1
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Saunders SH, Ahmed AM. ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency. Nucleic Acids Res 2024; 52:e43. [PMID: 38587185 PMCID: PMC11077079 DOI: 10.1093/nar/gkae227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 02/28/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024] Open
Abstract
Microbiology and synthetic biology depend on reverse genetic approaches to manipulate bacterial genomes; however, existing methods require molecular biology to generate genomic homology, suffer from low efficiency, and are not easily scaled to high throughput. To overcome these limitations, we developed a system for creating kilobase-scale genomic modifications that uses DNA oligonucleotides to direct the integration of a non-replicating plasmid. This method, Oligonucleotide Recombineering followed by Bxb-1 Integrase Targeting (ORBIT) was pioneered in Mycobacteria, and here we adapt and expand it for Escherichia coli. Our redesigned plasmid toolkit for oligonucleotide recombineering achieved significantly higher efficiency than λ Red double-stranded DNA recombineering and enabled precise, stable knockouts (≤134 kb) and integrations (≤11 kb) of various sizes. Additionally, we constructed multi-mutants in a single transformation, using orthogonal attachment sites. At high throughput, we used pools of targeting oligonucleotides to knock out nearly all known transcription factor and small RNA genes, yielding accurate, genome-wide, single mutant libraries. By counting genomic barcodes, we also show ORBIT libraries can scale to thousands of unique members (>30k). This work demonstrates that ORBIT for E. coli is a flexible reverse genetic system that facilitates rapid construction of complex strains and readily scales to create sophisticated mutant libraries.
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Affiliation(s)
- Scott H Saunders
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75320, USA
| | - Ayesha M Ahmed
- Green Center for Systems Biology - Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75320, USA
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2
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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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3
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Mulla Y, Bollenbach T. Invade to evade: E. coli's gutsy survival strategies. Cell Host Microbe 2024; 32:300-301. [PMID: 38484709 DOI: 10.1016/j.chom.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 03/19/2024]
Abstract
Antibiotic resistance is often studied in vitro, limiting the understanding of in vivo mechanisms that affect antibiotic treatment. In this issue of Cell Host & Microbe, Rodrigues et al. show that specific mutations allow bacteria to invade intestinal cells in a mouse model, thereby evading antibiotic treatment.
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Affiliation(s)
- Yuval Mulla
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany; Molecular Microbiology Section, Amsterdam Institute for Life and Environment (A-Life), Vrije Universiteit, 1081BT Amsterdam, The Netherlands
| | - Tobias Bollenbach
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany; Center for Data and Simulation Science, University of Cologne, 50931 Cologne, Germany.
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4
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Wong DPGH, Good BH. Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking. Nat Commun 2024; 15:1605. [PMID: 38383538 PMCID: PMC10881964 DOI: 10.1038/s41467-024-45792-0] [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] [Received: 09/21/2022] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Gut microbiota can adapt to their host environment by rapidly acquiring new mutations. However, the dynamics of this process are difficult to characterize in dominant gut species in their complex in vivo environment. Here we show that the fine-scale dynamics of genome-wide transposon libraries can enable quantitative inferences of these in vivo evolutionary forces. By analyzing >400,000 lineages across four human Bacteroides strains in gnotobiotic mice, we observed positive selection on thousands of cryptic variants - most of which were unrelated to their original gene knockouts. The spectrum of fitness benefits varied between species, and displayed diverse tradeoffs over time and in different dietary conditions, enabling inferences of their underlying function. These results suggest that within-host adaptations arise from an intense competition between numerous contending variants, which can strongly influence their emergent evolutionary tradeoffs.
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Affiliation(s)
- Daniel P G H Wong
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA
| | - Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, 94158, USA.
