201
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Yin K, Qiu JL. Genome editing for plant disease resistance: applications and perspectives. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180322. [PMID: 30967029 PMCID: PMC6367152 DOI: 10.1098/rstb.2018.0322] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2018] [Indexed: 12/16/2022] Open
Abstract
Diseases severely affect crop yield and quality, thereby threatening global food security. Genetic improvement of plant disease resistance is essential for sustainable agriculture. Genome editing has been revolutionizing plant biology and biotechnology by enabling precise, targeted genome modifications. Editing provides new methods for genetic improvement of plant disease resistance and accelerates resistance breeding. Here, we first summarize the challenges for breeding resistant crops. Next, we focus on applications of genome editing technology in generating plants with resistance to bacterial, fungal and viral diseases. Finally, we discuss the potential of genome editing for breeding crops that present novel disease resistance in the future. This article is part of the theme issue 'Biotic signalling sheds light on smart pest management'.
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Affiliation(s)
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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202
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Rodríguez Amor D, Dal Bello M. Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities. Life (Basel) 2019; 9:E22. [PMID: 30813538 PMCID: PMC6462982 DOI: 10.3390/life9010022] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/01/2019] [Accepted: 02/14/2019] [Indexed: 12/25/2022] Open
Abstract
Microbial cooperation pervades ecological scales, from single-species populations to host-associated microbiomes. Understanding the mechanisms promoting the stability of cooperation against potential threats by cheaters is a major question that only recently has been approached experimentally. Synthetic biology has helped to uncover some of these basic mechanisms, which were to some extent anticipated by theoretical predictions. Moreover, synthetic cooperation is a promising lead towards the engineering of novel functions and enhanced productivity of microbial communities. Here, we review recent progress on engineered cooperation in microbial ecosystems. We focus on bottom-up approaches that help to better understand cooperation at the population level, progressively addressing the challenges of tackling higher degrees of complexity: spatial structure, multispecies communities, and host-associated microbiomes. We envisage cooperation as a key ingredient in engineering complex microbial ecosystems.
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Affiliation(s)
- Daniel Rodríguez Amor
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Martina Dal Bello
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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203
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Tscherner M, Giessen TW, Markey L, Kumamoto CA, Silver PA. A Synthetic System That Senses Candida albicans and Inhibits Virulence Factors. ACS Synth Biol 2019; 8:434-444. [PMID: 30608638 DOI: 10.1021/acssynbio.8b00457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Due to a limited set of antifungals available and problems in early diagnosis, invasive fungal infections caused by Candida species are among the most common hospital-acquired infections with staggering mortality rates. Here, we describe an engineered system able to sense and respond to the fungal pathogen Candida albicans, the most common cause of candidemia. In doing so, we identified hydroxyphenylacetic acid (HPA) as a novel molecule secreted by C. albicans. Furthermore, we engineered E. coli to be able to sense HPA produced by C. albicans. Finally, we constructed a sense-and-respond system by coupling the C. albicans sensor to the production of an inhibitor of hypha formation, thereby reducing filamentation, virulence factor expression, and fungal-induced epithelial damage. This system could be used as a basis for the development of novel prophylactic approaches to prevent fungal infections.
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Affiliation(s)
- Michael Tscherner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Tobias W. Giessen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Laura Markey
- Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences and Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts 02111, United States
| | - Carol A. Kumamoto
- Graduate Program in Molecular Microbiology, Sackler School of Graduate Biomedical Sciences and Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts 02111, United States
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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204
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McCarty NS, Ledesma-Amaro R. Synthetic Biology Tools to Engineer Microbial Communities for Biotechnology. Trends Biotechnol 2019; 37:181-197. [PMID: 30497870 PMCID: PMC6340809 DOI: 10.1016/j.tibtech.2018.11.002] [Citation(s) in RCA: 235] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Microbial consortia have been used in biotechnology processes, including fermentation, waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly engineering microbial consortia for diverse applications, including the bioproduction of medicines, biofuels, and biomaterials from inexpensive carbon sources. An improved understanding of natural microbial ecosystems, and the development of new tools to construct synthetic consortia and program their behaviors, will vastly expand the functions that can be performed by communities of interacting microorganisms. Here, we review recent advancements in synthetic biology tools and approaches to engineer synthetic microbial consortia, discuss ongoing and emerging efforts to apply consortia for various biotechnological applications, and suggest future applications.
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Affiliation(s)
- Nicholas S. McCarty
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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205
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Abstract
The composite members of the microbiota face a range of selective pressures and must adapt to persist in the host. We highlight recent work characterizing the evolution and transfer of genetic information across nested scales of host-associated microbiota, which enable resilience to biotic and abiotic perturbations. At the strain level, we consider the preservation and diversification of adaptive information in progeny lineages. At the community level, we consider genetic exchange between distinct microbes in the ecosystem. Finally, we frame microbiomes as open systems subject to acquisition of novel information from foreign ecosystems through invasion by outsider microbes.
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206
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Lee YJ, Kim SJ, Amrofell MB, Moon TS. Establishing a Multivariate Model for Predictable Antisense RNA-Mediated Repression. ACS Synth Biol 2019; 8:45-56. [PMID: 30517781 DOI: 10.1021/acssynbio.8b00227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent advances in our understanding of RNA folding and functions have facilitated the use of regulatory RNAs such as synthetic antisense RNAs (asRNAs) to modulate gene expression. However, despite the simple and universal complementarity rule, predictable asRNA-mediated repression is still challenging due to the intrinsic complexity of native asRNA-mediated gene regulation. To address this issue, we present a multivariate model, based on the change in free energy of complex formation (Δ GCF) and percent mismatch of the target binding region, which can predict synthetic asRNA-mediated repression efficiency in diverse contexts. First, 69 asRNAs that bind to multiple target mRNAs were designed and tested to create the predictive model. Second, we showed that the same model is effective predicting repression of target genes in both plasmids and chromosomes. Third, using our model, we designed asRNAs that simultaneously modulated expression of a toxin and its antitoxin to demonstrate tunable control of cell growth. Fourth, we tested and validated the same model in two different biotechnologically important organisms: Escherichia coli Nissle 1917 and Bacillus subtilis 168. Last, multiple parameters, including target locations, the presence of an Hfq binding site, GC contents, and gene expression levels, were revisited to define the conditions under which the multivariate model should be used for accurate prediction. Together, 434 different strain-asRNA combinations were tested, validating the predictive model in a variety of contexts, including multiple target genes and organisms. The result presented in this study is an important step toward achieving predictable tunability of asRNA-mediated repression.
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Affiliation(s)
- Young Je Lee
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Soo-Jung Kim
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Matthew B. Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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207
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Cao X, Hamilton JJ, Venturelli OS. Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities. Biochemistry 2019; 58:94-107. [PMID: 30457843 PMCID: PMC6733022 DOI: 10.1021/acs.biochem.8b01006] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbiomes impact nearly every environment on Earth by modulating the molecular composition of the environment. Temporally changing environmental stimuli and spatial organization are major variables shaping the structure and function of microbiomes. The web of interactions among members of these communities and between the organisms and the environment dictates microbiome functions. Microbial interactions are major drivers of microbiomes and are modulated by spatiotemporal parameters. A mechanistic and quantitative understanding of ecological, molecular, and environmental forces shaping microbiomes could inform strategies to control microbiome dynamics and functions. Major challenges for harnessing the potential of microbiomes for diverse applications include the development of predictive modeling frameworks and tools for precise manipulation of microbiome behaviors.
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Affiliation(s)
| | | | - Ophelia S. Venturelli
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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208
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209
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Timmis K, Timmis JK, Brüssow H, Fernández LÁ. Synthetic consortia of nanobody-coupled and formatted bacteria for prophylaxis and therapy interventions targeting microbiome dysbiosis-associated diseases and co-morbidities. Microb Biotechnol 2019; 12:58-65. [PMID: 30575298 PMCID: PMC6302794 DOI: 10.1111/1751-7915.13355] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Designed nanobody-linked synthetic consortia for microbiota dysbiosis therapies. A. Nanobodies (Nb) are selected for specific antigens on target bacteria destined for a synthetic therapy consortium that may consist of two (B) or multiple (C) members. For the treatment of dysbiosis co-morbidities requiring two functionally distinct consortia, these may be linked through a common member to generate a single bi-functional microbiota therapy (D).
