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Thompson J, Johansen R, Dunbar J, Munsky B. Machine learning to predict microbial community functions: An analysis of dissolved organic carbon from litter decomposition. PLoS One 2019; 14:e0215502. [PMID: 31260460 PMCID: PMC6602172 DOI: 10.1371/journal.pone.0215502] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/07/2019] [Indexed: 12/20/2022] Open
Abstract
Microbial communities are ubiquitous and often influence macroscopic properties of the ecosystems they inhabit. However, deciphering the functional relationship between specific microbes and ecosystem properties is an ongoing challenge owing to the complexity of the communities. This challenge can be addressed, in part, by integrating the advances in DNA sequencing technology with computational approaches like machine learning. Although machine learning techniques have been applied to microbiome data, use of these techniques remains rare, and user-friendly platforms to implement such techniques are not widely available. We developed a tool that implements neural network and random forest models to perform regression and feature selection tasks on microbiome data. In this study, we applied the tool to analyze soil microbiome (16S rRNA gene profiles) and dissolved organic carbon (DOC) data from a 44-day plant litter decomposition experiment. The microbiome data includes 1709 total bacterial operational taxonomic units (OTU) from 300+ microcosms. Regression analysis of predicted and actual DOC for a held-out test set of 51 samples yield Pearson's correlation coefficients of.636 and.676 for neural network and random forest approaches, respectively. Important taxa identified by the machine learning techniques are compared to results from a standard tool (indicator species analysis) widely used by microbial ecologists. Of 1709 bacterial taxa, indicator species analysis identified 285 taxa as significant determinants of DOC concentration. Of the top 285 ranked features determined by machine learning methods, a subset of 86 taxa are common to all feature selection techniques. Using this subset of features, prediction results for random permutations of the data set are at least equally accurate compared to predictions determined using the entire feature set. Our results suggest that integration of multiple methods can aid identification of a robust subset of taxa within complex communities that may drive specific functional outcomes of interest.
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Affiliation(s)
- Jaron Thompson
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States of America
| | - Renee Johansen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Brian Munsky
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, United States of America
- Keck Scholar, School of Biomedical Engineering, Colorado State University, Fort Collins, CO, United States of America
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202
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Pittayanon R, Lau JT, Yuan Y, Leontiadis GI, Tse F, Surette M, Moayyedi P. Gut Microbiota in Patients With Irritable Bowel Syndrome-A Systematic Review. Gastroenterology 2019; 157:97-108. [PMID: 30940523 DOI: 10.1053/j.gastro.2019.03.049] [Citation(s) in RCA: 382] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/23/2019] [Accepted: 03/15/2019] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Irritable bowel syndrome (IBS) is common but difficult to treat. Altering the gut microbiota has been proposed as a strategy for treatment of IBS, but the association between the gut microbiome and IBS symptoms has not been well established. We performed a systematic review to explore evidence for this association. METHODS We searched databases, including MEDLINE, EMBASE, Cochrane CDSR, and CENTRAL, through April 2, 2018 for case-control studies comparing the fecal or colon microbiomes of adult or pediatric patients with IBS with microbiomes of healthy individuals (controls). The primary outcome was differences in specific gut microbes between patients with IBS and controls. RESULTS The search identified 2631 citations; 24 studies from 22 articles were included. Most studies evaluated adults presenting with various IBS subtypes. Family Enterobacteriaceae (phylum Proteobacteria), family Lactobacillaceae, and genus Bacteroides were increased in patients with IBS compared with controls, whereas uncultured Clostridiales I, genus Faecalibacterium (including Faecalibacterium prausnitzii), and genus Bifidobacterium were decreased in patients with IBS. The diversity of the microbiota was either decreased or not different in IBS patients compared with controls. More than 40% of included studies did not state whether cases and controls were comparable (did not describe sex and/or age characteristics). CONCLUSIONS In a systematic review, we identified specific bacteria associated with microbiomes of patients with IBS vs controls. Studies are needed to determine whether these microbes are a product or cause of IBS.
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Affiliation(s)
- Rapat Pittayanon
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada; Division of Gastroenterology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, The Thai Red Cross, Bangkok, Thailand
| | - Jennifer T Lau
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Yuhong Yuan
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Grigorios I Leontiadis
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Frances Tse
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Michael Surette
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Paul Moayyedi
- Department of Medicine, Division of Gastroenterology and Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
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203
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Wei T, Dang Y, Cao J, Wu Z, He J, Sun Y, Pan D, Tian Z. Different duck products protein on rat physiology and gut microbiota. J Proteomics 2019; 206:103436. [PMID: 31265922 DOI: 10.1016/j.jprot.2019.103436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/20/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
We report the effects of protein from different duck products on the intestinal flora and physiology of rats. After 30 days of feeding, rats fed water-boiled salted duck protein had the lowest gut microbial diversity and richness. Allobaculum, Lactobacillus, Coprococcus and Eubacterium increased in rats fed wine-cured duck protein, while rats fed water-boiled salted and wine-cured duck protein showed increased serum urea (UREA) concentrations and serum cholesterol (CHOL) to HDL-cholesterol (HDLC) ratios, but decreased retroperitoneal white adipose tissue (rWAT) and perirenal white adipose tissue (pWAT) to body weight ratios. The changes in gut bacteria were mainly associated with the fat-mass index (weight of rWAT or pWAT to body weight ratio), accompanied by the opposite correlation with UREA content. SIGNIFICANCE: It showed that protein from different duck products impacted the intestinal flora and caused physiological changes in rats. Different sources of processed protein vary in their digestibility and digestive kinetics, all of which can affect the intestinal microbiota and physiology. We report the effects is an effort to map the complex interactions of "host physiology-nutrition-microbiota" in order to provide some insights into that food processing can be improved to promote beneficial gut microbes and enhance human health.
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Affiliation(s)
- Taotao Wei
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo 315800, PR China; Food & Pharmaceutical Sciences College of Ningbo University, Ningbo 315800, PR China
| | - Yali Dang
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo 315800, PR China; Food & Pharmaceutical Sciences College of Ningbo University, Ningbo 315800, PR China
| | - Jinxuan Cao
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo 315800, PR China; Food & Pharmaceutical Sciences College of Ningbo University, Ningbo 315800, PR China
| | - Zhen Wu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo 315800, PR China; Food & Pharmaceutical Sciences College of Ningbo University, Ningbo 315800, PR China
| | - Jun He
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo 315800, PR China; Food & Pharmaceutical Sciences College of Ningbo University, Ningbo 315800, PR China
| | - Yangying Sun
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo 315800, PR China; Food & Pharmaceutical Sciences College of Ningbo University, Ningbo 315800, PR China
| | - Daodong Pan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo 315211, China; Key laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo 315800, PR China; Food & Pharmaceutical Sciences College of Ningbo University, Ningbo 315800, PR China.
| | - Zhenwen Tian
- Hubei Xiaohu Duck Food Co., Ltd, Jingzhou 434000, PR China
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Astudillo-García C, Hermans SM, Stevenson B, Buckley HL, Lear G. Microbial assemblages and bioindicators as proxies for ecosystem health status: potential and limitations. Appl Microbiol Biotechnol 2019; 103:6407-6421. [DOI: 10.1007/s00253-019-09963-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 01/04/2023]
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Kassiri B, Shrestha E, Kasprenski M, Antonescu C, Florea LD, Sfanos KS, Wang MH. A Prospective Study of the Urinary and Gastrointestinal Microbiome in Prepubertal Males. Urology 2019; 131:204-210. [PMID: 31195012 DOI: 10.1016/j.urology.2019.05.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/12/2019] [Accepted: 05/24/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To determine if urinary microbial communities similar to those described in adults exist in children and to profile the urinary and gastrointestinal microbiome in children presenting to urology for both routine and complex urologic procedures. METHODS Prepubertal boys (n = 20, ages 3 months-8 years; median age 15 months) who required elective urologic procedures were eligible. Urine samples were collected via sterile catheterization and fecal samples were obtained by rectal swabs. DNA was extracted from urine pellet and fecal samples and subjected to bacterial profiling via 16S rDNA Illumina sequencing and 16S rDNA quantitative polymerase chain reaction. We assessed within and between sample diversity and differential species abundance between samples. RESULTS Urine samples had low bacterial biomass that reflected the presence of bacterial populations. The most abundant genera detected in urine samples are not common to skin microbiota and several of the genera have been previously identified in the urinary microbiome of adults. We report presumably atypical compositional differences in both the urinary and gastrointestinal microbiome in children with prior antibiotic exposure and highlight an important case of a child who had undergone lifelong antibiotic treatment as prophylaxis for congenital abnormalities. CONCLUSION This study provides one of the first characterizations of the urinary microbiome in prepubertal males. Defining the baseline healthy microbiome in children may lay the foundation for understanding the long-term impact of factors such as antibiotic use in the development of a healthy microbiome as well as the development of future urologic and gastrointestinal diseases.
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Affiliation(s)
- Borna Kassiri
- Department of Urology, the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eva Shrestha
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Matthew Kasprenski
- Department of Urology, the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Corina Antonescu
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Baltimore, MD
| | - Liliana D Florea
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Baltimore, MD
| | - Karen S Sfanos
- Department of Urology, the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287.
| | - Ming-Hsien Wang
- Department of Urology, the James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD; Department of Urology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX
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Chin YX, Mi Y, Cao WX, Lim PE, Xue CH, Tang QJ. A Pilot Study on Anti-Obesity Mechanisms of Kappaphycus Alvarezii: The Role of Native κ-Carrageenan and the Leftover Sans-Carrageenan Fraction. Nutrients 2019; 11:E1133. [PMID: 31117266 PMCID: PMC6566674 DOI: 10.3390/nu11051133] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 05/10/2019] [Accepted: 05/17/2019] [Indexed: 12/15/2022] Open
Abstract
Kappaphycus is a commercially important edible red alga widely cultivated for carrageenan production. Here, we aimed to investigate the anti-obesity mechanism of Kappaphycus alvarezii by comparing the effects of whole seaweed (T), extracted native κ-carrageenan (CGN), and the leftover fraction sans-carrageenan (SCGN) supplementations (5%, w/w) on diet-induced obese C57BL/6J mice. A high-fat diet induced both a raised body fat percentage and serum cholesterol level, increased adipocytes size, abnormal levels of adipocytokines, and promoted gut dysbiosis. Our results showed that, overall, both CGN and SCGN were more effective in reversing obesity and related metabolic syndromes to normal levels than T. Furthermore, these findings suggested that CGN- and SCGN-modulated gut dysbiosis induced by a high-fat diet, which may play an influencing role in adiponectin dysregulation. Our data also showed some evidence that CGN and SCGN have distinct effects on selected genes involved in lipid metabolism. In conclusion, both κ-carrageenan and SCGN have novel anti-obesity potential with possible different mechanisms of action.
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Affiliation(s)
- Yao Xian Chin
- Human Health Research Laboratory, College of Food Science and Engineering, University of China, Qingdao 266003, Shandong, China.
| | - Ye Mi
- Human Health Research Laboratory, College of Food Science and Engineering, University of China, Qingdao 266003, Shandong, China.
| | - Wan Xiu Cao
- Human Health Research Laboratory, College of Food Science and Engineering, University of China, Qingdao 266003, Shandong, China.
| | - Phaik Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Chang Hu Xue
- Human Health Research Laboratory, College of Food Science and Engineering, University of China, Qingdao 266003, Shandong, China.
| | - Qing Juan Tang
- Human Health Research Laboratory, College of Food Science and Engineering, University of China, Qingdao 266003, Shandong, China.
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Levi Mortera S, Soggiu A, Vernocchi P, Del Chierico F, Piras C, Carsetti R, Marzano V, Britti D, Urbani A, Roncada P, Putignani L. Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach. J Proteomics 2019; 203:103378. [PMID: 31102759 DOI: 10.1016/j.jprot.2019.103378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition. SIGNIFICANCE: This paper would represent a reference work for investigations on gut microbiota in early life, from both a microbiological and a functional proteomic point of view. We focused on the shaping of the mouse gut microbiota in dependence on the feeding modality, defining a reliable taxonomic description, highlighting some functional characteristics of the microbial community, and performing a first quantitative evaluation by data independent analysis in metaproteomics.
