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Montrose JA, Kurada S, Fischer M. Current and future microbiome-based therapies in inflammatory bowel disease. Curr Opin Gastroenterol 2024; 40:258-267. [PMID: 38841848 DOI: 10.1097/mog.0000000000001027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
PURPOSE OF REVIEW The role of the microbiome and dysbiosis is increasingly recognized in the pathogenesis of inflammatory bowel disease (IBD). Intestinal microbiota transplant (IMT), previously termed fecal microbiota transplant has demonstrated efficacy in restoring a healthy microbiome and promoting gut health in recurrent Clostridioides difficile infection. Several randomized trials (RCTs) highlighted IMT's potential in treating ulcerative colitis, while smaller studies reported on its application in managing Crohn's disease and pouchitis. RECENT FINDINGS This review delves into the current understanding of dysbiosis in IBD, highlighting the distinctions in the microbiota of patients with IBD compared to healthy controls. It explores the mechanisms by which IMT can restore a healthy microbiome and provides a focused analysis of recent RCTs using IMT for inducing and maintaining remission in IBD. Lastly, we discuss the current knowledge gaps that limit its widespread use. SUMMARY The body of evidence supporting the use of IMT in IBD is growing. The lack of a standardized protocol impedes its application beyond clinical trials. Further research is needed to identify patient profile and disease phenotypes that benefit from IMT, to delineate key donor characteristics, optimize the delivery route, dosage, and frequency.
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Affiliation(s)
| | - Satya Kurada
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Monika Fischer
- Department of Medicine, Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Foppa C, Rizkala T, Repici A, Hassan C, Spinelli A. Microbiota and IBD: Current knowledge and future perspectives. Dig Liver Dis 2024; 56:911-922. [PMID: 38008696 DOI: 10.1016/j.dld.2023.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 11/28/2023]
Abstract
Inflammatory Bowel Disease (IBD) is a chronic relapsing-remitting disease with a remarkable increase in incidence worldwide and a substantial disease burden. Although the pathophysiology is not fully elucidated yet an aberrant immune reaction against the intestinal microbiota and the gut microbial dysbiosis have been identified to play a major role. The composition of gut microbiota in IBD patients is distinct from that of healthy individuals, with certain organisms predominating over others. Differences in the microbial dysbiosis have been also observed between Crohn Disease (CD) and Ulcerative Colitis (UC). A disruption of the microbiota's balance can lead to inflammation and intestinal damage. Microbiota composition in IBD can be affected both by endogenous (i.e., interaction with the immune system and intestinal epithelial cells) and exogenous (i.e., medications, surgery, diet) factors. The complex interplay between the gut microbiota and IBD is an area of great interest for understanding disease pathogenesis and developing new treatments. The purpose of this review is to summarize the latest evidence on the role of microbiota in IBD pathogenesis and to explore possible future areas of research.
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Affiliation(s)
- Caterina Foppa
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Colon and Rectal Surgery, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Tommy Rizkala
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy
| | - Alessandro Repici
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Gastroenterology and Digestive Endoscopy Unit, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Cesare Hassan
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Gastroenterology and Digestive Endoscopy Unit, via Manzoni 56, Rozzano, 20089, Milan, Italy
| | - Antonino Spinelli
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20090, Milan, Italy; IRCCS Humanitas Research Hospital, Division of Colon and Rectal Surgery, via Manzoni 56, Rozzano, 20089, Milan, Italy.
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3
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Xu C, Jiang H, Feng LJ, Jiang MZ, Wang YL, Liu SJ. Christensenella minuta interacts with multiple gut bacteria. Front Microbiol 2024; 15:1301073. [PMID: 38440147 PMCID: PMC10910051 DOI: 10.3389/fmicb.2024.1301073] [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: 09/24/2023] [Accepted: 01/30/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction Gut microbes form complex networks that significantly influence host health and disease treatment. Interventions with the probiotic bacteria on the gut microbiota have been demonstrated to improve host well-being. As a representative of next-generation probiotics, Christensenella minuta (C. minuta) plays a critical role in regulating energy balance and metabolic homeostasis in human bodies, showing potential in treating metabolic disorders and reducing inflammation. However, interactions of C. minuta with the members of the networked gut microbiota have rarely been explored. Methods In this study, we investigated the impact of C. minuta on fecal microbiota via metagenomic sequencing, focusing on retrieving bacterial strains and coculture assays of C. minuta with associated microbial partners. Results Our results showed that C. minuta intervention significantly reduced the diversity of fecal microorganisms, but specifically enhanced some groups of bacteria, such as Lactobacillaceae. C. minuta selectively enriched bacterial pathways that compensated for its metabolic defects on vitamin B1, B12, serine, and glutamate synthesis. Meanwhile, C. minuta cross-feeds Faecalibacterium prausnitzii and other bacteria via the production of arginine, branched-chain amino acids, fumaric acids and short-chain fatty acids (SCFAs), such as acetic. Both metagenomic data analysis and culture experiments revealed that C. minuta negatively correlated with Klebsiella pneumoniae and 14 other bacterial taxa, while positively correlated with F. prausnitzii. Our results advance our comprehension of C. minuta's in modulating the gut microbial network. Conclusions C. minuta disrupts the composition of the fecal microbiota. This disturbance is manifested through cross-feeding, nutritional competition, and supplementation of its own metabolic deficiencies, resulting in the specific enrichment or inhibition of the growth of certain bacteria. This study will shed light on the application of C. minuta as a probiotic for effective interventions on gut microbiomes and improvement of host health.