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Affiliation(s)
- Kenneth Timmis
- Institute of MicrobiologyTechnical University BraunschweigBraunschweigGermany
| | | | - Harald Brüssow
- Division of Animal and Human Health EngineeringDepartment of BiosystemsKatholieke Universiteit LeuvenLeuvenBelgium
| | - Luis Ángel Fernández
- Department of Microbial BiotechnologyCentro Nacional de BiotecnologíaConsejo Superior de Investigaciones CientíficasMadridSpain
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210
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Chavira A, Belda-Ferre P, Kosciolek T, Ali F, Dorrestein PC, Knight R. The Microbiome and Its Potential for Pharmacology. Handb Exp Pharmacol 2019; 260:301-326. [PMID: 31820171 DOI: 10.1007/164_2019_317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The human microbiota (the microscopic organisms that inhabit us) and microbiome (their genes) hold considerable potential for improving pharmacological practice. Recent advances in multi-"omics" techniques have dramatically improved our understanding of the constituents of the microbiome and their functions. The implications of this research for human health, including microbiome links to obesity, drug metabolism, neurological diseases, cancer, and many other health conditions, have sparked considerable interest in exploiting the microbiome for targeted therapeutics. Links between microbial pathways and disease states further highlight a rich potential for companion diagnostics and precision medicine approaches. For example, the success of fecal microbiota transplantation to treat Clostridium difficile infection has already started to redefine standard of care with a microbiome-directed therapy. In this review we briefly discuss the nature of human microbial ecosystems and with pathologies and biological processes linked to the microbiome. We then review emerging computational metagenomic, metabolomic, and wet lab techniques researchers are using today to learn about the roles host-microbial interactions have with respect to pharmacological purposes and vice versa. Finally, we describe how drugs affect the microbiome, how the microbiome can impact drug response in different people, and the potential of the microbiome itself as a source of new therapeutics.
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Affiliation(s)
- Aries Chavira
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tomasz Kosciolek
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Farhana Ali
- Division of Gastroenterology, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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211
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Mukherjee S, Joardar N, Sengupta S, Sinha Babu SP. Gut microbes as future therapeutics in treating inflammatory and infectious diseases: Lessons from recent findings. J Nutr Biochem 2018; 61:111-128. [PMID: 30196243 PMCID: PMC7126101 DOI: 10.1016/j.jnutbio.2018.07.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 02/07/2023]
Abstract
The human gut microbiota has been the interest of extensive research in recent years and our knowledge on using the potential capacity of these microbes are growing rapidly. Microorganisms colonized throughout the gastrointestinal tract of human are coevolved through symbiotic relationship and can influence physiology, metabolism, nutrition and immune functions of an individual. The gut microbes are directly involved in conferring protection against pathogen colonization by inducing direct killing, competing with nutrients and enhancing the response of the gut-associated immune repertoire. Damage in the microbiome (dysbiosis) is linked with several life-threatening outcomes viz. inflammatory bowel disease, cancer, obesity, allergy, and auto-immune disorders. Therefore, the manipulation of human gut microbiota came out as a potential choice for therapeutic intervention of the several human diseases. Herein, we review significant studies emphasizing the influence of the gut microbiota on the regulation of host responses in combating infectious and inflammatory diseases alongside describing the promises of gut microbes as future therapeutics.
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Affiliation(s)
- Suprabhat Mukherjee
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Nikhilesh Joardar
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Subhasree Sengupta
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Santi P Sinha Babu
- Parasitology Laboratory, Department of Zoology (Centre for Advanced Studies), Siksha-Bhavana, Visva-Bharati University, Santiniketan, West Bengal, 731235, India.
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212
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Abstract
Measuring biological data across time and space is critical for understanding complex biological processes and for various biosurveillance applications. However, such data are often inaccessible or difficult to directly obtain. Less invasive, more robust and higher-throughput biological recording tools are needed to profile cells and their environments. DNA-based cellular recording is an emerging and powerful framework for tracking intracellular and extracellular biological events over time across living cells and populations. Here, we review and assess DNA recorders that utilize CRISPR nucleases, integrases and base-editing strategies, as well as recombinase and polymerase-based methods. Quantitative characterization, modelling and evaluation of these DNA-recording modalities can guide their design and implementation for specific application areas.
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Affiliation(s)
- Ravi U Sheth
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
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213
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Pedrolli DB, Ribeiro NV, Squizato PN, de Jesus VN, Cozetto DA. Engineering Microbial Living Therapeutics: The Synthetic Biology Toolbox. Trends Biotechnol 2018; 37:100-115. [PMID: 30318171 DOI: 10.1016/j.tibtech.2018.09.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/31/2022]
Abstract
Microbes can be engineered to act like living therapeutics designed to perform specific actions in the human body. From fighting and preventing infections to eliminating tumors and treating metabolic disorders, engineered living systems are the next generation of therapeutics. In recent years, synthetic biologists have greatly expanded the genetic toolbox for microbial living therapeutics, adding sensors, regulators, memory circuits, delivery devices, and kill switches. These advances have paved the way for successful engineering of fully functional living therapeutics, with sensing, production, and biocontainment devices. However, some important tools are still missing from the box. In this review, we cover the most recent biological parts and approaches developed and describe the missing tools needed to build robust living therapeutics.
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Affiliation(s)
- Danielle B Pedrolli
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017.
| | - Nathan V Ribeiro
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Patrick N Squizato
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Victor N de Jesus
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
| | - Daniel A Cozetto
- Universidade Estadual Paulista (UNESP), School of Pharmaceutical Sciences, Department of Bioprocess and Biotechnology, 14800-903 Araraquara, Brazil; Members of Team AQA Unesp at iGEM 2017
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214
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Isabella VM, Ha BN, Castillo MJ, Lubkowicz DJ, Rowe SE, Millet YA, Anderson CL, Li N, Fisher AB, West KA, Reeder PJ, Momin MM, Bergeron CG, Guilmain SE, Miller PF, Kurtz CB, Falb D. Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria. Nat Biotechnol 2018; 36:857-864. [DOI: 10.1038/nbt.4222] [Citation(s) in RCA: 251] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 07/20/2018] [Indexed: 01/01/2023]
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215
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Lim YP, Go MK, Raida M, Inoue T, Wenk MR, Keasling JD, Chang MW, Yew WS. Synthetic Enzymology and the Fountain of Youth: Repurposing Biology for Longevity. ACS OMEGA 2018; 3:11050-11061. [PMID: 30320257 PMCID: PMC6173508 DOI: 10.1021/acsomega.8b01620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Caloric restriction (CR) is an intervention that can increase maximal lifespan in organisms, but its application to humans remains challenging. A more feasible approach to achieve lifespan extension is to develop CR mimetics that target biochemical pathways affected by CR. Recent studies in the engineering and structural characterization of polyketide synthases (PKSs) have facilitated their use as biocatalysts to produce novel polyketides. Here, we show that by establishing a combinatorial biosynthetic route in Escherichia coli and exploring the substrate promiscuity of a mutant PKS from alfalfa, 413 potential anti-ageing polyketides were biosynthesized. In this approach, novel acyl-coenzyme A (CoA) precursors generated by promiscuous acid-CoA ligases were utilized by PKS to generate polyketides which were then fed to Caenorhabditis elegans to study their potential efficacy in lifespan extension. It was found that CR mimetics like resveratrol can counter the age-associated decline in mitochondrial function and increase the lifespan of C. elegans. Using the mitochondrial respiration profile of C. elegans supplemented for 8 days with 50 μM resveratrol as a blueprint, we can screen our novel polyketides for potential CR mimetics with improved potency. This study highlights the utility of synthetic enzymology in the development of novel anti-ageing therapeutics.
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Affiliation(s)
- Yan Ping Lim
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Maybelle K. Go
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Manfred Raida
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Takao Inoue
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
| | - Markus R. Wenk
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Jay D. Keasling
- Department
of Chemical & Biomolecular Engineering, University of California at Berkeley, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Matthew W. Chang
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Wen Shan Yew
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, 117597, Singapore
- NUS
Synthetic Biology for Clinical and Technological Innovation,
Centre for Life Sciences, and Singapore Lipidomics Incubator, Life Sciences
Institute, National University of Singapore, 28 Medical Drive, 117456, Singapore
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216
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Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
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Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
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217
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McKay R, Ghodasra M, Schardt J, Quan D, Pottash AE, Shang W, Jay SM, Payne GF, Chang MW, March JC, Bentley WE. A platform of genetically engineered bacteria as vehicles for localized delivery of therapeutics: Toward applications for Crohn's disease. Bioeng Transl Med 2018; 3:209-221. [PMID: 30377661 PMCID: PMC6195910 DOI: 10.1002/btm2.10113] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/22/2018] [Accepted: 08/22/2018] [Indexed: 12/14/2022] Open
Abstract
For therapies targeting diseases of the gastrointestinal tract, we and others envision probiotic bacteria that synthesize and excrete biotherapeutics at disease sites. Toward this goal, we have engineered commensal E. coli that selectively synthesize and secrete a model biotherapeutic in the presence of nitric oxide (NO), an intestinal biomarker for Crohn's disease (CD). This is accomplished by co‐expressing the pore forming protein TolAIII with the biologic, granulocyte macrophage‐colony stimulating factor (GM‐CSF). We have additionally engineered these bacteria to accumulate at sites of elevated NO by engineering their motility circuits and controlling pseudotaxis. Importantly, because we have focused on in vitro test beds, motility and biotherapeutics production are spatiotemporally characterized. Together, the targeted recognition, synthesis, and biomolecule delivery comprises a “smart” probiotics platform that may have utility in the treatment of CD. Further, this platform could be modified to accommodate other pursuits by swapping the promoter and therapeutic gene to reflect other disease biomarkers and treatments, respectively.
