DOCSLIB.ORG

Interaction Between Drugs and the Gut Microbiome Gut: First Published As 10.1136/Gutjnl-2019-320204 on 14 May 2020

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Interaction Between Drugs and the Gut Microbiome Gut: First Published As 10.1136/Gutjnl-2019-320204 on 14 May 2020 Recent advances in basic science Interaction between drugs and the gut microbiome Gut: first published as 10.1136/gutjnl-2019-320204 on 14 May 2020. Downloaded from Rinse K Weersma ,1 Alexandra Zhernakova,2 Jingyuan Fu2,3 1Department of ABStract Gastroenterology and The human gut microbiome is a complex ecosystem Key messages Hepatology, University of Groningen, University Medical that can mediate the interaction of the human host There is a complex bidirectional interaction Centre Groningen, Groningen, with their environment. The interaction between gut ► The Netherlands microbes and commonly used non-antibiotic drugs is between commonly used non- antibiotic drugs 2Department of Genetics, complex and bidirectional: gut microbiome composition and the gut microbiome. University of Groningen and can be influenced by drugs, but, vice versa, the gut ► Commonly used drugs such as proton pump University Medical Center inhibitors, metformin, selective serotonin Groningen, Groningen, The microbiome can also influence an individual’s response Netherlands to a drug by enzymatically transforming the drug’s reuptake inhibitors and laxatives influence gut 3Department of Pediatrics, structure and altering its bioavailability, bioactivity or microbiome composition and function. University Medical Center toxicity (pharmacomicrobiomics). The gut microbiome ► Proton pump inhibitor- induced changes in Groningen, Groningen, The the gut microbiome can lead to decreased Netherlands can also indirectly impact an individual’s response to immunotherapy in cancer treatment. In this review we colonisation resistance and the development of enteric infections, including Clostridium Difficile Correspondence to discuss the bidirectional interactions between microbes Dr Rinse K Weersma, and drugs, describe the changes in gut microbiota infections. Gastroenterology and induced by commonly used non-antibiotic drugs, and ► Gut microbiome composition is associated with Hepatology, University of their potential clinical consequences and summarise how antitumour response and the clinical efficacy of Groningen, University Medical treatment with immune checkpoint inhibition. Centre Groningen, Groningen the microbiome impacts drug effectiveness and its role Gut microbes can contribute to drug efficacy 9700 RB, The Netherlands; in immunotherapy. Understanding how the microbiome ► r. k. weersma@ umcg. nl metabolises drugs and reduces treatment efficacy will and safety by enzymatically transforming drug unlock the possibility of modulating the gut microbiome structure and altering drug bioavailability, Received 30 March 2020 to improve treatment. bioactivity or toxicity. Revised 21 April 2020 ► Insights into how the gut microbiome interacts Accepted 28 April 2020 Published Online First with commonly used drugs enable interventions 14 May 2020 to modulate the gut microbiome and optimise treatment efficacy. INTRODUCTION In the past decade we have witnessed exciting http://gut.bmj.com/ discoveries linking the composition and function of the human gut microbiome to numerous common Finally, the gut microbiome can indirectly impact an diseases and phenotypes. Association studies have individual’s response to immunotherapy in cancer documented changes in the abundance of various treatment via its influence on the host’s general 13 gut bacteria in individuals with gastrointestinal immune status. These exciting new insights into phenotypes, including inflammatory bowel disease, the bidirectional interaction between non- antibiotic irritable bowel syndrome and colorectal cancer, and drugs and the gut microbiome are the focus of the on September 28, 2021 by guest. Protected copyright. with diseases of other systems and organs, including current review. cardiovascular and metabolic conditions, auto- immune conditions and psychiatric disorders.1–9 BackGROUND In addition to association analyses, intervention The development of gut microbiome research studies and animal studies have proven not only the Just a few decades ago our ability to analyse the association but also the causality of the gut micro- role of the gut microbiome in relation to human biome in relation to several diseases.10 Moreover, health was mainly defined by large technical chal- the influence of intrinsic and extrinsic factors on lenges. Historically, microbiome studies were gut microbiome composition is increasingly being performed using culturing methods in which one, understood. or a few, bacterial species were isolated and studied One very important recent finding is that many in relation to a disease. This research produced commonly used