1
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Voogdt CGP, Tripathi S, Bassler SO, McKeithen-Mead SA, Guiberson ER, Koumoutsi A, Bravo AM, Buie C, Zimmermann M, Sonnenburg JL, Typas A, Deutschbauer AM, Shiver AL, Huang KC. Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics. Cell Rep 2024; 43:113519. [PMID: 38142398 DOI: 10.1016/j.celrep.2023.113519] [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: 07/17/2023] [Revised: 10/22/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
The critical role of the intestinal microbiota in human health and disease is well recognized. Nevertheless, there are still large gaps in our understanding of the functions and mechanisms encoded in the genomes of most members of the gut microbiota. Genome-scale libraries of transposon mutants are a powerful tool to help us address this gap. Recent advances in barcoded transposon mutagenesis have dramatically lowered the cost of mutant fitness determination in hundreds of in vitro and in vivo experimental conditions. In an accompanying review, we discuss recent advances and caveats for the construction of pooled and arrayed barcoded transposon mutant libraries in human gut commensals. In this review, we discuss how these libraries can be used across a wide range of applications, the technical aspects involved, and expectations for such screens.
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Affiliation(s)
- Carlos Geert Pieter Voogdt
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stefan Oliver Bassler
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, Grabengasse 1, 69117 Heidelberg, Germany
| | - Saria A McKeithen-Mead
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emma R Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Koumoutsi
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Afonso Martins Bravo
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Cullen Buie
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Athanasios Typas
- Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Structural and Computational Biology Unit, EMBL, Heidelberg, Germany.
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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2
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Shiver AL, Sun J, Culver R, Violette A, Wynter C, Nieckarz M, Mattiello SP, Sekhon PK, Friess L, Carlson HK, Wong D, Higginbottom S, Weglarz M, Wang W, Knapp BD, Guiberson E, Sanchez J, Huang PH, Garcia PA, Buie CR, Good B, DeFelice B, Cava F, Scaria J, Sonnenburg J, Sinderen DV, Deutschbauer AM, Huang KC. A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555234. [PMID: 37693407 PMCID: PMC10491234 DOI: 10.1101/2023.08.29.555234] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Bifidobacteria commonly represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest as a probiotic therapy, predicting the nutritional requirements and health-promoting effects of Bifidobacteria is challenging due to major knowledge gaps. To overcome these deficiencies, we used large-scale genetics to create a compendium of mutant fitness in Bifidobacterium breve (Bb). We generated a high density, randomly barcoded transposon insertion pool in Bb, and used this pool to determine Bb fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. To enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1462 genes. We leveraged these tools to improve models of metabolic pathways, reveal unexpected host- and diet-specific requirements for colonization, and connect the production of immunomodulatory molecules to growth benefits. These resources will greatly reduce the barrier to future investigations of this important beneficial microbe.
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Affiliation(s)
- Anthony L. Shiver
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Rebecca Culver
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Arvie Violette
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Charles Wynter
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
| | - Marta Nieckarz
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Samara Paula Mattiello
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- College of Mathematics and Science, The University of Tennessee Southern, Pulaski TN 38478, USA
| | - Prabhjot Kaur Sekhon
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Lisa Friess
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Hans K. Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Daniel Wong
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
| | - Steven Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, California, USA
| | - Weigao Wang
- Department of Chemical Engineering, Stanford University, Stanford CA 94305, USA
| | | | - Emma Guiberson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Po-Hsun Huang
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Paulo A. Garcia
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Cullen R. Buie
- Department of Mechanical Engineering, Laboratory for Energy and Microsystems Innovation, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, 02139, MA, USA
| | - Benjamin Good
- Department of Applied Physics, Stanford University, Stanford CA 94305, USA
| | | | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, SE-90187, Sweden
| | - Joy Scaria
- Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK, 74074, USA
| | - Justin Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Douwe Van Sinderen
- School of Microbiology, University College Cork, Ireland
- APC Microbiome Ireland, University College Cork, Ireland
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158
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3
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Dudek NK, Galaz-Montoya JG, Shi H, Mayer M, Danita C, Celis AI, Viehboeck T, Wu GH, Behr B, Bulgheresi S, Huang KC, Chiu W, Relman DA. Previously uncharacterized rectangular bacterial structures in the dolphin mouth. Nat Commun 2023; 14:2098. [PMID: 37055390 PMCID: PMC10102025 DOI: 10.1038/s41467-023-37638-y] [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: 11/01/2021] [Accepted: 03/23/2023] [Indexed: 04/15/2023] Open
Abstract
Much remains to be explored regarding the diversity of uncultured, host-associated microbes. Here, we describe rectangular bacterial structures (RBSs) in the mouths of bottlenose dolphins. DNA staining revealed multiple paired bands within RBSs, suggesting the presence of cells dividing along the longitudinal axis. Cryogenic transmission electron microscopy and tomography showed parallel membrane-bound segments that are likely cells, encapsulated by an S-layer-like periodic surface covering. RBSs displayed unusual pilus-like appendages with bundles of threads splayed at the tips. We present multiple lines of evidence, including genomic DNA sequencing of micromanipulated RBSs, 16S rRNA gene sequencing, and fluorescence in situ hybridization, suggesting that RBSs are bacterial and distinct from the genera Simonsiella and Conchiformibius (family Neisseriaceae), with which they share similar morphology and division patterning. Our findings highlight the diversity of novel microbial forms and lifestyles that await characterization using tools complementary to genomics such as microscopy.
