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Kim K, Kang M, Cho BK. Systems and synthetic biology-driven engineering of live bacterial therapeutics. Front Bioeng Biotechnol 2023; 11:1267378. [PMID: 37929193 PMCID: PMC10620806 DOI: 10.3389/fbioe.2023.1267378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
The past decade has seen growing interest in bacterial engineering for therapeutically relevant applications. While early efforts focused on repurposing genetically tractable model strains, such as Escherichia coli, engineering gut commensals is gaining traction owing to their innate capacity to survive and stably propagate in the intestine for an extended duration. Although limited genetic tractability has been a major roadblock, recent advances in systems and synthetic biology have unlocked our ability to effectively harness native gut commensals for therapeutic and diagnostic purposes, ranging from the rational design of synthetic microbial consortia to the construction of synthetic cells that execute "sense-and-respond" logic operations that allow real-time detection and therapeutic payload delivery in response to specific signals in the intestine. In this review, we outline the current progress and latest updates on microbial therapeutics, with particular emphasis on gut commensal engineering driven by synthetic biology and systems understanding of their molecular phenotypes. Finally, the challenges and prospects of engineering gut commensals for therapeutic applications are discussed.
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Affiliation(s)
- Kangsan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Minjeong Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
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52
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Huang X. Treatment and management for children with urea cycle disorder in chronic stage. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:744-750. [PMID: 37807629 PMCID: PMC10764184 DOI: 10.3724/zdxbyxb-2023-0378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/27/2023] [Indexed: 10/10/2023]
Abstract
Urea cycle disorder (UCD) is a group of inherited metabolic diseases with high disability or fatality rate, which need long-term drug treatment and diet management. Except those with Citrin deficiency or liver transplantation, all pediatric patients require lifelong low protein diet with safe levels of protein intake and adequate energy and lipids supply for their corresponding age; supplementing essential amino acids and protein-free milk are also needed if necessary. The drugs for long-term use include nitrogen scavengers (sodium benzoate, sodium phenylbutyrate, glycerol phenylbutyrate), urea cycle activation/substrate supplementation agents (N-carbamylglutamate, arginine, citrulline), etc. Liver transplantation is recommended for pediatric patients not responding to standard diet and drug treatment, and those with severe progressive liver disease and/or recurrent metabolic decompensations. Gene therapy, stem cell therapy, enzyme therapy and other novel technologies may offer options for treatment in UCD patients. The regular biochemical assessments like blood ammonia, liver function and plasma amino acid profile are needed, and physical growth, intellectual development, nutritional intake should be also evaluated for adjusting treatment in time.
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Affiliation(s)
- Xinwen Huang
- Department of Genetics and Metabolism, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
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53
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Yu M, Hu S, Tang B, Yang H, Sun D. Engineering Escherichia coli Nissle 1917 as a microbial chassis for therapeutic and industrial applications. Biotechnol Adv 2023; 67:108202. [PMID: 37343690 DOI: 10.1016/j.biotechadv.2023.108202] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/19/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
Genetically engineered microbes, especially Escherichia coli, have been widely used in the biosynthesis of proteins and metabolites for medical and industrial applications. As a traditional probiotic with a well-established safety record, E. coli Nissle 1917 (EcN) has recently emerged as a microbial chassis for generating living therapeutics, drug delivery vehicles, and microbial platforms for industrial production. Despite the availability of genetic tools for engineering laboratory E. coli K-12 and B strains, new genetic engineering systems are still greatly needed to expand the application range of EcN. In this review, we have summarized the latest progress in the development of genetic engineering systems in EcN, as well as their applications in the biosynthesis and delivery of valuable small molecules and biomacromolecules of medical and/or industrial interest, followed by a glimpse of how this rapidly growing field will evolve in the future.
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Affiliation(s)
- Mingjing Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Shilong Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Biao Tang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Hua Yang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
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54
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Jensen BAH, Heyndrickx M, Jonkers D, Mackie A, Millet S, Naghibi M, Pærregaard SI, Pot B, Saulnier D, Sina C, Sterkman LGW, Van den Abbeele P, Venlet NV, Zoetendal EG, Ouwehand AC. Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration. Cell Rep Med 2023; 4:101190. [PMID: 37683651 PMCID: PMC10518632 DOI: 10.1016/j.xcrm.2023.101190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/12/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Research on gut microbiota has generally focused on fecal samples, representing luminal content of the large intestine. However, nutrient uptake is restricted to the small intestine. Abundant immune cell populations at this anatomical site combined with diminished mucus secretion and looser junctions (partly to allow for more efficient fluid and nutrient absorption) also results in intimate host-microbe interactions despite more rapid transit. It is thus crucial to dissect key differences in both ecology and physiology between small and large intestine to better leverage the immense potential of human gut microbiota imprinting, including probiotic engraftment at biological sensible niches. Here, we provide a detailed review unfolding how the physiological and anatomical differences between the small and large intestine affect gut microbiota composition, function, and plasticity. This information is key to understanding how gut microbiota manipulation, including probiotic administration, may strain-dependently transform host-microbe interactions at defined locations.
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Affiliation(s)
| | - Marc Heyndrickx
- Flanders Research Institute of Agriculture, Fisheries and Food, Belgium & Ghent University, Department Pathobiology, Pharmacology and Zoological Medicine, B-9090 Melle, 9820 Merelbeke, Belgium
| | - Daisy Jonkers
- Division Gastroenterology-Hepatology, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht 6229 ER, the Netherlands
| | - Alan Mackie
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, UK
| | - Sam Millet
- Flanders Research Institute of Agriculture, Fisheries and Food, 9090 Melle, Belgium
| | | | - Simone Isling Pærregaard
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bruno Pot
- Yakult Europe BV, 1332 Almere, the Netherlands
| | | | - Christian Sina
- Institute of Nutritional Medicine, University Medical Center of Schleswig-Holstein & University of Lübeck, 23538 Lübeck, Germany
| | | | | | - Naomi Vita Venlet
- International Life Science Institute, European Branch, Brussels, Belgium.