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Affiliation(s)
| | - Alessio Soggiu
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Pamela Vernocchi
- Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Cristian Piras
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Rita Carsetti
- B cell Pathophysiology Unit, Immunology Research Area and Unit of Diagnostic Immunology, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Marzano
- Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Domenico Britti
- C.I.S. - Interdepartmental Services Centre of Veterinary for Human and Animal Health, University of Catanzaro "Magna Græcia", Catanzaro, Italy.; Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Andrea Urbani
- Catholic University of Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Paola Roncada
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Lorenza Putignani
- Parasitology Unit and Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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208
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Ding FCL, Karkhaneh M, Zorzela L, Jou H, Vohra S. Probiotics for paediatric functional abdominal pain disorders: A rapid review. Paediatr Child Health 2019; 24:383-394. [PMID: 31528110 DOI: 10.1093/pch/pxz036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 02/15/2019] [Indexed: 12/17/2022] Open
Abstract
Background Functional abdominal pain disorders (FAPD) are prevalent in the paediatric population, however, there is currently no consensus regarding best practices for treatment. The use of probiotics is becoming popular to treat FAPD. The goal of this rapid review is to synthesize the best evidence on the use of probiotics in children with FAPD. Methods Searches were conducted on five main databases. Randomized controlled trials (RCTs) of probiotic use in children (0 to 18 years) with FAPD were searched. Populations of interest were patients with functional abdominal pain (FAP), irritable bowel syndrome (IBS), and functional dyspepsia (FD), recruited based on Rome criteria. Outcomes of interest were changes in abdominal pain severity, frequency, and duration. Findings Eleven RCTs with 829 participants with the diagnosis of FAP (n=400), IBS (n=329), FD (n=45), and mixed population (n=55) were included. Of six studies of children with FAP, two (n=103) used Lactobacillus rhamnosus GG (LGG) and reported no significant effects on pain, and four (n=281) used Lactobacillus (L) reuteri DSM 17938, of which three (n=229) reported significant positive effects on either severity or frequency of pain. Of six trials of children with IBS, four (n=219) used LGG, of which three (n=168) reported a positive effect. One (n=48) used bifidobacteria and one used VSL #3 (n=59), both demonstrating positive effects with probiotics. Two studies of FD reported no benefit. No adverse events were attributed to probiotics. Conclusions There is preliminary evidence for use of probiotics, particularly LGG, in reducing abdominal pain in children with IBS. There are inconsistent positive effects of other probiotics, including L. reuteri DSM 17938, in reducing pain in patients with FAP, IBS, or FD. More RCTs with rigorous methodology using single or combination probiotics are warranted.
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Affiliation(s)
- Fang Chao Linda Ding
- Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, Manitoba
| | - Mohammad Karkhaneh
- Department of Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta
| | - Liliane Zorzela
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta
| | - Hsing Jou
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta
| | - Sunita Vohra
- Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta
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209
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Hollister EB, Oezguen N, Chumpitazi BP, Luna RA, Weidler EM, Rubio-Gonzales M, Dahdouli M, Cope JL, Mistretta TA, Raza S, Metcalf GA, Muzny DM, Gibbs RA, Petrosino JF, Heitkemper M, Savidge TC, Shulman RJ, Versalovic J. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. J Mol Diagn 2019; 21:449-461. [PMID: 31005411 PMCID: PMC6504675 DOI: 10.1016/j.jmoldx.2019.01.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/30/2018] [Accepted: 01/06/2019] [Indexed: 02/06/2023] Open
Abstract
Accurate diagnosis and stratification of children with irritable bowel syndrome (IBS) remain challenging. Given the central role of recurrent abdominal pain in IBS, we evaluated the relationships of pediatric IBS and abdominal pain with intestinal microbes and fecal metabolites using a comprehensive clinical characterization and multiomics strategy. Using rigorous clinical phenotyping, we identified preadolescent children (aged 7 to 12 years) with Rome III IBS (n = 23) and healthy controls (n = 22) and characterized their fecal microbial communities using whole-genome shotgun metagenomics and global unbiased fecal metabolomic profiling. Correlation-based approaches and machine learning algorithms identified associations between microbes, metabolites, and abdominal pain. IBS cases differed from controls with respect to key bacterial taxa (eg, Flavonifractor plautii and Lachnospiraceae bacterium 7_1_58FAA), metagenomic functions (eg, carbohydrate metabolism and amino acid metabolism), and higher-order metabolites (eg, secondary bile acids, sterols, and steroid-like compounds). Significant associations between abdominal pain frequency and severity and intestinal microbial features were identified. A random forest classifier built on metagenomic and metabolic markers successfully distinguished IBS cases from controls (area under the curve, 0.93). Leveraging multiple lines of evidence, intestinal microbes, genes/pathways, and metabolites were associated with IBS, and these features were capable of distinguishing children with IBS from healthy children. These multi-omics features, and their links to childhood IBS coupled with nutritional interventions, may lead to new microbiome-guided diagnostic and therapeutic strategies.
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Affiliation(s)
- Emily B Hollister
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Diversigen, Inc., Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Bruno P Chumpitazi
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas
| | - Ruth Ann Luna
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Erica M Weidler
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas; Children's Nutrition Research Center, Houston, Texas
| | - Michelle Rubio-Gonzales
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Mahmoud Dahdouli
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Julia L Cope
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Toni-Ann Mistretta
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Sabeen Raza
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas; Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas
| | - Margaret Heitkemper
- Department of Biobehavioral Nursing and Health Informatics, University of Washington, Seattle, Washington
| | - Tor C Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Robert J Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas; Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Texas Children's Hospital, Houston, Texas; Children's Nutrition Research Center, Houston, Texas
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas; Department of Pathology, Texas Children's Hospital, Houston, Texas; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas.
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Tsiaoussis J, Antoniou MN, Koliarakis I, Mesnage R, Vardavas CI, Izotov BN, Psaroulaki A, Tsatsakis A. Effects of single and combined toxic exposures on the gut microbiome: Current knowledge and future directions. Toxicol Lett 2019; 312:72-97. [PMID: 31034867 DOI: 10.1016/j.toxlet.2019.04.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/08/2019] [Accepted: 04/11/2019] [Indexed: 12/12/2022]
Abstract
Human populations are chronically exposed to mixtures of toxic chemicals. Predicting the health effects of these mixtures require a large amount of information on the mode of action of their components. Xenobiotic metabolism by bacteria inhabiting the gastrointestinal tract has a major influence on human health. Our review aims to explore the literature for studies looking to characterize the different modes of action and outcomes of major chemical pollutants, and some components of cosmetics and food additives, on gut microbial communities in order to facilitate an estimation of their potential mixture effects. We identified good evidence that exposure to heavy metals, pesticides, nanoparticles, polycyclic aromatic hydrocarbons, dioxins, furans, polychlorinated biphenyls, and non-caloric artificial sweeteners affect the gut microbiome and which is associated with the development of metabolic, malignant, inflammatory, or immune diseases. Answering the question 'Who is there?' is not sufficient to define the mode of action of a toxicant in predictive modeling of mixture effects. Therefore, we recommend that new studies focus to simulate real-life exposure to diverse chemicals (toxicants, cosmetic/food additives), including as mixtures, and which combine metagenomics, metatranscriptomics and metabolomic analytical methods achieving in that way a comprehensive evaluation of effects on human health.
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Affiliation(s)
- John Tsiaoussis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion, Greece
| | - Michael N Antoniou
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Ioannis Koliarakis
- Laboratory of Anatomy-Histology-Embryology, Medical School, University of Crete, 71110 Heraklion, Greece
| | - Robin Mesnage
- Gene Expression and Therapy Group, King's College London, Faculty of Life Sciences & Medicine, Department of Medical and Molecular Genetics, 8th Floor, Tower Wing, Guy's Hospital, Great Maze Pond, London SE1 9RT, United Kingdom
| | - Constantine I Vardavas
- Laboratory of Toxicology, Medical School, University of Crete, Voutes, 71409 Heraklion, Crete, Greece
| | - Boris N Izotov
- Department of Analytical, Toxicology, Pharmaceutical Chemistry and Pharmacognosy, Sechenov University, 119991 Moscow, Russia
| | - Anna Psaroulaki
- Department of Clinical Microbiology and Microbial Pathogenesis, Medical School, University of Crete, 71110 Heraklion, Greece
| | - Aristidis Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, Voutes, 71409 Heraklion, Crete, Greece; Department of Analytical, Toxicology, Pharmaceutical Chemistry and Pharmacognosy, Sechenov University, 119991 Moscow, Russia.
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211
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Mills S, Stanton C, Lane JA, Smith GJ, Ross RP. Precision Nutrition and the Microbiome, Part I: Current State of the Science. Nutrients 2019; 11:nu11040923. [PMID: 31022973 PMCID: PMC6520976 DOI: 10.3390/nu11040923] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/10/2019] [Accepted: 04/17/2019] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota is a highly complex community which evolves and adapts to its host over a lifetime. It has been described as a virtual organ owing to the myriad of functions it performs, including the production of bioactive metabolites, regulation of immunity, energy homeostasis and protection against pathogens. These activities are dependent on the quantity and quality of the microbiota alongside its metabolic potential, which are dictated by a number of factors, including diet and host genetics. In this regard, the gut microbiome is malleable and varies significantly from host to host. These two features render the gut microbiome a candidate ‘organ’ for the possibility of precision microbiomics—the use of the gut microbiome as a biomarker to predict responsiveness to specific dietary constituents to generate precision diets and interventions for optimal health. With this in mind, this two-part review investigates the current state of the science in terms of the influence of diet and specific dietary components on the gut microbiota and subsequent consequences for health status, along with opportunities to modulate the microbiota for improved health and the potential of the microbiome as a biomarker to predict responsiveness to dietary components. In particular, in Part I, we examine the development of the microbiota from birth and its role in health. We investigate the consequences of poor-quality diet in relation to infection and inflammation and discuss diet-derived microbial metabolites which negatively impact health. We look at the role of diet in shaping the microbiome and the influence of specific dietary components, namely protein, fat and carbohydrates, on gut microbiota composition.
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Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland.
| | - Catherine Stanton
- APC Microbiome Ireland, Teagasc Food Research Centre, Fermoy P61 C996, Co Cork, Ireland.
| | - Jonathan A Lane
- H&H Group, Technical Centre, Global Research and Technology Centre, Cork P61 C996, Ireland.
| | - Graeme J Smith
- H&H Group, Technical Centre, Global Research and Technology Centre, Cork P61 C996, Ireland.
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland.
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212
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Morell Miranda P, Bertolini F, Kadarmideen HN. Investigation of gut microbiome association with inflammatory bowel disease and depression: a machine learning approach. F1000Res 2019. [DOI: 10.12688/f1000research.15091.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background: Inflammatory bowel disease (IBD) is a group of chronic diseases related to inflammatory processes in the digestive tract generally associated with an immune response to an altered gut microbiome in genetically predisposed subjects. For years, both researchers and clinicians have been reporting increased rates of anxiety and depression disorders in IBD, and these disorders have also been linked to an altered microbiome. However, the underlying pathophysiological mechanisms of comorbidity are poorly understood at the gut microbiome level. Methods: Metagenomic and metatranscriptomic data were retrieved from the Inflammatory Bowel Disease Multi-Omics Database. Samples from 70 individuals that had answered to a self-reported depression and anxiety questionnaire were selected and classified by their IBD diagnosis and their questionnaire results, creating six different groups. The cross-validation random forest algorithm was used in 90% of the individuals (training set) to retain the most important species involved in discriminating the samples without losing predictive power. The validation set that represented the remaining 10% of the samples equally distributed across the six groups was used to train a random forest using only the species selected in order to evaluate their predictive power. Results: A total of 24 species were identified as the most informative in discriminating the 6 groups. Several of these species were frequently described in dysbiosis cases, such as species from the genus Bacteroides and Faecalibacterium prausnitzii. Despite the different compositions among the groups, no common patterns were found between samples classified as depressed. However, distinct taxonomic profiles within patients of IBD depending on their depression status were detected. Conclusions: The machine learning approach is a promising approach for investigating the role of microbiome in IBD and depression. Abundance and functional changes in these species suggest that depression should be considered as a factor in future research on IBD.