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Affiliation(s)
- Natasha K Dudek
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
- Quantori, Cambridge, MA, 02142, USA
| | | | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Megan Mayer
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Cristina Danita
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Arianna I Celis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tobias Viehboeck
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, and Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Gong-Her Wu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Barry Behr
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Silvia Bulgheresi
- Department of Functional and Evolutionary Ecology, Environmental Cell Biology Group, University of Vienna, Vienna, Austria
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA.
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4
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Zhang J, Xue J, Luo N, Chen F, Chen B, Zhao Y. Microwell array chip-based single-cell analysis. LAB ON A CHIP 2023; 23:1066-1079. [PMID: 36625143 DOI: 10.1039/d2lc00667g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell profiling is key to uncover the cellular heterogeneity and drives deep understanding of cell fate. In recent years, microfluidics has become an ideal tool for single-cell profiling owing to its benefits of high throughput and automation. Among various microfluidic platforms, microwell has the advantages of simple operation and easy integration with in situ analysis ability, making it an ideal technique for single-cell studies. Herein, recent advances of single-cell analysis based on microwell array chips are summarized. We first introduce the design and preparation of different microwell chips. Then microwell-based cell capture and lysis strategies are discussed. We finally focus on advanced microwell-based analysis of single-cell proteins, nucleic acids, and metabolites. The challenges and opportunities for the development of microwell-based single-cell analysis are also presented.
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Affiliation(s)
- Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Ningfeng Luo
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Badong Chen
- Institute of Artificial Intelligence and Robotics and the College of Artificial Intelligence, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
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5
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Arjes HA, Sun J, Liu H, Nguyen TH, Culver RN, Celis AI, Walton SJ, Vasquez KS, Yu FB, Xue KS, Newton D, Zermeno R, Weglarz M, Deutschbauer A, Huang KC, Shiver AL. Construction and characterization of a genome-scale ordered mutant collection of Bacteroides thetaiotaomicron. BMC Biol 2022; 20:285. [PMID: 36527020 PMCID: PMC9758874 DOI: 10.1186/s12915-022-01481-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Ordered transposon-insertion collections, in which specific transposon-insertion mutants are stored as monocultures in a genome-scale collection, represent a promising tool for genetic dissection of human gut microbiota members. However, publicly available collections are scarce and the construction methodology remains in early stages of development. RESULTS Here, we describe the assembly of a genome-scale ordered collection of transposon-insertion mutants in the model gut anaerobe Bacteroides thetaiotaomicron VPI-5482 that we created as a resource for the research community. We used flow cytometry to sort single cells from a pooled library, located mutants within this initial progenitor collection by applying a pooling strategy with barcode sequencing, and re-arrayed specific mutants to create a condensed collection with single-insertion strains covering >2500 genes. To demonstrate the potential of the condensed collection for phenotypic screening, we analyzed growth dynamics and cell morphology. We identified both growth defects and altered cell shape in mutants disrupting sphingolipid synthesis and thiamine scavenging. Finally, we analyzed the process of assembling the B. theta condensed collection to identify inefficiencies that limited coverage. We demonstrate as part of this analysis that the process of assembling an ordered collection can be accurately modeled using barcode sequencing data. CONCLUSION We expect that utilization of this ordered collection will accelerate research into B. theta physiology and that lessons learned while assembling the collection will inform future efforts to assemble ordered mutant collections for an increasing number of gut microbiota members.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Rebecca N Culver
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Arianna I Celis
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sophie Jean Walton
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Katherine S Xue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel Newton
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ricardo Zermeno
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Meredith Weglarz
- Stanford Shared FACS Facility, Center for Molecular and Genetic Medicine, Stanford University, Stanford, CA, USA
| | - Adam Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Biophysics Training Program, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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6
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Thomson EE, Harfouche M, Kim K, Konda PC, Seitz CW, Cooke C, Xu S, Jacobs WS, Blazing R, Chen Y, Sharma S, Dunn TW, Park J, Horstmeyer RW, Naumann EA. Gigapixel imaging with a novel multi-camera array microscope. eLife 2022; 11:e74988. [PMID: 36515989 PMCID: PMC9917455 DOI: 10.7554/elife.74988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
The dynamics of living organisms are organized across many spatial scales. However, current cost-effective imaging systems can measure only a subset of these scales at once. We have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from structures that approach the cellular scale to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies with a field of view over hundreds of square centimeters at an optical resolution of 18 µm. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. Further, the MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Overall, by removing the bottlenecks imposed by single-camera image acquisition systems, the MCAM provides a powerful platform for investigating detailed biological features and behavioral processes of small model organisms across a wide range of spatial scales.
