DOCSLIB.ORG

Original Research Long-­Term Dietary Patterns Are Associated with Pro-­ Gut: First Published As 10.1136/Gutjnl-2020-322670 on 2 April 2021

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Original Research Long-­Term Dietary Patterns Are Associated with Pro-­ Gut: First Published As 10.1136/Gutjnl-2020-322670 on 2 April 2021 Gut microbiota Original research Long- term dietary patterns are associated with pro- Gut: first published as 10.1136/gutjnl-2020-322670 on 2 April 2021. Downloaded from inflammatory and anti- inflammatory features of the gut microbiome Laura A Bolte ,1,2 Arnau Vich Vila ,1,2 Floris Imhann,1,2 Valerie Collij,1,2 Ranko Gacesa,1,2 Vera Peters,1 Cisca Wijmenga,2 Alexander Kurilshikov,2 Marjo J E Campmans-K uijpers,1 Jingyuan Fu,2,3 Gerard Dijkstra,1 Alexandra Zhernakova,2 Rinse K Weersma 1 ► Additional material is ABSTRACT Significance of this study published online only. To view, Objective The microbiome directly affects the balance please visit the journal online of pro-inflammatory and anti-inflammatory responses (http:// dx. doi. org/ 10. 1136/ What is already known on this subject? gutjnl- 2020- 322670). in the gut. As microbes thrive on dietary substrates, ► Western diet and low- grade intestinal 1 the question arises whether we can nourish an anti- Department of inflammation are implicated in a growing Gastroenterology and inflammatory gut ecosystem. We aim to unravel number of immune- mediated inflammatory Hepatology, University of interactions between diet, gut microbiota and their Groningen and University functional ability to induce intestinal inflammation. diseases. Medical Centre Groningen, Design We investigated the relation between 173 ► Diet quantity, content and timing play a major Groningen, The Netherlands role in shaping gut microbial composition and 2 dietary factors and the microbiome of 1425 individuals Department of Genetics, function. University of Groningen and spanning four cohorts: Crohn’s disease, ulcerative colitis, University Medical Centre irritable bowel syndrome and the general population. ► Dysbiosis, shifts in metabolites and Groningen, Groningen, The Shotgun metagenomic sequencing was performed translocation of microbial products contribute Netherlands to profile gut microbial composition and function. to immune activation. 3Department of Pediatrics, Dietary intake was assessed through food frequency ► Research has been focused on anti- University of Groningen and inflammatory properties of isolated compounds, University Medical Centre questionnaires. We performed unsupervised clustering Groningen, Groningen, The to identify dietary patterns and microbial clusters. with limited efficacy. http://gut.bmj.com/ Netherlands Associations between diet and microbial features were What are the new findings? explored per cohort, followed by a meta- analysis and ► Diet- gut microbiome associations are consistent Correspondence to heterogeneity estimation. Prof Dr Rinse K Weersma, across patients with intestinal disease (Crohn’s Department of Gastroenterology Results We identified 38 associations between dietary disease, UC, IBS) and the general population. patterns and microbial clusters. Moreover, 61 individual and Hepatology, University ► Higher intake of animal foods, processed of Groningen and University foods and nutrients were associated with 61 species foods, alcohol and sugar, corresponds to a on September 30, 2021 by guest. Protected copyright. Medical Centre Groningen, P.O. and 249 metabolic pathways in the meta- analysis across microbial environment that is characteristic of Box 30.001, Groningen 9700 healthy individuals and patients with IBS, Crohn’s disease RB, The Netherlands; inflammation, and is associated with higher r. k. weersma@ umcg. nl and UC (false discovery rate<0.05). Processed foods and levels of intestinal inflammatory markers. animal- derived foods were consistently associated with ► Plant- based foods are linked to short- chain LAB and AVV are joint first higher abundances of Firmicutes, Ruminococcus species authors. fatty acid (SCFA)- producers, microbial of the Blautia genus and endotoxin synthesis pathways. metabolism of polysaccharides and a lower Received 28 July 2020 The opposite was found for plant foods and fish, abundance of pathobionts. Revised 13 February 2021 which were positively associated with short- chain fatty Accepted 15 February 2021 acid- producing commensals and pathways of nutrient metabolism. Conclusion We identified dietary patterns that in the intestine. Microbial competition for