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213
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214
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Fisher K, Hutcheon D, Ziegler J. Elimination of Fermentable Carbohydrates to Reduce Gastrointestinal Symptoms in Pediatric Patients With Irritable Bowel Syndrome: A Narrative Review. Nutr Clin Pract 2019; 35:231-245. [PMID: 30937981 DOI: 10.1002/ncp.10269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Irritable bowel syndrome (IBS) is classified as a functional gastrointestinal (GI) disorder characterized by abdominal pain, bloating, and changes in bowel function. Although the pathophysiology of IBS is incompletely understood, fermentable carbohydrates are implicated as a potential cause of symptoms. An elimination diet, such as a low-FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet, represents a potential intervention for reducing GI symptoms in patients with IBS. The role of fermentable carbohydrates in symptom onset is well studied in adult patients with IBS; however, less research exists in the pediatric population. This review sought to explore evidence for the role of dietary fermentable carbohydrate elimination to reduce GI symptoms (abdominal pain, stool changes, abdominal bloating) in children and adolescents (4-19 years of age) diagnosed with IBS based on Rome III or IV criteria. Five studies of neutral to positive quality rating were identified and analyzed using the Academy of Nutrition and Dietetics Evidence Analysis Process. These studies demonstrate that dietary elimination of fermentable carbohydrates, such as through a low-FODMAP diet, reduces the severity of 1 or more GI symptoms in about one-quarter to one-half of pediatric patients with IBS. Patients without improvement are considered "nonresponders" and may require an alternative intervention. More research is needed to establish the best way to identify patients who would respond to elimination diets vs other IBS treatment strategies.
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Affiliation(s)
- Kelly Fisher
- Department of Clinical and Preventive Nutrition Sciences, School of Health Professions, Rutgers University, Newark, New Jersey, USA
| | - Deborah Hutcheon
- Department of Clinical and Preventive Nutrition Sciences, School of Health Professions, Rutgers University, Newark, New Jersey, USA
| | - Jane Ziegler
- Department of Clinical and Preventive Nutrition Sciences, School of Health Professions, Rutgers University, Newark, New Jersey, USA
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215
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Parida S, Sharma D. The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer. Biochim Biophys Acta Rev Cancer 2019; 1871:392-405. [PMID: 30981803 PMCID: PMC8769497 DOI: 10.1016/j.bbcan.2019.04.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/22/2022]
Abstract
Disparate occurrence of breast cancer remains an intriguing question since only a subset of women with known risk factors develop cancer. Recent studies suggest an active role of local and distant microbiota in breast cancer initiation, progression, and overall prognosis. A dysbiotic microbiota predisposes the body to develop cancer by inducing genetic instability, initiating DNA damage and proliferation of the damaged progeny, eliciting favorable immune response, metabolic dysregulation and altered response to therapy. In this review, we present our analyses of the existing datasets and discuss the local dysbiosis observed in breast cancer patients and different aspects of breast carcinogenesis that can be potentially influenced by local breast microbiota. Striking differences between microbial community compositions in breast of cancer patients compared to healthy individuals were noted. Differences in microbiome were also apparent between benign and malignant disease and between nipple aspirate fluid of healthy individuals and breast survivors. We also discuss the identification of distinct bacterial, fungal, viral as well as parasite signatures for breast cancer. These microbes are capable of producing numerous secondary metabolites that can act as signaling mediators effecting breast cancer progression. We review how microbes potentially alter response to therapy affecting drug metabolism, pharmacokinetics, anti-tumor effects and toxicity. In conclusion, breast harbors a community of microbes that can communicate with the host cells inducing downstream signaling pathways and modulating various aspects of breast cancer growth and metastatic progression and an improved understanding of microbial dysbiosis can potentially reduce breast cancer risk and improve outcomes of breast cancer patients. The human microbiome, now referred to as, the "forgotten organ" contains a metagenome that is 100-fold more diverse compared to the human genome, thereby, is critically associated with human health [1,2]. With the revelations of the human microbiome project and advent of deep sequencing techniques, a plethora of information has been acquired in recent years. Body sites like stomach, bladder and lungs, once thought to be sterile, are now known to harbor millions of indigenous microbial species. Approximately 80% of the healthy microbiome consists of Firmicutes and Bacteroidetes accompanied by Verrucomicrobia, Actinobacteria, Proteobacteria, Tenericutes and Cyanobacteria [2-7]. The role of microbiome in diabetes, obesity and even neurodegenerative diseases was greatly appreciated in the last decade [1,7-14] and now it has been established that microbiome significantly contributes to many organ specific cancers [1,15,16].
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Affiliation(s)
- Sheetal Parida
- Department of Oncology, Johns Hopkins University School of Medicine and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA
| | - Dipali Sharma
- Department of Oncology, Johns Hopkins University School of Medicine and the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA.
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216
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Glutamatergic Signaling Along The Microbiota-Gut-Brain Axis. Int J Mol Sci 2019; 20:ijms20061482. [PMID: 30934533 PMCID: PMC6471396 DOI: 10.3390/ijms20061482] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/04/2019] [Accepted: 03/21/2019] [Indexed: 12/21/2022] Open
Abstract
A complex bidirectional communication system exists between the gastrointestinal tract and the brain. Initially termed the “gut-brain axis” it is now renamed the “microbiota-gut-brain axis” considering the pivotal role of gut microbiota in maintaining local and systemic homeostasis. Different cellular and molecular pathways act along this axis and strong attention is paid to neuroactive molecules (neurotransmitters, i.e., noradrenaline, dopamine, serotonin, gamma aminobutyric acid and glutamate and metabolites, i.e., tryptophan metabolites), sustaining a possible interkingdom communication system between eukaryota and prokaryota. This review provides a description of the most up-to-date evidence on glutamate as a neurotransmitter/neuromodulator in this bidirectional communication axis. Modulation of glutamatergic receptor activity along the microbiota-gut-brain axis may influence gut (i.e., taste, visceral sensitivity and motility) and brain functions (stress response, mood and behavior) and alterations of glutamatergic transmission may participate to the pathogenesis of local and brain disorders. In this latter context, we will focus on two major gut disorders, such as irritable bowel syndrome and inflammatory bowel disease, both characterized by psychiatric co-morbidity. Research in this area opens the possibility to target glutamatergic neurotransmission, either pharmacologically or by the use of probiotics producing neuroactive molecules, as a therapeutic approach for the treatment of gastrointestinal and related psychiatric disorders.
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217
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Degenhardt F, Seifert S, Szymczak S. Evaluation of variable selection methods for random forests and omics data sets. Brief Bioinform 2019; 20:492-503. [PMID: 29045534 PMCID: PMC6433899 DOI: 10.1093/bib/bbx124] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/06/2017] [Indexed: 12/28/2022] Open
Abstract
Machine learning methods and in particular random forests are promising approaches for prediction based on high dimensional omics data sets. They provide variable importance measures to rank predictors according to their predictive power. If building a prediction model is the main goal of a study, often a minimal set of variables with good prediction performance is selected. However, if the objective is the identification of involved variables to find active networks and pathways, approaches that aim to select all relevant variables should be preferred. We evaluated several variable selection procedures based on simulated data as well as publicly available experimental methylation and gene expression data. Our comparison included the Boruta algorithm, the Vita method, recurrent relative variable importance, a permutation approach and its parametric variant (Altmann) as well as recursive feature elimination (RFE). In our simulation studies, Boruta was the most powerful approach, followed closely by the Vita method. Both approaches demonstrated similar stability in variable selection, while Vita was the most robust approach under a pure null model without any predictor variables related to the outcome. In the analysis of the different experimental data sets, Vita demonstrated slightly better stability in variable selection and was less computationally intensive than Boruta. In conclusion, we recommend the Boruta and Vita approaches for the analysis of high-dimensional data sets. Vita is considerably faster than Boruta and thus more suitable for large data sets, but only Boruta can also be applied in low-dimensional settings.
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Affiliation(s)
| | - Stephan Seifert
- Institute of Medical Informatics and Statistics, Kiel University, Germany
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, Germany
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218
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Hieke ASC, Hubert SM, Athrey G. Circadian disruption and divergent microbiota acquisition under extended photoperiod regimens in chicken. PeerJ 2019; 7:e6592. [PMID: 30886778 PMCID: PMC6421066 DOI: 10.7717/peerj.6592] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/09/2019] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota is crucial for metabolic homeostasis, immunity, growth and overall health, and it is recognized that early-life microbiota acquisition is a pivotal event for later-life health. Recent studies show that gut microbiota diversity and functional activity are synchronized with the host circadian rhythms in healthy individuals, and circadian disruption elicits dysbiosis in mammalian models. However, no studies have determined the associations between circadian disruption in early life, microbiota colonization, and the consequences for microbiota structure in birds. Chickens, as a major source of protein around the world, are one of the most important agricultural species, and their gut and metabolic health are significant concerns. The poultry industry routinely employs extended photoperiods (>18 h light) as a management tool, and their impacts on the chicken circadian, its role in gut microbiota acquisition in early life (first 3 weeks of life), and consequences for later life microbiota structure remain unknown. In this study, the objectives were to (a) characterize circadian activity under two different light regimes in layer chicken (12/12 h′ Light/Dark (LD) and 23/1 h LD), (b) characterize gut microbiota acquisition and composition in the first 4 weeks of life, (c) determine if gut microbiota oscillate in synchrony with the host circadian rhythm, and (d) to determine if fecal microbiota is representative of cecal microbiota in early life. Expression of clock genes (clock, bmal1, and per2) was assayed, and fecal and cecal microbiotas were characterized using 16S rRNA gene amplicon analyses from birds raised under two photoperiod treatments. Chickens raised under 12/12 LD photoperiods exhibited rhythmic clock gene activity, which was absent in birds raised under the extended (23/1 LD) photoperiod. There was differential microbiota acquisition under different photoperiod regimes in newly hatched chicks. Gut microbiota members showed a similar oscillating pattern as the host, but this association was not as strong as found in mammals. Finally, the fecal microbiota was found to be not representative of cecal microbiota membership and structure in young birds. This is one of the first studies to demonstrate the use of photoperiods to modulate microbiota acquisition in newly hatched chicks, and show their potential as a tool to promote the colonization of beneficial microorganisms.
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Affiliation(s)
| | | | - Giridhar Athrey
- Poultry Science Department, Texas A&M University, College Station, TX, USA.,Faculty of Ecology and Evolutionary Biology, Texas A&M University, College Station, TX, USA
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219
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Nonceliac Wheat Sensitivity: An Immune-Mediated Condition with Systemic Manifestations. Gastroenterol Clin North Am 2019; 48:165-182. [PMID: 30711208 PMCID: PMC6364564 DOI: 10.1016/j.gtc.2018.09.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Non-celiac wheat sensitivity (NCWS) is characterized by gastrointestinal and extra-intestinal symptoms following the ingestion of gluten-containing cereals in subjects without celiac disease or wheat allergy. The identity of the molecular triggers in these cereals responsible for the symptoms of NCWS remains to be delineated. Recent research has identified a biological basis for the condition, with the observation of systemic immune activation in response to microbial translocation that appears to be linked to intestinal barrier defects. Ongoing research efforts are aimed at further characterizing the etiology, mechanism, and biomarkers of the condition.
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220
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Abstract
The gut microbiome is implicated in the pathophysiology of a wide range of psychological disorders. Preclinical studies have provided us with key insights into the mechanisms by which the microbiome influences bidirectional gut-brain communication. There are many signaling pathways involved, including the hypothalamic-pituitary-adrenal axis, immune modulation, tryptophan and serotonin metabolism, bile acid transformation, microbial production of neuroactive compounds, and regulation of the endocannabinoid system. The complex and widespread influence of the microbiome on many physiological and psychological processes has generated a keen interest in its therapeutic potential for depression, anxiety, autism, and other psychiatric disorders. It has been shown that the microbiome composition of people suffering with such conditions differs significantly from that of healthy controls, and although the area is in its infancy, interventional studies that alter a person's microbiome through the use of probiotics, prebiotics, or dietary change can alleviate psychopathological symptoms.
