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Arun KB, Madhavan A, Sindhu R, Emmanual S, Binod P, Pugazhendhi A, Sirohi R, Reshmy R, Awasthi MK, Gnansounou E, Pandey A. Probiotics and gut microbiome - Prospects and challenges in remediating heavy metal toxicity. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126676. [PMID: 34329091 DOI: 10.1016/j.jhazmat.2021.126676] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/02/2021] [Accepted: 07/15/2021] [Indexed: 05/26/2023]
Abstract
The gut microbiome, often referred to as "super organ", comprises up to a hundred trillion microorganisms, and the species diversity may vary from person to person. They perform a decisive role in diverse biological functions related to metabolism, immunity and neurological responses. However, the microbiome is sensitive to environmental pollutants, especially heavy metals. There is continuous interaction between heavy metals and the microbiome. Heavy metal exposure retards the growth and changes the structure of the phyla involved in the gut microbiome. Meanwhile, the gut microbiome tries to detoxify the heavy metals by altering the physiological conditions, intestinal permeability, enhancing enzymes for metabolizing heavy metals. This review summarizes the effect of heavy metals in altering the gut microbiome, the mechanism by which gut microbiota detoxifies heavy metals, diseases developed due to heavy metal-induced dysbiosis of the gut microbiome, and the usage of probiotics along with advancements in developing improved recombinant probiotic strains for the remediation of heavy metal toxicity.
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Affiliation(s)
- K B Arun
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, Kerala, India
| | - Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, Kerala, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695019, Kerala, India
| | - Shibitha Emmanual
- Department of Zoology, St. Joseph's College, Thrissur 680121, Kerala, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695019, Kerala, India
| | - Arivalagan Pugazhendhi
- School of Renewable Energy, Maejo University, Chiang Mai 50290, Thailand; College of Medical and Health Science, Asia University, Taichung, Taiwan ROC
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea; Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, North West A & F University, Yangling, Shaanxi 712100, China
| | - Edgard Gnansounou
- Ecole Polytechnique Federale de Lausanne, ENAC GR-GN, CH-1015 Lausanne, Switzerland
| | - Ashok Pandey
- Centre for Innovation and Translational Research, CSIR, Indian Institute for Toxicology Research, Lucknow 226001, Uttar Pradesh, India; Centre for Energy and Environmental Sustainability, Lucknow 226029, Uttar Pradesh, India.
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Abstract
The steadfast advance of the synthetic biology field has enabled scientists to use genetically engineered cells, instead of small molecules or biologics, as the basis for the development of novel therapeutics. Cells endowed with synthetic gene circuits can control the localization, timing and dosage of therapeutic activities in response to specific disease biomarkers and thus represent a powerful new weapon in the fight against disease. Here, we conceptualize how synthetic biology approaches can be applied to programme living cells with therapeutic functions and discuss the advantages that they offer over conventional therapies in terms of flexibility, specificity and predictability, as well as challenges for their development. We present notable advances in the creation of engineered cells that harbour synthetic gene circuits capable of biological sensing and computation of signals derived from intracellular or extracellular biomarkers. We categorize and describe these developments based on the cell scaffold (human or microbial) and the site at which the engineered cell exerts its therapeutic function within its human host. The design of cell-based therapeutics with synthetic biology is a rapidly growing strategy in medicine that holds great promise for the development of effective treatments for a wide variety of human diseases.
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Construction of a sustainable 3-hydroxybutyrate-producing probiotic Escherichia coli for treatment of colitis. Cell Mol Immunol 2021; 18:2344-2357. [PMID: 34480146 PMCID: PMC8484604 DOI: 10.1038/s41423-021-00760-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/08/2021] [Indexed: 02/07/2023] Open
Abstract
Colitis is a common disease of the colon that is very difficult to treat. Probiotic bacteria could be an effective treatment. The probiotic Escherichia coli Nissle 1917 (EcN) was engineered to synthesize the ketone body (R)-3-hydroxybutyrate (3HB) for sustainable production in the gut lumen of mice suffering from colitis. Components of heterologous 3HB synthesis routes were constructed, expressed, optimized, and inserted into the EcN genome, combined with deletions in competitive branch pathways. The genome-engineered EcN produced the highest 3HB level of 0.6 g/L under microaerobic conditions. The live therapeutic was found to colonize the mouse gastrointestinal tract over 14 days, elevating gut 3HB and short-chain-length fatty acid (SCFA) levels 8.7- and 3.1-fold compared to those of wild-type EcN, respectively. The sustainable presence of 3HB in mouse guts promoted the growth of probiotic bacteria, especially Akkermansia spp., to over 31% from the initial 2% of all the microbiome. As a result, the engineered EcN termed EcNL4 ameliorated colitis induced via dextran sulfate sodium (DSS) in mice. Compared to wild-type EcN or oral administration of 3HB, oral EcNL4 uptake demonstrated better effects on mouse weights, colon lengths, occult blood levels, gut tissue myeloperoxidase activity and proinflammatory cytokine concentrations. Thus, a promising live bacterium was developed to improve colonic microenvironments and further treat colitis. This proof-of-concept design can be employed to treat other diseases of the colon.
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Mejía-Pitta A, Broset E, de la Fuente-Nunez C. Probiotic engineering strategies for the heterologous production of antimicrobial peptides. Adv Drug Deliv Rev 2021; 176:113863. [PMID: 34273423 PMCID: PMC8440409 DOI: 10.1016/j.addr.2021.113863] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/10/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022]
Abstract
Engineered probiotic bacteria represent an innovative approach for treating and detecting a wide range of diseases including those caused by infectious agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics for combating antibiotic-resistant infections. These molecules can be delivered orally to the gut by using engineered probiotics, which confer protection against AMP degradation, thus enabling numerous applications including treating drug-resistant enteric pathogens and remodeling the microbiota in real time. Here, we provide an update on the current state of the art on AMP-producing probiotics, discuss methods to enhance gut colonization, and end by outlining future perspectives.