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Affiliation(s)
- Eric E Thomson
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | | | - Kanghyun Kim
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Pavan C Konda
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Catherine W Seitz
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Colin Cooke
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Shiqi Xu
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Whitney S Jacobs
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Robin Blazing
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Yang Chen
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | | | - Timothy W Dunn
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | | | - Roarke W Horstmeyer
- Ramona Optics IncDurhamUnited States
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Eva A Naumann
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
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7
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Aranda-Díaz A, Ng KM, Thomsen T, Real-Ramírez I, Dahan D, Dittmar S, Gonzalez CG, Chavez T, Vasquez KS, Nguyen TH, Yu FB, Higginbottom SK, Neff NF, Elias JE, Sonnenburg JL, Huang KC. Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota. Cell Host Microbe 2022; 30:260-272.e5. [PMID: 35051349 PMCID: PMC9082339 DOI: 10.1016/j.chom.2021.12.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/27/2021] [Accepted: 12/10/2021] [Indexed: 12/16/2022]
Abstract
Efforts to probe the role of the gut microbiota in disease would benefit from a system in which patient-derived bacterial communities can be studied at scale. We addressed this by validating a strategy to propagate phylogenetically complex, diverse, stable, and highly reproducible stool-derived communities in vitro. We generated hundreds of in vitro communities cultured from diverse stool samples in various media; certain media generally preserved inoculum composition, and inocula from different subjects yielded source-specific community compositions. Upon colonization of germ-free mice, community composition was maintained, and the host proteome resembled the host from which the community was derived. Treatment with ciprofloxacin in vivo increased susceptibility to Salmonella invasion in vitro, and the in vitro response to ciprofloxacin was predictive of compositional changes observed in vivo, including the resilience and sensitivity of each Bacteroides species. These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.
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Affiliation(s)
- Andrés Aranda-Díaz
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Tani Thomsen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Dylan Dahan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susannah Dittmar
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Carlos Gutierrez Gonzalez
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taylor Chavez
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Taylor H Nguyen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Norma F Neff
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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8
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Sun J, Shi H, Huang KC. Hyperosmotic Shock Transiently Accelerates Constriction Rate in Escherichia coli. Front Microbiol 2021; 12:718600. [PMID: 34489908 PMCID: PMC8418109 DOI: 10.3389/fmicb.2021.718600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial cells in their natural environments encounter rapid and large changes in external osmolality. For instance, enteric bacteria such as Escherichia coli experience a rapid decrease when they exit from host intestines. Changes in osmolality alter the mechanical load on the cell envelope, and previous studies have shown that large osmotic shocks can slow down bacterial growth and impact cytoplasmic diffusion. However, it remains unclear how cells maintain envelope integrity and regulate envelope synthesis in response to osmotic shocks. In this study, we developed an agarose pad-based protocol to assay envelope stiffness by measuring population-averaged cell length before and after a hyperosmotic shock. Pad-based measurements exhibited an apparently larger length change compared with single-cell dynamics in a microfluidic device, which we found was quantitatively explained by a transient increase in division rate after the shock. Inhibiting cell division led to consistent measurements between agarose pad-based and microfluidic measurements. Directly after hyperosmotic shock, FtsZ concentration and Z-ring intensity increased, and the rate of septum constriction increased. These findings establish an agarose pad-based protocol for quantifying cell envelope stiffness, and demonstrate that mechanical perturbations can have profound effects on bacterial physiology.
