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Nie Y, Lin T, Yang Y, Liu W, Hu Q, Chen G, Huang L, Wu H, Kong C, Lei Z, Guo J. The downregulation of tight junction proteins and pIgR in the colonic epithelium causes the susceptibility of EpCAM +/- mice to colitis and gut microbiota dysbiosis. Front Mol Biosci 2024; 11:1442611. [PMID: 39188786 PMCID: PMC11345229 DOI: 10.3389/fmolb.2024.1442611] [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: 06/02/2024] [Accepted: 07/29/2024] [Indexed: 08/28/2024] Open
Abstract
Background The genetic factors play important roles on the pathogenesis of inflammatory bowel disease (IBD). EpCAM is highly expressed in the intestinal epithelium. It is still unclear if the decrease or somatic mutation of EpCAM could cause IBD. Methods The WT and EpCAM+/- mice were administrated with DSS intermittently for nearly 8 weeks. The colon, liver and feces were harvested to check the morphological and histological changes, the expression of inflammatory genes and the gut microbiota via H&E staining, immunofluorescence, qPCR, western blot and 16S rDNA sequence assays. Results The DSS administration induced more serious inflammation in the colon of EpCAM+/- mice than WT mice. Compared to DSS-induced WT mice, the transcriptional levels of IL-6, F4/80, Ly6g, Ly6d and Igha were significantly higher in the colon of DSS-induced EpCAM+/- mice. The protein levels of MMP7 and MMP8 and the activation of JNK, ERK1/2 and p38 were significantly increased in the colon of DSS-induced EpCAM+/- mice. The protein levels of CLDN1, CLDN2, CLDN3, CLDN7, OCLD, ZO-1 and pIgR were significantly decreased in the colon of DSS-induced EpCAM+/- mice. The serum concentration of LPS was significantly higher in the DSS-induced EpCAM+/- mice which caused the acute inflammation in the liver of them. The expression of Pigr was significantly reduced in the liver of DSS-induced EpCAM+/- mice. The ratio of Firmicutes/Bacteroidetes at the phylum level was higher in the gut microbiota of EpCAM+/- mice than WT mice. Conclusion In conclusion, the heterozygous mutation of EpCAM increased the susceptibility to colitis, gut microbiota dysbiosis and liver injury.
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Affiliation(s)
- Ya Nie
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Ting Lin
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yanhong Yang
- The First Affiliated Hospital, School of Clinical Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wanwan Liu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qing Hu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
| | - Guibin Chen
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
| | - Li Huang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Huijuan Wu
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Cunjie Kong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Zili Lei
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiao Guo
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, Guangdong Pharmaceutical University, Guangzhou, China
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2
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Ignatiou A, Pitsouli C. Host-diet-microbiota interplay in intestinal nutrition and health. FEBS Lett 2024. [PMID: 38946050 DOI: 10.1002/1873-3468.14966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
The intestine is populated by a complex and dynamic assortment of microbes, collectively called gut microbiota, that interact with the host and contribute to its metabolism and physiology. Diet is considered a key regulator of intestinal microbiota, as ingested nutrients interact with and shape the resident microbiota composition. Furthermore, recent studies underscore the interplay of dietary and microbiota-derived nutrients, which directly impinge on intestinal stem cells regulating their turnover to ensure a healthy gut barrier. Although advanced sequencing methodologies have allowed the characterization of the human gut microbiome, mechanistic studies assessing diet-microbiota-host interactions depend on the use of genetically tractable models, such as Drosophila melanogaster. In this review, we first discuss the similarities between the human and fly intestines and then we focus on the effects of diet and microbiota on nutrient-sensing signaling cascades controlling intestinal stem cell self-renewal and differentiation, as well as disease. Finally, we underline the use of the Drosophila model in assessing the role of microbiota in gut-related pathologies and in understanding the mechanisms that mediate different whole-body manifestations of gut dysfunction.
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Affiliation(s)
- Anastasia Ignatiou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Chrysoula Pitsouli
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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3
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Chowdhury F, Hill L, Shah N, Popov J, Cheveldayoff P, Pai N. Intestinal microbiome in short bowel syndrome: diagnostic and therapeutic opportunities. Curr Opin Gastroenterol 2023; 39:463-471. [PMID: 37751391 DOI: 10.1097/mog.0000000000000970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
PURPOSE OF REVIEW The intestinal microbiome plays a strong, complementary role in the development and integrity of the intestinal epithelium. This biology is crucial for intestinal adaptation, particularly after the mucosal insults that lead to short bowel syndrome (SBS). The purpose of this review is to discuss relationships between the intestinal microbiota and the physiology of intestinal adaptation. RECENT FINDINGS We will address interactions between the intestinal microbiome and nutritional metabolism, factors leading to dysbiosis in SBS, and common compositional differences of the gut microbiome in SBS patients as compared to healthy controls. We will also discuss novel opportunities to expand diagnostic and therapeutic interventions in this population, by using our knowledge of the microbiome to manipulate luminal bacteria and study their resultant metabolites. As microbial therapeutics advance across so many fields of medicine, this review is timely in its advocacy for ongoing research that focuses on the SBS population.Our review will discuss 4 key areas: 1) physiology of the intestinal microbiome in SBS, 2) clinical and therapeutic insults that lead to a state of dysbiosis, 3) currently available evidence on microbiome-based approaches to SBS management, and 4) opportunities and innovations to inspire future research. SUMMARY The clinical implications of this review are both current, and potential. Understanding how the microbiome impacts intestinal adaptation and host physiology may enhance our understanding of why we experience such clinical variability in SBS patients' outcomes. This review may also expand clinicians' understanding of what 'personalized medicine' can mean for this patient population, and how we may someday consider our nutritional, therapeutic, and prognostic recommendations based on our patients' host, and microbial physiology.
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Affiliation(s)
- Fariha Chowdhury
- Department of Pediatrics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario
| | - Lee Hill
- Department of Pediatrics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario
- Department of Pediatrics, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Nyah Shah
- Department of Pediatrics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario
| | - Jelena Popov
- Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paige Cheveldayoff
- Department of Pediatrics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario
- Centre for Metabolism, Obesity and Diabetes Research
| | - Nikhil Pai
- Department of Pediatrics, Faculty of Health Sciences, McMaster University, Hamilton, Ontario
- Centre for Metabolism, Obesity and Diabetes Research
- Farncombe Family Digestive Health Research Institute, McMaster University
- Division of Pediatric Gastroenterology & Nutrition, McMaster Children's Hospital, Hamilton, Ontario, Canada
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4
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Fourati S, de Dreuille B, Bettolo J, Hutinet C, Le Gall M, Bado A, Joly F, Le Beyec J. Hyperphagia is prominent in adult patients with short bowel syndrome: A role for the colon? Clin Nutr 2023; 42:2109-2115. [PMID: 37751660 DOI: 10.1016/j.clnu.2023.09.003] [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: 06/09/2023] [Revised: 08/24/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
RATIONALE Short Bowel Syndrome (SBS) is the major cause of chronic intestinal failure (IF) and requires parenteral nutrition (PN). After bowel resection, some patients develop spontaneous intestinal adaptations and hyperphagia. Since promoting oral energy intake contributes to PN weaning, this study aims to characterize hyperphagia in patients with SBS and identify its determinants. METHODS This observational retrospective study included adult patients with SBS who were followed at an expert PN center between 2006 and 2019, with at least 2 separate nutritional assessments. Exclusion criteria were: active neoplasia, alternative treatment for IF or appetite-affecting medication. Resting energy expenditure (REE) was calculated for each patient using the Harris-Benedict equation. Food Intake Ratio (FIR) was calculated by dividing the highest caloric oral intake by REE and hyperphagia was defined as FIR >1.5. RESULTS Among the 59 patients with SBS included in this study, 82.6% had a FIR >1.5, including 15.5% with a FIR >3. Protein supplied approximately 16% of total energy intake while fat and carbohydrates provided 36% and 48%, respectively. The FIR was independent of gender and whether patients received oral nutrition alone (n = 28) or combined with PN (n = 31). The FIR was also not associated with residual small bowel length, nor the proportion of preserved colon. However, it was negatively correlated with the body mass index (BMI) of these patients (r = -0.533, p < 0.001), whether they had PN support or not. Patients with either a jejuno-colonic (n = 31) or a jejuno-ileal anastomosis (n = 9), had a significantly higher FIR compared to those with an end-jejunostomy (n = 18) (p < 0.05). However, no difference was found in the proportion of calories provided by protein, fat and carbohydrate between the 3 patients groups divided according to the SBS anatomical type. CONCLUSION A large majority of patients with SBS exhibited a hyperphagia regardless of PN dependence or bowel length, which was inversely correlated with BMI. The presence of the colon in continuity, thus in contact with the nutritional flow, seems to favor a higher oral intake which is beneficial for the nutritional autonomy of patients. This raises the question of a role of colonic microbiota and hormones in this behavior. Finally, this study also revealed an unexpected discrepancy between recommended energy intakes from protein, fat and carbohydrate and the actual intake of patients with SBS.