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Affiliation(s)
- Chang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Li-Juan Feng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Lin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Chechushkov A, Desyukevich P, Yakovlev T, Al Allaf L, Shrainer E, Morozov V, Tikunova N. Sterile Fecal Microbiota Transplantation Boosts Anti-Inflammatory T-Cell Response in Ulcerative Colitis Patients. Int J Mol Sci 2024; 25:1886. [PMID: 38339169 PMCID: PMC10856413 DOI: 10.3390/ijms25031886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Ulcerative colitis is a chronic immune-mediated disease of unclear etiology, affecting people of different ages and significantly reducing the quality of life. Modern methods of therapy are mainly represented by anti-inflammatory drugs and are not aimed at a specific pathogenetic factor. In this study, we investigated the effect of transplantation of sterile stool filtrate from healthy donors on the induction of anti-inflammatory immune mechanisms. It was shown that performing such a procedure in patients with ulcerative colitis caused the appearance of T helper cells in the blood, which reacted to the content of sterile stool filtrates in an antigen-specific manner and produced IL-10. At the same time, cells of the same patients before therapy in response to the addition of sterile stool filtrates were less reactive and predominantly produced IL-4, indicating its pro-inflammatory skewing. The obtained data demonstrated the effect of an anti-inflammatory shift in the T-helper response after transplantation of sterile stool filtrate, which increased and persisted for at least three months after the procedure.
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Affiliation(s)
- Anton Chechushkov
- Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (E.S.); (V.M.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Pavel Desyukevich
- Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (E.S.); (V.M.)
| | - Timir Yakovlev
- Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (E.S.); (V.M.)
| | - Lina Al Allaf
- Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (E.S.); (V.M.)
| | - Evgeniya Shrainer
- Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (E.S.); (V.M.)
- Autonomous Non-Commercial Organization “Center of New Medical Technologies in Akademgorodok”, 630090 Novosibirsk, Russia
| | - Vitalyi Morozov
- Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (E.S.); (V.M.)
| | - Nina Tikunova
- Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia (E.S.); (V.M.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Fu Y, Lyu J, Wang S. The role of intestinal microbes on intestinal barrier function and host immunity from a metabolite perspective. Front Immunol 2023; 14:1277102. [PMID: 37876938 PMCID: PMC10591221 DOI: 10.3389/fimmu.2023.1277102] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
The gut is colonized by many commensal microorganisms, and the diversity and metabolic patterns of microorganisms profoundly influence the intestinal health. These microbial imbalances can lead to disorders such as inflammatory bowel disease (IBD). Microorganisms produce byproducts that act as signaling molecules, triggering the immune system in the gut mucosa and controlling inflammation. For example, metabolites like short-chain fatty acids (SCFA) and secondary bile acids can release inflammatory-mediated signals by binding to specific receptors. These metabolites indirectly affect host health and intestinal immunity by interacting with the intestinal epithelial and mucosal immune cells. Moreover, Tryptophan-derived metabolites also play a role in governing the immune response by binding to aromatic hydrocarbon receptors (AHR) located on the intestinal mucosa, enhancing the intestinal epithelial barrier. Dietary-derived indoles, which are synthetic precursors of AHR ligands, work together with SCFA and secondary bile acids to reduce stress on the intestinal epithelium and regulate inflammation. This review highlights the interaction between gut microbial metabolites and the intestinal immune system, as well as the crosstalk of dietary fiber intake in improving the host microbial metabolism and its beneficial effects on the organism.
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Affiliation(s)
- Yifeng Fu
- Department of Cardiology, The Affiliated Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling, Zhejiang, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Jin Lyu
- Department of Pathology, the First People’s Hospital of Foshan, Foshan, Guangdong, China
| | - Shuangshuang Wang
- Department of Cardiology, The Affiliated Wenling Hospital of Wenzhou Medical University (The First People’s Hospital of Wenling), Wenling, Zhejiang, China
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Rojas CA, Entrolezo Z, Jarett JK, Jospin G, Kingsbury DD, Martin A, Eisen JA, Ganz HH. Microbiome Responses to Fecal Microbiota Transplantation in Cats with Chronic Digestive Issues. Vet Sci 2023; 10:561. [PMID: 37756083 PMCID: PMC10537086 DOI: 10.3390/vetsci10090561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 09/02/2023] [Indexed: 09/28/2023] Open
Abstract
There is growing interest in the application of fecal microbiota transplants (FMTs) in small animal medicine, but there are few published studies that have tested their effects in the domestic cat (Felis catus). Here we use 16S rRNA gene sequencing to examine fecal microbiome changes in 46 domestic cats with chronic digestive issues that received FMTs using lyophilized stool that was delivered in oral capsules. Fecal samples were collected from FMT recipients before and two weeks after the end of the full course of 50 capsules, as well as from their stool donors (N = 10), and other healthy cats (N = 113). The fecal microbiomes of FMT recipients varied with host clinical signs and dry kibble consumption, and shifts in the relative abundances of Clostridium, Collinsella, Megamonas, Desulfovibrio and Escherichia were observed after FMT. Overall, donors shared 13% of their bacterial amplicon sequence variants (ASVs) with FMT recipients and the most commonly shared ASVs were classified as Prevotella 9, Peptoclostridium, Bacteroides, and Collinsella. Lastly, the fecal microbiomes of cats with diarrhea became more similar to the microbiomes of age-matched and diet-matched healthy cats compared to cats with constipation. Overall, our results suggest that microbiome responses to FMT may be modulated by the FMT recipient's initial presenting clinical signs, diet, and their donor's microbiome.
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Affiliation(s)
- Connie A. Rojas
- Genome Center, University of California, Davis, CA 95616, USA; (C.A.R.); (J.A.E.)
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Zhandra Entrolezo
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Jessica K. Jarett
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Guillaume Jospin
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Dawn D. Kingsbury
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Alex Martin
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
| | - Jonathan A. Eisen
- Genome Center, University of California, Davis, CA 95616, USA; (C.A.R.); (J.A.E.)
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Holly H. Ganz
- AnimalBiome, Oakland, CA 94609, USA; (Z.E.); (J.K.J.); (G.J.); (A.M.)
