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Blondeaux A, Valibouze C, Speca S, Rousseaux C, Dubuquoy C, Blanquart H, Zerbib P, Desreumaux P, Foligné B, Titécat M. Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management. Int J Mol Sci 2024; 25:2164. [PMID: 38396840 PMCID: PMC10889215 DOI: 10.3390/ijms25042164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/02/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
The therapeutic management of Crohn's disease (CD), a chronic relapsing-remitting inflammatory bowel disease (IBD), is highly challenging. Surgical resection is sometimes a necessary procedure even though it is often associated with postoperative recurrences (PORs). Tofacitinib, an orally active small molecule Janus kinase inhibitor, is an anti-inflammatory drug meant to limit PORs in CD. Whereas bidirectional interactions between the gut microbiota and the relevant IBD drug are crucial, little is known about the impact of tofacitinib on the gut microbiota. The HLA-B27 transgenic rat is a good preclinical model used in IBD research, including for PORs after ileocecal resection (ICR). In the present study, we used shotgun metagenomics to first delineate the baseline composition and determinants of the fecal microbiome of HLA-B27 rats and then to evaluate the distinct impact of either tofacitinib treatment, ileocecal resection or the cumulative effect of both interventions on the gut microbiota in these HLA-B27 rats. The results confirmed that the microbiome of the HLA-B27 rats was fairly different from their wild-type littermates. We demonstrated here that oral treatment with tofacitinib does not affect the gut microbial composition of HLA-B27 rats. Of note, we showed that ICR induced an intense loss of bacterial diversity together with dramatic changes in taxa relative abundances. However, the oral treatment with tofacitinib neither modified the alpha-diversity nor exacerbated significant modifications in bacterial taxa induced by ICR. Collectively, these preclinical data are rather favorable for the use of tofacitinib in combination with ICR to address Crohn's disease management when considering microbiota.
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Affiliation(s)
- Aurélie Blondeaux
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
- Department of Hepato-Gastroenterology, Lille University Hospital, 59037 Lille, France
| | - Caroline Valibouze
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
- Department of Hepato-Gastroenterology, Lille University Hospital, 59037 Lille, France
| | - Silvia Speca
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
| | - Christel Rousseaux
- Intestinal Biotech Development, 1 Avenue Oscar Lambret, 59045 Lille, France; (C.R.); (C.D.)
| | - Caroline Dubuquoy
- Intestinal Biotech Development, 1 Avenue Oscar Lambret, 59045 Lille, France; (C.R.); (C.D.)
| | | | - Philippe Zerbib
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
- Department of Hepato-Gastroenterology, Lille University Hospital, 59037 Lille, France
| | - Pierre Desreumaux
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
- Department of Hepato-Gastroenterology, Lille University Hospital, 59037 Lille, France
| | - Benoît Foligné
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
| | - Marie Titécat
- U1286—INFINITE—Institute for Translational Research in Inflammation, CHU Lille, Inserm, Univ. Lille, F-59000 Lille, France; (A.B.); (C.V.); (S.S.); (P.Z.); (P.D.); (M.T.)
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Senanayake T, Makanyengo S, Hoedt EC, Goggins B, Smith SR, Keely S. Influence of the bile acid/microbiota axis in ileal surgery: a systematic review. Colorectal Dis 2024; 26:243-257. [PMID: 38177086 DOI: 10.1111/codi.16837] [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: 04/02/2023] [Revised: 09/21/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024]
Abstract
AIM The gastrointestinal bile acid (BA)/microbiota axis has emerged as a potential mediator of health and disease, particularly in relation to pathologies such as inflammatory bowel disease (IBD) and colorectal cancer. Whilst it presents an exciting new avenue for therapies, it has not yet been characterized in surgical resection of the ileum, where BA reabsorption occurs. The identification of BA/microbiota signatures may provide future therapies with perioperative personalized medicine. In this work we conduct a systematic review with the aim of investigating the microbiome and BA changes that are associated with resection of the ileum. METHOD The databases included were MEDLINE, EMBASE, Web of Science and Cochrane libraries. The outcomes of interest were faecal microbiome and BA signatures after ileal resection. RESULTS Of the initial 3106 articles, three studies met the inclusion/exclusion criteria for data extraction. A total of 257 patients (46% surgery, 54% nonsurgery controls) were included in the three studies. Two studies included patients with short bowel syndrome and the other included patients with IBD. Large-scale microbiota changes were reported. In general, alpha diversity had decreased amongst patients with ileal surgery. Phylum-level changes included decreased Bacteroidetes and increased Proteobacteria and Fusobacteria in patients with an intestinal resection. Surgery was associated with increased total faecal BAs, cholic acid and chenodeoxycholic acid. There were decreases in deoxycholic acid and glycine and taurine conjugated bile salts. Integrated BA and microbiota data identified correlations with several bacterial families and BA. CONCLUSION The BA/microbiota axis is still a novel area with minimal observational data in surgery. Further mechanistic research is necessary to further explore this and identify its role in improving perioperative outcomes.
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Affiliation(s)
- Tharindu Senanayake
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- Surgical and Perioperative Care Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
| | - Samwel Makanyengo
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- Surgical and Perioperative Care Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
| | - Emily C Hoedt
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
| | - Bridie Goggins
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
| | - Stephen R Smith
- Surgical and Perioperative Care Research Program, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Simon Keely
- NHMRC Centre of Research Excellence in Digestive Health, New Lambton Heights, New South Wales, Australia
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, New Lambton Heights, New South Wales, Australia
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Jiang L, Xu J, Cheng SY, Wang Y, Cai W. The gut microbiome and intestinal failure-associated liver disease. Hepatobiliary Pancreat Dis Int 2023; 22:452-457. [PMID: 37453856 DOI: 10.1016/j.hbpd.2023.07.002] [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: 04/25/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Intestinal failure-associated liver disease (IFALD) is a common hepatobiliary complication resulting from long-term parenteral nutrition (PN) in patients with intestinal failure. The spectrum of IFALD ranges from cholestasis, steatosis, portal fibrosis, to cirrhosis. Development of IFALD is a multifactorial process, in which gut dysbiosis plays a critical role in its initiation and progression in conjunction with increased intestinal permeability, activation of hepatic immune responses, and administration of lipid emulsion. Gut microbiota manipulation including pre/probiotics, fecal microbiota transplantation, and antibiotics has been studied in IFALD with varying success. In this review, we summarize current knowledge on the taxonomic and functional changes of gut microbiota in preclinical and clinical studies of IFALD. We also review the function of microbial metabolites and associated signalings in the context of IFALD. By providing microbiota-targeted interventions aiming to optimize PN-induced liver injury, our review provides perspectives for future basic and translational investigations in the field.
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Affiliation(s)
- Lu Jiang
- Division of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China; Shanghai Institute for Pediatric Research, Shanghai 200092, China; Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China
| | - Juan Xu
- Division of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Si-Yang Cheng
- Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Ying Wang
- Division of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China; Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China
| | - Wei Cai
- Division of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China; Shanghai Institute for Pediatric Research, Shanghai 200092, China; Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China; Department of Pediatric Surgery, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China.
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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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Witte MB, Saupe J, Reiner J, Bannert K, Schafmayer C, Lamprecht G, Berlin P. Ileocolonic Healing after Small Ileocecal Resection in Mice: NOD2 Deficiency Impairs Anastomotic Healing by Local Mechanisms. J Clin Med 2023; 12:3601. [PMID: 37240707 PMCID: PMC10219437 DOI: 10.3390/jcm12103601] [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: 04/03/2023] [Revised: 05/12/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Ileocecal resection (ICR) is frequently performed in Crohn's disease (CD). NOD2 mutations are risk factors for CD. Nod2 knockout (ko) mice show impaired anastomotic healing after extended ICR. We further investigated the role of NOD2 after limited ICR. C57B16/J (wt) and Nod2 ko littermates underwent limited ICR including 1-2 cm terminal ileum and were randomly assigned to vehicle or MDP treatment. Bursting pressure was measured on POD 5, and the anastomosis was analyzed for matrix turn-over and granulation tissue. Wound fibroblasts from subcutaneously implanted sponges were used for comparison. The M1/M2 macrophage plasma cytokines were analyzed. Mortality was not different between groups. Bursting pressure was significantly decreased in ko mice. This was associated with less granulation tissue but was not affected by MDP. However, anastomotic leak (AL) rate tended to be lower in MDP-treated ko mice (29% vs. 11%, p = 0.07). mRNA expression of collagen-1α (col1 α), collagen-3α (col3 α), matrix metalloproteinase (mmp)2 and mmp9 was increased in ko mice, indicating increased matrix turn-over, specifically in the anastomosis. Systemic TNF-α expression was significantly lower in ko mice. Ileocolonic healing is impaired in Nod2 ko mice after limited ICR by local mechanisms maybe including local dysbiosis.
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Affiliation(s)
- Maria B. Witte
- Department of General, Visceral, Thoracic, Vascular and Transplant Surgery, Rostock University Medical Center, Schillingallee 35, 18057 Rostock, Germany
| | - Johannes Saupe
- Division of Gastroenterology and Endocrinology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Strasse 6, 18057 Rostock, Germany
| | - Johannes Reiner
- Division of Gastroenterology and Endocrinology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Strasse 6, 18057 Rostock, Germany
| | - Karen Bannert
- Division of Gastroenterology and Endocrinology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Strasse 6, 18057 Rostock, Germany
| | - Clemens Schafmayer
- Department of General, Visceral, Thoracic, Vascular and Transplant Surgery, Rostock University Medical Center, Schillingallee 35, 18057 Rostock, Germany
| | - Georg Lamprecht
- Division of Gastroenterology and Endocrinology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Strasse 6, 18057 Rostock, Germany
| | - Peggy Berlin
- Division of Gastroenterology and Endocrinology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Strasse 6, 18057 Rostock, Germany
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Zhang X, Cao Z, Yang H, Wang Y, Wang W, Li S. Analysis of serum antioxidant capacity and gut microbiota in calves at different growth stages in Tibet. Front Microbiol 2023; 13:1089488. [PMID: 36798869 PMCID: PMC9927023 DOI: 10.3389/fmicb.2022.1089488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/22/2022] [Indexed: 01/31/2023] Open
Abstract
Introduction The hypoxic environment at high altitudes poses a major physiological challenge to animals, especially young animals, as it disturbs the redox state and induces intestinal dysbiosis. Information about its effects on Holstein calves is limited. Methods Here, serum biochemical indices and next-generation sequencing were used to explore serum antioxidant capacity, fecal fermentation performance, and fecal microbiota in Holstein calves aged 1, 2, 3, 4, 5, and 6 months in Tibet. Results and Discussion Serum antioxidant capacity changed with age, with the catalase and malondialdehyde levels significantly decreasing (p < 0.05), and superoxide dismutase levels significantly increasing (p < 0.05) with age. No significant differences (p > 0.05) in total volatile fatty acid levels were noted between the groups. In all groups, Firmicutes, Bacteroidetes, and Actinobacteria were the three most dominant phyla in the gut. Gut microbial alpha diversity significantly increased (p < 0.05) with age. Principal coordinate analysis plot based on Bray-Curtis dissimilarity revealed significant differences (p = 0.001) among the groups. Furthermore, the relative abundance of various genera changed dynamically with age, and the serum antioxidant capacity was associated with certain gut bacteria. The study provides novel insights for feeding Holstein calves in high-altitude regions.
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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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Kimmel M, Jin W, Xia K, Lun K, Azcarate-Peril A, Plantinga A, Wu M, Ataei S, Rackers H, Carroll I, Meltzer-Brody S, Fransson E, Knickmeyer R. Metabolite trajectories across the perinatal period and mental health: A preliminary study of tryptophan-related metabolites, bile acids and microbial composition. Behav Brain Res 2021; 418:113635. [PMID: 34755640 DOI: 10.1016/j.bbr.2021.113635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/26/2021] [Accepted: 10/18/2021] [Indexed: 01/06/2023]
Abstract
Depression and anxiety during pregnancy and postpartum are common, but affected women differ in timing, trajectories, and extent of symptoms. The objective of this pilot, feasibility study is to analyze trajectories of serotonin and tryptophan-related metabolites, bile acid metabolites, and microbial composition, in relation to psychiatric history and current symptoms across the perinatal period. Serum and fecal samples were collected from 30 women at three times points in the perinatal period and assayed with LC-MS/MS and 16S sequencing respectively. We defined mean trajectories for each metabolite, clustered individuals by metabolite trajectories, tested associations between metabolites, and examined metabolite levels in relation to microbial composition. Findings of note include: (1) changes in kynurenine and the ratio of kynurenic acid to kynurenine from second trimester to third trimester were strongly associated with baseline primary and secondary bile acids. (2) Secondary bile acid UDCA and its conjugated forms were associated with lower bacterial diversity and levels of Lachnospiraceae, a taxa known to produce Short Chain Fatty Acids. (3) History of anxiety was associated with UDCA levels, but history of major depression was not associated with any of the bile acids. (4) There was a trend towards lower dietary fiber for those with history of anxiety or depression. Overall, our results reveal substantial temporal variation in tryptophan-related metabolites and in bile acid metabolites over the perinatal period, with marked inter-individual variability. Trajectories of TRP -related metabolites, primary and secondary bile acids, and the absence or presence of microbes that produce Short Chain Fatty Acids (SCFAs) considered in concert have the potential to differentiate individuals based on perinatal adaptations that may impact mental and overall health.