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Affiliation(s)
- Salma Fourati
- UMR-S 1149 Centre de Recherche sur l'Inflammation Inserm, Université Paris Cité, 75018 Paris, France; Service de Biochimie Endocrinienne et Oncologique, Hôpital de la Pitié-Salpêtrière-Charles Foix, Sorbonne Université, 75013 Paris, France.
| | - Brune de Dreuille
- UMR-S 1149 Centre de Recherche sur l'Inflammation Inserm, Université Paris Cité, 75018 Paris, France
| | - Joanna Bettolo
- Department of Gastroenterology and Nutritional Support, Center for Intestinal Failure, Reference Centre of Rare Disease MarDI, AP-HP Beaujon Hospital, University of Paris Inserm UMR 1149, Paris, France
| | - Coralie Hutinet
- Department of Gastroenterology and Nutritional Support, Center for Intestinal Failure, Reference Centre of Rare Disease MarDI, AP-HP Beaujon Hospital, University of Paris Inserm UMR 1149, Paris, France
| | - Maude Le Gall
- UMR-S 1149 Centre de Recherche sur l'Inflammation Inserm, Université Paris Cité, 75018 Paris, France
| | - André Bado
- UMR-S 1149 Centre de Recherche sur l'Inflammation Inserm, Université Paris Cité, 75018 Paris, France
| | - Francisca Joly
- UMR-S 1149 Centre de Recherche sur l'Inflammation Inserm, Université Paris Cité, 75018 Paris, France; Department of Gastroenterology and Nutritional Support, Center for Intestinal Failure, Reference Centre of Rare Disease MarDI, AP-HP Beaujon Hospital, University of Paris Inserm UMR 1149, Paris, France
| | - Johanne Le Beyec
- UMR-S 1149 Centre de Recherche sur l'Inflammation Inserm, Université Paris Cité, 75018 Paris, France; Service de Biochimie Endocrinienne et Oncologique, Hôpital de la Pitié-Salpêtrière-Charles Foix, Sorbonne Université, 75013 Paris, France
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5
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Salvi PS, Shaughnessy MP, Sumigray KD, Cowles RA. Antibiotic-induced microbial depletion enhances murine small intestinal epithelial growth in a serotonin-dependent manner. Am J Physiol Gastrointest Liver Physiol 2023; 325:G80-G91. [PMID: 37158470 DOI: 10.1152/ajpgi.00113.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/06/2023] [Accepted: 01/28/2023] [Indexed: 05/10/2023]
Abstract
Regulation of small intestinal epithelial growth by endogenous and environmental factors is critical for intestinal homeostasis and recovery from insults. Depletion of the intestinal microbiome increases epithelial proliferation in small intestinal crypts, similar to the effects observed in animal models of serotonin potentiation. Based on prior evidence that the microbiome modulates serotonin activity, we hypothesized that microbial depletion-induced epithelial proliferation is dependent on host serotonin activity. A mouse model of antibiotic-induced microbial depletion (AIMD) was employed. Serotonin potentiation was achieved through either genetic knockout of the serotonin transporter (SERT) or pharmacological SERT inhibition, and inhibition of serotonin synthesis was achieved with para-chlorophenylalanine. AIMD and serotonin potentiation increased intestinal villus height and crypt proliferation in an additive manner, but the epithelial proliferation observed after AIMD was blocked in the absence of endogenous serotonin. Using Lgr5-EGFP-reporter mice, we evaluated intestinal stem cell (ISC) quantity and proliferation. AIMD increased the number of ISCs per crypt and ISC proliferation compared with controls, and changes in ISC number and proliferation were dependent on the presence of host serotonin. Furthermore, Western blotting demonstrated that AIMD reduced epithelial SERT protein expression compared with controls. In conclusion, host serotonin activity is necessary for microbial depletion-associated changes in villus height and ISC proliferation in crypts, and microbial depletion produces a functional serotonin-potentiated state through reduced SERT protein expression. These findings provide an understanding of how changes to the microbiome contribute to intestinal pathology and can be applied therapeutically.NEW & NOTEWORTHY Antibiotic-induced microbial depletion of the murine small intestine results in a state of potentiated serotonin activity through reduced epithelial expression of the serotonin transporter. Specifically, serotonin-dependent mechanisms lead to increased intestinal surface area and intestinal stem cell proliferation. Furthermore, the absence of endogenous serotonin leads to blunting of small intestinal villi, suggesting that serotonin signaling is required for epithelial homeostasis.
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Affiliation(s)
- Pooja S Salvi
- Division of Pediatric Surgery, Department of Surgery, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Matthew P Shaughnessy
- Division of Pediatric Surgery, Department of Surgery, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Kaelyn D Sumigray
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Robert A Cowles
- Division of Pediatric Surgery, Department of Surgery, Yale University School of Medicine, New Haven, Connecticut, United States
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6
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Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S, Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity 2023; 56:1376-1392.e8. [PMID: 37164013 DOI: 10.1016/j.immuni.2023.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Phage-displayed immunoprecipitation sequencing (PhIP-seq) has enabled high-throughput profiling of human antibody repertoires. However, a comprehensive overview of environmental and genetic determinants shaping human adaptive immunity is lacking. In this study, we investigated the effects of genetic, environmental, and intrinsic factors on the variation in human antibody repertoires. We characterized serological antibody repertoires against 344,000 peptides using PhIP-seq libraries from a wide range of microbial and environmental antigens in 1,443 participants from a population cohort. We detected individual-specificity, temporal consistency, and co-housing similarities in antibody repertoires. Genetic analyses showed the involvement of the HLA, IGHV, and FUT2 gene regions in antibody-bound peptide reactivity. Furthermore, we uncovered associations between phenotypic factors (including age, cell counts, sex, smoking behavior, and allergies, among others) and particular antibody-bound peptides. Our results indicate that human antibody epitope repertoires are shaped by both genetics and environmental exposures and highlight specific signatures of distinct phenotypes and genotypes.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Angel J Ruiz-Moreno
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Karina de Leeuw
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Suzanne Arends
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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7
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Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity 2023; 56:1393-1409.e6. [PMID: 37164015 DOI: 10.1016/j.immuni.2023.04.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/14/2023] [Indexed: 05/12/2023]
Abstract
Inflammatory bowel diseases (IBDs), e.g., Crohn's disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. Using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq), we identified antibodies against 344,000 antimicrobial, immune, and food antigens in 497 individuals with IBD compared with 1,326 controls. IBD was characterized by 373 differentially abundant antibody responses (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD, and 28% unique to UC. Antibody reactivities against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease, and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (area under the curve [AUC] = 0.89), and similar discrimination was achieved when using only ten antibodies (AUC = 0.87). Individuals with IBD thus show a distinct antibody repertoire against selected peptides, allowing clinical stratification and discovery of immunological targets.
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Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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8
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Huang Y, Jiao J, Yao D, Guo F, Li Y. Altered fecal microbiome and metabolome profiles in rat models of short bowel syndrome. Front Microbiol 2023; 14:1185463. [PMID: 37362931 PMCID: PMC10289890 DOI: 10.3389/fmicb.2023.1185463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Short bowel syndrome (SBS) is featured by impaired nutrients and fluids absorption due to massive small intestine resection. Gut dysbiosis has been implicated in SBS, this study aimed to characterize the metagenomic and metabolomic profiles of SBS and identify potential therapeutic targets. Methods Fecal samples from SBS and Sham rats (n = 8 per group) were collected for high-throughput metagenomic sequencing. Fecal metabolomics was measured by untargeted liquid chromatography-mass spectrometry. Results We found that the species-level α-diversity significantly decreased in SBS rats, accompanied by altered microbiome compositions. The beneficial anaerobes from Firmicutes and Bacteroidetes were depleted while microorganisms from Lactobacillus, Escherichia, Enterococcus, and Streptococcus were enriched in faces from SBS rats. LEfSe analysis identified 17 microbial species and 38 KEGG modules that were remarkably distinct between SBS and Sham rats. In total, 1,577 metabolites with known chemical identity were detected from all samples, among them, 276 metabolites were down-regulated and 224 metabolites were up-regulated in SBS group. The typical signatures of SBS fecal metabolome comprised reduced short-chain fatty acids and products of amino acid metabolism (indole derivatives and p-cresol), as well as altered bile acid spectrum. We revealed 215 robust associations between representative differentially abundant microbial species and metabolites, the species with the same changing trend tended to have a similar correlation with some certain metabolites. Conclusion The fecal microbiome and metabolome significantly altered in SBS. Our findings may lay the foundation for developing new strategies to facilitate intestinal adaptation in SBS patients.
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Affiliation(s)
- Yuhua Huang
- Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jian Jiao
- Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Danhua Yao
- Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Feilong Guo
- Department of General Surgery, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Yousheng Li
- Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
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9
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Ma T, Xue X, Tian H, Zhou X, Wang J, Zhao Z, Wang M, Song J, Feng R, Li L, Jing C, Tian F. Effect of the gut microbiota and their metabolites on postoperative intestinal motility and its underlying mechanisms. J Transl Med 2023; 21:349. [PMID: 37237321 DOI: 10.1186/s12967-023-04215-2] [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: 03/11/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Gut microbiota is closely related to human health and disease because, together with their metabolites, gut microbiota maintain normal intestinal peristalsis. The use of antibiotics or opioid anesthetics, or both, during surgical procedures can lead to dysbiosis and affect intestinal motility; however, the underlying mechanisms are not fully known. This review aims to discuss the effect of gut microbiota and their metabolites on postoperative intestinal motility, focusing on regulating the enteric nervous system, 5-hydroxytryptamine neurotransmitter, and aryl hydrocarbon receptor.
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Affiliation(s)
- TianRong Ma
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - XiaoLei Xue
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
- Department of Pharmacy, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China
| | - Hui Tian
- Department of Gastroenterology, Liaocheng People's Hospital, Shandong First Medical University, Liaocheng, 252000, China
| | - XinXiu Zhou
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - JunKe Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - ZhiWen Zhao
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
| | - MingFei Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - JiYuan Song
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - RenXiang Feng
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China
| | - Changqing Jing
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China.
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China.
| | - Feng Tian
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China.
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, China.