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Affiliation(s)
- Adriana Mejía-Pitta
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Esther Broset
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America; Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, United States of America; Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, United States of America.
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56
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Xu Y. Phage and phage lysins: New era of bio-preservatives and food safety agents. J Food Sci 2021; 86:3349-3373. [PMID: 34302296 DOI: 10.1111/1750-3841.15843] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/09/2021] [Accepted: 06/14/2021] [Indexed: 01/21/2023]
Abstract
There has been an increase in the search and application of new antimicrobial agents as alternatives to use of chemical preservatives and antibiotic-like compounds by the food industry. The massive use of antibiotic has created a reservoir of antibiotic-resistant bacteria that find their way from farm to humans. Thus, there exists an imperative need to explore new antibacterial options and bacteriophages perfectly fit into the class of safe and potent antimicrobials. Phage bio-control has come a long way owing to advances with use of phage cocktails, recombinant phages, and phage lysins; however, there still exists unmet challenges that restrict the number of phage-based products reaching the market. Hence, further studies are required to explore for more efficient phage-based bio-control strategies that can become an integral part of food safety protocols. This review thus aims to highlight the recent developments made in the application of phages and phage enzymes covering pre-harvest as well as post-harvest usage. It further focuses on the major issues in both phage and phage lysin research hindering their optimum use while detailing out the advances made by researchers lately in this direction for full exploitation of phages and phage lysins in the food sector.
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Affiliation(s)
- Yingmin Xu
- Food Technology College Jiangsu Vocational College of Agriculture and Forestry, China
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Chen J, Li X, Liu Y, Su T, Lin C, Shao L, Li L, Li W, Niu G, Yu J, Liu L, Li M, Yu X, Wang Q. Engineering a probiotic strain of Escherichia coli to induce the regression of colorectal cancer through production of 5-aminolevulinic acid. Microb Biotechnol 2021; 14:2130-2139. [PMID: 34272828 PMCID: PMC8449674 DOI: 10.1111/1751-7915.13894] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 06/03/2021] [Accepted: 07/03/2021] [Indexed: 01/30/2023] Open
Abstract
Bacterial vectors can be engineered to generate microscopic living therapeutics to produce and deliver anticancer agents. Escherichia coli Nissle 1917 (Nissle 1917) is a promising candidate with probiotic properties. Here, we used Nissle 1917 to develop a metabolic strategy to produce 5‐aminolevulinic acid (5‐ALA) from glucose as 5‐ALA plays an important role in the photodynamic therapy of cancers. The coexpression of hemAM and hemL using a low copy‐number plasmid led to remarkable accumulation of 5‐ALA. The downstream pathway of 5‐ALA biosynthesis was inhibited by levulinic acid (LA). Small‐scale cultures of engineered Nissle 1917 produced 300 mg l−1 of 5‐ALA. Recombinant Nissle 1917 was applied to deliver 5‐ALA to colorectal cancer cells, in which it induced the accumulation of antineoplastic protoporphyrin X (PpIX) and specific cytotoxicity towards colorectal cancer cells irradiated with a 630 nm laser. Moreover, this novel combination therapy proved effective in a mouse xenograft model and was not cytotoxic to normal tissues. These findings suggest that Nissle 1917 will serve as a potential carrier to effectively deliver 5‐ALA for cancer therapy. We combined the biosynthetic and tumor‐targeting features of the probiotic Escherichia coli Nissle 1917 with PDT to deliver 5‐ALA to colorectal cancer cells. E. coli Nissle 1917 was engineered to produce 5‐ALA, and delivered 5‐ALA to colorectal cancer cells to inhibit growth.
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Affiliation(s)
- Junhao Chen
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Xiaohong Li
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Yumei Liu
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong, 266237, China
| | - Changsen Lin
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, China
| | - Lijun Shao
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Lanhua Li
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Wanwei Li
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Guoyu Niu
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jing Yu
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250014, China
| | - Ling Liu
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Miaomiao Li
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Xiaoli Yu
- School of Public Health, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, Shandong, 266237, China
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58
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Gangadharan S, Raman K. The art of molecular computing: Whence and whither. Bioessays 2021; 43:e2100051. [PMID: 34101866 DOI: 10.1002/bies.202100051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/11/2021] [Accepted: 05/18/2021] [Indexed: 12/30/2022]
Abstract
An astonishingly diverse biomolecular circuitry orchestrates the functioning machinery underlying every living cell. These biomolecules and their circuits have been engineered not only for various industrial applications but also to perform other atypical functions that they were not evolved for-including computation. Various kinds of computational challenges, such as solving NP-complete problems with many variables, logical computation, neural network operations, and cryptography, have all been attempted through this unconventional computing paradigm. In this review, we highlight key experiments across three different ''eras'' of molecular computation, beginning with molecular solutions, transitioning to logic circuits and ultimately, more complex molecular networks. We also discuss a variety of applications of molecular computation, from solving NP-hard problems to self-assembled nanostructures for delivering molecules, and provide a glimpse into the exciting potential that molecular computing holds for the future. Also see the video abstract here: https://youtu.be/9Mw0K0vCSQw.
