanopore), and OPERA-MS (Illumina and Nanopore). Hybrid metagenome assembly was shown to generate contigs with almost same sizes comparable to those produced using Illumina reads alone, but was more contiguous, informative, and longer compared with those assembled with Illumina reads only. In addition, hybrid metagenome assembly enables us to obtain complete plasmid sequences and much more AMR gene-encoding contigs than the Illumina method. Most importantly, using our workflow, 58 novel high-quality metagenome bins were obtained from four assembly algorithms, particularly hybrid assembly (47/58), although metaSPAdes could provide 11 high-quality bins independently. Among them, 29 bins were currently uncultured bacterial metagenome-assembled genomes. These findings were highly consistent and supported by mock community data tested. In the analysis of biosynthetic gene clusters (BGCs), the number of BGCs in the contigs from hybridSPAdes (241) is higher than that of contigs from metaSPAdes (233). In conclusion, hybrid metagenome assembly could significantly enhance the efficiency of contig assembly, taxonomic binning, and genome construction compared with procedures using Illumina short-read data alone, indicating that nanopore long reads are highly useful in metagenomic applications. This technique could be used to create high-resolution references for future human metagenome studies.
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Affiliation(s)
- Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ning Dong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Wenguang Xiong
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Heng Heng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Edward Wai Chi Chan
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- *Correspondence: Sheng Chen,
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16
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Gu M, Samuelson DR, de la Rua NM, Charles TP, Taylor CM, Luo M, Siggins RW, Shellito JE, Welsh DA. Host innate and adaptive immunity shapes the gut microbiota biogeography. Microbiol Immunol 2022; 66:330-341. [PMID: 35067963 DOI: 10.1111/1348-0421.12963] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 11/29/2022]
Abstract
The gut microbiota has a fundamental role in the development and the maturation of the host immune system. Both innate and adaptive immune cells have critical functions in microbial pathogen containment and clearance, but the regulation of the commensal microbiome ecosystem in the gastrointestinal tract by these major immune cell populations is incompletely defined. We investigated the role of specific innate and adaptive immune cell in the regulation of the microbiota in the intestinal tract biogeographically. Dendritic cells, macrophages, CD4+ T-cells, CD8+ T-cells, and B-cells were depleted using monoclonal antibodies and clodronate liposomes, and the microbial communities was determined by 16S rRNA gene sequencing. With specific immune cell depletion, distinct microbiota changes were observed. In general, immune cell depleted mice had higher microbiota richness and evenness at all gut anatomical sites. At each gut segment, samples from immune cell-depleted animals clustered away from the Isotype/Liposome control mice. This was especially dramatic for small intestinal microbiota. Specifically, Enterobacteriaceae, Bacteroides acidifaciens and Mucispirillum schaedleri were highly enriched in the mucosa and lumen of the small intestine in immune cell-deficient animals. Further, the mucosal microbiota had higher microbiota evenness compared to luminal microbiota at all gut segments, and the UniFrac distance between B cell depleted and isotype control mice was the largest in duodenum followed by ileum and colon. Taken together, our data suggest that innate and adaptive immune cells specifically contribute to the regulation of the gut microbiota's biogeographical distribution along the gastrointestinal tract, and microbiota in duodenum mucosa are more responsive to host immune changes compared to other anatomical sites. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Min Gu
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Derrick R Samuelson
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Internal Medicine, Division of Pulmonary, Critical Care, & Sleep, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nicholas M de la Rua
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Tysheena P Charles
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Meng Luo
- Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Robert W Siggins
- Department of Physiology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - Judd E Shellito
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
| | - David A Welsh
- Department of Internal Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Science Center, New Orleans, LA, USA.,Department of Microbiology, Immunology, & Parasitology, Louisiana State University Health Science Center, New Orleans, LA, USA
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17
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Ren R, Gao X, Shi Y, Li J, Peng L, Sun G, Wang Z, Yan B, Zhi J, Yang Y. Long-Term Efficacy of Low-Intensity Single Donor Fecal Microbiota Transplantation in Ulcerative Colitis and Outcome-Specific Gut Bacteria. Front Microbiol 2021; 12:742255. [PMID: 34867859 PMCID: PMC8635752 DOI: 10.3389/fmicb.2021.742255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
Aims: To assess the long-term efficacy and safety of single-donor, low-intensity fecal microbiota transplantation (FMT) in treating ulcerative colitis (UC), and to identify the outcome-specific gut bacteria. Design: Thirty-one patients with active UC (Mayo scores ≥ 3) were recruited, and all received FMT twice, at the start of the study and 2∼3 months later, respectively, with a single donor and a long-term follow-up. The fecal microbiome profile was accessed via 16S rRNA sequencing before and after FMT. Results: After the first FMT, 22.58% (7/31) of patients achieved clinical remission and endoscopy remission, with the clinical response rate of 67.74% (21/31), which increased to 55% (11/20) and 80% (16/20), respectively, after the second FMT. No serious adverse events occurred in all patients. During 4 years of follow-up, the mean remission period of patients was 26.5 ± 19.98 m; the relapse rate in the 12 remission patients was 33.33% within 1 year, and 58.3% within 4 years. At baseline, UC patients showed an enrichment in some proinflammatory microorganisms compared to the donor, such as Bacteroides fragilis, Clostridium difficile, and Ruminococcus gnavus, and showed reduced amounts of short-chain fatty acid (SCFA) producing bacteria especially Faecalibacterium prausnitzii. FMT induced taxonomic compositional changes in the recipient gut microbiota, resulting in a donor-like state. Given this specific donor, UC recipients with different outcomes showed distinct gut microbial features before and after FMT. In prior to FMT, relapse was characterized by higher abundances of Bacteroides fragilis and Lachnospiraceae incertae sedis, together with lower abundances of Bacteroides massiliensis, Roseburia, and Ruminococcus; Prevotella copri was more abundant in the non-responders (NR); and the patients with sustained remission (SR) had a higher abundance of Bifidobacterium breve. After FMT, the NR patients had a lower level of Bifidobacterium compared to those with relapse (Rel) and SR, while a higher level of Bacteroides spp. was observed in the Rel group. Conclusion: Low-intensity single donor FMT could induce long remission in active UC. The gut microbiota composition in UC patients at baseline may be predictive of therapeutic response to FMT.
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Affiliation(s)
- Rongrong Ren
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xuefeng Gao
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen, China
- Central Laboratory, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen, China
| | - Yichao Shi
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jianfeng Li
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Lihua Peng
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Gang Sun
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zikai Wang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Bin Yan
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Junli Zhi
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yunsheng Yang
- Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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18
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Coquant G, Aguanno D, Pham S, Grellier N, Thenet S, Carrière V, Grill JP, Seksik P. Gossip in the gut: Quorum sensing, a new player in the host-microbiota interactions. World J Gastroenterol 2021; 27:7247-7270. [PMID: 34876787 PMCID: PMC8611211 DOI: 10.3748/wjg.v27.i42.7247] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/17/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
Bacteria are known to communicate with each other and regulate their activities in social networks by secreting and sensing signaling molecules called autoinducers, a process known as quorum sensing (QS). This is a growing area of research in which we are expanding our understanding of how bacteria collectively modify their behavior but are also involved in the crosstalk between the host and gut microbiome. This is particularly relevant in the case of pathologies associated with dysbiosis or disorders of the intestinal ecosystem. This review will examine the different QS systems and the evidence for their presence in the intestinal ecosystem. We will also provide clues on the role of QS molecules that may exert, directly or indirectly through their bacterial gossip, an influence on intestinal epithelial barrier function, intestinal inflammation, and intestinal carcinogenesis. This review aims to provide evidence on the role of QS molecules in gut physiology and the potential shared by this new player. Better understanding the impact of intestinal bacterial social networks and ultimately developing new therapeutic strategies to control intestinal disorders remains a challenge that needs to be addressed in the future.
