1
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Brasino M, Wagnell E, Ozdemir ES, Ranganathan S, Merritt J. Mutation of the peptide-regulated transcription factor ComR for amidated peptide specificity and heterologous function in Lactiplantibacillus plantarum WCFS1. Microbiol Spectr 2024; 12:e0051724. [PMID: 38687019 DOI: 10.1128/spectrum.00517-24] [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: 03/11/2024] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
There is a growing interest in the use of probiotic bacteria as biosensors for the detection of disease. However, there is a lack of bacterial receptors developed for specific disease biomarkers. Here, we have investigated the use of the peptide-regulated transcription factor ComR from Streptococcus spp. for specific peptide biomarker detection. ComR exhibits a number of attractive features that are potentially exploitable to create a biomolecular switch for engineered biosensor circuitry within the probiotic organism Lactiplantibacillus plantarum WCFS1. Through iterative design-build-test cycles, we developed a genomically integrated, ComR-based biosensor circuit that allowed WCFS1 to detect low nanomolar concentrations of ComR's cognate peptide XIP. By screening a library of ComR proteins with mutant residues substituted at the K100 position, we identified mutations that increased the specificity of ComR toward an amidated version of its cognate peptide, demonstrating the potential for ComR to detect this important class of biomarker.IMPORTANCEUsing bacteria to detect disease is an exciting possibility under active study. Detecting extracellular peptides with specific amino acid sequences would be particularly useful as these are important markers of health and disease (biomarkers). In this work, we show that a probiotic bacteria (Lactiplantibacillus plantarum) can be genetically engineered to detect specific extracellular peptides using the protein ComR from Streptococcus bacteria. In its natural form, ComR allowed the probiotic bacteria to detect a specific peptide, XIP. We then modified XIP to be more like the peptide biomarkers found in humans and engineered ComR so that it activated with this modified XIP and not the original XIP. This newly engineered ComR also worked in the probiotic bacteria, as expected. This suggests that with additional engineering, ComR might be able to activate with human peptide biomarkers and be used by genetically engineered probiotic bacteria to better detect disease.
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Affiliation(s)
- Michael Brasino
- Cancer Early Detection Advanced Research (CEDAR) Center, Knight Cancer Institute, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Eli Wagnell
- Cancer Early Detection Advanced Research (CEDAR) Center, Knight Cancer Institute, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - E Sila Ozdemir
- Cancer Early Detection Advanced Research (CEDAR) Center, Knight Cancer Institute, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Srivathsan Ranganathan
- Cancer Early Detection Advanced Research (CEDAR) Center, Knight Cancer Institute, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Justin Merritt
- Department of Biomaterial and Biomedical Sciences, School of Dentistry, Oregon Health and Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, Oregon, USA
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2
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Murali SK, Mansell TJ. Next generation probiotics: Engineering live biotherapeutics. Biotechnol Adv 2024; 72:108336. [PMID: 38432422 DOI: 10.1016/j.biotechadv.2024.108336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 02/10/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, also called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.
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Affiliation(s)
- Sanjeeva Kumar Murali
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA.
| | - Thomas J Mansell
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA.
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3
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Parvin T, Sadras SR. Advanced probiotics: bioengineering and their therapeutic application. Mol Biol Rep 2024; 51:361. [PMID: 38403783 DOI: 10.1007/s11033-024-09309-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024]
Abstract
The role of gut bacteria in human health has long been acknowledged and dysbiosis of the gut microbiota has been correlated with a variety of disorders. Synthetic biology has rapidly grown over the past few years offering a variety of biological applications such as harnessing the relationship between bacteria and human health. Lactic acid bacteria (LAB) are thought to be appropriate chassis organisms for genetic modification with potential biomedical applications. A thorough understanding of the molecular mechanisms behind their beneficial qualities is essential to assist the multifunctional medicinal sectors. Effective genome editing will aid in the creation of next-generation designer probiotics with enhanced resilience and specialized capabilities, furthering our knowledge of the molecular mechanisms behind the physiological impacts of probiotics and their interactions with the host and microbiota. The goal of this review is to provide a brief overview of the methods used to create modified probiotics with the scientific rationale behind gene editing technology, the mechanism of action of engineered probiotics along with their application to treat conditions like inflammatory bowel disease, cancer, bacterial infections, and various metabolic diseases. In addition, application concerns and future directions are also presented.
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Affiliation(s)
- Tamanna Parvin
- Department of Biochemistry and Molecular Biology, School of Life Science, Pondicherry University, Puducherry, India.
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, School of Life Science, Pondicherry University, Puducherry, India
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4
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Prajapati N, Patel J, Singh S, Yadav VK, Joshi C, Patani A, Prajapati D, Sahoo DK, Patel A. Postbiotic production: harnessing the power of microbial metabolites for health applications. Front Microbiol 2023; 14:1306192. [PMID: 38169918 PMCID: PMC10758465 DOI: 10.3389/fmicb.2023.1306192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Postbiotics, which are bioactive substances derived from the metabolic processes of beneficial microbes, have received considerable attention in the field of microbiome science in recent years, presenting a promising path for exploration and innovation. This comprehensive analysis looks into the multidimensional terrain of postbiotic production, including an extensive examination of diverse postbiotic classes, revealing their sophisticated mechanisms of action and highlighting future applications that might significantly affect human health. The authors thoroughly investigate the various mechanisms that support postbiotic production, ranging from conventional fermentation procedures to cutting-edge enzyme conversion and synthetic biology approaches. The review, as an acknowledgment of the field's developing nature, not only highlights current achievements but also navigates through the problems inherent in postbiotic production. In order to successfully include postbiotics in therapeutic interventions and the production of functional food ingredients, emphasis is given to critical elements, including improving yields, bolstering stability, and assuring safety. The knowledge presented herein sheds light on the expanding field of postbiotics and their potential to revolutionize the development of novel therapeutics and functional food ingredients.
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Affiliation(s)
- Nidhi Prajapati
- Department of Biotechnology, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, Gujarat, India
| | - Jinil Patel
- Department of Microbiology, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, Gujarat, India
| | - Sachidanand Singh
- Department of Biotechnology, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, Gujarat, India
- Department of Biotechnology, School of Energy and Technology, Pandit Deendayal Energy University, Knowledge Corridor, Gandhinagar, Gujarat, India
| | - Virendra Kumar Yadav
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Chinmayi Joshi
- Department of Biotechnology, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, Gujarat, India
| | - Anil Patani
- Department of Biotechnology, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, Gujarat, India
| | - Dharmendra Prajapati
- Department of Biotechnology, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, Gujarat, India
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | - Ashish Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
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5
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Arbel-Groissman M, Menuhin-Gruman I, Naki D, Bergman S, Tuller T. Fighting the battle against evolution: designing genetically modified organisms for evolutionary stability. Trends Biotechnol 2023; 41:1518-1531. [PMID: 37442714 DOI: 10.1016/j.tibtech.2023.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Synthetic biology has made significant progress in many areas, but a major challenge that has received limited attention is the evolutionary stability of synthetic constructs made of heterologous genes. The expression of these constructs in microorganisms, that is, production of proteins that are not necessary for the organism, is a metabolic burden, leading to a decrease in relative fitness and make the synthetic constructs unstable over time. This is a significant concern for the synthetic biology community, particularly when it comes to bringing this technology out of the laboratory. In this review, we discuss the issue of evolutionary stability in synthetic biology and review the available tools to address this challenge.
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Affiliation(s)
- Matan Arbel-Groissman
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Itamar Menuhin-Gruman
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Naki
- Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shaked Bergman
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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6
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Arcidiacono S, Spangler JR, Litteral V, Doherty LA, Stamps B, Walper S, Goodson M, Soares JW. In Vitro Fermentation Evaluation of Engineered Sense and Respond Probiotics in Polymicrobial Communities. ACS Biomater Sci Eng 2023; 9:5176-5185. [PMID: 37642529 DOI: 10.1021/acsbiomaterials.3c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Synthetic biology provides a means of engineering tailored functions into probiotic bacteria. Of particular interest is introducing microbial sense and response functions; however, techniques for testing in physiologically relevant environments, such as those for the intended use, are still lacking. Typically, engineered probiotics are developed and tested in monoculture or in simplified cocultures still within ideal environments. In vitro fermentation models using simplified microbial communities now allow us to simulate engineered organism behavior, specifically organism persistence and intended functionality, within more physiologically relevant, tailored microbial communities. Here, probiotic bacteria Escherichia coli Nissle and Lactobacillus plantarum engineered with sense and response functionalities were evaluated for the ability to persist and function without adverse impact on commensal bacteria within simplified polymicrobial communities with increasing metabolic competition that simulate gut microbe community dynamics. Probiotic abundance and plasmid stability, measured by viability qPCR, decreased for engineered E. coli Nissle relative to monocultures as metabolic competition increased; functional output was not affected. For engineered L. plantarum, abundance and plasmid stability were not adversely impacted; however, functional output was decreased universally as metabolic competition was introduced. For both organisms, adverse effects on select commensals were not evident. Testing engineered probiotics in more physiologically relevant in vitro test beds can provide critical knowledge for circuit design feedback and functional validation prior to the transition to more costly and time-consuming higher-fidelity testing in animal or human studies.