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Shtossel O, Turjeman S, Riumin A, Goldberg MR, Elizur A, Bekor Y, Mor H, Koren O, Louzoun Y. Recipient-independent, high-accuracy FMT-response prediction and optimization in mice and humans. MICROBIOME 2023; 11:181. [PMID: 37580821 PMCID: PMC10424414 DOI: 10.1186/s40168-023-01623-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 07/14/2023] [Indexed: 08/16/2023]
Abstract
BACKGROUND Some microbiota compositions are associated with negative outcomes, including among others, obesity, allergies, and the failure to respond to treatment. Microbiota manipulation or supplementation can restore a community associated with a healthy condition. Such interventions are typically probiotics or fecal microbiota transplantation (FMT). FMT donor selection is currently based on donor phenotype, rather than the anticipated microbiota composition in the recipient and associated health benefits. However, the donor and post-transplant recipient conditions differ drastically. We here propose an algorithm to identify ideal donors and predict the expected outcome of FMT based on donor microbiome alone. We also demonstrate how to optimize FMT for different required outcomes. RESULTS We show, using multiple microbiome properties, that donor and post-transplant recipient microbiota differ widely and propose a tool to predict the recipient post-transplant condition (engraftment success and clinical outcome), using only the donors' microbiome and, when available, demographics for transplantations from humans to either mice or other humans (with or without antibiotic pre-treatment). We validated the predictor using a de novo FMT experiment highlighting the possibility of choosing transplants that optimize an array of required goals. We then extend the method to characterize a best-planned transplant (bacterial cocktail) by combining the predictor and a generative genetic algorithm (GA). We further show that a limited number of taxa is enough for an FMT to produce a desired microbiome or phenotype. CONCLUSIONS Off-the-shelf FMT requires recipient-independent optimized FMT selection. Such a transplant can be from an optimal donor or from a cultured set of microbes. We have here shown the feasibility of both types of manipulations in mouse and human recipients. Video Abstract.
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Affiliation(s)
- Oshrit Shtossel
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel.
| | - Sondra Turjeman
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Alona Riumin
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael R Goldberg
- Yitzhak Shamir Medical Center (Assaf Harofeh), Zerifin, Israel
- Department of Pediatrics, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Arnon Elizur
- Yitzhak Shamir Medical Center (Assaf Harofeh), Zerifin, Israel
- Department of Pediatrics, Sackler Faculty of Medicine, Tel Aviv, Israel
| | - Yarin Bekor
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Hadar Mor
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, 52900, Israel.
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Kriger-Sharabi O, Malnick SDH, Fisher D. Manipulation of the intestinal microbiome-a slow journey to primetime. World J Clin Cases 2023; 11:4975-4988. [PMID: 37583860 PMCID: PMC10424025 DOI: 10.12998/wjcc.v11.i21.4975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/17/2023] [Accepted: 06/30/2023] [Indexed: 07/26/2023] Open
Abstract
The gut microbiota has important functions in the regulation of normal body functions. Alterations of the microbiota are being increasingly linked to various disease states. The microbiome has been manipulated via the administration of stool from animals or humans, for more than 1000 years. Currently, fecal microbiota transplantation can be performed via endoscopic administration of fecal matter to the duodenum or colon or via capsules of lyophilized stools. More recently fecal microbial transplantation has been shown to be very effective for recurrent Clostridoides difficile infection (CDI). In addition there is some evidence of efficacy in the metabolic syndrome and its hepatic manifestation, metabolic associated fatty liver disease (MAFLD), irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD). We review the current literature regarding the microbiome and the pathogenesis and treatment of CDI, MAFLD, IBS and IBD.
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Affiliation(s)
- Ofra Kriger-Sharabi
- Institute of Gastroenterology, Assuta Medical Center, Ashdod 7747629, Israel
| | - Stephen D H Malnick
- Department of Internal Medicine, Kaplan Medical Center, Rehovot 76100, Israel
| | - David Fisher
- Department of Endocrinology, Soroka Medical Center, Beer Sheva POB 151, Israel
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Chen Q, Fan Y, Zhang B, Yan C, Zhang Q, Ke Y, Chen Z, Wang L, Shi H, Hu Y, Huang Q, Su J, Xie C, Zhang X, Zhou L, Ren J, Xu H. Capsulized Fecal Microbiota Transplantation Induces Remission in Patients with Ulcerative Colitis by Gut Microbial Colonization and Metabolite Regulation. Microbiol Spectr 2023; 11:e0415222. [PMID: 37093057 PMCID: PMC10269780 DOI: 10.1128/spectrum.04152-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/30/2023] [Indexed: 04/25/2023] Open
Abstract
Fecal microbiota transplantation (FMT) can induce clinical remission in ulcerative colitis (UC) patients. Enemas, nasoduodenal tubes, and colonoscopies are the most common routes for FMT administration. However, there is a lack of definitive evidence regarding the effectiveness of capsulized FMT treatment in UC patients. In this study, we administered capsulized FMT to 22 patients with active UC to assess the efficiency of capsulized FMT and determine the specific bacteria and metabolite factors associated with the response to clinical remission. Our results showed that the use of capsulized FMT was successful in the treatment of UC patients. Capsulized FMT induced clinical remission and clinical response in 57.1% (12 of 21) and 76.2% (16 of 21) of UC patients, respectively. Gut bacterial richness was increased after FMT in patients who achieved remission. Patients in remission after FMT exhibited enrichment of Alistipes sp. and Odoribacter splanchnicus, along with increased levels of indolelactic acid. Patients who did not achieve remission exhibited enrichment of Escherichia coli and Klebsiella and increased levels of biosynthesis of 12,13-DiHOME (12,13-dihydroxy-9Z-octadecenoic acid) and lipopolysaccharides. Furthermore, we identified a relationship between specific bacteria and metabolites and the induction of remission in patients. These findings may provide new insights into FMT in UC treatment and provide reference information about therapeutic microbial manipulation of FMT to enhance its effects. (This study has been registered at ClinicalTrails.gov under registration no. NCT03426683). IMPORTANCE Fecal microbiota transplantation has been successfully used in patients. Recently, capsulized FMT was reported to induce a response in patients with UC. However, limited patients were enrolled in such studies, and the functional factors of capsulized FMT have not been reported in the remission of patients with UC. In this study, we prospectively recruited patients with UC to receive capsulized FMT. First, we found that capsulized FMT could induce clinical remission in 57.1% of patients and clinical response in 76.2% after 12 weeks, which was more acceptable. Second, we found a relationship between the decrease of opportunistic pathogen and lipopolysaccharide synthesis in patients in remission after capsulized FMT. We also identified an association between specific bacteria and metabolites and remission induction in patients after capsulized FMT. These findings put forward a possibility for patients to receive FMT at home and provide reference information about therapeutic microbial manipulation of FMT to enhance its effects.