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Affiliation(s)
- Garance Coquant
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, Paris 75012, France
| | - Doriane Aguanno
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, Paris 75012, France
- EPHE, PSL University, Paris 75014, France
| | - Sandrine Pham
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, Paris 75012, France
- EPHE, PSL University, Paris 75014, France
| | - Nathan Grellier
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, Paris 75012, France
| | - Sophie Thenet
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, Paris 75012, France
- EPHE, PSL University, Paris 75014, France
| | - Véronique Carrière
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, Paris 75012, France
| | - Jean-Pierre Grill
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, Paris 75012, France
| | - Philippe Seksik
- Centre de Recherche Saint-Antoine, INSERM, Sorbonne Université, Paris 75012, France
- Department of Gastroenterology and Nutrition, Saint-Antoine Hospital, APHP, Paris 75012, France
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19
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Deng M, Wu X, Duan X, Xu J, Yang X, Sheng X, Lou P, Shao C, Lv C, Yu Z. Lactobacillus paracasei L9 improves colitis by expanding butyrate-producing bacteria that inhibit the IL-6/STAT3 signaling pathway. Food Funct 2021; 12:10700-10713. [PMID: 34605504 DOI: 10.1039/d1fo02077c] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic intestinal inflammation that is currently incurable. Increasing evidence indicates that supplementation with probiotics could improve the symptoms of IBD. It is scientifically significant to identify novel and valid strains for treating IBD. It has been reported that the probiotic Lactobacillus paracasei L9 (L9), which is identified from the gut of healthy centenarians, can modulate host immunity and plays an anti-allergic role. Here, we demonstrated that L9 alleviates the pathological phenotypes of experimental colitis by expanding the abundance of butyrate-producing bacteria. Oral administration of sodium butyrate in experimental colitis recapitulates the L9 anti-inflammatory phenotypes. Mechanistically, sodium butyrate ameliorated the inflammatory responses by inhibiting the IL-6/STAT3 signaling pathway in colitis. Overall, these findings demonstrated that L9 alleviates the DSS-induced colitis development by enhancing the abundance of butyrate-producing bacterial strains that produce butyrate to suppress the IL-6/STAT3 signaling pathway, providing new insight into a promising therapeutic target for the remission of IBD.
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Affiliation(s)
- Min Deng
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Xi Wu
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Xiaoyue Duan
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jiuzhi Xu
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Xu Yang
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Xiaole Sheng
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Pengbo Lou
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Chunlei Shao
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Cong Lv
- Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China.
| | - Zhengquan Yu
- State Key Laboratories for Agrobiotechnology, Department of Nutrition and Health, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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20
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Dai ZF, Ma XY, Yang RL, Wang HC, Xu DD, Yang JN, Guo XB, Meng SS, Xu R, Li YX, Xu Y, Li K, Lin XH. Intestinal flora alterations in patients with ulcerative colitis and their association with inflammation. Exp Ther Med 2021; 22:1322. [PMID: 34630676 DOI: 10.3892/etm.2021.10757] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Ulcerative colitis (UC), which is a type of inflammatory bowel disease, is a chronic intestinal disorder of multifactorial etiology. Numerous studies have indicated an association between UC and intestinal bacteria. However, a limited number of studies regarding the expression of interleukin-17 (IL-17) and interleukin-23 (IL-23) in association with intestinal bacteria have been performed. The aim of the current study was to investigate the gut microbiota alterations in patients with UC, at a number of taxonomic levels, and their relationship with intestinal inflammation by analyzing the protein expression of IL-17 and IL-23. Specimens were collected from 10 healthy controls and 16 patients with UC. A histological examination was performed in colonic tissues, IL-17 and IL-23 protein expression was detected by immunohistochemistry, fecal samples were sequenced using 16S rDNA sequencing and bioinformatics analysis was performed. The UC group exhibited an increased histological score (P<0.01) and upregulated IL-17 and IL-23 expression (P<0.01). At the order level, the bacterial diversity of the UC group was decreased. β-diversity analyses, including principal component analysis, principal coordinate analysis and non-metric multidimensional scaling, demonstrated that the two groups of samples were separated into two taxonomic categories, as distinct variations were observed in the analysis of group differences (P=0.001). Regarding the differences in species composition between the groups, Enterococcus was indicated to be the species with the greatest difference in abundance compared with the healthy control group (P<0.01), followed by Lactobacillus (P<0.05), Escherichia-Shigella (P<0.05), Bifidobacterium and Bacteroides. In addition, the average optical density of IL-17 was positively correlated with the histological score (ρ=0.669; P=0.035), Enterococcus (r=0.843; P<0.001), Lactobacillus (r=0.737; P=0.001), Bifidobacterium (r=0.773; P<0.001) and Escherichia-Shigella (r=0.663; P=0.005), and the average optical density of IL-23 was positively correlated with the histological score (ρ=0.733; P=0.016), Enterococcus (r=0.771; P<0.001), Lactobacillus (r=0.566; P=0.022), Bifidobacterium (r=0.517; P=0.041) and Escherichia-Shigella (r=0.613; P=0.012). The results of the present study indicated that the intestinal microbiota of patients with UC differed from that of healthy controls at multiple taxonomic levels. The alterations of the intestinal microflora were closely associated with the degree of inflammation. The IL-23/IL-17 axis, as a key factor in the development of UC, maybe associated with the alterations of intestinal microflora. The interaction between intestinal microflora and the IL-23/IL-17 axis may serve an important role in the pathogenesis of UC.
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Affiliation(s)
- Zhi Feng Dai
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Xu Yuan Ma
- Department of Gastroenterology, People's Hospital of Xuchang, Xuchang, Henan 461000, P.R. China
| | - Rui Lin Yang
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Hui Chao Wang
- Department of Nephrology, The First Affiliated Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Dan Dan Xu
- Department of Dermatology, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Jing Nan Yang
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Xiao Bing Guo
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450002, P.R. China
| | - Shuang Shuang Meng
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Rui Xu
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Yu Xia Li
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Yao Xu
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Kun Li
- Department of Pathophysiology, Institute of Digestive Disease, Tongji University School of Medicine, Shanghai 200092, P.R. China
| | - Xu Hong Lin
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
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21
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Association of LRRK2 rs11564258 single nucleotide polymorphisms with type and extent of gastrointestinal mycobiome in ulcerative colitis: a case-control study. Gut Pathog 2021; 13:56. [PMID: 34593025 PMCID: PMC8482594 DOI: 10.1186/s13099-021-00453-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/20/2021] [Indexed: 12/02/2022] Open
Abstract
Background Recently, the role of endogenous microbiota and the genotype-microbiota correlation in inflammatory bowel disease (IBD) pathogenesis have been highlighted. However, fungi, as the second most prevalent residents of the intestine, and their primary receptor, Dectin-1, are underrated. Thus, we conducted the first human study investigating the association of Leucine-rich repeat kinase 2 (LRRK2) polymorphism (rs11564258) with type and the extent of intestinal fungi in IBD patients. Material and methods A case–control study was performed on 79 ulcerative colitis (UC)-patients (case group) and 58 healthy subjects (HS group). DNA was extracted from blood samples of both groups and amplified with the primers designed for the specific locus containing the LRRK2 polymorphism (rs11564258) and then sequenced. Dectin-1 and LRRK2 mRNA expression levels were also determined. Furthermore, the type and prevalence of fecal yeast species were surveyed in case and control groups. Results A positive correlation was observed between rs11564258 polymorphism and UC susceptibility (p = 0.008 vs. HS). Patients with active UC had the highest rate of isolated fungal colonies (50.41%), followed by patients with non-active UC (24.6%) and HS (25%). These results showed a relationship between UC severity with the increased fungal load. Candida albicans had the highest prevalence in both UC (78.7%) and HS groups (55.8%). Whereas Saccharomyces cerevisiae was the second most common species detected in HS (15.23%), it was significantly reduced in the UC patient group (1.68%) (P = 0.0001). On the other hand, single nucleotide polymorphism (SNP, rs11564258) was not correlated with the increased fungal flora in the UC patients. The expression of LRRK2 and Dectin-1 mRNA detected in blood samples was notably higher in the UC patients (P < 0.01) than in the HS group, without being affected by rs11564258 polymorphism. Conclusions Here, we disclosed that LRRK2 mediates Dectin-1 signaling pathway activation and subsequent inflammation in the UC patients without being affected by the presence of SNP rs11564258. Our data showed an increased global fungal load in the UC patients along with elevated UC susceptibility in cases carrying rs11564258 polymorphism. However, more clinical investigations, particularly in larger populations with different ethnic groups, are required to support this conclusion.