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Affiliation(s)
- Sahana Gangadharan
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India
| | - Karthik Raman
- Bhupat and Jyoti Mehta School of Biosciences, Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India.,Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai, India.,Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), Indian Institute of Technology Madras, Chennai, India
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59
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Characterization of Lysozyme-Like Effector TseP Reveals the Dependence of Type VI Secretion System (T6SS) Secretion on Effectors in Aeromonas dhakensis Strain SSU. Appl Environ Microbiol 2021; 87:e0043521. [PMID: 33837015 DOI: 10.1128/aem.00435-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread weapon employed by Gram-negative bacteria for interspecies interaction in complex communities. Analogous to a contractile phage tail, the double-tubular T6SS injects toxic effectors into prokaryotic and eukaryotic neighboring cells. Although effectors dictate T6SS functions, their identities remain elusive in many pathogens. Here, we report the lysozyme-like effector TseP in Aeromonas dhakensis, a waterborne pathogen that can cause severe gastroenteritis and systemic infection. Using secretion, competition, and enzymatic assays, we demonstrate that TseP is a T6SS-dependent effector with cell wall-lysing activities, and TsiP is its cognate immunity protein. Triple deletion of tseP and two known effector genes, tseI and tseC, abolished T6SS-mediated secretion, while complementation with any single effector gene partially restored bacterial killing and Hcp secretion. In contrast to whole-gene deletions, the triple-effector inactivation in the 3effc mutant abolished antibacterial killing but not T6SS secretion. We further demonstrate that the 3effc mutation abolished T6SS-mediated toxicity of SSU to Dictyostelium discoideum amoebae, suggesting that the T6SS physical puncture is nontoxic to eukaryotic cells. These data highlight not only the necessity of possessing functionally diverse effectors for survival in multispecies communities but also that effector inactivation would be an efficient strategy to detoxify the T6SS while preserving its delivery efficiency, converting the T6SS to a platform for protein delivery to a variety of recipient cells. IMPORTANCE Delivery of cargo proteins via protein secretion systems has been shown to be a promising tool in various applications. However, secretion systems are often used by pathogens to cause disease. Thus, strategies are needed to detoxify secretion systems while preserving their efficiency. The T6SS can translocate proteins through physical puncture of target cells without specific surface receptors and can target a broad range of recipients. In this study, we identified a cell wall-lysing effector, and by inactivating it and the other two known effectors, we have built a detoxified T6SS-active strain that may be used for protein delivery to prokaryotic and eukaryotic recipient cells.
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60
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Durmusoglu D, Al’Abri IS, Collins SP, Cheng J, Eroglu A, Beisel CL, Crook N. In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii. ACS Synth Biol 2021; 10:1039-1052. [PMID: 33843197 DOI: 10.1021/acssynbio.0c00562] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Saccharomyces boulardii is a probiotic yeast that exhibits rapid growth at 37 °C, is easy to transform, and can produce therapeutic proteins in the gut. To establish its ability to produce small molecules encoded by multigene pathways, we measured the amount and variance in protein expression enabled by promoters, terminators, selective markers, and copy number control elements. We next demonstrated efficient (>95%) CRISPR-mediated genome editing in this strain, allowing us to probe engineered gene expression across different genomic sites. We leveraged these strategies to assemble pathways enabling a wide range of vitamin precursor (β-carotene) and drug (violacein) titers. We found that S. boulardii colonizes germ-free mice stably for over 30 days and competes for niche space with commensal microbes, exhibiting short (1-2 day) gut residence times in conventional and antibiotic-treated mice. Using these tools, we enabled β-carotene synthesis (194 μg total) in the germ-free mouse gut over 14 days, estimating that the total mass of additional β-carotene recovered in feces was 56-fold higher than the β-carotene present in the initial probiotic dose. This work quantifies heterologous small molecule production titers by S. boulardii living in the mammalian gut and provides a set of tools for modulating these titers.
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Affiliation(s)
- Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Ibrahim S. Al’Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Scott P. Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Junrui Cheng
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Room 3204, Kannapolis, North Carolina 28081, United States
| | - Abdulkerim Eroglu
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Room 3204, Kannapolis, North Carolina 28081, United States
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, 120 Broughton Drive, Room 351, Raleigh, North Carolina 27695-7622, United States
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg 97080, Germany
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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Liu X, Wu M, Wang M, Duan Y, Phan C, Qi G, Tang G, Liu B. Metabolically engineered bacteria as light-controlled living therapeutics for anti-angiogenesis tumor therapy. MATERIALS HORIZONS 2021; 8:1454-1460. [PMID: 34846453 DOI: 10.1039/d0mh01582b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A living therapeutic system based on attenuated Salmonella was developed via metabolic engineering using an aggregation-induced emission (AIE) photosensitizer MA. The engineered bacteria could localize in the tumor tissues and continue to colonize and express exogenous genes. Under light irradiation, the encoded VEGFR2 gene was released and expressed in tumor tissues, which can suppress angiogenesis induced by a T cell-mediated autoimmune response and inhibit tumor growth.
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Affiliation(s)
- Xingang Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Engineering Drive 4, 117585, Singapore.
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David F, Davis AM, Gossing M, Hayes MA, Romero E, Scott LH, Wigglesworth MJ. A Perspective on Synthetic Biology in Drug Discovery and Development-Current Impact and Future Opportunities. SLAS DISCOVERY 2021; 26:581-603. [PMID: 33834873 DOI: 10.1177/24725552211000669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The global impact of synthetic biology has been accelerating, because of the plummeting cost of DNA synthesis, advances in genetic engineering, growing understanding of genome organization, and explosion in data science. However, much of the discipline's application in the pharmaceutical industry remains enigmatic. In this review, we highlight recent examples of the impact of synthetic biology on target validation, assay development, hit finding, lead optimization, and chemical synthesis, through to the development of cellular therapeutics. We also highlight the availability of tools and technologies driving the discipline. Synthetic biology is certainly impacting all stages of drug discovery and development, and the recognition of the discipline's contribution can further enhance the opportunities for the drug discovery and development value chain.