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Affiliation(s)
- Mary Kimmel
- University of North Carolina-Chapel Hill Department of Psychiatry, United States; Uppsala University, Department of Women and Children's Health, Sweden.
| | - Wanting Jin
- University of North Carolina-Chapel Hill Department of Psychiatry, United States
| | - Kai Xia
- University of North Carolina-Chapel Hill Department of Psychiatry, United States
| | - Kun Lun
- University of North Carolina-Chapel Hill Gillings School of Public Health, United States
| | - Andrea Azcarate-Peril
- University of North Carolina-Chapel Hill Department of Medicine and UNC Microbiome Core, United States
| | - Anna Plantinga
- Williams College Department of Mathematics and Statistics, United States
| | - Michael Wu
- University of North Carolina-Chapel Hill Department of Psychiatry, United States
| | - Shirin Ataei
- University of North Carolina-Chapel Hill Department of Psychiatry, United States
| | - Hannah Rackers
- University of North Carolina-Chapel Hill Department of Psychiatry, United States
| | - Ian Carroll
- University of North Carolina-Chapel Hill School of Public Health Department of Nutrition, United States
| | | | - Emma Fransson
- Uppsala University, Department of Women and Children's Health, Sweden; Department of Microbiology, Tumor and Cell Biology, Karolinska Insitutet Centre for Translational Microbiome Research, Sweden
| | - Rebecca Knickmeyer
- University of North Carolina-Chapel Hill Department of Psychiatry, United States; Michigan State University Department of Pediatrics and Human Development, United States
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Greiner M, Anagnostopoulos A, Pohl D, Zbinden R, Zbinden A. A rare case of severe gastroenteritis caused by Aeromonas hydrophila after colectomy in a patient with anti-Hu syndrome: a case report. BMC Infect Dis 2021; 21:1097. [PMID: 34689748 PMCID: PMC8543949 DOI: 10.1186/s12879-021-06784-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 10/12/2021] [Indexed: 11/26/2022] Open
Abstract
Background Aeromonas hydrophila is a gram-negative facultative anaerobic coccobacillus, which is an environmental opportunistic pathogen. A. hydrophila are involved in several infectious diseases such as gastroenteritis, septicemia and wound infections. However, gastroenteritis caused by Aeromonas spp. are rare and the clinical relevance of Aeromonas species in stool specimens is still under debate. Case presentation Our case concerns a 32-year-old woman who presented at hospital with a worsening watery diarrhea and fever requiring intensive care. A cholera-like illness was diagnosed. The patient had a past history of an anti-Hu syndrome with a myenteric ganglionitis. A molecular multiplex RT-PCR (QIAstat-Dx Gastrointestinal Panel, QIAGEN) covering a broad spectrum of diverse gastrointestinal pathogens performed directly from the stool was negative but the stool culture revealed growth of A. hydrophila. Further investigations of the A. hydrophila strain in cell cultures revealed the presence of a cytotoxic enterotoxin. Conclusions Although A. hydrophila rarely causes gastroenteritis, Aeromonas spp. should be considered as a causative agent of severe gastroenteritis with a cholera-like presentation. This case highlights the need to perform culture methods from stool samples when PCR-based methods are negative and gastrointestinal infection is suspected.
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Affiliation(s)
- Michael Greiner
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Alexia Anagnostopoulos
- Division of Infectious Diseases and Hospital Epidemiology, University of Zurich, University Hospital of Zurich, Zurich, Switzerland
| | - Daniel Pohl
- Division of Gastroenterology, University of Zurich, University Hospital of Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland.
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10
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Vomhof-DeKrey EE, Stover A, Basson MD. Microbiome diversity declines while distinct expansions of Th17, iNKT, and dendritic cell subpopulations emerge after anastomosis surgery. Gut Pathog 2021; 13:51. [PMID: 34376235 PMCID: PMC8353768 DOI: 10.1186/s13099-021-00447-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Anastomotic failure causes morbidity and mortality even in technically correct anastomoses. Initial leaks must be prevented by mucosal reapproximation across the anastomosis. Healing is a concerted effort between intestinal epithelial cells (IECs), immune cells, and commensal bacteria. IEC TLR4 activation and signaling is required for mucosal healing, leading to inflammatory factor release that recruits immune cells to limit bacteria invasion. TLR4 absence leads to mucosal damage from loss in epithelial proliferation, attenuated inflammatory response, and bacteria translocation. We hypothesize after anastomosis, an imbalance in microbiota will occur due to a decrease in TLR4 expression and will lead to changes in the immune milieu. RESULTS We isolated fecal content and small intestinal leukocytes from murine, Roux-en-Y and end-to-end anastomoses, to identify microbiome changes and subsequent alterations in the regulatory and pro-inflammatory immune cells 3 days post-operative. TLR4+ IECs were impaired after anastomosis. Microbiome diversity was reduced, with Firmicutes, Bacteroidetes, and Saccharibacteria decreased and Proteobacteria increased. A distinct TCRβhi CD4+ T cells subset after anastomosis was 10-20-fold greater than in control mice. 84% were Th17 IL-17A/F+ IL-22+ and/or TNFα+. iNKT cells were increased and TCRβhi. 75% were iNKT IL-10+ and 13% iNKTh17 IL-22+. Additionally, Treg IL-10+ and IL-22+ cells were increased. A novel dendritic cell subset was identified in anastomotic regions that was CD11bhi CD103mid and was 93% IL-10+. CONCLUSIONS This anastomotic study demonstrated a decrease in IEC TLR4 expression and microbiome diversity which then coincided with increased expansion of regulatory and pro-inflammatory immune cells and cytokines. Defining the anastomotic mucosal environment could help inform innovative therapeutics to target excessive pro-inflammatory invasion and microbiome imbalance.
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Affiliation(s)
- Emilie E. Vomhof-DeKrey
- Department of Surgery, University of North Dakota School of Medicine and the Health Sciences, 1301 North Columbia Road, Stop 9037, Grand Forks, ND 58202 USA
- Department of Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, 1301 North Columbia Road, Stop 9037, Grand Forks, ND 58202 USA
| | - Allie Stover
- Department of Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, 1301 North Columbia Road, Stop 9037, Grand Forks, ND 58202 USA
| | - Marc D. Basson
- Department of Surgery, University of North Dakota School of Medicine and the Health Sciences, 1301 North Columbia Road, Stop 9037, Grand Forks, ND 58202 USA
- Department of Biomedical Sciences, University of North Dakota School of Medicine and the Health Sciences, 1301 North Columbia Road, Stop 9037, Grand Forks, ND 58202 USA
- Department of Pathology, University of North Dakota School of Medicine and the Health Sciences, 1301 North Columbia Road, Stop 9037, Grand Forks, ND 58202 USA
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11
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Vetreno RP, Massey V, Crews FT. Long-lasting microbial dysbiosis and altered enteric neurotransmitters in adult rats following adolescent binge ethanol exposure. Addict Biol 2021; 26:e12869. [PMID: 31880056 PMCID: PMC7319904 DOI: 10.1111/adb.12869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 12/09/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Human alcoholism and ethanol exposure of adult mice cause acute microbial dysbiosis. Adolescent binge drinking is common, but the effect of adolescent ethanol exposure on the adult microbiome and enteric neurotransmitters has not been studied. In the current study, male Wistar rats received adolescent intermittent ethanol (AIE) treatment, and fecal samples were collected on postnatal day (P)54 and P95 for bacterial 16S rRNA amplicon sequencing. Cecal tissue was collected on P95 for analysis of innate immune and neurotransmitter marker expression. At the genus level, AIE treatment altered the relative abundance of several microbes, including decreased relative abundance of Dehalobacterium and CF231 (a member of the Paraprevotellaceae family) that persisted into adulthood. Across aging, the relative abundance of several microbes was altered in both control- and AIE-treated rats. At P95, AIE exposure was associated with increased cecal serotonin levels and reduced choline acetyltransferase gene expression. Taxonomic shifts at P54 and at P95 suggest that AIE causes both immediate and lasting microbial dysbiosis. The lasting microbial dysbiosis was accompanied by alterations of enteric neurotransmitters.
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Affiliation(s)
- Ryan P. Vetreno
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hi, Chapel Hill, North Carolina, USA
| | - Veronica Massey
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Fulton T. Crews
- Bowles Center for Alcohol Studies, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hi, Chapel Hill, North Carolina, USA
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12
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Hamilton AL, Kamm MA, De Cruz P, Wright EK, Feng H, Wagner J, Sung JJY, Kirkwood CD, Inouye M, Teo SM. Luminal microbiota related to Crohn's disease recurrence after surgery. Gut Microbes 2020; 11:1713-1728. [PMID: 32564657 PMCID: PMC7524166 DOI: 10.1080/19490976.2020.1778262] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Microbial factors are likely to be involved in the recurrence of Crohn's disease (CD) after bowel resection. We investigated the luminal microbiota before and longitudinally after surgery, in relation to disease recurrence, using 16S metagenomic techniques. METHODS In the prospective Post-Operative Crohn's Endoscopic Recurrence (POCER) study, fecal samples were obtained before surgery and 6, 12, and 18 months after surgery from 130 CD patients. Endoscopy was undertaken to detect disease recurrence, defined as Rutgeerts score ≥i2, at 6 months in two-thirds of patients and all patients at 18 months after surgery. The V2 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Cluster analysis was performed at family level, assessing microbiome community differences between patients with and without recurrence. RESULTS Six microbial cluster groups were identified. The cluster associated with maintenance of remission was enriched for the Lachnospiraceae family [adjusted OR 0.47 (0.27-0.82), P = .007]. The OTU diversity of Lachnospiraceae within this cluster was significantly greater than in all other clusters. The cluster enriched for Enterobacteriaceae was associated with an increased risk of disease recurrence [adjusted OR 6.35 (1.24-32.44), P = .026]. OTU diversity of Enterobacteriaceae within this cluster was significantly greater than in other clusters. CONCLUSIONS Luminal bacterial communities are associated with protection from, and the occurrence of, Crohn's disease recurrence after surgery. Recurrence may relate to a higher abundance of facultatively anaerobic pathobionts from the Enterobacteriaceae family. The ecologic change of depleted Lachnospiraceae, a genus of butyrate-producing bacteria, may permit expansion of Enterobacteriaceae through luminal environmental perturbation.
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Affiliation(s)
- Amy L. Hamilton
- Department of Gastroenterology, St Vincent’s Hospital and Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Michael A. Kamm
- Department of Gastroenterology, St Vincent’s Hospital and Department of Medicine, University of Melbourne, Melbourne, Australia,CONTACT Michael A. Kamm St Vincent’s Hospital, Melbourne, Australia
| | - Peter De Cruz
- Department of Gastroenterology, St Vincent’s Hospital and Department of Medicine, University of Melbourne, Melbourne, Australia,Department of Gastroenterology, Austin Health, Melbourne, Australia
| | - Emily K. Wright
- Department of Gastroenterology, St Vincent’s Hospital and Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Hai Feng
- The Chinese University of Hong Kong, Hong Kong, China,Enteric Virus Group, Murdoch Children’s Research Institute, Melbourne, Australia,School of Pharmacy, Harbin Medical University, Harbin, China
| | - Josef Wagner
- Enteric Virus Group, Murdoch Children’s Research Institute, Melbourne, Australia,Peter Doherty Institute for Infection and Immunity, Royal Melbourne Hospital, Melbourne, Australia
| | | | - Carl D. Kirkwood
- Enteric Virus Group, Murdoch Children’s Research Institute, Melbourne, Australia,Enteric and Diarrheal Diseases Global Health, Bill and Melinda Gates Foundation, SeattleUSA, WA, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia and Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Shu-Mei Teo
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia and Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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13
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Ghouri YA, Tahan V, Shen B. Secondary causes of inflammatory bowel diseases. World J Gastroenterol 2020; 26:3998-4017. [PMID: 32821067 PMCID: PMC7403802 DOI: 10.3748/wjg.v26.i28.3998] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/15/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBD), conventionally consist of Crohn’s disease (CD) and ulcerative colitis. They occur in individuals with high risk genotype for the disease in the setting of appropriate environmental factors. The pathogenesis of IBD involves a dysregulated autoimmune response to gut dysbiosis, which in turn is triggered due to exposure to various inciting environmental factors. But there is no clearly defined etiology of IBD and this type of disease is termed as “idiopathic IBD”, “classic IBD”, or “primary IBD”. We reviewed the current medical literature and found that certain etiological factors may be responsible for the development of IBD or IBD-like conditions, and we consider this form of de novo IBD as “secondary IBD”. Currently known factors that are potentially responsible for giving rise to secondary IBD are medications; bowel altering surgeries and transplantation of organs, stem cells or fecal microbiome. Medications associated with the development of secondary IBD include; immunomodulators, anti-tumor necrosis factor alpha agents, anti-interleukin agents, interferons, immune stimulating agents and checkpoint inhibitors. Colectomy can in some cases give rise to de novo CD, pouchitis of the ileal pouch, or postcolectomy enteritis syndrome. After solid organ transplantation or hematopoietic stem cell transplantation, the recipient may develop de novo IBD or IBD flare. Fecal microbiota transplantation has been widely used to treat patients suffering from recurrent Clostridium difficile infection but can also causes IBD flares.