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22
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Ditto MC, Parisi S, Landolfi G, Borrelli R, Realmuto C, Finucci A, Caviglia GP, Ribaldone DG, Astegiano M, Zanetti A, Carrara G, Scirè CA, Antivalle M, Sarzi-Puttini P, Fusaro E. Intestinal microbiota changes induced by TNF-inhibitors in IBD-related spondyloarthritis. RMD Open 2021; 7:rmdopen-2021-001755. [PMID: 34489323 PMCID: PMC8422478 DOI: 10.1136/rmdopen-2021-001755] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/30/2021] [Indexed: 12/14/2022] Open
Abstract
Background The close relationship between joints and gut inflammation has long been known and several data suggest that dysbiosis could link spondyloarthritis (SpA) to inflammatory bowel diseases (IBD). The introduction of biological drugs, in particular tumour necrosis factor inhibitors (TNFi), revolutionised the management of both these diseases. While the impact of conventional drugs on gut microbiota is well known, poor data are available about TNFi. Aim To investigate the impact of TNFi on gut microbiota. Methods We evaluated 20 patients affected by enteropathic arthritis, naïve for biological drugs, treated with TNFi at baseline and after 6 months of therapy. All patients followed a Mediterranean diet. Patients performed self-sampling of a faecal sample at baseline and after 6 months of therapy. NGS-based ITS and 16S rRNA gene sequencing was performed, followed by the taxonomic bioinformatics analysis. Results After 6 months of therapy, we detected a remarkable increase in Lachnospiraceae family (Δ +10.3, p=0.04) and Coprococcus genus (Δ +2.8, p=0.003). We also noted a decreasing trend in Proteobacteria (Δ −8.0, p=0.095) and Gammaproteobacteria (Δ −9, p=0.093) and an increasing trend in Clostridia (Δ +8.2, p=0.083). We did not find differences between TNFi responders (SpA improvement or IBD remission achieved) and non-responders in terms of alpha and beta diversity. Conclusions Our findings are consistent with the hypothesis that TNFi therapy tends to restore the intestinal eubiosis.
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Affiliation(s)
- Maria Chiara Ditto
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Simone Parisi
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | | | - Richard Borrelli
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Cristina Realmuto
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Annacarla Finucci
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Gian Paolo Caviglia
- Gastroenterology Unit, University of Turin Department of Medical Sciences, Turin, Italy
| | - Davide Giuseppe Ribaldone
- Gastroenterology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Marco Astegiano
- Gastroenterology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Anna Zanetti
- Epidemiology Unit, Italian Society of Rheumatology, Milan, Italy
| | - Greta Carrara
- Epidemiology Unit, Italian Society of Rheumatology, Milan, Italy
| | | | | | | | - Enrico Fusaro
- Rheumatology Unit, Azienda Ospedaliero Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
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23
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Chen G, Shen J. Artificial Intelligence Enhances Studies on Inflammatory Bowel Disease. Front Bioeng Biotechnol 2021; 9:635764. [PMID: 34307315 PMCID: PMC8297505 DOI: 10.3389/fbioe.2021.635764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/09/2021] [Indexed: 12/18/2022] Open
Abstract
Inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn’s disease (CD), is an idiopathic condition related to a dysregulated immune response to commensal intestinal microflora in a genetically susceptible host. As a global disease, the morbidity of IBD reached a rate of 84.3 per 100,000 persons and reflected a continued gradual upward trajectory. The medical cost of IBD is also notably extremely high. For example, in Europe, it has €3,500 in CD and €2,000 in UC per patient per year, respectively. In addition, taking into account the work productivity loss and the reduced quality of life, the indirect costs are incalculable. In modern times, the diagnosis of IBD is still a subjective judgment based on laboratory tests and medical images. Its early diagnosis and intervention is therefore a challenging goal and also the key to control its progression. Artificial intelligence (AI)-assisted diagnosis and prognosis prediction has proven effective in many fields including gastroenterology. In this study, support vector machines were utilized to distinguish the significant features in IBD. As a result, the reliability of IBD diagnosis due to its impressive performance in classifying and addressing region problems was improved. Convolutional neural networks are advanced image processing algorithms that are currently in existence. Digestive endoscopic images can therefore be better understood by automatically detecting and classifying lesions. This study aims to summarize AI application in the area of IBD, objectively evaluate the performance of these methods, and ultimately understand the algorithm–dataset combination in the studies.
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Affiliation(s)
- Guihua Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Shanghai Institute of Digestive Disease, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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24
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Li H, Christman LM, Li R, Gu L. Synergic interactions between polyphenols and gut microbiota in mitigating inflammatory bowel diseases. Food Funct 2021; 11:4878-4891. [PMID: 32490857 DOI: 10.1039/d0fo00713g] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel diseases (IBD) are a group of chronic and recurring inflammatory conditions in the colon and intestine. Their etiology is not fully understood but involves the combination of gut dysbiosis, genetics, immune functions, and environmental factors including diet. Polyphenols from plant-based food synergistically interact with gut microbiota to suppress inflammation and alleviate symptoms of IBD. Polyphenols increase the diversity of gut microbiota, improve the relative abundance of beneficial bacteria, and inhibit the pathogenic species. Polyphenols not absorbed in the small intestine are catabolized in the colon by microbiota into microbial metabolites, many of which have higher anti-inflammatory activity and bioavailability than their precursors. The polyphenols and their microbial metabolites alleviate IBD through reduction of oxidative stress, inhibition of inflammatory cytokines secretion (TNF-α, IL-6, IL-8, and IL-1β), suppression of NF-κB, upregulation of Nrf2, gut barrier protection, and modulation of immune function. Future studies are needed to discover unknown microbial metabolites of polyphenols and correlate specific gut microbes with microbial metabolites and IBD mitigating activity. A better knowledge of the synergistic interactions between polyphenols and gut microbiota will help to devise more effective prevention strategies for IBD. This review focuses on the role of polyphenols, gut microbiota and their synergistic interactions on the alleviation of IBD as well as current trends and future directions of IBD management.
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Affiliation(s)
- Hao Li
- Food Science and Human Nutrition Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, USA.
| | - Lindsey M Christman
- Food Science and Human Nutrition Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, USA.
| | - Ruiqi Li
- Food Science and Human Nutrition Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, USA.
| | - Liwei Gu
- Food Science and Human Nutrition Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, USA.
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25
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Somineni HK, Weitzner JH, Venkateswaran S, Dodd A, Prince J, Karikaran A, Sauer CG, Abramowicz S, Zwick ME, Cutler DJ, Okou DT, Chopra P, Kugathasan S. Site- and Taxa-Specific Disease-Associated Oral Microbial Structures Distinguish Inflammatory Bowel Diseases. Inflamm Bowel Dis 2021; 27:1889-1900. [PMID: 34002220 PMCID: PMC8599042 DOI: 10.1093/ibd/izab082] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND The gut and oral microbiome have independently been shown to be associated with inflammatory bowel disease (IBD). However, it is not known to what extent gut and oral microbial disease markers converge in terms of their composition in IBD. Further, the spatial and temporal variation within the oral microenvironments of IBD remain to be elucidated. PATIENTS AND METHODS We used a prospectively recruited cohort of patients with IBD (n = 47) and unrelated healthy control patients (n = 18) to examine the spatial and temporal distribution of microbiota within the various oral microenvironments, represented by saliva, tongue, buccal mucosa, and plaque, and compared them with stool. Microbiome characterization was performed using 16S rRNA gene sequencing. RESULTS The oral microbiome displayed IBD-associated dysbiosis, in a site- and taxa-specific manner. Plaque samples depicted a relatively severe degree of dysbiosis, and the disease-associated dysbiotic bacterial groups were predominantly the members of the phylum Firmicutes. Our 16S rRNA gene analyses show that oral microbiota can distinguish patients with IBD from healthy control patients, with salivary microbiota performing the best, closely matched by stool and other oral sites. Longitudinal profiles of microbial composition suggest that some taxa are more consistently perturbed than others, preferentially in a site-dependent fashion. CONCLUSIONS Collectively, these data indicate the potential of using oral microbial profiles in screening and monitoring patients with IBD. Furthermore, these results support the importance of spatial and longitudinal microbiome sampling to interpret disease-associated dysbiotic states and eventually to gain insights into disease pathogenesis.