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Affiliation(s)
- Florian David
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrew M Davis
- Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Cambridge, UK
| | - Michael Gossing
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Martin A Hayes
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elvira Romero
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Louis H Scott
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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Lorente-Picón M, Laguna A. New Avenues for Parkinson's Disease Therapeutics: Disease-Modifying Strategies Based on the Gut Microbiota. Biomolecules 2021; 11:433. [PMID: 33804226 PMCID: PMC7998286 DOI: 10.3390/biom11030433] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
Parkinson's disease (PD) is a multifactorial neurodegenerative disorder that currently affects 1% of the population over the age of 60 years, and for which no disease-modifying treatments exist. Neurodegeneration and neuropathology in different brain areas are manifested as both motor and non-motor symptoms in patients. Recent interest in the gut-brain axis has led to increasing research into the gut microbiota changes in PD patients and their impact on disease pathophysiology. As evidence is piling up on the effects of gut microbiota in disease development and progression, another front of action has opened up in relation to the potential usage of microbiota-based therapeutic strategies in treating gastrointestinal alterations and possibly also motor symptoms in PD. This review provides status on the different strategies that are in the front line (i.e., antibiotics; probiotics; prebiotics; synbiotics; dietary interventions; fecal microbiota transplantation, live biotherapeutic products), and discusses the opportunities and challenges the field of microbiome research in PD is facing.
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Affiliation(s)
- Marina Lorente-Picón
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute (VHIR)-Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Ariadna Laguna
- Neurodegenerative Diseases Research Group, Vall d'Hebron Research Institute (VHIR)-Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
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Chiang CJ, Huang PH. Metabolic engineering of probiotic Escherichia coli for cytolytic therapy of tumors. Sci Rep 2021; 11:5853. [PMID: 33712706 PMCID: PMC7971005 DOI: 10.1038/s41598-021-85372-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/28/2021] [Indexed: 12/13/2022] Open
Abstract
Bacterial cancer therapy was developed using probiotic Escherichia coli Nissle 1917 (EcN) for medical intervention of colorectal cancer. EcN was armed with HlyE, a small cytotoxic protein, under the control of the araBAD promoter (PBAD). The intrinsic limitation of PBAD for the gene expression is known to be negated by glucose and afflicted with all-or-nothing induction in host bacteria. This issue was addressed by metabolic engineering of EcN to uncouple the glucose-mediated control circuit and the L-arabinose transport-induction loop and to block L-arabinose catabolism. As a result, the reprogrammed strain (designated EcNe) enabled efficient expression of HlyE in a temporal control manner. The HlyE production was insensitive to glucose and reached a saturated level in response to L-arabinose at 30-50 μM. Moreover, the administrated EcNe exhibited tumor-specific colonization with the tumor-to-organ ratio of 106:1. Equipped with HlyE, EcNe significantly caused tumor regression in mice xenografted with human colorectal cancer cells. Overall, this study proposes a new strategy for the bacteria-mediated delivery of therapeutic proteins to tumors.
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Affiliation(s)
- Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402, Taiwan.
| | - Po-Han Huang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402, Taiwan
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Brooks SM, Alper HS. Applications, challenges, and needs for employing synthetic biology beyond the lab. Nat Commun 2021; 12:1390. [PMID: 33654085 PMCID: PMC7925609 DOI: 10.1038/s41467-021-21740-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
Synthetic biology holds great promise for addressing global needs. However, most current developments are not immediately translatable to 'outside-the-lab' scenarios that differ from controlled laboratory settings. Challenges include enabling long-term storage stability as well as operating in resource-limited and off-the-grid scenarios using autonomous function. Here we analyze recent advances in developing synthetic biological platforms for outside-the-lab scenarios with a focus on three major application spaces: bioproduction, biosensing, and closed-loop therapeutic and probiotic delivery. Across the Perspective, we highlight recent advances, areas for further development, possibilities for future applications, and the needs for innovation at the interface of other disciplines.
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Affiliation(s)
- Sierra M Brooks
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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66
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Tan X, Letendre JH, Collins JJ, Wong WW. Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics. Cell 2021; 184:881-898. [PMID: 33571426 PMCID: PMC7897318 DOI: 10.1016/j.cell.2021.01.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
Synthetic biology is a design-driven discipline centered on engineering novel biological functions through the discovery, characterization, and repurposing of molecular parts. Several synthetic biological solutions to critical biomedical problems are on the verge of widespread adoption and demonstrate the burgeoning maturation of the field. Here, we highlight applications of synthetic biology in vaccine development, molecular diagnostics, and cell-based therapeutics, emphasizing technologies approved for clinical use or in active clinical trials. We conclude by drawing attention to recent innovations in synthetic biology that are likely to have a significant impact on future applications in biomedicine.
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Affiliation(s)
- Xiao Tan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - Justin H Letendre
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Synthetic Biology Center, MIT, 77 Massachusetts Ave., Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
| | - Wilson W Wong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA.
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67
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Build a Sustainable Vaccines Industry with Synthetic Biology. Trends Biotechnol 2021; 39:866-874. [PMID: 33431228 PMCID: PMC7834237 DOI: 10.1016/j.tibtech.2020.12.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/21/2020] [Accepted: 12/09/2020] [Indexed: 12/24/2022]
Abstract
The vaccines industry has not changed appreciably in decades regarding technology, and has struggled to remain viable, with large companies withdrawing from production. Meanwhile, there has been no let-up in outbreaks of viral disease, at a time when the biopharmaceuticals industry is discussing downsizing. The distributed manufacturing model aligns well with this, and the advent of synthetic biology promises much in terms of vaccine design. Biofoundries separate design from manufacturing, a hallmark of modern engineering. Once designed in a biofoundry, digital code can be transferred to a small-scale manufacturing facility close to the point of care, rather than physically transferring cold-chain-dependent vaccine. Thus, biofoundries and distributed manufacturing have the potential to open up a new era of biomanufacturing, one based on digital biology and information systems. This seems a better model for tackling future outbreaks and pandemics.