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Affiliation(s)
- Steven Arcidiacono
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
| | - Joseph R Spangler
- Center for Bio/Molecular Science & Engineering, US Naval Research Laboratory, Washington, D.C.20375, United States
| | - Vaughn Litteral
- UES Inc, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Laurel A Doherty
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
| | - Blake Stamps
- 711th Human Performance Wing, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Scott Walper
- Center for Bio/Molecular Science & Engineering, US Naval Research Laboratory, Washington, D.C.20375, United States
| | - Michael Goodson
- 711th Human Performance Wing, US Air Force Research Laboratory, Wright-Patterson Air Force Base, Ohio 45433, United States
| | - Jason W Soares
- Soldier Effectiveness Directorate, US Army DEVCOM Soldier Center, Natick, Massachusetts 01760, United States
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7
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Singh A, Alexander SG, Martin S. Gut microbiome homeostasis and the future of probiotics in cancer immunotherapy. Front Immunol 2023; 14:1114499. [PMID: 37261348 PMCID: PMC10228691 DOI: 10.3389/fimmu.2023.1114499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/17/2023] [Indexed: 06/02/2023] Open
Abstract
The gut microbiome has an impact on cancer immune surveillance and immunotherapy, with recent studies showing categorical differences between immunotherapy-sensitive and immunotherapy-resistant cancer patient cohorts. Although probiotics are traditionally being supplemented to promote treatments or sustain therapeutic benefits; the FDA has not approved any for use with immunotherapy. The first step in developing probiotics for immunotherapy is identifying helpful or harmful bacteria down to the strain level. The gut microbiome's heterogeneity before and during treatment is also being investigated to determine microbial strains that are important for immunotherapy. Moreover, Dietary fiber intake, prebiotic supplementation and fecal microbiota transplantation (FMT) were found to enhance intratumoral CD8+ T cell to T-reg ratio in the clinics. The possibility of probiotic immunotherapy as a "living adjuvant" to CAR treatment and checkpoint blockade resistance is actively being investigated.
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8
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Rooney J, Cantacessi C, Sotillo J, Cortés A. Gastrointestinal worms and bacteria: From association to intervention. Parasite Immunol 2023; 45:e12955. [PMID: 36300732 DOI: 10.1111/pim.12955] [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: 09/15/2022] [Revised: 10/17/2022] [Accepted: 10/24/2022] [Indexed: 11/28/2022]
Abstract
A plethora of studies, both experimental and epidemiological, have indicated the occurrence of associations between infections by gastrointestinal (GI) helminths and the composition and function of the host gut microbiota. Given the worldwide risk and spread of anthelmintic resistance, particularly for GI parasites of livestock, a better understanding of the mechanisms underpinning the relationships between GI helminths and the gut microbiome, and between the latter and host health, may assist the development of novel microbiome-targeting and other bacteria-based strategies for parasite control. In this article, we review current and prospective methods to manipulate the host gut microbiome, and/or to exploit the immune stimulatory and modulatory properties of gut bacteria (and their products) to counteract the negative impact of GI worm infections; we also discuss the potential applications of these intervention strategies in programmes aimed to aid the fight against helminth diseases of humans and livestock.
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Affiliation(s)
- James Rooney
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Javier Sotillo
- Parasitology Reference and Research Laboratory, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Alba Cortés
- Departament de Farmàcia i Tecnologia Farmacèutica i Parasitologia, Universitat de València, València, Spain
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9
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Synthetic biology-inspired cell engineering in diagnosis, treatment, and drug development. Signal Transduct Target Ther 2023; 8:112. [PMID: 36906608 PMCID: PMC10007681 DOI: 10.1038/s41392-023-01375-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 03/13/2023] Open
Abstract
The fast-developing synthetic biology (SB) has provided many genetic tools to reprogram and engineer cells for improved performance, novel functions, and diverse applications. Such cell engineering resources can play a critical role in the research and development of novel therapeutics. However, there are certain limitations and challenges in applying genetically engineered cells in clinical practice. This literature review updates the recent advances in biomedical applications, including diagnosis, treatment, and drug development, of SB-inspired cell engineering. It describes technologies and relevant examples in a clinical and experimental setup that may significantly impact the biomedicine field. At last, this review concludes the results with future directions to optimize the performances of synthetic gene circuits to regulate the therapeutic activities of cell-based tools in specific diseases.
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10
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Recent advances in genetic tools for engineering probiotic lactic acid bacteria. Biosci Rep 2023; 43:232386. [PMID: 36597861 PMCID: PMC9842951 DOI: 10.1042/bsr20211299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/05/2023] Open
Abstract
Synthetic biology has grown exponentially in the last few years, with a variety of biological applications. One of the emerging applications of synthetic biology is to exploit the link between microorganisms, biologics, and human health. To exploit this link, it is critical to select effective synthetic biology tools for use in appropriate microorganisms that would address unmet needs in human health through the development of new game-changing applications and by complementing existing technological capabilities. Lactic acid bacteria (LAB) are considered appropriate chassis organisms that can be genetically engineered for therapeutic and industrial applications. Here, we have reviewed comprehensively various synthetic biology techniques for engineering probiotic LAB strains, such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 mediated genome editing, homologous recombination, and recombineering. In addition, we also discussed heterologous protein expression systems used in engineering probiotic LAB. By combining computational biology with genetic engineering, there is a lot of potential to develop next-generation synthetic LAB with capabilities to address bottlenecks in industrial scale-up and complex biologics production. Recently, we started working on Lactochassis project where we aim to develop next generation synthetic LAB for biomedical application.
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11
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Rivera-Tarazona LK, Sivaperuman Kalairaj M, Corazao T, Javed M, Zimmern PE, Subashchandrabose S, Ware TH. Controlling shape morphing and cell release in engineered living materials. BIOMATERIALS ADVANCES 2022; 143:213182. [PMID: 36375222 PMCID: PMC11005089 DOI: 10.1016/j.bioadv.2022.213182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/14/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Engineered living materials (ELMs) derive functionality from both a polymer matrix and the behavior of living cells within the material. The long-term goal of this work is to enable a system of ELM-based medical devices with both mechanical and bioactive functionality. Here, we fabricate multifunctional, stimuli-responsive ELMs comprised of acrylic hydrogel matrix and Escherichia coli. These ELMs undergo controlled changes in form and have a controlled release of bacteria from the composite. We hypothesize that the mechanical forces associated with cell proliferation within a covalently-crosslinked, non-degradable hydrogel are responsible for both phenomena. At constant cell loading, increased hydrogel elastic modulus significantly reduces both cell delivery and volume change associated with cell proliferation. ELMs that change volume over 100 % also result in ~106 colony forming units/mL in the growth medium over 2 h after 1 day of growth. At constant monomer feed ratios, increased cell loading leads to significantly increased cell delivery. Finally, these prokaryotic ELMs were investigated for their potential to deliver a probiotic that can reduce the proliferation of a uropathogen in vitro. Controlling the long-term delivery of bacteria could potentially be used in biomedical applications to modulate microbial communities within the human body.
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Affiliation(s)
| | | | - Tyler Corazao
- Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Mahjabeen Javed
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Philippe E Zimmern
- Department of Urology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Taylor H Ware
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA; Department of Materials Science and Engineering, Texas A&M University, College Station, TX 77843, USA.
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Xiao L, Yang Y, Han S, Rui X, Ma K, Zhang C, Wang G, Li W. Effects of genes required for exopolysaccharides biosynthesis in Lacticaseibacillus paracasei S-NB on cell surface characteristics and probiotic properties. Int J Biol Macromol 2022; 224:292-305. [DOI: 10.1016/j.ijbiomac.2022.10.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
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13
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Russell BJ, Brown SD, Siguenza N, Mai I, Saran AR, Lingaraju A, Maissy ES, Dantas Machado AC, Pinto AFM, Sanchez C, Rossitto LA, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Gonzalez DJ, Saghatelian A, Knight R, Zarrinpar A. Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes. Cell 2022; 185:3263-3277.e15. [PMID: 35931082 PMCID: PMC9464905 DOI: 10.1016/j.cell.2022.06.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/15/2022] [Accepted: 06/25/2022] [Indexed: 12/26/2022]
Abstract
Live bacterial therapeutics (LBTs) could reverse diseases by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally raised (CR) hosts have been unsuccessful because engineered microbial organisms (i.e., chassis) have difficulty in colonizing the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli bacteria isolated from the stool cultures of CR mice were modified to express functional genes. The reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect physiology of and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to “knock in” specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts and enables LBT with curative intent. Native E. coli strains isolated from mouse stool are genetically engineered for long-term engraftment in the conventional mouse gut and enable long-term systemic effects on the host, such as improvements in insulin sensitivity in mouse models of type 2 diabetes.