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Affiliation(s)
- Mary I Butler
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork T12 K8AF, Ireland; .,APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork T12 K8AF, Ireland
| | - Timothy G Dinan
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork T12 K8AF, Ireland; .,APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland
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221
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Huang TT, Lai JB, Du YL, Xu Y, Ruan LM, Hu SH. Current Understanding of Gut Microbiota in Mood Disorders: An Update of Human Studies. Front Genet 2019; 10:98. [PMID: 30838027 PMCID: PMC6389720 DOI: 10.3389/fgene.2019.00098] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023] Open
Abstract
Gut microbiota plays an important role in the bidirectional communication between the gut and the central nervous system. Mounting evidence suggests that gut microbiota can influence the brain function via neuroimmune and neuroendocrine pathways as well as the nervous system. Advances in gene sequencing techniques further facilitate investigating the underlying relationship between gut microbiota and psychiatric disorders. In recent years, researchers have preliminarily explored the gut microbiota in patients with mood disorders. The current review aims to summarize the published human studies of gut microbiota in mood disorders. The findings showed that microbial diversity and taxonomic compositions were significantly changed compared with healthy individuals. Most of these findings revealed that short-chain fatty acids-producing bacterial genera were decreased, while pro-inflammatory genera and those involved in lipid metabolism were increased in patients with depressive episodes. Interestingly, the abundance of Actinobacteria, Enterobacteriaceae was increased and Faecalibacterium was decreased consistently in patients with either bipolar disorder or major depressive disorder. Some studies further indicated that specific bacteria were associated with clinical characteristics, inflammatory profiles, metabolic markers, and pharmacological treatment. These studies present preliminary evidence of the important role of gut microbiota in mood disorders, through the brain-gut-microbiota axis, which emerges as a promising target for disease diagnosis and therapeutic interventions in the future.
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Affiliation(s)
- Ting-Ting Huang
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian-Bo Lai
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Mental Disorder's Management of Zhejiang Province, Hangzhou, China.,Brain Research Institute of Zhejiang University, Hangzhou, China
| | - Yan-Li Du
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Xu
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Mental Disorder's Management of Zhejiang Province, Hangzhou, China.,Brain Research Institute of Zhejiang University, Hangzhou, China
| | - Lie-Min Ruan
- Department of Mental Health, Ningbo First Hospital, Ningbo, China
| | - Shao-Hua Hu
- Department of Psychiatry, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The Key Laboratory of Mental Disorder's Management of Zhejiang Province, Hangzhou, China.,Brain Research Institute of Zhejiang University, Hangzhou, China
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222
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Yitbarek A, Weese JS, Alkie TN, Parkinson J, Sharif S. Influenza A virus subtype H9N2 infection disrupts the composition of intestinal microbiota of chickens. FEMS Microbiol Ecol 2019; 94:4705883. [PMID: 29228270 DOI: 10.1093/femsec/fix165] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/30/2017] [Indexed: 12/26/2022] Open
Abstract
The impact of low pathogenic influenza viruses such as subtype H9N2, which infect the respiratory and the gastrointestinal tracts of chickens, on microbial composition are not known. Twenty-day-old specific pathogen-free chickens were assigned to two treatment groups, control (uninfected) and H9N2-infected (challenged via the oral-nasal route). Fecal genomic DNA was extracted, and the V3-V4 regions of the 16S rRNA gene were sequenced using the Illumina Miseq® platform. Sequences were curated using Mothur as described in the MiSeq SOP. Infection of chickens with H9N2 resulted in an increase in phylum Proteobacteria, and differential enrichment with the genera Vampirovibrio, Pseudoflavonifractor, Ruminococcus, Clostridium cluster XIVb and Isobaculum while control chickens were differentially enriched with genera Novosphingobium, Sphingomonas, Bradyrhizobium and Bifidobacterium. Analysis of pre- and post-H9N2 infection of the same chickens showed that, before infection, the fecal microbiota was characterized by Lachnospiracea and Ruminococcaceae family and the genera Clostridium sensu stricto, Roseburia and Lachnospiraceae incertae sedis. However, post-H9N2 infection, class Deltaproteobacteria, orders Clostridiales and Bacteroidiales and the genus Alistipes were differentially enriched. Findings from the current study show that influenza virus infection in chickens results in the shift of the gut microbiota, and the disruption of the host-microbial homeostasis in the gut might be one of the mechanisms by which influenza virus infection is established in chickens.
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Affiliation(s)
- Alexander Yitbarek
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - J Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Tamiru Negash Alkie
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - John Parkinson
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.,Division of Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Departments of Biochemistry and Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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223
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Brasili E, Hassimotto NMA, Del Chierico F, Marini F, Quagliariello A, Sciubba F, Miccheli A, Putignani L, Lajolo F. Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1381-1391. [PMID: 30644740 DOI: 10.1021/acs.jafc.8b05408] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We have investigated the effect of intake of two different orange juices from Citrus sinensis cv. "Cara Cara" and cv. "Bahia" on faecal microbiota and metabolome using an integrated meta-omics approach. Following a randomized crossover design, healthy subjects daily consumed 500 mL of orange juice from Cara Cara or Bahia juices or an isocaloric control drink. Stools were collected at baseline (T0) and after a week (T7) of intervention. Operational taxonomic units (OTUs) were pyrosequenced targeting 16S rRNA, and faecal metabolites were analyzed by an untargeted metabolomics approach based on 1H NMR spectroscopy. The major shift observed in microbiota composition after orange juice intake was the increased abundance of a network of Clostridia OTUs from Mogibacteriaceae, Tissierellaceae, Veillonellaceae, Odoribacteraceae, and Ruminococcaceae families, whose members were differently affected by Cara Cara or Bahia juice consumption. A core of six metabolites such as inositol, choline, lysine, arginine, urocanic acid, and formate significantly increased in Cara Cara compared to the Bahia group.
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Affiliation(s)
- Elisa Brasili
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Science , University of São Paulo , São Paulo 05508-000, Brazil
- Food Research Center (FoRC) , CEPID-FAPESP (Research Innovation and Dissemination Centers Sao Paulo Research Foundation) , São Paulo 05468-901 , Brazil
| | - Neuza Mariko Aymoto Hassimotto
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Science , University of São Paulo , São Paulo 05508-000, Brazil
- Food Research Center (FoRC) , CEPID-FAPESP (Research Innovation and Dissemination Centers Sao Paulo Research Foundation) , São Paulo 05468-901 , Brazil
| | - Federica Del Chierico
- Unit of Human Microbiome , Children's Hospital and Research Institute Bambino Gesù , Rome 00165 , Italy
| | - Federico Marini
- Department of Chemistry , University of Rome "La Sapienza" , Rome 00185 , Italy
| | - Andrea Quagliariello
- Unit of Human Microbiome , Children's Hospital and Research Institute Bambino Gesù , Rome 00165 , Italy
| | - Fabio Sciubba
- Department of Chemistry , University of Rome "La Sapienza" , Rome 00185 , Italy
| | - Alfredo Miccheli
- Department of Chemistry , University of Rome "La Sapienza" , Rome 00185 , Italy
| | - Lorenza Putignani
- Unit of Human Microbiome , Children's Hospital and Research Institute Bambino Gesù , Rome 00165 , Italy
- Unit of Parasitology , Children's Hospital and Research Institute Bambino Gesù , Rome 00165 , Italy
| | - Franco Lajolo
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Science , University of São Paulo , São Paulo 05508-000, Brazil
- Food Research Center (FoRC) , CEPID-FAPESP (Research Innovation and Dissemination Centers Sao Paulo Research Foundation) , São Paulo 05468-901 , Brazil
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224
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Flowers SA, Baxter NT, Ward KM, Kraal AZ, McInnis MG, Schmidt TM, Ellingrod VL. Effects of Atypical Antipsychotic Treatment and Resistant Starch Supplementation on Gut Microbiome Composition in a Cohort of Patients with Bipolar Disorder or Schizophrenia. Pharmacotherapy 2019; 39:161-170. [PMID: 30620405 DOI: 10.1002/phar.2214] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
STUDY OBJECTIVE Previous studies identified shifts in gut microbiota associated with atypical antipsychotic (AAP) treatment that may link AAPs to metabolic burden. Dietary prebiotics such as resistant starch may be beneficial in obesity and glucose regulation, but little is known mechanistically about their ability to modify gut microbiota in AAP-treated individuals. This investigation was undertaken to delineate mechanistically the effects of AAP treatment and resistant starch supplementation on gut microbiota in a psychiatric population. DESIGN Cross-sectional cohort study. SETTING The study was performed in an outpatient setting. PATIENTS A total of 37 adults with a diagnosis of bipolar disorder or schizophrenia who were treated with an AAP (clozapine, olanzapine, risperidone, quetiapine, or ziprasidone [21 patients]) or lithium and/or lamotrigine (16 patients) for at least 6 months. INTERVENTION Patients in the AAP group received raw unmodified potato starch (resistant starch) daily for 14 days. MEASUREMENTS AND MAIN RESULTS Of the 37 patients, the mean ± SD age was 52.2 ± 12.5 years, and 57% were male. The primary outcome was gut microbiome DNA composition. Microbiome DNA obtained from stool samples from all patients was subject to 16S ribosomal RNA (rRNA) gene sequencing before and during resistant starch supplementation. Inter- and intragroup microbial diversity measures were performed by permutational multivariate analysis of variance and the Inverse Simpson Diversity Index, respectively. Differentially abundant organisms were detected by using linear discriminant analysis effect size. Although no significant difference in overall microbiota composition was detected at baseline between AAP users and nonusers, non-AAP users showed increased fractional representation of Alistipes. AAP-treated women exhibited decreased diversity compared with non-AAP-treated women. Although the microbiome of AAP-treated patients varied with resistant starch administration, an increased abundance of the Actinobacteria phylum was observed. CONCLUSION These data suggest that AAP treatment is associated with measurable differences in gut microbiota, particularly in female AAP-treated patients in whom reduced species richness was observed. Additionally, variable microbiome responses to resistant starch supplementation were seen, with a significant increase in starch degraders.
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Affiliation(s)
- Stephanie A Flowers
- Department of Pharmacy Practice, University of Illinois at Chicago, Chicago, Illinois
| | - Nielson T Baxter
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Kristen M Ward
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
| | - A Zarina Kraal
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan
| | - Thomas M Schmidt
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Vicki L Ellingrod
- Department of Clinical Pharmacy, University of Michigan, Ann Arbor, Michigan
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225
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Zhuang L, Chen H, Zhang S, Zhuang J, Li Q, Feng Z. Intestinal Microbiota in Early Life and Its Implications on Childhood Health. GENOMICS, PROTEOMICS & BIOINFORMATICS 2019; 17:13-25. [PMID: 30986482 PMCID: PMC6522475 DOI: 10.1016/j.gpb.2018.10.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/07/2018] [Accepted: 10/10/2018] [Indexed: 02/07/2023]
Abstract
Trillions of microbes reside in the human body and participate in multiple physiological and pathophysiological processes that affect host health throughout the life cycle. The microbiome is hallmarked by distinctive compositional and functional features across different life periods. Accumulating evidence has shown that microbes residing in the human body may play fundamental roles in infant development and the maturation of the immune system. Gut microbes are thought to be essential for the facilitation of infantile and childhood development and immunity by assisting in breaking down food substances to liberate nutrients, protecting against pathogens, stimulating or modulating the immune system, and exerting control over the hypothalamic-pituitary-adrenal axis. This review aims to summarize the current understanding of the colonization and development of the gut microbiota in early life, highlighting the recent findings regarding the role of intestinal microbes in pediatric diseases. Furthermore, we also discuss the microbiota-mediated therapeutics that can reconfigure bacterial communities to treat dysbiosis.
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Affiliation(s)
- Lu Zhuang
- Affiliated Bayi Children's Hospital, The Seventh Medical Center of PLA General Hospital, Beijing 100700, China; National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing 100700, China; Beijing Key Laboratory of Pediatric Organ Failure, Beijing 100700, China
| | - Haihua Chen
- Affiliated Bayi Children's Hospital, The Seventh Medical Center of PLA General Hospital, Beijing 100700, China; The First Clinical Academy of Dalian Medical University, Dalian 116011, China
| | - Sheng Zhang
- Affiliated Bayi Children's Hospital, The Seventh Medical Center of PLA General Hospital, Beijing 100700, China; National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing 100700, China; Beijing Key Laboratory of Pediatric Organ Failure, Beijing 100700, China
| | - Jiahui Zhuang
- College of the Environment, Northeast Normal University, Changchun 130117, China
| | - Qiuping Li
- Affiliated Bayi Children's Hospital, The Seventh Medical Center of PLA General Hospital, Beijing 100700, China; National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing 100700, China; Beijing Key Laboratory of Pediatric Organ Failure, Beijing 100700, China.
| | - Zhichun Feng
- Affiliated Bayi Children's Hospital, The Seventh Medical Center of PLA General Hospital, Beijing 100700, China; National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing 100700, China; Beijing Key Laboratory of Pediatric Organ Failure, Beijing 100700, China.