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Affiliation(s)
- Yezaz A Ghouri
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri- School of Medicine, Columbia, MO 65201, United States
| | - Veysel Tahan
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri- School of Medicine, Columbia, MO 65201, United States
| | - Bo Shen
- Department of Medicine and Surgery, Interventional IBD Center, Columbia University Irving Medical Center/New York Presbyterian Hospital, New York, NY 10032, United States
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14
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Longitudinal Investigation of the Gut Microbiota in Goat Kids from Birth to Postweaning. Microorganisms 2020; 8:microorganisms8081111. [PMID: 32722119 PMCID: PMC7463816 DOI: 10.3390/microorganisms8081111] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 01/12/2023] Open
Abstract
Early microbial colonization in the gut impacts animal performance and lifelong health. However, research on gut microbial colonization and development in young ruminants, especially after weaning, is currently limited. In this study, next-generation sequencing technology was performed to investigate the temporal dynamic changes of the microbial community in the jejunum and colon of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days (d) of age. As age increased, significant increases in microbial diversity, including the number of Observed OTUs and the Shannon Index, were observed in both the jejunum and colon. Regarding beta diversity, significant shifts in community membership and structure from d1 to d84 were observed based on both Bray–Curtis and Jaccard distances. With increasing age, dominant genera in the jejunum shifted from Lactobacillus to unclassified Ruminococcaceae, unclassified Lachnospiraceae and unclassified Clostridiales through starter supplementation, whereas colonic dominant genera changed from Lactobacillus and Butyricicoccus, within d1–d28, to unclassified Ruminococcaceae, unclassified Clostridiales and Campylobacter after solid diet supplementation. The linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed bacterial features that are stage-specific in the jejunum and colon, respectively. In the jejunum and colon, a significantly distinct structure and membership of the microbiota was observed across all ages. The growth stage-associated microbiota in each gut compartment was also identified as a marker for biogeography. Our data indicate the temporal and spatial differences of the gut microbiota in goats are important for their performance and health. Early microbial colonization can influence microbial composition in later life (e.g., post-weaning phase). This study provides insights that the temporal dynamics of gut microbiota development from newborn to post-weaning can aid in developing feeding strategies to improve goat health and production.
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15
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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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16
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Grillot J, Ait S, Bergoin C, Couronne T, Blond E, Peraldi C, Barnoud D, Chambrier C, Lauverjat M. Vitamin C in Home Parenteral Nutrition: A Need for Monitoring. Nutrients 2020; 12:nu12061667. [PMID: 32503297 PMCID: PMC7352530 DOI: 10.3390/nu12061667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 11/16/2022] Open
Abstract
To date, there are no recommendations about screening plasma vitamin C concentration and adjust its supplementation in patients on long-term home parenteral nutrition (HPN). The aim of this study was to evaluate vitamin C status and determine if a commercial multivitamin preparation (CMVP) containing 125 mg of vitamin C is sufficient in stable patients on HPN. All clinically stable patients receiving HPN or an intravenous fluid infusion at least two times per week for at least 6 months, hospitalized for nutritional assessment, were retrospectively included, for a total of 186 patients. We found that 29% of the patients had vitamin C insufficiency (i.e., <25 µmol/L). In univariate analysis, C-reactive protein (CRP) (p = 0.002) and intake of only 125 mg of vitamin C (p = 0.001) were negatively associated with vitamin C levels, and duration of follow-up in our referral center (p = 0.009) was positively associated with vitamin C levels. In multivariate analysis, only CRP (p = 0.001) and intake of 125 mg of vitamin C (p < 0.0001) were independently associated with low plasma vitamin C concentration. Patients receiving only CMVP with a low plasma vitamin C level significantly received personal compounded HPN (p = 0.008) and presented an inflammatory syndrome (p = 0.002). Vitamin C insufficiency is frequent in individuals undergoing home parenteral nutrition; therefore, there is a need to monitor plasma vitamin C levels, especially in patients on HPN with an inflammatory syndrome and only on CMVP.
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Affiliation(s)
- Julienne Grillot
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
- CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, CEDEX, 69921 Oullins, France;
- Correspondence: ; Tel.: +33-478-86-39-91
| | - Sabrina Ait
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
| | - Charlotte Bergoin
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
| | - Thomas Couronne
- Department of Gastroenterology, Hospices Civils de Lyon, CEDEX, F-69495 Pierre Benite, France;
| | - Emilie Blond
- CarMeN Laboratory, INSERM, INRA, INSA Lyon, Université Claude Bernard Lyon 1, CEDEX, 69921 Oullins, France;
- Biochemistry Department, Lyon Sud Hospital, Hospices Civils de Lyon, F-69495 Pierre Benite, France
| | - Catherine Peraldi
- Centre Agréé de Nutrition Parentérale à Domicile, Hospices Civils de Lyon, CEDEX, F-69495 Pierre Benite, France; (C.P.); (M.L.)
| | - Didier Barnoud
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
| | - Cécile Chambrier
- Nutrition Intensive Care Unit, Hospices Civil de Lyon, CEDEX, F-69495 Pierre Benite, France; (S.A.); (C.B.); (D.B.); (C.C.)
- Centre Agréé de Nutrition Parentérale à Domicile, Hospices Civils de Lyon, CEDEX, F-69495 Pierre Benite, France; (C.P.); (M.L.)
| | - Madeleine Lauverjat
- Centre Agréé de Nutrition Parentérale à Domicile, Hospices Civils de Lyon, CEDEX, F-69495 Pierre Benite, France; (C.P.); (M.L.)
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17
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Hawkins KG, Casolaro C, Brown JA, Edwards DA, Wikswo JP. The Microbiome and the Gut-Liver-Brain Axis for Central Nervous System Clinical Pharmacology: Challenges in Specifying and Integrating In Vitro and In Silico Models. Clin Pharmacol Ther 2020; 108:929-948. [PMID: 32347548 PMCID: PMC7572575 DOI: 10.1002/cpt.1870] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
The complexity of integrating microbiota into clinical pharmacology, environmental toxicology, and opioid studies arises from bidirectional and multiscale interactions between humans and their many microbiota, notably those of the gut. Hosts and each microbiota are governed by distinct central dogmas, with genetics influencing transcriptomics, proteomics, and metabolomics. Each microbiota's metabolome differentially modulates its own and the host's multi‐omics. Exogenous compounds (e.g., drugs and toxins), often affect host multi‐omics differently than microbiota multi‐omics, shifting the balance between drug efficacy and toxicity. The complexity of the host‐microbiota connection has been informed by current methods of in vitro bacterial cultures and in vivo mouse models, but they fail to elucidate mechanistic details. Together, in vitro organ‐on‐chip microphysiological models, multi‐omics, and in silico computational models have the potential to supplement the established methods to help clinical pharmacologists and environmental toxicologists unravel the myriad of connections between the gut microbiota and host health and disease.
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Affiliation(s)
- Kyle G Hawkins
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee, USA
| | - Caleb Casolaro
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Jacquelyn A Brown
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee, USA
| | - David A Edwards
- Department of Anesthesiology and Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John P Wikswo
- Department of Physics and Astronomy, Vanderbilt University, Nashville, Tennessee, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, Tennessee, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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18
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Yan Y, Drew DA, Markowitz A, Lloyd-Price J, Abu-Ali G, Nguyen LH, Tran C, Chung DC, Gilpin KK, Meixell D, Parziale M, Schuck M, Patel Z, Richter JM, Kelsey PB, Garrett WS, Chan AT, Stadler ZK, Huttenhower C. Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. Cell Host Microbe 2020; 27:585-600.e4. [PMID: 32240601 PMCID: PMC7453618 DOI: 10.1016/j.chom.2020.03.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/22/2019] [Accepted: 03/10/2020] [Indexed: 12/12/2022]
Abstract
The gut microbiota has been associated with colorectal cancer (CRC), but causal alterations preceding CRC have not been elucidated. To prospectively assess microbiome changes prior to colorectal neoplasia, we investigated samples from 100 Lynch syndrome patients using 16S rRNA gene sequencing of colon biopsies, coupled with metagenomic and metatranscriptomic sequencing of feces. Colectomy and CRC history represented the largest effects on microbiome profiles. A subset of Clostridiaceae were depleted in stool corresponding with baseline adenomas, while Desulfovibrio was enriched both in stool and in mucosal biopsies. A classifier leveraging stool metatranscriptomes resulted in modest power to predict interval development of preneoplastic colonic adenoma. Predictive transcripts corresponded with a shift in flagellin contributors and oxidative metabolic microenvironment, potentially factors in local CRC pathogenesis. This suggests that the effectiveness of prospective microbiome monitoring for adenomas may be limited but supports the potential causality of these consistent, early microbial changes in colonic neoplasia.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David A Drew
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Arnold Markowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason Lloyd-Price
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Galeb Abu-Ali
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Christina Tran
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel C Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine K Gilpin
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dana Meixell
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Melanie Parziale
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Madeline Schuck
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zalak Patel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James M Richter
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter B Kelsey
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wendy S Garrett
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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19
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Severe Intestinal Dysbiosis in Rat Models of Short Bowel Syndrome with Ileocecal Resection. Dig Dis Sci 2020; 65:431-441. [PMID: 31441001 DOI: 10.1007/s10620-019-05802-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Short bowel syndrome (SBS) resulting from extensive intestinal resection is thought to significantly affect gut microbiota. Data are limited on the signatures of the intestinal microbiome in SBS with different anatomical types. AIMS The aim of our investigation was to characterize the composition and function of gut microbiota in SBS with or without ileocecal resection (ICR). METHODS Six-week-old male Sprague-Dawley rats underwent 75% small bowel resection (SBR) with the ileocecal junction intact (SBR group, jejunoileal anastomosis, n = 10) or removed (ICR group, jejunocolic anastomosis, n = 10), or sham surgery (sham group, n = 10). Colonic contents of the rats were collected 28 days after operation, and 16S rRNA gene sequencing was performed on the MiSeq Illumina platform to analyze bacterial composition. RESULTS Overall structures of the gut microbiome differed significantly among the three groups. The bacterial α-diversity of the ICR group was remarkably lower than that of the sham group. ICR rats were enriched with Lactobacillus and opportunistic pathogens from Proteobacteria but depleted of commensal genera belonging to the Lachnospiraceae, Ruminococcaceae and Erysipelotrichaceae families. Genera from the Bacteroidales S24-7 group, Porphyromonadaceae, Prevotellaceae, Rikenellaceae and Christensenellaceae were prevalent in SBR rats. Functional pathways of branched-chain and aromatic amino acid biosynthesis, lipopolysaccharide biosynthesis and infectious diseases were abundant in the ICR group, while SBR rats featured pathways of C5 branched dibasic acid metabolism, biotin metabolism and one carbon pool folate. CONCLUSIONS ICR causes dramatically more severe intestinal dysbiosis than SBR only in SBS rat models, resulting in altered functional profiles of the gut microbiome.
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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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Muñiz Pedrogo DA, Chen J, Hillmann B, Jeraldo P, Al-Ghalith G, Taneja V, Davis JM, Knights D, Nelson H, Faubion WA, Raffals L, Kashyap PC. An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study. Inflamm Bowel Dis 2019; 25:902-913. [PMID: 30321331 PMCID: PMC6458525 DOI: 10.1093/ibd/izy318] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Inflammatory bowel diseases (IBDs) are a group of heterogeneous inflammatory conditions affecting the gastrointestinal tract. Although there is considerable evidence linking the gut microbiota to intestinal inflammation, there is limited knowledge on its potential role in the development of extraintestinal manifestations of IBD. METHODS Four groups of patients were included: IBD-associated arthropathy (IBD-A); IBD without arthropathy (IBD-N); rheumatoid arthritis (RA); and non-IBD, nonarthritis controls. DNA from stool samples was isolated and sequenced using the Illumina platform. Paired-end reads were quality-controlled using SHI7 and processed with SHOGUN. Abundance and diversity analyses were performed using QIIME, and compositional biomarker identification was performed using LEfSe. RESULTS One hundred eighty patients were included in the analysis. IBD-A was associated with an increased abundance of microbial tyrosine degradation pathways when compared with IBD-N (P = 0.02), whereas IBD-A and RA patients both shared an increased abundance of Clostridiaceae when compared with controls (P = 0.045). We found that history of bowel surgery was a significant source of variability (P = 0.001) among all IBD patients and was associated with decreased alpha diversity and increased abundance of Enterobacteriaceae (P = 0.004). CONCLUSIONS An increased abundance of gut microbial tyrosine degradation pathways was associated with IBD-A. An increased abundance of Clostridiaceae was shared by both IBD-A and RA patients and suggests a potentially common microbial link for inflammatory arthritis. The increased abundance of Enterobacteriaceae, previously reported in IBD, may be due to the effects of previous bowel surgery and highlights the importance of controlling for this variable in future studies.
