1
|
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] [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.
Collapse
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
| | | |
Collapse
|
2
|
von Strempel A, Weiss AS, Wittmann J, Salvado Silva M, Ring D, Wortmann E, Clavel T, Debarbieux L, Kleigrewe K, Stecher B. Bacteriophages targeting protective commensals impair resistance against Salmonella Typhimurium infection in gnotobiotic mice. PLoS Pathog 2023; 19:e1011600. [PMID: 37603558 PMCID: PMC10470868 DOI: 10.1371/journal.ppat.1011600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 08/31/2023] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
Gut microbial communities protect the host against a variety of major human gastrointestinal pathogens. Bacteriophages (phages) are ubiquitous in nature and frequently ingested via food and drinking water. Moreover, they are an attractive tool for microbiome engineering due to the lack of known serious adverse effects on the host. However, the functional role of phages within the gastrointestinal microbiome remain poorly understood. Here, we investigated the effects of microbiota-directed phages on infection with the human enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm), using a gnotobiotic mouse model (OMM14) for colonization resistance (CR). We show, that phage cocktails targeting Escherichia coli and Enterococcus faecalis acted in a strain-specific manner. They transiently reduced the population density of their respective target before establishing coexistence for up to 9 days. Infection susceptibility to S. Tm was markedly increased at an early time point after challenge with both phage cocktails. Surprisingly, OMM14 mice were also susceptible 7 days after a single phage inoculation, when the targeted bacterial populations were back to pre-phage administration density. Concluding, our work shows that phages that dynamically modulate the density of protective members of the gut microbiota can provide opportunities for invasion of bacterial pathogens, in particular at early time points after phage application. This suggests, that phages targeting protective members of the microbiota may increase the risk for Salmonella infection.
Collapse
Affiliation(s)
- Alexandra von Strempel
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Anna S. Weiss
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Marta Salvado Silva
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Diana Ring
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Esther Wortmann
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris, France
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| |
Collapse
|
3
|
Gül E, Bakkeren E, Salazar G, Steiger Y, Abi Younes A, Clerc M, Christen P, Fattinger SA, Nguyen BD, Kiefer P, Slack E, Ackermann M, Vorholt JA, Sunagawa S, Diard M, Hardt WD. The microbiota conditions a gut milieu that selects for wild-type Salmonella Typhimurium virulence. PLoS Biol 2023; 21:e3002253. [PMID: 37651408 PMCID: PMC10499267 DOI: 10.1371/journal.pbio.3002253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/13/2023] [Accepted: 07/13/2023] [Indexed: 09/02/2023] Open
Abstract
Salmonella Typhimurium elicits gut inflammation by the costly expression of HilD-controlled virulence factors. This inflammation alleviates colonization resistance (CR) mediated by the microbiota and thereby promotes pathogen blooms. However, the inflamed gut-milieu can also select for hilD mutants, which cannot elicit or maintain inflammation, therefore causing a loss of the pathogen's virulence. This raises the question of which conditions support the maintenance of virulence in S. Typhimurium. Indeed, it remains unclear why the wild-type hilD allele is dominant among natural isolates. Here, we show that microbiota transfer from uninfected or recovered hosts leads to rapid clearance of hilD mutants that feature attenuated virulence, and thereby contributes to the preservation of the virulent S. Typhimurium genotype. Using mouse models featuring a range of microbiota compositions and antibiotic- or inflammation-inflicted microbiota disruptions, we found that irreversible disruption of the microbiota leads to the accumulation of hilD mutants. In contrast, in models with a transient microbiota disruption, selection for hilD mutants was prevented by the regrowing microbiota community dominated by Lachnospirales and Oscillospirales. Strikingly, even after an irreversible microbiota disruption, microbiota transfer from uninfected donors prevented the rise of hilD mutants. Our results establish that robust S. Typhimurium gut colonization hinges on optimizing its manipulation of the host: A transient and tempered microbiota perturbation is favorable for the pathogen to both flourish in the inflamed gut and also minimize loss of virulence. Moreover, besides conferring CR, the microbiota may have the additional consequence of maintaining costly enteropathogen virulence mechanisms.