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Affiliation(s)
- Baylee J Russell
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Steven D Brown
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicole Siguenza
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Irene Mai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anand R Saran
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amulya Lingaraju
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Erica S Maissy
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ana C Dantas Machado
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Concepcion Sanchez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yukiko Miyamoto
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - R Alexander Richter
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Samuel B Ho
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA; VA Health Sciences San Diego, La Jolla, CA 92161, USA
| | - Lars Eckmann
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA 92093, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093, USA; VA Health Sciences San Diego, La Jolla, CA 92161, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
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14
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Lai Y, Hayashi N, Lu TK. Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology. Curr Opin Chem Biol 2022; 70:102178. [PMID: 35759819 DOI: 10.1016/j.cbpa.2022.102178] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/24/2022] [Accepted: 05/28/2022] [Indexed: 11/29/2022]
Abstract
The role of the microbiome in health and disease is attracting the attention of researchers seeking to engineer microorganisms for diagnostic and therapeutic applications. Recent progress in synthetic biology may enable the dissection of host-microbiota interactions. Sophisticated genetic circuits that can sense, compute, memorize, and respond to signals have been developed for the stable commensal bacterium Bacteroides thetaiotaomicron, dominant in the human gut. In this review, we highlight recent advances in expanding the genetic toolkit for B. thetaiotaomicron and foresee several applications of this species for microbiome engineering. We provide our perspective on the challenges and future opportunities for the engineering of human gut-associated bacteria as living therapeutic agents.
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Affiliation(s)
- Yong Lai
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA
| | - Naoki Hayashi
- JSR-Keio University Medical and Chemical Innovation Center (JKiC), JSR Corp., 35 Shinanomachi, Shinjuku, Tokyo 160-8582, Japan
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Research Laboratory of Electronics, MIT, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Senti Biosciences, 2 Corporate Drive South San Francisco, CA 94080, USA.
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15
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Cruz KCP, Enekegho LO, Stuart DT. Bioengineered Probiotics: Synthetic Biology Can Provide Live Cell Therapeutics for the Treatment of Foodborne Diseases. Front Bioeng Biotechnol 2022; 10:890479. [PMID: 35656199 PMCID: PMC9152101 DOI: 10.3389/fbioe.2022.890479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/29/2022] [Indexed: 11/15/2022] Open
Abstract
The rising prevalence of antibiotic resistant microbial pathogens presents an ominous health and economic challenge to modern society. The discovery and large-scale development of antibiotic drugs in previous decades was transformational, providing cheap, effective treatment for what would previously have been a lethal infection. As microbial strains resistant to many or even all antibiotic drug treatments have evolved, there is an urgent need for new drugs or antimicrobial treatments to control these pathogens. The ability to sequence and mine the genomes of an increasing number of microbial strains from previously unexplored environments has the potential to identify new natural product antibiotic biosynthesis pathways. This coupled with the power of synthetic biology to generate new production chassis, biosensors and “weaponized” live cell therapeutics may provide new means to combat the rapidly evolving threat of drug resistant microbial pathogens. This review focuses on the application of synthetic biology to construct probiotic strains that have been endowed with functionalities allowing them to identify, compete with and in some cases kill microbial pathogens as well as stimulate host immunity. Weaponized probiotics may have the greatest potential for use against pathogens that infect the gastrointestinal tract: Vibrio cholerae, Staphylococcus aureus, Clostridium perfringens and Clostridioides difficile. The potential benefits of engineered probiotics are highlighted along with the challenges that must still be met before these intriguing and exciting new therapeutic tools can be widely deployed.
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16
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Romero-Luna HE, Hernández-Mendoza A, González-Córdova AF, Peredo-Lovillo A. Bioactive peptides produced by engineered probiotics and other food-grade bacteria: A review. Food Chem X 2022; 13:100196. [PMID: 35498967 PMCID: PMC9039921 DOI: 10.1016/j.fochx.2021.100196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/09/2021] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Synthetic biology improves probiotics therapeutic approaches. Engineering technologies contribute to design probiotics mechanisms of action. Edition of proteolytic systems induce the generation of specific bioactive peptides. Engineered probiotics should be evaluated as therapeutic agents in clinical trials. Therapeutical and technological uses of engineered probiotics are still controversial.
Synthetic biology is employed for the study and design of engineered microbes with new and improved therapeutic functions. The main advantage of synthetic biology is the selective genetic manipulation of living organisms with desirable beneficial effects such as probiotics. Engineering technologies have contributed to the edition of metabolic processes involved in the mechanisms of action of probiotics, such as the generation of bioactive peptides. Hence, current information related to bioactive peptides, produced by different engineering probiotics, with antimicrobial, antiviral, antidiabetic, and antihypertensive activities, as well as their potential use as functional ingredients, is discussed here. Besides, the effectiveness and safety aspects of these bioactive peptides were also described.
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Affiliation(s)
- Haydee Eliza Romero-Luna
- Subdirección de Posgrado e Investigación, Instituto Tecnológico Superior de Xalapa, Xalapa 91096, Veracruz, Mexico
| | - Adrián Hernández-Mendoza
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD, A.C.), Hermosillo 83304, Sonora, Mexico
| | - Aarón Fernando González-Córdova
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD, A.C.), Hermosillo 83304, Sonora, Mexico
| | - Audry Peredo-Lovillo
- Subdirección de Posgrado e Investigación, Instituto Tecnológico Superior de Xalapa, Xalapa 91096, Veracruz, Mexico
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17
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Brennan AM. Development of Synthetic Biotics as Treatments for Human Diseases. Synth Biol (Oxf) 2022; 7:ysac001. [PMID: 35350191 PMCID: PMC8944296 DOI: 10.1093/synbio/ysac001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/19/2021] [Accepted: 01/29/2022] [Indexed: 12/02/2022] Open
Abstract
Advances in synthetic biology have allowed the generation of strains of bacteria that are genetically altered to have specific therapeutic benefits. These synthetic biotics, also widely referred to as engineered living therapeutics, have tremendous potential as a new therapeutic modality, and several have advanced into the clinic and human testing. This review outlines some of the unique attributes of synthetic biotics as well as some of the challenges in their development as prescription products. Regulatory considerations are discussed, and a case study of a program that has advanced into Phase 2 testing is provided: SYNB1618 for the treatment of PKU.
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18
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Kwak S, Mahmud B, Dantas G. A Tunable and Expandable Transactivation System in Probiotic Yeast Saccharomyces boulardii. ACS Synth Biol 2022; 11:508-514. [PMID: 34939781 PMCID: PMC9013468 DOI: 10.1021/acssynbio.1c00384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Precise transcriptional modulation is a key requirement for developing synthetic probiotics with predictably tunable functionalities. In this study, an expandable and tunable transactivation system was constructed and validated in probiotic yeast Saccharomyces boulardii. The use of nuclease-null Cas9 and scaffold RNA (scRNA) directed regulation enabled transactivation under the control of a synthetic promoter in S. boulardii. A synthetic promoter consisting of the scRNA target sequence and the core GAL7 promoter region restricted interference from the native galactose regulon. The system was readily expanded by introducing new target sequences to the promoter and scRNA. Complementarity between the promoter and scRNA, and binding specificity between scRNA and transcriptional activator, served as two layers of orthogonality of the transactivation. In addition, activator expression under the control of an inducible promoter enabled control of the transactivation via chemical inducer. The described system has the potential to enable engineering of probiotic yeast to more precisely perform therapeutic functions.
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Affiliation(s)
- Suryang Kwak
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA, 63110,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA, 63110
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA, 63110
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA, 63110,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA, 63110,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA, 63130,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA, 63110,Corresponding author (after review): G.D. ()
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19
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Zhang Y, Zhou L, Xia J, Dong C, Luo X. Human Microbiome and Its Medical Applications. Front Mol Biosci 2022; 8:703585. [PMID: 35096962 PMCID: PMC8793671 DOI: 10.3389/fmolb.2021.703585] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022] Open
Abstract
The commensal microbiome is essential for human health and is involved in many processes in the human body, such as the metabolism process and immune system activation. Emerging evidence implies that specific changes in the microbiome participate in the development of various diseases, including diabetes, liver diseases, tumors, and pathogen infections. Thus, intervention on the microbiome is becoming a novel and effective method to treat such diseases. Synthetic biology empowers researchers to create strains with unique and complex functions, making the use of engineered microbes for clinical applications attainable. The aim of this review is to summarize recent advances about the roles of the microbiome in certain diseases and the underlying mechanisms, as well as the use of engineered microbes in the prevention, detection, and treatment of various diseases.