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Affiliation(s)
- Ryan McKay
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Monil Ghodasra
- Fischell Dept. of Bioengineering University of Maryland College Park MD
| | - John Schardt
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health Bethesda MD
| | - David Quan
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Alex Eli Pottash
- Fischell Dept. of Bioengineering University of Maryland College Park MD
| | - Wu Shang
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Steven M Jay
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute National Institutes of Health Bethesda MD.,Marlene and Stewart Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine Baltimore MD.,Program in Molecular and Cellular Biology University of Maryland College Park MD
| | - Gregory F Payne
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
| | - Matthew Wook Chang
- Dept. of Biochemistry, Yong Loo Lin School of Medicine National University of Singapore Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation, Life Sciences Institute National University of Singapore Singapore
| | - John C March
- Dept. of Biological and Environmental Engineering Cornell University Ithaca NY
| | - William E Bentley
- Fischell Dept. of Bioengineering University of Maryland College Park MD.,Institute for Bioscience and Biotechnology Research University of Maryland College Park MD
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218
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Kim S, Kerns SJ, Ziesack M, Bry L, Gerber GK, Way JC, Silver PA. Quorum Sensing Can Be Repurposed To Promote Information Transfer between Bacteria in the Mammalian Gut. ACS Synth Biol 2018; 7:2270-2281. [PMID: 30125499 DOI: 10.1021/acssynbio.8b00271] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The gut microbiome is intricately involved with establishing and maintaining the health of the host. Engineering of gut microbes aims to add new functions and expand the scope of control over the gut microbiome. To create systems that can perform increasingly complex tasks in the gut, it is necessary to harness the ability of the bacteria to communicate in the gut environment. Interestingly, acyl-homoserine lactone (acyl-HSL)-mediated Gram-negative bacterial quorum sensing, a widely used mode of intercellular signaling system in nature, has not been identified in normal healthy mammalian gut. It remains unknown whether the gut bacteria that do not natively use quorum sensing can be engineered to successfully signal to other bacteria using acyl-HSLs in the gut environment. Here, we repurposed quorum sensing to create an information transfer system between native gut Escherichia coli and attenuated Salmonella enterica serovar Typhimurium. Specifically, we functionalized one species with inducible signal production and the other with signal detection and recording using genomically integrated circuits. The information transfer system demonstrated successful intra- and interspecies signaling in the murine gut. This study provides a basis for further understanding of interbacterial interactions in an otherwise hard-to-study environment as well as a basis for further investigation of the potential of acyl-HSLs as intercellular signaling molecules of engineered gut consortia.
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Affiliation(s)
- Suhyun Kim
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - S. Jordan Kerns
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Marika Ziesack
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Lynn Bry
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Georg K. Gerber
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States
| | - Jeffrey C. Way
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States
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219
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Engineered Stochastic Adhesion Between Microbes as a Protection Mechanism Against Environmental Stress. Cell Mol Bioeng 2018; 11:367-382. [PMID: 31719890 DOI: 10.1007/s12195-018-0552-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 08/29/2018] [Indexed: 01/14/2023] Open
Abstract
Introduction Microbes aggregate when they display adhesive proteins on their outer membrane surfaces, which then form bridges between microbes. Aggregation protects the inner microbes from harsh environmental conditions such as high concentrations of antibiotics, high salt conditions, and fluctuations in pH. The protective effects of microbial aggregation make it an attractive target for improving the ability of probiotic strains to persist in the gut environment. However, it remains challenging to achieve synthetic microbial aggregation using natural adhesive proteins because these proteins frequently mediate microbial virulence. Objectives Construction of synthetic proteins that mediate aggregation between microbes to enhance the survival of cells delivered to stressful environments. Methods We construct synthetic adhesins by fusing adhesive protein domains to surface display peptides. The resulting aggregated populations of bacteria are characterized using immunofluorescence, microscopy, flow cytometry, and quantification of colony forming units. Results We assemble a series of synthetic adhesins, demonstrate their display on the outer membrane of Escherichia coli, and show that they mediate bacterial aggregation. Further engineering of the size and motif composition of the adhesive domain shows that principles from natural adhesins can be applied to our synthetic adhesins. Finally, we show that aggregation allows E. coli cells to resist treatment with antimicrobial peptides and survive inside the gut of Caenorhabditis elegans. Conclusions Our results demonstrate that synthetic aggregation can allow bacteria to resist biocidal environmental conditions. Synthetic adhesins may be used to facilitate microbial colonization of previously inaccessible environmental niches, either in remote natural environments or inside living organisms.
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220
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Geldart KG, Kommineni S, Forbes M, Hayward M, Dunny GM, Salzman NH, Kaznessis YN. Engineered E. coli Nissle 1917 for the reduction of vancomycin-resistant Enterococcus in the intestinal tract. Bioeng Transl Med 2018; 3:197-208. [PMID: 30377660 PMCID: PMC6195901 DOI: 10.1002/btm2.10107] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/22/2018] [Accepted: 07/09/2018] [Indexed: 12/22/2022] Open
Abstract
Vancomycin-resistant Enterococcus (VRE) poses a serious threat in hospitals where they densely colonize the intestinal tracts of patients. In vulnerable hosts, these pathogens may translocate to the bloodstream and become lethal. The ability to selectively reduce VRE in the intestinal tracts of patients could potentially prevent many of these translocation events and reduce the spread of the pathogen. Herein, we have engineered Escherichia. coli Nissle 1917 to produce and secrete three antimicrobial peptides, Enterocin A, Enterocin B, and Hiracin JM79, to specifically target and kill Enterococcus. These peptides exhibited potent activity against both Enterococcus faecium and Enterococcus faecalis, the two most prominent species responsible for VRE infections. We first discuss the optimization of the system used to express and secrete the peptides. We then show that by simultaneously expressing these peptides, both E. faecium and E. faecalis were drastically inhibited. We then demonstrate a suppression of the development of resistance when supernatant from the E. coli producer strains was used to treat E. faecium. Finally, we tested the efficacy of the probiotic in a VRE colonization model in mice. These studies showed that administration of the engineered probiotic significantly reduced the levels of both E. faecium and E. faecalis in the feces of male Balb/cJ mice.
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Affiliation(s)
- Kathryn G. Geldart
- General Probiotics Inc.St. PaulMN 55114
- Department of Microbiology and ImmunologyUniversity of MinnesotaMinneapolisMN 55455
| | | | | | - Michael Hayward
- Department of PediatricsMedical College of WisconsinMilwaukeeWI 53226
| | - Gary M. Dunny
- Department of Microbiology and ImmunologyUniversity of MinnesotaMinneapolisMN 55455
| | - Nita H. Salzman
- Department of PediatricsMedical College of WisconsinMilwaukeeWI 53226
- Department of Microbiology and ImmunologyMedical College of WisconsinMilwaukeeWI 53226
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Hwang IY, Lee HL, Huang JG, Lim YY, Yew WS, Lee YS, Chang MW. Engineering microbes for targeted strikes against human pathogens. Cell Mol Life Sci 2018; 75:2719-2733. [PMID: 29736607 PMCID: PMC11105496 DOI: 10.1007/s00018-018-2827-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/06/2018] [Accepted: 04/23/2018] [Indexed: 12/24/2022]
Abstract
Lack of pathogen specificity in antimicrobial therapy causes non-discriminant microbial cell killing that disrupts the microflora present. As a result, potentially helpful microbial cells are killed along with the pathogen, altering the biodiversity and dynamic interactions within the population. Moreover, the unwarranted exposure of antibiotics to microbes increases the likelihood of developing resistance and perpetuates the emergence of multidrug resistance. Synthetic biology offers an alternative solution where specificity can be conferred to reduce the non-specific, non-targeted activity of currently available antibiotics, and instead provides targeted therapy against specific pathogens and minimising collateral damage to the host's inherent microbiota. With a greater understanding of the microbiome and the available genetic engineering tools for microbial cells, it is possible to devise antimicrobial strategies for novel antimicrobial therapy that are able to precisely and selectively remove infectious pathogens. Herein, we review the strategies developed by unlocking some of the natural mechanisms used by the microbes and how these may be utilised in targeted antimicrobial therapy, with the promise of reducing the current global bane of multidrug antimicrobial resistance.