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Affiliation(s)
- Jiawei Sun
- Department of Bioengineering, Stanford University, Stanford, CA, United States
| | - Handuo Shi
- Department of Bioengineering, Stanford University, Stanford, CA, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, United States.,Chan Zuckerberg Biohub, San Francisco, CA, United States
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9
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Han K, Sun M, Zhang J, Fu W, Hu R, Liu D, Liu W. Large-scale investigation of single cell activities and response dynamics in a microarray chip with a microfluidics-fabricated microporous membrane. Analyst 2021; 146:4303-4313. [PMID: 34105525 DOI: 10.1039/d1an00784j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microengineering technology involving microfabrication, micropatterning and microfluidics enables promising advances in single cell manipulation and analysis. Herein, we describe a parallel, large-scale, and temporal investigation of diverse single cell activities and response dynamics using a facile-assembled microwell array chip with a microfluidics-molded microporous membrane. We demonstrated that the versatility with respect to geometrical homogeneity and diversity of microporous membrane fabrication, as well as the stability, repeatability, and reproducibility rely on the well-improved molding. Serial and practical operations including controllable single cell trapping, array-like culture or chemical stimulation, and temporal monitoring can be smoothly completed in the chip. We confirmed that the microwell array chip allowed an efficient construction of a single cell array. Using the cell array, on-chip detection of single cell behaviours under various culture and drug therapy conditions to explore phenotypic heterogeneity was achieved in massive and dynamic manners. These achievements provide a facile and reliable methodology for fabricating microporous membranes with precise control and for developing universal microplatforms to perform robust manipulation and versatile analysis of single cells. This work also offers an insight into the development of easy to fabricate/use and market-oriented microsystems for single cell research, pharmaceutical development, and high-throughput screening.
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Affiliation(s)
- Kai Han
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China.
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10
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Zhu L, Rajendram M, Huang KC. Effects of fixation on bacterial cellular dimensions and integrity. iScience 2021; 24:102348. [PMID: 33912815 PMCID: PMC8066382 DOI: 10.1016/j.isci.2021.102348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/25/2021] [Accepted: 03/18/2021] [Indexed: 11/22/2022] Open
Abstract
Fixation facilitates imaging of subcellular localization and cell morphology, yet it remains unknown how fixation affects cellular dimensions and intracellular fluorescence patterns, particularly during long-term storage. Here, we characterized the effects of multiple fixatives on several bacterial species. Fixation generally reduced cell length by 5-15%; single-cell tracking in microfluidics revealed that the length decrease was an aggregate effect of many steps in the fixation protocol and that fluorescence of cytoplasmic GFP but not membrane-bound MreB-msfGFP was rapidly lost with formaldehyde-based fixatives. Cellular dimensions were preserved in formaldehyde-based fixatives for ≥4 days, but methanol caused length to decrease. Although methanol preserved cytoplasmic fluorescence better than formaldehyde-based fixatives, some Escherichia coli cells were able to grow directly after fixation. Moreover, methanol fixation caused lysis in a subpopulation of cells, with virtually all Bacillus subtilis cells lysing after one day. These findings highlight tradeoffs between maintenance of fluorescence and membrane integrity for future applications of fixation.
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Affiliation(s)
- Lillian Zhu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Manohary Rajendram
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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11
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Lawson M, Elf J. Imaging-based screens of pool-synthesized cell libraries. Nat Methods 2021; 18:358-365. [PMID: 33589838 DOI: 10.1038/s41592-020-01053-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Mapping a genetic perturbation to a change in phenotype is at the core of biological research. Advances in microscopy have transformed these studies, but they have largely been confined to examining a few strains or cell lines at a time. In parallel, there has been a revolution in creating synthetic libraries of genetically altered cells with relative ease. Here we describe methods that combine these powerful tools to perform live-cell imaging of pool-generated strain libraries for improved biological discovery.