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, the Netherlands
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55
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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56
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Lebovich M, Zeng M, Andrews LB. Algorithmic Programming of Sequential Logic and Genetic Circuits for Recording Biochemical Concentration in a Probiotic Bacterium. ACS Synth Biol 2023; 12:2632-2649. [PMID: 37581922 PMCID: PMC10510703 DOI: 10.1021/acssynbio.3c00232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 08/16/2023]
Abstract
Through the implementation of designable genetic circuits, engineered probiotic microorganisms could be used as noninvasive diagnostic tools for the gastrointestinal tract. For these living cells to report detected biomarkers or signals after exiting the gut, the genetic circuits must be able to record these signals by using genetically encoded memory. Complex memory register circuits could enable multiplex interrogation of biomarkers and signals. A theory-based approach to create genetic circuits containing memory, known as sequential logic circuits, was previously established for a model laboratory strain of Escherichia coli, yet how circuit component performance varies for nonmodel and clinically relevant bacterial strains is poorly understood. Here, we develop a scalable computational approach to design robust sequential logic circuits in probiotic strain Escherichia coli Nissle 1917 (EcN). In this work, we used TetR-family transcriptional repressors to build genetic logic gates that can be composed into sequential logic circuits, along with a set of engineered sensors relevant for use in the gut environment. Using standard methods, 16 genetic NOT gates and nine sensors were experimentally characterized in EcN. These data were used to design and predict the performance of circuit designs. We present a set of genetic circuits encoding both combinational logic and sequential logic and show that the circuit outputs are in close agreement with our quantitative predictions from the design algorithm. Furthermore, we demonstrate an analog-like concentration recording circuit that detects and reports three input concentration ranges of a biochemical signal using sequential logic.
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Affiliation(s)
- Matthew Lebovich
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Min Zeng
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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57
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Nelson MT, Coia HG, Holt C, Greenwood ES, Narayanan L, Robinson PJ, Merrill EA, Litteral V, Goodson MS, Saldanha RJ, Grogg MW, Mauzy CA. Evaluation of Human Performance Aiding Live Synthetically Engineered Bacteria in a Gut-on-a-Chip. ACS Biomater Sci Eng 2023; 9:5136-5150. [PMID: 36198112 DOI: 10.1021/acsbiomaterials.2c00774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Synbiotics are a new class of live therapeutics employing engineered genetic circuits. The rapid adoption of genetic editing tools has catalyzed the expansion of possible synbiotics, exceeding traditional testing paradigms in terms of both throughput and model complexity. Herein, we present a simplistic gut-chip model using common Caco2 and HT-29 cell lines to establish a dynamic human screening platform for a cortisol sensing tryptamine producing synbiotic for cognitive performance sustainment. The synbiotic, SYN, was engineered from the common probiotic E. coli Nissle 1917 strain. It had the ability to sense cortisol at physiological concentrations, resulting in the activation of a genetic circuit that produces tryptophan decarboxylase and converts bioavailable tryptophan to tryptamine. SYN was successfully cultivated within the gut-chip showing log-phase growth comparable to the wild-type strain. Tryptophan metabolism occurred quickly in the gut compartment when exposed to 5 μM cortisol, resulting in the complete conversion of bioavailable tryptophan into tryptamine. The flux of tryptophan and tryptamine from the gut to the vascular compartment of the chip was delayed by 12 h, as indicated by the detectable tryptamine in the vascular compartment. The gut-chip provided a stable environment to characterize the sensitivity of the cortisol sensor and dynamic range by altering cortisol and tryptophan dosimetry. Collectively, the human gut-chip provided human relevant apparent permeability to assess tryptophan and tryptamine metabolism, production, and transport, enabled host analyses of cellular viability and pro-inflammatory cytokine secretion, and succeeded in providing an efficacy test of a novel synbiotic. Organ-on-a-chip technology holds promise in aiding traditional therapeutic pipelines to more rapidly down select high potential compounds that reduce the failure rate and accelerate the opportunity for clinical intervention.
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Affiliation(s)
- M Tyler Nelson
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Heidi G Coia
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
- National Research Council, The National Academies of Sciences, Engineering, and Medicine, 500 Fifth Street N.W., Washington, D.C. 20001, United States
| | - Corey Holt
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Eric S Greenwood
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
- Oak Ridge Institute for Science and Education, 1299 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Latha Narayanan
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
- The Henry M. Jackson Foundation, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Peter J Robinson
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
- The Henry M. Jackson Foundation, 6720A Rockledge Drive, Bethesda, Maryland 20817, United States
| | - Elaine A Merrill
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Vaughn Litteral
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
- UES Inc., 4401 Dayton-Xenia Road, Dayton, Ohio 45432, United States
| | - Michael S Goodson
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Roland J Saldanha
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Matthew W Grogg
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
| | - Camilla A Mauzy
- United States Air Force Research Laboratory, 711th Human Performance Wing, 2510 N 5th Street, Bldg. 840, Wright-Patterson AFB, Ohio 45433, United States
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58
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Chen C, Zhu Z. Recent Advances in the Nanoshells Approach for Encapsulation of Single Probiotics. Drug Des Devel Ther 2023; 17:2763-2774. [PMID: 37705759 PMCID: PMC10497064 DOI: 10.2147/dddt.s419897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
The intestine, often referred to as the "second brain" of the human body, houses a vast microbial community that plays a crucial role in maintaining the host's balance and directly impacting overall health. Probiotics, a type of beneficial microorganism, offer various health benefits when consumed. However, probiotics face challenges such as acidic conditions in the stomach, bile acids, enzymes, and other adverse factors before they can colonize the intestinal tissues. At present, pills, dry powder, encapsulation, chemically modified bacteria, and genetically engineered bacteria have emerged as the preferred method for the stable and targeted delivery of probiotics. In particular, the use of nanoshells on the surface of single probiotics has shown promise in regulating their growth and differentiation. These nanoshells can detach from the probiotics' surface upon reaching the intestine, facilitating direct contact between the probiotics and intestinal mucosa. In this perspective, we provide an overview of the current developments in the formation of nanoshells mediated by single probiotics. We also discuss the advantages and disadvantages of different nanocoating strategies and explore future trends in probiotic protection.