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Affiliation(s)
- Qiongyun Chen
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Yanyun Fan
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Bangzhou Zhang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Changsheng Yan
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Qiang Zhang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yuhao Ke
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Zhangran Chen
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Lin Wang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Huaxiu Shi
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yiqun Hu
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Qingwen Huang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jingling Su
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Chenxi Xie
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Xu Zhang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Lixiang Zhou
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jianlin Ren
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Zhongshan Hospital of Xiamen University, Xiamen, China
- Department of Digestive Disease, School of Medicine, Xiamen University, Xiamen, China
| | - Hongzhi Xu
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Zhongshan Hospital of Xiamen University, Xiamen, China
- Department of Digestive Disease, School of Medicine, Xiamen University, Xiamen, China
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Xue JC, Yuan S, Meng H, Hou XT, Li J, Zhang HM, Chen LL, Zhang CH, Zhang QG. The role and mechanism of flavonoid herbal natural products in ulcerative colitis. Biomed Pharmacother 2023; 158:114086. [PMID: 36502751 DOI: 10.1016/j.biopha.2022.114086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory disease of the intestine that presents clinically with abdominal pain, mucopurulent stools, and posterior urgency. The lesions of UC are mainly concentrated in the rectal and colonic mucosa and submucosa. For patients with mild to moderate UC, the best pharmacological treatment includes glucocorticoids, immunosuppressants, antibiotics, and biologics, but the long-term application can have serious toxic side effects. Currently, nearly 40% of UC patients are treated with herbal natural products in combination with traditional medications to reduce the incidence of toxic side effects. Flavonoid herbal natural products are the most widely distributed polyphenols in plants and fruits, which have certain antioxidant and anti-inflammatory activities. Flavonoid herbal natural products have achieved remarkable efficacy in the treatment of UC. The pharmacological mechanisms are related to anti-inflammation, promotion of mucosal healing, maintenance of intestinal immune homeostasis, and regulation of intestinal flora. In this paper, we summarize the flavonoid components of anti-ulcerative colitis and their mechanisms reported in the past 10 years, to provide a basis for rational clinical use and the development of new anti-ulcerative colitis drugs.
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Affiliation(s)
- Jia-Chen Xue
- Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, Jilin Province 133002, China
| | - Shuo Yuan
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning Province 116622, China; Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin Province 133002, China
| | - Huan Meng
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning Province 116622, China
| | - Xiao-Ting Hou
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning Province 116622, China
| | - Jiao Li
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning Province 116622, China
| | - Hua-Min Zhang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning Province 116622, China; Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin Province 133002, China
| | - Li-Li Chen
- Jinan People's Hospital, Jinan, Shandong Province 271100, China
| | - Cheng-Hao Zhang
- Department of Oral Teaching and Research, Yanbian University, Yanji, Jilin Province 133000, China.
| | - Qing-Gao Zhang
- Department of Immunology and Pathogenic Biology, Yanbian University College of Basic Medicine, Yanji, Jilin Province 133002, China; Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning Province 116622, China.
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11
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DuPont HL, Jiang ZD, Alexander AS, DuPont AW, Brown EL. Intestinal IgA-Coated Bacteria in Healthy- and Altered-Microbiomes (Dysbiosis) and Predictive Value in Successful Fecal Microbiota Transplantation. Microorganisms 2022; 11:microorganisms11010093. [PMID: 36677385 PMCID: PMC9862469 DOI: 10.3390/microorganisms11010093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/17/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
IgA-coated bacteria in the gut (IgA-biome) provide a homeostatic function in healthy people through inhibition of microbial invaders and by protecting the epithelial monolayer of the gut. The laboratory methods used to detect this group of bacteria require flow cytometry and DNA sequencing (IgA-Seq). With dysbiosis (reduced diversity of the microbiome), the IgA-biome also is impaired. In the presence of enteric infection, oral vaccines, or an intestinal inflammatory disorder, the IgA-biome focuses on the pathogenic bacteria or foreign antigens, while in other chronic diseases associated with dysbiosis, the IgA-biome is reduced in capacity. Fecal microbiota transplantation (FMT), the use of fecal product from well-screened, healthy donors administered to patients with dysbiosis, has been successful in engrafting the intestine with healthy microbiota and metabolites leading to improve health. Through FMT, IgA-coated bacteria have been transferred to recipients retaining their immune coating. The IgA-biome should be evaluated in FMT studies as these mucosal-associated bacteria are more likely to be associated with successful transplantation than free luminal organisms. Studies of the microbiome pre- and post-FMT should employ metagenomic methods that identify bacteria at least at the species level to better identify organisms of interest while allowing comparisons of microbiota data between studies.
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Affiliation(s)
- Herbert L. DuPont
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX 77030, USA
- Kelsey Research Foundation, Houston, TX 77005, USA
- Correspondence: ; Tel.: +1-713-500-9366
| | - Zhi-Dong Jiang
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
| | | | - Andrew W. DuPont
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Eric L. Brown
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, USA
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12
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Huang Z, Liu K, Ma W, Li D, Mo T, Liu Q. The gut microbiome in human health and disease-Where are we and where are we going? A bibliometric analysis. Front Microbiol 2022; 13:1018594. [PMID: 36590421 PMCID: PMC9797740 DOI: 10.3389/fmicb.2022.1018594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022] Open
Abstract
Background There are trillions of microbiota in our intestinal tract, and they play a significant role in health and disease via interacting with the host in metabolic, immune, neural, and endocrine pathways. Over the past decades, numerous studies have been published in the field of gut microbiome and disease. Although there are narrative reviews of gut microbiome and certain diseases, the whole field is lack of systematic and quantitative analysis. Therefore, we outline research status of the gut microbiome and disease, and present insights into developments and characteristics of this field to provide a holistic grasp and future research directions. Methods An advanced search was carried out in the Web of Science Core Collection (WoSCC), basing on the term "gut microbiome" and its synonyms. The current status and developing trends of this scientific domain were evaluated by bibliometric methodology. CiteSpace was used to perform collaboration network analysis, co-citation analysis and citation burst detection. Results A total of 29,870 articles and 13,311 reviews were retrieved from the database, which involve 42,900 keywords, 176 countries/regions, 19,065 institutions, 147,225 authors and 4,251 journals. The gut microbiome and disease research is active and has received increasing attention. Co-cited reference analysis revealed the landmark articles in the field. The United States had the largest number of publications and close cooperation with other countries. The current research mainly focuses on gastrointestinal diseases, such as inflammatory bowel disease (IBD), ulcerative colitis (UC) and Crohn's disease (CD), while extra-intestinal diseases are also rising, such as obesity, diabetes, cardiovascular disease, Alzheimer's disease, Parkinson's disease. Omics technologies, fecal microbiota transplantation (FMT) and metabolites linked to mechanism would be more concerned in the future. Conclusion The gut microbiome and disease has been a booming field of research, and the trend is expected to continue. Overall, this research field shows a multitude of challenges and great opportunities.