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Affiliation(s)
- David A Muñiz Pedrogo
- Center for Clinical and Translational Science, Mayo Clinic, Rochester, Minnesota,University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Benjamin Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | | | - Gabriel Al-Ghalith
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, Minnesota
| | - John M Davis
- Division of Rheumatology, Mayo Clinic, Rochester, Minnesota
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Laura Raffals
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota,Address correspondence to: Purna C. Kashyap, MBBS, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905 ()
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Thompson AL, Houck KM, Jahnke JR. Pathways linking caesarean delivery to early health in a dual burden context: Immune development and the gut microbiome in infants and children from Galápagos, Ecuador. Am J Hum Biol 2019; 31:e23219. [PMID: 30693586 PMCID: PMC6661198 DOI: 10.1002/ajhb.23219] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 11/29/2018] [Accepted: 12/28/2018] [Indexed: 01/19/2023] Open
Abstract
OBJECTIVES Global increases in caesarean deliveries are exposing more infants to perinatal environments that are evolutionarily novel and potentially increasing their risks for inflammatory conditions. Yet, the pathways linking caesareans to later health outcomes are not well understood, particularly in dual burden contexts. We test two of the hypothesized pathways, altered immune function and gut microbiota, which may link delivery mode to later health outcomes and test whether these associations persist when controlling for postnatal nutritional and pathogenic exposures. METHODS Data come from infants, aged 0 to 2 (n = 41), and young children, aged 2 to 11 (n = 135), from the Galápagos, Ecuador. Differences in morbidity, C-reactive protein (CRP), and gut microbiota by delivery type were tested using linear and logistic regression models adjusted for nutritional and pathogenic exposures and infant age. RESULTS Over half of infants and over 40% of children were delivered by caesarean. Morbidity and CRP did not differ between infants or children born by caesarean or vaginally. Microbial taxa abundance differed by delivery mode. Infants born by caesarean had a higher abundance of Firmicutes and a lower relative abundance of Bacteroidales. Children born by caesarean had a higher abundance of Proteobacteria and Enterobacteriales. These differences remained after adjustment for environmental exposure. CONCLUSIONS Caesarean delivery is associated with differences in gut microbiota across childhood even in this dual burden context. Our results highlight the importance of examining caesarean delivery across diverse contexts to better understand the impact of perinatal interventions on short- and longer-term health outcomes.
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Affiliation(s)
- Amanda L. Thompson
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly M Houck
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Johanna R. Jahnke
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Berlin P, Reiner J, Wobar J, Bannert K, Glass Ä, Walter M, Bastian M, Willenberg HS, Vollmar B, Klar E, Seidler U, Lamprecht G, Witte M. Villus Growth, Increased Intestinal Epithelial Sodium Selectivity, and Hyperaldosteronism Are Mechanisms of Adaptation in a Murine Model of Short Bowel Syndrome. Dig Dis Sci 2019; 64:1158-1170. [PMID: 30569336 PMCID: PMC6548203 DOI: 10.1007/s10620-018-5420-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 12/07/2018] [Indexed: 12/09/2022]
Abstract
BACKGROUND Short bowel syndrome results from extensive small bowel resection and induces adaptation of the remaining intestine. Ileocecal resection (ICR) is the most frequent situation in humans. Villus hypertrophy is one hallmark of mucosal adaptation, but the functional mechanisms of mucosal adaptation are incompletely understood. AIMS The aim of the study was to characterize a clinically relevant model of short bowel syndrome but not intestinal failure in mice and to identify outcome predictors and mechanisms of adaptation. METHODS Male C57BL6/J mice underwent 40% ICR and were followed for 7 or 14 days. Small bowel transection served as control. All mice underwent autopsy. Survival, body weight, wellness score, stool water content, plasma aldosterone concentrations, and paracellular permeability were recorded. RESULTS Unlike controls, resected mice developed significant diarrhea with increased stool water. This was accompanied by sustained weight loss throughout follow-up. Villus length increased but did not correlate positively with adaptation. Plasma aldosterone concentrations correlated inversely with body weight at day 14. After ICR, intestinal epithelial (i.e., tight junctional) sodium permeability was increased. CONCLUSIONS 40% ICR results in moderate to severe short bowel syndrome. Successful adaptation to the short bowel situation involves villus elongation but does not correlate with the degree of villus elongation alone. In addition, increased intestinal epithelial sodium permeability facilitates sodium-coupled solute transport. Hyperaldosteronism correlates with the severity of weight loss, indicates volume depletion, and counterregulates water loss.
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Affiliation(s)
- Peggy Berlin
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057 Rostock, Germany
| | - Johannes Reiner
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057 Rostock, Germany
| | - Jakob Wobar
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057 Rostock, Germany
| | - Karen Bannert
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057 Rostock, Germany
| | - Änne Glass
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany
| | - Michael Walter
- Institute for Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057 Rostock, Germany
| | - Manuela Bastian
- Institute for Clinical Chemistry and Laboratory Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057 Rostock, Germany
| | - Holger Sven Willenberg
- Division of Endocrinology and Metabolism, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057 Rostock, Germany
| | - Brigitte Vollmar
- Institute of Experimental Surgery, Rostock University Medical Center, Schillingallee 69a, 18057 Rostock, Germany
| | - Ernst Klar
- Department of General, Thoracic, Vascular and Transplantation Surgery, Rostock University Medical Center, Schillingallee 35, 18057 Rostock, Germany
| | - Ursula Seidler
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Georg Lamprecht
- Division of Gastroenterology, Department of Medicine II, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057 Rostock, Germany
| | - Maria Witte
- Department of General, Thoracic, Vascular and Transplantation Surgery, Rostock University Medical Center, Schillingallee 35, 18057 Rostock, Germany
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Endospore forming bacteria may be associated with maintenance of surgically-induced remission in Crohn's disease. Sci Rep 2018; 8:9734. [PMID: 29950676 PMCID: PMC6021420 DOI: 10.1038/s41598-018-28071-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/14/2018] [Indexed: 12/28/2022] Open
Abstract
Crohn’s disease (CD) patients who undergo ileocolonic resection (ICR) typically have disease recurrence at the anastomosis which has been linked with a gut dysbiosis. The aims of this study were to define the mucosa-associated microbiota at the time of ICR and to determine if microbial community structure at the time of surgery was predictive of future disease relapse. Ileal biopsies were obtained at surgery and after 6 months from CD subjects undergoing ICR. Composition and function of mucosal-associated microbiota was assessed by 16S rRNA sequencing and PICRUSt analysis. Endoscopic recurrence was assessed using the Rutgeerts score. Analysis of mucosal biopsies taken at the time of surgery showed that decreased Clostridiales together with increased Enterobacteriales predicted disease recurrence. An increase in the endospore-forming Lachnospiraceae from surgery to 6 months post-ICR was associated with remission. A ratio of 3:1 between anaerobic endospore-forming bacterial families and aerobic families within the Firmicutes phylum was predictive of maintenance of remission. Gut recolonization following ICR is facilitated by microbes which are capable of either aerobic respiration or endospore formation. The relative proportions of these species at the time of surgery may be predictive of subsequent microbial community restoration and disease recurrence.
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25
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Abstract
Short-bowel syndrome represents the most common cause of intestinal failure and occurs when the remaining intestine cannot support fluid and nutrient needs to sustain adequate physiology and development without the use of supplemental parenteral nutrition. After intestinal loss or damage, the remnant bowel undergoes multifactorial compensatory processes, termed adaptation, which are largely driven by intraluminal nutrient exposure. Previous studies have provided insight into the biological processes and mediators after resection, however, there still remains a gap in the knowledge of more comprehensive mechanisms that drive the adaptive responses in these patients. Recent data support the microbiota as a key mediator of gut homeostasis and a potential driver of metabolism and immunomodulation after intestinal loss. In this review, we summarize the emerging ideas related to host-microbiota interactions in the intestinal adaptation processes.
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Key Words
- Adaptive Responses
- CONV, conventional
- ENS, enteric nervous system
- Enteric Flora
- GF, germ-free
- GI, gastrointestinal
- GLP-2, glucagon-like peptide 2
- IBD, inflammatory bowel disease
- ICR, ileocecal resection
- IF, intestinal failure
- IL, interleukin
- Immune System
- Intestinal Failure
- Microbial Metabolites
- NEC, necrotizing enterocolitis
- PN, parenteral nutrition
- SBR, small bowel resection
- SBS, short-bowel syndrome
- SCFA, short-chain fatty acid
- SFB, segmented filamentous bacteria
- TGR5, Takeda-G-protein-receptor 5
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26
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Laffin M, Perry T, Park H, Hotte N, Fedorak RN, Thiesen A, Dicken B, Madsen KL. Prebiotic Supplementation Following Ileocecal Resection in a Murine Model is Associated With a Loss of Microbial Diversity and Increased Inflammation. Inflamm Bowel Dis 2018; 24:101-110. [PMID: 29272494 PMCID: PMC6176898 DOI: 10.1093/ibd/izx033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND Individuals with Crohn's disease frequently require ileocecal resection (ICR), and inflammation often recurs in the neoterminal ileum following surgery. Fructooligosaccharide (FOS) is a fermentable prebiotic that stimulates the growth of bifidobacteria and may promote anti-inflammatory activity. The aim of this study was to determine if supplementation of a postICR diet with FOS in a mouse model would be effective in stimulating the growth of bifidobacteria and reducing systemic and local inflammation. METHODS ICR was performed in IL10-/- mice (129S1/SvlmJ) with colitis. Following surgery, nonICR control and ICR mice were fed a chow diet ± 10% FOS for 28 days. Serum, colon, and terminal ileum (TI) were analyzed for cytokine expression by MesoScale discovery platform. DNA extracted from stool was analyzed using 16s rRNA sequencing and qPCR. Expression of occludin and ZO1 was assessed using qPCR. Short-chain fatty acid (SCFA) concentrations were assessed using gas chromatography. RESULTS ICR led to increased systemic inflammation (P < 0.05) and a significant decline in fecal microbial diversity (P < 0.05). Mice on the FOS diet had a greater reduction in microbial diversity and also had worsened inflammation as evidenced by increased serum IL-6 (P < 0.05) and colonic IFNγ and TNFα (P < 0.05). Expression of occludin and ZO1 were significantly reduced in FOS-supplemented mice. There was a correlation between loss of diversity and the bifidogenic effectiveness of FOS (r = -0.61, P < 0.05). CONCLUSIONS FOS-supplementation of a postICR diet resulted in a decrease in fecal bacterial diversity, reduction in barrier function, and increased gut inflammation.
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Affiliation(s)
| | - Troy Perry
- Department of Surgery, University of Alberta
| | - Heekuk Park
- Department of Medicine, University of Alberta,The Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta
| | - Naomi Hotte
- The Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta
| | - Richard N Fedorak
- Department of Medicine, University of Alberta,The Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta
| | - Aducio Thiesen
- Department of Laboratory Medicine, University of Alberta
| | | | - Karen L Madsen
- Department of Medicine, University of Alberta,The Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR), University of Alberta,Address correspondence to: Karen L. Madsen, PhD, 7-142K Katz Building, University of Alberta, Edmonton, Alberta T6G 2E1. E-mail:
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27
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Huang Y, Guo F, Li Y, Wang J, Li J. Fecal microbiota signatures of adult patients with different types of short bowel syndrome. J Gastroenterol Hepatol 2017; 32:1949-1957. [PMID: 28425133 DOI: 10.1111/jgh.13806] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIM Short bowel syndrome (SBS) is a common cause of intestinal failure and can be divided into three types depending on intestinal anatomy. Gut dysbiosis has been observed in pediatric SBS patients and is associated with impaired outcome. Little is known about the changes in gut microbiota of adult SBS patients. Therefore, we aim to characterize the fecal microbiota of adult patients with different types of SBS. METHODS Fifteen fecal samples from healthy controls and adult patients with type II or type III SBS were collected (five in each group). Fecal microbial compositions were determined by high-throughput sequencing, and functional potential was predicted by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States. RESULTS Bacterial α-diversity significantly decreased in SBS patients and positively correlated to the remaining small bowel length. SBS II patients were enriched with Proteobacteria but deficient in Firmicutes and Bacteroidetes. Whereas Lactobacillus and Prevotella dominated the microbiomes of SBS III patients, commensal bacteria from Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae declined in SBS patients. The parenteral nutrition duration of SBS patients was positively related to the proportion of Enterobacteriaceae but negatively related to Lactobacillus. Functional pathways of citrate cycle and branched-chain and aromatic amino acid biosynthesis were abundant in SBS II patients, while functional profiles of pyrimidine and purine metabolism were dominant in SBS III patients. CONCLUSIONS Short bowel syndrome patients have a marked intestinal dysbiosis with type II SBS characterized by Proteobacteria and type III SBS featured by Lactobacillus, resulting in altered functional profiles of fecal microbiomes.
