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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Roybal KT, Williams JZ, Morsut L, Rupp LJ, Kolinko I, Choe JH, Walker WJ, McNally KA, Lim WA. Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. Cell 2016; 167:419-432.e16. [PMID: 27693353 DOI: 10.1016/j.cell.2016.09.011] [Citation(s) in RCA: 429] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 07/12/2016] [Accepted: 09/06/2016] [Indexed: 01/17/2023]
Abstract
Redirecting T cells to attack cancer using engineered chimeric receptors provides powerful new therapeutic capabilities. However, the effectiveness of therapeutic T cells is constrained by the endogenous T cell response: certain facets of natural response programs can be toxic, whereas other responses, such as the ability to overcome tumor immunosuppression, are absent. Thus, the efficacy and safety of therapeutic cells could be improved if we could custom sculpt immune cell responses. Synthetic Notch (synNotch) receptors induce transcriptional activation in response to recognition of user-specified antigens. We show that synNotch receptors can be used to sculpt custom response programs in primary T cells: they can drive a la carte cytokine secretion profiles, biased T cell differentiation, and local delivery of non-native therapeutic payloads, such as antibodies, in response to antigen. SynNotch T cells can thus be used as a general platform to recognize and remodel local microenvironments associated with diverse diseases.
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Affiliation(s)
- Kole T Roybal
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Jasper Z Williams
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Leonardo Morsut
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Levi J Rupp
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Isabel Kolinko
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Joseph H Choe
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Whitney J Walker
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Krista A McNally
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Wendell A Lim
- Department of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA.
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Kolinko I, Lohße A, Borg S, Raschdorf O, Jogler C, Tu Q, Pósfai M, Tompa E, Plitzko JM, Brachmann A, Wanner G, Müller R, Zhang Y, Schüler D. Biosynthesis of magnetic nanostructures in a foreign organism by transfer of bacterial magnetosome gene clusters. Nat Nanotechnol 2014; 9:193-197. [PMID: 24561353 DOI: 10.1038/nnano.2014.13] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/16/2014] [Indexed: 06/03/2023]
Abstract
The synthetic production of monodisperse single magnetic domain nanoparticles at ambient temperature is challenging. In nature, magnetosomes--membrane-bound magnetic nanocrystals with unprecedented magnetic properties--can be biomineralized by magnetotactic bacteria. However, these microbes are difficult to handle. Expression of the underlying biosynthetic pathway from these fastidious microorganisms within other organisms could therefore greatly expand their nanotechnological and biomedical applications. So far, this has been hindered by the structural and genetic complexity of the magnetosome organelle and insufficient knowledge of the biosynthetic functions involved. Here, we show that the ability to biomineralize highly ordered magnetic nanostructures can be transferred to a foreign recipient. Expression of a minimal set of genes from the magnetotactic bacterium Magnetospirillum gryphiswaldense resulted in magnetosome biosynthesis within the photosynthetic model organism Rhodospirillum rubrum. Our findings will enable the sustainable production of tailored magnetic nanostructures in biotechnologically relevant hosts and represent a step towards the endogenous magnetization of various organisms by synthetic biology.
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Affiliation(s)
- Isabel Kolinko
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Anna Lohße
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Sarah Borg
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Oliver Raschdorf
- 1] Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany [2] Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christian Jogler
- 1] Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany [2]
| | - Qiang Tu
- 1] Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany [2] Shandong University - Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Life Science College, Shandong University, Jinan 250100, China
| | - Mihály Pósfai
- University of Pannonia, Department of Earth and Environmental Sciences, Veszprém, H-8200 Hungary
| | - Eva Tompa
- University of Pannonia, Department of Earth and Environmental Sciences, Veszprém, H-8200 Hungary
| | - Jürgen M Plitzko
- 1] Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany [2] Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Andreas Brachmann
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Gerhard Wanner
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Youming Zhang
- Shandong University - Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Life Science College, Shandong University, Jinan 250100, China
| | - Dirk Schüler
- Ludwig-Maximilians-Universität München, Department of Biology I, Großhaderner Straße 2-4, 82152 Martinsried, Germany
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