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5
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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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6
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Jiang G, Zhang Y, Chen M, Ramoneda J, Han L, Shi Y, Peyraud R, Wang Y, Shi X, Chen X, Ding W, Jousset A, Hikichi Y, Ohnishi K, Zhao FJ, Xu Y, Shen Q, Dini-Andreote F, Zhang Y, Wei Z. Effects of plant tissue permeability on invasion and population bottlenecks of a phytopathogen. Nat Commun 2024; 15:62. [PMID: 38167266 PMCID: PMC10762237 DOI: 10.1038/s41467-023-44234-7] [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] [Received: 03/28/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Pathogen genetic diversity varies in response to environmental changes. However, it remains unclear whether plant barriers to invasion could be considered a genetic bottleneck for phytopathogen populations. Here, we implement a barcoding approach to generate a pool of 90 isogenic and individually barcoded Ralstonia solanacearum strains. We used 90 of these strains to inoculate tomato plants with different degrees of physical permeability to invasion (intact roots, wounded roots and xylem inoculation) and quantify the phytopathogen population dynamics during invasion. Our results reveal that the permeability of plant roots impacts the degree of population bottleneck, genetic diversity, and composition of Ralstonia populations. We also find that selection is the main driver structuring pathogen populations when barriers to infection are less permeable, i.e., intact roots, the removal of root physical and immune barriers results in the predominance of stochasticity in population assembly. Taken together, our study suggests that plant root permeability constitutes a bottleneck for phytopathogen invasion and genetic diversity.
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Affiliation(s)
- Gaofei Jiang
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yuling Zhang
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Min Chen
- College of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, China
| | - Josep Ramoneda
- Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Liangliang Han
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Rémi Peyraud
- iMEAN, Ramonville Saint Agne, Occitanie, FR, France
| | - Yikui Wang
- Vegetable Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
| | - Xiaojun Shi
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Xinping Chen
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Wei Ding
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Alexandre Jousset
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yasufumi Hikichi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Japan
| | - Kouhei Ohnishi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Japan
| | - Fang-Jie Zhao
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yangchun Xu
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Yong Zhang
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China.
- College of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, China.
| | - Zhong Wei
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China.
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7
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Helsen J, Sherlock G, Dey G. Experimental evolution for cell biology. Trends Cell Biol 2023; 33:903-912. [PMID: 37188561 PMCID: PMC10592577 DOI: 10.1016/j.tcb.2023.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
Evolutionary cell biology explores the origins, principles, and core functions of cellular features and regulatory networks through the lens of evolution. This emerging field relies heavily on comparative experiments and genomic analyses that focus exclusively on extant diversity and historical events, providing limited opportunities for experimental validation. In this opinion article, we explore the potential for experimental laboratory evolution to augment the evolutionary cell biology toolbox, drawing inspiration from recent studies that combine laboratory evolution with cell biological assays. Primarily focusing on approaches for single cells, we provide a generalizable template for adapting experimental evolution protocols to provide fresh insight into long-standing questions in cell biology.
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Affiliation(s)
- Jana Helsen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Gautam Dey
- Cell Biology and Biophysics, European Molecular Biology Laboratory, Heidelberg, Germany.
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8
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Theodosiou L, Farr AD, Rainey PB. Barcoding Populations of Pseudomonas fluorescens SBW25. J Mol Evol 2023; 91:254-262. [PMID: 37186220 PMCID: PMC10275814 DOI: 10.1007/s00239-023-10103-6] [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: 09/26/2022] [Accepted: 03/13/2023] [Indexed: 05/17/2023]
Abstract
In recent years, evolutionary biologists have developed an increasing interest in the use of barcoding strategies to study eco-evolutionary dynamics of lineages within evolving populations and communities. Although barcoded populations can deliver unprecedented insight into evolutionary change, barcoding microbes presents specific technical challenges. Here, strategies are described for barcoding populations of the model bacterium Pseudomonas fluorescens SBW25, including the design and cloning of barcoded regions, preparation of libraries for amplicon sequencing, and quantification of resulting barcoded lineages. In so doing, we hope to aid the design and implementation of barcoding methodologies in a broad range of model and non-model organisms.
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Affiliation(s)
- Loukas Theodosiou
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding, Cologne, Germany.
| | - Andrew D Farr
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Paul B Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Laboratory of Biophysics and Evolution, CBI, ESPCI Paris, Université PSL, CNRS, Paris, France
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9
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Johnson MS, Venkataram S, Kryazhimskiy S. Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes. J Mol Evol 2023; 91:263-280. [PMID: 36651964 PMCID: PMC10276077 DOI: 10.1007/s00239-022-10083-z] [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: 09/08/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023]
Abstract
Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.
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Affiliation(s)
- Milo S Johnson
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Sandeep Venkataram
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sergey Kryazhimskiy
- Department of Ecology, Behavior and Evolution, University of California San Diego, La Jolla, CA, 92093, USA.