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Affiliation(s)
- Cheng Chen
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Danyang, Jiangsu Province, 212300, People’s Republic of China
| | - Ziyu Zhu
- The Affiliated Huai’an Hospital of Xuzhou Medical University and the Second People’s Hospital of Huai’an, Huai’an, 223002, People’s Republic of China
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59
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Gao J, Nie R, Chang H, Yang W, Ren Q. A meta-analysis of microbiome therapies for hepatic encephalopathy. Eur J Gastroenterol Hepatol 2023; 35:927-937. [PMID: 37505972 DOI: 10.1097/meg.0000000000002596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Microbiome therapies may be reported to be effective in hepatic encephalopathy (HE). We thus did a meta-analysis of randomized controlled trials to assess the effect of microbiome therapies for HE. We systematically searched PubMed, Web of Science, EMBASE, and Cochrane Library for randomized controlled trials that compared the different treatments for HE including probiotics, symbiotics, and fecal microbiota transplant (FMT). Meta-analysis was performed to calculate pooled odds ratios (ORs) with corresponding 95% confidence intervals (CIs). Twenty-one studies met our inclusion criteria (N = 1746 participants). Probiotics, synbiotics and FMT significantly reversed minimal HE (MHE) (OR: 0.41, 95% CI: 0.19-0.90, P = 0.03), reduced overt HE (OHE) development (OR, 0.41; 95% CI: 0.28-0.61 P < 0.00001)and the frequency of serious adverse events(SAEs) (OR:0.14, 95% CI: 0.04-0.47, P = 0.001), meanwhile decreased ammonia levels (WMD: -9.26, 95% CI: -16.92 to -1.61; P = 0.02), NCT level (MD = -4.41, 95% CI: -0.87 to -0.22, P = 0.04) and hospitalization rates (OR, 0.38; 95% CI: 0.19-0.79, P = 0.009) compared with placebo/no treatment. Finally, we conclude that microbiome therapies were more effective in improving MHE and preventing progression to OHE, reducing the frequency of SAEs, and decreasing ammonia levels, NCT level, and hospitalization rates when compared to placebo/no treatment.
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Affiliation(s)
- Jie Gao
- Lanzhou University
- Department of Gastroenterology, the First Hospital of Lanzhou University
| | - Rui Nie
- Lanzhou University
- Department of Gastroenterology, the First Hospital of Lanzhou University
| | - Hong Chang
- Lanzhou University
- Department of Gastroenterology, the First Hospital of Lanzhou University
| | - Wei Yang
- Lanzhou University
- Department of Gastroenterology, the First Hospital of Lanzhou University
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University, Lanzhou, China
| | - Qian Ren
- Lanzhou University
- Department of Gastroenterology, the First Hospital of Lanzhou University
- Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University, Lanzhou, China
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60
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Effendi SSW, Ng IS. Prospective and challenges of live bacterial therapeutics from a superhero Escherichia coli Nissle 1917. Crit Rev Microbiol 2023; 49:611-627. [PMID: 35947523 DOI: 10.1080/1040841x.2022.2109405] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/02/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022]
Abstract
Escherichia coli Nissle 1917 (EcN), the active component of Mutaflor(R), is a notable probiotic from Gram-negative to treat Crohn's disease and irritable bowel syndrome. Therefore, a comprehensive genomic database maximizes the systemic probiotic assessment to discover EcN's role in human health. Recently, advanced synthetic and genetic tools have opened up a rich area to execute EcN as "living medicines" with controllable functions. Incorporating unique biomarkers allows the engineered EcN to switch genes on and off in response to environmental cues. Since EcN holds promise as a safe nature vehicle, more studies are desired to fully realize a wide range of probiotic potential for disease treatment. This review aims to deliver a historical origin of EcN, discuss the recent promising genetic toolbox in the rational design of probiotics, and pinpoint the clinical translation and evaluation of engineered EcN in vitro and in vivo. The summary of safety concerns, strategies of biotherapeutics development, and the challenges and prospects of engineered EcN is also concluded.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
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61
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Li P, Roos S, Luo H, Ji B, Nielsen J. Metabolic engineering of human gut microbiome: Recent developments and future perspectives. Metab Eng 2023; 79:1-13. [PMID: 37364774 DOI: 10.1016/j.ymben.2023.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/10/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
Many studies have demonstrated that the gut microbiota is associated with human health and disease. Manipulation of the gut microbiota, e.g. supplementation of probiotics, has been suggested to be feasible, but subject to limited therapeutic efficacy. To develop efficient microbiota-targeted diagnostic and therapeutic strategies, metabolic engineering has been applied to construct genetically modified probiotics and synthetic microbial consortia. This review mainly discusses commonly adopted strategies for metabolic engineering in the human gut microbiome, including the use of in silico, in vitro, or in vivo approaches for iterative design and construction of engineered probiotics or microbial consortia. Especially, we highlight how genome-scale metabolic models can be applied to advance our understanding of the gut microbiota. Also, we review the recent applications of metabolic engineering in gut microbiome studies as well as discuss important challenges and opportunities.
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Affiliation(s)
- Peishun Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Stefan Roos
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE75007, Uppsala, Sweden
| | - Hao Luo
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden
| | - Boyang Ji
- BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen, Denmark
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200, Copenhagen, Denmark.
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62
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Wu H, Wei J, Zhao X, Liu Y, Chen Z, Wei K, Lu J, Chen W, Jiang M, Li S, Chen T. Neuroprotective effects of an engineered Escherichia coli Nissle 1917 on Parkinson's disease in mice by delivering GLP-1 and modulating gut microbiota. Bioeng Transl Med 2023; 8:e10351. [PMID: 37693045 PMCID: PMC10487327 DOI: 10.1002/btm2.10351] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/06/2022] [Indexed: 09/12/2023] Open
Abstract
Considerable evidence suggests that insulin resistance is closely linked to Parkinson's disease (PD), leading to agents aiming at treating diabetes can be regarded as new neuroprotective strategies in PD, notably glucagon-like peptide-1 (GLP-1). However, the extremely short half-life of GLP-1 due to degradation by the ubiquitous proteolytic enzyme limits its clinical application. In this study, we engineered the recombinant integrant probiotic strain Escherichia coli Nissle 1917 (EcN) to create a strain EcN-GLP-1 that effectively delivers the heterologous GLP-1 molecule. Subsequently, we assessed its neuroprotective effects on 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP)-induced PD mice. We demonstrated that EcN-GLP-1 treatment could improve motor deficits, increase tyrosine hydroxylase-positive neurons, suppress microglia and astrocyte activation, reduce brain and colon inflammation, and ameliorate colonic barrier function damaged by MPTP induction. Meanwhile, we confirmed that the oral administration of EcN-GLP-1 could restore the disturbance of gut microbiota in the MPTP-induced PD mice, by reducing the relative abundances of Akkermansia and Oscillospira, and increasing the level of Prevotella in the gut. These results support further development of an engineered probiotic platform in which production of GLP-1 for gut-brain disorders, such as PD.