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13
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Zhang X, Ishikawa D, Ohkusa T, Fukuda S, Nagahara A. Hot topics on fecal microbiota transplantation for the treatment of inflammatory bowel disease. Front Med (Lausanne) 2022; 9:1068567. [PMID: 36530877 PMCID: PMC9755187 DOI: 10.3389/fmed.2022.1068567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/21/2022] [Indexed: 11/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic intestinal mucosal inflammatory disease with complex etiology. Traditional anti-inflammatory treatment regimens have yielded unsatisfactory results. As research continues to deepen, it has been found that the gut microbiota of patients with IBD is generally altered. The presence of microorganisms in the human gastrointestinal tract is inextricably linked to the regulation of health and disease. Disruption of the microbiotic balance of microbiota in the gastrointestinal tract is called dysbiosis, which leads to disease. Therefore, in recent years, the exploration of therapeutic methods to restore the homeostasis of the gut microbiota has attracted attention. Moreover, the use of the well-established fecal microbiota transplantation (FMT) regimen for the treatment of Clostridioides difficile infection has attracted the interest of IBD researchers. Therefore, there are an increasing number of clinical studies regarding FMT for IBD treatment. However, a series of questions regarding FMT in the treatment of IBD warrants further investigation and discussion. By reviewing published studies, this review explored hot topics such as the efficacy, safety, and administration protocol flow of FMT in the treatment of IBD. Different administration protocols have generally shown reassuring results with significant efficacy and safety. However, the FMT treatment regimen needs to be further optimized. We believe that in the future, individual customized or standard FMT implementation will further enhance the relevance of FMT in the treatment of IBD.
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Affiliation(s)
- Xiaochen Zhang
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo, Japan
| | - Dai Ishikawa
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo, Japan
- Department of Regenerative Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Toshifumi Ohkusa
- Department of Microbiota Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Gastroenterology and Hepatology, The Jikei University Kashiwa Hospital, Chiba, Japan
| | - Shinji Fukuda
- Department of Regenerative Microbiology, Juntendo University School of Medicine, Tokyo, Japan
| | - Akihito Nagahara
- Department of Gastroenterology, Juntendo University School of Medicine, Tokyo, Japan
- Department of Regenerative Microbiology, Juntendo University School of Medicine, Tokyo, Japan
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14
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Biazzo M, Deidda G. Fecal Microbiota Transplantation as New Therapeutic Avenue for Human Diseases. J Clin Med 2022; 11:jcm11144119. [PMID: 35887883 PMCID: PMC9320118 DOI: 10.3390/jcm11144119] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
The human body is home to a variety of micro-organisms. Most of these microbial communities reside in the gut and are referred to as gut microbiota. Over the last decades, compelling evidence showed that a number of human pathologies are associated with microbiota dysbiosis, thereby suggesting that the reinstatement of physiological microflora balance and composition might ameliorate the clinical symptoms. Among possible microbiota-targeted interventions, pre/pro-biotics supplementations were shown to provide effective results, but the main limitation remains in the limited microbial species available as probiotics. Differently, fecal microbiota transplantation involves the transplantation of a solution of fecal matter from a donor into the intestinal tract of a recipient in order to directly change the recipient's gut microbial composition aiming to confer a health benefit. Firstly used in the 4th century in traditional Chinese medicine, nowadays, it has been exploited so far to treat recurrent Clostridioides difficile infections, but accumulating data coming from a number of clinical trials clearly indicate that fecal microbiota transplantation may also carry the therapeutic potential for a number of other conditions ranging from gastrointestinal to liver diseases, from cancer to inflammatory, infectious, autoimmune diseases and brain disorders, obesity, and metabolic syndrome. In this review, we will summarize the commonly used preparation and delivery methods, comprehensively review the evidence obtained in clinical trials in different human conditions and discuss the variability in the results and the pivotal importance of donor selection. The final aim is to stimulate discussion and open new therapeutic perspectives among experts in the use of fecal microbiota transplantation not only in Clostridioides difficile infection but as one of the first strategies to be used to ameliorate a number of human conditions.
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Affiliation(s)
- Manuele Biazzo
- The BioArte Limited, Life Sciences Park, Triq San Giljan, SGN 3000 San Gwann, Malta;
- SienabioACTIVE, University of Siena, Via Aldo Moro 1, 53100 Siena, Italy
| | - Gabriele Deidda
- Department of Biomedical Sciences, University of Padua, Via U. Bassi 58/B, 35131 Padova, Italy
- Correspondence: ; Tel.: +39-049-827-6125
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15
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Wu J, Zhou B, Pang X, Song X, Gu Y, Xie R, Liu T, Xu X, Wang B, Cao H. Clostridium butyricum, a butyrate-producing potential probiotic, alleviates experimental colitis through epidermal growth factor receptor activation. Food Funct 2022; 13:7046-7061. [PMID: 35678197 DOI: 10.1039/d2fo00478j] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel disease (IBD) is an idiopathic inflammatory bowel disease. Modulation of gut microbiota with dietary and nutritional targets is a feasible strategy for the prevention and treatment of IBD. In this study, we focused on Clostridium butyricum Prazmowski (CB), a butyrate-producing potential probiotic. We found that CB feeding decreased the disease activity index, colon inflammation/injury score and cell apoptosis in an experimental colitis mouse model, as well as elevated the level of SCFAs in cecal feces. CB could also balance the inflammatory cytokines, protect tight junctions, and increase the number of goblet cells and MUC2 production in mice, accompanied by EGFR signaling activation triggered by heparin-binding epidermal growth factor (HB-EGF) and amphiregulin (AREG). From the perspective of mechanism, the CB supernatant (CBS) stimulated EGFR activation in colon epithelial cell lines in concentration-dependent and time-dependent manners. CBS reduced the damage of tight junctions induced by H2O2, and inhibition of EGFR could suppress the protective effect of CBS. In conclusion, CB could protect the gut barrier and alleviate experimental colitis through the transactivation of EGFR signaling in intestinal epithelial cells induced by ligands (HB-EGF and AREG). This study identified the potential efficacy of CB as a preventive strategy for IBD and showed the broad prospect of CB as a food supplement.