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226
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Yang C, Fang X, Zhan G, Huang N, Li S, Bi J, Jiang R, Yang L, Miao L, Zhu B, Luo A, Hashimoto K. Key role of gut microbiota in anhedonia-like phenotype in rodents with neuropathic pain. Transl Psychiatry 2019; 9:57. [PMID: 30705252 PMCID: PMC6355832 DOI: 10.1038/s41398-019-0379-8] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 12/15/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023] Open
Abstract
Patients with chronic neuropathic pain frequently suffer from symptoms of anhedonia, which is a core symptom of depression. Accumulating studies suggest that gut microbiota may play a role in depression via gut-microbiota-brain axis. However, it is unknown whether gut microbiota plays a role in neuropathic pain-associated anhedonia. Here, we used a rat model of spared nerve injury (SNI). Hierarchical cluster analysis of sucrose preference test (SPT) results was used to classify the SNI rats with or without anhedonia-like phenotype. The 16S ribosomal RNA sequencing analysis showed abnormal composition of gut microbiota in the anhedonia susceptible compared to sham-operated rats and resilient rats. Furthermore, antibiotics-treated mice showed pain as well as depression-like and anhedonia-like phenotypes, suggesting a role of gut microbiota in these abnormal behaviors. Transplantation of fecal microbiota from anhedonia susceptible rats into antibiotics-treated pseudo-germ-free mice significantly exaggerated pain and depression-like phenotypes, including anhedonia. In contrast, transplantation of fecal microbiota from resilient rats into antibiotics-treated pseudo-germ-free mice significantly improved pain and depression-like phenotypes, including anhedonia. In conclusion, this study suggests that abnormal composition of gut microbiota may contribute to anhedonia susceptibility post SNI surgery, and that gut microbiota also plays a role in the pain as well as depression-like phenotypes. Interestingly, fecal microbiota transplantation from SNI rats with or without anhedonia can alter pain, depression-like and anhedonia-like phenotypes in the pseudo-germ-free mice. Therefore, it is likely that gut microbiota plays a key role in the pain as well as depression-like phenotypes including anhedonia in rodents with neuropathic pain.
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Affiliation(s)
- Chun Yang
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Fang
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Gaofeng Zhan
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Niannian Huang
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan Li
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiangjiang Bi
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Riyue Jiang
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Ling Yang
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Liying Miao
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Bin Zhu
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Ailin Luo
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba, Japan.
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227
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Chouliaras G, Kondyli C, Bouzios I, Spyropoulos N, Chrousos GP, Roma-Giannikou E. Dietary Habits and Abdominal Pain-related Functional Gastrointestinal Disorders: A School-based, Cross-sectional Analysis in Greek Children and Adolescents. J Neurogastroenterol Motil 2019; 25:113-122. [PMID: 30646482 PMCID: PMC6326206 DOI: 10.5056/jnm17113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 04/03/2018] [Accepted: 09/28/2018] [Indexed: 12/15/2022] Open
Abstract
Background/Aims The abdominal pain-related functional gastrointestinal disorders (AP-FGIDs) affect a significant proportion of the pediatric population and consist 1 of the most frequent causes for seeking medical advice. In this study, we aimed to assess the relation of dietary habits with the likelihood of AP-FGIDs. Methods This was a school-based, cross-sectional study approved by the Greek Government authorities, after obtaining informed consent by the legal representatives of the children. Diagnoses of AP-FGIDs were based on the Greek official translation of the Rome III questionnaire. Demographic, socioeconomic and dietary data were collected through self-reporting or parent-reporting questionnaires. Associations between the probability of AP-FGIDs and dietary practices were assessed after adjusting for known confounders through a multiple logistic regression analysis. Results A total of 1365 children (147 AP-FGIDs and 1218 controls, 52.4% females, mean age: 12.8 ± 2.8 years) were included. Multiple regression analysis identified the following statistically significant confounders: victimization, the presence of a person with a severe health problem at home, female sex, engaging in limited physical exercise, and living in a single adult family. Subsequently, logistic regression, adjusted for the abovementioned confounders, showed that reduced fish and increased junk food consumption were related to a higher likelihood of AP-FGIDs. Conclusions Children with AP-FGIDs report excessive junk-food and reduced fish intake compared to controls. Further studies are needed in order to clarify the nature of this observation.
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Affiliation(s)
- Giorgos Chouliaras
- First Department of Pediatrics, University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Christina Kondyli
- First Department of Pediatrics, University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Ilias Bouzios
- First Department of Pediatrics, University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Nick Spyropoulos
- First Department of Pediatrics, University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - George P Chrousos
- First Department of Pediatrics, University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Eleftheria Roma-Giannikou
- First Department of Pediatrics, University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
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228
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Andrews K, Gonzalez A. Contextual risk factors impacting the colonization and development of the intestinal microbiota: Implications for children in low- and middle-income countries. Dev Psychobiol 2019; 61:714-728. [PMID: 30663777 DOI: 10.1002/dev.21823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 12/11/2022]
Abstract
Early adversities, such as poverty, maternal stress, and malnutrition, can affect the structure and functioning of the developing brain with implications for biological systems such as the intestinal microbiota. To date, most studies examining the impact of these risk factors on the development and functioning of the intestinal microbiota have primarily been conducted in high-income countries. However, arguably, children in low- and middle-income countries may be at increased risk given cumulative biological and psychosocial adversities during their development. Accumulating evidence in low- and middle-income countries has linked dysbiosis of the intestinal microbiota to child health outcomes such as stunting, malnutrition, and diarrheal diseases characterized by reduced microbial diversity and elevated pathogenic bacteria, which has implications for psychosocial outcomes. This review summarizes empirical findings that highlight the association between risk factors prevalent in low- and middle-income countries and the intestinal microbiota of children. Additionally, we briefly survey the current evidence regarding the effect of nutritional interventions on the microbial composition of children in low- and middle-income countries. We conclude that these empirical studies have the capacity to inform future research investigating the influence of preventive interventions on biological systems by targeting the predominant risk factors faced by children in low- and middle-income countries.
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Affiliation(s)
- Krysta Andrews
- Neuroscience Graduate Program, McMaster University, Hamilton, Ontario, Canada.,Offord Centre for Child Studies, McMaster University, Hamilton, Ontario, Canada
| | - Andrea Gonzalez
- Offord Centre for Child Studies, McMaster University, Hamilton, Ontario, Canada.,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
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229
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Interactions between Host PPARs and Gut Microbiota in Health and Disease. Int J Mol Sci 2019; 20:ijms20020387. [PMID: 30658440 PMCID: PMC6359605 DOI: 10.3390/ijms20020387] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/28/2018] [Accepted: 01/05/2019] [Indexed: 12/12/2022] Open
Abstract
The human gastrointestinal tract is inhabited by many types of microbiota, including bacteria, viruses, and fungi. Dysregulations of their microenvironment are associated with various health problems, not only limited to gastrointestinal disorders, such as inflammatory bowel disease, but to impacts beyond the intestine. For example, intestinal microbiota can affect the liver in non-alcoholic fatty liver disease, visceral adipose tissue during adipogenesis, and the heart in atherosclerosis. The factors contributing to these pathogeneses involve the gut microbiota and the effector organs of the host, and everything in between. The nuclear receptor peroxisome proliferator-activated receptors (PPARs) are pivotal for the modulation of many of the pathogeneses mentioned above. It is, therefore, conceivable that, in the process of host-microbiota interactions, PPARs play important roles. In this review, we focus on the interactions between host PPARs in different organs and gut microbiota and their impacts on maintaining health and various diseases.
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230
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Brett BE, de Weerth C. The microbiota-gut-brain axis: A promising avenue to foster healthy developmental outcomes. Dev Psychobiol 2019; 61:772-782. [PMID: 30640409 PMCID: PMC6617777 DOI: 10.1002/dev.21824] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/09/2018] [Accepted: 12/11/2018] [Indexed: 12/14/2022]
Abstract
Fostering healthy developmental growth in the first years of life is associated with numerous favorable cognitive, social, and economic outcomes. Funding and promoting research aimed at identifying potential targets for early intervention should be a top priority for lawmakers and funders. One promising avenue of research and potential early intervention is the microbiota–gut–brain axis. In this report, we briefly examine the role of the gut microbiota in human life, focusing on links with health, cognition, and behavior. We then discuss the development of the gut microbiota and the critical early window in which colonization occurs. Then, we review current nonnutritive means of influencing the gut microbiota in early life. Finally, we discuss the implications this work has for early intervention in low‐income communities and end with recommendations regarding further research and research funding priorities.
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Affiliation(s)
- Bonnie E Brett
- Behavioral Science Institute, Radboud University, Nijmegen, The Netherlands
| | - Carolina de Weerth
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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231
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Xu M, Xu X, Li J, Li F. Association Between Gut Microbiota and Autism Spectrum Disorder: A Systematic Review and Meta-Analysis. Front Psychiatry 2019; 10:473. [PMID: 31404299 PMCID: PMC6673757 DOI: 10.3389/fpsyt.2019.00473] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 06/13/2019] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is characterized by stereotyped behavior and deficits in communication and social interactions. Gastrointestinal (GI) dysfunction is an ASD-associated comorbidity, implying a potential role of the gut microbiota in ASD GI pathophysiology. Several recent studies found that autistic individuals harbor an altered bacterial gut microbiota. In some cases, remodeling the gut microbiota by antibiotic administration and microbiota transfer therapy reportedly alleviated the symptoms of ASD. However, there is little consensus on specific bacterial species that are similarly altered across individual studies. The aim of this study is to summarize previously published data and analyze the alteration of the relative abundance of bacterial genera in the gut microbiota in controls and individuals with ASD using meta-analysis. We analyzed nine studies, including 254 patients with ASD, and found that children with ASD had lower percentages of Akkermansia, Bacteroides, Bifidobacterium, and Parabacteroides and a higher percentage of Faecalibacterium in the total detected microflora compared to controls. In contrast, children with ASD had lower abundance of Enterococcus, Escherichia coli, Bacteroides, and Bifidobacterium and higher abundance of Lactobacillus. This meta-analysis suggests an association between ASD and alteration of microbiota composition and warrants additional prospective cohort studies to evaluate the association of bacterial changes with ASD symptoms, which would provide further evidence for the precise microbiological treatment of ASD.
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Affiliation(s)
- Mingyu Xu
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefeng Xu
- Department of Pulmonology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jijun Li
- Department of Integrative Medicine on Pediatrics, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Li
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Institute of Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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232
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He Z, Wu J, Xiao B, Xiao S, Li H, Wu K. The Initial Oral Microbiota of Neonates Among Subjects With Gestational Diabetes Mellitus. Front Pediatr 2019; 7:513. [PMID: 31921726 PMCID: PMC6914726 DOI: 10.3389/fped.2019.00513] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
Objective: The objective was to investigate the potential effect of gestational diabetes mellitus on the initial neonatal oral microbiome community structure. Methods: Oral samples were collected from 20 full-term, vaginally delivered newborns with sterile swabs. Nine of them had mothers diagnosed with gestational diabetes mellitus (GDM group), while 11 had non-diabetic mothers (NDM group). The oral microbiota was analyzed using multi-barcode 16S rRNA sequencing on Illumina MiSeq system. Results: The results showed that the birth weight, gestational age and gestational weight gain were significantly higher in NDM group. There was a significant correlation between gestational age and birth weight. Neonatal oral microbiome was composed of five dominant phyla from Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Tenericutes. Compared to NDM group, a higher alpha diversity and reduction of phylum Firmicutes were observed in GDM group. Genus Lactobacillus dominated in NDM group, while Alistipes, Streptococcus, and Faecalibacterium were overabundant in GDM group. Additionally, carbohydrate metabolism increased in NDM group, whereas amino acid metabolism, vitamin metabolism and lipopolysaccharide biosynthesis were more abundant in GDM group. Conclusions: This study showed a distinct oral microbiota profile in neonates born to mothers with GDM, which indicated that maternal diabetes status played an important role in neonatal initial oral microbiota.