non- antibiotic drugs—such as numerous important findings, but our ability to proton pump inhibitors (PPIs) and metformin— analyse other components of the gut ecosystem change microbiome composition and function.11 12 was limited. The development of the technique to These changes can influence health outcomes (in sequence the bacterial 16S ribosomal RNA gene the case of PPIs) or reduce drug efficacy (in the case allowed overall taxonomic assessment of the gut © Author(s) (or their of metformin). At the same time, more data has microbiome, and this has dramatically increased employer(s)) 2020. Re- use become available showing that the gut microbiome our knowledge of the broad variations in micro- permitted under CC BY. can directly influence an individual’s response to bial composition. More recently, whole genome Published by BMJ. a specific drug by enzymatically transforming the shotgun sequencing, or metagenomic sequencing To cite: Weersma RK, drug’s structure and altering its bioavailability, (MGS), has become a powerful methodology for Zhernakova A, Fu J. Gut bioactivity or toxicity—a phenomenon now studying the microbiome. MGS allows identifica- 2020;69:1510–1519. referred to as pharmacomicrobiomics (figure 1). tion of not only bacteria, but also viruses, protozoa 1510 Weersma RK, et al. Gut 2020;69:1510–1519. doi:10.1136/gutjnl-2019-320204 Recent advances in basic science Gut: first published as 10.1136/gutjnl-2019-320204 on 14 May 2020. Downloaded from http://gut.bmj.com/ Figure 1 Schematic overview of different interactions between the gut microbiome and commonly used non- antibiotic drugs. SCFA, short- chain fatty acids. and fungi, and it enables focussed analysis of bacterial genes and Human cohort- based analysis has further shown that the predicted biological pathways. However, as with all sequencing- dynamic nature of the gut ecosystem reflects a complex inter- based methods, MGS results are very dependent on the method action of the host with lifestyle, dietary, ecological and other on September 28, 2021 by guest. Protected copyright. used to isolate DNA from stool samples, and this is the major factors. Hundreds of intrinsic and environmental factors influ- source of the technical variability in the results of microbiome ence the gut microbiome in healthy individuals, including diet, studies.14 Other omics approaches, such as metatranscriptomics, medication, smoking, lifestyle, host genetics and diseases.15 17 metametabolomics and metaproteomics, are also increasingly Among all environmental factors, commonly used drugs play a being used to get a comprehensive picture of the gut ecosystem. particularly important role in the gut ecosystem. Finally, culturomics analysis, which allows deep characterisation of individual associated species and strains, is again becoming an important method to understand the role of specific taxa in Association of gut microbiome composition with commonly relation to diseases. used drugs in human cohorts Several human cohort studies have reported associations between Intrinsic and extrinsic factors influencing the gut microbiome use of specific drugs and altered microbial composition and func- With the aid of next-generating sequencing, gut microbiome tional profiles (summarised in table 1). One of the first studies analysis has been applied to several human cohorts. One to see this was conducted in the Dutch LifeLines-DEEP cohort, important finding is the large interindividual variability of the and this study reported microbial associations to 19 out of 42 17 gut ecosystem: only a minority of gut microbes are shared across commonly used drugs. In addition to antibiotics, many human- the majority of individuals. For example, in a European data targeted non- antibiotic drugs were associated with changes in set of 3000 samples, only 17 bacteria were identified as a core microbial composition. The top microbiome- associated drugs microbiome present in >95% of all samples.15 The majority of included PPIs, lipid- lowering statins, laxatives, metformin, beta- bacteria are rare. Of the 639 species identified in a population blockers and ACE inhibitors, and selective serotonin reuptake study of 1135 Dutch individuals, 469 (73%) were present in inhibitor antidepressants, and similar associations were also fewer than 10 individuals.16 This high interindividual variability observed in a Belgium Flemish cohort15 and in the TwinsUK potentially leads to variations in the metabolic functions carried cohort18 (table 1). It is also worth noting that these drug- microbe out by the gut microbiome. associations were mostly assessed for individual drugs. However, Weersma RK, et al. Gut 2020;69:1510–1519. doi:10.1136/gutjnl-2019-320204 1511 1512 Recent advancesinbasicscience Table 1 Effect of common drugs on the microbiome in population studies NL% UK% Effect on Effect on beta- div/prop. Name (analogue UK) n=1124 n=2737 alpha div of core genera