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Singh NK, Beckett JM, Kalpurath K, Ishaq M, Ahmad T, Eri RD. Synbiotics as Supplemental Therapy for the Alleviation of Chemotherapy-Associated Symptoms in Patients with Solid Tumours. Nutrients 2023; 15:nu15071759. [PMID: 37049599 PMCID: PMC10096799 DOI: 10.3390/nu15071759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Chemotherapy is still the first line of treatment for most cancer patients. Patients receiving chemotherapy are generally prone to infections, which result in complications, such as sepsis, mucositis, colitis, and diarrhoea. Several nutritional approaches have been trialled to counter the chemotherapy-associated side effects in cancer patients, but none have yet been approved for routine clinical use. One of the approaches to reduce or avoid chemotherapy-associated complications is to restore the gut microbiota. Gut microbiota is essential for the healthy functioning of the immune system, metabolism, and the regulation of other molecular responses in the body. Chemotherapy erodes the mucosal layer of the gastrointestinal tract and results in the loss of gut microbiota. One of the ways to restore the gut microbiota is through the use of probiotics. Probiotics are the ‘good’ bacteria that may provide health benefits if consumed in appropriate amounts. Some studies have highlighted that the consumption of probiotics in combination with prebiotics, known as synbiotics, may provide better health benefits when compared to probiotics alone. This review discusses the different nutritional approaches that have been studied in an attempt to combat chemotherapy-associated side effects in cancer patients with a particular focus on the use of pre-, pro- and synbiotics.
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Affiliation(s)
- Neeraj K. Singh
- School of Health Sciences, University of Tasmania, Newnham, Launceston 7248, Australia
| | - Jeffrey M. Beckett
- School of Health Sciences, University of Tasmania, Newnham, Launceston 7248, Australia
| | - Krishnakumar Kalpurath
- School of Health Sciences, University of Tasmania, Newnham, Launceston 7248, Australia
- Mersey Community Hospital, Latrobe 7307, Australia
| | - Muhammad Ishaq
- School of Health Sciences, University of Tasmania, Newnham, Launceston 7248, Australia
| | - Tauseef Ahmad
- School of Health Sciences, University of Tasmania, Newnham, Launceston 7248, Australia
| | - Rajaraman D. Eri
- School of Health Sciences, University of Tasmania, Newnham, Launceston 7248, Australia
- School of Science, STEM College, RMIT University, Melbourne 3083, Australia
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Cerdó T, García-Santos JA, Rodríguez-Pöhnlein A, García-Ricobaraza M, Nieto-Ruíz A, G. Bermúdez M, Campoy C. Impact of Total Parenteral Nutrition on Gut Microbiota in Pediatric Population Suffering Intestinal Disorders. Nutrients 2022; 14:4691. [PMID: 36364953 PMCID: PMC9658482 DOI: 10.3390/nu14214691] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 08/10/2023] Open
Abstract
Parenteral nutrition (PN) is a life-saving therapy providing nutritional support in patients with digestive tract complications, particularly in preterm neonates due to their gut immaturity during the first postnatal weeks. Despite this, PN can also result in several gastrointestinal complications that are the cause or consequence of gut mucosal atrophy and gut microbiota dysbiosis, which may further aggravate gastrointestinal disorders. Consequently, the use of PN presents many unique challenges, notably in terms of the potential role of the gut microbiota on the functional and clinical outcomes associated with the long-term use of PN. In this review, we synthesize the current evidence on the effects of PN on gut microbiome in infants and children suffering from diverse gastrointestinal diseases, including necrotizing enterocolitis (NEC), short bowel syndrome (SBS) and subsequent intestinal failure, liver disease and inflammatory bowel disease (IBD). Moreover, we discuss the potential use of pre-, pro- and/or synbiotics as promising therapeutic strategies to reduce the risk of severe gastrointestinal disorders and mortality. The findings discussed here highlight the need for more well-designed studies, and harmonize the methods and its interpretation, which are critical to better understand the role of the gut microbiota in PN-related diseases and the development of efficient and personalized approaches based on pro- and/or prebiotics.
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Affiliation(s)
- Tomás Cerdó
- Maimonides Institute for Research in Biomedicine of Córdoba (IMIBIC), Reina Sofia University Hospital, University of Córdoba, 14004 Córdoba, Spain
| | - José Antonio García-Santos
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, 18016 Granada, Spain
- Department of Paediatrics, School of Medicine, University of Granada, Avda. Investigación 11, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs-GRANADA, Health Sciences Technological Park, 18012 Granada, Spain
| | - Anna Rodríguez-Pöhnlein
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, 18016 Granada, Spain
- Department of Paediatrics, School of Medicine, University of Granada, Avda. Investigación 11, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs-GRANADA, Health Sciences Technological Park, 18012 Granada, Spain
| | - María García-Ricobaraza
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, 18016 Granada, Spain
- Department of Paediatrics, School of Medicine, University of Granada, Avda. Investigación 11, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs-GRANADA, Health Sciences Technological Park, 18012 Granada, Spain
| | - Ana Nieto-Ruíz
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, 18016 Granada, Spain
- Department of Paediatrics, School of Medicine, University of Granada, Avda. Investigación 11, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs-GRANADA, Health Sciences Technological Park, 18012 Granada, Spain
| | - Mercedes G. Bermúdez
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, 18016 Granada, Spain
- Department of Paediatrics, School of Medicine, University of Granada, Avda. Investigación 11, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs-GRANADA, Health Sciences Technological Park, 18012 Granada, Spain
| | - Cristina Campoy
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, 18016 Granada, Spain
- Department of Paediatrics, School of Medicine, University of Granada, Avda. Investigación 11, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria Ibs-GRANADA, Health Sciences Technological Park, 18012 Granada, Spain
- Spanish Network of Biomedical Research in Epidemiology and Public Health (CIBERESP), Granada’s Node, Carlos III Health Institute, Avda. Monforte de Lemos 5, 28028 Madrid, Spain
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Teduglutide in pediatric intestinal failure: A position statement of the Italian society of pediatric gastroenterology, hepatology and nutrition (SIGENP). Dig Liver Dis 2022; 54:1320-1327. [PMID: 35654733 DOI: 10.1016/j.dld.2022.04.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/05/2022] [Accepted: 04/29/2022] [Indexed: 12/29/2022]
Abstract
In recent years, the spectrum of possible treatments for Intestinal Failure (IF)-Short Bowel Syndrome (SBS) has been enriched by the implementation of GLP-2 analogues. In Italy, teduglutide (Ted), an analogue of GLP-2, was approved in January 2021 by the Italian Regulatory Agency for Drugs (AIFA) for IF-SBS patients ≥1 year old. According to the Agency indications, Ted can now be prescribed by regional reference centers, with costs fully charged to the National Health Service. Following pediatric-use approval in our country and in light of scarce evidence in childhood, the pediatric network for IF of the Italian Society for Pediatric Gastroenterology, Hepatology and Nutrition (SIGENP) planned to share management methods of Ted in pediatric IF. The main purpose was to identify the best candidates from a cost-effective perspective. Thus, focusing on available literature and on expert opinions, the present position statement provides consensus-based recommendations on the use of Ted for pediatric gastroenterologists and nutritionists treating children with SBS.
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13
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Hu Y, Cai M, Chu W, Hu Y. Dysbiosis of Gut Microbiota and Lipidomics of Content Induced by Dietary Methionine Restriction in Rice Field Eel (Monopterus albus). Front Microbiol 2022; 13:917051. [PMID: 35875587 PMCID: PMC9301281 DOI: 10.3389/fmicb.2022.917051] [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: 04/10/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
An 8-week feeding trial was conducted using the rice field eel (Monopterus albus) with six isonitrogenous and isoenergetic experimental diets of basic feed supplemented with different levels of methionine (0, 2, 4, 6, 8, or 10 g/kg). This study built upon previous research findings that showed dietary methionine restriction (M0, 0 g/kg) inhibited hepatic fatty acid metabolism and intestinal fatty acid transportation, but both are improved by dietary supplementation with a suitable level of methionine (M8, 8 g/kg). Hence, M0 and M8 were selected to investigate how methionine regulates the gut microbiota and lipidomics of M. albus. Compared with M0, values for gut bacterial Sobs, Shannon, ACE, and Chao1 indices of M8 were remarkably increased (p < 0.05), with Fusobacteria, Firmicutes, and Proteobacteria the dominant phyla and Cetobacterium, Plesiomonas, and Bacillus the main genera in the community under the M0 vs. M8 treatments. However, compared with M0, the proportion of phyla consisting of Fusobacteria decreased in M8, as did the Cetobacterium and Lactococcus at the genus level; conversely, the proportions corresponding to Firmicutes, Proteobacteria, and Chioroflexi phyla increased in M8, as did the Clostridium and Streptococcus genera. Many edges appeared in the circus and networks, demonstrating the interspecies interactions among different operational taxonomic units (OTUs). In addition, various OTUs within the same phylum were clustered within one module. Cooperative interactions were predominant in the two networks, while competitive interactions were prevalent in their submodules. Gut microbiota mainly played roles in nutrition (lipid, amino acid, and carbohydrate) transport and metabolism under the M0 vs. M8 treatments. The PLS-DA scores indicated a significant difference in the main lipidomic components between the M0 and M8 treatment groups. Namely, the TG(26:0/16:0/17:0), TG(28:0/16:0/16:0), TG(26:0/16:0/16:0), and TG(30:0/16:0/16:0)—among others—comprising the gut content were reduced under the M8 treatment (p < 0.001). The genus Clostridium was positively correlated with TG(18:1/18:1/22:5), TG(16:0/17:0/18:1), TG(18:0/18:1/20:3), and other compounds, yet negatively correlated with TG(18:0/17:0/20:0), TG(16:0/17:0/24:0), and TG(16:0/16:0/24:0), among others as well. According to the lipidomics analysis, the predicted KEGG pathways mainly included lipid and glycan biosynthesis and metabolism, and digestive, sensory, and immune systems. In conclusion, methionine restriction disturbed the microbial community balance and induced microbial dysfunctions, whereas methionine supplementation improved the homeostasis of gut microbiota and lipid metabolism of the rice eel.