Collapse
Affiliation(s)
- Ersin Gül
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Department of Biology, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Guillem Salazar
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Microbiology and Swiss Institute of Bioinformatics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Yves Steiger
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Andrew Abi Younes
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Melanie Clerc
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Philipp Christen
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Stefan A. Fattinger
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Bidong D. Nguyen
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Emma Slack
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute for Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag, Duebendorf, Switzerland
| | - Julia A. Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Microbiology and Swiss Institute of Bioinformatics, Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Médéric Diard
- Biozentrum, University of Basel, Basel, Switzerland
- Botnar Research Centre for Child Health, Basel, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
4
|
Gül E, Abi Younes A, Huuskonen J, Diawara C, Nguyen BD, Maurer L, Bakkeren E, Hardt WD. Differences in carbon metabolic capacity fuel co-existence and plasmid transfer between Salmonella strains in the mouse gut. Cell Host Microbe 2023; 31:1140-1153.e3. [PMID: 37348498 DOI: 10.1016/j.chom.2023.05.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/12/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Antibiotic resistance plasmids can be disseminated between different Enterobacteriaceae in the gut. Here, we investigate how closely related Enterobacteriaceae populations with similar nutrient needs can co-bloom in the same gut and thereby facilitate plasmid transfer. Using different strains of Salmonella Typhimurium (S.Tm SL1344 and ATCC14028) and mouse models of Salmonellosis, we show that the bloom of one strain (i.e., recipient) from very low numbers in a gut pre-occupied by the other strain (i.e., donor) depends on strain-specific utilization of a distinct carbon source, galactitol or arabinose. Galactitol-dependent growth of the recipient S.Tm strain promotes plasmid transfer between non-isogenic strains and between E. coli and S.Tm. In mice stably colonized by a defined microbiota (OligoMM12), galactitol supplementation similarly facilitates co-existence of two S.Tm strains and promotes plasmid transfer. Our work reveals a metabolic strategy used by Enterobacteriaceae to expand in a pre-occupied gut and provides promising therapeutic targets for resistance plasmids spread.
Collapse
Affiliation(s)
- Ersin Gül
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.
| | - Andrew Abi Younes
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jemina Huuskonen
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Cheickna Diawara
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Bidong D Nguyen
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Luca Maurer
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, 8093 Zurich, Switzerland.
| |
Collapse
|
5
|
Gül E, Enz U, Maurer L, Abi Younes A, Fattinger SA, Nguyen BD, Hausmann A, Furter M, Barthel M, Sellin ME, Hardt WD. Intraluminal neutrophils limit epithelium damage by reducing pathogen assault on intestinal epithelial cells during Salmonella gut infection. PLoS Pathog 2023; 19:e1011235. [PMID: 37384776 DOI: 10.1371/journal.ppat.1011235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023] Open
Abstract
Recruitment of neutrophils into and across the gut mucosa is a cardinal feature of intestinal inflammation in response to enteric infections. Previous work using the model pathogen Salmonella enterica serovar Typhimurium (S.Tm) established that invasion of intestinal epithelial cells by S.Tm leads to recruitment of neutrophils into the gut lumen, where they can reduce pathogen loads transiently. Notably, a fraction of the pathogen population can survive this defense, re-grow to high density, and continue triggering enteropathy. However, the functions of intraluminal neutrophils in the defense against enteric pathogens and their effects on preventing or aggravating epithelial damage are still not fully understood. Here, we address this question via neutrophil depletion in different mouse models of Salmonella colitis, which differ in their degree of enteropathy. In an antibiotic pretreated mouse model, neutrophil depletion by an anti-Ly6G antibody exacerbated epithelial damage. This could be linked to compromised neutrophil-mediated elimination and reduced physical blocking of the gut-luminal S.Tm population, such that the pathogen density remained high near the epithelial surface throughout the infection. Control infections with a ssaV mutant and gentamycin-mediated elimination of gut-luminal pathogens further supported that neutrophils are protecting the luminal surface of the gut epithelium. Neutrophil depletion in germ-free and gnotobiotic mice hinted that the microbiota can modulate the infection kinetics and ameliorate epithelium-disruptive enteropathy even in the absence of neutrophil-protection. Together, our data indicate that the well-known protective effect of the microbiota is augmented by intraluminal neutrophils. After antibiotic-mediated microbiota disruption, neutrophils are central for maintaining epithelial barrier integrity during acute Salmonella-induced gut inflammation, by limiting the sustained pathogen assault on the epithelium in a critical window of the infection.