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Affiliation(s)
- Michael Lawson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Johan Elf
- Department of Cell and Molecular Biology Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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12
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Cambré A, Aertsen A. Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria. Microbiol Mol Biol Rev 2020; 84:e00008-20. [PMID: 33115939 PMCID: PMC7599038 DOI: 10.1128/mmbr.00008-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The rise in fluorescence-based imaging techniques over the past 3 decades has improved the ability of researchers to scrutinize live cell biology at increased spatial and temporal resolution. In microbiology, these real-time vivisections structurally changed the view on the bacterial cell away from the "watery bag of enzymes" paradigm toward the perspective that these organisms are as complex as their eukaryotic counterparts. Capitalizing on the enormous potential of (time-lapse) fluorescence microscopy and the ever-extending pallet of corresponding probes, initial breakthroughs were made in unraveling the localization of proteins and monitoring real-time gene expression. However, later it became clear that the potential of this technique extends much further, paving the way for a focus-shift from observing single events within bacterial cells or populations to obtaining a more global picture at the intra- and intercellular level. In this review, we outline the current state of the art in fluorescence-based vivisection of bacteria and provide an overview of important case studies to exemplify how to use or combine different strategies to gain detailed information on the cell's physiology. The manuscript therefore consists of two separate (but interconnected) parts that can be read and consulted individually. The first part focuses on the fluorescent probe pallet and provides a perspective on modern methodologies for microscopy using these tools. The second section of the review takes the reader on a tour through the bacterial cell from cytoplasm to outer shell, describing strategies and methods to highlight architectural features and overall dynamics within cells.
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Affiliation(s)
- Alexander Cambré
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
| | - Abram Aertsen
- KU Leuven, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, Leuven, Belgium
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13
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de Wet TJ, Winkler KR, Mhlanga M, Mizrahi V, Warner DF. Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes. eLife 2020; 9:e60083. [PMID: 33155979 PMCID: PMC7647400 DOI: 10.7554/elife.60083] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/03/2020] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium tuberculosis possesses a large number of genes of unknown or predicted function, undermining fundamental understanding of pathogenicity and drug susceptibility. To address this challenge, we developed a high-throughput functional genomics approach combining inducible CRISPR-interference and image-based analyses of morphological features and sub-cellular chromosomal localizations in the related non-pathogen, M. smegmatis. Applying automated imaging and analysis to 263 essential gene knockdown mutants in an arrayed library, we derive robust, quantitative descriptions of bacillary morphologies consequent on gene silencing. Leveraging statistical-learning, we demonstrate that functionally related genes cluster by morphotypic similarity and that this information can be used to inform investigations of gene function. Exploiting this observation, we infer the existence of a mycobacterial restriction-modification system, and identify filamentation as a defining mycobacterial response to histidine starvation. Our results support the application of large-scale image-based analyses for mycobacterial functional genomics, simultaneously establishing the utility of this approach for drug mechanism-of-action studies.
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Affiliation(s)
- Timothy J de Wet
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Kristy R Winkler
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
| | - Musa Mhlanga
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Department of Integrative Biomedical Sciences, University of Cape TownCape TownSouth Africa
| | - Valerie Mizrahi
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape TownCape TownSouth Africa
| | - Digby F Warner
- SAMRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Department of Pathology, University of Cape TownCape TownSouth Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape TownSouth Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape TownCape TownSouth Africa
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14
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Yan Y, Nguyen LH, Franzosa EA, Huttenhower C. Strain-level epidemiology of microbial communities and the human microbiome. Genome Med 2020; 12:71. [PMID: 32791981 PMCID: PMC7427293 DOI: 10.1186/s13073-020-00765-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023] Open
Abstract
The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and “culturomics” technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.
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Affiliation(s)
- Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, MA, 02115, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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15
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Arjes HA, Vo L, Dunn CM, Willis L, DeRosa CA, Fraser CL, Kearns DB, Huang KC. Biosurfactant-Mediated Membrane Depolarization Maintains Viability during Oxygen Depletion in Bacillus subtilis. Curr Biol 2020; 30:1011-1022.e6. [PMID: 32059765 PMCID: PMC7153240 DOI: 10.1016/j.cub.2020.01.073] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/09/2019] [Accepted: 01/23/2020] [Indexed: 12/26/2022]
Abstract
The presence or absence of oxygen in the environment is a strong effector of cellular metabolism and physiology. Like many eukaryotes and some bacteria, Bacillus subtilis primarily utilizes oxygen during respiration to generate ATP. Despite the importance of oxygen for B. subtilis survival, we know little about how populations adapt to shifts in oxygen availability. Here, we find that when oxygen was depleted from stationary phase B. subtilis cultures, ∼90% of cells died while the remaining cells maintained colony-forming ability. We discover that production of the antimicrobial surfactin confers two oxygen-related fitness benefits: it increases aerobic growth yield by increasing oxygen diffusion, and it maintains viability during oxygen depletion by depolarizing the membrane. Strains unable to produce surfactin exhibited an ∼50-fold reduction in viability after oxygen depletion. Surfactin treatment of these cells led to membrane depolarization and reduced ATP production. Chemical and genetic perturbations that alter oxygen consumption or redox state support a model in which surfactin-mediated membrane depolarization maintains viability through slower oxygen consumption and/or a shift to a more reduced metabolic profile. These findings highlight the importance of membrane potential in regulating cell physiology and growth, and demonstrate that antimicrobials that depolarize cell membranes can benefit cells when the terminal electron acceptor in respiration is limiting. This foundational knowledge has deep implications for environmental microbiology, clinical anti-bacterial therapy, and industrial biotechnology.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Lam Vo
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Caroline M Dunn
- Department of Biology, 1001 E 3rd Street, Indiana University, Bloomington, IN 47405, USA
| | - Lisa Willis
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Christopher A DeRosa
- Department of Chemistry, McCormick Road, University of Virginia, Charlottesville, VA 22904, USA
| | - Cassandra L Fraser
- Department of Chemistry, McCormick Road, University of Virginia, Charlottesville, VA 22904, USA
| | - Daniel B Kearns
- Department of Biology, 1001 E 3rd Street, Indiana University, Bloomington, IN 47405, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA.