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Affiliation(s)
- Hari K Somineni
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA,Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia, USA
| | - Jordan H Weitzner
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Anne Dodd
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Jarod Prince
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Arjuna Karikaran
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Cary G Sauer
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Shelly Abramowicz
- Department of Surgery, Division of Oral and Maxillofacial Surgery, Emory University, Atlanta, Georgia, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - David T Okou
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, Georgia, USA,Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia, USA,Department of Human Genetics, Emory University, Atlanta, Georgia, USA,Address correspondence to: Subra Kugathasan, MD, Division of Pediatric Gastroenterology, Emory University School of Medicine and Children’s Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA 30322 ()
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26
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Romano-Keeler J, Zhang J, Sun J. The Life-Long Role of Nutrition on the Gut Microbiome and Gastrointestinal Disease. Gastroenterol Clin North Am 2021; 50:77-100. [PMID: 33518170 PMCID: PMC7863586 DOI: 10.1016/j.gtc.2020.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Bacterial colonization of the intestines occurs during the first 2 years of life. Homeostasis of the gut microbiome is established to foster normal intestinal immune development for adulthood. Derangements in this process can interfere with immune function and increase an individual's risk for gastrointestinal disorders. We discuss the role of diet and the microbiome on the onset of such disorders. We examine how micronutrients, prebiotics, and probiotics modulate disease pathogenesis. We discuss how diet and abnormal microbial colonization impact extraintestinal organs. Understanding the communication of nutrition and the microbiome offers exciting opportunities for therapeutics.
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Affiliation(s)
- Joann Romano-Keeler
- Division of Neonatology, Department of Pediatrics, University of Illinois at Chicago, 840 South Wood Street, MC 856, Suite 1252, Chicago, IL 60612, USA
| | - Jilei Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, 840 South Wood Street, Room 704 CSB, MC716, Chicago, IL 60612, USA
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, 840 South Wood Street, Room 704 CSB, MC716, Chicago, IL 60612, USA; University of Illinois Cancer Center, 818 South Wolcott Avenue, Chicago, IL 60612, USA.
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27
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Franzin M, Stefančič K, Lucafò M, Decorti G, Stocco G. Microbiota and Drug Response in Inflammatory Bowel Disease. Pathogens 2021; 10:211. [PMID: 33669168 PMCID: PMC7919657 DOI: 10.3390/pathogens10020211] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
A mutualistic relationship between the composition, function and activity of the gut microbiota (GM) and the host exists, and the alteration of GM, sometimes referred as dysbiosis, is involved in various immune-mediated diseases, including inflammatory bowel disease (IBD). Accumulating evidence suggests that the GM is able to influence the efficacy of the pharmacological therapy of IBD and to predict whether individuals will respond to treatment. Additionally, the drugs used to treat IBD can modualate the microbial composition. The review aims to investigate the impact of the GM on the pharmacological therapy of IBD and vice versa. The GM resulted in an increase or decrease in therapeutic responses to treatment, but also to biotransform drugs to toxic metabolites. In particular, the baseline GM composition can help to predict if patients will respond to the IBD treatment with biologic drugs. On the other hand, drugs can affect the GM by incrementing or reducing its diversity and richness. Therefore, the relationship between the GM and drugs used in the treatment of IBD can be either beneficial or disadvantageous.
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Affiliation(s)
- Martina Franzin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Katja Stefančič
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (K.S.); (G.S.)
| | - Marianna Lucafò
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Giuliana Decorti
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy;
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (K.S.); (G.S.)
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28
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Morales Fénero C, Amaral MA, Xavier IK, Padovani BN, Paredes LC, Takiishi T, Lopes-Ferreira M, Lima C, Colombo A, Saraiva Câmara NO. Short chain fatty acids (SCFAs) improves TNBS-induced colitis in zebrafish. CURRENT RESEARCH IN IMMUNOLOGY 2021; 2:142-154. [PMID: 35492385 PMCID: PMC9040093 DOI: 10.1016/j.crimmu.2021.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/20/2022] Open
Affiliation(s)
- Camila Morales Fénero
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Corresponding author.
| | | | - Izabella Karina Xavier
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Barbara Nunes Padovani
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Lais Cavalieri Paredes
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Tatiana Takiishi
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles, Brussels, Belgium
| | - Mônica Lopes-Ferreira
- Center of Toxins, Immune Response and Cellular Signalling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Carla Lima
- Center of Toxins, Immune Response and Cellular Signalling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Alicia Colombo
- Department of Pathologic Anatomy, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Niels Olsen Saraiva Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Medicine, Nephrology Division, Federal University of São Paulo, Brazil
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29
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Stalla FM, Astegiano M, Ribaldone DG, Saracco GM, Pellicano R. The small intestine: barrier, permeability and microbiota. Minerva Gastroenterol (Torino) 2020; 68:98-110. [PMID: 33267569 DOI: 10.23736/s2724-5985.20.02808-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In recent years, there has been growing interest in the comprehension of the physiology of intestinal permeability and microbiota; and how these elements could influence the pathogenesis of diseases. The term intestinal permeability describes all the processes that allow the passage of molecules as water, electrolytes and nutrients through the intestinal barrier by the paracellular or the transcellular transport systems with several implications for self-tolerance and not-self immunity. An increased permeability might induce a more significant interaction of the immune system with unknown external antigens. This might favor the onset of several immune-related extra-intestinal diseases including coeliac disease, diabetes mellitus type 1, bronchial asthma and inflammatory bowel diseases. Furthermore, the intestinal permeability interacts every day with microbiota, the complex system of mutualistic inhabitants and commensal microorganisms living in the healthy gut. Microbiota is implicated in physiological functions by actively participating in digestion, absorption, synthesis of vitamins and protection from external aggressions. The critical site where these processes occur is the small intestine to which this updated review is dedicated. Understanding its anatomy, its barrier structure and permeability modulation and its microbiota composition is the essential skill to comprehend the complex pathogenesis of several - not only gastroenterological - diseases.
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Affiliation(s)
| | | | | | - Giorgio M Saracco
- Department of Medical Sciences, University of Turin, Turin, Italy.,Unit of Gastroenterology, Molinette Hospital, Turin, Italy
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30
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Sankarasubramanian J, Ahmad R, Avuthu N, Singh AB, Guda C. Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease. Front Med (Lausanne) 2020; 7:606298. [PMID: 33330572 PMCID: PMC7729129 DOI: 10.3389/fmed.2020.606298] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Inflammatory bowel disease (IBD) represents multifactorial chronic inflammatory conditions in the gastrointestinal tract and includes Crohn's disease (CD) and ulcerative colitis (UC). Despite similarities in pathobiology and disease symptoms, UC and CD represent distinct diseases and exhibit diverse therapeutic responses. While studies have now confirmed that IBD is associated with dramatic changes in the gut microbiota, specific changes in the gut microbiome and associated metabolic effects on the host due to CD and UC are less well-understood. Methods: To address this knowledge gap, we performed an extensive unbiased meta-analysis of the gut microbiome data from five different IBD patient cohorts from five different countries using QIIME2, DIAMOND, and STAMP bioinformatics platforms. In-silico profiling of the metabolic pathways and community metabolic modeling were carried out to identify disease-specific association of the metabolic fluxes and signaling pathways. Results: Our results demonstrated a highly conserved gut microbiota community between healthy individuals and IBD patients at higher phylogenetic levels. However, at or below the order level in the taxonomic rank, we found significant disease-specific alterations. Similarly, we identified differential enrichment of the metabolic pathways in CD and UC, which included enriched pathways related to amino acid and glycan biosynthesis and metabolism, in addition to other metabolic pathways. Conclusions: In conclusion, this study highlights the prospects of harnessing the gut microbiota to improve understanding of the etiology of CD and UC and to develop novel prognostic, and therapeutic approaches.