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Affiliation(s)
- Yajun Hu
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Minglang Cai
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Wuying Chu
- Department of Bioengneering and Environmental Science, Changsha University, Changsha, China
| | - Yi Hu
- Hunan Engineering Technology Research Center of Featured Aquatic Resources Utilization, Hunan Agricultural University, Changsha, China
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
- *Correspondence: Yi Hu,
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14
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Pauline M, Fouhse J, Hinchliffe T, Wizzard P, Patrick Nation, Huynh H, Wales P, Willing B, Turner J. Probiotic Treatment Versus Empiric Oral Antibiotics for Managing Dysbiosis in Short Bowel Syndrome: Impact on the Mucosal and Stool Microbiota, Short Chain Fatty Acids and Adaptation. JPEN J Parenter Enteral Nutr 2022; 46:1828-1838. [PMID: 35383975 DOI: 10.1002/jpen.2377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Infants and children with short bowel syndrome (SBS) are presumed to be at risk of gut microbial dysbiosis with potential sequelae of bacterial overgrowth that include sepsis, D-lactic acidosis, mucosal inflammation and malabsorption. In neonatal piglets with SBS, we compared intestinal microbial composition, short chain fatty acids (SCFA) and adaptation given probiotic treatment (Lactobacillus and Bifidobacterium spp.) versus oral metronidazole. METHODS Following 75% distal small intestinal resection, piglets were allocated to: probiotic (PRO, 500mg BID n=7), metronidazole (MET, 15mg/kg BID n=8) and placebo (PLA, 500mg BID n=8). After 10 days of parenteral and enteral nutrition, 16S rRNA gene amplicon sequencing (colon tissue and stool) were undertaken and SCFA analysis (stool and colon effluent) performed using gas chromatography. RESULTS In colon, Shannon diversity was higher for PRO compared to MET and PLA (p=0.002). PRO and PLA increased abundance of Bacteroidetes species (e.g. Bacteroides fragilis), compared to MET (p<0.001). PRO compared to PLA increased abundance of Firmicutes species (e.g. Lactobacillus fermentum) (p<0.001). MET increased abundance of Proteobacteria members, predominately Enterobacteriaceae compared to PRO (p=0.004). In stool, microbial findings were similar and SCFA (butyrate) concentrations were highest for PRO (p=0.003) compared to MET. CONCLUSION In pediatric SBS, the empiric use of oral antibiotics, such as metronidazole, is common for presumed clinical consequences of microbial dysbiosis. In this study of SBS piglets, that approach was associated with decreased microbial diversity and increased abundance of potentially inflammatory Proteobacteria. In contrast, a probiotic treatment using Lactobacillus and Bifidobacterium spp. increased both diversity and SCFAs. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mirielle Pauline
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Janelle Fouhse
- Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tierah Hinchliffe
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Pamela Wizzard
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Patrick Nation
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Hien Huynh
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Paul Wales
- Department of Surgery, Cincinnati Children's Hospital Medical Center and University of Cincinnati
| | - Benjamin Willing
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Justine Turner
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
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Portincasa P, Bonfrate L, Vacca M, De Angelis M, Farella I, Lanza E, Khalil M, Wang DQH, Sperandio M, Di Ciaula A. Gut Microbiota and Short Chain Fatty Acids: Implications in Glucose Homeostasis. Int J Mol Sci 2022; 23:ijms23031105. [PMID: 35163038 PMCID: PMC8835596 DOI: 10.3390/ijms23031105] [Citation(s) in RCA: 253] [Impact Index Per Article: 126.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 02/07/2023] Open
Abstract
Gut microbiota encompasses a wide variety of commensal microorganisms consisting of trillions of bacteria, fungi, and viruses. This microbial population coexists in symbiosis with the host, and related metabolites have profound effects on human health. In this respect, gut microbiota plays a pivotal role in the regulation of metabolic, endocrine, and immune functions. Bacterial metabolites include the short chain fatty acids (SCFAs) acetate (C2), propionate (C3), and butyrate (C4), which are the most abundant SCFAs in the human body and the most abundant anions in the colon. SCFAs are made from fermentation of dietary fiber and resistant starch in the gut. They modulate several metabolic pathways and are involved in obesity, insulin resistance, and type 2 diabetes. Thus, diet might influence gut microbiota composition and activity, SCFAs production, and metabolic effects. In this narrative review, we discuss the relevant research focusing on the relationship between gut microbiota, SCFAs, and glucose metabolism.
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Affiliation(s)
- Piero Portincasa
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (I.F.); (E.L.); (M.K.); (A.D.C.)
- Correspondence: (P.P.); (L.B.)
| | - Leonilde Bonfrate
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (I.F.); (E.L.); (M.K.); (A.D.C.)
- Correspondence: (P.P.); (L.B.)
| | - Mirco Vacca
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (M.V.); (M.D.A.)
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (M.V.); (M.D.A.)
| | - Ilaria Farella
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (I.F.); (E.L.); (M.K.); (A.D.C.)
| | - Elisa Lanza
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (I.F.); (E.L.); (M.K.); (A.D.C.)
| | - Mohamad Khalil
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (I.F.); (E.L.); (M.K.); (A.D.C.)
| | - David Q.-H. Wang
- Department of Medicine and Genetics, Division of Gastroenterology and Liver Diseases, Marion Bessin Liver Research Center, Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA;
| | - Markus Sperandio
- Biomedical Center (BMC), Institute for Cardiovascular Physiology and Pathophysiology, Walter Brendel Center for Experimental Medicine (WBex), Faculty of Medicine, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany;
| | - Agostino Di Ciaula
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy; (I.F.); (E.L.); (M.K.); (A.D.C.)
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Wang Y, Zheng L, Zhou Z, Yao D, Huang Y, Liu B, Duan Y, Li Y. Review article: insights into the bile acid-gut microbiota axis in intestinal failure-associated liver disease-redefining the treatment approach. Aliment Pharmacol Ther 2022; 55:49-63. [PMID: 34713470 DOI: 10.1111/apt.16676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 06/04/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Intestinal failure-associated liver disease (IFALD) increases mortality of patients with intestinal failure (IF), but lacks effective prevention or treatment approaches. Bile acids, gut microbiota and the host have close and complex interactions, which play a central role in modulating host immune and metabolic homeostasis. Increasing evidence suggests that derangement of the bile acid-gut microbiota (BA-GM) axis contributes to the development of IFALD. AIMS To review the BA-GM axis in the pathogenesis and clinical applications of IFALD, and to explore future directions for effective disease management. METHODS We conducted a literature search on bile acid and gut microbiota in IF and liver diseases. RESULTS The BA-GM axis demonstrates a unique IF signature manifesting as an increase in primary-to-secondary bile acids ratio, disturbed enterohepatic circulation, blunted bile acid signalling pathways, gut microbial dysbiosis, and altered microbial metabolic outputs. Bile acids and gut microbiota shape the compositional and functional alterations of each other in IF; collaboratively, they promote immune dysfunction and metabolic aberration in the liver. Diagnostic markers and treatments targeting the BA-GM axis showed promising potential in the management of IFALD. CONCLUSIONS Bile acids and gut microbiota play a central role in the development of IFALD and make attractive biomarkers as well as therapeutic targets. A multitarget, individualised therapy aiming at different parts of the BA-GM axis may provide optimal clinical benefits and requires future investigation.
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Affiliation(s)
- Yaoxuan Wang
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Lei Zheng
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Zhiyuan Zhou
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Danhua Yao
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Yuhua Huang
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Bin Liu
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Yantao Duan
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
| | - Yousheng Li
- Department of General Surgery, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai, China
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Portincasa P, Bonfrate L, Khalil M, Angelis MD, Calabrese FM, D’Amato M, Wang DQH, Di Ciaula A. Intestinal Barrier and Permeability in Health, Obesity and NAFLD. Biomedicines 2021; 10:83. [PMID: 35052763 PMCID: PMC8773010 DOI: 10.3390/biomedicines10010083] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 02/07/2023] Open
Abstract
The largest surface of the human body exposed to the external environment is the gut. At this level, the intestinal barrier includes luminal microbes, the mucin layer, gastrointestinal motility and secretion, enterocytes, immune cells, gut vascular barrier, and liver barrier. A healthy intestinal barrier is characterized by the selective permeability of nutrients, metabolites, water, and bacterial products, and processes are governed by cellular, neural, immune, and hormonal factors. Disrupted gut permeability (leaky gut syndrome) can represent a predisposing or aggravating condition in obesity and the metabolically associated liver steatosis (nonalcoholic fatty liver disease, NAFLD). In what follows, we describe the morphological-functional features of the intestinal barrier, the role of major modifiers of the intestinal barrier, and discuss the recent evidence pointing to the key role of intestinal permeability in obesity/NAFLD.
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Affiliation(s)
- Piero Portincasa
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari Medical School, 70124 Bari, Italy; (L.B.); (M.K.); (A.D.C.)
| | - Leonilde Bonfrate
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari Medical School, 70124 Bari, Italy; (L.B.); (M.K.); (A.D.C.)
| | - Mohamad Khalil
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari Medical School, 70124 Bari, Italy; (L.B.); (M.K.); (A.D.C.)
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (M.D.A.); (F.M.C.)
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (M.D.A.); (F.M.C.)
| | - Francesco Maria Calabrese
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (M.D.A.); (F.M.C.)
| | - Mauro D’Amato
- Gastrointestinal Genetics Lab, CIC bioGUNE-BRTA, 48160 Derio, Spain;
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - David Q.-H. Wang
- Department of Medicine and Genetics, Division of Gastroenterology and Liver Diseases, Marion Bessin Liver Research Center, Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, New York, NY 10461, USA;
| | - Agostino Di Ciaula
- Clinica Medica “A. Murri”, Department of Biomedical Sciences & Human Oncology, University of Bari Medical School, 70124 Bari, Italy; (L.B.); (M.K.); (A.D.C.)