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16
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Zahir T, Camacho R, Vitale R, Ruckebusch C, Hofkens J, Fauvart M, Michiels J. High-throughput time-resolved morphology screening in bacteria reveals phenotypic responses to antibiotics. Commun Biol 2019; 2:269. [PMID: 31341968 PMCID: PMC6650389 DOI: 10.1038/s42003-019-0480-9] [Citation(s) in RCA: 25] [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: 03/03/2019] [Accepted: 05/21/2019] [Indexed: 11/09/2022] Open
Abstract
Image-based high-throughput screening strategies for quantifying morphological phenotypes have proven widely successful. Here we describe a combined experimental and multivariate image analysis approach for systematic large-scale phenotyping of morphological dynamics in bacteria. Using off-the-shelf components and software, we established a workflow for high-throughput time-resolved microscopy. We then screened the single-gene deletion collection of Escherichia coli for antibiotic-induced morphological changes. Using single-cell quantitative descriptors and supervised classification methods, we measured how different cell morphologies developed over time for all strains in response to the β-lactam antibiotic cefsulodin. 191 strains exhibit significant variations under antibiotic treatment. Phenotypic clustering provided insights into processes that alter the antibiotic response. Mutants with stable bulges show delayed lysis, contributing to antibiotic tolerance. Lipopolysaccharides play a crucial role in bulge stability. This study demonstrates how multiparametric phenotyping by high-throughput time-resolved imaging and computer-aided cell classification can be used for comprehensively studying dynamic morphological transitions in bacteria.
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Affiliation(s)
- Taiyeb Zahir
- Centre of Microbial and Plant Genetics, KU Leuven—University of Leuven, Leuven, 3001 Belgium
- VIB-KU Leuven Center of Microbiology, Leuven, 3001 Belgium
| | - Rafael Camacho
- Department of Chemistry, KU Leuven—University of Leuven, Leuven, 3001 Belgium
| | - Raffaele Vitale
- Department of Chemistry, KU Leuven—University of Leuven, Leuven, 3001 Belgium
- LASIR CNRS, Université de Lille, Lille, F-59000 France
| | | | - Johan Hofkens
- Department of Chemistry, KU Leuven—University of Leuven, Leuven, 3001 Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven—University of Leuven, Leuven, 3001 Belgium
- VIB-KU Leuven Center of Microbiology, Leuven, 3001 Belgium
- imec, Leuven, 3001 Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven—University of Leuven, Leuven, 3001 Belgium
- VIB-KU Leuven Center of Microbiology, Leuven, 3001 Belgium
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17
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Godinez WJ, Chan H, Hossain I, Li C, Ranjitkar S, Rasper D, Simmons RL, Zhang X, Feng BY. Morphological Deconvolution of Beta-Lactam Polyspecificity in E. coli. ACS Chem Biol 2019; 14:1217-1226. [PMID: 31184469 DOI: 10.1021/acschembio.9b00141] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Beta-lactams comprise one of the earliest classes of antibiotic therapies. These molecules covalently inhibit enzymes from the family of penicillin-binding proteins (PBPs), which are essential in construction of the bacterial cell wall. As a result, beta-lactams cause striking changes to cellular morphology, the nature of which varies by the range of PBPs simultaneously engaged in the cell. The traditional method of exploring beta-lactam polyspecificity is a gel-based binding assay which is low-throughput and typically is run ex situ in cell extracts. Here, we describe a medium-throughput, image-based assay combined with machine learning methods to automatically profile the activity of beta-lactams in E. coli cells. By testing for morphological change across a panel of strains with perturbations to individual PBP enzymes, our approach automatically and quantifiably relates different beta-lactam antibiotics according to their preferences for individual PBPs in cells. We show the potential of our approach for guiding the design of novel inhibitors toward different PBP-binding profiles by predicting the mechanisms of two recently reported PBP inhibitors.