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Affiliation(s)
- In Young Hwang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Hui Ling Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - James Guoxian Huang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Yvonne Yijuan Lim
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore, 119074, Singapore
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117596, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
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222
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Ritter SC, Yang ML, Kaznessis YN, Hackel BJ. Multispecies activity screening of microcin J25 mutants yields antimicrobials with increased specificity toward pathogenic Salmonella species relative to human commensal Escherichia coli. Biotechnol Bioeng 2018; 115:2394-2404. [PMID: 29940080 DOI: 10.1002/bit.26772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/05/2018] [Accepted: 06/18/2018] [Indexed: 12/13/2022]
Abstract
Modern large-scale agricultural practices that incorporate high density farming with subtherapeutic antibiotic dosing are considered a major contributor to the rise of antibiotic-resistant bacterial infections of humans with species of Salmonella being a leading agriculture-based bacterial infection. Microcin J25, a potent and highly stable antimicrobial peptide active against Enterobacteriaceae, is a candidate antimicrobial against multiple Salmonella species. Emerging evidence supports the hypothesis that the composition of the microbiota of the gastrointestinal tract prevents a variety of diseases by preventing infectious agents from proliferating. Reducing clearance of off-target bacteria may decrease susceptibility to secondary infection. Of the Enterobacteriaceae susceptible to microcin J25, Escherichia coli are the most abundant within the human gut. To explore the modulation of specificity, a collection of 207 mutants encompassing 12 positions in both the ring and loop of microcin J25 was built and tested for activity against Salmonella and E. coli strains. As has been found previously, mutational tolerance of ring residues was lower than loop residues, with 22% and 51% of mutations, respectively, retaining activity toward at least one target within the target organism test panel. The multitarget screening elucidated increased mutational tolerance at position G2, G3, and G14 than previously identified in panels composed of single targets. Multiple mutations conferred differential response between the different targets. Examination of specificity differences between mutants found that 30% showed significant improvements to specificity toward any of the targets. Generation and testing of a combinatorial library designed from the point-mutant study revealed that microcin J25I13T reduces off-target activity toward commensal human-derived E. coli isolates by 81% relative to Salmonella enterica serovar Enteritidis. These in vitro specificity improvements are likely to improve in vivo treatment efficacy by reducing clearance of commensal bacteria in the gastrointestinal tract of hosts.
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Affiliation(s)
- Seth C Ritter
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Mike L Yang
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Yiannis N Kaznessis
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota
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McKay R, Hauk P, Quan D, Bentley WE. Development of Cell-Based Sentinels for Nitric Oxide: Ensuring Marker Expression and Unimodality. ACS Synth Biol 2018; 7:1694-1701. [PMID: 29975512 PMCID: PMC7025431 DOI: 10.1021/acssynbio.8b00146] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We generated "sentinel" bacteria that respond to the biomarker nitric oxide (NO) and produce a homogeneous and strong fluorescent response. Our dual-plasmid system consists of a signal "relay" vector that employs an NO-responsive promoter that amplifies the native signal (via expression of T7 Polymerase (T7Pol)) to a second vector responsible for GFP expression. Importantly, to achieve an optimal "sentinel" response, we developed strategies that balance the transcriptional load within cells by altering (i) translation and (ii) activity of the T7Pol. Our optimized genetic circuitry was then used to transform commensal E. coli Nissle, as a proof-of-concept toward an ingestible cell-based sensor for Crohn's disease (CD) that, in turn, is marked by elevated levels of intestinal NO. Thus, the "biosensors" demonstrated here may serve as a simple diagnostic tool, contrasting the standard of care including colonoscopies or biopsies.
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Affiliation(s)
- Ryan McKay
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - Pricila Hauk
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - David Quan
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
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224
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Mimee M, Nadeau P, Hayward A, Carim S, Flanagan S, Jerger L, Collins J, McDonnell S, Swartwout R, Citorik RJ, Bulović V, Langer R, Traverso G, Chandrakasan AP, Lu TK. An ingestible bacterial-electronic system to monitor gastrointestinal health. Science 2018; 360:915-918. [PMID: 29798884 DOI: 10.1126/science.aas9315] [Citation(s) in RCA: 256] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 04/20/2018] [Indexed: 12/22/2022]
Abstract
Biomolecular monitoring in the gastrointestinal tract could offer rapid, precise disease detection and management but is impeded by access to the remote and complex environment. Here, we present an ingestible micro-bio-electronic device (IMBED) for in situ biomolecular detection based on environmentally resilient biosensor bacteria and miniaturized luminescence readout electronics that wirelessly communicate with an external device. As a proof of concept, we engineer heme-sensitive probiotic biosensors and demonstrate accurate diagnosis of gastrointestinal bleeding in swine. Additionally, we integrate alternative biosensors to demonstrate modularity and extensibility of the detection platform. IMBEDs enable new opportunities for gastrointestinal biomarker discovery and could transform the management and diagnosis of gastrointestinal disease.
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Affiliation(s)
- Mark Mimee
- Microbiology Program, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.,Synthetic Biology Center, MIT, Cambridge, MA 02139, USA
| | - Phillip Nadeau
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Alison Hayward
- Division of Comparative Medicine, MIT, Cambridge, MA 02139, USA.,Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Sean Carim
- Synthetic Biology Center, MIT, Cambridge, MA 02139, USA
| | - Sarah Flanagan
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Logan Jerger
- Synthetic Biology Center, MIT, Cambridge, MA 02139, USA.,Division of Pediatric Gastroentrology, Hepatology, and Nutrition, Department of Pediatrics, MassGeneral Hospital for Children, Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA
| | - Joy Collins
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Shane McDonnell
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
| | - Richard Swartwout
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Robert J Citorik
- Microbiology Program, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.,Synthetic Biology Center, MIT, Cambridge, MA 02139, USA
| | - Vladimir Bulović
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Robert Langer
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA.,Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Giovanni Traverso
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA.,Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA.,Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Anantha P Chandrakasan
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA.
| | - Timothy K Lu
- Synthetic Biology Center, MIT, Cambridge, MA 02139, USA. .,Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA.,Department of Biological Engineering, MIT, Cambridge, MA 02139, USA
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225
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Synthetic biology toolkits and applications in Saccharomyces cerevisiae. Biotechnol Adv 2018; 36:1870-1881. [PMID: 30031049 DOI: 10.1016/j.biotechadv.2018.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/10/2018] [Accepted: 07/16/2018] [Indexed: 12/26/2022]
Abstract
Synthetic biologists construct biological components and systems to look into biological phenomena and drive a myriad of practical applications that aim to tackle current global challenges in energy, healthcare and the environment. While most tools have been established in bacteria, particularly Escherichia coli, recent years have seen parallel developments in the model yeast strain Saccharomyces cerevisiae, one of the most well-understood eukaryotic biological system. Here, we outline the latest advances in yeast synthetic biology tools based on a framework of abstraction hierarchies of parts, circuits and genomes. In brief, the creation and characterization of biological parts are explored at the transcriptional, translational and post-translational levels. Using characterized parts as building block units, the designing of functional circuits is elaborated with examples. In addition, the status and potential applications of synthetic genomes as a genome level platform for biological system construction are also discussed. In addition to the development of a toolkit, we describe how those tools have been applied in the areas of drug production and screening, study of disease mechanisms, pollutant sensing and bioremediation. Finally, we provide a future outlook of yeast as a workhorse of eukaryotic genetics and a chosen chassis in this field.
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226
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Paalanne N, Husso A, Salo J, Pieviläinen O, Tejesvi MV, Koivusaari P, Pirttilä AM, Pokka T, Mattila S, Jyrkäs J, Turpeinen A, Uhari M, Renko M, Tapiainen T. Intestinal microbiome as a risk factor for urinary tract infections in children. Eur J Clin Microbiol Infect Dis 2018; 37:1881-1891. [PMID: 30006660 DOI: 10.1007/s10096-018-3322-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/04/2018] [Indexed: 12/24/2022]
Abstract
As urinary tract infection (UTI) pathogens originate from the gut, we hypothesized that the gut environment reflected by intestinal microbiome influences the risk of UTI. Our prospective case-control study compared the intestinal microbiomes of 37 children with a febrile UTI with those of 69 healthy children. We sequenced the regions of the bacterial 16S rRNA gene and used the LefSe algorithm to calculate the size of the linear discriminant analysis (LDA) effect. We measured fecal lactoferrin and iron concentrations and quantitative PCR for Escherichia coli. At the phylum level, there were no significant differences. At the genus level, Enterobacter was more abundant in UTI patients with an LDA score > 3 (log 10), while Peptostreptococcaceae were more abundant in healthy subjects with an LDA score > 3 (log 10). In total, 20 OTUs with significantly different abundances were observed. Previous use of antimicrobials did not associate with intestinal microbiome. The relative abundance of E. coli was 1.9% in UTI patients and 0.5% in controls (95% CI of the difference-0.8 to 3.6%). The mean concentration of E.coli in quantitative PCR was 0.14 ng/μl in the patients and 0.08 ng/μl in the controls (95% CI of the difference-0.04 to 0.16). Fecal iron and lactoferrin concentrations were similar between the groups. At the family and genus level, we noted several differences in the intestinal microbiome between children with UTI and healthy children, which may imply that the gut environment is linked with the risk of UTI in children.