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18
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Alonso García E, de la Fuente Ordoñez JJ, Lavilla Lerma L, Estudillo-Martínez MD, Castillo-Gutiérrez S, Benomar N, Knapp CW, Abriouel H. Transcriptomic Profile and Probiotic Properties of Lactiplantibacillus pentosus Pre-adapted to Edible Oils. Front Microbiol 2021; 12:747043. [PMID: 34721347 PMCID: PMC8553220 DOI: 10.3389/fmicb.2021.747043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, we determined whether pre-adapting Lactiplantibacillus pentosus strains, isolated from Aloreña green table olives, to vegetable-based edible oils improved their robustness and functionality; this may have great importance on their stress response during fermentation, storage, and digestion. Pre-adapting the strains to the corresponding oils significantly increased their probiotic functionality (e.g., auto-aggregation, co-aggregation with pathogens, and mucin adhesion), although results depended on the strain and the oil used for pre-adaptation. As such, we selected olive-adapted (TO) L. pentosus AP2-16, which exhibited improved functionality, and subjected it to transcriptomic profiling with the aim to understand the molecular mechanisms involved in the adaptation and the increased functionality. Global transcriptomic analysis of oil-adapted (olive or almond) and non-adapted (control) L. pentosus AP2-16 realized that 3,259 genes were expressed, with 2,779 mapped to the reference database. Comparative transcriptomic analysis showed that 125 genes (olive vs. control) and 108 genes (olive vs. almond) became significantly differentially expressed. TO L. pentosus AP2-16 responded by rerouting its metabolic pathways to balance energy production and storage, cell growth and survivability, host interactions (glycoconjugates), and other physiological features. As such, the pre-adaptation of lactobacilli with olive oil switches their transcriptional network to regulate robustness and functionality, possibly representing a novel approach toward the design and manufacture of probiotic products with improved stability and functionality.
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Affiliation(s)
- Esther Alonso García
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Juan José de la Fuente Ordoñez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Leyre Lavilla Lerma
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - María D Estudillo-Martínez
- Área de Estadística e Investigación Operativa, Departamento de Estadística e Investigación Operativa, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Sonia Castillo-Gutiérrez
- Área de Estadística e Investigación Operativa, Departamento de Estadística e Investigación Operativa, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Charles W Knapp
- Centre for Water, Environment, Sustainability and Public Health, Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom
| | - Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
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19
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Josyabhatla R, Imseis EM. Pediatric intestinal failure and the microbiome. Semin Perinatol 2021; 45:151453. [PMID: 34332780 DOI: 10.1016/j.semperi.2021.151453] [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: 01/10/2023]
Abstract
Neonatal intestinal failure is a complex medical condition that is associated with the need for long term parenteral nutrition and its associated complications. The microbiome in this diseased state is different from what is now understood to be a healthy microbiome. The effect of this dysbiotic microbiome on the complications of intestinal failure are only starting to be understood. The ability to modulate the microbiome with enteral/parenteral nutrients, as well probiotics to a healthier state, is an exciting opportunity that holds promise.
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Affiliation(s)
- Rohit Josyabhatla
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Texas Health Science Center at Houston, TX, USA
| | - Essam M Imseis
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Texas Health Science Center at Houston, TX, USA.
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20
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Zhang Y, Li JX, Zhang Y, Wang YL. Intestinal microbiota participates in nonalcoholic fatty liver disease progression by affecting intestinal homeostasis. World J Clin Cases 2021; 9:6654-6662. [PMID: 34447812 PMCID: PMC8362529 DOI: 10.12998/wjcc.v9.i23.6654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/25/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disease with a pathogenesis that has not been fully elucidated. With the development of the theory of the gut-liver axis and the deepening of related research, the role of the intestinal tract in the pathogenesis of NAFLD has been investigated more. Intestinal microbiota, intestinal metabolites, and intestinal epithelial and immune-based barriers constitute the intestinal environment, which uses crosstalk to maintain the homeostasis of the intestinal environment. This paper reviews the progress in the study of intestinal microbiota, intestinal environment, and NAFLD and suggests that repair of intestinal functional balance may be a new idea for early prevention and intervention of NAFLD.
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Affiliation(s)
- Yang Zhang
- Department of Gastroenterology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing 100078, China
| | - Jun-Xiang Li
- Department of Gastroenterology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing 100078, China
| | - Yan Zhang
- Department of Gastroenterology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing 100078, China
| | - Yun-Liang Wang
- Department of Gastroenterology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing 100078, China
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21
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Kayama H, Okumura R, Takeda K. Interaction Between the Microbiota, Epithelia, and Immune Cells in the Intestine. Annu Rev Immunol 2021; 38:23-48. [PMID: 32340570 DOI: 10.1146/annurev-immunol-070119-115104] [Citation(s) in RCA: 310] [Impact Index Per Article: 103.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The gastrointestinal tract harbors numerous commensal bacteria, referred to as the microbiota, that benefit host health by digesting dietary components and eliminating pathogens. The intestinal microbiota maintains epithelial barrier integrity and shapes the mucosal immune system, balancing host defense and oral tolerance with microbial metabolites, components, and attachment to host cells. To avoid aberrant immune responses, epithelial cells segregate the intestinal microbiota from immune cells by constructing chemical and physical barriers, leading to the establishment of host-commensal mutualism. Furthermore, intestinal immune cells participate in the maintenance of a healthy microbiota community and reinforce epithelial barrier functions. Perturbations of the microbiota composition are commonly observed in patients with autoimmune diseases and chronic inflammatory disorders. An understanding of the intimate interactions between the intestinal microbiota, epithelial cells, and immune cells that are crucial for the maintenance of intestinal homeostasis might promote advances in diagnostic and therapeutic approaches for various diseases.
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Affiliation(s)
- Hisako Kayama
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; , , .,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan.,Institute for Advanced Co-Creation Studies, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryu Okumura
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; , , .,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kiyoshi Takeda
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; , , .,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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22
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Neelis EG, de Koning BAE, Hulst JM, Papadopoulou R, Kerbiriou C, Rings EHHM, Wijnen RMH, Nichols B, Gerasimidis K. Gut microbiota and its diet-related activity in children with intestinal failure receiving long-term parenteral nutrition. JPEN J Parenter Enteral Nutr 2021; 46:693-708. [PMID: 33982321 PMCID: PMC9255855 DOI: 10.1002/jpen.2188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background This study characterized gut microbiota and its diet‐related activity in children with intestinal failure (IF) receiving parenteral nutrition (PN) compared with those of healthy controls (HC) and in relation to disease characteristics. Methods The fecal microbiota and short‐chain fatty acids (SCFAs) were measured in 15 IF patients (n = 68) and 25 HC (n = 25). Results Patients with IF had a lower bacterial load (P = .003), diversity (P < .001), evenness (P < .001) and richness (P = 0.006) than HC. Patients with surgical IF had lower diversity (P < .039) than those with functional IF. Propionic acid and butyric acid (p < .001) were lower and d‐lactate and l‐lactate were higher (p < 0.001) in IF patients than in HC. The energy supplied by PN (%PN) was negatively associated with microbiota diversity and SCFA profile. IF patients had more Escherichia‐Shigella (P = .006), Cronobacter (P = .001), and Staphylococcus (Operational Taxonomic Unit 14, P < .001) and less Faecalibacterium (P < 0.001) and Ruminococcus 1 and 2 (P < .001). Duration of PN (P = .005), %PN (P = .005), and fiber intake (P = .011) were predictive of microbiota structure. Higher intake of enteral nutrition was associated with microbiota structure and function closer to those of HC. Conclusions Microbiota composition and its diet‐related function are altered in IF, with depletion of beneficial SCFAs and species and supraphysiological increase of potentially harmful pathobionts. The influence of this compositional and functional microbial dysbiosis on patients’ outcomes and management warrants further exploration.
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Affiliation(s)
- Esther G Neelis
- Department of Pediatric Gastroenterology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Barbara A E de Koning
- Department of Pediatric Gastroenterology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Jessie M Hulst
- Department of Pediatric Gastroenterology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands.,Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rodanthi Papadopoulou
- Human Nutrition, School of Medicine, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Caroline Kerbiriou
- Human Nutrition, School of Medicine, College of Medicine, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Edmond H H M Rings
- Department of Pediatric Gastroenterology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands.,Department of Pediatric Gastroenterology, Leiden University Medical Center-Willem Alexander Children's Hospital, Leiden, The Netherlands
| | - René M H Wijnen
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Ben Nichols
- Department of Pediatric Gastroenterology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Konstantinos Gerasimidis
- Department of Pediatric Gastroenterology, Erasmus Medical Center-Sophia Children's Hospital, Rotterdam, The Netherlands
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23
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miRNA Profiling in the Chicken Liver under the Influence of Early Microbiota Stimulation with Probiotic, Prebiotic, and Synbiotic. Genes (Basel) 2021; 12:genes12050685. [PMID: 34062867 PMCID: PMC8147272 DOI: 10.3390/genes12050685] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is a form of interaction of the external environment on reading and transcription of genetic information encoded in nucleic acids. We provided evidence that early stimulation of the chicken microbiota with in ovo delivered synbiotics influenced gene expression and DNA methylation in the liver. Therefore, we hypothesize that the stimulation of microbiota by administering bioactive substances in ovo also affects the activity of miRNA in liver. For the analysis of miRNA activity, RNA was isolated from liver of adult broiler chicken and native chicken breed. The animals received a prebiotic, probiotic and synbiotic in ovo on day 12 of egg incubation. The analysis of miRNA expression was performed using the LNA method on a miRNA panel selected on the basis of previous microarray experiments. We have found increased miRNA expression activity after probiotic and synbiotic administration, especially in native chicken breed. Our results suggest that prebiotics reduce or do not affect miRNA activity. We have also shown that miRNA activity is regulated by the substance and genotype of the chicken. We can conclude that miRNAs constitute an important component of the molecular mechanism of host–probiotic interaction in liver.