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10
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Li F, Mahadevan A, Sherlock G. An improved algorithm for inferring mutational parameters from bar-seq evolution experiments. BMC Genomics 2023; 24:246. [PMID: 37149606 PMCID: PMC10164349 DOI: 10.1186/s12864-023-09345-x] [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] [Received: 11/08/2022] [Accepted: 04/27/2023] [Indexed: 05/08/2023] Open
Abstract
BACKGROUND Genetic barcoding provides a high-throughput way to simultaneously track the frequencies of large numbers of competing and evolving microbial lineages. However making inferences about the nature of the evolution that is taking place remains a difficult task. RESULTS Here we describe an algorithm for the inference of fitness effects and establishment times of beneficial mutations from barcode sequencing data, which builds upon a Bayesian inference method by enforcing self-consistency between the population mean fitness and the individual effects of mutations within lineages. By testing our inference method on a simulation of 40,000 barcoded lineages evolving in serial batch culture, we find that this new method outperforms its predecessor, identifying more adaptive mutations and more accurately inferring their mutational parameters. CONCLUSION Our new algorithm is particularly suited to inference of mutational parameters when read depth is low. We have made Python code for our serial dilution evolution simulations, as well as both the old and new inference methods, available on GitHub ( https://github.com/FangfeiLi05/FitMut2 ), in the hope that it can find broader use by the microbial evolution community.
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Affiliation(s)
- Fangfei Li
- Department of Genetics, Stanford University, Stanford, California, US
| | - Aditya Mahadevan
- Department of Physics, Stanford University, Stanford, California, US
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, California, US.
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11
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Zhou S, Wu Y, Zhao Y, Zhang Z, Jiang L, Liu L, Zhang Y, Tang J, Yuan YJ. Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization. Natl Sci Rev 2023; 10:nwad073. [PMID: 37223244 PMCID: PMC10202648 DOI: 10.1093/nsr/nwad073] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/07/2022] [Accepted: 02/02/2023] [Indexed: 11/12/2023] Open
Abstract
Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary processes. Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural variations. Here, we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes (synII, synIII, synV, circular synVI, synIXR and synX). Remarkably, we find that the rearrangement events exhibit a specific landscape of frequency. We further reveal that the landscape is shaped by the combined effects of chromatin accessibility and spatial contact probability. The rearrangements tend to occur in 3D spatially proximal and chromatin-accessible regions. The enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution, and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.
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Affiliation(s)
- Sijie Zhou
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yu Zhao
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Zhen Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Limin Jiang
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Lin Liu
- Epigenetic Group, FrasergenBioinformatics Co., Ltd., Wuhan 430000, China
| | - Yan Zhang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jijun Tang
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
- Department of Computer Science, University of South Carolina, Columbia, SC 29208, USA
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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12
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Kantak M, Batra P, Shende P. Integration of DNA barcoding and nanotechnology in drug delivery. Int J Biol Macromol 2023; 230:123262. [PMID: 36646350 DOI: 10.1016/j.ijbiomac.2023.123262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/15/2023]
Abstract
In recent years' development in nanotechnology utilization of DNA barcodes with potential benefit of nanoparticulate system is a hallmark for novel advancement in healthcare, biomedical and research sector. Interplay of biological barcoding with nanodimensional system encompasses innovative technologies to offer unique advantages of ultra-sensitivity, error-free, accuracy with minimal label reagents, and less time consumption in comparison to conventional techniques like ELISA, PCR, culture media, electrophoresis. DNA barcoding systems used as universal novel tool for identification and multiplex structural detection of proteins, DNAs, toxins, allergens, and nucleic acids of humans, viruses, animals, bacteria, plants as well as personalized treatment in ovarian cancer, AIDS-related Kaposi sarcoma, breast cancer and cardiovascular diseases. Barcoding tools offer substantial attention in drug delivery, in-vivo screening, gene transport for theranostics, bioimaging, and nano-biosensors applications. This review article outlines the recent advances in nano-mediated DNA barcodes to explore various applications in detection of cancer markers, tumor cells, pathogens, allergens, as theranostics, biological sensors, and plant authentication. Furthermore, it summarizes the diverse newer technologies such as bio-barcode amplification (BBA), Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) and CRISPR-Cas9 gene knockout and their applications as sensors for detections of antigens, allergens, and other specimens.