nutri- consistently correlate with groups of bacteria with shared ents plays a key role in controlling this balance.1 functional roles in both, health and disease. Moreover, Inflammatory bowel disease (IBD) is the archetyp- specific foods and nutrients were associated with species ical disease in which the homoeostasis between the known to infer mucosal protection and anti-inflammatory gut microbiota and the intestinal immune system is © Author(s) (or their lost. Beyond the local immune responses, the gut employer(s)) 2021. Re- use effects. We propose microbial mechanisms through which permitted under CC BY. the diet affects inflammatory responses in the gut as a microbiota also affect systemic immune compo- Published by BMJ. rationale for future intervention studies. nents and are implicated in a growing number of immune- mediated inflammatory diseases (IMIDs), To cite: Bolte LA, Vich Vila A, ranging from diabetes to arthritis and systemic Imhann F, et al. Gut Epub 2 ahead of print: [please lupus erythematosus. Gut dysbiosis and associated include Day Month Year]. INTRODUCTION inflammation have also been implicated in cancer doi:10.1136/ The gut microbiome directly affects the balance of and cardiometabolic disorders.3 4 Epidemiological gutjnl-2020-322670 pro- inflammatory and anti- inflammatory responses studies uncovered several dietary factors associated Bolte LA, et al. Gut 2021;0:1–12. doi:10.1136/gutjnl-2020-322670 1 Gut microbiota replicability of diet-microbiome associations in different disease Significance of this study contexts. We propose pro- inflammatory and anti- inflammatory mechanisms through which specific foods and dietary patterns Gut: first published as 10.1136/gutjnl-2020-322670 on 2 April 2021. Downloaded from How might it impact on clinical practice in the foreseeable could affect inflammatory responses in the gut as a rational basis future? for designing dietary interventions. ► Modulation of gut microbiota through diets enriched in vegetables, legumes, grains, nuts and fish and a higher MATERIALS AND METHODS intake of plant over animal foods, has a potential to prevent Study design and cohort description intestinal inflammatory processes at the core of many chronic We associated the diet to the gut microbiome composition and diseases. function of 1425 individuals from the general population and Whole food- based dietary patterns could increase the anti- ► patients with intestinal diseases, using two independent cohorts inflammatory capacity of nutrients through synergistic effects from the northern Netherlands. Cohort 1 consists of 331 on the gut microbiome. patients with IBD from the 1000IBD cohort of the University Sources of n-3 PUFAs (omega-3 polyunsaturated fatty acids) 20 ► Medical Center Groningen (UMCG). Patients were diagnosed and polyphenols may be used to potentiate the abundance of by their treating physician based on accepted radiological, endo- SCFA- producers. scopic and histopathological evaluation and were classified as Replacement of animal protein by plant protein has a ► either Crohn’s disease or ulcerative colitis. Cohort 2 consists potential to reduce intestinal inflammatory processes by of 1094 individuals from the Dutch general- population-based targeting microbial pathways involved. 21 cohort LifeLines DEEP. The LifeLines DEEP cohort comprises 223 individuals with irritable bowel syndrome (IBS) according to a symptom questionnaire based on Rome- III criteria. Due with the onset of these diseases. However, the mechanisms to known differences in the gut microbiome composition and underlying this relationship remain largely unknown. dietary preferences between healthy individuals and patients As microbes rely on dietary substrates in the intestine, the gut with IBD and IBS, participants were divided into four sub- microbiome is often proposed as a mediator through which foods cohorts, namely Crohn’s disease (CD, n=205), ulcerative colitis exert their pro- inflammatory and anti- inflammatory effects. For (UC, n=126), IBS (n=223) and healthy controls (HC, n=871) example, animal experiments demonstrated that foods containing (table 1).22–25 To explore consistency and heterogeneity across 5 6 7 8 high levels of saturated fats, dietary heme, sugar, salt and low these different contexts, all analyses were performed separately 1 levels of fibre induce inflammation and autoimmunity through per cohort, followed by a meta-analysis. microbial mechanisms such as induction of T- helper 17 (TH17) cells. Other studies in mice and humans implicated that