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Affiliation(s)
- Yangming Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Linguang Zhou
- Department of Pharmacy, Peking University International Hospital, Beijing, China
| | - Jialin Xia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Ce Dong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- *Correspondence: Xiaozhou Luo,
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20
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Liu CY, Cham CM, Chang EB. Epithelial wound healing in inflammatory bowel diseases: the next therapeutic frontier. Transl Res 2021; 236:35-51. [PMID: 34126257 PMCID: PMC8380699 DOI: 10.1016/j.trsl.2021.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/25/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023]
Abstract
Patients with one of the many chronic inflammatory disorders broadly classified as inflammatory bowel disease (IBD) now have a diverse set of immunomodulatory therapies at their disposal. Despite these recent medical advances, complete sustained remission of disease remains elusive for most patients. The full healing of the damaged intestinal mucosa is the primary goal of all therapies. Achieving this requires not just a reduction of the aberrant immunological response, but also wound healing of the epithelium. No currently approved therapy directly targets the epithelium. Epithelial repair is compromised in IBD and normally facilitates re-establishment of the homeostatic barrier between the host and the microbiome. In this review, we summarize the evidence that epithelial wound healing represents an important yet underdeveloped therapeutic modality for IBD. We highlight 3 general approaches that are promising for developing a new class of epithelium-targeted therapies: epithelial stem cells, cytokines, and microbiome engineering. We also provide a frank discussion of some of the challenges that must be overcome for epithelial repair to be therapeutically leveraged. A concerted approach by the field to develop new therapies targeting epithelial wound healing will offer patients a game-changing, complementary class of medications and could dramatically improve outcomes.
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Affiliation(s)
- Cambrian Y Liu
- Department of Medicine, The University of Chicago, Chicago, Illinois.
| | - Candace M Cham
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Eugene B Chang
- Department of Medicine, The University of Chicago, Chicago, Illinois.
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21
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Kunjapur AM, Napolitano MG, Hysolli E, Noguera K, Appleton EM, Schubert MG, Jones MA, Iyer S, Mandell DJ, Church GM. Synthetic auxotrophy remains stable after continuous evolution and in coculture with mammalian cells. SCIENCE ADVANCES 2021; 7:eabf5851. [PMID: 34215581 PMCID: PMC11060021 DOI: 10.1126/sciadv.abf5851] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Understanding the evolutionary stability and possible context dependence of biological containment techniques is critical as engineered microbes are increasingly under consideration for applications beyond biomanufacturing. While synthetic auxotrophy previously prevented Escherichia coli from exhibiting detectable escape from batch cultures, its long-term effectiveness is unknown. Here, we report automated continuous evolution of a synthetic auxotroph while supplying a decreasing concentration of essential biphenylalanine (BipA). After 100 days of evolution, triplicate populations exhibit no observable escape and exhibit normal growth rates at 10-fold lower BipA concentration than the ancestral synthetic auxotroph. Allelic reconstruction reveals the contribution of three genes to increased fitness at low BipA concentrations. Based on its evolutionary stability, we introduce the progenitor strain directly to mammalian cell culture and observe containment of bacteria without detrimental effects on HEK293T cells. Overall, our findings reveal that synthetic auxotrophy is effective on time scales and in contexts that enable diverse applications.
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Affiliation(s)
- Aditya M Kunjapur
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA.
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, CLB 215, Newark, DE 19716, USA
| | - Michael G Napolitano
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA
| | - Eriona Hysolli
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA
| | - Karen Noguera
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA
| | - Evan M Appleton
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA
| | - Max G Schubert
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA
| | - Michaela A Jones
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy Street, CLB 215, Newark, DE 19716, USA
| | - Siddharth Iyer
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA
| | - Daniel J Mandell
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, NRB 238, Boston, MA 02115, USA.
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22
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Arcidiacono S, Breedon AME, Goodson MS, Doherty LA, Lyon W, Jimenez G, Pantoja-Feliciano IG, Soares JW. In vitro fermentation test bed for evaluation of engineered probiotics in polymicrobial communities. J Biol Methods 2021; 8:e147. [PMID: 34104665 PMCID: PMC8175340 DOI: 10.14440/jbm.2021.347] [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: 10/23/2020] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/25/2022] Open
Abstract
In vitro fermentation systems offer significant opportunity for deconvoluting complex metabolic dynamics within polymicrobial communities, particularly those associated with the human gut microbiome. In vitro gut models have broad experimental capacity allowing rapid evaluation of multiple parameters, generating knowledge to inform design of subsequent in vivo studies. Here, our method describes an in vitro fermentation test bed to provide a physiologically-relevant assessment of engineered probiotics circuit design functions. Typically, engineered probiotics are evaluated under pristine, mono- or co-culture conditions and transitioned directly into animal or human studies, commonly resulting in a loss of desired function when introduced to complex gut communities. Our method encompasses a systematic workflow entailing fermentation, molecular and functional characterization, and statistical analyses to validate an engineered probiotic’s persistence, plasmid stability and reporter response. To demonstrate the workflow, simplified polymicrobial communities of human gut microbial commensals were utilized to investigate the probiotic Escherichia coli Nissle 1917 engineered to produce a fluorescent reporter protein. Commensals were assembled with increasing complexity to produce a mock community based on nutrient utilization. The method assesses engineered probiotic persistence in a competitive growth environment, reporter production and function, effect of engineering on organism growth and influence on commensal composition. The in vitro test bed represents a new element within the Design-Build-Test-Learn paradigm, providing physiologically-relevant feedback for circuit re-design and experimental validation for transition of engineered probiotics to higher fidelity animal or human studies.
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Affiliation(s)
- Steven Arcidiacono
- Soldier Effectiveness Directorate, DEVCOM Soldier Center, Natick, MA 01760, USA
| | - Amy M Ehrenworth Breedon
- 711 th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA.,UES, Inc., Dayton, OH 45432, USA
| | - Michael S Goodson
- 711 th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
| | - Laurel A Doherty
- Soldier Effectiveness Directorate, DEVCOM Soldier Center, Natick, MA 01760, USA
| | - Wanda Lyon
- 711 th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA
| | - Grace Jimenez
- 711 th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH 45433, USA.,UES, Inc., Dayton, OH 45432, USA
| | | | - Jason W Soares
- Soldier Effectiveness Directorate, DEVCOM Soldier Center, Natick, MA 01760, USA
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23
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Aavani F, Biazar E, Heshmatipour Z, Arabameri N, Kamalvand M, Nazbar A. Applications of bacteria and their derived biomaterials for repair and tissue regeneration. Regen Med 2021; 16:581-605. [PMID: 34030458 DOI: 10.2217/rme-2020-0116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Microorganisms such as bacteria and their derived biopolymers can be used in biomaterials and tissue regeneration. Various methods have been applied to regenerate damaged tissues, but using probiotics and biomaterials derived from bacteria with improved economic-production efficiency and highly applicable properties can be a new solution in tissue regeneration. Bacteria can synthesize numerous types of biopolymers. These biopolymers possess many desirable properties such as biocompatibility and biodegradability, making them good candidates for tissue regeneration. Here, we reviewed different types of bacterial-derived biopolymers and highlight their applications for tissue regeneration.
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Affiliation(s)
- Farzaneh Aavani
- Biomedical Engineering Faculty, Amirkabir University of Technology (Tehran Polytechnic), 15916-34311 Tehran, Iran
| | - Esmaeil Biazar
- Department of Biomedical Engineering, Tissue Engineering Group, Tonekabon Branch, Islamic Azad University, 46841-61167 Tonekabon, Iran
| | - Zoheir Heshmatipour
- Department of Microbiology, Tonekabon Branch, Islamic Azad University, 46841-61167 Tonekabon, Iran
| | - Nasibeh Arabameri
- Department of Microbiology, Tonekabon Branch, Islamic Azad University, 46841-61167 Tonekabon, Iran
| | - Mahshad Kamalvand
- Department of Biomedical Engineering, Tissue Engineering Group, Tonekabon Branch, Islamic Azad University, 46841-61167 Tonekabon, Iran
| | - Abolfazl Nazbar
- National Cell Bank, Pasteur Institute of Iran, 13169-43551 Tehran, Iran
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24
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Parker MT, Kunjapur AM. Deployment of Engineered Microbes: Contributions to the Bioeconomy and Considerations for Biosecurity. Health Secur 2021; 18:278-296. [PMID: 32816583 DOI: 10.1089/hs.2020.0010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Engineering at microscopic scales has an immense effect on the modern bioeconomy. Microbes contribute to such disparate markets as chemical manufacturing, fuel production, crop optimization, and pharmaceutical synthesis, to name a few. Due to new and emerging synthetic biology technologies, and the sophistication and control afforded by them, we are on the brink of deploying engineered microbes to not only enhance traditional applications but also to introduce these microbes to sectors, contexts, and formats not previously attempted. In microbially managed medicine, microbial engineering holds promise for increasing efficacy, improving tissue penetration, and sustaining treatment. In the environment, the most effective areas for deployment are in the management of crops and protection of ecosystems. However, caution is warranted before introducing engineered organisms to new environments where they may proliferate without control and could cause unforeseen effects. We summarize ideas and data that can inform identification and assessment of the risks that these tools present to ensure that realistic hazards are described and unrealistic ones do not hinder advancement. Further, because modes of containment are crucial complements to deployment, we describe the state of the art in microbial biocontainment strategies, current gaps, and how these gaps might be addressed through technological advances in synthetic engineering. Collectively, this work highlights engineered microbes as a foundational and expanding facet of the bioeconomy, projects their utility in upcoming deployments outside the laboratory, and identifies knowns and unknowns that will be necessary considerations and points of focus in this endeavor.