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Affiliation(s)
- Maithili Kantak
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India
| | - Priyanka Batra
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India
| | - Pravin Shende
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS, V. L. Mehta Road, Vile Parle (W), Mumbai, India.
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13
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Aggarwal SD, Lees JA, Jacobs NT, Bee GCW, Abruzzo AR, Weiser JN. BlpC-mediated selfish program leads to rapid loss of Streptococcus pneumoniae clonal diversity during infection. Cell Host Microbe 2023; 31:124-134.e5. [PMID: 36395758 PMCID: PMC9839470 DOI: 10.1016/j.chom.2022.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/27/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022]
Abstract
Successful colonization of a host requires bacterial adaptation through genetic and population changes that are incompletely defined. Using chromosomal barcoding and high-throughput sequencing, we investigate the population dynamics of Streptococcus pneumoniae during infant mouse colonization. Within 1 day post inoculation, diversity was reduced >35-fold with expansion of a single clonal lineage. This loss of diversity was not due to immune factors, microbiota, or exclusive genetic drift. Rather, bacteriocins induced by the BlpC-quorum sensing pheromone resulted in predation of kin cells. In this intra-strain competition, the subpopulation reaching a quorum likely eliminates others that have yet to activate the blp locus. Additionally, this reduced diversity restricts the number of unique clones that establish colonization during transmission between hosts. Genetic variation in the blp locus was also associated with altered transmissibility in a human population, further underscoring the importance of BlpC in clonal selection and its role as a selfish element.
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Affiliation(s)
- Surya D Aggarwal
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - John A Lees
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA; European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK; MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London W12 7TA, UK
| | - Nathan T Jacobs
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Gavyn Chern Wei Bee
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Annie R Abruzzo
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jeffrey N Weiser
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA.
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14
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McMullen JG, Lennon JT. Mark-recapture of microorganisms. Environ Microbiol 2023; 25:150-157. [PMID: 36310117 DOI: 10.1111/1462-2920.16267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 01/21/2023]
Affiliation(s)
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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15
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Ganti K, Bagga A, Carnaccini S, Ferreri LM, Geiger G, Joaquin Caceres C, Seibert B, Li Y, Wang L, Kwon T, Li Y, Morozov I, Ma W, Richt JA, Perez DR, Koelle K, Lowen AC. Influenza A virus reassortment in mammals gives rise to genetically distinct within-host subpopulations. Nat Commun 2022; 13:6846. [PMID: 36369504 PMCID: PMC9652339 DOI: 10.1038/s41467-022-34611-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
Influenza A virus (IAV) genetic exchange through reassortment has the potential to accelerate viral evolution and has played a critical role in the generation of multiple pandemic strains. For reassortment to occur, distinct viruses must co-infect the same cell. The spatio-temporal dynamics of viral dissemination within an infected host therefore define opportunity for reassortment. Here, we used wild type and synonymously barcoded variant viruses of a pandemic H1N1 strain to examine the within-host viral dynamics that govern reassortment in guinea pigs, ferrets and swine. The first two species are well-established models of human influenza, while swine are a natural host and a frequent conduit for cross-species transmission and reassortment. Our results show reassortment to be pervasive in all three hosts but less frequent in swine than in ferrets and guinea pigs. In ferrets, tissue-specific differences in the opportunity for reassortment are also evident, with more reassortants detected in the nasal tract than the lower respiratory tract. While temporal trends in viral diversity are limited, spatial patterns are clear, with heterogeneity in the viral genotypes detected at distinct anatomical sites revealing extensive compartmentalization of reassortment and replication. Our data indicate that the dynamics of viral replication in mammals allow diversification through reassortment but that the spatial compartmentalization of variants likely shapes their evolution and onward transmission.