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Affiliation(s)
- Heng Wu
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational MedicineNanchang UniversityNanchangJiangxiChina
| | - Jing Wei
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational MedicineNanchang UniversityNanchangJiangxiChina
| | - Xiumiao Zhao
- Queen Mary SchoolNanchang UniversityNanchangJiangxiChina
| | - Ying Liu
- Institute of Life ScienceNanchang UniversityNanchangJiangxiChina
| | - Zhihang Chen
- Queen Mary SchoolNanchang UniversityNanchangJiangxiChina
| | - Kehong Wei
- Queen Mary SchoolNanchang UniversityNanchangJiangxiChina
| | - Jiachen Lu
- Queen Mary SchoolNanchang UniversityNanchangJiangxiChina
| | - Wenjie Chen
- Queen Mary SchoolNanchang UniversityNanchangJiangxiChina
| | - Meixiu Jiang
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational MedicineNanchang UniversityNanchangJiangxiChina
| | - Shengjie Li
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational MedicineNanchang UniversityNanchangJiangxiChina
| | - Tingtao Chen
- National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational MedicineNanchang UniversityNanchangJiangxiChina
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Sanmarco LM, Rone JM, Polonio CM, Fernandez Lahore G, Giovannoni F, Ferrara K, Gutierrez-Vazquez C, Li N, Sokolovska A, Plasencia A, Faust Akl C, Nanda P, Heck ES, Li Z, Lee HG, Chao CC, Rejano-Gordillo CM, Fonseca-Castro PH, Illouz T, Linnerbauer M, Kenison JE, Barilla RM, Farrenkopf D, Stevens NA, Piester G, Chung EN, Dailey L, Kuchroo VK, Hava D, Wheeler MA, Clish C, Nowarski R, Balsa E, Lora JM, Quintana FJ. Lactate limits CNS autoimmunity by stabilizing HIF-1α in dendritic cells. Nature 2023; 620:881-889. [PMID: 37558878 PMCID: PMC10725186 DOI: 10.1038/s41586-023-06409-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
Abstract
Dendritic cells (DCs) have a role in the development and activation of self-reactive pathogenic T cells1,2. Genetic variants that are associated with the function of DCs have been linked to autoimmune disorders3,4, and DCs are therefore attractive therapeutic targets for such diseases. However, developing DC-targeted therapies for autoimmunity requires identification of the mechanisms that regulate DC function. Here, using single-cell and bulk transcriptional and metabolic analyses in combination with cell-specific gene perturbation studies, we identify a regulatory loop of negative feedback that operates in DCs to limit immunopathology. Specifically, we find that lactate, produced by activated DCs and other immune cells, boosts the expression of NDUFA4L2 through a mechanism mediated by hypoxia-inducible factor 1α (HIF-1α). NDUFA4L2 limits the production of mitochondrial reactive oxygen species that activate XBP1-driven transcriptional modules in DCs that are involved in the control of pathogenic autoimmune T cells. We also engineer a probiotic that produces lactate and suppresses T cell autoimmunity through the activation of HIF-1α-NDUFA4L2 signalling in DCs. In summary, we identify an immunometabolic pathway that regulates DC function, and develop a synthetic probiotic for its therapeutic activation.
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Affiliation(s)
- Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Joseph M Rone
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Carolina M Polonio
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Gonzalo Fernandez Lahore
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Federico Giovannoni
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Kylynne Ferrara
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Cristina Gutierrez-Vazquez
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Ning Li
- Synlogic Therapeutics, Cambridge, MA, USA
| | | | - Agustin Plasencia
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Camilo Faust Akl
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Payal Nanda
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Evelin S Heck
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Hong-Gyun Lee
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Chun-Cheih Chao
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Claudia M Rejano-Gordillo
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Pedro H Fonseca-Castro
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Tomer Illouz
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Linnerbauer
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Jessica E Kenison
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Rocky M Barilla
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Farrenkopf
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Nikolas A Stevens
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Gavin Piester
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth N Chung
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Lucas Dailey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay K Kuchroo
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - David Hava
- Synlogic Therapeutics, Cambridge, MA, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roni Nowarski
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Eduardo Balsa
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Dong X, Wu W, Pan P, Zhang XZ. Engineered Living Materials for Advanced Diseases Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2304963. [PMID: 37436776 DOI: 10.1002/adma.202304963] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/13/2023]
Abstract
Natural living materials serving as biotherapeutics exhibit great potential for treating various diseases owing to their immunoactivity, tissue targeting, and other biological activities. In this review, the recent developments in engineered living materials, including mammalian cells, bacteria, viruses, fungi, microalgae, plants, and their active derivatives that are used for treating various diseases are summarized. Further, the future perspectives and challenges of such engineered living material-based biotherapeutics are discussed to provide considerations for future advances in biomedical applications.
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Affiliation(s)
- Xue Dong
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, P. R. China
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, P. R. China
| | - Wei Wu
- Medical Center of Hematology, Xinqiao Hospital, State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 400037, P. R. China
| | - Pei Pan
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
| | - Xian-Zheng Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, P. R. China
- Key Laboratory of Biomedical Polymers of Ministry of Education and Department of Chemistry, Wuhan University, Wuhan, 430072, P. R. China
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65
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Gong T, Wu J. Synthetic engineered bacteria for cancer therapy. Expert Opin Drug Deliv 2023; 20:993-1013. [PMID: 37497622 DOI: 10.1080/17425247.2023.2241367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/10/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023]
Abstract
INTRODUCTION Cancer mortality worldwide highlights the urgency for advanced therapeutic methods to fill the gaps in conventional cancer therapies. Bacteriotherapy is showing great potential in tumor regression due to the motility and colonization tendencies of bacteria. However, the complicated in vivo environment and tumor pathogenesis hamper the therapeutic outcomes. Synthetic engineering methods endow bacteria with flexible abilities both at the extracellular and intracellular levels to meet treatment requirements. In this review, we introduce synthetic engineering methods for bacterial modifications. We highlight the recent progress in engineered bacteria and explore how these synthetic methods endow bacteria with superior abilities in cancer therapy. The current clinical translations are further discussed. Overall, this review may shed light on the advancement of engineered bacteria for cancer therapy. AREAS COVERED Recent progress in synthetic methods for bacterial engineering and specific examples of their applications in cancer therapy are discussed in this review. EXPERT OPINION Bacteriotherapy bridges the gaps of conventional cancer therapies through the natural motility and colonization tendency of bacteria, as well as their synthetic engineering. Nevertheless, to fulfill the bacteriotherapy potential and move into clinical trials, more research focusing on its safety concerns should be conducted.
