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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Hockenberry A, Slack E, Stadtmueller BM. License to Clump: Secretory IgA Structure-Function Relationships Across Scales. Annu Rev Microbiol 2023; 77:645-668. [PMID: 37713459 DOI: 10.1146/annurev-micro-032521-041803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
Secretory antibodies are the only component of our adaptive immune system capable of attacking mucosal pathogens topologically outside of our bodies. All secretory antibody classes are (a) relatively resistant to harsh proteolytic environments and (b) polymeric. Recent elucidation of the structure of secretory IgA (SIgA) has begun to shed light on SIgA functions at the nanoscale. We can now begin to unravel the structure-function relationships of these molecules, for example, by understanding how the bent conformation of SIgA enables robust cross-linking between adjacent growing bacteria. Many mysteries remain, such as the structural basis of protease resistance and the role of noncanonical bacteria-IgA interactions. In this review, we explore the structure-function relationships of IgA from the nano- to the metascale, with a strong focus on how the seemingly banal "license to clump" can have potent effects on bacterial physiology and colonization.
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Affiliation(s)
- Alyson Hockenberry
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
- Department of Environmental Systems Science (D-USYS), ETH Zürich, Zürich, Switzerland;
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland;
- Botnar Research Centre for Child Health, Basel, Switzerland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Beth M Stadtmueller
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA;
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois, Urbana, Illinois, USA
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Hockenberry A, Radiom M, Arnoldini M, Turgay Y, Dunne M, Adamcik J, Stadtmueller B, Mezzenga R, Ackermann M, Slack E. Nanoscale clustering by O-antigen-Secretory Immunoglobulin-A binding limits outer membrane diffusion by encaging individual Salmonella cells. bioRxiv 2023:2023.07.13.548943. [PMID: 37503073 PMCID: PMC10369997 DOI: 10.1101/2023.07.13.548943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Secreted immunoglobulins, predominantly SIgA, influence the colonization and pathogenicity of mucosal bacteria. While part of this effect can be explained by SIgA-mediated bacterial aggregation, we have an incomplete picture of how SIgA binding influences cells independently of aggregation. Here we show that akin to microscale crosslinking of cells, SIgA targeting the Salmonella Typhimurium O-antigen extensively crosslinks the O-antigens on the surface of individual bacterial cells at the nanoscale. This crosslinking results in an essentially immobilized bacterial outer membrane. Membrane immobilization, combined with Bam-complex mediated outer membrane protein insertion results in biased inheritance of IgA-bound O-antigen, concentrating SIgA-bound O-antigen at the oldest poles during cell growth. By combining empirical measurements and simulations, we show that this SIgA-driven biased inheritance increases the rate at which phase-varied daughter cells become IgA-free: a process that can accelerate IgA escape via phase-variation of O-antigen structure. Our results show that O-antigen-crosslinking by SIgA impacts workings of the bacterial outer membrane, helping to mechanistically explain how SIgA may exert aggregation-independent effects on individual microbes colonizing the mucosae.
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Diard M, Bakkeren E, Lentsch V, Rocker A, Bekele NA, Hoces D, Aslani S, Arnoldini M, Böhi F, Schumann-Moor K, Adamcik J, Piccoli L, Lanzavecchia A, Stadtmueller BM, Donohue N, van der Woude MW, Hockenberry A, Viollier PH, Falquet L, Wüthrich D, Bonfiglio F, Loverdo C, Egli A, Zandomeneghi G, Mezzenga R, Holst O, Meier BH, Hardt WD, Slack E. A rationally designed oral vaccine induces immunoglobulin A in the murine gut that directs the evolution of attenuated Salmonella variants. Nat Microbiol 2021; 6:830-841. [PMID: 34045711 PMCID: PMC7611113 DOI: 10.1038/s41564-021-00911-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
The ability of gut bacterial pathogens to escape immunity by antigenic variation-particularly via changes to surface-exposed antigens-is a major barrier to immune clearance1. However, not all variants are equally fit in all environments2,3. It should therefore be possible to exploit such immune escape mechanisms to direct an evolutionary trade-off. Here, we demonstrate this phenomenon using Salmonella enterica subspecies enterica serovar Typhimurium (S.Tm). A dominant surface antigen of S.Tm is its O-antigen: a long, repetitive glycan that can be rapidly varied by mutations in biosynthetic pathways or by phase variation4,5. We quantified the selective advantage of O-antigen variants in the presence and absence of O-antigen-specific immunoglobulin A and identified a set of evolutionary trajectories allowing immune escape without an associated fitness cost in naive mice. Through the use of rationally designed oral vaccines, we induced immunoglobulin A responses blocking all of these trajectories. This selected for Salmonella mutants carrying deletions of the O-antigen polymerase gene wzyB. Due to their short O-antigen, these evolved mutants were more susceptible to environmental stressors (detergents or complement) and predation (bacteriophages) and were impaired in gut colonization and virulence in mice. Therefore, a rationally induced cocktail of intestinal antibodies can direct an evolutionary trade-off in S.Tm. This lays the foundations for the exploration of mucosal vaccines capable of setting evolutionary traps as a prophylactic strategy.
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Affiliation(s)
- Médéric Diard
- Biozentrum, University of Basel, Basel, Switzerland.
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Zoology, University of Oxford, Oxford, UK
| | - Verena Lentsch
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | | | | | - Daniel Hoces
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Selma Aslani
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Markus Arnoldini
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Flurina Böhi
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Department of Molecular Mechanisms of Disease, University of Zürich, Zürich, Switzerland
| | - Kathrin Schumann-Moor
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.,Division of Surgical Research, University Hospital of Zürich, Zürich, Switzerland
| | - Jozef Adamcik
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Beth M Stadtmueller
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nicholas Donohue
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK.,Department of Orthopedics and Trauma, Medical University of Graz, Graz, Austria
| | - Marjan W van der Woude
- York Biomedical Research Institute, Hull York Medical School, University of York, York, UK
| | - Alyson Hockenberry
- Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland.,Department of Environmental Sciences, ETH Zürich, Zürich, Switzerland
| | - Patrick H Viollier
- Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Laurent Falquet
- Department of Biology, University of Fribourg, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wüthrich
- Infection Biology, University Hospital of Basel, Basel, Switzerland
| | | | - Claude Loverdo
- Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Adrian Egli
- Infection Biology, University Hospital of Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Raffaele Mezzenga
- Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.,Department of Materials, ETH Zürich, Zürich, Switzerland
| | - Otto Holst
- Forschungszentrum Borstel, Borstel, Germany
| | - Beat H Meier
- Institute for Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Emma Slack
- Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland. .,Institute of Food, Nutrition and Health, D-HEST, ETH Zürich, Zürich, Switzerland.
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