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Abstract
Bacteria possess many unique properties in treating cancer that are unachievable with standard methods, including specific tumor targeting, deep tissue penetration, and programmable therapeutic efficacy. Bacteria species such as Salmonella, Escherichia, Clostridium, and Listeria have been demonstrated to restrict tumor growth with improved prognosis in mice models. Moreover, some bacterial strains were advanced to clinical trials. This Spotlight on Applications summarizes general strategies for engineering living bacteria to fight cancer and provides examples to illustrate different approaches to engineer bacteria for safety and therapeutic index improvement.
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Affiliation(s)
- Lei Rong
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China.,Institute of Pharmaceutical Sciences, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Qi Lei
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China.,School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, People's Republic of China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan 430072, People's Republic of China
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69
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Kelly VW, Liang BK, Sirk SJ. Living Therapeutics: The Next Frontier of Precision Medicine. ACS Synth Biol 2020; 9:3184-3201. [PMID: 33205966 DOI: 10.1021/acssynbio.0c00444] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Modern medicine has long studied the mechanism and impact of pathogenic microbes on human hosts, but has only recently shifted attention toward the complex and vital roles that commensal and probiotic microbes play in both health and dysbiosis. Fueled by an enhanced appreciation of the human-microbe holobiont, the past decade has yielded countless insights and established many new avenues of investigation in this area. In this review, we discuss advances, limitations, and emerging frontiers for microbes as agents of health maintenance, disease prevention, and cure. We highlight the flexibility of microbial therapeutics across disease states, with special consideration for the rational engineering of microbes toward precision medicine outcomes. As the field advances, we anticipate that tools of synthetic biology will be increasingly employed to engineer functional living therapeutics with the potential to address longstanding limitations of traditional drugs.
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Affiliation(s)
- Vince W. Kelly
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Benjamin K. Liang
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Shannon J. Sirk
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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70
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Zou Y, Chen T. Engineered Akkermansia muciniphila: A promising agent against diseases (Review). Exp Ther Med 2020; 20:285. [PMID: 33209129 PMCID: PMC7668130 DOI: 10.3892/etm.2020.9415] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/15/2020] [Indexed: 12/23/2022] Open
Abstract
Achieving a harmonious gut microbial ecosystem has been hypothesized to be a successful method for alleviating metabolic disorders. The administration of probiotics, such as Lactobacillus and Bifidobacteria, is a known traditional and safe pathway to regulate human commensal microbes. With advancements in genetic sequencing and genetic editing tools, more bacteria are able to function as engineered probiotics with multiple therapeutic properties. As one of the next-generation probiotic candidates, Akkermansia muciniphila (A. muciniphila) has been discovered to enhance the gut barrier function and moderate inflammatory responses, exhibit improved effects with pasteurization and display beneficial probiotic effects in individuals with obesity, type 2 diabetes, atherosclerosis and autism-related gastrointestinal disturbances. In view of this knowledge, the present review aimed to summarize the effects of A. muciniphila in the treatment of metabolic disorders and to discuss several mature recombination systems for the genetic modification of A. muciniphila. From gaining an enhanced understanding of its genetic background, ingested A. muciniphila is expected to be used in various applications, including as a diagnostic tool, and in the site-specific delivery of therapeutic drugs.
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Affiliation(s)
- Yixuan Zou
- Institute of Translational Medicine, National Engineering Research Center for Bioengineering Drugs and Technologies, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Tingtao Chen
- Institute of Translational Medicine, National Engineering Research Center for Bioengineering Drugs and Technologies, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
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71
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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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72
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Wu ZC, Feng HX, Wu L, Zhang M, Zhou WL. Quorum Sensing System in Bacteroides thetaiotaomicron Strain Identified by Genome Sequence Analysis. ACS OMEGA 2020; 5:27502-27513. [PMID: 33134713 PMCID: PMC7594123 DOI: 10.1021/acsomega.0c03986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 09/29/2020] [Indexed: 06/11/2023]
Abstract
This study is a bioinformatics assay on the microbial genome of Bacteroides thetaiotaomicron. The study focuses on the problem of quorum sensing as a result of adverse factors such as chemotherapy and antibiotic therapy. In patients with severe intestinal diseases, two strains of microorganisms were identified that were distinguished as new. Strains were investigated by conducting genome sequencing. The current concepts concerned with the quorum sensing system regulation by stationary-phase sigma factor and their coregulation of target genes in B. thetaiotaomicron were considered. The study suggested using bioinformatics data for the diagnosis of gastrointestinal disorders. In the course of the study, 402 genes having a greater than twofold change were identified with the 95% confidence level. The shortest and longest coding genes were predicted; the noncoding genes were detected. Biological pathways (KEGG pathways) were classified into the following categories: cellular processes, environmental information processing, genetic information processing, human disease, metabolism, and organismic systems. Among notable changes in the biofilm population observed in parallel to the planktonic B. thetaiotaomicron was the expression of genes in the polysaccharide utilization loci that were involved in the synthesis of O-glycans.
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Affiliation(s)
- Zhi Cheng Wu
- Department
of Laboratory, First Affiliated Hospital
of Hainan Medical College, 31 Longhua Road, Haikou, Hainan 570102, China
| | - Hong Xin Feng
- School
of Tropical and Laboratory Medicine, Hainan
Medical University, Haikou, Hainan 571199, China
| | - Lin Wu
- School
of Tropical and Laboratory Medicine, Hainan
Medical University, Haikou, Hainan 571199, China
- Department
of Biotechnology and Biotechnics, National
Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic
Institute”, Kyiv 03056, Ukraine
- Key
Laboratory of Tropical Translational Medicine, Ministry of Education, Hainan Medical University, Haikou Hainan 571199, China
| | - Meng Zhang
- Sanya
People’s Hospital, Jiefang Third Road, 558, Sanya 572000, China
| | - Wei Lan Zhou
- Department
of Laboratory, First Affiliated Hospital
of Hainan Medical College, 31 Longhua Road, Haikou, Hainan 570102, China
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73
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Lammens EM, Nikel PI, Lavigne R. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nat Commun 2020; 11:5294. [PMID: 33082347 PMCID: PMC7576135 DOI: 10.1038/s41467-020-19124-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022] Open
Abstract
Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.