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Affiliation(s)
- Jagadesan Sankarasubramanian
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Nagavardhini Avuthu
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Amar B. Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
- VA Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| | - Chittibabu Guda
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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31
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Thompson C, Taleban S. Incorporating Frailty in the Treatment Program of Elderly Patients with Gastrointestinal Disease. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s11938-020-00310-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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32
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Yu P, Ke C, Guo J, Zhang X, Li B. Lactobacillus plantarum L15 Alleviates Colitis by Inhibiting LPS-Mediated NF-κB Activation and Ameliorates DSS-Induced Gut Microbiota Dysbiosis. Front Immunol 2020; 11:575173. [PMID: 33123156 PMCID: PMC7566170 DOI: 10.3389/fimmu.2020.575173] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022] Open
Abstract
Previous studies have suggested that the Lactobacillus plantarum bacteria strain could be effective in ulcerative colitis (UC) management. However, its effects are strain-specific and the related mechanisms for its attenuating effects on UC remain unclear. This study aimed to elucidate the underlying mechanisms for the protective effect of L. plantarum on UC. Firstly, 15 L. plantarum strains were screened for potential probiotic characteristics with good tolerance to simulated human gastrointestinal transit and adhesion. Secondly, the inflammatory response of selected strains to the Caco-2 cells induced by lipopolysaccharide (LPS) was measured. Finally, an in vivo mouse model induced by dextran sulfate sodium (DSS) was used to assess the beneficial effects and likely action mechanisms the successfully screened in vitro strain, L. plantarum L15. In vitro results showed that L. plantarum L15 possessed the highest gastrointestinal transit tolerance, adhesion and reduction of pro-inflammatory abilities compared to the other screened strains. In vivo, high dose of L. plantarum L15 supplementation increased the body weight, colon length and anti-inflammatory cytokine production. Pro-inflammatory cytokine production, disease activity index (DAI) levels and myeloperoxidase (MPO) parameters decreased using this strain. In addition, L. plantarum L15 alleviated the histopathological changes in colon, modulated the gut microbiota, and decreased LPS secretion. The activities of this strain down-regulated the expression of TLR4 and MyD88 genes as well as genes associated with NF-κB signaling pathway. Our findings present L. plantarum L15 as a new probiotic, with promising application for UC management.
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Affiliation(s)
- Peng Yu
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Chuxin Ke
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Jiaxin Guo
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xiuling Zhang
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Bailiang Li
- College of Food Science, Northeast Agricultural University, Harbin, China.,Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin, China
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33
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Wang G, Huang S, Cai S, Yu H, Wang Y, Zeng X, Qiao S. Lactobacillus reuteri Ameliorates Intestinal Inflammation and Modulates Gut Microbiota and Metabolic Disorders in Dextran Sulfate Sodium-Induced Colitis in Mice. Nutrients 2020; 12:nu12082298. [PMID: 32751784 PMCID: PMC7468961 DOI: 10.3390/nu12082298] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/11/2022] Open
Abstract
Lactobacillus reuteri, a commensal intestinal bacteria, has various health benefits including the regulation of immunity and intestinal microbiota. We examined whether L. reuteri I5007 could protect mice against colitis in ameliorating inflammation, modulating microbiota, and metabolic composition. In vitro, HT-29 cells were cultured with L. reuteri I5007 or lipopolysaccharide treatment under three different conditions, i.e., pre-, co- (simultaneous), and posttreatment. Pretreatment with L. reuteri I5007 effectively relieves inflammation in HT-29 cells challenged with lipopolysaccharide. In vivo, mice were given L. reuteri I5007 by gavage throughout the study, starting one week prior to dextran sulfate sodium (DSS) treatment for one week followed by two days without DSS. L. reuteri I5007 improved DSS-induced colitis, which was confirmed by reduced weight loss, colon length shortening, and histopathological damage, restored the mucus layer, as well as reduced pro-inflammatory cytokines levels. Analysis of 16S rDNA sequences and metabolome demonstrates that L. reuteri I5007 significantly alters colonic microbiota and metabolic structural and functional composition. Overall, the results demonstrate that L. reuteri I5007 pretreatment could effectively alleviate intestinal inflammation by regulating immune responses and altering the composition of gut microbiota structure and function, as well as improving metabolic disorders in mice with colitis.
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Affiliation(s)
- Gang Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (G.W.); (S.H.); (S.C.); (H.Y.); (Y.W.); (X.Z.)
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing 100193, China
| | - Shuo Huang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (G.W.); (S.H.); (S.C.); (H.Y.); (Y.W.); (X.Z.)
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing 100193, China
| | - Shuang Cai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (G.W.); (S.H.); (S.C.); (H.Y.); (Y.W.); (X.Z.)
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing 100193, China
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (G.W.); (S.H.); (S.C.); (H.Y.); (Y.W.); (X.Z.)
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing 100193, China
| | - Yuming Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (G.W.); (S.H.); (S.C.); (H.Y.); (Y.W.); (X.Z.)
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing 100193, China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (G.W.); (S.H.); (S.C.); (H.Y.); (Y.W.); (X.Z.)
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing 100193, China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (G.W.); (S.H.); (S.C.); (H.Y.); (Y.W.); (X.Z.)
- Beijing Key Laboratory of Biological Feed Additive, China Agricultural University, Beijing 100193, China
- Correspondence: ; Tel.: +86-10-6273-1456
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34
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Zhang Z, Cao H, Shen P, Liu J, Cao Y, Zhang N. Ping weisan alleviates chronic colitis in mice by regulating intestinal microbiota composition. JOURNAL OF ETHNOPHARMACOLOGY 2020; 255:112715. [PMID: 32114163 DOI: 10.1016/j.jep.2020.112715] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/28/2020] [Accepted: 02/23/2020] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ping weisan (PWS), a complex formulation used in traditional Chinese medicine, is first described in 1107 AD and published in the Prescriptions of Taiping Benevolent Dispensary. We have previously confirmed that PWS has the effect of alleviating DSS-induced chronic ulcerative colitis (UC) in mice. AIM OF THE STUDY We aimed to examine whether PWS protects mice from chronic UC by regulating intestinal microbiota composition. MATERIALS AND METHODS Chronic colitis was induced in C57BL/6 mice with 2.5% DSS in drinking water. PWS (8 g/kg) was orally administered throughout the experiment. Body weight changes, stool consistency and myeloperoxidase (MPO) activity were measured in these mice. Interleukin-17A (IL-17A) and interferon gamma (IFN-γ) mRNA levels were detected by qRT-PCR. The alterations of fecal microflora were investigated by 16S rRNA sequencing. Furthermore, intestinal tight junction protein including occludin, and serum lipopolysaccharide (LPS) level were also detected. RESULTS PWS relieved DSS-induced loss of body weight, and improved stool consistency and MPO activity in mice. The levels of IL-17A and IFN-γ mRNA were also reduced after treatment with PWS. PWS not only regulated occludin level but also decreased serum LPS. We further showed DSS-induced changes in intestinal microbial composition and richness are significantly regulated by PWS. PWS treatment significantly decreased the abundance of Bacteroidetes, but increased the abundance of Firmicutes in chronic UC mice induced by DSS. CONCLUSIONS Combining with our previous results, we found that PWS could exert anti-UC role by rebalancing intestinal bacteria.
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Affiliation(s)
- Zecai Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China; Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Hongyang Cao
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Peng Shen
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiuxi Liu
- College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yongguo Cao
- College of Veterinary Medicine, Jilin University, Changchun, China; Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China.
| | - Naisheng Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China.
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35
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Zatorski H, Nakov R. Faecal Microbiota Transplantation in Inflammatory Bowel Disease: Current Concepts and Future Challenges. Curr Drug Targets 2020; 21:1440-1447. [PMID: 32484770 DOI: 10.2174/1389450121666200602125507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/26/2022]
Abstract
Dysbiosis has been repeatedly observed in inflammatory bowel disease (IBD) and is now recognized as an essential factor in the gut inflammatory process. IBD is a significant burden to health-care systems, mainly due to treatment-related costs. Available treatments have several limitations: up to 30% of patients are primary non-responders, and between 10 and 20% lose response per year, requiring a dose-escalation or a switch to another biologic. Hence, the current IBD treatment is not sufficient, and there is an urgent need to introduce new therapies in the management of these patients. Recently, the correction of dysbiosis has become an attractive approach from a therapeutic point of view. Faecal microbiota transplantation (FMT) appears as a reliable and potentially beneficial therapy in IBD patients. There is developing data that FMT for mild-to-moderately active UC is a safe and efficient therapy for the induction of remission. However, the current studies have different designs and have a short follow up, which makes clinical interpretation significantly difficult. There is a need for RCTs with a well-defined study cohort using FMT for the therapy of CD patients. The location, behavior, and severity of the disease should be taken into account. The goal of this manuscript is to review the data currently available on FMT and IBD, to explain FMT principles and methodology in IBD patients and to discuss some unresolved issues.
