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Daniel BBJ, Steiger Y, Sintsova A, Field CM, Nguyen BD, Schubert C, Cherrak Y, Sunagawa S, Hardt WD, Vorholt JA. Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags. Nat Microbiol 2024; 9:1103-1116. [PMID: 38503975 PMCID: PMC10994841 DOI: 10.1038/s41564-024-01634-9] [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: 09/19/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed that they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intrastrain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. We observed colonization resistance against late-arriving strains of Salmonella Typhimurium in the mouse gut, whereas the phyllosphere accommodated Sphingomonas latecomers in a manner proportional to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems.
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Affiliation(s)
| | - Yves Steiger
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Anna Sintsova
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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Sintsova A, Ruscheweyh HJ, Field CM, Feer L, Nguyen BD, Daniel B, Hardt WD, Vorholt JA, Sunagawa S. mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations. Bioinformatics 2024; 40:btae078. [PMID: 38341646 PMCID: PMC10885212 DOI: 10.1093/bioinformatics/btae078] [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: 07/31/2023] [Revised: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 02/12/2024] Open
Abstract
MOTIVATION DNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization, and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills. RESULTS Here, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups. The tool is seamlessly integrated with an intuitive web app for interactive data exploration via the STRING and KEGG databases to accelerate scientific discovery. AVAILABILITY AND IMPLEMENTATION The tool is implemented in Python. The source code is freely available (https://github.com/MicrobiologyETHZ/mbarq) and the web app can be accessed at: https://microbiomics.io/tools/mbarq-app.
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Affiliation(s)
- Anna Sintsova
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Christopher M Field
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Lilith Feer
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Bidong D Nguyen
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Benjamin Daniel
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Wolf-Dietrich Hardt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Julia A Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
- Department of Biology, Institute of Microbiology, Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
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Tawk C, Lim B, Bencivenga-Barry NA, Lees HJ, Ramos RJF, Cross J, Goodman AL. Infection leaves a genetic and functional mark on the gut population of a commensal bacterium. Cell Host Microbe 2023; 31:811-826.e6. [PMID: 37119822 PMCID: PMC10197903 DOI: 10.1016/j.chom.2023.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/04/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023]
Abstract
Gastrointestinal infection changes microbiome composition and gene expression. In this study, we demonstrate that enteric infection also promotes rapid genetic adaptation in a gut commensal. Measurements of Bacteroides thetaiotaomicron population dynamics within gnotobiotic mice reveal that these populations are relatively stable in the absence of infection, and the introduction of the enteropathogen Citrobacter rodentium reproducibly promotes rapid selection for a single-nucleotide variant with increased fitness. This mutation promotes resistance to oxidative stress by altering the sequence of a protein, IctA, that is essential for fitness during infection. We identified commensals from multiple phyla that attenuate the selection of this variant during infection. These species increase the levels of vitamin B6 in the gut lumen. Direct administration of this vitamin is sufficient to significantly reduce variant expansion in infected mice. Our work demonstrates that a self-limited enteric infection can leave a stable mark on resident commensal populations that increase fitness during infection.
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Affiliation(s)
- Caroline Tawk
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Bentley Lim
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Natasha A Bencivenga-Barry
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Hannah J Lees
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruben J F Ramos
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Justin Cross
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT 06510, USA.
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Blois S, Goetz BM, Bull JJ, Sullivan CS. Interpreting and de-noising genetically engineered barcodes in a DNA virus. PLoS Comput Biol 2022; 18:e1010131. [PMID: 36413582 PMCID: PMC9725130 DOI: 10.1371/journal.pcbi.1010131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 12/06/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5,000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe the challenges faced with interpreting the barcode sequences obtained from the library. Our Illumina NextSeq sequencing recalled much greater variation in barcode sequencing reads than the expected 5,000 barcodes-necessarily stemming from the Illumina library processing and sequencing error. Using data from defined control virus genomes cloned into plasmid backbones we develop a vetted post-sequencing method to cluster the erroneous reads around the true virus genome barcodes. These findings may foreshadow problems with randomized barcodes in other microbial systems and provide a useful approach for future work utilizing nucleic acid barcoded pathogens.