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Affiliation(s)
- Eveline-Marie Lammens
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium
| | - Pablo Ivan Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, DK, Denmark
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, BE, Belgium.
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74
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75
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De Maesschalck V, Gutiérrez D, Paeshuyse J, Lavigne R, Briers Y. Advanced engineering of third-generation lysins and formulation strategies for clinical applications. Crit Rev Microbiol 2020; 46:548-564. [PMID: 32886565 DOI: 10.1080/1040841x.2020.1809346] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
One of the possible solutions for the current antibiotic resistance crisis may be found in (often bacteriophage-derived) peptidoglycan hydrolases. The first clinical trials of these natural enzymes, coined here as first-generation lysins, are currently ongoing. Moving beyond natural endolysins with protein engineering established the second generation of lysins. In second-generation lysins, the focus lies on improving antibacterial and biochemical properties such as antimicrobial activity and stability, as well as expanding their activities towards Gram-negative pathogens. However, solutions to particular key challenges regarding clinical applications are only beginning to emerge in the third generation of lysins, in which protein and biochemical engineering efforts focus on improving properties relevant under clinical conditions. In addition, increasingly advanced formulation strategies are developed to increase the bioavailability, antibacterial activity, and half-life, and to reduce pro-inflammatory responses. This review focuses on third-generation and advanced formulation strategies that are developed to treat infections, ranging from topical to systemic applications. Together, these efforts may fully unlock the potential of lysin therapy and will propel it as a true antibiotic alternative or supplement.
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Affiliation(s)
- Vincent De Maesschalck
- Department of Biosystems, KU Leuven, Leuven, Belgium.,Department of Biotechnology, Ghent University, Gent, Belgium
| | - Diana Gutiérrez
- Department of Biotechnology, Ghent University, Gent, Belgium
| | - Jan Paeshuyse
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Yves Briers
- Department of Biotechnology, Ghent University, Gent, Belgium
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76
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Tanna T, Ramachanderan R, Platt RJ. Engineered bacteria to report gut function: technologies and implementation. Curr Opin Microbiol 2020; 59:24-33. [PMID: 32828048 DOI: 10.1016/j.mib.2020.07.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 12/15/2022]
Abstract
Advances in synthetic biology and microbiology have enabled the creation of engineered bacteria which can sense and report on intracellular and extracellular signals. When deployed in vivo these whole-cell bacterial biosensors can act as sentinels to monitor biomolecules of interest in human health and disease settings. This is particularly interesting in the context of the gut microbiota, which interacts extensively with the human host throughout time and transit of the gut and can be accessed from feces without requiring invasive collection. Leveraging rational engineering approaches for genetic circuits as well as an expanding catalog of disease-associated biomarkers, bacterial biosensors can act as non-invasive and easy-to-monitor reporters of the gut. Here, we summarize recent engineering approaches applied in vivo in animal models and then highlight promising technologies for designing the next generation of bacterial biosensors.
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Affiliation(s)
- Tanmay Tanna
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Computer Science, ETH Zurich, Universitätstrasse 6, 8092 Zürich, Switzerland
| | - Raghavendra Ramachanderan
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland; Department of Chemistry, University of Basel, Petersplatz 1, 4003 Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland.
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77
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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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78
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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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79
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Liu Y, Chen J, Crisante D, Jaramillo Lopez JM, Mahadevan R. Dynamic Cell Programming with Quorum Sensing-Controlled CRISPRi Circuit. ACS Synth Biol 2020; 9:1284-1291. [PMID: 32485106 DOI: 10.1021/acssynbio.0c00148] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Synthetic biology is enabling rapid advances in the areas of biomanufacturing and live therapeutics. Dynamic circuits that can be used to regulate cellular resources and microbial community behavior represent a defining focus of synthetic biology, and have attracted tremendous interest. However, the existing dynamic circuits are mostly gene editing-dependent or cell lysis-based, which limits their broad and convenient application, and in some cases, such lysis-based circuits can suffer from genetic instability due to evolution. There is limited research in quorum sensing-assisted CRISPRi, which can function in a gene editing-independent manner. Here, we constructed a series of quorum sensing controlled CRISPRi systems (Q-CRISPRi), which can dynamically program bacteria by using customized sgRNA without introducing cell lysis. We successfully applied Q-CRISPRi circuits to dynamically program gene expression, population density, phenotype, physical property, and community composition of microbial consortia. The strategies reported here represent methods for dynamic cell programming and could be effective in programming industrially and medically important microorganisms to offer better control of their metabolism and behavior.
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Affiliation(s)
- Yilan Liu
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Jinjin Chen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - David Crisante
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Jhoselyn Marisol Jaramillo Lopez
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 200 College Street, Toronto, Ontario M5S 3E5, Canada
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80
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Yu X, Lin C, Yu J, Qi Q, Wang Q. Bioengineered Escherichia coli Nissle 1917 for tumour-targeting therapy. Microb Biotechnol 2020; 13:629-636. [PMID: 31863567 PMCID: PMC7111071 DOI: 10.1111/1751-7915.13523] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 12/19/2022] Open
Abstract
Bacterial vectors, as microscopic living 'robotic factories', can be reprogrammed into microscopic living 'robotic factories', using a top-down bioengineering approach to produce and deliver anticancer agents. Most of the current research has focused on bacterial species such as Salmonella typhimurium or Clostridium novyi. However, Escherichia coli Nissle 1917 (EcN) is another promising candidate with probiotic properties. EcN offers increased applicability for cancer treatment with the development of new molecular biology and complete genome sequencing techniques. In this review, we discuss the genetics and physical properties of EcN. We also summarize and analyse recent studies regarding tumour therapy mediated by EcN. Many challenges remain in the development of more promising strategies for combatting cancer with EcN.