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Affiliation(s)
- William J. Godinez
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Basel, Switzerland
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States
| | - Helen Chan
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States
| | - Imtiaz Hossain
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Cindy Li
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States
| | - Srijan Ranjitkar
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States
| | - Dita Rasper
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States
| | - Robert L. Simmons
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States
| | - Xian Zhang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Brian Y. Feng
- Infectious Diseases, Novartis Institutes for BioMedical Research, Emeryville, California, United States
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18
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Hart SFM, Skelding D, Waite AJ, Burton JC, Shou W. High-throughput quantification of microbial birth and death dynamics using fluorescence microscopy. QUANTITATIVE BIOLOGY 2019; 7:69-81. [PMID: 31598381 PMCID: PMC6785046 DOI: 10.1007/s40484-018-0160-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 08/31/2018] [Accepted: 09/21/2018] [Indexed: 10/27/2022]
Abstract
BACKGROUND Microbes live in dynamic environments where nutrient concentrations fluctuate. Quantifying fitness in terms of birth rate and death rate in a wide range of environments is critical for understanding microbial evolution and ecology. METHODS Here, using high-throughput time-lapse microscopy, we have quantified how Saccharomyces cerevisiae mutants incapable of synthesizing an essential metabolite (auxotrophs) grow or die in various concentrations of the required metabolite. We establish that cells normally expressing fluorescent proteins lose fluorescence upon death and that the total fluorescence in an imaging frame is proportional to the number of live cells even when cells form multiple layers. We validate our microscopy approach of measuring birth and death rates using flow cytometry, cell counting, and chemostat culturing. RESULTS For lysine-requiring cells, very low concentrations of lysine are not detectably consumed and do not support cell birth, but delay the onset of death phase and reduce the death rate compared to no lysine. In contrast, in low hypoxanthine, hypoxanthine-requiring cells can produce new cells, yet also die faster than in the absence of hypoxanthine. For both strains, birth rates under various metabolite concentrations are better described by the sigmoidal-shaped Moser model than the well-known Monod model, while death rates can vary with metabolite concentration and time. CONCLUSIONS Our work reveals how time-lapse microscopy can be used to discover non-intuitive microbial birth and death dynamics and to quantify growth rates in many environments.
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Affiliation(s)
| | | | | | | | - Wenying Shou
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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19
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Abstract
The gut microbiota plays a central role in human health. Studies by Tramontano et al. (2018) and Maier et al. (2018) improve our understanding of the metabolism and pharmaceutical impact of human gut bacteria through high-throughput screening of growth in the presence of different nutrients and drugs, respectively.
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Affiliation(s)
- Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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20
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Rapidly moving new bacteria to model-organism status. Curr Opin Biotechnol 2018; 51:116-122. [DOI: 10.1016/j.copbio.2017.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/11/2017] [Indexed: 11/23/2022]
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21
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Priest DG, Tanaka N, Tanaka Y, Taniguchi Y. Micro-patterned agarose gel devices for single-cell high-throughput microscopy of E. coli cells. Sci Rep 2017; 7:17750. [PMID: 29269838 PMCID: PMC5740163 DOI: 10.1038/s41598-017-17544-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/22/2017] [Indexed: 11/25/2022] Open
Abstract
High-throughput microscopy of bacterial cells elucidated fundamental cellular processes including cellular heterogeneity and cell division homeostasis. Polydimethylsiloxane (PDMS)-based microfluidic devices provide advantages including precise positioning of cells and throughput, however device fabrication is time-consuming and requires specialised skills. Agarose pads are a popular alternative, however cells often clump together, which hinders single cell quantitation. Here, we imprint agarose pads with micro-patterned ‘capsules’, to trap individual cells and ‘lines’, to direct cellular growth outwards in a straight line. We implement this micro-patterning into multi-pad devices called CapsuleHotel and LineHotel for high-throughput imaging. CapsuleHotel provides ~65,000 capsule structures per mm2 that isolate individual Escherichia coli cells. In contrast, LineHotel provides ~300 line structures per mm that direct growth of micro-colonies. With CapsuleHotel, a quantitative single cell dataset of ~10,000 cells across 24 samples can be acquired and analysed in under 1 hour. LineHotel allows tracking growth of > 10 micro-colonies across 24 samples simultaneously for up to 4 generations. These easy-to-use devices can be provided in kit format, and will accelerate discoveries in diverse fields ranging from microbiology to systems and synthetic biology.