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Affiliation(s)
- Niko Paalanne
- Department of Pediatrics and Adolescence, Oulu University Hospital, Oulu, Finland. .,PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland.
| | - Aleksi Husso
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Jarmo Salo
- Department of Pediatrics and Adolescence, Oulu University Hospital, Oulu, Finland.,PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Oskari Pieviläinen
- Department of Pediatrics and Adolescence, Oulu University Hospital, Oulu, Finland.,PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Mysore V Tejesvi
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland.,Chain Antimicrobials Ltd, Teknologiantie 2, 90590, Oulu, Finland
| | - Pirjo Koivusaari
- Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | | | - Tytti Pokka
- Department of Pediatrics and Adolescence, Oulu University Hospital, Oulu, Finland.,PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Sampo Mattila
- Research Unit in Sustainable Chemistry, University of Oulu, Oulu, Finland
| | - Juha Jyrkäs
- Research Unit in Sustainable Chemistry, University of Oulu, Oulu, Finland
| | - Ari Turpeinen
- Research Unit in Sustainable Chemistry, University of Oulu, Oulu, Finland
| | - Matti Uhari
- Department of Pediatrics and Adolescence, Oulu University Hospital, Oulu, Finland.,PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Marjo Renko
- Department of Pediatrics and Adolescence, Oulu University Hospital, Oulu, Finland.,PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Terhi Tapiainen
- Department of Pediatrics and Adolescence, Oulu University Hospital, Oulu, Finland.,PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu, Oulu, Finland
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Lee HL, Shen H, Hwang IY, Ling H, Yew WS, Lee YS, Chang MW. Targeted Approaches for In Situ Gut Microbiome Manipulation. Genes (Basel) 2018; 9:E351. [PMID: 30002345 PMCID: PMC6071227 DOI: 10.3390/genes9070351] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/07/2018] [Accepted: 07/09/2018] [Indexed: 12/17/2022] Open
Abstract
Microbial communities and their collective genomes form the gut microbiome, of which bacteria are the major contributor. Through their secreted metabolites, bacteria interact with the host, influencing human health and physiology. Perturbation of the microbiota and metabolome has been associated with various diseases and metabolic conditions. As knowledge on fundamental host-microbiome interactions and genetic engineering tools becomes readily available, targeted manipulation of the gut microbiome for therapeutic applications gains favourable attention. Manipulation of the gut microbiome can be achieved by altering the microbiota population and composition, or by modifying the functional metabolic activity of the microbiome to promote health and restore the microbiome balance. In this article, we review current works that demonstrate various strategies employed to manipulate the gut microbiome in situ to various degrees of precision.
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Affiliation(s)
- Hui Ling Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, 8 Medical Drive, Singapore 117596, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Haosheng Shen
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore 119074, Singapore.
| | - In Young Hwang
- Department of Biochemistry, Yong Loo Lin School of Medicine, 8 Medical Drive, Singapore 117596, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, 8 Medical Drive, Singapore 117596, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, 8 Medical Drive, Singapore 117596, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Yung Seng Lee
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Rd, Singapore 119074, Singapore.
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Rd, Singapore 119074, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, 8 Medical Drive, Singapore 117596, Singapore.
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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Ozdemir T, Fedorec AJ, Danino T, Barnes CP. Synthetic Biology and Engineered Live Biotherapeutics: Toward Increasing System Complexity. Cell Syst 2018; 7:5-16. [DOI: 10.1016/j.cels.2018.06.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/31/2018] [Accepted: 06/15/2018] [Indexed: 12/31/2022]
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229
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Yang X, Li Z, Xiao H, Wang N, Li Y, Xu X, Chen Z, Tan H, Li J. A Universal and Ultrastable Mineralization Coating Bioinspired from Biofilms. ADVANCED FUNCTIONAL MATERIALS 2018. [DOI: 10.1002/adfm.201802730] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Xiao Yang
- College of Polymer Science and Engineering; State Key Laboratory of Polymer Materials Engineering; Sichuan University; No. 24, South Section One of Yinhuan Road Chengdu 610065 P. R. China
| | - Zhenhua Li
- State Key Laboratory of Supramolecular Structure and Materials; Institute of Theoretical Chemistry; Jilin University; 2699 Qianjin Street Changchun 130012 P. R. China
| | - Hong Xiao
- Department of Pain Management; West China Hospital; Sichuan University; No. 37, GuoXue Xiang Chengdu 610041 P. R. China
| | - Ning Wang
- Regenerative Medicine Research Center; West China Hospital; Sichuan University; No. 37, GuoXue Xiang Chengdu 61004 P. R. China
| | - Yanpu Li
- College of Polymer Science and Engineering; State Key Laboratory of Polymer Materials Engineering; Sichuan University; No. 24, South Section One of Yinhuan Road Chengdu 610065 P. R. China
| | - Xinyuan Xu
- College of Polymer Science and Engineering; State Key Laboratory of Polymer Materials Engineering; Sichuan University; No. 24, South Section One of Yinhuan Road Chengdu 610065 P. R. China
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure and Materials; Institute of Theoretical Chemistry; Jilin University; 2699 Qianjin Street Changchun 130012 P. R. China
| | - Hong Tan
- College of Polymer Science and Engineering; State Key Laboratory of Polymer Materials Engineering; Sichuan University; No. 24, South Section One of Yinhuan Road Chengdu 610065 P. R. China
| | - Jianshu Li
- College of Polymer Science and Engineering; State Key Laboratory of Polymer Materials Engineering; Sichuan University; No. 24, South Section One of Yinhuan Road Chengdu 610065 P. R. China
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230
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Praveschotinunt P, Dorval Courchesne NM, den Hartog I, Lu C, Kim JJ, Nguyen PQ, Joshi NS. Tracking of Engineered Bacteria In Vivo Using Nonstandard Amino Acid Incorporation. ACS Synth Biol 2018; 7:1640-1650. [PMID: 29791796 PMCID: PMC6415965 DOI: 10.1021/acssynbio.8b00135] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The rapidly growing field of microbiome research presents a need for better methods of monitoring gut microbes in vivo with high spatial and temporal resolution. We report a method of tracking microbes in vivo within the gastrointestinal tract by programming them to incorporate nonstandard amino acids (NSAA) and labeling them via click chemistry. Using established machinery constituting an orthogonal translation system (OTS), we engineered Escherichia coli to incorporate p-azido-l-phenylalanine (pAzF) in place of the UAG (amber) stop codon. We also introduced a mutant gene encoding for a cell surface protein (CsgA) that was altered to contain an in-frame UAG codon. After pAzF incorporation and extracellular display, the engineered strains could be covalently labeled via copper-free click reaction with a Cy5 dye conjugated to the dibenzocyclooctyl (DBCO) group. We confirmed the functionality of the labeling strategy in vivo using a murine model. Labeling of the engineered strain could be observed using oral administration of the dye to mice several days after colonization of the gastrointestinal tract. This work sets the foundation for the development of in vivo tracking microbial strategies that may be compatible with noninvasive imaging modalities and are capable of longitudinal spatiotemporal monitoring of specific microbial populations.