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Affiliation(s)
- Xiaoli Yu
- School of Public Health and ManagementWeifang Medical UniversityWeifang261053ShandongChina
| | - Changsen Lin
- State Key Laboratory of Microbial TechnologyNational Glycoengineering Research CenterShandong UniversityQingdao266237ShandongChina
- Affiliated Hospital of Shandong University of Traditional Chinese MedicineJinan250014ShandongChina
| | - Jing Yu
- Affiliated Hospital of Shandong University of Traditional Chinese MedicineJinan250014ShandongChina
| | - Qingsheng Qi
- State Key Laboratory of Microbial TechnologyNational Glycoengineering Research CenterShandong UniversityQingdao266237ShandongChina
| | - Qian Wang
- State Key Laboratory of Microbial TechnologyNational Glycoengineering Research CenterShandong UniversityQingdao266237ShandongChina
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81
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Developing a new class of engineered live bacterial therapeutics to treat human diseases. Nat Commun 2020; 11:1738. [PMID: 32269218 PMCID: PMC7142098 DOI: 10.1038/s41467-020-15508-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/13/2020] [Indexed: 12/29/2022] Open
Abstract
A complex interplay of metabolic and immunological mechanisms underlies many diseases that represent a substantial unmet medical need. There is an increasing appreciation of the role microbes play in human health and disease, and evidence is accumulating that a new class of live biotherapeutics comprised of engineered microbes could address specific mechanisms of disease. Using the tools of synthetic biology, nonpathogenic bacteria can be designed to sense and respond to environmental signals in order to consume harmful compounds and deliver therapeutic effectors. In this perspective, we describe considerations for the design and development of engineered live biotherapeutics to achieve regulatory and patient acceptance. The role microbes play in human health and the ability of synthetic biology to engineer microbial properties opens up new ways of treating disease. In this perspective, the authors describe the design and development of these living therapeutics.
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82
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Inducible cell-to-cell signaling for tunable dynamics in microbial communities. Nat Commun 2020; 11:1193. [PMID: 32132536 PMCID: PMC7055273 DOI: 10.1038/s41467-020-15056-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 01/06/2020] [Indexed: 11/09/2022] Open
Abstract
The last decade has seen bacteria at the forefront of biotechnological innovation, with applications including biomolecular computing, living therapeutics, microbiome engineering and microbial factories. These emerging applications are all united by the need to precisely control complex microbial dynamics in spatially extended environments, requiring tools that can bridge the gap between intracellular and population-level coordination. To address this need, we engineer an inducible quorum sensing system which enables precise tunability of bacterial dynamics both at the population and community level. As a proof-of-principle, we demonstrate the advantages of this system when genetically equipped for cargo delivery. In addition, we exploit the absence of cross-talk with respect to the majority of well-characterized quorum sensing systems to demonstrate inducibility of multi-strain communities. More broadly, this work highlights the unexplored potential of remotely inducible quorum sensing systems which, coupled to any gene of interest, may facilitate the translation of circuit designs into applications.
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83
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Chowdhury S, Castro S, Coker C, Hinchliffe TE, Arpaia N, Danino T. Programmable bacteria induce durable tumor regression and systemic antitumor immunity. Nat Med 2019; 25:1057-1063. [PMID: 31270504 PMCID: PMC6688650 DOI: 10.1038/s41591-019-0498-z] [Citation(s) in RCA: 324] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/24/2019] [Indexed: 12/12/2022]
Abstract
Synthetic biology is driving a new era of medicine through the genetic programming of living cells1,2. This transformative approach allows for the creation of engineered systems that intelligently sense and respond to diverse environments, ultimately adding specificity and efficacy that extends beyond the capabilities of molecular-based therapeutics3–6. One particular focus area has been the engineering of bacteria as therapeutic delivery systems to selectively release therapeutic payloads in vivo7–11. Here, we engineered a non-pathogenic E. coli to specifically lyse within the tumor microenvironment and release an encoded nanobody antagonist of CD47 (CD47nb)12, an anti-phagocytic receptor commonly overexpressed in several human cancers13,14. We show that delivery of CD47nb by tumor-colonizing bacteria increases activation of tumor-infiltrating T cells, stimulates rapid tumor regression, prevents metastasis, and leads to long-term survival in a syngeneic tumor model. Moreover, we report that local injection of CD47nb bacteria stimulates systemic tumor antigen–specific immune responses that reduce the growth of untreated tumors – providing, to the best of our knowledge, the first demonstration of an abscopal effect induced by an engineered bacterial immunotherapy. Thus, engineered bacteria may be used for safe and local delivery of immunotherapeutic payloads leading to systemic antitumor immunity.
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Affiliation(s)
- Sreyan Chowdhury
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.,Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Samuel Castro
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Courtney Coker
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Taylor E Hinchliffe
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Nicholas Arpaia
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA. .,Data Science Institute, Columbia University, New York, NY, USA.
