Current Topics in Microbiology and Immunology
Volume 358
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Klaus AktoriesMedizinische Fakultät, Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Abt. IAlbert-Ludwigs-Universität Freiburg, Albertstr. 25, 79104 Freiburg, Germany
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Ulrich Dobrindt • Jörg H. HackerCatharina SvanborgEditors
Between Pathogenicityand Commensalism
Responsible Series Editor: Fritz Melchers
123
EditorsUlrich DobrindtInstitut für HygieneUniversitätsklinikum MünsterMünsterGermany
Jörg H. HackerNationale Akademie der WissenschaftenDeutsche Akademie der Naturforscher
LeopoldinaHalleGermany
Catharina SvanborgSection of Microbiology, Immunology
and GlycobiologyLund UniversityLundSweden
ISSN 0070-217XISBN 978-3-642-36559-1 ISBN 978-3-642-36560-7 (eBook)DOI 10.1007/978-3-642-36560-7Springer Heidelberg New York Dordrecht London
Library of Congress Control Number: 2013933115
� Springer-Verlag Berlin Heidelberg 2013This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part ofthe material is concerned, specifically the rights of translation, reprinting, reuse of illustrations,recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission orinformation storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodology now known or hereafter developed. Exempted from this legal reservation are briefexcerpts in connection with reviews or scholarly analysis or material supplied specifically for thepurpose of being entered and executed on a computer system, for exclusive use by the purchaser of thework. Duplication of this publication or parts thereof is permitted only under the provisions ofthe Copyright Law of the Publisher’s location, in its current version, and permission for use mustalways be obtained from Springer. Permissions for use may be obtained through RightsLink at theCopyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law.The use of general descriptive names, registered names, trademarks, service marks, etc. in thispublication does not imply, even in the absence of a specific statement, that such names are exemptfrom the relevant protective laws and regulations and therefore free for general use.While the advice and information in this book are believed to be true and accurate at the date ofpublication, neither the authors nor the editors nor the publisher can accept any legal responsibility forany errors or omissions that may be made. The publisher makes no warranty, express or implied, withrespect to the material contained herein.
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Preface
Microbes colonize nearly every biotic and abiotic niche on our planet. Thisincludes also our human body which is densely populated with microbes, themajority of which interacts with us in a commensal, sometimes even mutualistic,relationship. Only a minority of our microbiota represents pathogenic organismswith the ability to cause infection.
Traditionally, the microbiota colonizing a niche or the entire body is usuallydistinguished into non-pathogenic and pathogenic organisms based on theirpotential to cause disease. Based on Jakob Henle’s assumption that microorgan-isms are the causative agents of infectious diseases (Henle 1840), his studentRobert Koch and Friedrich Loeffler formulated already in 1884 four criteria, toestablish a causal relationship between a causative microbe and a disease (Koch1884; Loeffler 1884). According to the so-called Henle–Koch postulates, bacteriaisolated from disease cases have been compared with isolates from healthy indi-viduals with regard to the presence of virulence-associated traits that contribute tothe establishment of an infection in healthy hosts and that distinguish pathogenicfrom non-pathogenic variants.
The term commensalism has been introduced in the second half of the nine-teenth century by Pierre-Joseph van Beneden, defining a relation between indi-viduals of two species where one species obtains benefits from the other withoutharming or benefiting the latter. The commensal, which benefits from the asso-ciation, may obtain nutrients, shelter, or locomotion from the host species, which issubstantially unaffected (Boucher 1985).
Whereas the Henle–Koch postulates and the definition of commensalismallow(ed) to categorize obligate pathogens, this is often difficult for opportunisticpathogens which may belong to the normal microbiota of healthy individuals.Successful infection by such facultative pathogens does often not only rely onvirulence-associated bacterial traits, but also requires susceptible hosts with animpaired mucosal barrier and/or immune response defects. Identifying individualhost susceptibility factors as well as the characterization of compositional changes
v
of the microbiota, their gene expression and metabolic profiles in patient subsetswill thus be essential for an improved treatment of infectious diseases in the future.