ingredi- Fecal sample collection and processing ents added during food processing including dietary emulsifiers,9 For each participant one stool sample was collected. Participants antimicrobial additives10 and artificial sweeteners,11 promote gut were asked to collect and immediately freeze their sample at permeability and intestinal inflammation through an increase in http://gut.bmj.com/ home. Samples were then picked up, transported on dry ice and mucolytic bacteria and endotoxins. In contrast, a high intake of stored at –80°C. All samples were processed according to the tryptophan12 and fibre13 generally leads to immune states associ- same pipeline in one laboratory (UMCG, Groningen). Intestinal ated with colonic health. inflammatory markers were measured in the same sample. The The
Load more

Recommended publications
  • The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio In
    microorganisms Review The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease Spase Stojanov 1,2, Aleš Berlec 1,2 and Borut Štrukelj 1,2,* 1 Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; [email protected] (S.S.); [email protected] (A.B.) 2 Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia * Correspondence: borut.strukelj@ffa.uni-lj.si Received: 16 September 2020; Accepted: 31 October 2020; Published: 1 November 2020 Abstract: The two most important bacterial phyla in the gastrointestinal tract, Firmicutes and Bacteroidetes, have gained much attention in recent years. The Firmicutes/Bacteroidetes (F/B) ratio is widely accepted to have an important influence in maintaining normal intestinal homeostasis. Increased or decreased F/B ratio is regarded as dysbiosis, whereby the former is usually observed with obesity, and the latter with inflammatory bowel disease (IBD). Probiotics as live microorganisms can confer health benefits to the host when administered in adequate amounts. There is considerable evidence of their nutritional and immunosuppressive properties including reports that elucidate the association of probiotics with the F/B ratio, obesity, and IBD. Orally administered probiotics can contribute to the restoration of dysbiotic microbiota and to the prevention of obesity or IBD. However, as the effects of different probiotics on the F/B ratio differ, selecting the appropriate species or mixture is crucial. The most commonly tested probiotics for modifying the F/B ratio and treating obesity and IBD are from the genus Lactobacillus. In this paper, we review the effects of probiotics on the F/B ratio that lead to weight loss or immunosuppression.
    [Show full text]
  • Evaluation of 16S Rrna Primer Sets for Characterisation of Microbiota in Paediatric Patients with Autism Spectrum Disorder L
    www.nature.com/scientificreports OPEN Evaluation of 16S rRNA primer sets for characterisation of microbiota in paediatric patients with autism spectrum disorder L. Palkova1,2, A. Tomova3, G. Repiska3, K. Babinska3, B. Bokor4, I. Mikula5, G. Minarik2, D. Ostatnikova3 & K. Soltys4,6* Abstract intestinal microbiota is becoming a signifcant marker that refects diferences between health and disease status also in terms of gut-brain axis communication. Studies show that children with autism spectrum disorder (ASD) often have a mix of gut microbes that is distinct from the neurotypical children. Various assays are being used for microbiota investigation and were considered to be universal. However, newer studies showed that protocol for preparing DNA sequencing libraries is a key factor infuencing results of microbiota investigation. The choice of DNA amplifcation primers seems to be the crucial for the outcome of analysis. In our study, we have tested 3 primer sets to investigate diferences in outcome of sequencing analysis of microbiota in children with ASD. We found out that primers detected diferent portion of bacteria in samples especially at phylum level; signifcantly higher abundance of Bacteroides and lower Firmicutes were detected using 515f/806r compared to 27f/1492r and 27f*/1495f primers. So, the question is whether a gold standard of Firmicutes/Bacteroidetes ratio is a valuable and reliable universal marker, since two primer sets towards 16S rRNA can provide opposite information. Moreover, signifcantly higher relative abundance of Proteobacteria was detected using 27f/1492r. The beta diversity of sample groups difered remarkably and so the number of observed bacterial genera. An advent of massively parallel sequencing (MPS) technologies has revolutionized an investigating of human microbiota1.