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24
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Thänert R, Thänert A, Ou J, Bajinting A, Burnham CAD, Engelstad HJ, Tecos ME, Ndao IM, Hall-Moore C, Rouggly-Nickless C, Carl MA, Rubin DC, Davidson NO, Tarr PI, Warner BB, Dantas G, Warner BW. Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. Gut Microbes 2021; 13:1940792. [PMID: 34264786 PMCID: PMC8284144 DOI: 10.1080/19490976.2021.1940792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 02/08/2023] Open
Abstract
Surgical removal of the intestine, lifesaving in catastrophic gastrointestinal disorders of infancy, can result in a form of intestinal failure known as short bowel syndrome (SBS). Bloodstream infections (BSIs) are a major challenge in pediatric SBS management. BSIs require frequent antibiotic therapy, with ill-defined consequences for the gut microbiome and childhood health. Here, we combine serial stool collection, shotgun metagenomic sequencing, multivariate statistics and genome-resolved strain-tracking in a cohort of 19 patients with surgically-induced SBS to show that antibiotic-driven intestinal dysbiosis in SBS enriches for persistent intestinal colonization with BSI causative pathogens in SBS. Comparing the gut microbiome composition of SBS patients over the first 4 years of life to 19 age-matched term and 18 preterm controls, we find that SBS gut microbiota diversity and composition was persistently altered compared to controls. Commensals including Ruminococcus, Bifidobacterium, Eubacterium, and Clostridium species were depleted in SBS, while pathobionts (Enterococcus) were enriched. Integrating clinical covariates with gut microbiome composition in pediatric SBS, we identified dietary and antibiotic exposures as the main drivers of these alterations. Moreover, antibiotic resistance genes, specifically broad-spectrum efflux pumps, were at a higher abundance in SBS, while putatively beneficial microbiota functions, including amino acid and vitamin biosynthesis, were depleted. Moreover, using strain-tracking we found that the SBS gut microbiome harbors BSI causing pathogens, which can persist intestinally throughout the first years of life. The association between antibiotic-driven gut dysbiosis and enrichment of intestinal pathobionts isolated from BSI suggests that antibiotic treatment may predispose SBS patients to infection. Persistence of pathobionts and depletion of beneficial microbiota and functionalities in SBS highlights the need for microbiota-targeted interventions to prevent infection and facilitate intestinal adaptation.
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Affiliation(s)
- Robert Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Anna Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jocelyn Ou
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Adam Bajinting
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Holly J. Engelstad
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Maria E. Tecos
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - I. Malick Ndao
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carla Hall-Moore
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Colleen Rouggly-Nickless
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mike A. Carl
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Deborah C. Rubin
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Nicholas O. Davidson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Phillip I. Tarr
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Barbara B. Warner
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Brad W. Warner
- Division of Pediatric Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
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25
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Gazit VA, Swietlicki EA, Liang MU, Surti A, McDaniel R, Geisman M, Alvarado DM, Ciorba MA, Bochicchio G, Ilahi O, Kirby J, Symons WJ, Davidson NO, Levin MS, Rubin DC. Stem cell and niche regulation in human short bowel syndrome. JCI Insight 2020; 5:137905. [PMID: 33141758 PMCID: PMC7714413 DOI: 10.1172/jci.insight.137905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 10/28/2020] [Indexed: 12/20/2022] Open
Abstract
Loss of functional small bowel surface area following surgical resection for disorders such as Crohn’s disease, intestinal ischemic injury, radiation enteritis, and in children, necrotizing enterocolitis, atresia, and gastroschisis, may result in short bowel syndrome, with attendant high morbidity, mortality, and health care costs in the United States. Following resection, the remaining small bowel epithelium mounts an adaptive response, resulting in increased crypt cell proliferation, increased villus height, increased crypt depth, and enhanced nutrient and electrolyte absorption. Although these morphologic and functional changes are well described in animal models, the adaptive response in humans is less well understood. Clinically the response is unpredictable and often inadequate. Here we address the hypotheses that human intestinal stem cell populations are expanded and that the stem cell niche is regulated following massive gut resection in short bowel syndrome (SBS). We use intestinal enteroid cultures from patients with SBS to show that the magnitude and phenotype of the adaptive stem cell response are both regulated by stromal niche cells, including intestinal subepithelial myofibroblasts, which are activated by intestinal resection to enhance epithelial stem and proliferative cell responses. Our data suggest that myofibroblast regulation of bone morphogenetic protein signaling pathways plays a role in the gut adaptive response after resection. LGR5+ stem cells are expanded and BMP signaling regulates the stem cell niche in human short bowel syndrome.
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Affiliation(s)
- Vered A Gazit
- Division of Gastroenterology, John T. Milliken Department of Medicine
| | | | - Miranda U Liang
- Division of Gastroenterology, John T. Milliken Department of Medicine
| | - Adam Surti
- Division of Gastroenterology, John T. Milliken Department of Medicine
| | - Raechel McDaniel
- Division of Gastroenterology, John T. Milliken Department of Medicine
| | - Mackenzie Geisman
- Division of Gastroenterology, John T. Milliken Department of Medicine
| | - David M Alvarado
- Division of Gastroenterology, John T. Milliken Department of Medicine
| | - Matthew A Ciorba
- Division of Gastroenterology, John T. Milliken Department of Medicine
| | | | | | | | | | - Nicholas O Davidson
- Division of Gastroenterology, John T. Milliken Department of Medicine.,Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Marc S Levin
- Division of Gastroenterology, John T. Milliken Department of Medicine.,Veterans Affairs Medical Center, St. Louis, Missouri, USA
| | - Deborah C Rubin
- Division of Gastroenterology, John T. Milliken Department of Medicine.,Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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26
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Chiplunker AJ, Chen L, Levin MS, Warner BW, Davidson NO, Rubin DC. Increased Adiposity and Reduced Lean Body Mass in Patients with Short Bowel Syndrome. Dig Dis Sci 2020; 65:3271-3279. [PMID: 31907775 PMCID: PMC7924810 DOI: 10.1007/s10620-019-06032-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 12/24/2019] [Indexed: 01/25/2023]
Abstract
BACKGROUND Few studies have examined the metabolic consequences of short bowel syndrome (SBS) and its effects on body composition in adults. We hypothesized that body composition of SBS patients is altered compared to a normal age-, race-, and sex-matched population, regardless of parenteral nutrition (PN) dependence. AIM To compare the body composition of adult patients with SBS to age-, sex-, and race-matched healthy controls. METHODS Twenty patients with SBS underwent body composition analysis using the GE Lunar iDXA scanner. Patients were age-, sex-, and race-matched to controls from the National Health and Nutrition Examination Survey (1999-2004). Mean differences in body mass index, fat-free mass, fat mass, percent body fat, visceral adipose tissue mass and volume, and bone mineral density were measured. Statistical analysis was performed using SAS 9.4 software. RESULTS Fifty-five percent of subjects had a history of PN use, and 30% were current PN users. Mean percent body fat for SBS patients was 35.1% compared to 30.9% for healthy controls (p = 0.043). Fat-free mass was reduced in SBS (p = 0.007). Patients with reduced bone mass had a trend toward significantly more years of PN exposure compared to those with normal bone mass (p = 0.094), and a trend toward older age (p = 0.075). CONCLUSIONS SBS is associated with increased percent body fat and reduced fat-free mass, suggesting that improved dietary and therapeutic interventions are needed to restore normal metabolic indices and avoid risk of metabolic syndrome in SBS patients.
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Affiliation(s)
- Adeeti J. Chiplunker
- Department of Medicine, Division of Gastroenterology, Washington University in St. Louis School of Medicine
| | - Ling Chen
- Division of Biostatistics, Washington University in St. Louis School of Medicine
| | - Marc S. Levin
- Department of Medicine, Division of Gastroenterology, Washington University in St. Louis School of Medicine.,VA St. Louis Health Care System, Washington University in St. Louis School of Medicine
| | - Brad W. Warner
- Division of Pediatric Surgery St. Louis Children’s Hospital, Washington University in St. Louis School of Medicine
| | - Nicholas O. Davidson
- Department of Medicine, Division of Gastroenterology, Washington University in St. Louis School of Medicine.,Department of Developmental Biology; Washington University in St. Louis School of Medicine
| | - Deborah C. Rubin
- Department of Medicine, Division of Gastroenterology, Washington University in St. Louis School of Medicine.,Department of Developmental Biology; Washington University in St. Louis School of Medicine
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Lin L, Wang Y, Xu L, Liu J, Zhu W, Mao S. Microbiome-host co-oscillation patterns in remodeling of colonic homeostasis during adaptation to a high-grain diet in a sheep model. Anim Microbiome 2020; 2:22. [PMID: 33499965 PMCID: PMC7807687 DOI: 10.1186/s42523-020-00041-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ruminant gastrointestinal tract homeostasis deploys interactive microbiome-host metabolic communication and signaling axes to underpin the fitness of the host. After this stable niche is destroyed by environmental triggers, remodeling of homeostasis can occur as a spontaneous physiological compensatory actor. RESULTS In this study, 20 sheep were randomly divided into four groups: a hay-fed control (CON) group and a high-grain (HG) diet group for 7, 14, or 28 days. Then, we examined 16S rRNA gene sequences and transcriptome sequences to outline the microbiome-host co-oscillation patterns in remodeling of colonic homeostasis in a sheep model during adaptation to a HG diet. Our data revealed that with durations of an HG diet, the higher starch levels directly affected the colonic lumen environment (lower pH and higher fermentation parameters), which in turn filtered lumen-specific functional taxonomic groups (HG-sensitive and HG-tolerant taxa). The colonic epithelium then gave rise to a new niche that triggered endoplasmic reticulum stress to activate unfolded protein response, if the duration of endoplasmic reticulum stress was overlong, this process would regulate cell apoptosis (Caspase-3, Caspase-8, and TNFRSF21) to achieve a functional transformation. CONCLUSIONS Our results provide a holistic view of the colonic microbial assemblages and epithelium functional profile co-oscillation patterns in remodeling of colonic homeostasis during adaptation to an HG diet in a sheep model. These findings also provide a proof of concept that the microbe-host collaboration is vital for maintaining hindgut homeostasis to adapt to dietary dichotomies.