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Affiliation(s)
- Tong Gong
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, China
| | - Jinhui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, China
- Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
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66
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Ciocan D, Elinav E. Engineering bacteria to modulate host metabolism. Acta Physiol (Oxf) 2023; 238:e14001. [PMID: 37222395 PMCID: PMC10909415 DOI: 10.1111/apha.14001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 05/25/2023]
Abstract
The microbial community of the gut, collectively termed the gut microbiota, modulates both host metabolism and disease development in a variety of clinical contexts. The microbiota can have detrimental effects and be involved in disease development and progression, but it can also offer benefits to the host. This has led in the last years to the development of different therapeutic strategies targeting the microbiota. In this review, we will focus on one of these strategies that involve the use of engineered bacteria to modulate gut microbiota in the treatment of metabolic disorders. We will discuss the recent developments and challenges in the use of these bacterial strains with an emphasis on their use for the treatment of metabolic diseases.
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Affiliation(s)
- Dragos Ciocan
- Systems Immunology DepartmentWeisman Institute of ScienceRehovotIsrael
- School of MedicineParis‐Saclay UniversityLe Kremlin‐BicêtreFrance
| | - Eran Elinav
- Systems Immunology DepartmentWeisman Institute of ScienceRehovotIsrael
- Microbiota & Cancer DivisionDKFZHeidelbergGermany
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67
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Abstract
Live biotherapeutic products (LBPs), including symbiotic and genetically engineered bacteria, are a promising class of emerging therapeutics that are widely investigated both preclinically and clinically for their oral delivery to the gastrointestinal (GI) tract. One emergent delivery strategy involves the direct functionalization of LBP surfaces through noncovalent or covalent modifications to control LBP interactions with the GI microenvironment, thereby improving their viability, attachment, or therapeutic effect. However, unlike other therapeutic modalities, LBPs are living organisms which present two unique challenges for surface modifications: (1) this approach can directly interfere with key LBP biological processes (e.g., colonization, metabolite secretion) and (2) modification can be variable due to the dynamic nature of LBP surfaces. Collectively, these factors remain uncharacterized as they relate to the oral delivery of LBPs. Herein, we leverage our previously reported surface modification platform, which enables LBP surface-presentation of targeting ligands, to broadly evaluate and characterize surface modifications on LBPs. Specifically, we evaluate how LBP growth affects the dilution of surface-presented targeting ligands and the subsequent loss of specific target attachment over time. Next, we describe key surface modification parameters (e.g., concentration, residence time) that can be optimized to facilitate LBP target attachment. We then characterize how bioconjugation influences the suitability of LBPs for oral delivery by evaluating their growth, viability, storage, toxicity against mammalian cells, and in vivo colonization. Broadly, we describe key parameters that influence the performance of surface modified LBPs and subsequently outline an experimental pipeline for characterizing and evaluating their suitability for oral delivery.
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Affiliation(s)
- Ava M. Vargason
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Aaron C. Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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68
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Yang Y, Hu T, Bian Y, Meng F, Yu S, Li H, Zhang Q, Gu L, Weng X, Tan C, Liang R. Coupling Probiotics with 2D CoCuMo-LDH Nanosheets as a Tumor-Microenvironment-Responsive Platform for Precise NIR-II Photodynamic Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211205. [PMID: 36913539 DOI: 10.1002/adma.202211205] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/07/2023] [Indexed: 06/09/2023]
Abstract
Photodynamic therapy (PDT) has become a promising cancer treatment approach with superior advantages. However, it remains a grand challenge to develop tumor microenvironment (TME)-responsive photosensitizers (PSs) for tumor-targeting precise PDT. Herein, the coupling Lactobacillus acidophilus (LA) probiotics with 2D CoCuMo layered-double-hydroxide (LDH) nanosheets (LA&LDH) is reported as a TME-responsive platform for precise NIR-II PDT. The CoCuMo-LDH nanosheets loaded on LA can be transformed from crystalline into amorphous through etching by the LA-metabolite-enabled low pH and overexpressed glutathione. The TME-induced in situ amorphization of CoCuMo-LDH nanosheets can boost its photodynamic activity for singlet oxygen (1 O2 ) generation under 1270 nm laser irradiation with relative 1 O2 quantum yield of 1.06, which is the highest among previously reported NIR-excited PSs. In vitro and in vivo assays prove that the LA&LDH can effectively achieve complete cell apoptosis and tumor eradication under 1270 nm laser irradiation. This study proves that the probiotics can be used as a tumor-targeting platform for highly efficient precise NIR-II PDT.
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Affiliation(s)
- Yu Yang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Tingting Hu
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
| | - Yixin Bian
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Fanqi Meng
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Shilong Yu
- Institute of Advanced Materials (IAM) and Key Laboratory of Flexible Electronics (KLoFE), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Hai Li
- Institute of Advanced Materials (IAM) and Key Laboratory of Flexible Electronics (KLoFE), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Qinghua Zhang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lin Gu
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Xisheng Weng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Chaoliang Tan
- Department of Chemistry and Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, P. R. China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, 518057, P. R. China
| | - Ruizheng Liang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, P. R. China
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Donati S, Mattanovich M, Hjort P, Jacobsen SAB, Blomquist SD, Mangaard D, Gurdo N, Pastor FP, Maury J, Hanke R, Herrgård MJ, Wulff T, Jakočiūnas T, Nielsen LK, McCloskey D. An automated workflow for multi-omics screening of microbial model organisms. NPJ Syst Biol Appl 2023; 9:14. [PMID: 37208327 DOI: 10.1038/s41540-023-00277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
Multi-omics datasets are becoming of key importance to drive discovery in fundamental research as much as generating knowledge for applied biotechnology. However, the construction of such large datasets is usually time-consuming and expensive. Automation might enable to overcome these issues by streamlining workflows from sample generation to data analysis. Here, we describe the construction of a complex workflow for the generation of high-throughput microbial multi-omics datasets. The workflow comprises a custom-built platform for automated cultivation and sampling of microbes, sample preparation protocols, analytical methods for sample analysis and automated scripts for raw data processing. We demonstrate possibilities and limitations of such workflow in generating data for three biotechnologically relevant model organisms, namely Escherichia coli, Saccharomyces cerevisiae, and Pseudomonas putida.