The vast majority of microbes colonizing a healthy host, can probably beconsidered commensals, although for most of them we still lack informationregarding the nature of their relationship with the host (whether they hurt orhelp…). Estimated 500–1000 bacterial species belong to the resident humanintestinal flora and the same holds true for the microbial consortium colonizing theskin (Grice et al. 2009; Sears 2005). The microorganisms living inside or on ‘‘us’’outnumber ‘‘our’’ somatic and germ cells by a factor of ten (Turnbaugh et al.2007), but so far only a minor fraction of this microbiota has been characterizedand identified (Marcy et al. 2007). The human microbiome project will help us tofurther increase our knowledge on the microbial diversity associated with ourhealthy body and the contribution of microbiota to disease and infection. Althoughwe already know that, e.g., the individual composition of the microbial flora differsfrom person to person, and that different diseases are associated with deviations inthe composition of the microbial community in the diseased niche, we are far fromunderstanding the commensals’ exact role for human development, physiology,protection against opportunistic pathogens, immunity, and nutrition.
This book covers various aspects of the interplay between commensal orpathogenic bacteria with their hosts. The chapters summarize the recent knowl-edge on geno- and phenotypic traits of opportunistic bacterial pathogens, such asEscherichia coli, staphylococci or Pseudomonas aeruginosa, as well as the impactof commensal and probiotic bacteria on intestinal physiology and health. Thedifferential interaction of pathogenic, commensal, or probiotic bacteria with theirhost is reviewed from the bacterial and from the host perspective to complete thiscompilation of articles on differences and similarities of pathogenic and com-mensal microorganisms.
Ulrich DobrindtJörg H. Hacker
Catharina Svanborg
References
Boucher DH (1985) The idea of mutualism, past and future. In: Boucher DH (ed) The biology ofmutualism: ecology and evolution, Oxford University Press, New York, pp. 1–28
Grice EA et al (2009) Topographical and temporal diversity of the human skin microbiome.Science 324:1190–1192
Henle J (1840) Von den Contagien und Miasmen und den contagiös-miasmatischen Krankheiten.Berlin
Koch R (1884) Die Aetiologie der Tuberkulose. Mittheilungen aus dem kaiserlichenGesundheitsamte 2:1–81
Loeffler F (1884) Untersuchung über die Bedeutung der Mikroorganismen für die Entstehung derDiphtherie beim Menschen, bei der Taube und beim Kalbe. Mittheilungen aus demkaiserlichen Gesundheitsamte 2:421–499
vi Preface
Marcy Y et al (2007). Dissecting biological ‘‘dark matter’’ with single-cell genetic analysis ofrare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA104:11889–11894
Sears CL (2005) A dynamic partnership: celebrating our gut flora. Anaerobe 11:247–251Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human
microbiome project. Nature 449:804–810
Preface vii
Contents
Part I Between Commensalism and Pathogenicity:Bacterial and Host Aspects
E. coli as an All-Rounder: The Thin Line Between Commensalismand Pathogenicity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3Andreas Leimbach, Jörg Hacker and Ulrich Dobrindt
What Distinguishes Highly Pathogenic Staphylococci fromMedium- and Non-pathogenic? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33Ralf Rosenstein and Friedrich Götz
Microevolution of Pseudomonas aeruginosa to a ChronicPathogen of the Cystic Fibrosis Lung . . . . . . . . . . . . . . . . . . . . . . . . . 91Michael Hogardt and Jürgen Heesemann
Lactobacillus: Host–Microbe Relationships . . . . . . . . . . . . . . . . . . . . . 119John O’Callaghan and Paul W. O’Toole
Bacterial Moonlighting Proteins and Bacterial Virulence . . . . . . . . . . 155Brian Henderson and Andrew Martin
Symbionts and Pathogens: What is the Difference?. . . . . . . . . . . . . . . 215Vicente Pérez-Brocal, Amparo Latorre and Andrés Moya
ix
Part II Host–Microbe Interaction in the Intestinal Tract
Ecology and Physiology of the Intestinal Tract . . . . . . . . . . . . . . . . . . 247Michael Blaut
The Gut Microflora and Its Variety of Roles in Health and Disease . . 273Julia-Stefanie Frick and Ingo B. Autenrieth
Host-Recognition of Pathogens and Commensalsin the Mammalian Intestine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291Oriana Rossi, Peter van Baarlen and Jerry M. Wells