Load more

Recommended publications
  • Intestinal Virome Changes Precede Autoimmunity in Type I Diabetes-Susceptible Children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D
    Correction MEDICAL SCIENCES Correction for “Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children,” by Guoyan Zhao, Tommi Vatanen, Lindsay Droit, Arnold Park, Aleksandar D. Kostic, Tiffany W. Poon, Hera Vlamakis, Heli Siljander, Taina Härkönen, Anu-Maaria Hämäläinen, Aleksandr Peet, Vallo Tillmann, Jorma Ilonen, David Wang, Mikael Knip, Ramnik J. Xavier, and Herbert W. Virgin, which was first published July 10, 2017; 10.1073/pnas.1706359114 (Proc Natl Acad Sci USA 114: E6166–E6175). The authors wish to note the following: “After publication, we discovered that certain patient-related information in the spreadsheets placed online had information that could conceiv- ably be used to identify, or at least narrow down, the identity of children whose fecal samples were studied. The article has been updated online to remove these potential privacy concerns. These changes do not alter the conclusions of the paper.” Published under the PNAS license. Published online November 19, 2018. www.pnas.org/cgi/doi/10.1073/pnas.1817913115 E11426 | PNAS | November 27, 2018 | vol. 115 | no. 48 www.pnas.org Downloaded by guest on September 26, 2021 Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children Guoyan Zhaoa,1, Tommi Vatanenb,c, Lindsay Droita, Arnold Parka, Aleksandar D. Kosticb,2, Tiffany W. Poonb, Hera Vlamakisb, Heli Siljanderd,e, Taina Härkönend,e, Anu-Maaria Hämäläinenf, Aleksandr Peetg,h, Vallo Tillmanng,h, Jorma Iloneni, David Wanga,j, Mikael Knipd,e,k,l, Ramnik J. Xavierb,m, and
    [Show full text]
  • The Impact of Sequence Database Choice on Metaproteomic Results in Gut Microbiota Studies
    Tanca et al. Microbiome (2016) 4:51 DOI 10.1186/s40168-016-0196-8 RESEARCH Open Access The impact of sequence database choice on metaproteomic results in gut microbiota studies Alessandro Tanca1, Antonio Palomba1, Cristina Fraumene1, Daniela Pagnozzi1, Valeria Manghina2, Massimo Deligios2, Thilo Muth3,4, Erdmann Rapp3, Lennart Martens5,6,7, Maria Filippa Addis1 and Sergio Uzzau1,2* Abstract Background: Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics, the study of the whole protein complement of a microbial community, can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Results: Here, we present a systematic investigation of variables concerning database construction and annotation and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. In particular, the contribution of experimental metagenomic databases was revealed to be mandatory when dealing with mouse samples. Moreover, the use of a “merged” database, containing all metagenomic sequences from the population under study, was found to be generally preferable over the use of sample-matched databases. We also observed that taxonomic and functional results are strongly database-dependent, in particular when analyzing the mouse gut microbiota.
    [Show full text]
  • Towards a Functional Hypothesis Relating Anti-Islet Cell Autoimmunity
    Endesfelder et al. Microbiome (2016) 4:17 DOI 10.1186/s40168-016-0163-4 RESEARCH Open Access Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production David Endesfelder1, Marion Engel1, Austin G. Davis-Richardson2, Alexandria N. Ardissone2, Peter Achenbach3, Sandra Hummel3, Christiane Winkler3, Mark Atkinson4, Desmond Schatz4, Eric Triplett2, Anette-Gabriele Ziegler3 and Wolfgang zu Castell1,5* Abstract Background: The development of anti-islet cell autoimmunity precedes clinical type 1 diabetes and occurs very early in life. During this early period, dietary factors strongly impact on the composition of the gut microbiome. At the same time, the gut microbiome plays a central role in the development of the infant immune system. A functional model of the association between diet, microbial communities, and the development of anti-islet cell autoimmunity can provide important new insights regarding the role of the gut microbiome in the pathogenesis of type 1 diabetes. Results: A novel approach was developed to enable the analysis of the microbiome on an aggregation level between a single microbial taxon and classical ecological measures analyzing the whole microbial population. Microbial co-occurrence networks were estimated at age 6 months to identify candidates for functional microbial communities prior to islet autoantibody development. Stratification of children based on these communities revealed functional associations between diet, gut microbiome, and islet autoantibody development. Two communities were strongly associated with breast-feeding and solid food introduction, respectively. The third community revealed a subgroup of children that was dominated by Bacteroides abundances compared to two subgroups with low Bacteroides and increased Akkermansia abundances.