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Affiliation(s)
- Stefano Donati
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Matthias Mattanovich
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark
| | - Pernille Hjort
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | | | - Sarah Dina Blomquist
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Drude Mangaard
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Nicolas Gurdo
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Felix Pacheco Pastor
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Jérôme Maury
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Rene Hanke
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Markus J Herrgård
- BioInnovation Institute, Ole Maaløes Vej 3, 2200, København, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Tadas Jakočiūnas
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Lars Keld Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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70
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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71
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Lynch JP, González-Prieto C, Reeves AZ, Bae S, Powale U, Godbole NP, Tremblay JM, Schmidt FI, Ploegh HL, Kansra V, Glickman JN, Leong JM, Shoemaker CB, Garrett WS, Lesser CF. Engineered Escherichia coli for the in situ secretion of therapeutic nanobodies in the gut. Cell Host Microbe 2023; 31:634-649.e8. [PMID: 37003258 PMCID: PMC10101937 DOI: 10.1016/j.chom.2023.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/20/2022] [Accepted: 03/08/2023] [Indexed: 04/03/2023]
Abstract
Drug platforms that enable the directed delivery of therapeutics to sites of diseases to maximize efficacy and limit off-target effects are needed. Here, we report the development of PROT3EcT, a suite of commensal Escherichia coli engineered to secrete proteins directly into their surroundings. These bacteria consist of three modular components: a modified bacterial protein secretion system, the associated regulatable transcriptional activator, and a secreted therapeutic payload. PROT3EcT secrete functional single-domain antibodies, nanobodies (Nbs), and stably colonize and maintain an active secretion system within the intestines of mice. Furthermore, a single prophylactic dose of a variant of PROT3EcT that secretes a tumor necrosis factor-alpha (TNF-α)-neutralizing Nb is sufficient to ablate pro-inflammatory TNF levels and prevent the development of injury and inflammation in a chemically induced model of colitis. This work lays the foundation for developing PROT3EcT as a platform for the treatment of gastrointestinal-based diseases.
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Affiliation(s)
- Jason P Lynch
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Coral González-Prieto
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Analise Z Reeves
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sena Bae
- Departments of Immunology and Infectious Diseases and Harvard T.H. Chan Center for the Microbiome in Public Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Urmila Powale
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Neha P Godbole
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jacqueline M Tremblay
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA
| | - Florian I Schmidt
- Institute of Innate Immunity, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Hidde L Ploegh
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - Jonathan N Glickman
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02115, USA
| | - John M Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA; Tufts Stuart B Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Boston, MA 02111, USA
| | - Charles B Shoemaker
- Department of Infectious Disease and Global Health, Tufts Cummings School of Veterinary Medicine, North Grafton, MA 01536, USA; Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Wendy S Garrett
- Departments of Immunology and Infectious Diseases and Harvard T.H. Chan Center for the Microbiome in Public Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cammie F Lesser
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Ragon Institute of Harvard and MIT, Cambridge, MA 02139, USA.
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De Oliveira FL, Salgaço MK, de Oliveira MT, Mesa V, Sartoratto A, Peregrino AM, Ramos WS, Sivieri K. Exploring the Potential of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 as Promising Psychobiotics Using SHIME. Nutrients 2023; 15:nu15061521. [PMID: 36986251 PMCID: PMC10056475 DOI: 10.3390/nu15061521] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Psychobiotics are probiotics that have the characteristics of modulating central nervous system (CNS) functions or reconciled actions by the gut-brain axis (GBA) through neural, humoral and metabolic pathways to improve gastrointestinal activity as well as anxiolytic and even antidepressant abilities. The aim of this work was to evaluate the effect of Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 on the gut microbiota of mildly anxious adults using SHIME®. The protocol included a one-week control period and two weeks of treatment with L. helveticus R0052 and B. longum R0175. Ammonia (NH4+), short chain fatty acids (SCFAs), gamma-aminobutyric acid (GABA), cytokines and microbiota composition were determined. Probiotic strains decreased significantly throughout the gastric phase. The highest survival rates were exhibited by L. helveticus R0052 (81.58%; 77.22%) after the gastric and intestinal phase when compared to B. longum (68.80%; 64.64%). At the genus level, a taxonomic assignment performed in the ascending colon in the SHIME® model showed that probiotics (7 and 14 days) significantly (p < 0.005) increased the abundance of Lactobacillus and Olsenella and significantly decreased Lachnospira and Escheria-Shigella. The probiotic treatment (7 and 14 days) decreased (p < 0.001) NH4+ production when compared to the control period. For SCFAs, we observed after probiotic treatment (14 days) an increase (p < 0.001) in acetic acid production and total SCFAs when compared to the control period. Probiotic treatment increased (p < 0.001) the secretion of anti-inflammatory (IL-6 and IL-10) and decreased (p < 0.001) pro-inflammatory cytokines (TNF-alpha) when compared to the control period. The gut-brain axis plays an important role in the gut microbiota, producing SCFAs and GABA, stimulating the production of anti-anxiety homeostasis. The signature of the microbiota in anxiety disorders provides a promising direction for the prevention of mental illness and opens a new perspective for using the psychobiotic as a main actor of therapeutic targets.