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Affiliation(s)
- Hubert Zatorski
- Department of Digestive Tract Diseasesx,Department of Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Radislav Nakov
- Clinic of Gastroenterology, Tsaritsa Yoanna University Hospital, Medical University of Sofia, Sofia, Bulgaria
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36
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Huang Y, Yu Y, Zhan S, Tomberlin JK, Huang D, Cai M, Zheng L, Yu Z, Zhang J. Dual oxidase Duox and Toll-like receptor 3 TLR3 in the Toll pathway suppress zoonotic pathogens through regulating the intestinal bacterial community homeostasis in Hermetia illucens L. PLoS One 2020; 15:e0225873. [PMID: 32352968 PMCID: PMC7192390 DOI: 10.1371/journal.pone.0225873] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/26/2020] [Indexed: 01/26/2023] Open
Abstract
Black soldier fly (BSF; Hermetia illucens L.) larvae can convert fresh pig manure into protein and fat-rich biomass, which can then be used as aquafeed for select species. Currently, BSF is the only approved insect for such purposes in Canada, USA, and the European Union. Pig manure could serve as a feed substrate for BSF; however, it is contaminated with zoonotic pathogens (e.g., Staphylococcus aureus and Salmonella spp.). Fortunately, BSF larvae inhibit many of these zoonotic pathogens; however, the mechanisms employed are unclear. We employed RNAi, qRT-PCR, and Illumina MiSeq 16S rDNA high-throughput sequencing to examine the interaction between two immune genes (Duox in Duox-reactive oxygen species [ROS] immune system and TLR3 in the Toll signaling pathway) and select pathogens common in pig manure to decipher the mechanisms resulting in pathogen suppression. Results indicate Bsf Duox-TLR3 RNAi increased bacterial load but decreased relative abundance of Providencia and Dysgonomonas, which are thought to be commensals in the BSF larval gut. Bsf Duox-TLR3 RNAi also inactivated the NF-κB signaling pathway, downregulated the expression of antimicrobial peptides, and diminished inhibitory effects on zoonotic pathogen. The resulting dysbiosis stimulated an immune response by activating BsfDuox and promoting ROS, which regulated the composition and structure of the gut bacterial community. Thus, BsfDuox and BsfTLR3 are important factors in regulating these key gut microbes, while inhibiting target zoonotic pathogens.
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Affiliation(s)
- Yaqing Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongqiang Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuai Zhan
- Institute of Plant Physiology & Ecology, SIBS, CAS, Shanghai, China
| | | | - Dian Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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37
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Chen T, Nomura K, Wang X, Sohrabi R, Xu J, Yao L, Paasch BC, Ma L, Kremer J, Cheng Y, Zhang L, Wang N, Wang E, Xin XF, He SY. A plant genetic network for preventing dysbiosis in the phyllosphere. Nature 2020; 580:653-657. [PMID: 32350464 PMCID: PMC7197412 DOI: 10.1038/s41586-020-2185-0] [Citation(s) in RCA: 218] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/19/2020] [Indexed: 12/31/2022]
Abstract
The aboveground parts of terrestrial plants, collectively called the phyllosphere, have a key role in the global balance of atmospheric carbon dioxide and oxygen. The phyllosphere represents one of the most abundant habitats for microbiota colonization. Whether and how plants control phyllosphere microbiota to ensure plant health is not well understood. Here we show that the Arabidopsis quadruple mutant (min7 fls2 efr cerk1; hereafter, mfec)1, simultaneously defective in pattern-triggered immunity and the MIN7 vesicle-trafficking pathway, or a constitutively activated cell death1 (cad1) mutant, carrying a S205F mutation in a membrane-attack-complex/perforin (MACPF)-domain protein, harbour altered endophytic phyllosphere microbiota and display leaf-tissue damage associated with dysbiosis. The Shannon diversity index and the relative abundance of Firmicutes were markedly reduced, whereas Proteobacteria were enriched in the mfec and cad1S205F mutants, bearing cross-kingdom resemblance to some aspects of the dysbiosis that occurs in human inflammatory bowel disease. Bacterial community transplantation experiments demonstrated a causal role of a properly assembled leaf bacterial community in phyllosphere health. Pattern-triggered immune signalling, MIN7 and CAD1 are found in major land plant lineages and are probably key components of a genetic network through which terrestrial plants control the level and nurture the diversity of endophytic phyllosphere microbiota for survival and health in a microorganism-rich environment.
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Affiliation(s)
- Tao Chen
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.,State Key Laboratory of Agriculture Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, China.,Howard Hughes Medical Institute, Michigan State University, East Lansing, MI, USA
| | - Kinya Nomura
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Xiaolin Wang
- National key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Reza Sohrabi
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, USA
| | - Lingya Yao
- National key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Bradley C. Paasch
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Li Ma
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - James Kremer
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Yuti Cheng
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.,Howard Hughes Medical Institute, Michigan State University, East Lansing, MI, USA
| | - Li Zhang
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.,Howard Hughes Medical Institute, Michigan State University, East Lansing, MI, USA
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida, USA
| | - Ertao Wang
- National key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiu-Fang Xin
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China. .,CAS-JIC Center of Excellence for Plant and Microbial Sciences (CEPAMS), Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Sheng Yang He
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, USA. .,Howard Hughes Medical Institute, Michigan State University, East Lansing, MI, USA. .,Plant Resilience Institute, Michigan State University, East Lansing, MI, USA.
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38
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Sung J. Inflammatory bowel disease: Is East really differ from West? J Gastroenterol Hepatol 2020; 35:357-358. [PMID: 32162386 DOI: 10.1111/jgh.15003] [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: 12/09/2022]
Affiliation(s)
- Joseph Sung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China.,Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
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39
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Attenuation of DSS induced colitis by Dictyophora indusiata polysaccharide (DIP) via modulation of gut microbiota and inflammatory related signaling pathways. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103641] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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40
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Aggeletopoulou I, Konstantakis C, Assimakopoulos SF, Triantos C. The role of the gut microbiota in the treatment of inflammatory bowel diseases. Microb Pathog 2019; 137:103774. [PMID: 31586663 DOI: 10.1016/j.micpath.2019.103774] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 02/07/2023]
Abstract
The human intestinal microbiota coevolves with its host through a symbiotic relationship and exerts great influence on substantial functions including aspects of physiology, metabolism, nutrition and regulation of immune responses leading to physiological homeostasis. Over the last years, several studies have been conducted toward the assessment of the host-gut microbiota interaction, aiming to elucidate the mechanisms underlying the pathogenesis of several diseases. A defect on the microbiota-host crosstalk and the concomitant dysregulation of immune responses combined with genetic and environmental factors have been implicated in the pathogenesis of inflammatory bowel diseases (IBD). To this end, novel therapeutic options based on the gut microbiota modulation have been an area of extensive research interest. In this review we present the recent findings on the association of dysbiosis with IBD pathogenesis, we focus on the role of gut microbiota on the treatment of IBD and discuss the novel and currently available therapeutic strategies in manipulating the composition and function of gut microbiota in IBD patients. Applicable and emerging microbiota treatment modalities, such as the use of antibiotics, prebiotics, probiotics, postbiotics, synbiotics and fecal microbiota transplantation (FMT) constitute promising therapeutic options. However, the therapeutic potential of the aforementioned approaches is a topic of investigation and further studies are needed to elucidate their position in the present treatment algorithms of IBD.
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Affiliation(s)
- Ioanna Aggeletopoulou
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, 26504, Greece.
| | - Christos Konstantakis
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, 26504, Greece.
| | | | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, 26504, Greece.