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Affiliation(s)
- Yuhua Huang
- Intestinal Rehabilitation and Transplant Center, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Feilong Guo
- Intestinal Rehabilitation and Transplant Center, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Yousheng Li
- Intestinal Rehabilitation and Transplant Center, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China.,Department of general surgery, Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Jian Wang
- Intestinal Rehabilitation and Transplant Center, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Jieshou Li
- Intestinal Rehabilitation and Transplant Center, Jinling Hospital, School of Medicine, Nanjing University, Nanjing, China
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Allali I, Arnold JW, Roach J, Cadenas MB, Butz N, Hassan HM, Koci M, Ballou A, Mendoza M, Ali R, Azcarate-Peril MA. A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome. BMC Microbiol 2017; 17:194. [PMID: 28903732 PMCID: PMC5598039 DOI: 10.1186/s12866-017-1101-8] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 08/29/2017] [Indexed: 12/16/2022] Open
Abstract
Background Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Results Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. Conclusions The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies. Electronic supplementary material The online version of this article (10.1186/s12866-017-1101-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Imane Allali
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.,Laboratory of Biochemistry & Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Jason W Arnold
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Jeffrey Roach
- Research Computing, University of North Carolina, Chapel Hill, NC, USA
| | - Maria Belen Cadenas
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Natasha Butz
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA
| | - Hosni M Hassan
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Matthew Koci
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Anne Ballou
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Mary Mendoza
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - Rizwana Ali
- Department of Poultry Science, North Carolina State University, Raleigh, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology, and Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Campus Box 7555, 332 Isaac Taylor Hall, Chapel Hill, NC, 27599-7545, USA.
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Wellman AS, Metukuri MR, Kazgan N, Xu X, Xu Q, Ren NSX, Czopik A, Shanahan MT, Kang A, Chen W, Azcarate-Peril MA, Gulati AS, Fargo DC, Guarente L, Li X. Intestinal Epithelial Sirtuin 1 Regulates Intestinal Inflammation During Aging in Mice by Altering the Intestinal Microbiota. Gastroenterology 2017; 153:772-786. [PMID: 28552621 PMCID: PMC5581719 DOI: 10.1053/j.gastro.2017.05.022] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 05/05/2017] [Accepted: 05/19/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Intestinal epithelial homeostasis is maintained by complex interactions among epithelial cells, commensal gut microorganisms, and immune cells. Disruption of this homeostasis is associated with disorders such as inflammatory bowel disease (IBD), but the mechanisms of this process are not clear. We investigated how Sirtuin 1 (SIRT1), a conserved mammalian NAD+-dependent protein deacetylase, senses environmental stress to alter intestinal integrity. METHODS We performed studies of mice with disruption of Sirt1 specifically in the intestinal epithelium (SIRT1 iKO, villin-Cre+, Sirt1flox/flox mice) and control mice (villin-Cre-, Sirt1flox/flox) on a C57BL/6 background. Acute colitis was induced in some mice by addition of 2.5% dextran sodium sulfate to drinking water for 5-9 consecutive days. Some mice were given antibiotics via their drinking water for 4 weeks to deplete their microbiota. Some mice were fed with a cholestyramine-containing diet for 7 days to sequester their bile acids. Feces were collected and proportions of microbiota were analyzed by 16S rRNA amplicon sequencing and quantitative PCR. Intestines were collected from mice and gene expression profiles were compared by microarray and quantitative PCR analyses. We compared levels of specific mRNAs between colon tissues from age-matched patients with ulcerative colitis (n=10) vs without IBD (n=8, controls). RESULTS Mice with intestinal deletion of SIRT1 (SIRT1 iKO) had abnormal activation of Paneth cells starting at the age of 5-8 months, with increased activation of NF-κB, stress pathways, and spontaneous inflammation at 22-24 months of age, compared with control mice. SIRT1 iKO mice also had altered fecal microbiota starting at 4-6 months of age compared with control mice, in part because of altered bile acid metabolism. Moreover, SIRT1 iKO mice with defective gut microbiota developed more severe colitis than control mice. Intestinal tissues from patients with ulcerative colitis expressed significantly lower levels of SIRT1 mRNA than controls. Intestinal tissues from SIRT1 iKO mice given antibiotics, however, did not have signs of inflammation at 22-24 months of age, and did not develop more severe colitis than control mice at 4-6 months. CONCLUSIONS In analyses of intestinal tissues, colitis induction, and gut microbiota in mice with intestinal epithelial disruption of SIRT1, we found this protein to prevent intestinal inflammation by regulating the gut microbiota. SIRT1 might therefore be an important mediator of host-microbiome interactions. Agents designed to activate SIRT1 might be developed as treatments for IBDs.
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Affiliation(s)
- Alicia S Wellman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Mallikarjuna R Metukuri
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Nevzat Kazgan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Xiaojiang Xu
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Qing Xu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Natalie S X Ren
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Agnieszka Czopik
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael T Shanahan
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ashley Kang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; NIEHS Scholars Connect Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Willa Chen
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology and Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ajay S Gulati
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Leonard Guarente
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina.
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Pascoe EL, Hauffe HC, Marchesi JR, Perkins SE. Network analysis of gut microbiota literature: an overview of the research landscape in non-human animal studies. ISME JOURNAL 2017; 11:2644-2651. [PMID: 28800135 DOI: 10.1038/ismej.2017.133] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/21/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022]
Abstract
A wealth of human studies have demonstrated the importance of gut microbiota to health. Research on non-human animal gut microbiota is now increasing, but what insight does it provide? We reviewed 650 publications from this burgeoning field (2009-2016) and determined that animals driving this research were predominantly 'domestic' (48.2%), followed by 'model' (37.5%), with least studies on 'wild' (14.3%) animals. Domestic studies largely experimentally perturbed microbiota (81.8%) and studied mammals (47.9%), often to improve animal productivity. Perturbation was also frequently applied to model animals (87.7%), mainly mammals (88.1%), for forward translation of outcomes to human health. In contrast, wild animals largely characterised natural, unperturbed microbiota (79.6%), particularly in pest or pathogen vectoring insects (42.5%). We used network analyses to compare the research foci of each animal group: 'diet' was the main focus in all three, but to different ends: to enhance animal production (domestic), to study non-infectious diseases (model), or to understand microbiota composition (wild). Network metrics quantified model animal studies as the most interdisciplinary, while wild animals incorporated the fewest disciplines. Overall, animal studies, especially model and domestic, cover a broad array of research. Wild animals, however, are the least investigated, but offer under-exploited opportunities to study 'real-life' microbiota.
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Affiliation(s)
- Emily L Pascoe
- Organisms and Environment Division, School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff University, Cardiff, UK.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Michele all' Adige (TN), Italy
| | - Heidi C Hauffe
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Michele all' Adige (TN), Italy
| | - Julian R Marchesi
- Organisms and Environment Division, School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff University, Cardiff, UK.,Centre for Digestive and Gut Health, Imperial College London, London, UK.,Department of Surgery and Cancer, Imperial College London, London, UK
| | - Sarah E Perkins
- Organisms and Environment Division, School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff University, Cardiff, UK.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Michele all' Adige (TN), Italy
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Impact of short-chain galactooligosaccharides on the gut microbiome of lactose-intolerant individuals. Proc Natl Acad Sci U S A 2017; 114:E367-E375. [PMID: 28049818 DOI: 10.1073/pnas.1606722113] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Directed modulation of the colonic bacteria to metabolize lactose effectively is a potentially useful approach to improve lactose digestion and tolerance. A randomized, double-blind, multisite placebo-controlled trial conducted in human subjects demonstrated that administration of a highly purified (>95%) short-chain galactooligosaccharide (GOS), designated "RP-G28," significantly improved clinical outcomes for lactose digestion and tolerance. In these individuals, stool samples were collected pretreatment (day 0), after GOS treatment (day 36), and 30 d after GOS feeding stopped and consumption of dairy products was encouraged (day 66). In this study, changes in the fecal microbiome were investigated using 16S rRNA amplicon pyrosequencing and high-throughput quantitative PCR. At day 36, bifidobacterial populations were increased in 27 of 30 of GOS subjects (90%), demonstrating a bifidogenic response in vivo. Relative abundance of lactose-fermenting Bifidobacterium, Faecalibacterium, and Lactobacillus were significantly increased in response to GOS. When dairy was introduced into the diet, lactose-fermenting Roseburia species increased from day 36 to day 66. The results indicated a definitive change in the fecal microbiome of lactose-intolerant individuals, increasing the abundance of lactose-metabolizing bacteria that were responsive to dietary adaptation to GOS. This change correlated with clinical outcomes of improved lactose tolerance.
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Muller CO, Rossignol G, Montalva L, Viala J, Martinez-Vinson C, Mosca A, Berrebi D, Bonnard A. Long-Term Outcome of Laparoscopic Duhamel Procedure for Extended Hirschsprung's Disease. J Laparoendosc Adv Surg Tech A 2016; 26:1032-1035. [DOI: 10.1089/lap.2016.0152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Cécile O. Muller
- Department of Pediatric Surgery, Hôpital Robert Debré, APHP, Paris, France
| | | | - Louise Montalva
- Department of Pediatric Surgery, Hôpital Robert Debré, APHP, Paris, France
| | - Jerome Viala
- Pediatric Gastroenterology, Hôpital Robert Debré, APHP, Paris, France
| | | | - Alexis Mosca
- Pediatric Gastroenterology, Hôpital Robert Debré, APHP, Paris, France
| | | | - Arnaud Bonnard
- Department of Pediatric Surgery, Hôpital Robert Debré, APHP, Paris, France
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Emerging Technologies for Gut Microbiome Research. Trends Microbiol 2016; 24:887-901. [PMID: 27426971 DOI: 10.1016/j.tim.2016.06.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/06/2016] [Accepted: 06/23/2016] [Indexed: 02/06/2023]
Abstract
Understanding the importance of the gut microbiome on modulation of host health has become a subject of great interest for researchers across disciplines. As an intrinsically multidisciplinary field, microbiome research has been able to reap the benefits of technological advancements in systems and synthetic biology, biomaterials engineering, and traditional microbiology. Gut microbiome research has been revolutionized by high-throughput sequencing technology, permitting compositional and functional analyses that were previously an unrealistic undertaking. Emerging technologies, including engineered organoids derived from human stem cells, high-throughput culturing, and microfluidics assays allowing for the introduction of novel approaches, will improve the efficiency and quality of microbiome research. Here, we discuss emerging technologies and their potential impact on gut microbiome studies.
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Mondot S, Lepage P, Seksik P, Allez M, Tréton X, Bouhnik Y, Colombel JF, Leclerc M, Pochart P, Doré J, Marteau P. Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery. Gut 2016; 65:954-62. [PMID: 26628508 PMCID: PMC4893116 DOI: 10.1136/gutjnl-2015-309184] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 11/01/2015] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Preventing postoperative recurrence after ileocolonic resection (ICR) for Crohn's disease (CD) is challenging. Defining the disturbances of the microbial composition and community structure after ICR and their link with early disease recurrence is crucial. DESIGN Microbiota composition (fingerprinting and 16S rDNA sequencing) and community structure (correlation networks of bacterial species) were assessed from ileal mucosa sampled in 20 patients undergoing ICR and 6 months later during endoscopy from above (neoterminal ileum) and below (subanastomotic colon) the surgical anastomosis. RESULTS ICR had a dramatic effect on gut microbial ecosystem. At surgery, CD mucosa harboured a dysbiotic microbiota with high proportions of α/β Proteobacteria and Bacilli. Six months later, half of the patients had recurrent lesions at ileocolonoscopy and presented higher numbers of Lachnospiraceae. Recurrence of endoscopic lesions was associated with enrichment in Enterococcus durans while patients in remission had increased proportions of Dorea longicatena and Bacteroides plebeius. Structural differences were striking between recurrence and remission microbiota; while the microbiota of patients with CD recurrence exhibited a loose community structure, the microbiota of patients in remission displayed communities that were robustly correlated to each other. Microbiota colonising the neoterminal ileum and subanastomotic colon 6 months after ICR only differed in patients with recurrence. CONCLUSIONS ICR modifies the gut microbiome. Remission after 6 months was associated with homogenous bacterial distribution around the anastomosis. Community structure and bacterial networks highlight target species, including Faecalibacterium prausnitzii and Ruminococcus gnavus, which may allow precise modulations of the overall microbial ecosystem towards remission pattern.
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Affiliation(s)
- S Mondot
- INRA, Micalis UMR1319, Jouy-en-Josas, France,AgroParisTech, Micalis UMR1319, Jouy-en-Josas, France,Institut Curie, U932, Paris, France
| | - P Lepage
- INRA, Micalis UMR1319, Jouy-en-Josas, France,AgroParisTech, Micalis UMR1319, Jouy-en-Josas, France
| | - P Seksik
- Sorbonne Universités—UPMC Univ Paris 06, INSERM ERL 1157, AP-HP, Hôpital Saint Antoine, CNRS UMR 7203 LBM, CHU Saint-Antoine, Paris, France
| | - M Allez
- Gastroenterology Department, Hôpital Saint Louis, APHP, INSERM U1160, Université Paris 7, GETAID, Paris, France
| | - X Tréton
- Gastroenterology Department, Hôpital Beaujon, Clichy, Université Paris 7, GETAID, Paris, France
| | - Y Bouhnik
- Gastroenterology Department, Hôpital Beaujon, Clichy, Université Paris 7, GETAID, Paris, France
| | - J F Colombel
- Department of Gastroenterology, Icahn School of Medicine, New York, New York, USA
| | - M Leclerc
- INRA, Micalis UMR1319, Jouy-en-Josas, France,AgroParisTech, Micalis UMR1319, Jouy-en-Josas, France
| | - P Pochart
- EA Laboratoire de Biologie, Conservatoire national des arts et métiers, Paris, France,EA4065 Université Paris V, Paris, France
| | - J Doré
- INRA, Micalis UMR1319, Jouy-en-Josas, France,AgroParisTech, Micalis UMR1319, Jouy-en-Josas, France
| | - P Marteau
- Gastroenterology Department, Hôpital Lariboisière & Université Denis Diderot—Paris 7, Sorbonne Paris Cité & GETAID, Paris, France
| | - the GETAID
- GETAID, Groupe d'Etude des Traitements des Affections Inflammatoires Digestives, Paris, France
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Warner BW. The Pathogenesis of Resection-Associated Intestinal Adaptation. Cell Mol Gastroenterol Hepatol 2016; 2:429-438. [PMID: 27722191 PMCID: PMC5042605 DOI: 10.1016/j.jcmgh.2016.05.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/06/2016] [Indexed: 12/14/2022]
Abstract
After massive small-bowel resection, the remnant bowel compensates by a process termed adaptation. Adaptation is characterized by villus elongation and crypt deepening, which increases the capacity for absorption and digestion per unit length. The mechanisms/mediators of this important response are multiple. The purpose of this review is to highlight the major basic contributions in elucidating a more comprehensive understanding of this process.