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Affiliation(s)
- Zhijiang He
- Shenzhen University General Hospital, Shenzhen, China
| | - Jiaman Wu
- Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Bin Xiao
- Shenzhen Children's Hospital, Shenzhen, China
| | - Shanqiu Xiao
- Bao an Maternal and Child Health Hospital, Jinan University, Shenzhen, China
| | - Hongping Li
- Shenzhen Children's Hospital, Shenzhen, China
| | - Kaifeng Wu
- Boluo Maternal and Child Health Family Planning Service Centre, Huizhou, China
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233
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Shulman RJ, Öhman L, Stridsberg M, Cain K, Simrén M, Heitkemper M. Evidence of increased fecal granins in children with irritable bowel syndrome and correlates with symptoms. Neurogastroenterol Motil 2019; 31:e13486. [PMID: 30298961 PMCID: PMC6296885 DOI: 10.1111/nmo.13486] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/30/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Granins have been implicated in the pathophysiology of irritable bowel syndrome (IBS) in adults. We sought to determine whether fecal granins are altered in children with IBS and associated with symptoms. METHODS Children (7-12 years of age) with IBS and healthy controls (HC) kept daily pain and stool diaries for 2 weeks. Stool samples were analyzed for chromogranins A and B (CgA, CgB) and secretogranins II and III (SgII, SgIII). Children also completed psychological measures to assess anxiety, depression, somatization, and internalizing symptoms. KEY RESULTS Fecal CgB and SgIII concentrations were higher in all the boys (IBS plus HC, n = 48) than in all the girls (IBS plus HC, n = 75) (P = 0.02 and P = 0.046, respectively). CgA and SgIII were greater in children with IBS (n = 52) vs HC (n = 69) (P = 0.01, P = 0.017, respectively). CgB and SgII did not differ between groups. In children with IBS, the number of pain episodes per week and mean daily pain rating correlated positively with all four granins. The number of stools per day correlated positively with CgB and SgII, and the percent of diarrheal stools (6 or 7 on the Bristol Scale) correlated inversely with all four granins in boys but not in girls. Fecal granins did not correlate with psychological measures. CONCLUSIONS AND INFERENCES As measured by fecal granins, there is evidence of neuroimmune activation in children with IBS. Granins are related to abdominal pain symptoms, stooling frequency, and stool form in children with IBS. Sex influences the fecal concentration of CgB and SgIII.
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Affiliation(s)
- Robert J. Shulman
- Children’s Nutrition Research Center, Baylor College of Medicine, Department of Pediatrics, Houston, TX
| | - Lena Öhman
- University of Gothenburg, Göteborg, Sweden
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234
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Pini Prato A, Bartow-McKenney C, Hudspeth K, Mosconi M, Rossi V, Avanzini S, Faticato MG, Ceccherini I, Lantieri F, Mattioli G, Larson D, Pavan W, De Filippo C, Di Paola M, Mavilio D, Cavalieri D. A Metagenomics Study on Hirschsprung's Disease Associated Enterocolitis: Biodiversity and Gut Microbial Homeostasis Depend on Resection Length and Patient's Clinical History. Front Pediatr 2019; 7:326. [PMID: 31448249 PMCID: PMC6696876 DOI: 10.3389/fped.2019.00326] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Objectives: Since 2010, several researches demonstrated that microbiota dynamics correlate and can even predispose to Hirschsprung (HSCR) associated enterocolitis (HAEC). This study aims at assessing the structure of the microbiota of HSCR patients in relation to extent of aganglionosis and HAEC status. Methods: All consecutive HSCR patients admitted to Gaslini Institute (Genova, Italy) between May 2012 and November 2014 were enrolled. Institutional review board (IRB) approval was obtained. Stools were sampled and 16S rDNA V3-V4 regions were sequenced using the Illumina-MiSeq. Taxonomy assignments were performed using QIIME RDP. Alpha diversity indexes were analyzed by Shannon and Simpson Indexes, and Phylogenetic Diversity. Results: We enrolled 20 patients. Male to female ratio was 4:1. Six patients suffered from Total Colonic Aganglionosis (TCSA). Considering sample site (i.e., extent of aganglionosis), we confirmed the known relationship between sample site and both biodiversity and composition of intestinal microbiota. Patients with TCSA showed lower biodiversity and increased Proteobacteria/Bacteroidetes relative abundance ratio. When addressing biodiversity, composition and dynamics of TCSA patients we could not find any significant relationship with regard to HAEC occurrences. Conclusions: The composition of HAEC predisposing microbiota is specific to each patient. We could confirm that total colon resections can change the composition of intestinal microbiota and to dramatically reduce microbial diversity. The subsequent reduction of system robustness could expose TCSA patients to environmental microbes that might not be part of the normal microbiota. Future long-term studies should investigate both patients and their family environment, as well as their disease history.
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Affiliation(s)
- Alessio Pini Prato
- Division of Pediatric Surgery, AON SS Antonio e Biagio e Cesare Arrigo, Alessandria, Italy.,Division of Pediatric Surgery, Giannina Gaslini Institute, Genoa, Italy
| | - Casey Bartow-McKenney
- Department of Dermatology and Microbiology, University of Pennsylvania, Philadelphia, PA, United States
| | - Kelly Hudspeth
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, Milan, Italy.,Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, Milan, Italy
| | - Manuela Mosconi
- Division of Pediatric Surgery, Giannina Gaslini Institute, Genoa, Italy
| | - Valentina Rossi
- Division of Pediatric Surgery, Giannina Gaslini Institute, Genoa, Italy
| | - Stefano Avanzini
- Division of Pediatric Surgery, Giannina Gaslini Institute, Genoa, Italy
| | - Maria G Faticato
- Division of Pediatric Surgery, Giannina Gaslini Institute, Genoa, Italy.,Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Science (DINOGMI), University of Genoa, Genoa, Italy
| | | | - Francesca Lantieri
- Biostatistics Section, Department of Health Science, University of Genoa, Genoa, Italy
| | - Girolamo Mattioli
- Division of Pediatric Surgery, Giannina Gaslini Institute, Genoa, Italy.,Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics and Maternal and Child Science (DINOGMI), University of Genoa, Genoa, Italy
| | - Denise Larson
- Genomics, Development and Disease Section, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - William Pavan
- Genomics, Development and Disease Section, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Carlotta De Filippo
- Institute of Agriculture Biology and Biotechnology, National Research Council, Pisa, Italy
| | - Monica Di Paola
- Department, of Biology, University of Florence, Firenze, Italy
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, Milan, Italy.,Department of Medical Biotechnologies and Translational Medicine (BioMeTra), University of Milan, Milan, Italy
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235
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Shin A, Preidis GA, Shulman R, Kashyap PC. The Gut Microbiome in Adult and Pediatric Functional Gastrointestinal Disorders. Clin Gastroenterol Hepatol 2019; 17:256-274. [PMID: 30153517 PMCID: PMC6314902 DOI: 10.1016/j.cgh.2018.08.054] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/23/2018] [Accepted: 08/21/2018] [Indexed: 02/07/2023]
Abstract
The importance of gut microbiota in gastrointestinal (GI) physiology was well described, but our ability to study gut microbial ecosystems in their entirety was limited by culture-based methods prior to the sequencing revolution. The advent of high-throughput sequencing opened new avenues, allowing us to study gut microbial communities as an aggregate, independent of our ability to culture individual microbes. Early studies focused on association of changes in gut microbiota with different disease states, which was necessary to identify a potential role for microbes and generate novel hypotheses. Over the past few years the field has moved beyond associations to better understand the mechanistic implications of the microbiome in the pathophysiology of complex diseases. This movement also has resulted in a shift in our focus toward therapeutic strategies, which rely on better understanding the mediators of gut microbiota-host cross-talk. It is not surprising the gut microbiome has been implicated in the pathogenesis of functional gastrointestinal disorders given its role in modulating physiological processes such as immune development, GI motility and secretion, epithelial barrier integrity, and brain-gut communication. In this review, we focus on the current state of knowledge and future directions in microbiome research as it pertains to functional gastrointestinal disorders. We summarize the factors that help shape the gut microbiome in human beings. We discuss data from animal models and human studies to highlight existing paradigms regarding the mechanisms underlying microbiota-mediated alterations in physiological processes and their relevance in human interventions. While translation of microbiome science is still in its infancy, the outlook is optimistic and we are advancing in the right direction toward precise mechanism-based microbiota therapies.
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Affiliation(s)
- Andrea Shin
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Geoffrey A Preidis
- Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Robert Shulman
- Section of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Purna C Kashyap
- Enteric Neuroscience Program, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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236
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Diagnosis of Bacterial Overgrowth Syndrome and Lactase Deficiency in Patients with Irritable Bowel Syndrome in Practice of a Family Doctor. Fam Med 2018. [DOI: 10.30841/2307-5112.6.2018.168481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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237
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Warda AK, Rea K, Fitzgerald P, Hueston C, Gonzalez-Tortuero E, Dinan TG, Hill C. Heat-killed lactobacilli alter both microbiota composition and behaviour. Behav Brain Res 2018; 362:213-223. [PMID: 30597248 DOI: 10.1016/j.bbr.2018.12.047] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/17/2018] [Accepted: 12/27/2018] [Indexed: 12/16/2022]
Abstract
Recently it has been proposed to expand the definition of psychobiotics (beneficial bacteria (probiotics) or support for such bacteria (prebiotics) that positively impact mental health) to any exogenous influence whose effect on the brain is bacterially-mediated. This definition would include inactivated microorganisms with anxiolytic and antidepressant effects. The use of inactivated microorganisms has several advantages over living organisms, including no risk of infection in vulnerable individuals and ease of use in terms of storage and delivery options. It has been reported that consumption of inactivated microorganisms can affect behaviour, particularly in chronic or prolonged stress situations, but effects on healthy populations have not been investigated to the same extent. Also, only limited data is available on the effects of inactivated microorganisms on the microbiota of healthy individuals (animal or human). Therefore, we investigated the effect of feeding a standard mouse chow which incorporates ADR-159, a heat-killed fermentate generated by two Lactobacillus strains, on the behaviour and microbiota of healthy mice. Prolonged consumption of ADR-159 diet had no adverse effect on anthropometrics or general health, but the ADR-159 fed animals demonstrated increased sociability and lower baseline corticosterone levels (stress hormone). The diet also led to subtle but significant changes in the microbiota, with less abundant taxa being most affected. The behavioural, biochemical and microbiological results provide a new light on the impact of inactivated microorganisms and their metabolites on the social behaviour and microbiota of healthy mice.
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Affiliation(s)
- Alicja K Warda
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Kieran Rea
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Cara Hueston
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry & Neurobehavioural Sciences, University College Cork, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland; School of Microbiology, University College Cork, Cork, Ireland.