Collapse
Affiliation(s)
- Ersin Gül
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ursina Enz
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Luca Maurer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Andrew Abi Younes
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Stefan A Fattinger
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Bidong D Nguyen
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Annika Hausmann
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Markus Furter
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Manja Barthel
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Mikael E Sellin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
6
|
Hoces D, Greter G, Arnoldini M, Stäubli ML, Moresi C, Sintsova A, Berent S, Kolinko I, Bansept F, Woller A, Häfliger J, Martens E, Hardt WD, Sunagawa S, Loverdo C, Slack E. Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide in the mouse gut depends on the resident microbiota. eLife 2023; 12:81212. [PMID: 36757366 PMCID: PMC10014078 DOI: 10.7554/elife.81212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 02/08/2023] [Indexed: 02/10/2023] Open
Abstract
Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. In this study, we used genetically barcoded Bacteroides thetaiotaomicron (B. theta) strains to quantify population bottlenecks experienced by a B. theta population during colonization of the mouse gut. As expected, this reveals an inverse relationship between microbiota complexity and the probability that an individual wildtype B. theta clone will colonize the gut. The polysaccharide capsule of B. theta is important for resistance against attacks from other bacteria, phage, and the host immune system, and correspondingly acapsular B. theta loses in competitive colonization against the wildtype strain. Surprisingly, the acapsular strain did not show a colonization defect in mice with a low-complexity microbiota, as we found that acapsular strains have an indistinguishable colonization probability to the wildtype strain on single-strain colonization. This discrepancy could be resolved by tracking in vivo growth dynamics of both strains: acapsular B.theta shows a longer lag phase in the gut lumen as well as a slightly slower net growth rate. Therefore, as long as there is no niche competitor for the acapsular strain, this has only a small influence on colonization probability. However, the presence of a strong niche competitor (i.e., wildtype B. theta, SPF microbiota) rapidly excludes the acapsular strain during competitive colonization. Correspondingly, the acapsular strain shows a similarly low colonization probability in the context of a co-colonization with the wildtype strain or a complete microbiota. In summary, neutral tagging and detailed analysis of bacterial growth kinetics can therefore quantify the mechanisms of colonization resistance in differently-colonized animals.
Collapse
Affiliation(s)
- Daniel Hoces
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Giorgia Greter
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Markus Arnoldini
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Melanie L Stäubli
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Claudia Moresi
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Anna Sintsova
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Sara Berent
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Isabel Kolinko
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Florence Bansept
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Aurore Woller
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Janine Häfliger
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| | - Eric Martens
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Shinichi Sunagawa
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Claude Loverdo
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP)ParisFrance
| | - Emma Slack
- Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH ZurichZürichSwitzerland
| |
Collapse
|
7
|
Herzog MKM, Cazzaniga M, Peters A, Shayya N, Beldi L, Hapfelmeier S, Heimesaat MM, Bereswill S, Frankel G, Gahan CG, Hardt WD. Mouse models for bacterial enteropathogen infections: insights into the role of colonization resistance. Gut Microbes 2023; 15:2172667. [PMID: 36794831 PMCID: PMC9980611 DOI: 10.1080/19490976.2023.2172667] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
Globally, enteropathogenic bacteria are a major cause of morbidity and mortality.1-3 Campylobacter, Salmonella, Shiga-toxin-producing Escherichia coli, and Listeria are among the top five most commonly reported zoonotic pathogens in the European Union.4 However, not all individuals naturally exposed to enteropathogens go on to develop disease. This protection is attributable to colonization resistance (CR) conferred by the gut microbiota, as well as an array of physical, chemical, and immunological barriers that limit infection. Despite their importance for human health, a detailed understanding of gastrointestinal barriers to infection is lacking, and further research is required to investigate the mechanisms that underpin inter-individual differences in resistance to gastrointestinal infection. Here, we discuss the current mouse models available to study infections by non-typhoidal Salmonella strains, Citrobacter rodentium (as a model for enteropathogenic and enterohemorrhagic E. coli), Listeria monocytogenes, and Campylobacter jejuni. Clostridioides difficile is included as another important cause of enteric disease in which resistance is dependent upon CR. We outline which parameters of human infection are recapitulated in these mouse models, including the impact of CR, disease pathology, disease progression, and mucosal immune response. This will showcase common virulence strategies, highlight mechanistic differences, and help researchers from microbiology, infectiology, microbiome research, and mucosal immunology to select the optimal mouse model.
