Current Topics in Microbiology and Immunology

Volume 358

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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

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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:ingo.autenrieth@med.uni-tuebingen.de

Peter van Baarlen Host Microbe Interactomics Group, Wageningen University,P.O. box 338, 6700 AH Wageningen, The Netherlands, e-mail: peter.vanbaarlen@wur.nl

Michael Blaut Department of Gastrointestinal Microbiology, German Institute ofHuman Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116,14558 Nuthetal, Germany, e-mail: blaut@dife.de

Jing Cheng Department of Veterinary Biosciences, University of Helsinki, P.O.Box 66, 00014 Helsinki, Finland, e-mail: jing.cheng@helsinki.fi

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: willem.devos@wur.nl

Ulrich Dobrindt Institute of Hygiene, University Hospital of Münster, Robert-Koch-Straße 41, 48149 Münster, Germany, e-mail: dobrindt@uni-muenster.de

Julia-Stefanie Frick Institute for Medical Microbiology and Hygiene, UniversityHospital of Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen, Germany, e-mail:julia-stefanie.frick@med.uni-tuebingen.de

Friedrich Götz Microbial Genetics, Institute of Microbiology and InfectionMedicine Tübingen, University of Tübingen, Waldhäuser Str. 70/8, 72076Tübingen, Germany, e-mail: friedrich.goetz@uni-tuebingen.de

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: heesemann@mvp.uni-muenchen.de

Brian Henderson Department of Microbial Diseases, UCL-Eastman DentalInstitute, University College London, 256 Gray’s Inn Road, London WC1X 8LD,UK, e-mail: Brian.Henderson@ucl.ac.uk

Michael Hogardt Department of Infectiology, Bavarian Health and Food SafetyAuthority, Veterinärstraße 2, 85764 Oberschleissheim, Germany, e-mail:Michael.Hogardt@lgl.bayern.de

Amparo Latorre Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Uni-versitat de València, Apartado Postal 22085, 46071 Valencia, Spain, e-mail:amparo.latorre@uv.es

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:andreas.leimbach@ukmuenster.de

Andrew C. R. Martin Institute of Structural and Molecular Biology, Division ofBiosciences, University College London, Darwin Building, Gower Street, WC1E6BT London, UK, e-mail: andrew.martin@ucl.ac.uk

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: andres.moya@uv.es

John O’Callaghan Department of Microbiology and Alimentary PharmabioticCentre, University College Cork, Cork, Ireland, e-mail: j.ocallaghan@ucc.ie

Paul W. O’Toole Department of Microbiology and Alimentary PharmabioticCentre, University College Cork, Cork, Ireland, e-mail: pwotoole@ucc.ie

Airi M. Palva Department of Veterinary Biosciences, University of Helsinki,P.O. Box 66, 00014 Helsinki, Finland, e-mail: airi.palva@helsinki.fi

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: perez_vicbro@gva.es

Ralf Rosenstein Microbial Genetics, Institute of Microbiology and InfectionMedicine Tübingen, University of Tübingen, Waldhäuser Str. 70/8, 72076Tübingen, Germany, e-mail: ralf.rosenstein@uni-tuebingen.de

xii Contributors

Oriana Rossi Host Microbe Interactomics Group, Wageningen University, P.O.box 338, 6700 AH Wageningen, The Netherlands, e-mail: oriana.rossi@wur.nl

Reetta Satokari Department of Veterinary Biosciences, University of Helsinki,P.O. Box 66, 00014 Helsinki, Finland, e-mail: reetta.satokari@helsinki.fi

Jerry M. Wells Host Microbe Interactomics Group, Wageningen University,P.O. box 338, 6700 AH Wageningen, The Netherlands, e-mail: jerry.wells@wur.nl

Contributors xiii