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Affiliation(s)
- Brad W. Warner
- Correspondence Address correspondence to: Brad W. Warner, MD, Washington University School of Medicine, St. Louis Children's Hospital, One Children's Place, Suite 5s40, St. Louis, Missouri 63110. fax: (314) 454-2442.Washington University School of MedicineSt. Louis Children's HospitalOne Children's PlaceSuite 5s40St. LouisMissouri 63110
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Mezoff EA, Hawkins JA, Ollberding NJ, Karns R, Morrow AL, Helmrath MA. The human milk oligosaccharide 2'-fucosyllactose augments the adaptive response to extensive intestinal. Am J Physiol Gastrointest Liver Physiol 2016; 310:G427-38. [PMID: 26702137 PMCID: PMC4796291 DOI: 10.1152/ajpgi.00305.2015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/22/2015] [Indexed: 01/31/2023]
Abstract
Intestinal resection resulting in short bowel syndrome (SBS) carries a heavy burden of long-term morbidity, mortality, and cost of care, which can be attenuated with strategies that improve intestinal adaptation. SBS infants fed human milk, compared with formula, have more rapid intestinal adaptation. We tested the hypothesis that the major noncaloric human milk oligosaccharide 2'-fucosyllactose (2'-FL) contributes to the adaptive response after intestinal resection. Using a previously described murine model of intestinal adaptation, we demonstrated increased weight gain from 21 to 56 days (P < 0.001) and crypt depth at 56 days (P < 0.0095) with 2'-FL supplementation after ileocecal resection. Furthermore, 2'-FL increased small bowel luminal content microbial alpha diversity following resection (P < 0.005) and stimulated a bloom in organisms of the genus Parabacteroides (log2-fold = 4.1, P = 0.035). Finally, transcriptional analysis of the intestine revealed enriched ontologies and pathways related to antimicrobial peptides, metabolism, and energy processing. We conclude that 2'-FL supplementation following ileocecal resection increases weight gain, energy availability through microbial community modulation, and histological changes consistent with improved adaptation.
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Affiliation(s)
- Ethan A. Mezoff
- 1Cincinnati Children's Hospital Medical Center, Division of Gastroenterology, Hepatology, and Nutrition;
| | - Jennifer A. Hawkins
- 2Cincinnati Children's Hospital Medical Center, Division of Pediatric General and Thoracic Surgery;
| | - Nicholas J. Ollberding
- 3Cincinnati Children's Hospital Medical Center, Division of Biostatistics and Epidemiology;
| | - Rebekah Karns
- 4Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics; and
| | - Ardythe L. Morrow
- 5Cincinnati Children's Hospital Medical Center, Division of Neonatology and Pulmonary Biology
| | - Michael A. Helmrath
- 2Cincinnati Children's Hospital Medical Center, Division of Pediatric General and Thoracic Surgery;
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Monteagudo-Mera A, Arthur JC, Jobin C, Keku T, Bruno-Barcena JM, Azcarate-Peril MA. High purity galacto-oligosaccharides enhance specific Bifidobacterium species and their metabolic activity in the mouse gut microbiome. Benef Microbes 2016; 7:247-64. [PMID: 26839072 DOI: 10.3920/bm2015.0114] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prebiotics are selectively fermented ingredients that result in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon the host health. The aim of this study was to evaluate the influence of a β(1-4)galacto-oligosaccharides (GOS) formulation consisting of 90% pure GOS (GOS90), on the composition and activity of the mouse gut microbiota. Germ-free mice were colonised with microbiota from four pathogen-free wt 129 mice donors (SPF), and stools were collected during a feeding trial in which GOS90 was delivered orally for 14 days. Pyrosequencing of 16S rDNA amplicons showed that Bifidobacterium and specific Lactobacillus, Bacteroides and Clostridiales were more prevalent in GOS90-fed mice after 14 days, although the prebiotic impact on Bifidobacterium varied among individual mice. Prebiotic feeding also resulted in decreased abundance of Bacteroidales, Helicobacter and Clostridium. High-throughput quantitative PCR showed an increased abundance of Bifidobacterium adolescentis, Bifidobacterium pseudocatenulatum, Bifidobacterium lactis and Bifidobacterium gallicum in the prebiotic-fed mice. Control female mice showed a higher diversity (phylogenetic diversity (PD) = 15.1 ± 3.4 in stools and PD = 13.0 ± 0.6 in intestinal contents) than control males (PD = 7.8 ± 1.6 in stool samples and PD = 9.5 ± 1.0 in intestinal contents). GOS90 did not modify inflammatory biomarkers (interleukin (IL)-6, IL-12, IL-1β, interferon gamma and tumour necrosis factor alpha). Decreased butyrate, acetate and lactate concentrations in stools of prebiotic fed mice suggested an increase in colonic absorption and reduced excretion. Overall, our results demonstrate that GOS90 is capable of modulating the intestinal microbiome resulting in expansion of the probiome (autochtonous commensal intestinal bacteria considered to have a beneficial influence on health).
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Affiliation(s)
- A Monteagudo-Mera
- 1 Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North Carolina, 312 Isaac Taylor Hall, Chapel Hill, NC 27599, USA
| | - J C Arthur
- 2 Department of Medicine, Division of Gastroenterology and Hepatology and Center for Gastrointestinal Biology and Disease, University of North Carolina, 312 Isaac Taylor Hall, Chapel Hill, NC 27599, USA
| | - C Jobin
- 2 Department of Medicine, Division of Gastroenterology and Hepatology and Center for Gastrointestinal Biology and Disease, University of North Carolina, 312 Isaac Taylor Hall, Chapel Hill, NC 27599, USA.,3 Department of Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of Florida, Box 100214, Gainesville, FL 32610-0214, USA
| | - T Keku
- 2 Department of Medicine, Division of Gastroenterology and Hepatology and Center for Gastrointestinal Biology and Disease, University of North Carolina, 312 Isaac Taylor Hall, Chapel Hill, NC 27599, USA
| | - J M Bruno-Barcena
- 4 Department of Plant and Microbial Biology, 4550A Thomas Hall, Campus Box 7615, Raleigh, NC 27695, USA
| | - M A Azcarate-Peril
- 1 Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North Carolina, 312 Isaac Taylor Hall, Chapel Hill, NC 27599, USA.,5 Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, 100 Mason Farm Road, Campus Box 7545, Chapel Hill, NC 27599-7545, USA
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Levesque CL, Turner J, Li J, Wizzard P, St Pierre B, Lim D, Wales P. In a Neonatal Piglet Model of Intestinal Failure, Administration of Antibiotics and Lack of Enteral Nutrition Have a Greater Impact on Intestinal Microflora Than Surgical Resection Alone. JPEN J Parenter Enteral Nutr 2016; 41:938-945. [PMID: 26838525 DOI: 10.1177/0148607115626903] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Data are limited on how short bowel syndrome (SBS) affects the healthy developing intestinal microbiome, with even less assessing different SBS anatomical surgical models. This study was conducted to describe the "ileal" and "colonic" microflora in 2 surgical models of SBS. MATERIALS AND METHODS Neonatal piglets (2-5 days old) underwent intestinal resection, leaving the ileum (JI anatomy, n = 6) or removing the ileum and ileocecal valve (JC anatomy, n = 5), or sham surgery (sham; n = 4). JI, JC, and sham piglets commenced parenteral nutrition on day 0 and received ampicillin and trimethoprim-sulfadoxine on days 0-4 for prevention of line sepsis. At day 7, ileal and colonic digesta were collected, and they were also collected from age-matched sow-fed piglets (n = 6). DNA extraction, sequencing, and annotation followed standard procedures. RESULTS Colonic and ileal bacterial genus diversity and relative bacterial abundance were greater ( P < .05) in sow-fed compared with JI, JC, and sham piglets; however, minor differences were observed in either location between sham, JI, and JC piglets and within the surgical model. In the colon, sow-fed piglets had higher ( P < .05) abundance of Lactobacillus (26%) and tended to have lower ( P = .06) abundance of Enterococcus (<.1%) than JI, JC, or sham piglets, in which Lactobacillus and Enterococcus abundance averaged <.1% and 9%, respectively. CONCLUSIONS Intestinal resection reduces bacterial diversity in the large bowel, and the difference is associated with the presence/absence of the ileum and ileocecal valve. The lack of enteral nutrition and antibiotic administration (ie, sow-fed vs surgery) had a greater influence on the observed shift in diversity and relative abundance than intestinal resection.
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Affiliation(s)
- Crystal L Levesque
- 1 Animal Science Department, South Dakota State University, Brookings, South Dakota, USA
| | - Justine Turner
- 2 Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Julang Li
- 3 Animal Science Department, University of Guelph, Guelph, Ontario, Canada
| | - Pamela Wizzard
- 2 Department of Agriculture, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Benoit St Pierre
- 1 Animal Science Department, South Dakota State University, Brookings, South Dakota, USA
| | - David Lim
- 4 Department of Surgery, University of Alberta, Canada
| | - Paul Wales
- 5 Division of General Surgery, Hospital for Sick Children, Toronto, Ontario, Canada.,6 Group for Improvement of Intestinal Function and Treatment, Hospital for Sick Children, Toronto, Ontario, Canada
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Till H, Castellani C, Moissl-Eichinger C, Gorkiewicz G, Singer G. Disruptions of the intestinal microbiome in necrotizing enterocolitis, short bowel syndrome, and Hirschsprung's associated enterocolitis. Front Microbiol 2015; 6:1154. [PMID: 26528281 PMCID: PMC4607865 DOI: 10.3389/fmicb.2015.01154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 10/05/2015] [Indexed: 12/22/2022] Open
Abstract
Next generation sequencing techniques are currently revealing novel insight into the microbiome of the human gut. This new area of research seems especially relevant for neonatal diseases, because the development of the intestinal microbiome already starts in the perinatal period and preterm infants with a still immature gut associated immune system may be harmed by a dysproportional microbial colonization. For most gastrointestinal diseases requiring pediatric surgery there is very limited information about the role of the intestinal microbiome. This review aims to summarize the current knowledge and outline future perspectives for important pathologies like necrotizing enterocolitis (NEC) of the newborn, short bowel syndrome (SBS), and Hirschsprung’s disease associated enterocolitis (HAEC). Only studies applying next generation sequencing techniques to analyze the diversity of the intestinal microbiome were included. In NEC patients intestinal dysbiosis could already be detected prior to any clinical evidence of the disease resulting in a reduction of the bacterial diversity. In SBS patients the diversity seems to be reduced compared to controls. In children with Hirschsprung’s disease the intestinal microbiome differs between those with and without episodes of enterocolitis. One common finding for all three diseases seems to be an overabundance of Proteobacteria. However, most human studies are based on fecal samples and experimental data question whether fecal samples actually represent the microbiome at the site of the diseased bowel and whether the luminal (transient) microbiome compares to the mucosal (resident) microbiome. In conclusion current studies already allow a preliminary understanding of the potential role of the intestinal microbiome in pediatric surgical diseases. Future investigations could clarify the interface between the intestinal epithelium, its immunological competence and mucosal microbiome. Advances in this field may have an impact on the understanding and non-operative treatment of such diseases in infancy.
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Affiliation(s)
- Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University of Graz Graz, Austria
| | - Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University of Graz Graz, Austria
| | | | | | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University of Graz Graz, Austria
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Sadaghian Sadabad M, Regeling A, de Goffau MC, Blokzijl T, Weersma RK, Penders J, Faber KN, Harmsen HJM, Dijkstra G. The ATG16L1-T300A allele impairs clearance of pathosymbionts in the inflamed ileal mucosa of Crohn's disease patients. Gut 2015; 64:1546-52. [PMID: 25253126 DOI: 10.1136/gutjnl-2014-307289] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 09/09/2014] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Crohn's disease (CD) is caused by a complex interplay among genetic, microbial and environmental factors. ATG16L1 is an important genetic factor involved in innate immunity, including autophagy and phagocytosis of microbial components from the gut. We investigated the effect of inflammation on the composition of microbiota in the ileal mucosa of CD patients in relation to the ATG16L1 risk status. DESIGN Biopsies (n=35) were obtained from inflamed and non-inflamed regions of the terminal ileum of 11 CD patients homozygous for the ATG16L1 risk allele (ATG16L1-T300A) and 9 CD patients homozygous for the ATG16L1 protective allele (ATG16L1-T300). Biopsy DNA was extracted and the bacterial composition analysed by pyrosequencing. Intracellular survival rates of adherent-invasive Escherichia coli (AIEC) were analysed by determining colony forming units after exposure to monocytes isolated from healthy volunteers homozygous for the ATG16L1 risk or protective allele. RESULTS Inflamed ileal tissue from patients homozygous for the ATG16L1 risk allele contained increased numbers of Fusobacteriaceae, whereas inflamed ileal tissue of patients homozygous for the ATG16L1 protective allele showed decreased numbers of Bacteroidaceae and Enterobacteriaceae and increased Lachnospiraceae. The ATG16L1 allele did not affect the bacterial composition in the non-inflamed ileal tissue. Monocytes homozygous for the ATG16L1 risk allele showed impaired killing of AIEC under inflammatory conditions compared with those homozygous for the ATG16L1 protective allele. CONCLUSIONS CD patients homozygous for the ATG16L1-T300A risk allele show impaired clearance of pathosymbionts in ileal inflammation indicating that ATG16L1 is essential for effective elimination of pathosymbionts upon inflammation.