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Affiliation(s)
- Pichet Praveschotinunt
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02138 , United States
- John A. Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Noémie-Manuelle Dorval Courchesne
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02138 , United States
- Department of Chemical Engineering , McGill University , Montréal , Québec H3A 0C5 , Canada
| | - Ilona den Hartog
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02138 , United States
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering , Eindhoven University of Technology , 5612 AZ Eindhoven , The Netherlands
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research , Leiden University , 2311 EZ Leiden , The Netherlands
| | - Chaochen Lu
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02138 , United States
- Dr. von Hauner Children's Hospital , 80337 Munich , Germany
- Medical Center of the University of Munich , 80539 Munich , Germany
- Ludwig Maximilians University , 80539 Munich , Germany
| | - Jessica J Kim
- Harvard College , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Peter Q Nguyen
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02138 , United States
| | - Neel S Joshi
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02138 , United States
- John A. Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , Massachusetts 02138 , United States
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231
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Mao N, Cubillos-Ruiz A, Cameron DE, Collins JJ. Probiotic strains detect and suppress cholera in mice. Sci Transl Med 2018; 10:eaao2586. [PMID: 29899022 PMCID: PMC7821980 DOI: 10.1126/scitranslmed.aao2586] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 01/22/2018] [Accepted: 05/08/2018] [Indexed: 12/18/2022]
Abstract
Microbiota-modulating interventions are an emerging strategy to promote gastrointestinal homeostasis. Yet, their use in the detection, prevention, and treatment of acute infections remains underexplored. We report the basis of a probiotic-based strategy to promote colonization resistance and point-of-need diagnosis of cholera, an acute diarrheal disease caused by the pathogen Vibrio cholerae Oral administration of Lactococcus lactis, a common dietary fermentative bacterium, reduced intestinal V. cholerae burden and improved survival in infected infant mice through the production of lactic acid. Furthermore, we engineered an L. lactis strain that specifically detects quorum-sensing signals of V. cholerae in the gut and triggers expression of an enzymatic reporter that is readily detected in fecal samples. We postulate that preventive dietary interventions with fermented foods containing natural and engineered L. lactis strains may hinder cholera progression and improve disease surveillance in populations at risk of cholera outbreaks.
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Affiliation(s)
- Ning Mao
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Andres Cubillos-Ruiz
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - D. Ewen Cameron
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02138, USA
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology (MIT), Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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232
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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233
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Ha JH, Hauk P, Cho K, Eo Y, Ma X, Stephens K, Cha S, Jeong M, Suh JY, Sintim HO, Bentley WE, Ryu KS. Evidence of link between quorum sensing and sugar metabolism in Escherichia coli revealed via cocrystal structures of LsrK and HPr. SCIENCE ADVANCES 2018; 4:eaar7063. [PMID: 29868643 PMCID: PMC5983913 DOI: 10.1126/sciadv.aar7063] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/18/2018] [Indexed: 05/30/2023]
Abstract
Quorum sensing (QS), a bacterial process that regulates population-scale behavior, is mediated by small signaling molecules, called autoinducers (AIs), that are secreted and perceived, modulating a "collective" phenotype. Because the autoinducer AI-2 is secreted by a wide variety of bacterial species, its "perception" cues bacterial behavior. This response is mediated by the lsr (LuxS-regulated) operon that includes the AI-2 transporter LsrACDB and the kinase LsrK. We report that HPr, a phosphocarrier protein central to the sugar phosphotransferase system of Escherichia coli, copurifies with LsrK. Cocrystal structures of an LsrK/HPr complex were determined, and the effects of HPr and phosphorylated HPr on LsrK activity were assessed. LsrK activity is inhibited when bound to HPr, revealing new linkages between QS activity and sugar metabolism. These findings help shed new light on the abilities of bacteria to rapidly respond to changing nutrient levels at the population scale. They also suggest new means of manipulating QS activity among bacteria and within various niches.
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Affiliation(s)
- Jung-Hye Ha
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, South Korea
- Department of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, South Korea
- New Drug Development Center, 80 Cheombok-ro, Dong-gu, Daegu-si 41061, South Korea
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Kun Cho
- Biomedical Omics Group, Korea Basic Science Institute, Chungcheongbuk-do 28119, South Korea
| | - Yumi Eo
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, South Korea
| | - Xiaochu Ma
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Kristina Stephens
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Soyoung Cha
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, South Korea
| | - Migyeong Jeong
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, South Korea
| | - Herman O. Sintim
- Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Kyoung-Seok Ryu
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, South Korea
- Department of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, South Korea
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234
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Designer cells programming quorum-sensing interference with microbes. Nat Commun 2018; 9:1822. [PMID: 29739943 PMCID: PMC5940823 DOI: 10.1038/s41467-018-04223-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/16/2018] [Indexed: 02/07/2023] Open
Abstract
Quorum sensing is a promising target for next-generation anti-infectives designed to address evolving bacterial drug resistance. The autoinducer-2 (AI-2) is a key quorum-sensing signal molecule which regulates bacterial group behaviors and is recognized by many Gram-negative and Gram-positive bacteria. Here we report a synthetic mammalian cell-based microbial-control device that detects microbial chemotactic formyl peptides through a formyl peptide sensor (FPS) and responds by releasing AI-2. The microbial-control device was designed by rewiring an artificial receptor-based signaling cascade to a modular biosynthetic AI-2 production platform. Mammalian cells equipped with the microbial-control gene circuit detect formyl peptides secreted from various microbes with high sensitivity and respond with robust AI-2 production, resulting in control of quorum sensing-related behavior of pathogenic Vibrio harveyi and attenuation of biofilm formation by the human pathogen Candida albicans. The ability to manipulate mixed microbial populations through fine-tuning of AI-2 levels may provide opportunities for future anti-infective strategies.
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235
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Dou J, Bennett MR. Synthetic Biology and the Gut Microbiome. Biotechnol J 2018; 13:e1700159. [PMID: 28976641 PMCID: PMC5882594 DOI: 10.1002/biot.201700159] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/23/2017] [Indexed: 12/19/2022]
Abstract
The gut microbiome plays a crucial role in maintaining human health. Functions performed by gastrointestinal microbes range from regulating metabolism to modulating immune and nervous system development. Scientists have attempted to exploit this importance through the development of engineered probiotics that are capable of producing and delivering small molecule therapeutics within the gut. However, existing synthetic probiotics are simplistic and fail to replicate the complexity and adaptability of native homeostatic mechanisms. In this review, the ways in which the tools and approaches of synthetic biology have been applied to improve the efficacy of therapeutic probiotics, and the ways in which they might be applied in the future is discussed. Simple devices, such as a bistable switches and integrase memory arrays, have been successfully implemented in the mammalian gut, and models for targeted delivery in this environment have also been developed. In the future, it will be necessary to introduce concepts such as logic-gating and biocontainment mechanisms into synthetic probiotics, as well as to expand the collection of relevant biosensors. Ideally, this will bring us closer to a reality in which engineered therapeutic microbes will be able to accurately diagnose and effectively respond to a variety of disease states.
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Affiliation(s)
- Jennifer Dou
- Department of Biosciences, Rice University, Houston, TX 77005
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, Houston, TX 77005
- Department of Bioengineering, Rice University, Houston, TX 77005
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236
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Kenny DJ, Balskus EP. Engineering chemical interactions in microbial communities. Chem Soc Rev 2018; 47:1705-1729. [PMID: 29210396 DOI: 10.1039/c7cs00664k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Microbes living within host-associated microbial communities (microbiotas) rely on chemical communication to interact with surrounding organisms. These interactions serve many purposes, from supplying the multicellular host with nutrients to antagonizing invading pathogens, and breakdown of chemical signaling has potentially negative consequences for both the host and microbiota. Efforts to engineer microbes to take part in chemical interactions represent a promising strategy for modulating chemical signaling within these complex communities. In this review, we discuss prominent examples of chemical interactions found within host-associated microbial communities, with an emphasis on the plant-root microbiota and the intestinal microbiota of animals. We then highlight how an understanding of such interactions has guided efforts to engineer microbes to participate in chemical signaling in these habitats. We discuss engineering efforts in the context of chemical interactions that enable host colonization, promote host health, and exclude pathogens. Finally, we describe prominent challenges facing this field and propose new directions for future engineering efforts.
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Affiliation(s)
- Douglas J Kenny
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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237
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Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics. Curr Opin Biotechnol 2018; 53:224-231. [PMID: 29550614 DOI: 10.1016/j.copbio.2018.01.028] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/22/2017] [Accepted: 01/24/2018] [Indexed: 12/19/2022]
Abstract
The trillions of microbes hosted by humans can dictate health or illness depending on a multitude of genetic, environmental, and lifestyle factors that help define the human ecosystem. As the human microbiota is characterized, so can the interconnectivity of microbe-host-disease be realized and manipulated. Designing microbes as therapeutic agents can not only enable targeted drug delivery but also restore homeostasis within a perturbed microbial community. Used for centuries in fermentation and preservation of food, lactic acid bacteria (LAB) have a long history of safe, and occasionally health promoting, interactions with the human gut, making them ideal candidates for engineered functionality. This review outlines available genetic tools, recent developments in biomedical applications, as well as potential future applications of synthetic biology to program LAB-based therapeutic systems.
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238
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Bober JR, Beisel CL, Nair NU. Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications. Annu Rev Biomed Eng 2018. [PMID: 29528686 DOI: 10.1146/annurev-bioeng-062117-121019] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An increasing number of studies have strongly correlated the composition of the human microbiota with many human health conditions and, in several cases, have shown that manipulating the microbiota directly affects health. These insights have generated significant interest in engineering indigenous microbiota community members and nonresident probiotic bacteria as biotic diagnostics and therapeutics that can probe and improve human health. In this review, we discuss recent advances in synthetic biology to engineer commensal and probiotic lactic acid bacteria, bifidobacteria, and Bacteroides for these purposes, and we provide our perspective on the future potential of these technologies.