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Affiliation(s)
- Michael T Parker
- Michael T. Parker, PhD, is an Assistant Dean, Office of the Dean, Georgetown University, Washington, DC. Aditya M. Kunjapur, PhD, is an Assistant Professor, Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
| | - Aditya M Kunjapur
- Michael T. Parker, PhD, is an Assistant Dean, Office of the Dean, Georgetown University, Washington, DC. Aditya M. Kunjapur, PhD, is an Assistant Professor, Chemical and Biomolecular Engineering, University of Delaware, Newark, DE
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25
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Ni ZJ, Zhang YG, Chen SX, Thakur K, Wang S, Zhang JG, Shang YF, Wei ZJ. Exploration of walnut components and their association with health effects. Crit Rev Food Sci Nutr 2021; 62:5113-5129. [PMID: 33567903 DOI: 10.1080/10408398.2021.1881439] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Traditionally, walnuts have occupied an imperative position in the functional food market with consistently recognized nutritious and functional properties. In the past years, the lipid profile of walnuts has brought much scientific attention via linking a cascade of biological attributes and health-promoting effects. Over time, researchers have focused on diversified composition (polyphenols and vitamins) of different parts of walnut (flower, pellicle, and kernel) and emphasized their physiological significance. Consequently, a plethora of reports has emerged on the potential role of walnut consumption against a series of diseases including cancer, gut dysbiosis, cardiovascular, and neurodegenerative diseases. Therefore, we accumulated the updated data on composition and classification, extraction methods, and utilization of different parts of walnuts as well as associated beneficial effects under in vivo and clinical studies. Altogether, this review summarized the ameliorative effects of a walnut-enriched diet in chronic diseases which can be designated to the synergistic or individual effects of walnut components mainly through anti-oxidative and anti-inflammatory role.
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Affiliation(s)
- Zhi-Jing Ni
- Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China.,School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Yi-Ge Zhang
- Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China.,School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Sheng-Xiong Chen
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Kiran Thakur
- Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China.,School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Shaoyun Wang
- College of Biological Science and Technology, Fuzhou University, Fuzhou, People's Republic of China
| | - Jian-Guo Zhang
- Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China.,School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Ya-Fang Shang
- School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Zhao-Jun Wei
- Collaborative Innovation Center for Food Production and Safety, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China.,School of Food Science and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
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26
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Liu ZS, Lin CF, Lee CP, Hsieh MC, Lu HF, Chen YF, Ku YW, Chen PW. A Single Plasmid of Nisin-Controlled Bovine and Human Lactoferrin Expressing Elevated Antibacterial Activity of Lactoferrin-Resistant Probiotic Strains. Antibiotics (Basel) 2021; 10:antibiotics10020120. [PMID: 33513782 PMCID: PMC7911973 DOI: 10.3390/antibiotics10020120] [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: 12/26/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 11/28/2022] Open
Abstract
Lactoferrin (LF) is a multifunctional protein found in mammals, and it shows broad-spectrum antimicrobial activity. To improve the functional properties of specific probiotics in order to provide both the beneficial characteristics of lactic acid bacteria and the biological activity of LF, cDNAs of bovine LF (BLF), human LF (HLF), or porcine LF (PLF) were cloned into a nisin-inducible plasmid. These were then transformed into the selected eight probiotics, which are LF-resistant hosts. Expression of recombinant LFs (rLFs) was analyzed via SDS-PAGE and Western blot analysis. Although the selected host strains may not contain the nisRK genes (NisK, the sensor kinase; NisR, the regulator protein), the components of autoregulation, a low level of LFs expression can be successfully induced by using nisin within bacterial cells in a time-dependent manner in three engineered clones, including Lactobacillus delbrueckii/HLF, L. delbrueckii/BLF, and L. gasseri/BLF. Lactobacillus delbrueckii and Lactobacillus gasseri originate from yogurt and human milk, respectively, and both strains are functional probiotic strains. Therefore, we further compared the antibacterial activities of disrupted recombinant probiotic clones, conventional strains (host control), and vector control ones by using agar diffusion and broth inhibition analysis, and the expression of rLFs in the above three clones considerately improved their antibacterial efficacies against four important food-borne pathogens, namely, Escherichia coli, Staphylococcus aureus, Enterococcus faecalis, and Salmonellaenterica. In conclusion, this study provides a simple strategy for the production of functional LFs (BLF and HLF) in both functional and LF-resistant hosts for applications in the field.
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Affiliation(s)
- Zhen-Shu Liu
- Department of Safety, Health and Environmental Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan; (Z.-S.L.); (M.-C.H.); (H.-F.L.)
- Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chiayi 61363, Taiwan
- Center for Environmental Sustainability and Human Health, Ming Chi University of Technology, New Taipei City, 24301, Taiwan
| | - Chuen-Fu Lin
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Chung-Pei Lee
- School of Nursing, National Taipei University of Nursing and Health Sciences, Taipei 11219, Taiwan;
| | - Min-Chi Hsieh
- Department of Safety, Health and Environmental Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan; (Z.-S.L.); (M.-C.H.); (H.-F.L.)
| | - Hung-Fu Lu
- Department of Safety, Health and Environmental Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan; (Z.-S.L.); (M.-C.H.); (H.-F.L.)
| | - Ying-Fang Chen
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40249, Taiwan; (Y.-F.C.); (Y.-W.K.)
| | - Yu-We Ku
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40249, Taiwan; (Y.-F.C.); (Y.-W.K.)
| | - Po-Wen Chen
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40249, Taiwan; (Y.-F.C.); (Y.-W.K.)
- Correspondence: ; Tel.: +886-4-22840368-36
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27
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Zuo F, Marcotte H. Advancing mechanistic understanding and bioengineering of probiotic lactobacilli and bifidobacteria by genome editing. Curr Opin Biotechnol 2021; 70:75-82. [PMID: 33445135 DOI: 10.1016/j.copbio.2020.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/02/2020] [Accepted: 12/17/2020] [Indexed: 12/01/2022]
Abstract
Typical traditional probiotics lactobacilli and bifidobacteria are gaining great interest to be developed as living diagnostics and therapeutics for improving human health. However, the mechanistic basis underlying their inherent health beneficial property remain incompletely understood which can slow down the translational pipeline in the functional food and pharmaceutical field. Efficient genome editing will advance the understanding of the molecular mechanism of the probiotics' physiological properties and their interaction with the host and the host microbiota, thereby further promote the development of next-generation designer probiotics with improved robustness and tailored functionalities. With the expansion of genome editing strategies such as CRISPR-Cas-based tools and IPSD assisted genome engineering as well as other synthetic biology technologies, the research and application of these health-promoting bacteria for the food and pharmaceutical industry will be further enhanced.
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Affiliation(s)
- Fanglei Zuo
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden; Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm SE-106 91, Sweden.
| | - Harold Marcotte
- Department of Laboratory Medicine, Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm SE-141 86, Sweden
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28
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Mays ZJS, Nair NU. A quantitative model for metabolic intervention using gut microbes. Biotechnol Prog 2021; 37:e3125. [PMID: 33426814 DOI: 10.1002/btpr.3125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 11/08/2022]
Abstract
As medicine shifts toward precision-based and personalized therapeutics, utilizing more complex biomolecules to treat increasingly difficult and rare conditions, microorganisms provide an avenue for realizing the production and processing necessary for novel drug pipelines. More so, probiotic microbes can be co-opted to deliver therapeutics by oral administration as living drugs, able to survive and safely transit the digestive tract. As living therapeutics are in their nascency, traditional pharmacokinetic-pharmacodynamic (PK-PD) models for evaluating drug candidates are not appropriate for this novel platform. Using a living therapeutic in late-stage clinical development for phenylketonuria (PKU) as a case study, we adapt traditional oral drug delivery models to properly evaluate and inform the engineering of living therapeutics. We develop the adapted for living therapeutics compartmental absorption and transit (ALT-CAT) model to provide metrics for drug efficacy across nine age groups of PKU patients and evaluate model parameters that are influenced by patient physiology, microbe selection and therapeutic production, and dosing formulations. In particular, the ALT-CAT model describes the mathematical framework to model the behavior of orally delivered engineered bacteria that act as living therapeutics by adapting similar methods that have been developed and widely-used for small molecular drug delivery and absorption.