Collapse
Affiliation(s)
- Mathias K.-M. Herzog
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Monica Cazzaniga
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Audrey Peters
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Nizar Shayya
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - University Medicine Berlin, Berlin, Germany
| | - Luca Beldi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Markus M. Heimesaat
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - University Medicine Berlin, Berlin, Germany
| | - Stefan Bereswill
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - University Medicine Berlin, Berlin, Germany
| | - Gad Frankel
- Department of Life Sciences, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Cormac G.M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- School of Pharmacy, University College Cork, Cork, Ireland
| | - Wolf-Dietrich Hardt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
8
|
Lv Q, Li Z, Sui A, Yang X, Han Y, Yao R. The role and mechanisms of gut microbiota in diabetic nephropathy, diabetic retinopathy and cardiovascular diseases. Front Microbiol 2022; 13:977187. [PMID: 36060752 PMCID: PMC9433831 DOI: 10.3389/fmicb.2022.977187] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/28/2022] [Indexed: 11/26/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) and T2DM-related complications [such as retinopathy, nephropathy, and cardiovascular diseases (CVDs)] are the most prevalent metabolic diseases. Intriguingly, overwhelming findings have shown a strong association of the gut microbiome with the etiology of these diseases, including the role of aberrant gut bacterial metabolites, increased intestinal permeability, and pathogenic immune function affecting host metabolism. Thus, deciphering the specific microbiota, metabolites, and the related mechanisms to T2DM-related complications by combined analyses of metagenomics and metabolomics data can lead to an innovative strategy for the treatment of these diseases. Accordingly, this review highlights the advanced knowledge about the characteristics of the gut microbiota in T2DM-related complications and how it can be associated with the pathogenesis of these diseases. Also, recent studies providing a new perspective on microbiota-targeted therapies are included.
Collapse
|
9
|
Xavier RGC, da Silva PHS, Trindade HD, Carvalho GM, Nicolino RR, Freitas PMC, Silva ROS. Characterization of Escherichia coli in Dogs with Pyometra and the Influence of Diet on the Intestinal Colonization of Extraintestinal Pathogenic E. coli (ExPEC). Vet Sci 2022; 9:vetsci9050245. [PMID: 35622773 PMCID: PMC9144190 DOI: 10.3390/vetsci9050245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 02/04/2023] Open
Abstract
Despite its high frequency and clinical relevance, the pathogenesis of canine pyometra remains poorly understood. The most accepted hypothesis is that bacteria involved ascend from the intestinal tract, causing the uterine infection. Extraintestinal pathogenic Escherichia coli (ExPEC) is the most frequent pathogen in canine pyometra, accounting for 57–100% of cases. The aim of the present study was to determine the frequency of phylogenetic groups and virulence factors in E. coli strains isolated from the uterine and rectal swabs of bitches with pyometra (n = 72) and from rectal swabs from healthy bitches fed commercial dry feed (n = 53) or a raw meat-based diet (RMBD; n = 38). A total of 512 strains of E. coli were isolated and divided into five categories according to the origin of the sample: 120 isolates from the uterine content of dogs with E. coli pyometra, 102 from the feces of bitches with E. coli pyometra, 75 from the feces of bitches without E. coli pyometra, 130 feces samples from healthy dogs fed commercial feed, and 85 feces samples from healthy dogs fed a raw meat-based diet. E. coli strains belonging to the B2 phylogroup and positive for virulence factor genes associated with adhesion (fimbriae type P [papC]) and production of toxins (α-hemolysin [hlyA] and uropathogenic specific protein [usp]) predominated in the uterine content and rectal swabs of bitches with E. coli pyometra. Interestingly, a lower growth rate of E. coli from the B2 phylogroup was observed in dogs fed a RMBD than in those fed commercial dry feed. The present study suggests that intestinal colonization by certain types of E. coli could be a risk factor for the occurrence of E. coli pyometra in bitches and that diet can influence intestinal colonization by such strains.