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Affiliation(s)
- Jingyi Wu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Bingqian Zhou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Xiaoqi Pang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Xueli Song
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Yu Gu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Runxiang Xie
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Xin Xu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China.
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16
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Pu D, Zhang Z, Feng B. Alterations and Potential Applications of Gut Microbiota in Biological Therapy for Inflammatory Bowel Diseases. Front Pharmacol 2022; 13:906419. [PMID: 35734396 PMCID: PMC9207480 DOI: 10.3389/fphar.2022.906419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/26/2022] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is a chronic immune-mediated inflammatory disorder of the gastrointestinal tract that is closely associated with dysbiosis of the intestinal microbiota. Currently, biologic agents are the mainstream therapies for IBD. With the increasing incidence of IBD, limitations of biologic agents have gradually emerged during treatment. Recent studies have indicated that gut microbiota is highly correlated with the efficacy of biologic agents. This review focuses on alterations in both the components and metabolites of gut microbiota during biological therapy for IBD, systematically summarises the specific gut microbiota closely related to the clinical efficacy, and compares current predictive models for the efficacy of biologics, further highlighting the predictive value of intestinal microbiota. Based on the mechanistic analysis of faecal microbiota transplantation (FMT) and biologic agents, a new therapeutic strategy, comprising a combination of FMT and biologics, has been proposed as a promising treatment for IBD with improved efficacy.
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Affiliation(s)
| | - Zhe Zhang
- *Correspondence: Zhe Zhang, ; Baisui Feng,
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17
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Benítez-Páez A, Hartstra AV, Nieuwdorp M, Sanz Y. Species- and strain-level assessment using rrn long-amplicons suggests donor's influence on gut microbial transference via fecal transplants in metabolic syndrome subjects. Gut Microbes 2022; 14:2078621. [PMID: 35604764 PMCID: PMC9132484 DOI: 10.1080/19490976.2022.2078621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Fecal microbiota transplantation (FMT) is currently used for treating Clostridium difficile infection and explored for other clinical applications in experimental trials. However, the effectiveness of this therapy could vary, and partly depend on the donor's bacterial species engraftment, whose evaluation is challenging because there are no cost-effective strategies for accurately tracking the microbe transference. In this regard, the precise identification of bacterial species inhabiting the human gut is essential to define their role in human health unambiguously. We used Nanopore-based device to sequence bacterial rrn operons (16S-ITS-23S) and to reveal species-level abundance changes in the human gut microbiota of a FMT trial. By assessing the donor and recipient microbiota before and after FMT, we further evaluated whether this molecular approach reveals strain-level genetic variation to demonstrate microbe transfer and engraftment. Strict control over sequencing data quality and major microbiota covariates was critical for accurately estimating the changes in gut microbial species abundance in the recipients after FMT. We detected strain-level variation via single-nucleotide variants (SNVs) at rrn regions in a species-specific manner. We showed that it was possible to explore successfully the donor-bacterial strain (e.g., Parabacteroides merdae) engraftment in recipients of the FMT by assessing the nucleotide frequencies at rrn-associated SNVs. Our findings indicate that the engraftment of donors' microbiota is to some extent correlated with the improvement of metabolic health in recipients and that parameters such as the baseline gut microbiota configuration, sex, and age of donors should be considered to ensure the success of FMT in humans. The study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).
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Affiliation(s)
- Alfonso Benítez-Páez
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain,Host-Microbe Interactions in Metabolic Health Laboratory, Principe Felipe Research Center (CIPF), Valencia, Spain,CONTACT Alfonso Benítez-Páez Host-Microbe Interactions in Metabolic Health Laboratory, Principe Felipe Research Center (CIPF), Valencia, Spain
| | - Annick V. Hartstra
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia, Spain,Yolanda Sanz Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna-Valencia46980, Spain
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18
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Smith BJ, Li X, Shi ZJ, Abate A, Pollard KS. Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts. FRONTIERS IN BIOINFORMATICS 2022; 2:867386. [PMID: 36304283 PMCID: PMC9580935 DOI: 10.3389/fbinf.2022.867386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022] Open
Abstract
While genome databases are nearing a complete catalog of species commonly inhabiting the human gut, their representation of intraspecific diversity is lacking for all but the most abundant and frequently studied taxa. Statistical deconvolution of allele frequencies from shotgun metagenomic data into strain genotypes and relative abundances is a promising approach, but existing methods are limited by computational scalability. Here we introduce StrainFacts, a method for strain deconvolution that enables inference across tens of thousands of metagenomes. We harness a “fuzzy” genotype approximation that makes the underlying graphical model fully differentiable, unlike existing methods. This allows parameter estimates to be optimized with gradient-based methods, speeding up model fitting by two orders of magnitude. A GPU implementation provides additional scalability. Extensive simulations show that StrainFacts can perform strain inference on thousands of metagenomes and has comparable accuracy to more computationally intensive tools. We further validate our strain inferences using single-cell genomic sequencing from a human stool sample. Applying StrainFacts to a collection of more than 10,000 publicly available human stool metagenomes, we quantify patterns of strain diversity, biogeography, and linkage-disequilibrium that agree with and expand on what is known based on existing reference genomes. StrainFacts paves the way for large-scale biogeography and population genetic studies of microbiomes using metagenomic data.