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Affiliation(s)
- Zachary J S Mays
- Department of Chemical & Biological Engineering, Tufts University, Medford, Massachusetts, USA
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, Massachusetts, USA
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29
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Wang R, Tang R, Li B, Ma X, Schnabl B, Tilg H. Gut microbiome, liver immunology, and liver diseases. Cell Mol Immunol 2021; 18:4-17. [PMID: 33318628 PMCID: PMC7852541 DOI: 10.1038/s41423-020-00592-6] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/08/2020] [Indexed: 02/08/2023] Open
Abstract
The gut microbiota is a complex and plastic consortium of microorganisms that are intricately connected with human physiology. The liver is a central immunological organ that is particularly enriched in innate immune cells and constantly exposed to circulating nutrients and endotoxins derived from the gut microbiota. The delicate interaction between the gut and liver prevents accidental immune activation against otherwise harmless antigens. Work on the interplay between the gut microbiota and liver has assisted in understanding the pathophysiology of various liver diseases. Of immense importance is the step from high-throughput sequencing (correlation) to mechanistic studies (causality) and therapeutic intervention. Here, we review the gut microbiota, liver immunology, and the interaction between the gut and liver. In addition, the impairment in the gut-liver axis found in various liver diseases is reviewed here, with an emphasis on alcohol-associated liver disease (ALD), nonalcoholic fatty liver disease (NAFLD), and autoimmune liver disease (AILD). On the basis of growing evidence from these preclinical studies, we propose that the gut-liver axis paves the way for targeted therapeutic modalities for liver diseases.
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Affiliation(s)
- Rui Wang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Bo Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, 200001, Shanghai, China
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, 200001, Shanghai, China.
| | - Bernd Schnabl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University Innsbruck, Innsbruck, Austria.
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30
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Engineer probiotic bifidobacteria for food and biomedical applications - Current status and future prospective. Biotechnol Adv 2020; 45:107654. [DOI: 10.1016/j.biotechadv.2020.107654] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/14/2020] [Accepted: 11/01/2020] [Indexed: 12/15/2022]
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31
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Kumar P, Sinha R, Shukla P. Artificial intelligence and synthetic biology approaches for human gut microbiome. Crit Rev Food Sci Nutr 2020; 62:2103-2121. [PMID: 33249867 DOI: 10.1080/10408398.2020.1850415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The gut microbiome comprises a variety of microorganisms whose genes encode proteins to carry out crucial metabolic functions that are responsible for the majority of health-related issues in human beings. The advent of the technological revolution in artificial intelligence (AI) assisted synthetic biology (SB) approaches will play a vital role in the modulating the therapeutic and nutritive potential of probiotics. This can turn human gut as a reservoir of beneficial bacterial colonies having an immense role in immunity, digestion, brain function, and other health benefits. Hence, in the present review, we have discussed the role of several gene editing tools and approaches in synthetic biology that have equipped us with novel tools like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas) systems to precisely engineer probiotics for diagnostic, therapeutic and nutritive value. A brief discussion over the AI techniques to understand the metagenomic data from the healthy and diseased gut microbiome is also presented. Further, the role of AI in potentially impacting the pace of developments in SB and its current challenges is also discussed. The review also describes the health benefits conferred by engineered microbes through the production of biochemicals, nutraceuticals, drugs or biotherapeutics molecules etc. Finally, the review concludes with the challenges and regulatory concerns in adopting synthetic biology engineered microbes for clinical applications. Thus, the review presents a synergistic approach of AI and SB toward human gut microbiome for better health which will provide interesting clues to researchers working in the area of rapidly evolving food and nutrition science.
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Affiliation(s)
- Prasoon Kumar
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, India.,Department of Medical Devices, National Institute of Pharmaceutical Education and Research, Ahmedabad, India
| | | | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India.,Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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32
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Davies JE, Behroozian S. An ancient solution to a modern problem. Mol Microbiol 2020; 113:546-549. [PMID: 32185831 DOI: 10.1111/mmi.14481] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 11/30/2022]
Abstract
The dearth of new antibiotics and escalating emergence of multidrug resistant bacteria have created a global healthcare crisis and highlight the drastic need for novel antimicrobial agents. Complementary and alternative strategies including the investigation of ancient medicinals could address this problem. Natural clay minerals with a long history of medicinal and biomedical applications have become an interest due to their broad-spectrum antimicrobial activity. Such untapped natural sources may provide new therapeutic agents in the battle against infectious diseases in the post-antibiotic era.
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Affiliation(s)
- Julian E Davies
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Shekooh Behroozian
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
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33
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Liu H, Robinson DS, Wu ZY, Kuo R, Yoshikuni Y, Blaby IK, Cheng JF. Bacterial genome editing by coupling Cre-lox and CRISPR-Cas9 systems. PLoS One 2020; 15:e0241867. [PMID: 33147260 PMCID: PMC7641437 DOI: 10.1371/journal.pone.0241867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/21/2020] [Indexed: 01/25/2023] Open
Abstract
The past decade has been a golden age for microbiology, marked by the discovery of an unprecedented increase in the number of novel bacterial species. Yet gaining biological knowledge of those organisms has not kept pace with sequencing efforts. To unlock this genetic potential there is an urgent need for generic (i.e. non-species specific) genetic toolboxes. Recently, we developed a method, termed chassis-independent recombinase-assisted genome engineering (CRAGE), enabling the integration and expression of large complex gene clusters directly into the chromosomes of diverse bacteria. Here we expand upon this technology by incorporating CRISPR-Cas9 allowing precise genome editing across multiple bacterial species. To do that we have developed a landing pad that carries one wild-type and two mutant lox sites to allow integration of foreign DNA at two locations through Cre-lox recombinase-mediated cassette exchange (RMCE). The first RMCE event is to integrate the Cas9 and the DNA repair protein genes RecET, and the second RMCE event enables the integration of customized sgRNA and a repair template. Following this workflow, we achieved precise genome editing in four different gammaproteobacterial species. We also show that the inserted landing pad and the entire editing machinery can be removed scarlessly after editing. We report here the construction of a single landing pad transposon and demonstrate its functionality across multiple species. The modular design of the landing pad and accessory vectors allows design and assembly of genome editing platforms for other organisms in a similar way. We believe this approach will greatly expand the list of bacteria amenable to genetic manipulation and provides the means to advance our understanding of the microbial world.
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Affiliation(s)
- Hualan Liu
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - David S. Robinson
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Zong-Yen Wu
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Rita Kuo
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Ian K. Blaby
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * E-mail:
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34
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Belizário JE, Sircili MP. Novel biotechnological approaches for monitoring and immunization against resistant to antibiotics Escherichia coli and other pathogenic bacteria. BMC Vet Res 2020; 16:420. [PMID: 33138825 PMCID: PMC7607641 DOI: 10.1186/s12917-020-02633-8] [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: 04/01/2019] [Accepted: 10/21/2020] [Indexed: 01/12/2023] Open
Abstract
The application of next-generation molecular, biochemical and immunological methods for developing new vaccines, antimicrobial compounds, probiotics and prebiotics for zoonotic infection control has been fundamental to the understanding and preservation of the symbiotic relationship between animals and humans. With increasing rates of antibiotic use, resistant bacterial infections have become more difficult to diagnose, treat, and eradicate, thereby elevating the importance of surveillance and prevention programs. Effective surveillance relies on the availability of rapid, cost-effective methods to monitor pathogenic bacterial isolates. In this opinion article, we summarize the results of some research program initiatives for the improvement of live vaccines against avian enterotoxigenic Escherichia coli using virulence factor gene deletion and engineered vaccine vectors based on probiotics. We also describe methods for the detection of pathogenic bacterial strains in eco-environmental headspace and aerosols, as well as samples of animal and human breath, based on the composition of volatile organic compounds and fatty acid methyl esters. We explain how the introduction of these low-cost biotechnologies and protocols will provide the opportunity to enhance co-operation between networks of resistance surveillance programs and integrated routine workflows of veterinary and clinical public health microbiology laboratories.
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Affiliation(s)
- José E Belizário
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo, Av. Lineu Prestes, 1524, São Paulo, SP, CEP 05508-900, Brazil.
| | - Marcelo P Sircili
- Laboratory of Genetics, Butantan Institute, Av. Vital Brazil, 1500, São Paulo, SP, CEP 05503-900, Brazil
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35
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Chappell TC, Nair NU. Engineered lactobacilli display anti-biofilm and growth suppressing activities against Pseudomonas aeruginosa. NPJ Biofilms Microbiomes 2020; 6:48. [PMID: 33127888 PMCID: PMC7599214 DOI: 10.1038/s41522-020-00156-6] [Citation(s) in RCA: 20] [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: 04/08/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022] Open
Abstract
Biofilms are an emerging target for new therapeutics in the effort to address the continued increase in resistance and tolerance to traditional antimicrobials. In particular, the distinct nature of the biofilm growth state often means that traditional antimcirobials, developed to combat planktonic cells, are ineffective. Biofilm treatments are designed to both reduce pathogen load at an infection site and decrease the development of resistance by rendering the embedded organisms more susceptible to treatment at lower antimicrobial concentrations. In this work, we developed a new antimicrobial treatment modality using engineered lactic acid bacteria (LAB). We first characterized the natural capacity of two lactobacilli, L. plantarum and L. rhamnosus, to inhibit P. aeruginosa growth, biofilm formation, and biofilm viability, which we found to be dependent upon the low pH generated during culture of the LAB. We further engineered these LAB to secrete enzymes known to degrade P. aeruginosa biofilms and show that our best performing engineered LAB, secreting a pathogen-derived enzyme (PelAh), degrades up to 85% of P. aeruginosa biofilm.