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Affiliation(s)
- Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anish Bagga
- Emory College of Arts and Sciences, Atlanta, GA, USA
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Lucas M Ferreri
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - C Joaquin Caceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Yonghai Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Liping Wang
- Department of Veterinary Pathobiology, and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Taeyong Kwon
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yuhao Li
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Igor Morozov
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Wenjun Ma
- Department of Veterinary Pathobiology, and Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
- St. Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, TN, USA
| | - Juergen A Richt
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
- St. Jude Center of Excellence for Influenza Research and Response (SJ-CEIRR), Memphis, TN, USA
| | - Daniel R Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
- The Center for Research on Influenza Pathogenesis and Transmission (CRIPT CEIRR), New York, NY, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, USA
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, GA, USA
| | - Anice C Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, GA, USA.
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16
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Wang Q, Olesen AK, Maccario L, Madsen JS. An easily modifiable conjugative plasmid for studying horizontal gene transfer. Plasmid 2022; 123-124:102649. [PMID: 36100085 DOI: 10.1016/j.plasmid.2022.102649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/03/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
Horizontal gene transfer is an important mechanism in bacterial evolution and can occur at striking frequencies when mediated by mobile genetic elements. Conjugative plasmids are mobile genetic elements that are main drivers of horizontal transfer and a major facilitator in the spread of antibiotic resistance genes. However, conjugative plasmid models that readily can be genetically modified with the aim to study horizontal transfer are not currently available. The aim of this study was to develop a conjugative plasmid model where the insertion of gene cassettes such as reporter genes (e.g., fluorescent proteins) or antibiotic resistance genes would be efficient and convenient. Here, we introduced a single attTn7 site into the conjugative broad-host-range IncP-1 plasmid pKJK5 in a non-disruptive manner. Furthermore, a version with lower transfer rate and a non-conjugative version of pKJK5-attTn7 were also constructed. The advantage of having the attTn7 sites is that genes of interest can be introduced in a single step with very high success rate using the Tn7 transposition system. In addition, larger genetic fragments can be inserted. To illustrate the efficacy of the constructed pKJK5 plasmids, they were complemented with sfGFP (a gene encoding superfolder green fluorescent protein) in addition to seven different β-lactamase genes representing the four known classes of β-lactamases.
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Affiliation(s)
- Qinqin Wang
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Asmus Kalckar Olesen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Lorrie Maccario
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
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17
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Brettner L, Ho WC, Schmidlin K, Apodaca S, Eder R, Geiler-Samerotte K. Challenges and potential solutions for studying the genetic and phenotypic architecture of adaptation in microbes. Curr Opin Genet Dev 2022; 75:101951. [PMID: 35797741 DOI: 10.1016/j.gde.2022.101951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 11/29/2022]
Abstract
All organisms are defined by the makeup of their DNA. Over billions of years, the structure and information contained in that DNA, often referred to as genetic architecture, have been honed by a multitude of evolutionary processes. Mutations that cause genetic elements to change in a way that results in beneficial phenotypic change are more likely to survive and propagate through the population in a process known as adaptation. Recent work reveals that the genetic targets of adaptation are varied and can change with genetic background. Further, seemingly similar adaptive mutations, even within the same gene, can have diverse and unpredictable effects on phenotype. These challenges represent major obstacles in predicting adaptation and evolution. In this review, we cover these concepts in detail and identify three emerging synergistic solutions: higher-throughput evolution experiments combined with updated genotype-phenotype mapping strategies and physiological models. Our review largely focuses on recent literature in yeast, and the field seems to be on the cusp of a new era with regard to studying the predictability of evolution.
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18
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Young E, Allen RJ. Lineage dynamics in growing biofilms: Spatial patterns of standing vs. de novo diversity. Front Microbiol 2022; 13:915095. [PMID: 35966660 PMCID: PMC9363821 DOI: 10.3389/fmicb.2022.915095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Microbial biofilms show high phenotypic and genetic diversity, yet the mechanisms underlying diversity generation and maintenance remain unclear. Here, we investigate how spatial patterns of growth activity within a biofilm lead to spatial patterns of genetic diversity. Using individual-based computer simulations, we show that the active layer of growing cells at the biofilm interface controls the distribution of lineages within the biofilm, and therefore the patterns of standing and de novo diversity. Comparing biofilms of equal size, those with a thick active layer retain more standing diversity, while de novo diversity is more evenly distributed within the biofilm. In contrast, equal-sized biofilms with a thin active layer retain less standing diversity, and their de novo diversity is concentrated at the top of the biofilm, and in fewer lineages. In the context of antimicrobial resistance, biofilms with a thin active layer may be more prone to generate lineages with multiple resistance mutations, and to seed new resistant biofilms via sloughing of resistant cells from the upper layers. Our study reveals fundamental "baseline" mechanisms underlying the patterning of diversity within biofilms.