Collapse
|
10
|
Bakkeren E, Gül E, Huisman JS, Steiger Y, Rocker A, Hardt WD, Diard M. Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium. Nat Commun 2022; 13:1939. [PMID: 35410999 PMCID: PMC9001671 DOI: 10.1038/s41467-022-29597-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Intestinal inflammation fuels the transmission of Salmonella Typhimurium (S.Tm). However, a substantial fitness cost is associated with virulence expression. Mutations inactivating transcriptional virulence regulators generate attenuated variants profiting from inflammation without enduring virulence cost. Such variants interfere with the transmission of fully virulent clones. Horizontal transfer of functional regulatory genes (HGT) into attenuated variants could nevertheless favor virulence evolution. To address this hypothesis, we cloned hilD, coding for the master regulator of virulence, into a conjugative plasmid that is highly transferrable during intestinal colonization. The resulting mobile hilD allele allows virulence to emerge from avirulent populations, and to be restored in attenuated mutants competing against virulent clones within-host. However, mutations inactivating the mobile hilD allele quickly arise. The stability of virulence mediated by HGT is strongly limited by its cost, which depends on the hilD expression level, and by the timing of transmission. We conclude that robust evolution of costly virulence expression requires additional selective forces such as narrow population bottlenecks during transmission. Salmonella Typhimurium virulence is costly and can be lost by mutation during infection. Bakkeren et al. show that virulence restoration via horizontal gene transfer is only transient while transmission bottlenecks promote long-term virulence stability.
Collapse
|
11
|
In vitro interaction network of a synthetic gut bacterial community. THE ISME JOURNAL 2022; 16:1095-1109. [PMID: 34857933 PMCID: PMC8941000 DOI: 10.1038/s41396-021-01153-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 10/27/2021] [Accepted: 11/10/2021] [Indexed: 02/07/2023]
Abstract
A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM12) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM12 interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM12 interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.
Collapse
|
12
|
Diet leaves a genetic signature in a keystone member of the gut microbiota. Cell Host Microbe 2022; 30:183-199.e10. [PMID: 35085504 DOI: 10.1016/j.chom.2022.01.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022]
Abstract
Switching from a low-fat and high-fiber diet to a Western-style high-fat and high-sugar diet causes microbiota imbalances that underlay many pathological conditions (i.e., dysbiosis). Although the effects of dietary changes on microbiota composition and functions are well documented, their impact in gut bacterial evolution remains unexplored. We followed the emergence of mutations in Bacteroides thetaiotaomicron, a prevalent fiber-degrading microbiota member, upon colonization of the murine gut under different dietary regimens. B. thetaiotaomicron evolved rapidly in the gut and Western-style diet selected for mutations that promote degradation of mucin-derived glycans. Periodic dietary changes caused fluctuations in the frequency of such mutations and were associated with metabolic shifts, resulting in the maintenance of higher intraspecies genetic diversity compared to constant dietary regimens. These results show that dietary changes leave a genetic signature in microbiome members and suggest that B. thetaiotaomicron genetic diversity could be a biomarker for dietary differences among individuals.