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Affiliation(s)
- Todd C Chappell
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
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36
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Challenges & opportunities for phage-based in situ microbiome engineering in the gut. J Control Release 2020; 326:106-119. [DOI: 10.1016/j.jconrel.2020.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 06/14/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022]
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37
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Huang FC, Lu YT, Liao YH. Beneficial effect of probiotics on Pseudomonas aeruginosa-infected intestinal epithelial cells through inflammatory IL-8 and antimicrobial peptide human beta-defensin-2 modulation. Innate Immun 2020; 26:592-600. [PMID: 32988256 DOI: 10.1177/1753425920959410] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The human pathogen Pseudomonas aeruginosa can rapidly induce fatal sepsis, even in previously healthy infants or children treated with appropriate antibiotics. To reduce antibiotic overuse, exploring novel complementary therapies, such as probiotics that reportedly protect patients against P. aeruginosa infection, would be particularly beneficial. However, the major mechanism underlying the clinical effects is not completely understood. We thus aimed to investigate how probiotics affect IL-8 and human beta-defensin 2 (hBD-2) in P. aeruginosa-infected intestinal epithelial cells (IECs). We infected SW480 IECs with wild type PAO1 P. aeruginosa following probiotic treatment with Lactobacillus rhamnosus GG or Bifidobacterium longum spp. infantis S12, and analysed the mRNA expression and secreted protein of IL-8 and hBD-2, Akt signalling and NOD1 receptor protein expression. We observed that probiotics enhanced hBD-2 expression but suppressed IL-8 responses when administered before infection. They also enhanced P. aeruginosa-induced membranous NOD1 protein expression and Akt activation. The siRNA-mediated Akt or NOD1 knockdown counteracted P. aeruginosa-induced IL-8 or hBD-2 expression, indicating regulatory effects of these probiotics. In conclusion, these data suggest that probiotics exert reciprocal regulation of inflammation and antimicrobial peptides in P. aeruginosa-infected IECs and provide supporting evidence for applying probiotics to reduce antibiotic overuse.
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Affiliation(s)
- Fu-Chen Huang
- Department of Paediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yi-Ting Lu
- Department of Paediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yu-Hsuan Liao
- Department of Paediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
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38
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Cortés A, Rooney J, Bartley DJ, Nisbet AJ, Cantacessi C. Helminths, hosts, and their microbiota: new avenues for managing gastrointestinal helminthiases in ruminants. Expert Rev Anti Infect Ther 2020; 18:977-985. [PMID: 32530331 DOI: 10.1080/14787210.2020.1782188] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Evidence is emerging of complex interactions occurring between gastrointestinal (GI) parasites of ruminants and the resident gut flora, with likely implications for the pathophysiology of worm infection and disease. Similarly, recent data point toward the occurrence of a GI nematode (GIN)-specific microbiota, with potential roles in worm fundamental physiology and reproduction. Parasite-microbiota relationships might represent potential targets for the development of novel parasiticides. AREAS COVERED In this article, we review current knowledge of the role(s) that host- and helminth-associated microbiota play in ruminant host-parasite relationships, and outline potential avenues for the control of GIN of farmed ruminants via the manipulation of resident microbial species with putative functions in infection establishment, host-immune modulation, and/or parasite fitness and survival. EXPERT OPINION In order for this knowledge to be translated into practical applications, we argue that several aspects of the nematode-microbiota cross-talk must be addressed, including (i) the causality of interactions between the parasite, the gut microbiota, and the host immune system, (ii) the modes of action of dietary prebiotics and probiotics, (iii) the mechanisms by which diet supplementation aids the development of resistance/tolerance to GI helminth infections and (iv) the composition of the GIN microbiome and its role(s) in parasite biology and physiology.
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Affiliation(s)
- Alba Cortés
- Departament de Farmàcia i Tecnologia Farmacèutica i Parasotologia, Facultat de Farmàcia, Universitat de València , València, Spain.,Department of Veterinary Medicine, University of Cambridge , Cambridge, UK
| | - James Rooney
- Department of Veterinary Medicine, University of Cambridge , Cambridge, UK
| | | | | | - Cinzia Cantacessi
- Department of Veterinary Medicine, University of Cambridge , Cambridge, UK
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39
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Feng W, Liu J, Ao H, Yue S, Peng C. Targeting gut microbiota for precision medicine: Focusing on the efficacy and toxicity of drugs. Am J Cancer Res 2020; 10:11278-11301. [PMID: 33042283 PMCID: PMC7532689 DOI: 10.7150/thno.47289] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Intra- and interindividual variation in drug responses is one major reason for the failure of drug therapy, drug toxicity, and even the death of patients. Precision medicine, or personalized medicine, is a field of medicine that customizes an individual's medical diagnosis and treatment based on his/her genes, microbiomes, environments, etc. Over the past decade, a large number of studies have demonstrated that gut microbiota can modify the efficacy and toxicity of drugs, and the extent of the modification varies greatly from person to person because of the variability of the gut microbiota. Personalized manipulation of gut microbiota is an important approach to rectify the abnormal drug response. In this review, we aim to improve drug efficacy and reduce drug toxicity by combining precision medicine and gut microbiota. After describing the interactions between gut microbiota and xenobiotics, we discuss (1) the effects of gut microbiota on drug efficacy and toxicity and the corresponding mechanisms, (2) the variability of gut microbiota, which leads to variation in drug responses, (3) the biomarkers used for the patient stratification and treatment decisions before the use of drugs, and (4) the methods used for the personalized manipulation of gut microbiota to improve drug outcomes. Overall, we hope to improve the drug response by incorporating the knowledge of gut microbiota into clinical practice.
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40
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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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41
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Lim YY, Lee YS, Ooi DSQ. Engineering the Gut Microbiome for Treatment of Obesity: A Review of Current Understanding and Progress. Biotechnol J 2020; 15:e2000013. [PMID: 32663372 DOI: 10.1002/biot.202000013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 07/07/2020] [Indexed: 12/13/2022]
Abstract
Obesity is a complex, multifactorial disease that is increasing in prevalence despite extensive research and efforts to curb it. Over the last decade, gut microbiome has emerged as an important contributor to the pathogenesis of obesity. Microbiome profile is altered in obese phenotype and the causative role of microbiome in obesity is demonstrated in fecal microbiota transplantation studies. Herein, recent evidences supporting the role of gut microbiome in obesity and the current therapies designed to engineer gut microbiome for treatment of obesity will be reviewed. The microbial enterotypes associated with obesity is outlined, and the gut microbiota-driven metabolism and low-grade inflammation linking gut microbiome and obesity is examined. How the different intrinsic and extrinsic factors such as host genetics, mode of childbirth delivery, diet, lifestyle habits and use of antibiotics influence the composition of the gut microbiome in the development of obesity is evaluated. Also, the efficacy of current microbiome-based therapies in the forms of prebiotics, probiotics and engineered microbes that are used to manipulate gut microbiome in treating obesity is discussed.
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Affiliation(s)
- Yvonne Yijuan Lim
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Division of Paediatric Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228, Singapore
| | - Yung Seng Lee
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Division of Paediatric Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228, Singapore
| | - Delicia Shu Qin Ooi
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Division of Paediatric Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore, 119228, Singapore
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42
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Shi Y, Li J, Shen Y, Sun Z. Using Probiotics to Mute Salmonella enteric Serovar Typhimurium: An Opinion. Front Bioeng Biotechnol 2020; 8:558. [PMID: 32656191 PMCID: PMC7324470 DOI: 10.3389/fbioe.2020.00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/07/2020] [Indexed: 01/03/2023] Open
Affiliation(s)
- Yang Shi
- Institute of Food and Drug Inspection, Zhoukou Normal University, Zhoukou, China
| | - Juan Li
- Institute of Food and Drug Inspection, Zhoukou Normal University, Zhoukou, China
| | - Yihao Shen
- Institute of Food and Drug Inspection, Zhoukou Normal University, Zhoukou, China
| | - Zhongke Sun
- Institute of Food and Drug Inspection, Zhoukou Normal University, Zhoukou, China.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, China
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43
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Egan S, Fukatsu T, Francino MP. Opportunities and Challenges to Microbial Symbiosis Research in the Microbiome Era. Front Microbiol 2020; 11:1150. [PMID: 32612581 PMCID: PMC7308722 DOI: 10.3389/fmicb.2020.01150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/06/2020] [Indexed: 01/04/2023] Open
Affiliation(s)
- Suhelen Egan
- Centre for Marine Science and Innovation (CMSI), School of Biological, Earth and Environmental Sciences (BEES), UNSW Sydney, Sydney, NSW, Australia
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - M Pilar Francino
- Joint Research Unit in Genomics and Health, Fundació per al Foment de la Investigació Sanitária i Biomèdica de la Comunitat Valenciana (FISABIO)/Institut de Biologia Integrativa de Sistemes (Universitat de València i Consejo Superior de Investigaciones Científicas), València, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain
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44
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Engineering microbial diagnostics and therapeutics with smart control. Curr Opin Biotechnol 2020; 66:11-17. [PMID: 32563763 DOI: 10.1016/j.copbio.2020.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 12/26/2022]
Abstract
Microbes have become an increasingly powerful chassis for developing diagnostic and therapeutic technologies. While many of the earlier engineering efforts used microbes that expressed relevant proteins constitutively, more microbes are being engineered to express them with region-selectivity and disease-responsiveness through biosensors. Such 'smart' microbes have been developed to diagnose and treat a wide range of disorders and diseases, including bacterial infections, cancers, inflammatory disorders, and metabolic disorders. In this review, we discuss synthetic biology technologies that have been applied to engineer microbes for biomedical applications, focusing on recent reports that demonstrate microbial sensing by using animal models or clinical samples. Advances in synthetic biology will enable engineered microbes to significantly improve the medical field.