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Affiliation(s)
- Ellen Young
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Rosalind J. Allen
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
- Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
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19
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Emergent evolutionary forces in spatial models of luminal growth and their application to the human gut microbiota. Proc Natl Acad Sci U S A 2022; 119:e2114931119. [PMID: 35787046 PMCID: PMC9282425 DOI: 10.1073/pnas.2114931119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The genetic composition of the gut microbiota is constantly reshaped by ecological and evolutionary forces. These strain-level dynamics are challenging to understand because they depend on complex spatial growth processes that take place within a host. Here we introduce a population genetic framework to predict how stochastic evolutionary forces emerge from simple models of microbial growth in spatially extended environments like the intestinal lumen. Our framework shows how fluid flow and longitudinal variation in growth rate combine to shape the frequencies of genetic variants in simulated fecal samples, yielding analytical expressions for the effective generation times, selection coefficients, and rates of genetic drift. We find that over longer timescales, the emergent evolutionary dynamics can often be captured by well-mixed models that lack explicit spatial structure, even when there is substantial spatial variation in species-level composition. By applying these results to the human colon, we find that continuous fluid flow and simple forms of wall growth alone are unlikely to create sufficient bottlenecks to allow large fluctuations in mutant frequencies within a host. We also find that the effective generation times may be significantly shorter than expected from traditional average growth rate estimates. Our results provide a starting point for quantifying genetic turnover in spatially extended settings like the gut microbiota and may be relevant for other microbial ecosystems where unidirectional fluid flow plays an important role.
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20
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Environmental selection and epistasis in an empirical phenotype-environment-fitness landscape. Nat Ecol Evol 2022; 6:427-438. [PMID: 35210579 DOI: 10.1038/s41559-022-01675-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
Fitness landscapes, mappings of genotype/phenotype to their effects on fitness, are invaluable concepts in evolutionary biochemistry. Although widely discussed, measurements of phenotype-fitness landscapes in proteins remain scarce. Here, we quantify all single mutational effects on fitness and phenotype (EC50) of VIM-2 β-lactamase across a 64-fold range of ampicillin concentrations. We then construct a phenotype-fitness landscape that takes variations in environmental selection pressure into account. We found that a simple, empirical landscape accurately models the ~39,000 mutational data points, suggesting that the evolution of VIM-2 can be predicted on the basis of the selection environment. Our landscape provides new quantitative knowledge on the evolution of the β-lactamases and proteins in general, particularly their evolutionary dynamics under subinhibitory antibiotic concentrations, as well as the mechanisms and environmental dependence of non-specific epistasis.
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21
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Robustness: linking strain design to viable bioprocesses. Trends Biotechnol 2022; 40:918-931. [PMID: 35120750 DOI: 10.1016/j.tibtech.2022.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/18/2022]
Abstract
Microbial cell factories are becoming increasingly popular for the sustainable production of various chemicals. Metabolic engineering has led to the design of advanced cell factories; however, their long-term yield, titer, and productivity falter when scaled up and subjected to industrial conditions. This limitation arises from a lack of robustness - the ability to maintain a constant phenotype despite the perturbations of such processes. This review describes predictable and stochastic industrial perturbations as well as state-of-the-art technologies to counter process variability. Moreover, we distinguish robustness from tolerance and discuss the potential of single-cell studies for improving system robustness. Finally, we highlight ways of achieving consistent and comparable quantification of robustness that can guide the selection of strains for industrial bioprocesses.