    [Show full text]
  • Dietary Supplementation with Inulin-Propionate Ester Or Inulin
    Gut microbiota ORIGINAL ARTICLE Dietary supplementation with inulin-propionate ester Gut: first published as 10.1136/gutjnl-2019-318424 on 10 April 2019. Downloaded from or inulin improves insulin sensitivity in adults with overweight and obesity with distinct effects on the gut microbiota, plasma metabolome and systemic inflammatory responses: a randomised cross- over trial Edward S Chambers, 1 Claire S Byrne,1 Douglas J Morrison,2 Kevin G Murphy,3 Tom Preston,2 Catriona Tedford,4 Isabel Garcia-Perez,5 Sofia Fountana,5 Jose Ivan Serrano-Contreras,5 Elaine Holmes,5 Catherine J Reynolds,6 Jordie F Roberts,6 Rosemary J Boyton,6 Daniel M Altmann,6 Julie A K McDonald, 7 Julian R Marchesi,7,8 Arne N Akbar,9 Natalie E Riddell,10 Gareth A Wallis,11 Gary S Frost1 ► Additional material is ABSTRact published online only. To view Objective To investigate the underlying mechanisms Significance of this study please visit the journal online behind changes in glucose homeostasis with delivery (http:// dx. doi. org/ 10. 1136/ What is already known on this subject? gutjnl- 2019- 318424). of propionate to the human colon by comprehensive and coordinated analysis of gut bacterial composition, ► Short-chain fatty acids (SCFA), derived from For numbered affiliations see fermentation of dietary fibre by the gut end of article. plasma metabolome and immune responses. Design Twelve non-diabetic adults with overweight microbiota, have been shown to improve host insulin sensitivity. Correspondence to and obesity received 20 g/day of inulin-propionate ester (IPE),
    [Show full text]
  • Characterization of Antibiotic Resistance Genes in the Species of the Rumen Microbiota
    ARTICLE https://doi.org/10.1038/s41467-019-13118-0 OPEN Characterization of antibiotic resistance genes in the species of the rumen microbiota Yasmin Neves Vieira Sabino1, Mateus Ferreira Santana1, Linda Boniface Oyama2, Fernanda Godoy Santos2, Ana Júlia Silva Moreira1, Sharon Ann Huws2* & Hilário Cuquetto Mantovani 1* Infections caused by multidrug resistant bacteria represent a therapeutic challenge both in clinical settings and in livestock production, but the prevalence of antibiotic resistance genes 1234567890():,; among the species of bacteria that colonize the gastrointestinal tract of ruminants is not well characterized. Here, we investigate the resistome of 435 ruminal microbial genomes in silico and confirm representative phenotypes in vitro. We find a high abundance of genes encoding tetracycline resistance and evidence that the tet(W) gene is under positive selective pres- sure. Our findings reveal that tet(W) is located in a novel integrative and conjugative element in several ruminal bacterial genomes. Analyses of rumen microbial metatranscriptomes confirm the expression of the most abundant antibiotic resistance genes. Our data provide insight into antibiotic resistange gene profiles of the main species of ruminal bacteria and reveal the potential role of mobile genetic elements in shaping the resistome of the rumen microbiome, with implications for human and animal health. 1 Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil. 2 Institute for Global Food Security, School of Biological
    [Show full text]
  • The Human Gut Microbiome in Early-Onset Type 1 Diabetes from the TEDDY Study Tommi Vatanen1*, Eric A