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45
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Cho SW, Yim J, Seo SW. Engineering Tools for the Development of Recombinant Lactic Acid Bacteria. Biotechnol J 2020; 15:e1900344. [DOI: 10.1002/biot.201900344] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/27/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Sung Won Cho
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Jaewoo Yim
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
| | - Sang Woo Seo
- School of Chemical and Biological EngineeringInstitute of Chemical ProcessesSeoul National University 1 Gwanak‐ro Gwanak‐gu Seoul 08826 Republic of Korea
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46
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Abstract
Mucus in the gastrointestinal (GI) tract is the primary point-of-interaction between humans and their gut microbiota. This intimates that mucus not only ensures protection against endogenous and exogenous opportunists but also provisions for the human microbiota to reside and flourish. With the emergence of living therapeutics, engineered microbes can deliver and produce increasingly complex medicine, and controlling the mucoadhesive properties of different microbial chassis can dictate dose-response in a patient. Here we present a redesigned, in vitro, plate-based assay to measure the mucus adhesion of various probiotics. Cell-mucus interactions were isolated by immobilizing mucus to the plate surface. Binding parameters were derived for each probiotic strain by measuring cell adhesion over a wide range of cell concentrations, providing dose-dependent adhesion metrics. Surface proteins and cell components known to influence mucoadhesion were then heterologously expressed or altered in Lactococcus lactis MG1363 and Escherichia coli Nissle 1917 to control mucus-binding capacity, avidity, and cooperativity.
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Affiliation(s)
- Zachary J. S. Mays
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Todd C. Chappell
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Nikhil U. Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, United States
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47
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Bencivenga-Barry NA, Lim B, Herrera CM, Trent MS, Goodman AL. Genetic Manipulation of Wild Human Gut Bacteroides. J Bacteriol 2020; 202:e00544-19. [PMID: 31712278 PMCID: PMC6964735 DOI: 10.1128/jb.00544-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/01/2019] [Indexed: 12/30/2022] Open
Abstract
Bacteroides is one of the most prominent genera in the human gut microbiome, and study of this bacterial group provides insights into gut microbial ecology and pathogenesis. In this report, we introduce a negative selection system for rapid and efficient allelic exchange in wild Bacteroides species that does not require any alterations to the genetic background or a nutritionally defined culture medium. In this approach, dual antibacterial effectors normally delivered via type VI secretion are targeted to the bacterial periplasm under the control of tightly regulated anhydrotetracycline (aTC)-inducible promoters. Introduction of aTC selects for recombination events producing the desired genetic modification, and the dual effector design allows for broad applicability across strains that may have immunity to one counterselection effector. We demonstrate the utility of this approach across 21 human gut Bacteroides isolates representing diverse species, including strains isolated directly from human donors. We use this system to establish that antimicrobial peptide resistance in Bacteroides vulgatus is determined by the product of a gene that is not included in the genomes of previously genetically tractable members of the human gut microbiome.IMPORTANCE Human gut Bacteroides species exhibit strain-level differences in their physiology, ecology, and impact on human health and disease. However, existing approaches for genetic manipulation generally require construction of genetically modified parental strains for each microbe of interest or defined medium formulations. In this report, we introduce a robust and efficient strategy for targeted genetic manipulation of diverse wild-type Bacteroides species from the human gut. This system enables genetic investigation of members of human and animal microbiomes beyond existing model organisms.
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Affiliation(s)
- Natasha A Bencivenga-Barry
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
| | - Bentley Lim
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
| | - Carmen M Herrera
- Department of Infectious Diseases, University of Georgia at Athens, College of Veterinary Medicine, Athens, Georgia, USA
- Center for Vaccines and Immunology, University of Georgia at Athens, College of Veterinary Medicine, Athens, Georgia, USA
| | - M Stephen Trent
- Department of Infectious Diseases, University of Georgia at Athens, College of Veterinary Medicine, Athens, Georgia, USA
- Center for Vaccines and Immunology, University of Georgia at Athens, College of Veterinary Medicine, Athens, Georgia, USA
- Department of Microbiology, University of Georgia at Athens, College of Arts and Sciences, Athens, Georgia, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
- Microbial Sciences Institute, Yale University, West Haven, Connecticut, USA
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48
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Chang HJ, Bonnet J. Synthetic receptors to understand and control cellular functions. Methods Enzymol 2020; 633:143-167. [DOI: 10.1016/bs.mie.2019.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Sabit H, Cevik E, Tombuloglu H. Colorectal cancer: The epigenetic role of microbiome. World J Clin Cases 2019; 7:3683-3697. [PMID: 31799293 PMCID: PMC6887622 DOI: 10.12998/wjcc.v7.i22.3683] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 10/23/2019] [Accepted: 10/30/2019] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer in men (746000 cases per year) and the second most common cancer in women globally (614000 cases per year). The incidence rate of CRC in developed countries (737000 cases per year) is higher than that in less developed countries (624000 cases per year). CRC can arise from genetic causes such as chromosomal instability and microsatellite instability. Several etiologic factors underlie CRC including age, diet, and lifestyle. Gut microbiota represent a proven cause of the disease, where they play pivotal roles in modulating and reshaping the host epigenome. Several active microbial metabolites have been found to drive carcinogenesis, invasion, and metastasis via modifying both the methylation landscape along with histone structure in intestinal cells. Gut microbiota, in response to diet, can exert both beneficial and harmful functions in humans, according to the intestinal balance of number and types of these bacteria. Although the intestinal microbial community is diverse among individuals, these microbes cumulatively produce 100-fold more proteins than the human genome itself, which calls for further studies to elaborate on the complicated interaction between these microorganisms and intestinal cells. Therefore, understanding the exact role that gut microbiota play in inducing CRC will help attain reliable strategies to precisely diagnose and treat this fatal disease.
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Affiliation(s)
- Hussein Sabit
- Department of Genetics, Institute for Medical Research and Consultations, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Emre Cevik
- Department of Genetics, Institute for Medical Research and Consultations, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics, Institute for Medical Research and Consultations, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
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50
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Yadav M, Mandeep, Shukla P. Probiotics of Diverse Origin and Their Therapeutic Applications: A Review. J Am Coll Nutr 2019; 39:469-479. [PMID: 31765283 DOI: 10.1080/07315724.2019.1691957] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The increased awareness about the harmful effects of excessive use of antibiotics has created an interest in probiotics due to its beneficial effects on gut microbiota. These advantages of probiotics have attracted researchers to find out effects on human metabolism and their role in the treatment of diverse types of diseases or disorders. Additionally, they are clinically used as biocontrol agents in the treatment of mental disorders, anticancer agents and in decreasing the threat of necrotizing enterocolitis in premature infants. In this review, we have focused on various kinds of probiotics and various nondairy substrates for their production. We have also included the importance of probiotics in the treatment of metabolic disorders, type II diabetes and infectious diseases. Furthermore, this review emphasizes applications of probiotics originated from different organisms. Their future health perspectives are discussed to gain insight into their applications.KEY TEACHING POINTSThe global market of probiotics is enormously rising day by day due to its highly beneficial effect on human microbiota.Additionally, these are used as biocontrol agents; mental disorders prevent cancer and decrease the threat of necrotizing enterocolitis (NEC) in premature infants.This review focuses on various kinds of sources of probiotics and various non-dairy substrates for the production of probiotics.The importance of probiotics in the treatment of metabolic disorders, type II diabetes control, cancer and treatment of infectious diseases are also described.It emphasizes diversified probiotics and their applications in various human health aspects and future perspectives.
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Affiliation(s)
- Monika Yadav
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Mandeep
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
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