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22
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Hogle SL, Hepolehto I, Ruokolainen L, Cairns J, Hiltunen T. Effects of phenotypic variation on consumer coexistence and prey community structure. Ecol Lett 2021; 25:307-319. [PMID: 34808704 PMCID: PMC9299012 DOI: 10.1111/ele.13924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/06/2021] [Accepted: 10/15/2021] [Indexed: 12/29/2022]
Abstract
A popular idea in ecology is that trait variation among individuals from the same species may promote the coexistence of competing species. However, theoretical and empirical tests of this idea have yielded inconsistent findings. We manipulated intraspecific trait diversity in a ciliate competing with a nematode for bacterial prey in experimental microcosms. We found that intraspecific trait variation inverted the original competitive hierarchy to favour the consumer with variable traits, ultimately resulting in competitive exclusion. This competitive outcome was driven by foraging traits (size, speed and directionality) that increased the ciliate's fitness ratio and niche overlap with the nematode. The interplay between consumer trait variation and competition resulted in non‐additive cascading effects—mediated through prey defence traits—on prey community assembly. Our results suggest that predicting consumer competitive population dynamics and the assembly of prey communities will require understanding the complexities of trait variation within consumer species.
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Affiliation(s)
- Shane L Hogle
- Department of Biology, University of Turku, Turku, Finland
| | - Iina Hepolehto
- Department of Microbiology, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lasse Ruokolainen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Johannes Cairns
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland.,Department of Computer Science, University of Helsinki, Finland
| | - Teppo Hiltunen
- Department of Biology, University of Turku, Turku, Finland
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23
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Hullahalli K, Waldor MK. Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during murine systemic infection. eLife 2021; 10:e70910. [PMID: 34636322 PMCID: PMC8545400 DOI: 10.7554/elife.70910] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022] Open
Abstract
The dissemination of pathogens through blood and their establishment within organs lead to severe clinical outcomes. However, the within-host dynamics that underlie pathogen spread to and clearance from systemic organs remain largely uncharacterized. In animal models of infection, the observed pathogen population results from the combined contributions of bacterial replication, persistence, death, and dissemination, each of which can vary across organs. Quantifying the contribution of each these processes is required to interpret and understand experimental phenotypes. Here, we leveraged STAMPR, a new barcoding framework, to investigate the population dynamics of extraintestinal pathogenic Escherichia coli, a common cause of bacteremia, during murine systemic infection. We show that while bacteria are largely cleared by most organs, organ-specific clearance failures are pervasive and result from dramatic expansions of clones representing less than 0.0001% of the inoculum. Clonal expansion underlies the variability in bacterial burden between animals, and stochastic dissemination of clones profoundly alters the pathogen population structure within organs. Despite variable pathogen expansion events, host bottlenecks are consistent yet highly sensitive to infection variables, including inoculum size and macrophage depletion. We adapted our barcoding methodology to facilitate multiplexed validation of bacterial fitness determinants identified with transposon mutagenesis and confirmed the importance of bacterial hexose metabolism and cell envelope homeostasis pathways for organ-specific pathogen survival. Collectively, our findings provide a comprehensive map of the population biology that underlies bacterial systemic infection and a framework for barcode-based high-resolution mapping of infection dynamics.
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Affiliation(s)
- Karthik Hullahalli
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Division of Infectious Diseases, Brigham & Women’s HospitalBostonUnited States
| | - Matthew K Waldor
- Department of Microbiology, Harvard Medical SchoolBostonUnited States
- Division of Infectious Diseases, Brigham & Women’s HospitalBostonUnited States
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24
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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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25
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26
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Kasimatis KR, Sánchez-Ramírez S, Stevenson ZC. Sexual Dimorphism through the Lens of Genome Manipulation, Forward Genetics, and Spatiotemporal Sequencing. Genome Biol Evol 2021; 13:evaa243. [PMID: 33587127 PMCID: PMC7883666 DOI: 10.1093/gbe/evaa243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2020] [Indexed: 11/14/2022] Open
Abstract
Sexual reproduction often leads to selection that favors the evolution of sex-limited traits or sex-specific variation for shared traits. These sexual dimorphisms manifest due to sex-specific genetic architectures and sex-biased gene expression across development, yet the molecular mechanisms underlying these patterns are largely unknown. The first step is to understand how sexual dimorphisms arise across the genotype-phenotype-fitness map. The emergence of "4D genome technologies" allows for efficient, high-throughput, and cost-effective manipulation and observations of this process. Studies of sexual dimorphism will benefit from combining these technological advances (e.g., precision genome editing, inducible transgenic systems, and single-cell RNA sequencing) with clever experiments inspired by classic designs (e.g., bulked segregant analysis, experimental evolution, and pedigree tracing). This perspective poses a synthetic view of how manipulative approaches coupled with cutting-edge observational methods and evolutionary theory are poised to uncover the molecular genetic basis of sexual dimorphism with unprecedented resolution. We outline hypothesis-driven experimental paradigms for identifying genetic mechanisms of sexual dimorphism among tissues, across development, and over evolutionary time.