    [Show full text]
  • Toward Defining the Autoimmune Microbiome for Type 1 Diabetes
    The ISME Journal (2011) 5, 82–91 & 2011 International Society for Microbial Ecology All rights reserved 1751-7362/11 www.nature.com/ismej ORIGINAL ARTICLE Toward defining the autoimmune microbiome for type 1 diabetes Adriana Giongo1, Kelsey A Gano1, David B Crabb1, Nabanita Mukherjee2, Luis L Novelo2, George Casella2, Jennifer C Drew1, Jorma Ilonen3,4,5, Mikael Knip5,6,7, Heikki Hyo¨ty5,8, Riitta Veijola5,9, Tuula Simell5,10, Olli Simell5,10, Josef Neu11, Clive H Wasserfall12, Desmond Schatz11, Mark A Atkinson12 and Eric W Triplett1 1Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA; 2Department of Statistics, University of Florida, Gainesville, FL, USA; 3Department of Clinical Microbiology, University of Kuopio, Kuopio, Finland; 4Immunogenetics Laboratory, University of Turku, Turku, Oulu, and Tampere, Finland; 5Juvenile Diabetes Research Foundation (JDRF), Center of Prevention of Type 1 Diabetes, Turku, Finland; 6Hospital for Children and Adolescents, University of Helsinki, Helsinki, Finland; 7Department of Pediatrics and Research Unit, Tampere University Hospital, Tampere, Finland; 8Department of Virology, University of Tampere, Medical School and Center for Laboratory Medicine, Tampere University Hospital, Tampere, Finland; 9Department of Pediatrics, University of Oulu, Oulu, Finland; 10Department of Pediatrics, Turku University Hospital, Turku, Finland; 11Department of Pediatrics, University of Florida, Gainesville, FL, USA and 12Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA Several studies have shown that gut bacteria have a role in diabetes in murine models. Specific bacteria have been correlated with the onset of diabetes in a rat model. However, it is unknown whether human intestinal microbes have a role in the development of autoimmunity that often leads to type 1 diabetes (T1D), an autoimmune disorder in which insulin-secreting pancreatic islet cells are destroyed.
    [Show full text]
  • The Influence of Diet on the Gut Microbiome
    South Dakota State University Open PRAIRIE: Open Public Research Access Institutional Repository and Information Exchange Health and Nutritional Sciences Graduate Students Plan B Capstone Projects Health and Nutritional Sciences 2020 The Influence of Diet on the Gut Microbiome Kayla Wede Follow this and additional works at: https://openprairie.sdstate.edu/hns_plan-b Part of the Human and Clinical Nutrition Commons The Influence of Diet on the Gut Microbiome Kayla Wede [email protected] [email protected] Kendra Kattelmann, PhD, RDN, LN, FAND Master of Science in Nutrition and Exercise Science, Department of Health and Nutritional Sciences, 2020 Department of Health and Nutritional Sciences Abstract: There is growing research that directly looks at the relationship between the human diet and the gut microbiome. This paper is a narrative review of the current literature on how the human diet can influence the gut microbiome. Without a healthy gut, bacterial imbalances can occur which have been linked to health complications. There are many factors that affect the gut microbiome such as diet, medications, and exercise. There is also limited research that looks at the macronutrients and their role in gut health. It is known that the type of food that people consume is a major influencer of the overall abundance and variety of bacteria in the microbiota. Keywords: gut microbiome, diet, lifestyle, gut microbiota, health, and disease 1 Introduction: There are over 100 trillion bacteria that live in the human gut along with viruses, fungi, and protozoa that all work together to make up the human intestinal tract. [1-3] The gut microbiome is thought to have a role in prevention and treatment for a variety of diseases including obesity, Alzheimer’s Disease, diabetes, and some types of cancer.