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Affiliation(s)
- Sylvain Blois
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
- Department of Biomedical Sciences, University of Cagliari, Monserrato, Cagliari, Italy
| | - Benjamin M. Goetz
- Center for Biomedical Research Support, The University of Texas at Austin, Austin, Texas, United States of America
| | - James J. Bull
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Christopher S. Sullivan
- Department of Molecular Biosciences, LaMontagne Center for Infectious Disease, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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Kammoun H, Kim M, Hafner L, Gaillard J, Disson O, Lecuit M. Listeriosis, a model infection to study host-pathogen interactions in vivo. Curr Opin Microbiol 2021; 66:11-20. [PMID: 34923331 DOI: 10.1016/j.mib.2021.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/27/2021] [Accepted: 11/30/2021] [Indexed: 12/19/2022]
Abstract
Listeria monocytogenes (Lm) is a foodborne pathogen and the etiological agent of listeriosis. This facultative intracellular Gram-positive bacterium has the ability to colonize the intestinal lumen, cross the intestinal, blood-brain and placental barriers, leading to bacteremia, neurolisteriosis and maternal-fetal listeriosis. Lm is a model microorganism for the study of the interplay between a pathogenic microbe, host tissues and microbiota in vivo. Here we review how animal models permissive to Lm-host interactions allow deciphering some of the key steps of the infectious process, from the intestinal lumen to the crossing of host barriers and dissemination within the host. We also highlight recent investigations using tagged Lm and clinically relevant strains that have shed light on within-host dynamics and the purifying selection of Lm virulence factors. Studying Lm infection in vivo is a way forward to explore host biology and unveil the mechanisms that have selected its capacity to closely associate with its vertebrate hosts.
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Affiliation(s)
- Hana Kammoun
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, 75015 Paris, France
| | - Minhee Kim
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, 75015 Paris, France
| | - Lukas Hafner
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, 75015 Paris, France
| | - Julien Gaillard
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, 75015 Paris, France
| | - Olivier Disson
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, 75015 Paris, France
| | - Marc Lecuit
- Institut Pasteur, Université de Paris, Inserm U1117, Biology of Infection Unit, 75015 Paris, France; Institut Pasteur, National Reference Centre and WHO Collaborating Centre Listeria, 75015 Paris, France; Necker-Enfants Malades University Hospital, Division of Infectious Diseases and Tropical Medicine, APHP, Institut Imagine, 75006 Paris, France.
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Abstract
Pathogen population dynamics during infection are critical determinants of infection susceptibility and define patterns of dissemination. However, deciphering these dynamics, particularly founding population sizes in host organs and patterns of dissemination between organs, is difficult because measuring bacterial burden alone is insufficient to observe these patterns. Introduction of allelic diversity into otherwise identical bacteria using DNA barcodes enables sequencing-based measurements of these parameters, in a method known as STAMP (Sequence Tag-based Analysis of Microbial Populations). However, bacteria often undergo unequal expansion within host organs, resulting in marked differences in the frequencies of barcodes in input and output libraries. Here, we show that these differences confound STAMP-based analyses of founding population sizes and dissemination patterns. We present STAMPR, a successor to STAMP, which accounts for such population expansions. Using data from systemic infection of barcoded extraintestinal pathogenic E. coli, we show that this new framework, along with the metrics it yields, enhances the fidelity of measurements of bottlenecks and dissemination patterns. STAMPR was also validated on an independent barcoded Pseudomonas aeruginosa data set, uncovering new patterns of dissemination within the data. This framework (available at https://github.com/hullahalli/stampr_rtisan), when coupled with barcoded data sets, enables a more complete assessment of within-host bacterial population dynamics. IMPORTANCE Barcoded bacteria are often employed to monitor pathogen population dynamics during infection. The accuracy of these measurements is diminished by unequal bacterial expansion rates. Here, we develop computational tools to circumvent this limitation and establish additional metrics that collectively enhance the fidelity of measuring within-host pathogen founding population sizes and dissemination patterns. These new tools will benefit future studies of the dynamics of pathogens and symbionts within their respective hosts and may have additional barcode-based applications beyond host-microbe interactions.
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