    OPEN LETTER https://doi.org/10.1038/s41586-018-0620-2 The human gut microbiome in early-onset type 1 diabetes from the TEDDY study Tommi Vatanen1*, Eric A. Franzosa1,2, Randall Schwager2, Surya Tripathi1, Timothy D. Arthur1, Kendra Vehik3, Åke Lernmark4, William A. Hagopian5, Marian J. Rewers6, Jin-Xiong She7, Jorma Toppari8,9, Anette-G. Ziegler10,11,12, Beena Akolkar13, Jeffrey P. Krischer3, Christopher J. Stewart14,15, Nadim J. Ajami14, Joseph F. Petrosino14, Dirk Gevers1,19, Harri Lähdesmäki16, Hera Vlamakis1, Curtis Huttenhower1,2,20* & Ramnik J. Xavier1,17,18,20* Type 1 diabetes (T1D) is an autoimmune disease that targets species, and deficiency of bacteria that produce short-chain fatty pancreatic islet beta cells and incorporates genetic and acids (SCFAs)7,8 in cases of T1D or islet autoimmunity (IA)8,11,15,18. environmental factors1, including complex genetic elements2, Corroborating these findings, decreased levels of SCFA-producing patient exposures3 and the gut microbiome4. Viral infections5 bacteria were found in adults with type 2 diabetes (T2D)19. In addi- and broader gut dysbioses6 have been identified as potential tion, increased intestinal permeability14 and decreased microbial diver- causes or contributing factors; however, human studies have not sity12 after IA but before T1D diagnosis have been reported. Studies yet identified microbial compositional or functional triggers that using the nonobese diabetic (NOD) mouse model have determined are predictive of islet autoimmunity or T1D. Here we analyse immune mechanisms that mediate the protective effects of SCFAs9 10,913 metagenomes in stool samples from 783 mostly white, non- and the microbiome-linked sex bias in autoimmunity20.
    [Show full text]
  • Effect of Fructans, Prebiotics and Fibres on the Human Gut Microbiome Assessed by 16S Rrna-Based Approaches: a Review
    Wageningen Academic Beneficial Microbes, 2020; 11(2): 101-129 Publishers Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review K.S. Swanson1, W.M. de Vos2,3, E.C. Martens4, J.A. Gilbert5,6, R.S. Menon7, A. Soto-Vaca7, J. Hautvast8#, P.D. Meyer9, K. Borewicz2, E.E. Vaughan10* and J.L. Slavin11 1Division of Nutritional Sciences, University of Illinois at Urbana-Champaign,1207 W. Gregory Drive, Urbana, IL 61801, USA; 2Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, the Netherlands; 3Human Microbiome Research Programme, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014, Helsinki, Finland; 4Department of Microbiology and Immunology, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI 48130, USA; 5Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL 60637, USA; 6Bioscience Division, Argonne National Laboratory, 9700 S Cass Ave, Lemont, IL 60439, USA; 7The Bell Institute of Health and Nutrition, General Mills Inc., 9000 Plymouth Ave N, Minneapolis, MN 55427, USA; 8Division Human Nutrition, Department Agrotechnology and Food Sciences, P.O. Box 17, 6700 AA, Wageningen University; 9Nutrition & Scientific Writing Consultant, Porfierdijk 27, 4706 MH Roosendaal, the Netherlands; 10Sensus (Royal Cosun), Oostelijke Havendijk 15, 4704 RA, Roosendaal, the Netherlands; 11Department of Food Science and Nutrition, University of Minnesota, 1334 Eckles Ave, St. Paul, MN 55108, USA; [email protected]; #Emeritus Professor Received: 27 May 2019 / Accepted: 15 December 2019 © 2020 Wageningen Academic Publishers OPEN ACCESS REVIEW ARTICLE Abstract The inherent and diverse capacity of dietary fibres, nondigestible oligosaccharides (NDOs) and prebiotics to modify the gut microbiota and markedly influence health status of the host has attracted rising interest.