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Affiliation(s)
- Byron J. Smith
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Xiangpeng Li
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Zhou Jason Shi
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, United States
- Chan-Zuckerberg Biohub, San Francisco, CA, United States
| | - Adam Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
- Chan-Zuckerberg Biohub, San Francisco, CA, United States
| | - Katherine S. Pollard
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
- Chan-Zuckerberg Biohub, San Francisco, CA, United States
- *Correspondence: Katherine S. Pollard,
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19
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Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N. Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis. Sci Rep 2022; 12:5517. [PMID: 35365713 PMCID: PMC8976058 DOI: 10.1038/s41598-022-09307-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 03/16/2022] [Indexed: 01/04/2023] Open
Abstract
Fecal microbiota transplant is a promising therapy for ulcerative colitis. Parameters maximizing effectiveness and tolerability are not yet clear, and it is not known how import the transmission of donor microbes to patients is. Here (clinicaltrails.gov: NCT03006809) we have tested the effects of antibiotic pretreatment and compared two modes of maintenance dose delivery, capsules versus enema, in a randomized, pilot, open-label, 2 × 2 factorial design with 22 patients analyzed with mild to moderate UC. Clinically, the treatment was well-tolerated with favorable safety profile. Of patients who received antibiotic pretreatment, 6 of 11 experienced remission after 6 weeks of treatment, versus 2 of 11 non-pretreated patients (log odds ratio: 1.69, 95% confidence interval: −0.25 to 3.62). No significant differences were found between maintenance dosing via capsules versus enema. In exploratory analyses, microbiome turnover at both the species and strain levels was extensive and significantly more pronounced in the pretreated patients. Associations were also revealed between taxonomic turnover and changes in the composition of primary and secondary bile acids. Together these findings suggest that antibiotic pretreatment contributes to microbiome engraftment and possibly clinical effectiveness, and validate longitudinal strain tracking as a powerful way to monitor the dynamics and impact of microbiota transfer.
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Affiliation(s)
- Byron J Smith
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | - Martin Zydek
- Division of Gastroenterology, University of California, San Francisco, CA, USA
| | - Bing Zhang
- Division of Gastroenterology, University of California, San Francisco, CA, USA.,Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lara Aboud Syriani
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, USA
| | - Jonathan P Terdiman
- Division of Gastroenterology, University of California, San Francisco, CA, USA
| | | | - Averil Ma
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Susan V Lynch
- Division of Gastroenterology, University of California, San Francisco, CA, USA.,Benioff Center for Microbiome Medicine, University of California, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Najwa El-Nachef
- Division of Gastroenterology, University of California, San Francisco, CA, USA.
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20
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Qiu P, Ishimoto T, Fu L, Zhang J, Zhang Z, Liu Y. The Gut Microbiota in Inflammatory Bowel Disease. Front Cell Infect Microbiol 2022; 12:733992. [PMID: 35273921 PMCID: PMC8902753 DOI: 10.3389/fcimb.2022.733992] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
Epidemiological surveys indicate that the incidence of inflammatory bowel disease (IBD) is increasing rapidly with the continuous growth of the economy. A large number of studies have investigated the relationship between the genetic factors related to the susceptibility to IBD and the gut microbiota of patients by using high-throughput sequencing. IBD is considered the outcome of the interaction between host and microorganisms, including intestinal microbial factors, abnormal immune response, and a damaged intestinal mucosal barrier. The imbalance of microbial homeostasis leads to the colonization and invasion of opportunistic pathogens in the gut, which increases the risk of the host immune response and promotes the development of IBD. It is critical to identify the specific pathogens related to the pathogenesis of IBD. An in-depth understanding of various pathogenic factors is of great significance for the early detection of IBD. This review highlights the role of gut microbiota in the pathogenesis of IBD and provides a theoretical basis for the personalized approaches that modulate the gut microbiota to treat IBD.
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Affiliation(s)
- Peng Qiu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Gastrointestinal Cancer Biology, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Lingfeng Fu
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Gastrointestinal Cancer Biology, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun Zhang
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
- Gastrointestinal Cancer Biology, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Zhenyong Zhang
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yang Liu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Yang Liu, ; orcid.org/0000-0002-2129-9086
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21
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Islam J, Tanimizu M, Shimizu Y, Goto Y, Ohtani N, Sugiyama K, Tatezaki E, Sato M, Makino E, Shimada T, Ueda C, Matsuo A, Suyama Y, Sakai Y, Furukawa M, Usami K, Yoneyama H, Aso H, Tanaka H, Nochi T. Development of a rational framework for the therapeutic efficacy of fecal microbiota transplantation for calf diarrhea treatment. MICROBIOME 2022; 10:31. [PMID: 35184756 PMCID: PMC8858662 DOI: 10.1186/s40168-021-01217-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 12/20/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Establishing fecal microbiota transplantation (FMT) to prevent multifactorial diarrhea in calves is challenging because of the differences in farm management practices, the lack of optimal donors, and recipient selection. In this study, the underlying factors of successful and unsuccessful FMT treatment cases are elucidated, and the potential markers for predicting successful FMT are identified using fecal metagenomics via 16S rRNA gene sequencing, fecal metabolomics via capillary electrophoresis time-of-flight mass spectrometry, and machine learning approaches. RESULTS Specifically, 20 FMT treatment cases, in which feces from healthy donors were intrarectally transferred into recipient diarrheal calves, were conducted with a success rate of 70%. Selenomonas was identified as a microorganism genus that showed significant donor-recipient compatibility in successful FMT treatments. A strong positive correlation between the microbiome and metabolome data, which is a prerequisite factor for FMT success, was confirmed by Procrustes analysis in successful FMT (r = 0.7439, P = 0.0001). Additionally, weighted gene correlation network analysis confirmed the positively or negatively correlated pairs of bacterial taxa (family Veillonellaceae) and metabolomic features (i.e., amino acids and short-chain fatty acids) responsible for FMT success. Further analysis aimed at establishing criteria for donor selection identified the genus Sporobacter as a potential biomarker in successful donor selection. Low levels of metabolites, such as glycerol 3-phosphate, dihydroxyacetone phosphate, and isoamylamine, in the donor or recipients prior to FMT, are predicted to facilitate FMT. CONCLUSIONS Overall, we provide the first substantial evidence of the factors related to FMT success or failure; these findings could improve the design of future microbial therapeutics for treating diarrhea in calves. Video abstract.