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Affiliation(s)
- Mehdi Sadaghian Sadabad
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anouk Regeling
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marcus C de Goffau
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tjasso Blokzijl
- Department of Laboratory Medicine, 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
| | - John Penders
- Department of Medical Microbiology, School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, 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
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Becker-Dreps S, Allali I, Monteagudo A, Vilchez S, Hudgens MG, Rogawski ET, Carroll IM, Zambrana LE, Espinoza F, Azcarate-Peril MA. Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery. Am J Trop Med Hyg 2015; 93:1187-93. [PMID: 26350452 DOI: 10.4269/ajtmh.15-0322] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/23/2015] [Indexed: 12/16/2022] Open
Abstract
Understanding how the gut microbiota is affected by diarrhea episodes may help explain alterations in intestinal function among children in low-income settings. This study examined the composition of the gut microbiome of Nicaraguan children both during diarrhea episodes and while free of diarrhea for at least 2 months. Relative abundances of bacterial taxa, phylogenetic diversity, and species richness were determined by 16S amplicon sequencing and compared between paired diarrhea and recovery samples. A total of 66 stools were provided by 25 children enrolled in a 1-year cohort study of diarrhea etiologies. Children in our cohort had a mean age of 21.9 months; 64% were breast-fed, and 10% had received an antibiotic during the diarrhea episode. Overall, phylogenetic diversity and species richness did not differ significantly between diarrhea and recovery stools. However, of children who had a bacterial enteropathogen detected in any diarrhea stool, none experienced an increase in phylogenetic diversity in recovery, whereas of those in whom no bacterial enteropathogens were detected in their diarrhea stool(s), 59% experienced an increase in phylogenetic diversity in recovery (P = 0.008). This preliminary study suggests that recovery of the gut microbiota after a diarrhea episode may take longer time than previously thought and may be pathogen specific.
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Affiliation(s)
- Sylvia Becker-Dreps
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Imane Allali
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Andrea Monteagudo
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Samuel Vilchez
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Michael G Hudgens
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Elizabeth T Rogawski
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Ian M Carroll
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Luis Enrique Zambrana
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Felix Espinoza
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - M Andrea Azcarate-Peril
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Laboratory of Biochemistry and Immunology, Faculty of Sciences, Mohammed V University, Rabat, Morocco; Department of Microbiology and Parasitology, National Autonomous University of Nicaragua, León, Nicaragua; Department of Biostatistics, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Epidemiology, University of North Carolina Gillings School of Global Public Health, Chapel Hill, North Carolina; Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Center for Demographic and Health Research, National Autonomous University of Nicaragua, León, Nicaragua; Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
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Ritchie LE, Taddeo SS, Weeks BR, Lima F, Bloomfield SA, Azcarate-Peril MA, Zwart SR, Smith SM, Turner ND. Space Environmental Factor Impacts upon Murine Colon Microbiota and Mucosal Homeostasis. PLoS One 2015; 10:e0125792. [PMID: 26083373 PMCID: PMC4470690 DOI: 10.1371/journal.pone.0125792] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/26/2015] [Indexed: 01/01/2023] Open
Abstract
Astronaut intestinal health may be impacted by microgravity, radiation, and diet. The aim of this study was to characterize how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota (determined by 16S rDNA pyrosequencing) and colon function. Three independent experiments were conducted to achieve these goals: 1) fractionated low LET γ radiation (137Cs, 3 Gy, RAD), high Fe diet (IRON) (650 mg/kg diet), and a combination of low LET γ radiation and high Fe diet (IRON+RAD) in male Sprague-Dawley rats; 2) high LET 38Si particle exposure (0.050 Gy), 1/6 G partial weight bearing (PWB), and a combination of high LET38Si particle exposure and PWB in female BalbC/ByJ mice; and 3) 13 d spaceflight in female C57BL/6 mice. Low LET radiation, IRON and spaceflight increased Bacteroidetes and decreased Firmicutes. RAD and IRON+RAD increased Lactobacillales and lowered Clostridiales compared to the control (CON) and IRON treatments. Low LET radiation, IRON, and spaceflight did not significantly affect diversity or richness, or elevate pathogenic genera. Spaceflight increased Clostridiales and decreased Lactobacillales, and similar trends were observed in the experiment using a ground-based model of microgravity, suggesting altered gravity may affect colonic microbiota. Although we noted no differences in colon epithelial injury or inflammation, spaceflight elevated TGFβ gene expression. Microbiota and mucosal characterization in these models is a first step in understanding the impact of the space environment on intestinal health.
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Affiliation(s)
- Lauren E. Ritchie
- Intercollegiate Faculty of Genetics, Texas A&M University, College Station, Texas, United States of America
| | - Stella S. Taddeo
- Nutrition & Food Science Department, Texas A&M University, College Station, Texas, United States of America
| | - Brad R. Weeks
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, United States of America
| | - Florence Lima
- Division of Nephrology, Department of Medicine, University of Kentucky, Lexington, Kentucky, United States of America
| | - Susan A. Bloomfield
- Department of Health and Kinesiology, Texas A&M University, College Station, Texas, United States of America
| | - M. Andrea Azcarate-Peril
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Sara R. Zwart
- Human Health and Performance Directorate, NASA Lyndon B. Johnson Space Center, Houston, Texas, United States of America
| | - Scott M. Smith
- Human Health and Performance Directorate, NASA Lyndon B. Johnson Space Center, Houston, Texas, United States of America
| | - Nancy D. Turner
- Intercollegiate Faculty of Genetics, Texas A&M University, College Station, Texas, United States of America
- Nutrition & Food Science Department, Texas A&M University, College Station, Texas, United States of America
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43
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Tzanetakis GN, Azcarate-Peril MA, Zachaki S, Panopoulos P, Kontakiotis EG, Madianos PN, Divaris K. Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing. J Endod 2015; 41:1226-33. [PMID: 25906920 DOI: 10.1016/j.joen.2015.03.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/11/2015] [Accepted: 03/16/2015] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Elucidating the microbial ecology of endodontic infections (EIs) is a necessary step in developing effective intracanal antimicrobials. The aim of the present study was to investigate the bacterial composition of symptomatic and asymptomatic primary and persistent infections in a Greek population using high-throughput sequencing methods. METHODS 16S amplicon pyrosequencing of 48 root canal bacterial samples was conducted, and sequencing data were analyzed using an oral microbiome-specific and a generic (Greengenes) database. Bacterial abundance and diversity were examined by EI type (primary or persistent), and statistical analysis was performed by using non-parametric and parametric tests accounting for clustered data. RESULTS Bacteroidetes was the most abundant phylum in both infection groups. Significant, albeit weak associations of bacterial diversity were found, as measured by UniFrac distances with infection type (analyses of similarity, R = 0.087, P = .005) and symptoms (analyses of similarity, R = 0.055, P = .047). Persistent infections were significantly enriched for Proteobacteria and Tenericutes compared with primary ones; at the genus level, significant differences were noted for 14 taxa, including increased enrichment of persistent infections for Lactobacillus, Streptococcus, and Sphingomonas. More but less abundant phyla were identified using the Greengenes database; among those, Cyanobacteria (0.018%) and Acidobacteria (0.007%) were significantly enriched among persistent infections. Persistent infections showed higher phylogenetic diversity (PD) (asymptomatic: PD = 9.2, standard error [SE] = 1.3; symptomatic: PD = 8.2, SE = 0.7) compared with primary infections (asymptomatic: PD = 5.9, SE = 0.8; symptomatic: PD = 7.4, SE = 1.0). CONCLUSIONS The present study revealed a high bacterial diversity of EI and suggests that persistent infections may have more diverse bacterial communities than primary infections.
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Affiliation(s)
- Giorgos N Tzanetakis
- Department of Endodontics, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece.
| | - M Andrea Azcarate-Peril
- Department of Cell Biology and Physiology and Microbiome Core Facility, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina
| | - Sophia Zachaki
- Laboratory of Health Physics, Radiobiology and Cytogenetics, NCSR "Demokritos", Athens, Greece
| | - Panos Panopoulos
- Department of Endodontics, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos G Kontakiotis
- Department of Endodontics, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Phoebus N Madianos
- Department of Periodontology, School of Dentistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Kimon Divaris
- Department of Pediatric Dentistry, School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina
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Allali I, Delgado S, Marron PI, Astudillo A, Yeh JJ, Ghazal H, Amzazi S, Keku T, Azcarate-Peril MA. Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain. Gut Microbes 2015; 6:161-72. [PMID: 25875428 PMCID: PMC4615176 DOI: 10.1080/19490976.2015.1039223] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer in the world and the second leading cause of cancer deaths in the US and Spain. The molecular mechanisms involved in the etiology of CRC are not yet elucidated due in part to the complexity of the human gut microbiota. In this study, we compared the microbiome composition of 90 tumor and matching adjacent tissue (adjacent) from cohorts from the US and Spain by 16S rRNA amplicon sequencing in order to determine the impact of the geographic origin on the CRC microbiome. Data showed a significantly (P < 0.05) higher Phylogenetic Diversity (PD) for the US (PD Adjacent = 26.3 ± 5.3, PD Tumor = 23.3 ± 6.2) compared to the Spanish cohort (PD Adjacent = 18.9 ± 5.9, PD Tumor = 18.7 ± 6.6) while no significant differences in bacterial diversity were observed between tumor and adjacent tissues for individuals from the same country. Adjacent tissues from the Spanish cohort were enriched in Firmicutes (SP = 43.9% and US = 22.2%, P = 0.0001) and Actinobacteria (SP = 1.6% and US = 0.5%, P = 0.0018) compared to US adjacent tissues, while adjacent tissues from the US had significantly higher abundances of Fusobacteria (US = 8.1% and SP = 1.5%, P = 0.0023) and Sinergistetes (US = 0.3% and SP = 0.1%, P = 0.0097). Comparisons between tumor and adjacent tissues in each cohort identified the genus Eikenella significantly over represented in US tumors (T = 0.024% and A = 0%, P = 0.03), and the genera Fusobacterium (T = 10.4% and A = 1.5%, P = <0.0001), Bulleida (T = 0.36% and A = 0.09%, P = 0.02), Gemella (T = 1.46% and A = 0.19%, P = 0.03), Parvimonas (T = 3.14% and A = 0.86%, P = 0.03), Campylobacter (T = 0.15% and A = 0.008%, P = 0.047), and Streptococcus (T = 2.84% and A = 2.19%, P = 0.05) significantly over represented in Spanish tumors. Predicted metagenome functional content from 16S rRNA surveys showed that bacterial motility proteins and proteins involved in flagellar assembly were over represented in adjacent tissues of both cohorts, while pathways involved in fatty acid biosynthesis, the MAPK signaling pathway, and bacterial toxins were over represented in tumors. Our study suggests that microbiome compositional and functional dissimilarities by geographic location should be taken in consideration when approaching CRC therapeutic options.