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Affiliation(s)
- Fellipe Lopes De Oliveira
- Graduate Program in Food, Nutrition, and Food Engineering, Campus Araraquara, São Paulo State University (UNESP), Araraquara 14800-060, SP, Brazil
| | - Mateus Kawata Salgaço
- Graduate Program in Food, Nutrition, and Food Engineering, Campus Araraquara, São Paulo State University (UNESP), Araraquara 14800-060, SP, Brazil
| | | | - Victoria Mesa
- Université Paris Cité, INSERM, UMR-S 1139 (3PHM), Faculty of Pharmacy, F-75006 Paris, France
- Food and Human Nutrition Research Group, School of Nutrition and Dietetics, Universidad de Antioquia (UdeA), Medellín 050010, Antioquia, Colombia
| | | | | | - Williams Santos Ramos
- APSEN Farmacêutica, Department of Medical Affairs, Santo Amaro 04753-001, SP, Brazil
| | - Katia Sivieri
- Graduate Program in Food, Nutrition, and Food Engineering, Campus Araraquara, São Paulo State University (UNESP), Araraquara 14800-060, SP, Brazil
- University of Araraquara-UNIARA, Araraquara 14801-320, SP, Brazil
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73
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Sanmarco LM, Rone JM, Polonio CM, Giovannoni F, Lahore GF, Ferrara K, Gutierrez-Vazquez C, Li N, Sokolovska A, Plasencia A, Akl CF, Nanda P, Heck ES, Li Z, Lee HG, Chao CC, Rejano-Gordillo CM, Fonseca-Castro PH, Illouz T, Linnerbauer M, Kenison JE, Barilla RM, Farrenkopf D, Piester G, Dailey L, Kuchroo VK, Hava D, Wheeler MA, Clish C, Nowarski R, Balsa E, Lora JM, Quintana FJ. Engineered probiotics limit CNS autoimmunity by stabilizing HIF-1α in dendritic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.532101. [PMID: 36993446 PMCID: PMC10055137 DOI: 10.1101/2023.03.17.532101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Dendritic cells (DCs) control the generation of self-reactive pathogenic T cells. Thus, DCs are considered attractive therapeutic targets for autoimmune diseases. Using single-cell and bulk transcriptional and metabolic analyses in combination with cell-specific gene perturbation studies we identified a negative feedback regulatory pathway that operates in DCs to limit immunopathology. Specifically, we found that lactate, produced by activated DCs and other immune cells, boosts NDUFA4L2 expression through a mechanism mediated by HIF-1α. NDUFA4L2 limits the production of mitochondrial reactive oxygen species that activate XBP1-driven transcriptional modules in DCs involved in the control of pathogenic autoimmune T cells. Moreover, we engineered a probiotic that produces lactate and suppresses T-cell autoimmunity in the central nervous system via the activation of HIF-1α/NDUFA4L2 signaling in DCs. In summary, we identified an immunometabolic pathway that regulates DC function, and developed a synthetic probiotic for its therapeutic activation.
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74
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Qiao JY, Li W, Zeng RY, Yu YJ, Chen QW, Liu XH, Cheng SX, Zhang XZ. An orally delivered bacteria-based coacervate antidote for alcohol detoxification. Biomaterials 2023; 296:122072. [PMID: 36878091 DOI: 10.1016/j.biomaterials.2023.122072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Alcohol intoxication causes serious diseases, whereas current treatments are mostly supportive and unable to convert alcohol into nontoxic products in the digestive tract. To address this issue, an oral intestinal-coating coacervate antidote containing acetic acid bacteria (AAB) and sodium alginate (SA) mixture was constructed. After oral administration, SA reduces absorption of ethanol and promotes the proliferation of AAB, and AAB converts ethanol to acetic acid or carbon dioxide and water by two sequential catalytic reactions in the presence of membrane-bound alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH). In vivo study shows that the bacteria-based coacervate antidote can significantly reduce the blood alcohol concentration (BAC) and effectively alleviates alcoholic liver injury in mice. Given the convenience and effectiveness of oral administration, AAB/SA can be used as a promising candidate antidote for relieving alcohol-induced acute liver injury.
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Affiliation(s)
- Ji-Yan Qiao
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Wen Li
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Run-Yao Zeng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Yun-Jian Yu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Qi-Wen Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Xin-Hua Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Si-Xue Cheng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China.
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75
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He L, Tang W, Huang L, Zhou W, Huang S, Zou L, Yuan L, Men D, Chen S, Hu Y. Rational design of a genome-based insulated system in Escherichia coli facilitates heterologous uricase expression for hyperuricemia treatment. Bioeng Transl Med 2023; 8:e10449. [PMID: 36925686 PMCID: PMC10013758 DOI: 10.1002/btm2.10449] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/18/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Hyperuricemia is a prevalent disease worldwide that is characterized by elevated urate levels in the blood owing to purine metabolic disorders, which can result in gout and comorbidities. To facilitate the treatment of hyperuricemia through the uricolysis, we engineered a probiotic Escherichia coli Nissle 1917 (EcN) named EcN C6 by inserting an FtsP-uricase cassette into an "insulated site" located between the uspG and ahpF genes. Expression of FtsP-uricase in this insulated region did not influence the probiotic properties or global gene transcription of EcN but strongly increased the enzymatic activity for urate degeneration, suggesting that the genome-based insulated system is an ideal strategy for EcN modification. Oral administration of EcN C6 successfully alleviated hyperuricemia, related symptoms and gut microbiota in a purine-rich food-induced hyperuricemia rat model and a uox-knockout mouse model. Together, our study provides an insulated site for heterologous gene expression in EcN strain and a recombinant EcN C6 strain as a safe and effective therapeutic candidate for hyperuricemia treatment.