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Affiliation(s)
- Jahidul Islam
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Masae Tanimizu
- East Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 1533 Naruto, Sanmu, Chiba, 289-1326, Japan
| | - Yu Shimizu
- East Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 1533 Naruto, Sanmu, Chiba, 289-1326, Japan
| | - Yoshiaki Goto
- North Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 99-1 Nira, Katori, Chiba, 289-0407, Japan
| | - Natsuki Ohtani
- North Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 99-1 Nira, Katori, Chiba, 289-0407, Japan
| | - Kentaro Sugiyama
- North Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 99-1 Nira, Katori, Chiba, 289-0407, Japan
| | - Eriko Tatezaki
- North Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 99-1 Nira, Katori, Chiba, 289-0407, Japan
| | - Masumi Sato
- West Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 154-11, Shisui-machi, Imba-gun, Chiba, 285-0902, Japan
| | - Eiji Makino
- West Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 154-11, Shisui-machi, Imba-gun, Chiba, 285-0902, Japan
| | - Toru Shimada
- Central Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 736 Amoda, Ichihara, Chiba, 299-0126, Japan
| | - Chise Ueda
- Central Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 736 Amoda, Ichihara, Chiba, 299-0126, Japan
| | - Ayumi Matsuo
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Yoshihisa Suyama
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Yoshifumi Sakai
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Mutsumi Furukawa
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Katsuki Usami
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Hiroshi Yoneyama
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Hisashi Aso
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan
| | - Hidekazu Tanaka
- North Veterinary Clinical Center, Chiba Prefectural Federation of Agricultural Mutual Aid Association, 99-1 Nira, Katori, Chiba, 289-0407, Japan.
| | - Tomonori Nochi
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8572, Japan.
- Division of Mucosal Vaccines, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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22
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Lima SF, Gogokhia L, Viladomiu M, Chou L, Putzel G, Jin WB, Pires S, Guo CJ, Gerardin Y, Crawford CV, Jacob V, Scherl E, Brown SE, Hambor J, Longman RS. Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation. Gastroenterology 2022; 162:166-178. [PMID: 34606847 PMCID: PMC8678328 DOI: 10.1053/j.gastro.2021.09.061] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/01/2021] [Accepted: 09/28/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) is an emerging treatment modality for ulcerative colitis (UC). Several randomized controlled trials have shown efficacy for FMT in the treatment of UC, but a better understanding of the transferable microbiota and their immune impact is needed to develop more efficient microbiome-based therapies for UC. METHODS Metagenomic analysis and strain tracking was performed on 60 donor and recipient samples receiving FMT for active UC. Sorting and sequencing of immunoglobulin (Ig) A-coated microbiota (called IgA-seq) was used to define immune-reactive microbiota. Colonization of germ-free or genetically engineered mice with patient-derived strains was performed to determine the mechanism of microbial impact on intestinal immunity. RESULTS Metagenomic analysis defined a core set of donor-derived transferable bacterial strains in UC subjects achieving clinical response, which predicted response in an independent trial of FMT for UC. IgA-seq of FMT recipient samples and gnotobiotic mice colonized with donor microbiota identified Odoribacter splanchnicus as a transferable strain shaping mucosal immunity, which correlated with clinical response and the induction of mucosal regulatory T cells. Colonization of mice with O splanchnicus led to an increase in Foxp3+/RORγt+ regulatory T cells, induction of interleukin (IL) 10, and production of short chain fatty acids, all of which were required for O splanchnicus to limit colitis in mouse models. CONCLUSIONS This work provides the first evidence of transferable, donor-derived strains that correlate with clinical response to FMT in UC and reveals O splanchnicus as a key component promoting both metabolic and immune cell protection from colitis. These mechanistic features will help enable strategies to enhance the efficacy of microbial therapy for UC. Clinicaltrials.gov ID NCT02516384.
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MESH Headings
- Animals
- Bacteroidetes/genetics
- Bacteroidetes/immunology
- Bacteroidetes/metabolism
- Clinical Trials as Topic
- Colitis/immunology
- Colitis/metabolism
- Colitis/microbiology
- Colitis/therapy
- Colitis, Ulcerative/diagnosis
- Colitis, Ulcerative/immunology
- Colitis, Ulcerative/metabolism
- Colitis, Ulcerative/microbiology
- Colon/immunology
- Colon/metabolism
- Colon/microbiology
- Disease Models, Animal
- Fecal Microbiota Transplantation
- Forkhead Transcription Factors/metabolism
- Gastrointestinal Microbiome/genetics
- Gastrointestinal Microbiome/immunology
- Germ-Free Life
- Humans
- Immunity, Mucosal
- Immunoglobulin A/genetics
- Immunoglobulin A/immunology
- Immunoglobulin A/metabolism
- Intestinal Mucosa/immunology
- Intestinal Mucosa/metabolism
- Intestinal Mucosa/microbiology
- Intraepithelial Lymphocytes/immunology
- Intraepithelial Lymphocytes/metabolism
- Intraepithelial Lymphocytes/microbiology
- Metagenome
- Metagenomics
- Mice, Inbred C57BL
- Mice, Knockout
- Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- T-Lymphocytes, Regulatory/microbiology
- Treatment Outcome
- Mice
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Affiliation(s)
- Svetlana F Lima
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Lasha Gogokhia
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York; St. Mary's Hospital, Department of Medicine, Waterbury, Connecticut
| | - Monica Viladomiu
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Lance Chou
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Gregory Putzel
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Wen-Bing Jin
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Silvia Pires
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Chun-Jun Guo
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | | | - Carl V Crawford
- Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Vinita Jacob
- Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York; Jill Roberts Center for IBD, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Ellen Scherl
- Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York; Jill Roberts Center for IBD, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York
| | - Su-Ellen Brown
- Boehringer Ingelheim SHINE Program, Ridgefield, Connecticut
| | - John Hambor
- Boehringer Ingelheim SHINE Program, Ridgefield, Connecticut
| | - Randy S Longman
- Jill Roberts Institute for Research in IBD, Weill Cornell Medicine, New York, New York; Division of Gastroenterology and Hepatology, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York; Jill Roberts Center for IBD, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, New York.
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