    [Show full text]
  • Covalent DNA Modifications in Phage and Bacterial Dynamics Alexandra Bryson University of Pennsylvania, [email protected]
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2016 Covalent DNA Modifications in Phage and Bacterial Dynamics Alexandra Bryson University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Microbiology Commons Recommended Citation Bryson, Alexandra, "Covalent DNA Modifications in Phage and Bacterial Dynamics" (2016). Publicly Accessible Penn Dissertations. 1627. https://repository.upenn.edu/edissertations/1627 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1627 For more information, please contact [email protected]. Covalent DNA Modifications in Phage and Bacterial Dynamics Abstract The microorganisms on and in the human body play a significant role in health and disease; however, little is known about how the interactions between these complex communities affect our wellbeing. This study examines how bacteria and phage interact through bacterial nucleases that restrict infection, such as restriction enzymes and CRISPR systems, and the covalent DNA modifications that neutralize them. Multiple targeted nucleases equip bacteria with an innate immune response against phage, and CRISPR systems provide an adaptive immune response. I report three main studies. 1) To study the human gut microbiome and virome (comprised predominately of phage), we collected fecal samples from a healthy individual over four years. From the fecal samples, total bacterial DNA and DNA from purified virus like particles (VLPs) were sequenced using Illumina and Pacific iosB cience single-molecule real-time (SMRT) sequencing to yield information about genome sequences and covalent modifications. Using computational methods we identified seven bacterial contigs and one phage contig with CRISPR arrays targeting phage contigs.
    [Show full text]
  • Genome-Based Taxonomic Classification Of
    ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia.
    [Show full text]
  • Different Bacteroides Species Colonise Human and Chicken
    microorganisms Article Different Bacteroides Species Colonise Human and Chicken Intestinal Tract Miloslava Kollarcikova 1, Marcela Faldynova 1, Jitka Matiasovicova 1, Eva Jahodarova 1, Tereza Kubasova 1, Zuzana Seidlerova 1, Vladimir Babak 1 , Petra Videnska 2, Alois Cizek 3 and Ivan Rychlik 1,* 1 Veterinary Research Institute, 62100 Brno, Czech Republic; [email protected] (M.K.); [email protected] (M.F.); [email protected] (J.M.); [email protected] (E.J.); [email protected] (T.K.); [email protected] (Z.S.); [email protected] (V.B.) 2 Faculty of Science, Masaryk’s University, 62500 Brno, Czech Republic; [email protected] 3 Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, 61242 Brno, Czech Republic; [email protected] * Correspondence: [email protected]; Tel.: +420-533331201 Received: 25 August 2020; Accepted: 24 September 2020; Published: 27 September 2020 Abstract: Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism.
    [Show full text]
  • Lytic Bacteroides Uniformis Bacteriophages Exhibiting Host Tropism Congruent with Diversity Generating Retroelement
    bioRxiv preprint doi: https://doi.org/10.1101/2020.10.09.334284; this version posted October 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 3 4 5 Lytic Bacteroides uniformis bacteriophages exhibiting host tropism congruent 6 with diversity generating retroelement 7 8 9 10 11 12 1 2 1,3* 13 Stina Hedzet , Tomaž Accetto , Maja Rupnik 14 15 16 1National laboratory for health, environment and food, NLZOH, Maribor, Slovenia 17 18 2University of Ljubljana, Biotechnical faculty, Animal science department 19 20 3University of Maribor, Faculty of Medicine, Maribor, Slovenia 21 22 23 24 25 26 Corresponding author*: 27 Maja Rupnik, NLZOH, [email protected] 28 29 30 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.10.09.334284; this version posted October 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 31 Abstract 32 Intestinal phages are abundant and important component of gut microbiota, but our knowledge 33 remains limited to only a few isolated and characterized representatives targeting numerically 34 dominant gut bacteria. Here we describe isolation of human intestinal phages infecting 35 Bacteroides uniformis. Bacteroides is one of the most common bacterial groups in the global 36 human gut microbiota, however, to date not many Bacteroides specific phages are known. Phages 37 isolated in this study belong to a novel viral genus, Bacuni, within Siphoviridae family and 38 represent the first lytic phages, genomes of which encode diversity generating retroelements 39 (DGR).