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Affiliation(s)
- Imane Allali
- Department of Cell Biology and Physiology, and Microbiome Core Facility; University of North Carolina School of Medicine; Chapel Hill, NC, USA,Laboratory of Biochemistry & Immunology; Faculty of Sciences; University Mohammed V; Rabat, Morocco,Laboratory of Genetics and Biotechnology; Faculty of Sciences of Oujda; University Mohammed Premier; Oujda, Morocco
| | - Susana Delgado
- Department of Microbiology and Biochemistry of Dairy Products; Instituto de Productos Lácteos de Asturias (IPLA-CSIC); Villaviciosa-Asturias, Spain
| | - Pablo Isidro Marron
- Instituto Universitario de Oncología del Principado de Asturias; Hospital Universitario Central de Asturias; Universidad de Oviedo; Asturias, Spain
| | - Aurora Astudillo
- Instituto Universitario de Oncología del Principado de Asturias; Hospital Universitario Central de Asturias; Universidad de Oviedo; Asturias, Spain
| | - Jen Jen Yeh
- Lineberger Comprehensive Cancer Center; Departments of Surgery and Pharmacology; University of North Carolina School of Medicine; Chapel Hill, NC, USA
| | - Hassan Ghazal
- Laboratory of Genetics and Biotechnology; Faculty of Sciences of Oujda; University Mohammed Premier; Oujda, Morocco,Polydisciplinary Faculty of Nador; University Mohammed Premier; Nador, Morocco
| | - Saaïd Amzazi
- Laboratory of Biochemistry & Immunology; Faculty of Sciences; University Mohammed V; Rabat, Morocco
| | - Temitope Keku
- Division of Gastroenterology & Hepatology; Department of Medicine; University of North Carolina School of Medicine; Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- Department of Cell Biology and Physiology, and Microbiome Core Facility; University of North Carolina School of Medicine; Chapel Hill, NC, USA,Correspondence to: M Andrea Azcarate-Peril
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Ritchie LE, Sturino JM, Carroll RJ, Rooney LW, Azcarate-Peril MA, Turner ND. Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis. FEMS Microbiol Ecol 2015; 91:fiv008. [PMID: 25764457 PMCID: PMC4573659 DOI: 10.1093/femsec/fiv008] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 11/05/2014] [Accepted: 01/08/2015] [Indexed: 02/07/2023] Open
Abstract
The microbiota affects host health, and dysbiosis is involved in colitis. Sorghum bran influences butyrate concentrations during dextran sodium sulfate (DSS) colitis, suggesting microbiota changes. We aimed to characterize the microbiota during colitis, and ascertain if polyphenol-rich sorghum bran diets mitigate these effects. Rats (n = 80) were fed diets containing 6% fiber from cellulose, or Black (3-deoxyanthocyanins), Sumac (condensed tannins), or Hi Tannin black (both) sorghum bran. Inflammation was induced three times using 3% DSS for 48 h (40 rats, 2 week separation), and the microbiota characterized by pyrosequencing. The Firmicutes/Bacteroidetes ratio was higher in Cellulose DSS rats. Colonic injury negatively correlated with Firmicutes, Actinobacteria, Lactobacillales and Lactobacillus, and positively correlated with Unknown/Unclassified. Post DSS#2, richness was significantly lower in Sumac and Hi Tannin black. Post DSS#3 Bacteroidales, Bacteroides, Clostridiales, Lactobacillales and Lactobacillus were reduced, with no Clostridium identified. Diet significantly affected Bacteroidales, Bacteroides, Clostridiales and Lactobacillus post DSS#2 and #3. Post DSS#3 diet significantly affected all genus, including Bacteroides and Lactobacillus, and diversity and richness increased. Sumac and Hi Tannin black DSS had significantly higher richness compared to controls. Thus, these sorghum brans may protect against alterations observed during colitis including reduced microbial diversity and richness, and dysbiosis of Firmicutes/Bacteroidetes.
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Affiliation(s)
- Lauren E Ritchie
- Intercollegiate Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA
| | - Joseph M Sturino
- Intercollegiate Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA Nutrition and Food Science Department, Texas A&M University, College Station, TX 77843-2253, USA
| | - Raymond J Carroll
- Department of Statistics, Texas A&M University, College Station, TX 77843-3143, USA
| | - Lloyd W Rooney
- Soil and Crop Sciences, Texas A&M University, College Station, TX 77843-2474, USA
| | - M Andrea Azcarate-Peril
- Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7545, USA
| | - Nancy D Turner
- Intercollegiate Faculty of Genetics, Texas A&M University, College Station, TX 77843-2253, USA Nutrition and Food Science Department, Texas A&M University, College Station, TX 77843-2253, USA
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Thompson AL, Monteagudo-Mera A, Cadenas MB, Lampl ML, Azcarate-Peril MA. Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome. Front Cell Infect Microbiol 2015; 5:3. [PMID: 25705611 PMCID: PMC4318912 DOI: 10.3389/fcimb.2015.00003] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/05/2015] [Indexed: 01/14/2023] Open
Abstract
The development of the infant intestinal microbiome in response to dietary and other exposures may shape long-term metabolic and immune function. We examined differences in the community structure and function of the intestinal microbiome between four feeding groups, exclusively breastfed infants before introduction of solid foods (EBF), non-exclusively breastfed infants before introduction of solid foods (non-EBF), EBF infants after introduction of solid foods (EBF+S), and non-EBF infants after introduction of solid foods (non-EBF+S), and tested whether out-of-home daycare attendance was associated with differences in relative abundance of gut bacteria. Bacterial 16S rRNA amplicon sequencing was performed on 49 stool samples collected longitudinally from a cohort of 9 infants (5 male, 4 female). PICRUSt metabolic inference analysis was used to identify metabolic impacts of feeding practices on the infant gut microbiome. Sequencing data identified significant differences across groups defined by feeding and daycare attendance. Non-EBF and daycare-attending infants had higher diversity and species richness than EBF and non-daycare attending infants. The gut microbiome of EBF infants showed increased proportions of Bifidobacterium and lower abundance of Bacteroidetes and Clostridiales than non-EBF infants. PICRUSt analysis indicated that introduction of solid foods had a marginal impact on the microbiome of EBF infants (24 enzymes overrepresented in EBF+S infants). In contrast, over 200 bacterial gene categories were overrepresented in non-EBF+S compared to non-EBF infants including several bacterial methyl-accepting chemotaxis proteins (MCP) involved in signal transduction. The identified differences between EBF and non-EBF infants suggest that breast milk may provide the gut microbiome with a greater plasticity (despite having a lower phylogenetic diversity) that eases the transition into solid foods.
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Affiliation(s)
- Amanda L. Thompson
- Department of Anthropology, University of North CarolinaChapel Hill, NC, USA
| | - Andrea Monteagudo-Mera
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
| | - Maria B. Cadenas
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
| | - Michelle L. Lampl
- Department of Anthropology and Center for the Study of Human Health, Emory UniversityAtlanta, GA, USA
| | - M. A. Azcarate-Peril
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
- Department of Cell Biology and Physiology, School of Medicine, University of North CarolinaChapel Hill, NC, USA
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De Cruz P, Kang S, Wagner J, Buckley M, Sim WH, Prideaux L, Lockett T, McSweeney C, Morrison M, Kirkwood CD, Kamm MA. Association between specific mucosa-associated microbiota in Crohn's disease at the time of resection and subsequent disease recurrence: a pilot study. J Gastroenterol Hepatol 2015; 30:268-78. [PMID: 25087692 DOI: 10.1111/jgh.12694] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/11/2014] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIM Crohn's disease pathogenesis involves alterations in the gut microbiota. We characterized the mucosa-associated microbiota at the time of surgical resection and 6 months later to identify bacterial profiles associated with recurrence and remission. METHODS Tissue samples were collected from surgical resection specimens in 12 Crohn's disease patients, and at 6 months postoperative colonoscopy from the neoterminal ileum and anastomosis. Endoscopic recurrence was assessed using the Rutgeerts score. Microbiota was characterized using microarray and 454 pyrosequencing. Longitudinal comparisons were made within patients, and cross-sectional comparisons made with colonoscopic biopsies from the terminal ileum and cecum of 10 healthy subjects. RESULTS Microbiota of healthy subjects had high diversity and was dominated by the Firmicutes, Bacteroidetes, and Proteobacteria phyla. Biodiversity was lower in Crohn's disease patients at the time of surgery, increased after surgery, but still differed from healthy subjects. Crohn's disease patients with recurrent disease retained a microbiota favoring proteolytic-fueled fermentation and lactic acid-producing bacteria, including Enterococcus and Veillonella spp., while those maintaining remission demonstrated predominant saccharolytic Bacteroides, Prevotella, and Parabacteroides spp., and saccharolytic, butyrate-producing Firmicutes. CONCLUSION In Crohn's disease, the mucosa-associated microbiota diversity is reduced at the time of surgery, but also differs between patients with different clinical outcomes at 6 months. These findings may provide prognostic information at the time of surgery, allowing identification of patients at increased risk of recurrence, and provide basis for a more targeted approach for therapeutic interventions after surgery.
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Affiliation(s)
- Peter De Cruz
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Victoria, Australia; Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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Small bowel resection induces long-term changes in the enteric microbiota of mice. J Gastrointest Surg 2015; 19:56-64; discussion 64. [PMID: 25183407 PMCID: PMC4576885 DOI: 10.1007/s11605-014-2631-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/11/2014] [Indexed: 01/31/2023]
Abstract
PURPOSE The enteric microbiome is known to play a major role in healthy gut homeostasis and several disease states. It may also contribute to both the intestinal recovery and complications that occur in patients with short bowel syndrome. The extent and nature of alterations to the gut microbiota following intestinal resection, however, are not well studied in a controlled setting. The purpose of this investigation is to characterize the effects of massive small bowel resection on the murine enteric microflora. METHODS Wild-type C57BL6 mice, following a week of acclamation to a liquid rodent diet, underwent either 50% proximal small bowel resection (SBR) or a sham operation. Mice were sacrificed, and enteric contents from the small bowel, cecum, and stool were harvested at 7 and 90 days post-operatively. DNA was isolated, and the V3-V5 regions of the 16s rRNA gene amplified and pyrosequenced on a Roche 454 platform. Sequences were clustered into operation taxonomic units and classified. Communities were then analyzed for diversity and phylogenic composition. RESULTS In the long-term group, the microbes inhabiting the ileum of mice undergoing SBR and sham operation differed significantly at the genus level (p < 0.001). Small bowel contents collected before and after SBR also differed significantly (p = 0.006). This was driven by an increase in Lactobacillus and decrease in Enterobacteriaceae species in mice undergoing SBR. No difference was seen in the long-term stool or in stool, cecal, or ileal contents in the short-term. No difference in microbial community diversity was found in any group. CONCLUSION Bowel resection induces long-term changes in the microbial community of the murine ileum, but not at more distal sites of the gastrointestinal tract. The increase in Lactobacillus encountered small bowel of resected mice correlates with limited previous studies. These changes may reflect an adaptive response of the microbiota to maximize energy extraction, but further studies are needed to establish the role played by this altered community.
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Sangild PT, Ney DM, Sigalet DL, Vegge A, Burrin D. Animal models of gastrointestinal and liver diseases. Animal models of infant short bowel syndrome: translational relevance and challenges. Am J Physiol Gastrointest Liver Physiol 2014; 307:G1147-68. [PMID: 25342047 PMCID: PMC4269678 DOI: 10.1152/ajpgi.00088.2014] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Intestinal failure (IF), due to short bowel syndrome (SBS), results from surgical resection of a major portion of the intestine, leading to reduced nutrient absorption and need for parenteral nutrition (PN). The incidence is highest in infants and relates to preterm birth, necrotizing enterocolitis, atresia, gastroschisis, volvulus, and aganglionosis. Patient outcomes have improved, but there is a need to develop new therapies for SBS and to understand intestinal adaptation after different diseases, resection types, and nutritional and pharmacological interventions. Animal studies are needed to carefully evaluate the cellular mechanisms, safety, and translational relevance of new procedures. Distal intestinal resection, without a functioning colon, results in the most severe complications and adaptation may depend on the age at resection (preterm, term, young, adult). Clinically relevant therapies have recently been suggested from studies in preterm and term PN-dependent SBS piglets, with or without a functional colon. Studies in rats and mice have specifically addressed the fundamental physiological processes underlying adaptation at the cellular level, such as regulation of mucosal proliferation, apoptosis, transport, and digestive enzyme expression, and easily allow exogenous or genetic manipulation of growth factors and their receptors (e.g., glucagon-like peptide 2, growth hormone, insulin-like growth factor 1, epidermal growth factor, keratinocyte growth factor). The greater size of rats, and especially young pigs, is an advantage for testing surgical procedures and nutritional interventions (e.g., PN, milk diets, long-/short-chain lipids, pre- and probiotics). Conversely, newborn pigs (preterm or term) and weanling rats provide better insights into the developmental aspects of treatment for SBS in infants owing to their immature intestines. The review shows that a balance among practical, economical, experimental, and ethical constraints will determine the choice of SBS model for each clinical or basic research question.
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Affiliation(s)
- Per T. Sangild
- 1Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark; ,2Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark;
| | - Denise M. Ney
- 3Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, Wisconsin;
| | | | - Andreas Vegge
- 1Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark; ,5Diabetes Pharmacology, Novo Nordisk, Måløv, Denmark; and
| | - Douglas Burrin
- 6USDA-ARS Children's Nutrition Research Center, Baylor College of Medicine, Houston, Texas
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50
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Perry T, Borowiec A, Dicken B, Fedorak R, Madsen K. Murine ileocolic bowel resection with primary anastomosis. J Vis Exp 2014:e52106. [PMID: 25406841 DOI: 10.3791/52106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Intestinal resections are frequently required for treatment of diseases involving the gastrointestinal tract, with Crohn's disease and colon cancer being two common examples. Despite the frequency of these procedures, a significant knowledge gap remains in describing the inherent effects of intestinal resection on host physiology and disease pathophysiology. This article provides detailed instructions for an ileocolic resection with primary end-to-end anastomosis in mice, as well as essential aspects of peri-operative care to maximize post-operative success. When followed closely, this procedure yields a 95% long-term survival rate, no failure to thrive, and minimizes post-operative complications of bowel obstruction and anastomotic leak. The technical challenges of performing the procedure in mice are a barrier to its wide spread use in research. The skills described in this article can be acquired without previous surgical experience. Once mastered, the murine ileocolic resection procedure will provide a reproducible tool for studying the effects of intestinal resection in models of human disease.
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Affiliation(s)
- Troy Perry
- Department of Surgery, University of Alberta;
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