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Affiliation(s)
- Katja R Kasimatis
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, USA
| | | | - Zachary C Stevenson
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
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27
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Cairns J, Jokela R, Becks L, Mustonen V, Hiltunen T. Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation. Nat Ecol Evol 2020; 4:1385-1394. [PMID: 32778754 DOI: 10.1038/s41559-020-1272-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/03/2020] [Indexed: 12/31/2022]
Abstract
In an era of pervasive anthropogenic ecological disturbances, there is a pressing need to understand the factors that constitute community response and resilience. A detailed understanding of disturbance response needs to go beyond associations and incorporate features of disturbances, species traits, rapid evolution and dispersal. Multispecies microbial communities that experience antibiotic perturbation represent a key system with important medical dimensions. However, previous microbiome studies on this theme have relied on high-throughput sequencing data from uncultured species without the ability to explicitly account for the role of species traits and immigration. Here, we serially passage a 34-species defined bacterial community through different levels of pulse antibiotic disturbance, manipulating the presence or absence of species immigration. To understand the ecological community response measured using amplicon sequencing, we combine initial trait data measured for each species separately and metagenome sequencing data revealing adaptive mutations during the experiment. We found that the ecological community response was highly repeatable within the experimental treatments, which could be attributed in part to key species traits (antibiotic susceptibility and growth rate). Increasing antibiotic levels were also coupled with an increasing probability of species extinction, making species immigration critical for community resilience. Moreover, we detected signals of antibiotic-resistance evolution occurring within species at the same time scale, leaving evolutionary changes in communities despite recovery at the species compositional level. Together, these observations reveal a disturbance response that presents as classic species sorting, but is nevertheless accompanied by rapid within-species evolution.
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Affiliation(s)
- Johannes Cairns
- Wellcome Sanger Institute, Cambridge, UK. .,Organismal and Evolutionary Biology Research Programme (OEB), Department of Computer Science, University of Helsinki, Helsinki, Finland. .,Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Roosa Jokela
- Department of Microbiology, University of Helsinki, Helsinki, Finland.,Human Microbiome Research Program (HUMI), Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lutz Becks
- Community Dynamics Group, Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Aquatic Ecology and Evolution, Limnological Institute University Konstanz, Konstanz, Germany
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme (OEB), Department of Computer Science, University of Helsinki, Helsinki, Finland.,Helsinki Institute for Information Technology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Teppo Hiltunen
- Department of Microbiology, University of Helsinki, Helsinki, Finland. .,Department of Biology, University of Turku, Turku, Finland.
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28
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van Dijk B, Hogeweg P, Doekes HM, Takeuchi N. Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements. eLife 2020; 9:e56801. [PMID: 32432548 PMCID: PMC7316506 DOI: 10.7554/elife.56801] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/15/2020] [Indexed: 12/11/2022] Open
Abstract
Horizontal gene transfer (HGT) and gene loss result in rapid changes in the gene content of bacteria. While HGT aids bacteria to adapt to new environments, it also carries risks such as selfish genetic elements (SGEs). Here, we use modelling to study how HGT of slightly beneficial genes impacts growth rates of bacterial populations, and if bacterial collectives can evolve to take up DNA despite selfish elements. We find four classes of slightly beneficial genes: indispensable, enrichable, rescuable, and unrescuable genes. Rescuable genes - genes with small fitness benefits that are lost from the population without HGT - can be collectively retained by a community that engages in costly HGT. While this 'gene-sharing' cannot evolve in well-mixed cultures, it does evolve in a spatial population like a biofilm. Despite enabling infection by harmful SGEs, the uptake of foreign DNA is evolutionarily maintained by the hosts, explaining the coexistence of bacteria and SGEs.
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Affiliation(s)
- Bram van Dijk
- Utrecht University, Theoretical BiologyUtrechtNetherlands
| | | | - Hilje M Doekes
- Utrecht University, Theoretical BiologyUtrechtNetherlands
| | - Nobuto Takeuchi
- University of Auckland, Biological SciencesAucklandNew Zealand
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