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238
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Zhang C, Zhang W, Zhang J, Jing Y, Yang M, Du L, Gao F, Gong H, Chen L, Li J, Liu H, Qin C, Jia Y, Qiao J, Wei B, Yu Y, Zhou H, Liu Z, Yang D, Li J. Gut microbiota dysbiosis in male patients with chronic traumatic complete spinal cord injury. J Transl Med 2018; 16:353. [PMID: 30545398 PMCID: PMC6293533 DOI: 10.1186/s12967-018-1735-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/06/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Neurogenic bowel dysfunction (NBD) is a major physical and psychological problem in patients with spinal cord injury (SCI), and gut dysbiosis is commonly occurs in SCI. Here, we document neurogenic bowel management of male patients with chronic traumatic complete SCI in our centre and perform comparative analysis of the gut microbiota between our patients and healthy males. METHODS A total of 43 male patients with chronic traumatic complete SCI (20 with quadriplegia and 23 with paraplegia) and 23 healthy male adults were enrolled. Clinical data and fresh stool specimens were collected from all participants. Face-to-face interviews were conducted to survey the neurogenic bowel management of 43 patients with SCI. Gut microbiomes were analysed by sequencing of the V3-V4 region of the 16S rRNA gene. RESULTS NBD was common in adult male patients with chronic traumatic complete SCI. Patients with quadriplegia exhibited a longer time to defecate than did those with paraplegia and had higher NBD scores and heavier neurogenic bowel symptoms. The diversity of the gut microbiota in the SCI group was reduced, and the structural composition was different from that of the healthy adult male group. The abundance of Veillonellaceae and Prevotellaceae increased, while Bacteroidaceae and Bacteroides decreased in the SCI group. The abundance of Bacteroidaceae and Bacteroides in the quadriplegia group and Acidaminococcaceae, Blautia, Porphyromonadaceae, and Lachnoclostridium in the paraplegia group were significantly higher than those in the healthy male group. Serum biomarkers (GLU, HDL, CR, and CRP), NBD defecation time and COURSE had significant correlations with microbial community structure. Microbial community structure was significantly associated with serum biomarkers (GLU, HDL, CR, and CRP), NBD defecation time, and COURSE. CONCLUSIONS This study presents a comprehensive landscape of the gut microbiota in adult male patients with chronic traumatic complete SCI and documents their neurogenic bowel management. Gut microbiota dysbiosis in SCI patients was correlated with serum biomarkers and NBD symptoms.
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Affiliation(s)
- Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Wenhao Zhang
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Jie Zhang
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Yingli Jing
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
- Institute of Rehabilitation Medicine, China Rehabilitation Research Center, Beijing, 100068 China
| | - Mingliang Yang
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Liangjie Du
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Huiming Gong
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Liang Chen
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Jun Li
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Hongwei Liu
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Yanmei Jia
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Jiali Qiao
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Bo Wei
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
- Department of Spinal Cord Injury Rehabilitation, China Rehabilitation Research Center, Beijing, 100068 China
| | - Yan Yu
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
- Institute of Rehabilitation Medicine, China Rehabilitation Research Center, Beijing, 100068 China
| | - Hongjun Zhou
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
- Department of Spinal Cord Injury Rehabilitation, China Rehabilitation Research Center, Beijing, 100068 China
| | - Zhizhong Liu
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
- Laboratory Medicine, China Rehabilitation Research Center, Beijing, 100068 China
| | - Degang Yang
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
| | - Jianjun Li
- School of Rehabilitation Medicine, Capital Medical University, No. 10 Jiaomen North Road, Fengtai District, Beijing, 100068 China
- Department of Spinal and Neural Function Reconstruction, China Rehabilitation Research Center, Beijing, 100068 China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, 100068 China
- China Rehabilitation Science Institute, Beijing, 100068 China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, 100068 China
- Institute of Rehabilitation Medicine, China Rehabilitation Research Center, Beijing, 100068 China
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239
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Pärtty A, Rautava S, Kalliomäki M. Probiotics on Pediatric Functional Gastrointestinal Disorders. Nutrients 2018; 10:nu10121836. [PMID: 30501103 PMCID: PMC6316480 DOI: 10.3390/nu10121836] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/22/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
The potential association between gut microbiota perturbations and childhood functional gastrointestinal disturbances opens interesting therapeutic and preventive possibilities with probiotics. The aim of this review was to evaluate current evidence on the efficacy of probiotics for the management of pediatric functional abdominal pain disorders, functional constipation and infantile colic. Thus far, no single strain, combination of strains or synbiotics can be recommended for the management of irritable bowel syndrome, functional abdominal pain or functional constipation in children. However, Lactobacillus reuteri DSM 17938 may be considered for the management of breastfed colic infants, while data on other probiotic strains, probiotic mixtures or synbiotics are limited in infantile colic.
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Affiliation(s)
- Anna Pärtty
- Department of Pediatrics, University of Turku, 20521 Turku, Finland.
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, 20521 Turku, Finland.
| | - Samuli Rautava
- Department of Pediatrics, University of Turku, 20521 Turku, Finland.
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, 20521 Turku, Finland.
| | - Marko Kalliomäki
- Department of Pediatrics, University of Turku, 20521 Turku, Finland.
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, 20521 Turku, Finland.
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240
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Possible Prevention of Diabetes with a Gluten-Free Diet. Nutrients 2018; 10:nu10111746. [PMID: 30428550 PMCID: PMC6266002 DOI: 10.3390/nu10111746] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023] Open
Abstract
Gluten seems a potentially important determinant in type 1 diabetes (T1D) and type 2 diabetes (T2D). Intake of gluten, a major component of wheat, rye, and barley, affects the microbiota and increases the intestinal permeability. Moreover, studies have demonstrated that gluten peptides, after crossing the intestinal barrier, lead to a more inflammatory milieu. Gluten peptides enter the pancreas where they affect the morphology and might induce beta-cell stress by enhancing glucose- and palmitate-stimulated insulin secretion. Interestingly, animal studies and a human study have demonstrated that a gluten-free (GF) diet during pregnancy reduces the risk of T1D. Evidence regarding the role of a GF diet in T2D is less clear. Some studies have linked intake of a GF diet to reduced obesity and T2D and suggested a role in reducing leptin- and insulin-resistance and increasing beta-cell volume. The current knowledge indicates that gluten, among many environmental factors, may be an aetiopathogenic factors for development of T1D and T2D. However, human intervention trials are needed to confirm this and the proposed mechanisms.
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241
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Mukherjee S, Joardar N, Sengupta S, Sinha Babu SP. Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings. J Nutr Biochem 2018; 61:111-128. [PMID: 30196243 PMCID: PMC7126101 DOI: 10.1016/j.jnutbio.2018.07.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 02/07/2023]
Abstract
The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.
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Affiliation(s)
- Suprabhat Mukherjee
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Nikhilesh Joardar
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Subhasree Sengupta
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Santi P Sinha Babu
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India.
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242
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Ihekweazu FD, Versalovic J. Development of the Pediatric Gut Microbiome: Impact on Health and Disease. Am J Med Sci 2018; 356:413-423. [PMID: 30384950 PMCID: PMC6268214 DOI: 10.1016/j.amjms.2018.08.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/10/2018] [Indexed: 02/07/2023]
Abstract
The intestinal microbiota are important in human growth and development. Microbial composition may yield insights into the temporal development of microbial communities and vulnerabilities to disorders of microbial ecology such as recurrent Clostridium difficile infection. Discoveries of key microbiome features of carbohydrate and amino acid metabolism are lending new insights into possible therapies or preventative strategies for inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). In this review, we summarize the current understanding of the development of the pediatric gastrointestinal microbiome, the influence of the microbiome on the developing brain through the gut-brain axis, and the impact of dysbiosis on disease development. Dysbiosis is explored in the context of pediatric allergy and asthma, recurrent C. difficile infection, IBD, IBS, and metabolic disorders. The central premise is that the human intestinal microbiome plays a vital role in health and disease, beginning in the prenatal period and extending throughout childhood.
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Affiliation(s)
- Faith D. Ihekweazu
- Pediatric Gastroenterology, Hepatology and Nutrition, Baylor College of Medicine, Texas Children’s Hospital, 1102 Bates St., Houston, TX, 77030, USA.
| | - James Versalovic
- Pediatric Pathology and Immunology, Baylor College of Medicine, Texas Children’s Hospital 1102 Bates St., Houston, TX, 77030, USA.
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243
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Oakley BB, Vasconcelos EJR, Diniz PPVP, Calloway KN, Richardson E, Meinersmann RJ, Cox NA, Berrang ME. The cecal microbiome of commercial broiler chickens varies significantly by season. Poult Sci 2018; 97:3635-3644. [PMID: 30016503 DOI: 10.3382/ps/pey214] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 04/30/2018] [Indexed: 12/23/2022] Open
Abstract
Next-generation DNA sequencing is rapidly becoming a powerful tool for food animal management. One valuable use of this technology is to re-examine long-standing observations of performance differences associated with animal husbandry practices to better understand how these differences may be modulated by the gastrointestinal (GI) microbiome. The influences of environmental parameters such as air temperature and relative humidity on broiler chicken performance have commonly been observed, but how the GI microbiome may respond to seasonal environmental changes remains largely unknown. The purposes of this study were therefore to: (1) characterize the cecal microflora of commercial broilers (N = 87) collected at harvest across all 4 seasons, and (2) identify any significant changes of the GI microbiome and specific taxa according to season and Campylobacter status. Finding taxa with significant positive or negative correlations with Campylobacter could be useful by identifying indicator or antagonistic taxa and could also inform inferences regarding the ecological niche of Campylobacter. Whole GI tracts were removed from commercial broilers representing 87 independent flocks between April 2013 and May 2014 in the U.S. state of Georgia. Intact ceca were separated, cultured for Campylobacter and cecal contents were frozen. The cecal microbiome was characterized using barcoded sequencing of 16S rRNA genes on the Illumina MiSeq platform. The composition of the microbiome measured at processing was generally not affected by Campylobacter status but was most significantly affected by season of grow-out. Significantly fewer bacterial genera were found in winter than spring or summer. Bacterial genera with prior evidence for both positive or negative influences on gut health outcomes were significantly less abundant in the fall. Identifying specific members of the GI microbiota that vary according to season may help develop novel interventions to improve husbandry practices and growth performance.
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Affiliation(s)
- Brian B Oakley
- College of Veterinary Medicine, Western University of Health Sciences, 309 E. 2nd St., Pomona, CA 91766-1854, USA
| | - Elton J R Vasconcelos
- College of Veterinary Medicine, Western University of Health Sciences, 309 E. 2nd St., Pomona, CA 91766-1854, USA
| | - Pedro P V P Diniz
- College of Veterinary Medicine, Western University of Health Sciences, 309 E. 2nd St., Pomona, CA 91766-1854, USA
| | - Kimberly N Calloway
- College of Veterinary Medicine, Western University of Health Sciences, 309 E. 2nd St., Pomona, CA 91766-1854, USA
| | - Ella Richardson
- College of Veterinary Medicine, Western University of Health Sciences, 309 E. 2nd St., Pomona, CA 91766-1854, USA
| | - Richard J Meinersmann
- USDA Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA 30605, USA
| | - Nelson A Cox
- USDA Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA 30605, USA
| | - Mark E Berrang
- USDA Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA 30605, USA
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Bretin A, Gewirtz AT. Aluminum Meddles With Visceral Pain Perception. Cell Mol Gastroenterol Hepatol 2018; 7:235-236. [PMID: 30539790 PMCID: PMC6282629 DOI: 10.1016/j.jcmgh.2018.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 12/10/2022]
Affiliation(s)
| | - Andrew T. Gewirtz
- Correspondence Address correspondence to: Andrew T. Gewirtz, PhD, Center for Inflammation, Immunity, and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia 30303.