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Affiliation(s)
- Josef R Bober
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, USA;
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Nikhil U Nair
- Department of Chemical and Biological Engineering, Tufts University, Medford, Massachusetts 02155, USA;
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239
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Rodiño-Janeiro BK, Vicario M, Alonso-Cotoner C, Pascua-García R, Santos J. A Review of Microbiota and Irritable Bowel Syndrome: Future in Therapies. Adv Ther 2018; 35:289-310. [PMID: 29498019 PMCID: PMC5859043 DOI: 10.1007/s12325-018-0673-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Indexed: 12/01/2022]
Abstract
Irritable bowel syndrome (IBS), one of the most frequent digestive disorders, is characterized by chronic and recurrent abdominal pain and altered bowel habit. The origin seems to be multifactorial and is still not well defined for the different subtypes. Genetic, epigenetic and sex-related modifications of the functioning of the nervous and immune-endocrine supersystems and regulation of brain-gut physiology and bile acid production and absorption are certainly involved. Acquired predisposition may act in conjunction with infectious, toxic, dietary and life event-related factors to enhance epithelial permeability and elicit mucosal microinflammation, immune activation and dysbiosis. Notably, strong evidence supports the role of bacterial, viral and parasitic infections in triggering IBS, and targeting microbiota seems promising in view of the positive response to microbiota-related therapies in some patients. However, the lack of highly predictive diagnostic biomarkers and the complexity and heterogeneity of IBS patients make management difficult and unsatisfactory in many cases, reducing patient health-related quality of life and increasing the sanitary burden. This article reviews specific alterations and interventions targeting the gut microbiota in IBS, including prebiotics, probiotics, synbiotics, non-absorbable antibiotics, diets, fecal transplantation and other potential future approaches useful for the diagnosis, prevention and treatment of IBS.
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Affiliation(s)
- Bruno K Rodiño-Janeiro
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain.
| | - María Vicario
- Translational Mucosal Immunology Group, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Subdirección General de Investigación Sanitaria, Ministerio de Economía, Industria y Competitividad, Madrid, Spain
| | - Carmen Alonso-Cotoner
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Subdirección General de Investigación Sanitaria, Ministerio de Economía, Industria y Competitividad, Madrid, Spain
| | | | - Javier Santos
- Laboratory of Neuro-Immuno-Gastroenterology, Digestive System Research Unit, Vall d'Hebron Institut de Recerca, Department of Gastroenterology, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona (Facultat de Medicina), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Subdirección General de Investigación Sanitaria, Ministerio de Economía, Industria y Competitividad, Madrid, Spain.
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240
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Pham PLH, Rooholghodos SA, Choy JS, Luo X. Constructing Synthetic Ecosystems with Biopolymer Fluitrodes. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201700180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Phu L. H. Pham
- Department of Mechanical Engineering The Catholic University of America 620 Michigan Ave NE Washington DC 20064 USA
| | - Seyed A. Rooholghodos
- Department of Mechanical Engineering The Catholic University of America 620 Michigan Ave NE Washington DC 20064 USA
| | - John S. Choy
- Department of Biology The Catholic University of America 620 Michigan Ave NE Washington DC 20064 USA
| | - Xiaolong Luo
- Department of Mechanical Engineering The Catholic University of America 620 Michigan Ave NE Washington DC 20064 USA
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241
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de Barros PP, Scorzoni L, Ribeiro FDC, Fugisaki LRDO, Fuchs BB, Mylonakis E, Jorge AOC, Junqueira JC, Rossoni RD. Lactobacillus paracasei 28.4 reduces in vitro hyphae formation of Candida albicans and prevents the filamentation in an experimental model of Caenorhabditis elegans. Microb Pathog 2018; 117:80-87. [PMID: 29432910 DOI: 10.1016/j.micpath.2018.02.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/13/2022]
Abstract
The objective of this study was to evaluate the influence of microbe-microbe interactions to identify a strain of Lactobacillus that could reduce the filamentation of Candida albicans ATCC 18804 using in vitro and in vivo models. Thus presenting a probiotic effect against the fungal pathogen. First, we analyzed the ability of 25 clinical isolates of Lactobacillus to reduce filamentation in C. albicans in vitro. We found that L. paracasei isolate 28.4 exhibited the greatest reduction of C. albicans hyphae (p = 0.0109). This reduction was confirmed by scanning electron microscopy analysis. The influence of C. albicans filamentation was found to be contributed through reduced gene expression of filament associated genes (TEC1 and UME6). In an in vivo study, prophylactic provisions with L. paracasei increased the survival of Caenorhabditis elegans worms infected with C. albicans (p = 0.0001) by 29%. Prolonged survival was accompanied by the prevention of cuticle rupture of 27% of the worms by filamentation of C. albicans, a phenotype that is characteristic of C. albicans killing of nematodes, compared to the control group. Lactobacillus paracasei isolate 28.4 reduced the filamentation of C. albicans in vitro by negatively regulating the TEC1 and UME6 genes that are essential for the production of hyphae. Prophylactic provision of Lactobacillus paracasei 28.4 protected C. elegans against candidiasis in vivo. L. paracasei 28.4 has the potential to be employed as an alternative method to control candidiasis.
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Affiliation(s)
- Patrícia Pimentel de Barros
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, UNESP - Univ Estadual Paulista, Francisco Jose Longo 777, Sao Dimas, Sao Jose dos Campos, CEP: 12245-000, SP, Brazil.
| | - Liliana Scorzoni
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, UNESP - Univ Estadual Paulista, Francisco Jose Longo 777, Sao Dimas, Sao Jose dos Campos, CEP: 12245-000, SP, Brazil.
| | - Felipe de Camargo Ribeiro
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, UNESP - Univ Estadual Paulista, Francisco Jose Longo 777, Sao Dimas, Sao Jose dos Campos, CEP: 12245-000, SP, Brazil.
| | - Luciana Ruano de Oliveira Fugisaki
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, UNESP - Univ Estadual Paulista, Francisco Jose Longo 777, Sao Dimas, Sao Jose dos Campos, CEP: 12245-000, SP, Brazil.
| | - Beth Burgwyn Fuchs
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI, 02903, USA.
| | - Eleftherios Mylonakis
- Division of Infectious Diseases, Rhode Island Hospital, Alpert Medical School of Brown University, Providence, RI, 02903, USA.
| | - Antonio Olavo Cardoso Jorge
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, UNESP - Univ Estadual Paulista, Francisco Jose Longo 777, Sao Dimas, Sao Jose dos Campos, CEP: 12245-000, SP, Brazil.
| | - Juliana Campos Junqueira
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, UNESP - Univ Estadual Paulista, Francisco Jose Longo 777, Sao Dimas, Sao Jose dos Campos, CEP: 12245-000, SP, Brazil.
| | - Rodnei Dennis Rossoni
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, UNESP - Univ Estadual Paulista, Francisco Jose Longo 777, Sao Dimas, Sao Jose dos Campos, CEP: 12245-000, SP, Brazil.
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Abstract
Our ability to generate bacterial strains with unique and increasingly complex functions has rapidly expanded in recent times. The capacity for DNA synthesis is increasing and costing less; new tools are being developed for fast, large-scale genetic manipulation; and more tested genetic parts are available for use, as is the knowledge of how to use them effectively. These advances promise to unlock an exciting array of 'smart' bacteria for clinical use but will also challenge scientists to better optimize preclinical testing regimes for early identification and validation of promising strains and strategies. Here, we review recent advances in the development and testing of engineered bacterial diagnostics and therapeutics. We highlight new technologies that will assist the development of more complex, robust and reliable engineered bacteria for future clinical applications, and we discuss approaches to more efficiently evaluate engineered strains throughout their preclinical development.