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84
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McCombe PA, Henderson RD, Lee A, Lee JD, Woodruff TM, Restuadi R, McRae A, Wray NR, Ngo S, Steyn FJ. Gut microbiota in ALS: possible role in pathogenesis? Expert Rev Neurother 2019; 19:785-805. [PMID: 31122082 DOI: 10.1080/14737175.2019.1623026] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: The gut microbiota has important roles in maintaining human health. The microbiota and its metabolic byproducts could play a role in the pathogenesis of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Areas covered: The authors evaluate the methods of assessing the gut microbiota, and also review how the gut microbiota affects the various physiological functions of the gut. The authors then consider how gut dysbiosis could theoretically affect the pathogenesis of ALS. They present the current evidence regarding the composition of the gut microbiota in ALS and in rodent models of ALS. Finally, the authors review therapies that could improve gut dysbiosis in the context of ALS. Expert opinion: Currently reported studies suggest some instances of gut dysbiosis in ALS patients and mouse models; however, these studies are limited, and more information with well-controlled larger datasets is required to make a definitive judgment about the role of the gut microbiota in ALS pathogenesis. Overall this is an emerging field that is worthy of further investigation. The authors advocate for larger studies using modern metagenomic techniques to address the current knowledge gaps.
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Affiliation(s)
- Pamela A McCombe
- Centre for Clinical Research, The University of Queensland , Brisbane , Australia.,Wesley Medical Research, Level 8 East Wing, The Wesley Hospital , Brisbane , Australia.,Department of Neurology, Royal Brisbane & Women's Hospital , Brisbane , Australia.,School of Medicine, The University of Queensland , Brisbane , Australia
| | - Robert D Henderson
- Wesley Medical Research, Level 8 East Wing, The Wesley Hospital , Brisbane , Australia.,Department of Neurology, Royal Brisbane & Women's Hospital , Brisbane , Australia.,School of Medicine, The University of Queensland , Brisbane , Australia.,Queensland Brain Institute, The University of Queensland , Brisbane , Australia
| | - Aven Lee
- Centre for Clinical Research, The University of Queensland , Brisbane , Australia
| | - John D Lee
- School of Biomedical Sciences, The University of Queensland , Brisbane , Australia
| | - Trent M Woodruff
- School of Biomedical Sciences, The University of Queensland , Brisbane , Australia
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Allan McRae
- Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Naomi R Wray
- Queensland Brain Institute, The University of Queensland , Brisbane , Australia.,Institute for Molecular Bioscience, The University of Queensland , Brisbane , Australia
| | - Shyuan Ngo
- Centre for Clinical Research, The University of Queensland , Brisbane , Australia.,Wesley Medical Research, Level 8 East Wing, The Wesley Hospital , Brisbane , Australia.,Department of Neurology, Royal Brisbane & Women's Hospital , Brisbane , Australia.,Queensland Brain Institute, The University of Queensland , Brisbane , Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane , Australia
| | - Frederik J Steyn
- Centre for Clinical Research, The University of Queensland , Brisbane , Australia.,Wesley Medical Research, Level 8 East Wing, The Wesley Hospital , Brisbane , Australia.,Department of Neurology, Royal Brisbane & Women's Hospital , Brisbane , Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane , Australia
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85
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Jiang B, Li Z, Ou B, Duan Q, Zhu G. Targeting ideal oral vaccine vectors based on probiotics: a systematical view. Appl Microbiol Biotechnol 2019; 103:3941-3953. [PMID: 30915504 DOI: 10.1007/s00253-019-09770-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 12/29/2022]
Abstract
Probiotics have great potential to be engineered into oral vaccine delivery systems, which can facilitate elicitation of mucosal immunity without latent risks of pathogenicity. Combined with the progressive understanding of probiotics and the mucosal immune system as well as the advanced biotechniques of genetic engineering, the development of promising oral vaccine vectors based on probiotics is available while complicated and demanding. Therefore, a systematical view on the design of practical probiotic vectors is necessary, which will help to logically analyze and resolve the problems that might be neglected during our exploration. Here, we attempt to systematically summarize several fundamental issues vital to the effectiveness of the vector of probiotics, including the stability of the engineered vectors, the optimization of antigen expression, the improvement of colonization, and the enhancement of immunoreactivity. We also compared the existent strategies and some developing ones, attempting to figure out an optimal strategy that might deserve to be referred in the future development of oral vaccine vectors based on probiotics.
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Affiliation(s)
- Boyu Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, 225009, China
| | - Zhendong Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, 225009, China
| | - Bingming Ou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, 225009, China.,College of Life Science, Zhaoqing University, Zhaoqing, 526061, China
| | - Qiangde Duan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, 225009, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China. .,Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, 225009, China.
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86
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Singh B, Mal G, Gautam SK, Mukesh M. Designer Probiotics: The Next-Gen High Efficiency Biotherapeutics. ADVANCES IN ANIMAL BIOTECHNOLOGY 2019. [PMCID: PMC7147453 DOI: 10.1007/978-3-030-21309-1_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The probiotic engineering is a cutting edge technology for improving disease diagnosis, treating gastrointestinal disorders and infectious diseases, and improving nutrition and ecological health. Use of bioengineered microorganisms in animals has different targets and prospects owing to differences in their anatomy, physiology, and feeding habits. In ruminants, the bioengineered microorganism is primarily aimed to enhance nutrient utilization, detoxify toxic plant metabolites, and lessen the enteric methanogenesis, while in non-ruminants, the bioengineered microorganisms are aimed to enhance nutrient utilizations, confer protection against pathogens, and inhibit infectious agents. Highlights The microorganisms can be engineered to enhance their metabolic efficiency The bioengineered microorganisms could solve the burgeoning problem of drug-resistant pathogens The recombinant probiotics are promising therapeutic agents against infectious diseases.
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Affiliation(s)
- Birbal Singh
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Gorakh Mal
- ICAR-Indian Veterinary Research Institute, Regional Station, Palampur, India
| | - Sanjeev K. Gautam
- Department of Biotechnology, Kurukshetra University, Kurukshetra, Haryana India
| | - Manishi Mukesh
- Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana India
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