    [Show full text]
  • A Novel Ruminococcus Gnavus Clade Enriched in Inflammatory Bowel
    Hall et al. Genome Medicine (2017) 9:103 DOI 10.1186/s13073-017-0490-5 RESEARCH Open Access A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients Andrew Brantley Hall1,2†, Moran Yassour1,2†, Jenny Sauk3,10, Ashley Garner1,2, Xiaofang Jiang1,4, Timothy Arthur1,2, Georgia K. Lagoudas1,5, Tommi Vatanen1,2, Nadine Fornelos1,2, Robin Wilson3, Madeline Bertha6, Melissa Cohen3, John Garber3, Hamed Khalili3, Dirk Gevers1,2,11, Ashwin N. Ananthakrishnan3, Subra Kugathasan6, Eric S. Lander1,7,8, Paul Blainey1,5, Hera Vlamakis1,2, Ramnik J. Xavier1,2,3,4* and Curtis Huttenhower1,9* Abstract Background: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes. Methods: We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn. Results: We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients.
    [Show full text]
  • Direct-Fed Microbial Supplementation Influences the Bacteria Community
    www.nature.com/scientificreports OPEN Direct-fed microbial supplementation infuences the bacteria community composition Received: 2 May 2018 Accepted: 4 September 2018 of the gastrointestinal tract of pre- Published: xx xx xxxx and post-weaned calves Bridget E. Fomenky1,2, Duy N. Do1,3, Guylaine Talbot1, Johanne Chiquette1, Nathalie Bissonnette 1, Yvan P. Chouinard2, Martin Lessard1 & Eveline M. Ibeagha-Awemu 1 This study investigated the efect of supplementing the diet of calves with two direct fed microbials (DFMs) (Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB) and Lactobacillus acidophilus BT1386 (LA)), and an antibiotic growth promoter (ATB). Thirty-two dairy calves were fed a control diet (CTL) supplemented with SCB or LA or ATB for 96 days. On day 33 (pre-weaning, n = 16) and day 96 (post- weaning, n = 16), digesta from the rumen, ileum, and colon, and mucosa from the ileum and colon were collected. The bacterial diversity and composition of the gastrointestinal tract (GIT) of pre- and post-weaned calves were characterized by sequencing the V3-V4 region of the bacterial 16S rRNA gene. The DFMs had signifcant impact on bacteria community structure with most changes associated with treatment occurring in the pre-weaning period and mostly in the ileum but less impact on bacteria diversity. Both SCB and LA signifcantly reduced the potential pathogenic bacteria genera, Streptococcus and Tyzzerella_4 (FDR ≤ 8.49E-06) and increased the benefcial bacteria, Fibrobacter (FDR ≤ 5.55E-04) compared to control. Other potential benefcial bacteria, including Rumminococcaceae UCG 005, Roseburia and Olsenella, were only increased (FDR ≤ 1.30E-02) by SCB treatment compared to control.
    [Show full text]
  • Microbiota and Drug Response in Inflammatory Bowel Disease
    pathogens Review Microbiota and Drug Response in Inflammatory Bowel Disease Martina Franzin 1,† , Katja Stefanˇciˇc 2,† , Marianna Lucafò 3, Giuliana Decorti 1,3,* and Gabriele Stocco 2 1 Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy; [email protected] 2 Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; [email protected] (K.S.); [email protected] (G.S.) 3 Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-3785362 † The authors contributed equally to the manuscript. Abstract: A mutualistic relationship between the composition, function and activity of the gut microbiota (GM) and the host exists, and the alteration of GM, sometimes referred as dysbiosis, is involved in various immune-mediated diseases, including inflammatory bowel disease (IBD). Accumulating evidence suggests that the GM is able to influence the efficacy of the pharmacological therapy of IBD and to predict whether individuals will respond to treatment. Additionally, the drugs used to treat IBD can modualate the microbial composition. The review aims to investigate the impact of the GM on the pharmacological therapy of IBD and vice versa. The GM resulted in an increase or decrease in therapeutic responses to treatment, but also to biotransform drugs to toxic metabolites. In particular, the baseline GM composition can help to predict if patients will respond to the IBD treatment with biologic drugs. On the other hand, drugs can affect the GM by incrementing or reducing its diversity and richness. Therefore, the relationship between the GM and drugs used in Citation: Franzin, M.; Stefanˇciˇc,K.; the treatment of IBD can be either beneficial or disadvantageous.