Collapse
|
13
|
Heras VL, Melgar S, MacSharry J, Gahan CG. The Influence of the Western Diet on Microbiota and Gastrointestinal Immunity. Annu Rev Food Sci Technol 2022; 13:489-512. [DOI: 10.1146/annurev-food-052720-011032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Diet exerts a major influence upon host immune function and the gastrointestinal microbiota. Although components of the human diet (including carbohydrates, fats, and proteins) are essential sources of nutrition for the host, they also influence immune function directly through interaction with innate and cell-mediated immune regulatory mechanisms. Regulation of the microbiota community structure also provides a mechanism by which food components influence host immune regulatory processes. Here, we consider the complex interplay between components of the modern (Western) diet, the microbiota, and host immunity in the context of obesity and metabolic disease, inflammatory bowel disease, and infection. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Vanessa Las Heras
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - John MacSharry
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- School of Medicine, University College Cork, Cork, Ireland
| | - Cormac G.M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- School of Pharmacy, University College Cork, Cork, Ireland
| |
Collapse
|
14
|
Bakkeren E, Herter JA, Huisman JS, Steiger Y, Gül E, Newson JPM, Brachmann AO, Piel J, Regoes R, Bonhoeffer S, Diard M, Hardt WD. Pathogen invasion-dependent tissue reservoirs and plasmid-encoded antibiotic degradation boost plasmid spread in the gut. eLife 2021; 10:e69744. [PMID: 34872631 PMCID: PMC8651294 DOI: 10.7554/elife.69744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 11/10/2021] [Indexed: 11/30/2022] Open
Abstract
Many plasmids encode antibiotic resistance genes. Through conjugation, plasmids can be rapidly disseminated. Previous work identified gut luminal donor/recipient blooms and tissue-lodged plasmid-bearing persister cells of the enteric pathogen Salmonella enterica serovar Typhimurium (S.Tm) that survive antibiotic therapy in host tissues, as factors promoting plasmid dissemination among Enterobacteriaceae. However, the buildup of tissue reservoirs and their contribution to plasmid spread await experimental demonstration. Here, we asked if re-seeding-plasmid acquisition-invasion cycles by S.Tm could serve to diversify tissue-lodged plasmid reservoirs, and thereby promote plasmid spread. Starting with intraperitoneal mouse infections, we demonstrate that S.Tm cells re-seeding the gut lumen initiate clonal expansion. Extended spectrum beta-lactamase (ESBL) plasmid-encoded gut luminal antibiotic degradation by donors can foster recipient survival under beta-lactam antibiotic treatment, enhancing transconjugant formation upon re-seeding. S.Tm transconjugants can subsequently re-enter host tissues introducing the new plasmid into the tissue-lodged reservoir. Population dynamics analyses pinpoint recipient migration into the gut lumen as rate-limiting for plasmid transfer dynamics in our model. Priority effects may be a limiting factor for reservoir formation in host tissues. Overall, our proof-of-principle data indicates that luminal antibiotic degradation and shuttling between the gut lumen and tissue-resident reservoirs can promote the accumulation and spread of plasmids within a host over time.
Collapse
Affiliation(s)
- Erik Bakkeren
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | | | - Jana Sanne Huisman
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH ZurichZurichSwitzerland
| | - Yves Steiger
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Ersin Gül
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | | | | | - Jörn Piel
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| | - Roland Regoes
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH ZurichZurichSwitzerland
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH ZurichZurichSwitzerland
| | - Médéric Diard
- Botnar Research Centre for Child HealthBaselSwitzerland
- Biozentrum, University of BaselBaselSwitzerland
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH ZurichZurichSwitzerland
| |
Collapse
|
15
|
Dietary Acrylamide Intake Alters Gut Microbiota in Mice and Increases Its Susceptibility to Salmonella Typhimurium Infection. Foods 2021; 10:foods10122990. [PMID: 34945541 PMCID: PMC8700958 DOI: 10.3390/foods10122990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/15/2021] [Accepted: 11/22/2021] [Indexed: 11/18/2022] Open
Abstract
Acrylamide (AA) has been extensively examined for its potential toxicological effects on humans and animals, but its impacts on gut microbiota and effects on hosts’ susceptibility to enteric infection remain elusive. The present study was designed to evaluate the effect of AA on gut microbiota of mice and susceptibility of mice to S. Typhimurium infection. After four weeks’ intervention, mice fed with AA exhibited significantly decreased body weight. Meanwhile, 16S rRNA gene sequencing showed reduced relative abundance of Firmicutes and increased abundance of Bacteroidetes in AA-treated mice prior to infection. In addition, we observed high relative abundance of Burkholderiales and Erysipelotrichales, more specifically the genus Sutterella and Allobaculum, respectively, in AA-treated mice before infection. Subsequently, the mice were orally infected with S. Typhimurium. The histological changes, systemic dissemination of S. Typhimurium, and inflammatory responses were examined. Compared to mice fed with normal diet, mice fed AA exhibited higher level of bacterial counts in liver, spleen, and ileum, which was consistent with exacerbated tissue damage determined by histological analyses. In addition, higher expression of pro-inflammaroty cytokines, p-IκBα, and p-P65 and lower mRNA expressions of mucin2, occludin, zo-1, claudin-1, and E-cadherin were detected in AA-treated mice. These findings provide novel insights into the potential health impact of AA consumption and the detailed mechanism for its effect on S. Typhimurium infection merit further exploration.