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41
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Pigneur B, Ruemmele FM. Nutritional interventions for the treatment of IBD: current evidence and controversies. Therap Adv Gastroenterol 2019; 12:1756284819890534. [PMID: 31803252 PMCID: PMC6878599 DOI: 10.1177/1756284819890534] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 10/22/2019] [Indexed: 02/04/2023] Open
Abstract
Environmental factors, particularly diet, are the focus of current research as potential triggers of inflammatory bowel disease (IBD). Epidemiological cohort data showing a rapid increase of IBD in western countries and the emergence of IBD in developing countries paralleling the introduction of a western diet are indirect arguments linking food and food behaviour to intestinal inflammation. The successful use of exclusive enteral nutrition (EEN), now considered as first-line induction therapy for paediatric Crohn's disease (CD), is the strongest argument for a link between diet and IBD. Mechanistic studies revealed that EEN impacts intestinal microbiota composition and together with the exclusion of potentially harmful food ingredients this allows the control of intestinal inflammation and induces mucosal healing. However, the exclusivity character of EEN is a major drawback. Based on the data of EEN, the search for more tolerable and still effective diets has begun. Recent reports on the new CD exclusion diet (CDED), CD-TREAT, as well as the specific carbohydrate diet (SCD) provide the first promising results, further underlining the potential of diet to control inflammation in patients with CD by excluding certain food components. Ongoing research is trying to combine nutritional interventions with analyses of intestinal microbiota and their metabolic functions with the aim of correcting the intestinal dysbiosis that characterizes IBD. This research is promising and gives new hope to patients that have been looking for decades for nutritional interventions with the aim of stabilizing their disease course. There might even be potential for disease prevention in high-risk patients by excluding potentially harmful food components.
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Affiliation(s)
- Bénédicte Pigneur
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France,Assistance Publique-Hôpitaux de Paris, Hôpital Necker-Enfants Malades, Service de Gastroentérologie pédiatrique, Paris, France
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Cai Y, Liu W, Lin Y, Zhang S, Zou B, Xiao D, Lin L, Zhong Y, Zheng H, Liao Q, Xie Z. Compound polysaccharides ameliorate experimental colitis by modulating gut microbiota composition and function. J Gastroenterol Hepatol 2019; 34:1554-1562. [PMID: 30589960 DOI: 10.1111/jgh.14583] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIM Inflammatory bowel disease results from a dysregulated immune response to intestinal microbial flora in individuals with genetic predisposition(s). This study aimed to determine the effects of compound polysaccharides (CP) containing yam polysaccharide and inulin on the rat model of colitis induced by 2,4,6-trinitrobenzenesulfonic acid (TNBS) and to explain the mechanism in terms of gut microbiota composition and function. METHODS Male SD rats were divided into three groups: the control group, the model group, and the CP group. Disease activity index, serum myeloperoxidase level, and the composition and function of gut microbiota were analyzed. RESULTS The data in the study showed CP reduced inflammation in the rat model of colitis induced by TNBS and ameliorated the experimental colitis. The results also indicated that CP not only reversed TNBS-induced gut dysbiosis-indexed by increased short-chain fatty acids (SCFAs)-producing bacteria, lactic acid-producing bacteria, and decreased Bacteroides, Proteobacteria as well as sulfate-reducing bacteria, but also restored the dysregulated microbiota function of colitic rats into a normal condition, including an improvement on basic metabolism and a reduction on oxidative stress, cell motility, signal transduction, xenobiotics biodegradation, and metabolism as well as pathogenesis processes. CONCLUSIONS Compound polysaccharides ameliorated the experimental colitis of rats induced by TNBS by modulating the gut microbiota composition and function profiles, which makes it possible to be used as prebiotic agents to treat gut dysbiosis in colitis individuals.
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Affiliation(s)
- Ying Cai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Wen Liu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Yixuan Lin
- School of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shaobao Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Baorong Zou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Dan Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Lei Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuping Zhong
- School of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haihui Zheng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiongfeng Liao
- School of Chinese Materia Medica, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhiyong Xie
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, China.,School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, China
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Pigneur B, Lepage P, Mondot S, Schmitz J, Goulet O, Doré J, Ruemmele FM. Mucosal Healing and Bacterial Composition in Response to Enteral Nutrition Vs Steroid-based Induction Therapy-A Randomised Prospective Clinical Trial in Children With Crohn's Disease. J Crohns Colitis 2019; 13:846-855. [PMID: 30541015 DOI: 10.1093/ecco-jcc/jjy207] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
AIMS Exclusive enteral nutrition [EEN] is as efficacious as corticosteroids [CS] to induce remission in Crohn's disease [CD], without their adverse effects. EEN seems to be more efficient than steroids to induce mucosal healing, but the underlying molecular mechanisms are only sparsely understood. We aimed in the present work to study the anti-inflammatory effects of EEN with Modulen IBD® vs CS in active paediatric CD, and to assess its modulatory effects on the intestinal microbiota as compared with steroids. MATERIALS AND METHODS Nineteen patients with new-onset active CD (Harvey-Bradshaw index [HBI] >5), aged from 6 to 17 years, were included in this prospective randomised induction trial with CS [n = 6] or EEN [n = 13]. Patients were assessed at Weeks 0 and 8 using clinical parameters HBI, endoscopic findings (Crohn's Disease Endoscopic Index of Severity [CDEIS] score) and analysis of faecal microbiota composition. RESULTS At 8 weeks, clinical remission [HBI <5] was achieved in 13/13 patients on EEN and 5/6 patients on steroids; the mucosal healing rate was significantly higher in the EEN [89%] compared with steroid group [17%]. There were no significant differences between groups regarding biological markers, but the intestinal microbiota profiles shifted upon EEN-induced remission to a higher proportion of Ruminococcus bacteria compared with steroid-induced remission [p = 0.049], and with higher proportions of bacteria belonging to Clostridium in EEN-treated patients. CONCLUSIONS Both steroid and EEN induced clinical remission. However, patients with EEN-induced remission showed a higher rate of mucosal healing and this was associated with a different gut microbiota compositional shift in these children.
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Affiliation(s)
- Bénédicte Pigneur
- Hôpital Necker Enfants Malades Université Sorbonne Paris Cité, Paris, APHP.,INSERM UMR1163, Laboratory of Intestinal Immunity, Institut Imagine, Paris, France
| | - Patricia Lepage
- Micalis Institute, INRA, University Paris-Saclay, Jouy-en-Josas, France
| | - Stanislas Mondot
- Micalis Institute, INRA, University Paris-Saclay, Jouy-en-Josas, France
| | - Jacques Schmitz
- Hôpital Necker Enfants Malades Université Sorbonne Paris Cité, Paris, APHP
| | - Olivier Goulet
- Hôpital Necker Enfants Malades Université Sorbonne Paris Cité, Paris, APHP
| | - Joël Doré
- INRA, Metagenopolis, Jouy-en-Josas, France
| | - Frank M Ruemmele
- Hôpital Necker Enfants Malades Université Sorbonne Paris Cité, Paris, APHP.,INSERM UMR1163, Laboratory of Intestinal Immunity, Institut Imagine, Paris, France
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Huang C, Shi G. Smoking and microbiome in oral, airway, gut and some systemic diseases. J Transl Med 2019; 17:225. [PMID: 31307469 PMCID: PMC6632217 DOI: 10.1186/s12967-019-1971-7] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/05/2019] [Indexed: 12/24/2022] Open
Abstract
The human microbiome harbors a diverse array of microbes which establishes a mutually beneficial relation with the host in healthy conditions, however, the dynamic homeostasis is influenced by both host and environmental factors. Smoking contributes to modifications of the oral, lung and gut microbiome, leading to various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn’s disease, ulcerative colitis and cancers. However, the exact causal relationship between smoking and microbiome alteration remains to be further explored.
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Affiliation(s)
- Chunrong Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025, People's Republic of China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025, People's Republic of China
| | - Guochao Shi
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025, People's Republic of China. .,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, 197, Rui Jin Er Road, Shanghai, 200025, People's Republic of China.
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Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol 2019; 4:293-305. [PMID: 30531976 PMCID: PMC6342642 DOI: 10.1038/s41564-018-0306-4] [Citation(s) in RCA: 929] [Impact Index Per Article: 185.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 10/25/2018] [Indexed: 12/13/2022]
Abstract
The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome-the molecular interface between host and microbiota-are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic 'guilt by association' (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.