Contribution of the Intestinal Microbiota to Human Health:From Birth to 100 Years of Age . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323Jing Cheng, Airi M. Palva, Willem M. de Vos and Reetta Satokari
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 347
x Contents
Contributors
Ingo B. Autenrieth Institute for Medical Microbiology and Hygiene, UniversityHospital of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany, e-mail:[email protected]
Peter van Baarlen Host Microbe Interactomics Group, Wageningen University,P.O. box 338, 6700 AH Wageningen, The Netherlands, e-mail: [email protected]
Michael Blaut Department of Gastrointestinal Microbiology, German Institute ofHuman Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116,14558 Nuthetal, Germany, e-mail: [email protected]
Jing Cheng Department of Veterinary Biosciences, University of Helsinki, P.O.Box 66, 00014 Helsinki, Finland, e-mail: [email protected]
Willem M. de Vos Department of Veterinary Biosciences and Department ofBacteriology and Immunology, University of Helsinki, Helsinki, Finland; Labo-ratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wa-geningen, The Netherlands, e-mail: [email protected]
Ulrich Dobrindt Institute of Hygiene, University Hospital of Münster, Robert-Koch-Straße 41, 48149 Münster, Germany, e-mail: [email protected]
Julia-Stefanie Frick Institute for Medical Microbiology and Hygiene, UniversityHospital of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany, e-mail:[email protected]
Friedrich Götz Microbial Genetics, Institute of Microbiology and InfectionMedicine Tübingen, University of Tübingen, Waldhäuser Str. 70/8, 72076Tübingen, Germany, e-mail: [email protected]
Jörg Hacker National German Academy of Sciences LeopoldinaEmil-Abderhalden-Straße 37, 06108 Halle/Saale, Germany, e-mail: joerg.hacker@leopoldina. de
xi
Jürgen Heesemann Max von Pettenkofer-Institut für Hygiene and MedicalMicrobiology, Ludwig-Maximilians-University Munich, Pettenkoferstraße 9a,80336 Munich, Germany, e-mail: [email protected]
Brian Henderson Department of Microbial Diseases, UCL-Eastman DentalInstitute, University College London, 256 Gray’s Inn Road, London WC1X 8LD,UK, e-mail: [email protected]
Michael Hogardt Department of Infectiology, Bavarian Health and Food SafetyAuthority, Veterinärstraße 2, 85764 Oberschleissheim, Germany, e-mail:[email protected]
Amparo Latorre Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Uni-versitat de València, Apartado Postal 22085, 46071 Valencia, Spain, e-mail:[email protected]
Andreas Leimbach Institute of Hygiene, University Hospital of Münster, Robert-Koch-Straße 41, 48149 Münster, Germany; Göttingen Genomics Laboratory,University of Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany, e-mail:[email protected]
Andrew C. R. Martin Institute of Structural and Molecular Biology, Division ofBiosciences, University College London, Darwin Building, Gower Street, WC1E6BT London, UK, e-mail: [email protected]
Andrés Moya Área de Genómica y Salud, Centro Superior de Investigación enSalud Pública (CSISP), Avenida de Cataluña 21, 46020 Valencia, Spain; InstitutCavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apar-tado Postal 22085, 46071 Valencia, Spain, e-mail: [email protected]
John O’Callaghan Department of Microbiology and Alimentary PharmabioticCentre, University College Cork, Cork, Ireland, e-mail: [email protected]
Paul W. O’Toole Department of Microbiology and Alimentary PharmabioticCentre, University College Cork, Cork, Ireland, e-mail: [email protected]
Airi M. Palva Department of Veterinary Biosciences, University of Helsinki,P.O. Box 66, 00014 Helsinki, Finland, e-mail: [email protected]
Vicente Pérez-Brocal Área de Genómica y Salud, Centro Superior de Investi-gación en Salud Pública (CSISP), Avenida de Cataluña 21, 46020 Valencia, Spain,e-mail: [email protected]
Ralf Rosenstein Microbial Genetics, Institute of Microbiology and InfectionMedicine Tübingen, University of Tübingen, Waldhäuser Str. 70/8, 72076Tübingen, Germany, e-mail: [email protected]
xii Contributors
Oriana Rossi Host Microbe Interactomics Group, Wageningen University, P.O.box 338, 6700 AH Wageningen, The Netherlands, e-mail: [email protected]
Reetta Satokari Department of Veterinary Biosciences, University of Helsinki,P.O. Box 66, 00014 Helsinki, Finland, e-mail: [email protected]
Jerry M. Wells Host Microbe Interactomics Group, Wageningen University,P.O. box 338, 6700 AH Wageningen, The Netherlands, e-mail: [email protected]
Contributors xiii