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243
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Palmer JD, Piattelli E, McCormick BA, Silby MW, Brigham CJ, Bucci V. Engineered Probiotic for the Inhibition of Salmonella via Tetrathionate-Induced Production of Microcin H47. ACS Infect Dis 2018; 4:39-45. [PMID: 28918634 PMCID: PMC5766358 DOI: 10.1021/acsinfecdis.7b00114] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Complications arising from antibiotic-resistant bacteria are becoming one of the key issues in modern medicine. Members of drug-resistant Enterobacteriaceae spp. include opportunistic pathogens (e.g., Salmonella spp.) that are among the leading causes of morbidity and mortality worldwide. Overgrowth of these bacteria is considered a hallmark of intestinal dysbiosis. Microcins (small antimicrobial peptides) produced by some gut commensals can potentially cure these conditions by inhibiting these pathogens and have been proposed as a viable alternative to antibiotic treatment. In this proof-of-concept work, we leverage this idea to develop a genetically engineered prototype probiotic to inhibit Salmonella spp. upon exposure to tetrathionate, a molecule produced in the inflamed gut during the course of Salmonella infection. We developed a plasmid-based system capable of conferring the ability to detect and utilize tetrathionate, while at the same time producing microcin H47. We transferred this plasmid-based system to Escherichia coli and demonstrated the ability of the engineered strain to inhibit growth of Salmonella in anaerobic conditions while in the presence of tetrathionate, with no detectable inhibition in the absence of tetrathionate. In direct competition assays between the engineered E. coli and Salmonella, the engineered E. coli had a considerable increase in fitness advantage in the presence of 1 mM tetrathionate as compared to the absence of tetrathionate. In this work, we have demonstrated the ability to engineer a strain of E. coli capable of using an environmental signal indicative of intestinal inflammation as an inducing molecule, resulting in production of a microcin capable of inhibiting the organism responsible for the inflammation.
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Affiliation(s)
- Jacob D. Palmer
- Department of Bioengineering, University of Massachusetts Dartmouth, 285 Old Westport Road, N. Dartmouth, Massachusetts 02747, United States
| | - Emma Piattelli
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, N. Dartmouth, Massachusetts 02747, United States
| | - Beth A. McCormick
- MaPS, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
- UMass, Center for Microbiome Research, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
| | - Mark W. Silby
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, N. Dartmouth, Massachusetts 02747, United States
- UMassD, Probiotic Discovery, Engineering and Manufacturing Pipeline, 285 Old Westport Road, N. Dartmouth, Massachusetts 02747, United States
| | - Christopher J. Brigham
- Department of Bioengineering, University of Massachusetts Dartmouth, 285 Old Westport Road, N. Dartmouth, Massachusetts 02747, United States
- UMassD, Probiotic Discovery, Engineering and Manufacturing Pipeline, 285 Old Westport Road, N. Dartmouth, Massachusetts 02747, United States
| | - Vanni Bucci
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, N. Dartmouth, Massachusetts 02747, United States
- UMass, Center for Microbiome Research, 55 Lake Avenue North, Worcester, Massachusetts 01655, United States
- UMassD, Probiotic Discovery, Engineering and Manufacturing Pipeline, 285 Old Westport Road, N. Dartmouth, Massachusetts 02747, United States
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244
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Intestinal microbiota profiles associated with low and high residual feed intake in chickens across two geographical locations. PLoS One 2017; 12:e0187766. [PMID: 29141016 PMCID: PMC5687768 DOI: 10.1371/journal.pone.0187766] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/25/2017] [Indexed: 01/01/2023] Open
Abstract
Intestinal microbe-host interactions can affect the feed efficiency (FE) of chickens. As inconsistent findings for FE-associated bacterial taxa were reported across studies, the present objective was to identify whether bacterial profiles and predicted metabolic functions that were associated with residual feed intake (RFI) and performance traits in female and male chickens were consistent across two different geographical locations. At six weeks of life, the microbiota in ileal, cecal and fecal samples of low (n = 34) and high (n = 35) RFI chickens were investigated by sequencing the V3-5 region of the 16S rRNA gene. Location-associated differences in α-diversity and relative abundances of several phyla and genera were detected. RFI-associated bacterial abundances were found at the phylum and genus level, but differed among the three intestinal sites and between males and females. Correlation analysis confirmed that, of the taxonomically classifiable bacteria, Lactobacillus (5% relative abundance) and two Lactobacillus crispatus-OTUs in feces were indicative for high RFI in females (P < 0.05). In males, Ruminococcus in cecal digesta (3.1% relative abundance) and Dorea in feces (<0.1% relative abundance) were best indicative for low RFI, whereas Acinetobacter in feces (<1.5% relative abundance) related to high RFI (P < 0.05). Predicted metabolic functions in feces of males confirmed compositional relationships as functions related to amino acid, fatty acid and vitamin metabolism correlated with low RFI, whereas an increasing abundance of bacterial signaling and interaction (i.e. cellular antigens) genes correlated with high RFI (P < 0.05). In conclusion, RFI-associated bacterial profiles could be identified across different geographical locations. Results indicated that consortia of low-abundance taxa in the ileum, ceca and feces may play a role for FE in chickens, whereby only bacterial FE-associations found in ileal and cecal digesta may serve as useful targets for dietary strategies.
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245
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Certain LK, Way JC, Pezone MJ, Collins JJ. Using Engineered Bacteria to Characterize Infection Dynamics and Antibiotic Effects In Vivo. Cell Host Microbe 2017; 22:263-268.e4. [PMID: 28867388 DOI: 10.1016/j.chom.2017.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/17/2017] [Accepted: 08/01/2017] [Indexed: 12/31/2022]
Abstract
Synthetic biology has focused on engineering microbes to synthesize useful products or to serve as living diagnostics and therapeutics. Here we utilize a host-derived Escherichia coli strain engineered with a genetic toggle switch as a research tool to examine in vivo replicative states in a mouse model of chronic infection, and to compare in vivo and in vitro bacterial behavior. In contrast to the effect of antibiotics in vitro, we find that the fraction of actively dividing bacteria remains relatively high throughout the course of a chronic infection in vivo and increases in response to antibiotics. Moreover, the presence of non-dividing bacteria in vivo does not necessarily lead to an antibiotic-tolerant infection, in contrast to expectations from in vitro experiments. These results demonstrate the utility of engineered bacteria for querying pathogen behavior in vivo, and the importance of validating in vitro studies of antibiotic effects with in vivo models.
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Affiliation(s)
- Laura K Certain
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Matthew J Pezone
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, 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, Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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246
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Higashikuni Y, Chen WC, Lu TK. Advancing therapeutic applications of synthetic gene circuits. Curr Opin Biotechnol 2017; 47:133-141. [PMID: 28750201 DOI: 10.1016/j.copbio.2017.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023]
Abstract
Synthetic biology aims to introduce new sense-and-respond capabilities into living cells, which would enable novel therapeutic strategies. The development of regulatory elements, molecular computing devices, and effector screening technologies has enabled researchers to design synthetic gene circuits in many organisms, including mammalian cells. Engineered gene networks, such as closed-loop circuits or Boolean logic gate circuits, can be used to program cells to perform specific functions with spatiotemporal control and restoration of homeostasis in response to the extracellular environment and intracellular signaling. In addition, genetically modified microbes can be designed as local delivery of therapeutic molecules. In this review, we will discuss recent advances in therapeutic applications of synthetic gene circuits, as well as challenges and future opportunities for biomedicine.
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Affiliation(s)
- Yasutomi Higashikuni
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA
| | - William Cw Chen
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Timothy K Lu
- Research Laboratory of Electronics, Massachusetts Institute of Technology, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, MA 02139, USA.
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247
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Ma B, Pan Q, Peppelenbosch MP. Genetically Engineered Bacteria for Treating Human Disease. Trends Pharmacol Sci 2017; 38:763-764. [PMID: 28760488 DOI: 10.1016/j.tips.2017.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 06/28/2017] [Accepted: 07/06/2017] [Indexed: 01/09/2023]
Abstract
Bacteria have now been harnessed to combat human diseases, especially to meet the challenge of antimicrobial resistance. Modulating the microbiome, particularly by genetically engineering the bacteria, has provided proof-of-concept as potential pharmacotherapy, but those involved in this field should engage in discussion as how to move forward.
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Affiliation(s)
- Buyun Ma
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands.
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248
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Álvarez B, Fernández LÁ. Sustainable therapies by engineered bacteria. Microb Biotechnol 2017; 10:1057-1061. [PMID: 28696008 PMCID: PMC5609241 DOI: 10.1111/1751-7915.12778] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 06/20/2017] [Indexed: 12/17/2022] Open
Abstract
The controlled in situ delivery of biologics (e.g. enzymes, cytokines, antibodies) by engineered bacteria of our microbiome will allow the sustainable production of these complex and expensive drugs locally in the human body, overcoming many of the technical and economical barriers currently associated with the global use of these potent medicines. We provide examples showing how engineered bacteria can be effective treatments against multiple pathologies, including autoimmune and inflammatory diseases, metabolic disorders, diabetes, obesity, infectious diseases and cancer, hence contributing to achieve the Global Sustainable Goal 3: ensure healthy lives and promote well‐being for all at all ages.
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Affiliation(s)
- Beatriz Álvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus UAM Cantoblanco, 28049, Madrid, Spain
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus UAM Cantoblanco, 28049, Madrid, Spain
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