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Affiliation(s)
- Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | | | | | | | - Henry J Haiser
- Novartis Institute for Biomedical Research Inc., Cambridge, MA, USA
| | - Stefan Reinker
- Novartis Institute for Biomedical Research Inc., Cambridge, MA, USA
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Himel Mallick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Lauren J McIver
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Jenny S Sauk
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robin G Wilson
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Betsy W Stevens
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Kerry Pierce
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy A Deik
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin Bullock
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jeffrey A Porter
- Novartis Institute for Biomedical Research Inc., Basel, Switzerland
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
| | - Clary B Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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The Microbiome in Patients With Inflammatory Diseases. Clin Gastroenterol Hepatol 2019; 17:243-255. [PMID: 30196163 DOI: 10.1016/j.cgh.2018.08.078] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/17/2018] [Accepted: 08/24/2018] [Indexed: 02/07/2023]
Abstract
Microbial dysbiosis characterized by alterations in the structure and function of the gut microbiome has long been implicated in the pathogenesis of inflammatory bowel disease (IBD). To date, most human IBD microbiome studies are focused on microbial composition rather than function, however, with the latest technical advancements complemented by the rapidly dropping costs, studies focusing on the functional aspects of microbial dysbiosis are on the rise. Several compelling and complimentary pieces of evidence support the notion that the gut microbiome and their metabolites play an important role in the development of IBD. Data from preclinical studies overwhelmingly support the notion that changes in the gut microbiome causally underlie IBD pathogenesis. Hence, there is considerable interest in modulating the state and function of the gut microbiome to achieve therapeutic benefits. While the causal potential of the gut microbiome remains an active area of current research in the clinical setting, accumulating correlative evidence support the view that microbial dysbiosis parallels increased incidence of IBD. In this review, we intend to provide a brief overview of the current human IBD microbiome findings, describe the cause-effect relationships between the gut microbiome and IBD, and discuss the possibility of using microbiome-based approaches in the diagnosis, therapy, and management of disease. In addition, the potential role of microbiome-based interventions in the treatment of human IBD is also discussed.
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Li Y, Xie Z, Gao T, Li L, Chen Y, Xiao D, Liu W, Zou B, Lu B, Tian X, Han B, Guo Y, Zhang S, Lin L, Wang M, Li P, Liao Q. A holistic view of gallic acid-induced attenuation in colitis based on microbiome-metabolomics analysis. Food Funct 2019; 10:4046-4061. [DOI: 10.1039/c9fo00213h] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GA enema can treat UC by influencing microbiota-mediated metabolism.
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48
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Metagenome Analysis as a Tool to Study Bacterial Infection Associated with Acute Surgical Abdomen. J Clin Med 2018; 7:jcm7100346. [PMID: 30322074 PMCID: PMC6210133 DOI: 10.3390/jcm7100346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/02/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022] Open
Abstract
Background: The purpose of this study was to profile the bacterium in the ascites and blood of patients with acute surgical abdomen by metagenome analysis. Methods: A total of 97 patients with acute surgical abdomen were included in this study. Accompanied with the standard culture procedures, ascites and blood samples were collected for metagenome analysis to measure the relative abundance of bacteria among groups of patients and between blood and ascites. Results: Metagenomic analysis identified 107 bacterial taxa from the ascites of patients. A principal component analysis (PCA) could separate the bacteria of ascites into roughly three groups: peptic ulcer, perforated or non-perforated appendicitis, and a group which included cholecystitis, small bowel lesion, and colon perforation. Significant correlation between the bacteria of blood and ascites was found in nine bacterial taxa both in blood and ascites with more than 500 sequence reads. However, the PCA failed to separate the variation in the bacteria of blood into different groups of patients, and the bacteria of metagenomic analysis is only partly in accordance with those isolated from a conventional culture method. Conclusion: This study indicated that the metagenome analysis can provide limited information regarding the bacteria in the ascites and blood of patients with acute surgical abdomen.
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Lopez-Siles M, Enrich-Capó N, Aldeguer X, Sabat-Mir M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects. Front Cell Infect Microbiol 2018; 8:281. [PMID: 30245977 PMCID: PMC6137959 DOI: 10.3389/fcimb.2018.00281] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 07/25/2018] [Indexed: 12/21/2022] Open
Abstract
Akkermansia muciniphila and Faecalibacterium prausnitzii, cohabitants in the intestinal mucosa, are considered members of a healthy microbiota and reduction of both species occurs in several intestinal disorders, including inflammatory bowel disease. Little is known however about a possible link between the reduction in quantity of these species, and in which circumstances this may occur. This study aims to determine the abundances and co-occurrence of the two species in order to elucidate conditions that may compromise their presence in the gut. Loads of A. muciniphila, total F. prausnitzii and its two phylogroup (16S rRNA gene copies) were determined by quantitative polymerase chain reaction in colonic biopsies from 17 healthy controls (H), 23 patients with ulcerative colitis (UC), 31 patients with Crohn's disease (CD), 3 with irritable bowel syndrome (IBS) and 3 with colorectal cancer (CRC). Data were normalized to total bacterial 16S rRNA gene copies in the same sample. Prevalence, relative abundances and correlation analyses were performed according to type of disease and considering relevant clinical characteristics of patients such as IBD location, age of disease onset, CD behavior, current medication and activity status. Co-occurrence of both species was found in 29% of H, 65% of UC and 29% of CD. Lower levels of total F. prausnitzii and phylogroups were found in subjects with CD, compared with H subjects (P ≤ 0.044). In contrast, no differences were found with the regard to A. muciniphila abundance across different disease states, but CD patients with disease onset below 16 years of age featured a marked depletion of this species. In CD patients, correlation between A. muciniphila and total F. prausnitzii (ρ = 0.362, P = 0.045) was observed, and particularly in those with non-stricturing, non-penetrating disease behavior and under moderate immunosuppressants therapy. Altogether, this study revealed that co-occurrence of both species differs between disease status. In addition, IBD patients featured a reduction of F. prausnitzii but similar loads of A. muciniphila when compared to H subjects, with the exception of those with early onset CD. Depletion of A. muciniphila in this subgroup of subjects suggests that it could be a potential biomarker to assist in pediatric CD diagnosis.
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Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Núria Enrich-Capó
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Xavier Aldeguer
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Spain
| | - Miriam Sabat-Mir
- Department of Gastroenterology, Hospital Santa Caterina, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, Aberdeen, United Kingdom
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
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Sunkara T, Rawla P, Ofosu A, Gaduputi V. Fecal microbiota transplant - a new frontier in inflammatory bowel disease. J Inflamm Res 2018; 11:321-328. [PMID: 30214266 PMCID: PMC6124474 DOI: 10.2147/jir.s176190] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic multifactorial disease that affects the gastrointestinal tract and results from an aberrant immune response toward luminal antigens in genetically susceptible people. Most of the current therapies for IBD focus on the management of the inflammation by using corticosteroids, immune modulators, and more recently, monoclonal antibodies (biological therapy). Although these therapies provide benefit in most cases, there are still a significant number of patients who do not respond or become refractory over time, suggesting the need for alternative therapeutic options. In the last decade, it has been recognized that "dysbiosis," an imbalanced gut microbiota, is a key element in IBD suggesting microbiome-based therapies as an attractive approach. Recently, fecal microbiota transplant (FMT) has been successfully used for the treatment of Clostridium difficile infection, and it is now under investigation for the treatment of IBD. Clinical trials data are still poor but strongly support a future introduction of FMT in therapy to manage IBD microbiome. More studies are needed to assess the optimal route of administration and the frequency of FMT, the best matched donor for each patient as well as the risks associated with FMT in IBD.
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Affiliation(s)
- Tagore Sunkara
- Division of Gastroenterology and Hepatology, The Brooklyn Hospital Center, Mount Sinai Health System, New York, NY, USA
| | - Prashanth Rawla
- Department of Internal Medicine, Sovah Health, Martinsville, VA, USA,
| | - Andrew Ofosu
- Division of Gastroenterology and Hepatology, The Brooklyn Hospital Center, Mount Sinai Health System, New York, NY, USA
| | - Vinaya Gaduputi
- Division of Gastroenterology, SBH Health System, Bronx, NY, USA
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