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Affiliation(s)
- Limei Lin
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration center of Animal Science, National Center for International Research on Animal Gut Nutrition, Centre for ruminant nutrition and feed engineering technology research, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yue Wang
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration center of Animal Science, National Center for International Research on Animal Gut Nutrition, Centre for ruminant nutrition and feed engineering technology research, Nanjing Agricultural University, Nanjing, 210095 China
| | - Lei Xu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration center of Animal Science, National Center for International Research on Animal Gut Nutrition, Centre for ruminant nutrition and feed engineering technology research, Nanjing Agricultural University, Nanjing, 210095 China
| | - Junhua Liu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration center of Animal Science, National Center for International Research on Animal Gut Nutrition, Centre for ruminant nutrition and feed engineering technology research, Nanjing Agricultural University, Nanjing, 210095 China
| | - Weiyun Zhu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration center of Animal Science, National Center for International Research on Animal Gut Nutrition, Centre for ruminant nutrition and feed engineering technology research, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shengyong Mao
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, Laboratory of Gastrointestinal Microbiology, National Experimental Teaching Demonstration center of Animal Science, National Center for International Research on Animal Gut Nutrition, Centre for ruminant nutrition and feed engineering technology research, Nanjing Agricultural University, Nanjing, 210095 China
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Le Beyec J, Billiauws L, Bado A, Joly F, Le Gall M. Short Bowel Syndrome: A Paradigm for Intestinal Adaptation to Nutrition? Annu Rev Nutr 2020; 40:299-321. [PMID: 32631145 DOI: 10.1146/annurev-nutr-011720-122203] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Short bowel syndrome (SBS) is a rare disease that results from extensive resection of the intestine. When the remaining absorption surface of the intestine cannot absorb enough macronutrients, micronutrients, and water, SBS results in intestinal failure (IF). Patients with SBS who suffer from IF require parenteral nutrition for survival, but long-term parenteral nutrition may lead to complications such as catheter sepsis and metabolic diseases. Spontaneous intestinal adaptation occurs weeks to months after resection, resulting in hyperplasia of the remnant gut, modification of gut hormone levels, dysbiosis, and hyperphagia. Oral nutrition and presence of the colon are two major positive drivers for this adaptation. This review aims to summarize the current knowledge of the mechanisms underlying spontaneous intestinal adaptation, particularly in response to modifications of luminal content, including nutrients. In the future, dietary manipulations could be used to treat SBS.
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Affiliation(s)
- Johanne Le Beyec
- Centre de Recherche sur l'Inflammation, INSERM UMRS-1149, Assistance Publique-Hôpitaux de Paris, Université de Paris, 75018 Paris, France; .,Service de Biochimie Endocrinienne et Oncologique, Hôpital Pitié-Salpêtrière-Charles Foix, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, 75013 Paris, France
| | - Lore Billiauws
- Centre de Recherche sur l'Inflammation, INSERM UMRS-1149, Assistance Publique-Hôpitaux de Paris, Université de Paris, 75018 Paris, France; .,Service de Gastroentérologie, MICI et Assistance Nutritive, Groupe Hospitalier Universitaire Paris Nord Val de Seine (GHUPNVS), Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Université de Paris, 92110 Clichy, France
| | - André Bado
- Centre de Recherche sur l'Inflammation, INSERM UMRS-1149, Assistance Publique-Hôpitaux de Paris, Université de Paris, 75018 Paris, France;
| | - Francisca Joly
- Centre de Recherche sur l'Inflammation, INSERM UMRS-1149, Assistance Publique-Hôpitaux de Paris, Université de Paris, 75018 Paris, France; .,Service de Gastroentérologie, MICI et Assistance Nutritive, Groupe Hospitalier Universitaire Paris Nord Val de Seine (GHUPNVS), Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Université de Paris, 92110 Clichy, France
| | - Maude Le Gall
- Centre de Recherche sur l'Inflammation, INSERM UMRS-1149, Assistance Publique-Hôpitaux de Paris, Université de Paris, 75018 Paris, France;
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Alterations in the Gut Microbiome and Suppression of Histone Deacetylases by Resveratrol Are Associated with Attenuation of Colonic Inflammation and Protection Against Colorectal Cancer. J Clin Med 2020; 9:jcm9061796. [PMID: 32526927 PMCID: PMC7355848 DOI: 10.3390/jcm9061796] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is known to significantly increase the risk for development of colorectal cancer (CRC), suggesting inflammation and cancer development are closely intertwined. Thus, agents that suppress inflammation may prevent the onset of cancer. In the current study, we used resveratrol, an anti-inflammatory stilbenoid, to study the role of microbiota in preventing inflammation-driven CRC. Resveratrol treatment in the azoxymethane (AOM) and dextran sodium sulphate (DSS) CRC murine model caused an increase in anti-inflammatory CD4 + FOXP3 + (Tregs) and CD4 + IL10 + cells, a decrease in proinflammatory Th1 and Th17 cells, and attenuated CRC development. Gut microbial profile studies demonstrated that resveratrol altered the gut microbiome and short chain fatty acid (SCFA), with modest increases in n-butyric acid and a potential butyrate precursor isobutyric acid. Fecal transfer from resveratrol-treated CRC mice and butyrate supplementation resulted in attenuation of disease and suppression of the inflammatory T cell response. Data also revealed both resveratrol and sodium butyrate (BUT) were capable of inhibiting histone deacetylases (HDACs), correlating with Treg induction. Analysis of The Cancer Genome Atlas (TCGA) datasets revealed increased expression of Treg-specific transcription factor FoxP3 or anti-inflammatory IL-10 resulted in an increase in 5-year survival of patients with CRC. These data suggest that alterations in the gut microbiome lead to an anti-inflammatory T cell response, leading to attenuation of inflammation-driven CRC.
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Metabolism and Interaction with Food Components. Int J Mol Sci 2020; 21:ijms21103688. [PMID: 32456257 PMCID: PMC7279363 DOI: 10.3390/ijms21103688] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
The human gut contains trillions of microbes that play a central role in host biology, including the provision of key nutrients from the diet. Food is a major source of precursors for metabolite production; in fact, diet modulates the gut microbiota (GM) as the nutrients, derived from dietary intake, reach the GM, affecting both the ecosystem and microbial metabolic profile. GM metabolic ability has an impact on human nutritional status from childhood. However, there is a wide variability of dietary patterns that exist among individuals. The study of interactions with the host via GM metabolic pathways is an interesting field of research in medicine, as microbiota members produce myriads of molecules with many bioactive properties. Indeed, much evidence has demonstrated the importance of metabolites produced by the bacterial metabolism from foods at the gut level that dynamically participate in various biochemical mechanisms of a cell as a reaction to environmental stimuli. Hence, the GM modulate homeostasis at the gut level, and the alteration in their composition can concur in disease onset or progression, including immunological, inflammatory, and metabolic disorders, as well as cancer. Understanding the gut microbe–nutrient interactions will increase our knowledge of how diet affects host health and disease, thus enabling personalized therapeutics and nutrition.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Viale San Paolo 15, 00146 Rome, Italy;
- Correspondence: ; Tel.: +39-0668-594061; Fax: +39-0668-592218
| | - Federica Del Chierico
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Viale San Paolo 15, 00146 Rome, Italy;
| | - Lorenza Putignani
- Unit of Parasitology and Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Piazza Sant’ Onofrio 4, 00165 Rome, Italy;
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31
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Zhang A, Sodhi CP, Wang M, Shores DR, Fulton W, Prindle T, Brosten S, O'Hare E, Lau A, Ding H, Jia H, Lu P, White JR, Hui J, Sears CL, Hackam DJ, Alaish SM. A Central Role for Lipocalin-2 in the Adaptation to Short-Bowel Syndrome Through Down-Regulation of IL22 in Mice. Cell Mol Gastroenterol Hepatol 2020; 10:309-326. [PMID: 32330729 PMCID: PMC7327842 DOI: 10.1016/j.jcmgh.2020.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/10/2022]
Abstract
BACKGROUND & AIMS In short-bowel syndrome (SBS), inadequate intestinal adaptation is responsible for the majority of complications, including sepsis, liver failure, and death. In this study, we sought to further delineate the adaptive response to identify potential therapeutic targets. METHODS We performed a 75% small-bowel resection (SBR) or sham operation on C57Bl/6J wild-type (WT), lipocalin-2 (LCN2)-/-, and interleukin 22 (IL22)-/- mice. Exogenous IL22 was administered to SBR WT mice. Cecal fecal matter from SBR WT and SBR LCN2-/- mice were transplanted into germ-free mice. Intestinal permeability, inflammation, proliferation, and the microbiome were evaluated 1 week after surgery. CD4+IL22+ laminal propria lymphocytes were sorted by flow cytometry. Naïve T cells were polarized to T-helper cells with or without LCN2. RESULTS A 75% SBR in a mouse re-creates the increased intestinal permeability, enterocyte proliferation, and intestinal dysbiosis seen in SBS. LCN2 expression increases after 75% SBR, and this increase can be abrogated with broad-spectrum antibiotic treatment. LCN2-/- mice have less intestinal inflammation, increased IL22 expression, and greater adaptation as evidenced by less intestinal permeability, increased carbohydrate enzyme expression, less weight loss, and less dysbiosis after 75% SBR than WT mice. The proinflammatory and anti-adaptive effects of LCN2 can be transferred to germ-free mice via a fecal transplant. Administration of exogenous IL22 improves adaptation and restores the normal microbiome after 75% SBR in WT mice. CONCLUSIONS LCN2 promotes inflammation and slows intestinal adaptation through changes in the microbiome and IL22 inhibition in a mouse SBS model. Strategies to reduce LCN2 may offer novel therapeutic approaches to enhance adaptation in SBS.