    [Show full text]
  • Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-Anal Pouch Resembles 2 That Observed in Crohn’S Disease
    medRxiv preprint doi: https://doi.org/10.1101/2020.09.23.20199315; this version posted September 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Dysbiosis in metabolic genes of the gut microbiomes of patients with an ileo-anal pouch resembles 2 that observed in Crohn’s Disease 4 Authors: Vadim Dubinsky1, Leah Reshef1, Keren Rabinowitz2,3, Karin Yadgar2,3, Lihi Godny2,3, Keren 6 Zonensain2,3, Nir Wasserberg4,5, Iris Dotan2,4*, Uri Gophna1* 8 Affiliation: 1The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, 10 Tel-Aviv University, Tel Aviv, Israel. 2The Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel. 12 3Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel. 4Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel. 14 5Colorectal Unit, the Division of Surgery, Rabin Medical Center, Petah-Tikva, Israel. 16 * Correspondence to [email protected]; [email protected] 18 20 22 24 26 28 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.09.23.20199315; this version posted September 25, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Diverse Hydrogen Production and Consumption Pathways Influence
    The ISME Journal (2019) 13:2617–2632 https://doi.org/10.1038/s41396-019-0464-2 ARTICLE Diverse hydrogen production and consumption pathways influence methane production in ruminants 1 2 3 1 3 1 Chris Greening ● Renae Geier ● Cecilia Wang ● Laura C. Woods ● Sergio E. Morales ● Michael J. McDonald ● 3 3 4 5 6 2 Rowena Rushton-Green ● Xochitl C. Morgan ● Satoshi Koike ● Sinead C. Leahy ● William J. Kelly ● Isaac Cann ● 5 3 2 Graeme T. Attwood ● Gregory M. Cook ● Roderick I. Mackie Received: 7 December 2018 / Revised: 3 June 2019 / Accepted: 7 June 2019 / Published online: 26 June 2019 © The Author(s) 2019. This article is published with open access Abstract Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H2 production or fi 1234567890();,: 1234567890();,: consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis con rmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep.
    [Show full text]
  • Altered Diversity and Composition of Gut Microbiota in Wilson's Disease
    www.nature.com/scientificreports OPEN Altered diversity and composition of gut microbiota in Wilson’s disease Xiangsheng Cai1,2,3,9*, Lin Deng4,9, Xiaogui Ma1,9, Yusheng Guo2, Zhiting Feng5, Minqi Liu2, Yubin Guan1, Yanting Huang1, Jianxin Deng6, Hongwei Li7, Hong Sang8, Fang Liu7* & Xiaorong Yang1* Wilson’s disease (WD) is an autosomal recessive inherited disorder of chronic copper toxicosis with high mortality and disability. Recent evidence suggests a correlation between dysbiosis in gut microbiome and multiple diseases such as genetic and metabolic disease. However, the impact of intestinal microbiota polymorphism in WD have not been fully elaborated and need to be explore for seeking some microbiota beneft for WD patients. In this study, the 16S rRNA sequencing was performed on fecal samples from 14 patients with WD and was compared to the results from 16 healthy individuals. The diversity and composition of the gut microbiome in the WD group were signifcantly lower than those in healthy individuals. The WD group presented unique richness of Gemellaceae, Pseudomonadaceae and Spirochaetaceae at family level, which were hardly detected in healthy controls. The WD group had a markedly lower abundance of Actinobacteria, Firmicutes and Verrucomicrobia, and a higher abundance of Bacteroidetes, Proteobacteria, Cyanobacteria and Fusobacteria than that in healthy individuals. The Firmicutes to Bacteroidetes ratio in the WD group was signifcantly lower than that of healthy control. In addition, the functional profle of the gut microbiome from WD patients showed a lower abundance of bacterial groups involved in the host immune and metabolism associated systems pathways such as transcription factors and ABC-type transporters, compared to healthy individuals.
    [Show full text]