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245
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Li X, Wu S, Li X, Yan T, Duan Y, Yang X, Duan Y, Sun Q, Yang X. Simultaneous Supplementation of Bacillus subtilis and Antibiotic Growth Promoters by Stages Improved Intestinal Function of Pullets by Altering Gut Microbiota. Front Microbiol 2018; 9:2328. [PMID: 30369910 PMCID: PMC6194165 DOI: 10.3389/fmicb.2018.02328] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/11/2018] [Indexed: 12/21/2022] Open
Abstract
Early nutrition of pullets could determine the overall development and the performance of laying hens. With the aim to reduce the use of antibiotic growth promoters (AGPs) and to maintain the growth and development of pullets, the effect of simultaneous short-termed supplementation of AGPs (bacitracin zinc 20 mg/kg and colistin sulfate 4 mg/kg) and Bacillus subtilis (B. subtilis) DSM17299 probiotic, as well as the effect of supplementation of AGPs (bacitracin zinc 20 mg/kg and colistin sulfate 4 mg/kg) during the whole period (0~16 weeks) on the overall growth and development, intestinal health, and caecal microbiota of pullets were evaluated. In the present study, a total of 630 one-day-old Hy-Line Brown layers were randomly distributed into five equal groups: including the AGPs group (supplemented with AGPs based on basal diets for 16 weeks), the BA3 group (supplemented with AGPs and B. subtilis based on basal diets for 3 weeks), the BA6 group (for 6 weeks), the BA12 group (for 12 weeks), and the BA16 group (for 16 weeks). When compared with the AGPs group, the supplementation of AGPs + B. subtilis for the first 3 weeks could maintain overall growth performance, including the average body weight, average feed intake, average daily weight gain, and feed conversion ratio of pullets at 3, 6, 12, and 16 weeks of age (P > 0.05). Meanwhile, the characteristic growth indexes in different periods were separately measured. At 3 weeks of age, the amylase activity in ileum was elevated (P = 0.028), and the length of tibia was up to the standard in the BA3 group. At 12 weeks of age, the increased villus height (P = 0.046) of jejunum, increased villus height (P = 0.023) and ratio of villus height to crypt depth (P = 0.012) of ileum, decreased crypt depth (P = 0.002) of ileum, and elevated mRNA levels of sucrase in jejunum (P < 0.05) were all identified in the BA3 group. At 16 weeks of age, the secreted immunoglobulin A (sIgA) content in the jejunum mucosa of the BA3 group was greater than the other groups (P < 0.001). Furthermore, altered intestinal microbiota was found in the BA3 group. Specifically, decreased amounts of Alistipes, Bacteroides, Odoribacter, Dehalobacterium, and Sutterella and increased amounts of Lactobacillus, Dorea, Ruminococcus, and Oscillospira were determined (P < 0.05) in the BA3 group at week 6. Meanwhile, decreased amounts of B. fragilis and C. leptum (P < 0.05) were identified in the BA3 group at week 12, which were found to be relevant for the improvement of intestinal morphology (P < 0.05) by Pearson analysis. In conclusion, simultaneous supplementation of AGP and B. subtilis for 0~3 weeks increased the relative abundance of beneficial microbiota in caecum in 0~6 weeks, then improved the intestinal morphology by elevating populations of B. fragilis and C. leptum in 7~16 weeks, and further upregulated sucrase expression and increased sIgA content in the intestinal mucosa in 13~16 weeks.
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Affiliation(s)
- Xueyuan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shengru Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Animal Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xinyi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Tao Yan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongle Duan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xin Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yulan Duan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qingzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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246
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Pickard JM, Zeng MY, Caruso R, Núñez G. Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease. Immunol Rev 2018; 279:70-89. [PMID: 28856738 DOI: 10.1111/imr.12567] [Citation(s) in RCA: 871] [Impact Index Per Article: 145.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The intestinal tract of mammals is colonized by a large number of microorganisms including trillions of bacteria that are referred to collectively as the gut microbiota. These indigenous microorganisms have co-evolved with the host in a symbiotic relationship. In addition to metabolic benefits, symbiotic bacteria provide the host with several functions that promote immune homeostasis, immune responses, and protection against pathogen colonization. The ability of symbiotic bacteria to inhibit pathogen colonization is mediated via several mechanisms including direct killing, competition for limited nutrients, and enhancement of immune responses. Pathogens have evolved strategies to promote their replication in the presence of the gut microbiota. Perturbation of the gut microbiota structure by environmental and genetic factors increases the risk of pathogen infection, promotes the overgrowth of harmful pathobionts, and the development of inflammatory disease. Understanding the interaction of the microbiota with pathogens and the immune system will provide critical insight into the pathogenesis of disease and the development of strategies to prevent and treat inflammatory disease.
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Affiliation(s)
- Joseph M Pickard
- Department of Pathology and Comprehensive Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Melody Y Zeng
- Department of Pathology and Comprehensive Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Roberta Caruso
- Department of Pathology and Comprehensive Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gabriel Núñez
- Department of Pathology and Comprehensive Cancer Center, The University of Michigan Medical School, Ann Arbor, MI, USA
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247
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Salvatore S, Pensabene L, Borrelli O, Saps M, Thapar N, Concolino D, Staiano A, Vandenplas Y. Mind the gut: probiotics in paediatric neurogastroenterology. Benef Microbes 2018; 9:883-898. [PMID: 30198327 DOI: 10.3920/bm2018.0013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The gut-brain axis has recently emerged as a key modulator of human health and the intestinal microbiome has a well-recognised pivotal role in this strong connection. The aim of this narrative review is to update and summarise the effect and clinical applicability of probiotics in paediatric neurogastroenterology. The Cochrane Database and PubMed were searched using keywords relating to different subtypes of functional gastrointestinal disorders (FGIDs) and their symptoms, those relating to the CNS and related neurological or behavioural dysfunction as well as 'probiotic' OR 'probiotics'. Included papers were limited to those including children (aged 0-18 years) and using English language. Although significant effects of specific strains have been reported in infants with FGIDs, heterogeneity amongst the studies (different products and concentrations used and FGID subtypes), has limited the ability to draw an overall conclusion on the clinical value of probiotics. According to different meta-analyses of randomised controlled trials, the use of Lactobacillus reuteri (DSM 17938) was associated with a significant decrease in average crying time in infantile colic. There is moderate evidence for this strain and LGG and limited evidence (based on one study each) for the beneficial effect of VSL#3 and a three-strain bifidobacteria mix in abdominal pain FGIDs, particularly in the irritable bowel disease subgroup of children, but not in functional dyspepsia. There is currently no clear evidence of positive effects of oral probiotics in autistic spectrum disorder. Efficacy and safety of other strains or beneficial effects in other conditions still need to be proven, as probiotic properties are strain-specific, and data cannot be extrapolated to other brain-gut or mood diseases or to other probiotics of the same or different species. To transform the use of probiotics from a tempting suggestion to a promising treatment modality in neurogastroenterological disorders more accurate differentiation of the efficacy-proven strains, clarification of dose, duration, and outcome and a careful selection of the target patients are still necessary.
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Affiliation(s)
- S Salvatore
- 1 Department of Pediatrics, University of Insubria, Via F. Del Ponte 19, 21100 Varese, Italy
| | - L Pensabene
- 2 Department of Medical and Surgical Sciences, Pediatric Unit, University Magna Graecia of Catanzaro, Viale Pio X, 88100 Catanzaro, Italy
| | - O Borrelli
- 3 Neurogastroenterology and Motility Unit, Department of Gastroenterology, Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, United Kingdom
| | - M Saps
- 4 Division of Pediatric Gastroenterology, Hepatology and Nutrition, University of Miami, 1601 NW 12. Ave, Miami FL 33136, USA
| | - N Thapar
- 3 Neurogastroenterology and Motility Unit, Department of Gastroenterology, Great Ormond Street Hospital for Children, Great Ormond St, London WC1N 3JH, United Kingdom
| | - D Concolino
- 2 Department of Medical and Surgical Sciences, Pediatric Unit, University Magna Graecia of Catanzaro, Viale Pio X, 88100 Catanzaro, Italy
| | - A Staiano
- 5 Department of Translational Medical Science, Section of Pediatrics, University of Naples 'Federico II', Via S. Pansini 5, 80131 Naples, Italy
| | - Y Vandenplas
- 6 KidZ Health Castle, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium
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248
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Microbiota dysbiosis and its pathophysiological significance in bowel obstruction. Sci Rep 2018; 8:13044. [PMID: 30177854 PMCID: PMC6120911 DOI: 10.1038/s41598-018-31033-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 08/07/2018] [Indexed: 02/06/2023] Open
Abstract
Bowel obstruction (OB) causes local and systemic dysfunctions. Here we investigated whether obstruction leads to alterations in microbiota community composition and total abundance, and if so whether these changes contribute to dysfunctions in OB. Partial colon obstruction was maintained in rats for 7 days. The mid colon and its intraluminal feces - proximal to the obstruction - were studied. OB did not cause bacterial overgrowth or mucosa inflammation, but induced profound changes in fecal microbiota composition and diversity. At the phylum level, the 16S rRNA sequencing showed a significant decrease in the relative abundance of Firmicutes with corresponding increases in Proteobacteria and Bacteroidetes in OB compared with sham controls. Daily treatment using broad spectrum antibiotics dramatically reduced total bacterial abundance, but increased the relative presence of Proteobacteria. Antibiotics eliminated viable bacteria in the spleen and liver, but not in the mesentery lymph node in OB. Although antibiotic treatment decreased muscle contractility in sham rats, it had little effect on OB-associated suppression of muscle contractility or inflammatory changes in the muscle layer. In conclusion, obstruction leads to marked dysbiosis in the colon. Antibiotic eradication of microbiota had limited effects on obstruction-associated changes in inflammation, motility, or bacterial translocation.
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249
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Nam Y, Min YS, Sohn UD. Recent advances in pharmacological research on the management of irritable bowel syndrome. Arch Pharm Res 2018; 41:955-966. [PMID: 30132170 DOI: 10.1007/s12272-018-1068-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 08/16/2018] [Indexed: 12/17/2022]
Abstract
Irritable bowel syndrome (IBS), a common gastrointestinal (GI) disorder, is associated with various factors, including lifestyle, infection, stress, intestinal flora, and related diseases. The pharmacotherapeutic stimulation of receptors and downstream signaling pathways is effective in reducing IBS symptoms; however, it is still associated with adverse effects. Various receptors related to GI motility and visceral hypersensitivity should be considered to enhance the benefit/risk ratio of IBS treatments. This review discusses recent pharmacological advances in IBS management. Several receptors related to GI motility and abdominal pain are investigated in various angles. 5-Hydroxytryptamine (5-HT) is an important neurotransmitter that activates the colonic mucosal 5-HT4 receptor without causing severe cardiovascular adverse effects. The clinical potential of ramosetron for diarrhea-predominant IBS has been suggested because of a lower risk of ischemic colitis than conventional 5-HT3 receptor antagonists. Toll-like receptors (TLRs), especially TLR2 and TLR4, show a significant effect on the post-infection symptoms and lipopolysaccharide-mediated regulation of GI motility. Histamine is a well-known nitrogenous compound that regulates inflammatory responses and visceral hypersensitivity. Histamine 1 receptor-mediated sensitization of the transient receptor potential vanilloid 1 is associated with IBS. Pharmacological approaches based on these signaling pathways could be useful in the development of novel IBS treatments.
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Affiliation(s)
- Yoonjin Nam
- Department of Pharmacology, College of Pharmacy, Chung-Ang University, 84 Heukseok-RO, Dongjak-Gu, Seoul, 06974, Republic of Korea
| | - Young Sil Min
- Department of Medical Plant Science, Jung Won University, 85 Munmu-ro, Goesan-eup, Goesan-gun, Chungbuk, 28024, Republic of Korea
| | - Uy Dong Sohn
- Department of Pharmacology, College of Pharmacy, Chung-Ang University, 84 Heukseok-RO, Dongjak-Gu, Seoul, 06974, Republic of Korea.
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250
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Wang G, Liu Q, Guo L, Zeng H, Ding C, Zhang W, Xu D, Wang X, Qiu J, Dong Q, Fan Z, Zhang Q, Pan J. Gut Microbiota and Relevant Metabolites Analysis in Alcohol Dependent Mice. Front Microbiol 2018; 9:1874. [PMID: 30158912 PMCID: PMC6104187 DOI: 10.3389/fmicb.2018.01874] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/25/2018] [Indexed: 12/21/2022] Open
Abstract
Alcohol abuse is a major public health crisis. Relative evidences supported that the gut microbiota (GM) played an important role in central nervous system (CNS) function, and the composition of them had changed after alcohol drinking. We sought to explore the changes of GM in alcohol dependence. In our study, the GM of mice with alcohol administration was detected through analyzed 16S rRNA gene sequencing and the fecal metabolites were analyzed by LC-MS. The microbial diversity was significantly higher in the alcohol administration group, the abundance of phylum Firmicutes and its class Clostridiales were elevated, meanwhile the abundance of Lachnospiraceae, Alistipes, and Odoribacter showed significant differences among the three groups. Based on LC-MS results, bile acid, secondary bile acid, serotonin and taurine level had varying degrees of changes in alcohol model. From paraffin sections, tissue damage was observed in liver and colon. These findings provide direct evidence that alcohol intake affects the composition of GM, enable a better understanding of the function of GM in the microbiota-gut-brain (MGB) axis, and give a new thought for alcohol addiction treatment.
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Affiliation(s)
- Guanhao Wang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qing Liu
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Liang Guo
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Haijuan Zeng
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Chengchao Ding
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Wentong Zhang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Dongpo Xu
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiang Wang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jingxuan Qiu
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Qingli Dong
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Ziquan Fan
- Thermo Fisher Scientific, Shanghai, China
| | - Qi Zhang
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jing Pan
- School of Medical Instruments and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
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