    [Show full text]
  • Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis
    Journal of Clinical Medicine Article Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis Kei Nomura 1 , Dai Ishikawa 1,2,* , Koki Okahara 1, Shoko Ito 1, Keiichi Haga 1, Masahito Takahashi 1, Atsushi Arakawa 3, Tomoyoshi Shibuya 1 , Taro Osada 1, Kyoko Kuwahara-Arai 4, Teruo Kirikae 4 and Akihito Nagahara 1,2 1 Department of Gastroenterology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; [email protected] (K.N.); [email protected] (K.O.); [email protected] (S.I.); [email protected] (K.H.); [email protected] (M.T.); [email protected] (T.S.); [email protected] (T.O.); [email protected] (A.N.) 2 Department of Intestinal Microbiota Therapy, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan 3 Department of Human Pathology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; [email protected] 4 Department of Microbiology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan; [email protected] (K.K.-A.); [email protected] (T.K.) * Correspondence: [email protected]; Tel.: +81-(0)3-5802-1060 Abstract: Fecal microbiota transplantation following triple-antibiotic therapy (amoxicillin/fosfomycin/ metronidazole) improves dysbiosis caused by reduced Bacteroidetes diversity in patients with ulcer- ative colitis (UC). We investigated the correlation between Bacteroidetes species abundance and UC activity. Fecal samples from 34 healthy controls and 52 patients with active UC (Lichtiger’s clinical activity index ≥5 or Mayo endoscopic subscore ≥1) were subjected to next-generation sequencing Citation: Nomura, K.; Ishikawa, D.; Okahara, K.; Ito, S.; Haga, K.; with HSP60 as a target in bacterial metagenome analysis.
    [Show full text]
  • View Statement on Interactions Between Xenobiotics and the Human Microbiota and Their Potential Toxicological Implications
    COMMITTEE ON TOXICITY OF CHEMICALS IN FOOD, CONSUMER PRODUCTS AND THE ENVIRONMENT Statement on interactions between xenobiotics and the human microbiota and their potential toxicological implications. Introduction 1 The term human microbiota refers to the population of microorganisms (bacteria, viruses, fungi, archea, protozoa) living in internal compartments and on the surface of human beings. This statement aims to describe the current state of knowledge of changes in the population and function of the gut microbiota1 caused by exposure to components of, and contaminants present in, the diet and the effects of the gut microbiota in modulating the toxicity of those substances. 2 There is a substantial body of literature on the microbiota, therefore this paper has used relatively narrow search terms and thus is a representative rather than comprehensive survey of the microbiota and their interaction with ingested xenobiotics Composition and distribution of the microbiota 3 The externally accessible compartments of the human body are inhabited by microorganisms. By far the greatest number and variety of microorganisms are present in the digestive tract, predominantly in the caecum. The most studied of these are bacteria that fall into the phyla of the Gram-negative Bacteroidetes and the Gram-positive Firmicutes. Other relatively abundant phyla are the Actinobacteria, the Proteobacteria and the Verrucomicrobia but the full range of species varies from site to site, from individual to individual and with diet (David et al, 2014) health, sex, ethnicity, age and geographical location. This statement concentrates on the bacterial population of the microbiome since the majority of the scientific literature relates to them.
    [Show full text]
  • Supplementary Table 8 Spearman's Correlations Between Targeted Urinary Urolithins and Microbiota
    Supplementary material Gut Supplementary Table 8 Spearman's correlations between targeted urinary urolithins and microbiota. Urolithin- Urolithin- Urolithin- Total A- B- C- Urolithins Family level Taxonomy glucuronid glucuronid glucuronid (A+B+C) e e e Actinobacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium adolescentis_msp_0263 -0.18 -0.09 -0.16 -0.18 Bifidobacteriaceae Bifidobacterium; Bifidobacterium adolescentis Actinobacteria; Actinobacteria; Bifidobacteriales; Bifidobacteriaceae; Bifidobacterium bifidum_msp_0419 -0.12 -0.2 -0.08 -0.13 Bifidobacteriaceae Bifidobacterium; Bifidobacterium bifidum Actinobacteria; Coriobacteriia; Coriobacteriales; Coriobacteriaceae; Collinsella; Collinsella aerofaciens_msp_1244 -0.15 -0.06 -0.04 -0.18 Coriobacteriaceae Collinsella aerofaciens Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Adlercreutzia; unclassified Adlercreutzia_msp_0396 0.09 0.01 0.16 0.12 Eggerthellaceae unclassified Adlercreutzia Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Eggerthella; Eggerthella lenta_msp_0573 0.03 -0.15 0.08 0.03 Eggerthellaceae Eggerthella lenta Actinobacteria; Coriobacteriia; Eggerthellales; Eggerthellaceae; Gordonibacter; Gordonibacter urolithinfaciens_msp_1339 0.19 -0.05 0.18 0.19 Eggerthellaceae Gordonibacter urolithinfaciens Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae; Bacteroides; Bacteroides cellulosilyticus_msp_0003 0.12 0.11 0.15 0.15 Bacteroidaceae Bacteroides cellulosilyticus Bacteroidetes; Bacteroidia; Bacteroidales;
    [Show full text]