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Affiliation(s)
- Ailan Zhang
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chhinder P Sodhi
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Menghan Wang
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Darla R Shores
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - William Fulton
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Thomas Prindle
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Serena Brosten
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elizabeth O'Hare
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexander Lau
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hua Ding
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hongpeng Jia
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peng Lu
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Justin Hui
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cynthia L Sears
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David J Hackam
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Samuel M Alaish
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Abstract
Understanding how health-promoting microbiota are established and their beneficial interactions with the host is of critical biomedical importance. The current high throughput data acquisition technologies allow for integrating components of the gut ecosystem. The richness of data types and large number of measured variables involved underscores the critical importance of the appropriate choice of analytical and computational methods that can be used to model this complex ecosystem. This review outlines currently used approaches to perform analyses of data obtained as a result of interrogation of the gut-microbiota ecosystem and the challenges associated with these methodological and computational efforts. The problem of large dimensionality versus small numbers of samples is explained with discussions of clustering, dimensionality reduction, and statistical testing. Predictive modeling and data integration specific to the gut ecosystem are also discussed.
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Affiliation(s)
- Ivan Ivanov
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, USA.
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33
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Berlin P, Reiner J, Witte M, Wobar J, Lindemann S, Barrantes I, Kreikemeyer B, Bastian M, Schäffler H, Bannert K, Jaster R, Lamprecht G. Nod2 deficiency functionally impairs adaptation to short bowel syndrome via alterations of the epithelial barrier function. Am J Physiol Gastrointest Liver Physiol 2019; 317:G727-G738. [PMID: 31509436 DOI: 10.1152/ajpgi.00117.2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) gene mutations are a risk factor for Crohn's disease and also associated with worse outcome in short bowel syndrome (SBS) patients independent of the underlying disease. The aim of this study was to analyze the effect of Nod2 deficiency on barrier function and stool microbiome after extensive ileocecal resection in mice. Male C57BL6/J wild-type (WT) and Nod2-knockout (KO) mice underwent 40% ileocecal resection. Sham control mice received simple transection of the ileum. Clinical outcome was monitored daily. Barrier function was measured with Ussing chambers using FITC-4-kDa-Dextran flux, transmucosal electrical resistance, and dilution potentials. Immunofluorescence of claudin-2 was studied. Composition of the stool microbiome was assessed by 16S rRNA gene sequencing. Resected Nod2-KO mice had impaired clinical outcome compared with resected WT mice. This was accompanied by increased stool water contents and increased plasma aldosterone. Histomorphological adaptation was independent of Nod2. Barrier function studies revealed impaired sodium to chloride permeability and altered claudin-2 localization in the absence of Nod2. Resection induced decreases of bacterial diversity and a shift of bacteriodetes-to-firmicutes ratios. Ileum and cecum resection-induced increase in proteobacteria was absent in Nod2-deficient mice. Verrucomicrobia were temporarily increased in Nod2-KO mice. Nod2 deficiency functionally impairs adaptation to short bowel syndrome via a lesser increase of epithelial sodium pore permeability, altered epithelial barrier function, and the microbiome.NEW & NOTEWORTHYNOD2 gene mutations are associated with the development of severe short bowel syndrome and intestinal failure. The influence of Nod2 mutations on intestinal adaptation in experimental short bowel syndrome has not been studied yet. Here, we provide data that Nod2 deficiency worsens clinical outcome and functional adaptation under SBS conditions in mice, indicating that NOD2 is required for successful adaptation after ileocecal resection.
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Affiliation(s)
- Peggy Berlin
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Johannes Reiner
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Maria Witte
- Department of General, Thoracic, Vascular, and Transplantation Surgery, Rostock University Medical Center, Rostock, Germany
| | - Jakob Wobar
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Sabeth Lindemann
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Israel Barrantes
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Bernd Kreikemeyer
- Institute for Microbiology, Virology, and Hygiene, University of Medicine Rostock, Rostock, Germany
| | - Manuela Bastian
- Institute for Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, Rostock, Germany
| | - Holger Schäffler
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Karen Bannert
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Robert Jaster
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
| | - Georg Lamprecht
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Rostock, Germany
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Zhu S, Liu S, Li H, Zhang Z, Zhang Q, Chen L, Zhao Y, Chen Y, Gu J, Min L, Zhang S. Identification of Gut Microbiota and Metabolites Signature in Patients With Irritable Bowel Syndrome. Front Cell Infect Microbiol 2019; 9:346. [PMID: 31681624 PMCID: PMC6813219 DOI: 10.3389/fcimb.2019.00346] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
Background and Aims: Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder. However, the underlying mechanism of IBS is not fully understood. The aim of this study was to investigate potential mechanism and novel biomarkers of IBS through evaluation of the metabolomic and microbiologic profile. Methods: Fecal samples were collected from 15 irritable bowel syndrome patients and 15 healthy controls. By using gas chromatography coupled to time-of-flight mass spectrometry (GC-TOFMS) and 16S rDNA amplicon sequencing, fecal metabolites and microbiota of healthy controls and the IBS patients were measured. Results: IBS patients had a significantly differential metabolite profile as compared to healthy controls, and 4 clusters with 31 metabolites, including a group of amino acids and fatty acids, were significantly up-regulated as compared to the healthy controls. In addition, 19 microbes were significantly up-regulated, and 12 microbes were down-regulated in the IBS group, when compared with the healthy controls. Some clusters of fecal metabolites or microorganisms were significantly correlated with the severity of IBS symptoms, such as the frequency of abdominal pain/discomfort and the number of bowel movements. Correlation of the metabolite levels with abundances of microbial genera showed some statistically significant metabolite-microbe associations. Four differentially abundant amino acids clustered together were positively correlated with some microbes, including Lachnospira, Clostridium, and so on. Conclusion: The finding of this study puts a global perspective on metabolomics and microbiota profiling in IBS patients and provides a theoretical basis for future research on pathophysiology of IBS.
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Affiliation(s)
- Shengtao Zhu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Si Liu
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Hengcun Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Zheng Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Qian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Lei Chen
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Yu Zhao
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Yang Chen
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic and Systems Biology, Department of Automation, BNRist, Tsinghua University, Beijing, China
| | - Junchao Gu
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Li Min
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, China
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Federici M. Gut microbiome and microbial metabolites: a new system affecting metabolic disorders. J Endocrinol Invest 2019; 42:1011-1018. [PMID: 30788772 DOI: 10.1007/s40618-019-01022-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/12/2019] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The gut microbiome is emerging as an important player in the field of metabolic disorders. MATERIALS AND METHODS Currently, several studies are ongoing to determine whether the effect of gut microbiome on obesity, type 2 diabetes, non-alcoholic fatty liver disease, and other metabolic diseases is determined by singular species or rather by a functional role of bacterial metabolism at higher taxonomical level. Deciphering if a single or more species are responsible for metabolic traits or rather microbial metabolic pathways are responsible for effects on host metabolism may help to identify appropriate dietary interventions to support microbial functions according to the prevalent host disease. Furthermore, the combination of metagenomics and metabolomics-based signature might be applied in the future to improve the risk prediction in healthy subjects. CONCLUSION In this review, I will summarize the current findings regarding the role of gut microbiome and metabolites in metabolic disorders to argue whether the current achievements may be translated into clinical practice.
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Affiliation(s)
- M Federici
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133, Rome, Italy.
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Park CJ, Armenia SJ, Shaughnessy MP, Greig CJ, Cowles RA. Potentiation of serotonin signaling leads to increased carbohydrate and lipid absorption in the murine small intestine. J Pediatr Surg 2019; 54:1245-1249. [PMID: 30879746 DOI: 10.1016/j.jpedsurg.2019.02.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 02/21/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Enteric serotonin influences intestinal homeostasis and functions as a mucosal growth factor. Previously, we demonstrated increased mucosal surface area and enhanced crypt cell proliferation in serotonin reuptake transporter (SERT)-deficient mice. Therefore, we hypothesized that serotonin-mediated mucosal growth would also result in enhanced carbohydrate and lipid absorption. MATERIAL AND METHODS Wild-type C57Bl/6 (WT) and SERT-knockout (SERTKO) mice were fasted then gavaged with D-xylose or boron-dipyrromethene (BODIPY) FL-C12 medium-chain fatty acid analog. Serum D-xylose and BODIPY concentrations were serially measured from blood drawn at 30 to 360 min post-gavage. Small intestine was harvested from both groups for comparison of morphometric parameters. Area under the curve of plotted graphs was calculated, and means were compared with Student's t-test to a significance of p < 0.05. RESULTS Villus height and crypt depth were significantly greater in the middle and distal small intestine of SERTKO animals compared to WT. Overall absorption of D-xylose and BODIPY was greater in SERTKO animals compared to WT animals. Absorption of D-xylose was persistently elevated in SERTKO animals, while there was an initial delay in BODIPY absorption followed by a sustained and significantly greater absorption in SERTKO animals at 60-360 min after gavage. CONCLUSION Potentiation of serotonin signaling in SERTKO mice results in small intestinal mucosal growth and enhanced carbohydrate and fat absorption in vivo. These functional increases support the concept of targeting the serotonin signaling system to augment intestinal adaptation in the setting of intestinal failure.
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Affiliation(s)
- Christine J Park
- Department of Surgery, Section of Pediatric Surgery at Yale University, New Haven, CT
| | - Sarah J Armenia
- Department of Surgery, Section of Pediatric Surgery at Yale University, New Haven, CT
| | - Matthew P Shaughnessy
- Department of Surgery, Section of Pediatric Surgery at Yale University, New Haven, CT
| | - Chasen J Greig
- Department of Surgery, Section of Pediatric Surgery at Yale University, New Haven, CT
| | - Robert A Cowles
- Department of Surgery, Section of Pediatric Surgery at Yale University, New Haven, CT.
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