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Affiliation(s)
- David G Priest
- Laboratory for Single Cell Gene Dynamics, Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Nobuyuki Tanaka
- Laboratory for Integrated Biodevice, Quantitative Biology Center (QBiC), RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yo Tanaka
- Laboratory for Integrated Biodevice, Quantitative Biology Center (QBiC), RIKEN, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuichi Taniguchi
- Laboratory for Single Cell Gene Dynamics, Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan. .,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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22
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Cesar S, Huang KC. Thinking big: the tunability of bacterial cell size. FEMS Microbiol Rev 2017; 41:672-678. [PMID: 28961755 DOI: 10.1093/femsre/fux026] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/10/2017] [Indexed: 11/13/2022] Open
Abstract
The determination of cell size is a fundamental challenge for all living organisms. In a given growth condition, cell size for a particular bacterial species typically falls within a narrow distribution. Nonetheless, size can vary enormously across species, and the size of a single bacterium can even vary substantially across growth conditions. Recent phenomenological studies have revived classic interest in how cells maintain their size and how they adjust their size with changes in growth rate. However, the mechanisms by which cells establish a particular size are relatively enigmatic. Here, we review existing knowledge on how size in rod-shaped bacteria is shaped by nutrient, mechanical, and genetic factors. We also examine obstacles to accurate size measurement and recent technologies that help to overcome these hurdles. Finally, we discuss the relevance of cell size to bacterial physiology.
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Affiliation(s)
- Spencer Cesar
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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23
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Shi H, Colavin A, Bigos M, Tropini C, Monds RD, Huang KC. Deep Phenotypic Mapping of Bacterial Cytoskeletal Mutants Reveals Physiological Robustness to Cell Size. Curr Biol 2017; 27:3419-3429.e4. [DOI: 10.1016/j.cub.2017.09.065] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 11/25/2022]
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24
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Caccamo PD, Brun YV. The Molecular Basis of Noncanonical Bacterial Morphology. Trends Microbiol 2017; 26:191-208. [PMID: 29056293 DOI: 10.1016/j.tim.2017.09.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/08/2017] [Accepted: 09/28/2017] [Indexed: 01/04/2023]
Abstract
Bacteria come in a wide variety of shapes and sizes. The true picture of bacterial morphological diversity is likely skewed due to an experimental focus on pathogens and industrially relevant organisms. Indeed, most of the work elucidating the genes and molecular processes involved in maintaining bacterial morphology has been limited to rod- or coccal-shaped model systems. The mechanisms of shape evolution, the molecular processes underlying diverse shapes and growth modes, and how individual cells can dynamically modulate their shape are just beginning to be revealed. Here we discuss recent work aimed at advancing our knowledge of shape diversity and uncovering the molecular basis for shape generation in noncanonical and morphologically complex bacteria.
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Affiliation(s)
- Paul D Caccamo
- Department of Biology, Indiana University, 1001 E. 3rd St, Bloomington, IN 47405, USA
| | - Yves V Brun
- Department of Biology, Indiana University, 1001 E. 3rd St, Bloomington, IN 47405, USA.
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25
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Lawson MJ, Camsund D, Larsson J, Baltekin Ö, Fange D, Elf J. In situ genotyping of a pooled strain library after characterizing complex phenotypes. Mol Syst Biol 2017; 13:947. [PMID: 29042431 PMCID: PMC5658705 DOI: 10.15252/msb.20177951] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/11/2017] [Accepted: 09/22/2017] [Indexed: 11/28/2022] Open
Abstract
In this work, we present a proof-of-principle experiment that extends advanced live cell microscopy to the scale of pool-generated strain libraries. We achieve this by identifying the genotypes for individual cells in situ after a detailed characterization of the phenotype. The principle is demonstrated by single-molecule fluorescence time-lapse imaging of Escherichia coli strains harboring barcoded plasmids that express a sgRNA which suppresses different genes in the E. coli genome through dCas9 interference. In general, the method solves the problem of characterizing complex dynamic phenotypes for diverse genetic libraries of cell strains. For example, it allows screens of how changes in regulatory or coding sequences impact the temporal expression, location, or function of a gene product, or how the altered expression of a set of genes impacts the intracellular dynamics of a labeled reporter.
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Affiliation(s)
- Michael J Lawson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Daniel Camsund
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jimmy Larsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Özden Baltekin
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - David Fange
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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