Collapse
|
16
|
Emerging technologies and infection models in cellular microbiology. Nat Commun 2021; 12:6764. [PMID: 34799563 PMCID: PMC8604907 DOI: 10.1038/s41467-021-26641-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/18/2021] [Indexed: 01/09/2023] Open
Abstract
The field of cellular microbiology, rooted in the co-evolution of microbes and their hosts, studies intracellular pathogens and their manipulation of host cell machinery. In this review, we highlight emerging technologies and infection models that recently promoted opportunities in cellular microbiology. We overview the explosion of microscopy techniques and how they reveal unprecedented detail at the host-pathogen interface. We discuss the incorporation of robotics and artificial intelligence to image-based screening modalities, biochemical mapping approaches, as well as dual RNA-sequencing techniques. Finally, we describe chips, organoids and animal models used to dissect biophysical and in vivo aspects of the infection process. As our knowledge of the infected cell improves, cellular microbiology holds great promise for development of anti-infective strategies with translational applications in human health.
Collapse
|
17
|
Le Guern R, Stabler S, Gosset P, Pichavant M, Grandjean T, Faure E, Karaca Y, Faure K, Kipnis E, Dessein R. Colonization resistance against multi-drug-resistant bacteria: a narrative review. J Hosp Infect 2021; 118:48-58. [PMID: 34492304 DOI: 10.1016/j.jhin.2021.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Colonization resistance by gut microbiota is a fundamental phenomenon in infection prevention and control. Hospitalized patients may be exposed to multi-drug-resistant bacteria when hand hygiene compliance among healthcare workers is not adequate. An additional layer of defence is provided by the healthy gut microbiota, which helps clear the exogenous bacteria and acts as a safety net when hand hygiene procedures are not followed. This narrative review focuses on the role of the gut microbiota in colonization resistance against multi-drug-resistant bacteria, and its implications for infection control. The review discusses the underlying mechanisms of colonization resistance (direct or indirect), the concept of resilience of the gut microbiota, the link between the antimicrobial spectrum and gut dysbiosis, and possible therapeutic strategies. Antimicrobial stewardship is crucial to maximize the effects of colonization resistance. Avoiding unnecessary antimicrobial therapy, shortening the antimicrobial duration as much as possible, and favouring antibiotics with low anti-anaerobe activity may decrease the acquisition and expansion of multi-drug-resistant bacteria. Even after antimicrobial therapy, the resilience of the gut microbiota often occurs spontaneously. Spontaneous resilience explains the existence of a window of opportunity for colonization of multi-drug-resistant bacteria during or just after antimicrobial therapy. Strategies favouring resilience of the gut microbiota, such as high-fibre diets or precision probiotics, should be evaluated.
Collapse
Affiliation(s)
- R Le Guern
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Laboratoire de Bactériologie-Hygiène, CHU Lille, Lille, France.
| | - S Stabler
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - P Gosset
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - M Pichavant
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - T Grandjean
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - E Faure
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - Y Karaca
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - K Faure
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - E Kipnis
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Réanimation Chirurgicale, CHU Lille, Lille, France
| | - R Dessein
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Laboratoire de Bactériologie-Hygiène, CHU Lille, Lille, France
| |
Collapse
|
18
|
Fattinger SA, Sellin ME, Hardt WD. Epithelial inflammasomes in the defense against Salmonella gut infection. Curr Opin Microbiol 2020; 59:86-94. [PMID: 33128958 DOI: 10.1016/j.mib.2020.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 02/06/2023]
Abstract
The gut epithelium prevents bacterial access to the host's tissues and coordinates a number of mucosal defenses. Here, we review the function of epithelial inflammasomes in the infected host and focus on their role in defense against Salmonella Typhimurium. This pathogen employs flagella to swim towards the epithelium and a type III secretion system (TTSS) to dock and invade intestinal epithelial cells. Flagella and TTSS components are recognized by the canonical NAIP/NLRC4 inflammasome, while LPS activates the non-canonical Caspase-4/11 inflammasome. The relative contributions of these inflammasomes, the activated cell death pathways and the elicited mucosal defenses are subject to environmental control and appear to change along the infection trajectory. It will be an important future task to explain how this may enable defense against the challenges imposed by diverse bacterial enteropathogens.
Collapse
Affiliation(s)
- Stefan A Fattinger
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mikael E Sellin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wolf-Dietrich Hardt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|