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Affiliation(s)
- Lina He
- CAS Key Laboratory of Special Pathogens and BiosafetyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Wei Tang
- CAS Key Laboratory of Special Pathogens and BiosafetyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
| | - Ling Huang
- CAS Key Laboratory of Special Pathogens and BiosafetyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Wei Zhou
- CAS Key Laboratory of Special Pathogens and BiosafetyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shaojia Huang
- CAS Key Laboratory of Special Pathogens and BiosafetyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Linxuan Zou
- CAS Key Laboratory of Special Pathogens and BiosafetyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lisha Yuan
- CAS Key Laboratory of Special Pathogens and BiosafetyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dong Men
- State Key Laboratory of VirologyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
| | - Shiyun Chen
- CAS Key Laboratory of Special Pathogens and BiosafetyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
| | - Yangbo Hu
- State Key Laboratory of VirologyWuhan Institute of Virology, Chinese Academy of SciencesWuhanChina
- Hubei Jiangxia LaboratoryWuhanChina
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76
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Hedin KA, Kruse V, Vazquez-Uribe R, Sommer MOA. Biocontainment strategies for in vivo applications of Saccharomyces boulardii. Front Bioeng Biotechnol 2023; 11:1136095. [PMID: 36890914 PMCID: PMC9986445 DOI: 10.3389/fbioe.2023.1136095] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
The human gastrointestinal tract is a complex and dynamic environment, playing a crucial role in human health. Microorganisms engineered to express a therapeutic activity have emerged as a novel modality to manage numerous diseases. Such advanced microbiome therapeutics (AMTs) must be contained within the treated individual. Hence safe and robust biocontainment strategies are required to prevent the proliferation of microbes outside the treated individual. Here we present the first biocontainment strategy for a probiotic yeast, demonstrating a multi-layered strategy combining an auxotrophic and environmental-sensitive strategy. We knocked out the genes THI6 and BTS1, causing thiamine auxotrophy and increased sensitivity to cold, respectively. The biocontained Saccharomyces boulardii showed restricted growth in the absence of thiamine above 1 ng/ml and exhibited a severe growth defect at temperatures below 20°C. The biocontained strain was well tolerated and viable in mice and demonstrated equal efficiency in peptide production as the ancestral non-biocontained strain. In combination, the data support that thi6∆ and bts1∆ enable biocontainment of S. boulardii, which could be a relevant chassis for future yeast-based AMTs.
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Affiliation(s)
| | | | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
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77
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Cao Z, Liu R, Wang C, Lin S, Wang L, Pang Y. Fluorescence-Activating and Absorption-Shifting Nanoprobes for Anaerobic Tracking of Gut Microbiota Derived Vesicles. ACS NANO 2023; 17:2279-2293. [PMID: 36735721 DOI: 10.1021/acsnano.2c08780] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Outer membrane vesicles (OMVs) are crucial for bacterial intercellular communication and the crosstalk between the gut microbiota and its host. Methods capable of visualizing gut microbiota derived OMVs would be of great significance but have been rarely reported. Here, nanoprobes carrying a fluorescence-activating and absorption-shifting tag are prepared by combining genetic engineering and antibiotic-boosted vesicle formation and release. Benefiting from their natural structure and molecular oxygen-independent emission, the resulting nanovesicles can be applied as endogenous fluorescence probes to anaerobically track gut microbiota associated OMVs. These nanoprobes show flexibility in on-demand fluorescence turn-on/off and reversibly switchable emission bands for intelligent and dual-color imaging. With these special characteristics, the behaviors of microbiota OMVs to not only inhibit specific pathogenic strains through membrane fusion but also repair the intestinal barrier via entering intestinal epithelia and promoting the expressions of tight junctions are tracked and identified in the gut. Based on these discoveries, OMVs are disclosed to be able to remit inflammation in a murine model of colitis following transplantation to the intestine by oral delivery. This work provides an approach to visualize the dynamics of the gut microbiota and disclose potential targets for disease intervention.
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Affiliation(s)
- Zhenping Cao
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Rui Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chuhan Wang
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
| | - Sisi Lin
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Wang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yan Pang
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
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78
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Kalantari A, James MJ, Renaud LA, Perreault M, Monahan CE, McDonald MN, Hava DL, Isabella VM. Robust performance of a live bacterial therapeutic chassis lacking the colibactin gene cluster. PLoS One 2023; 18:e0280499. [PMID: 36730255 PMCID: PMC9894410 DOI: 10.1371/journal.pone.0280499] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/29/2022] [Indexed: 02/03/2023] Open
Abstract
E. coli Nissle (EcN) is a non-pathogenic probiotic bacterium of the Enterobacteriaceae family that has been used for over a century to promote general gut health. Despite the history of safe usage of EcN, concerns have been raised regarding the presence of the pks gene cluster, encoding the genotoxin colibactin, due to its association with colorectal cancer. Here, we sought to determine the effect of pks island removal on the in vitro and in vivo robustness and activity of EcN and EcN-derived strains. A deletion of the pks island (Δpks) was constructed in wild type and engineered strains of EcN using lambda red recombineering. Mass spectrometric measurement of N-myristoyl-D-asparagine, released during colibactin maturation, confirmed that the pks deletion abrogated colibactin production. Growth curves were comparable between Δpks strains and their isogenic parents, and wild type EcN displayed no competitive advantage to the Δpks strain in mixed culture. Deletion of pks also had no effect on the activity of strains engineered to degrade phenylalanine (SYNB1618 and SYNB1934) or oxalate (SYNB8802). Furthermore, 1:1 mixed dosing of wild type and Δpks EcN in preclinical mouse and nonhuman primate models demonstrated no competitive disadvantage for the Δpks strain with regards to transit time or colonization. Importantly, there was no significant difference on in vivo strain performance between the clinical-stage strain SYNB1934 and its isogenic Δpks variant with regards to recovery of the quantitative strain-specific biomarkers d5- trans-cinnamic acid, and d5-hippuric acid. Taken together, these data support that the pks island is dispensable for Synthetic Biotic fitness and activity in vivo and that its removal from engineered strains of EcN will not have a deleterious effect on strain efficacy.
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Affiliation(s)
- Aida Kalantari
- Synlogic, Inc., Cambridge, Massachusetts, United States of America
- * E-mail: (VMI); (AK)
| | - Michael J. James
- Synlogic, Inc., Cambridge, Massachusetts, United States of America
| | - Lauren A. Renaud
- Synlogic, Inc., Cambridge, Massachusetts, United States of America
| | - Mylene Perreault
- Synlogic, Inc., Cambridge, Massachusetts, United States of America
| | | | - Mary N. McDonald
- Synlogic, Inc., Cambridge, Massachusetts, United States of America
| | - David L. Hava
- Synlogic, Inc., Cambridge, Massachusetts, United States of America
| | - Vincent M. Isabella
- Synlogic, Inc., Cambridge, Massachusetts, United States of America
- * E-mail: (VMI); (AK)
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79
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Chen H, Lei P, Ji H, Yang Q, Peng B, Ma J, Fang Y, Qu L, Li H, Wu W, Jin L, Sun D. Advances in Escherichia coli Nissle 1917 as a customizable drug delivery system for disease treatment and diagnosis strategies. Mater Today Bio 2023; 18:100543. [PMID: 36647536 PMCID: PMC9840185 DOI: 10.1016/j.mtbio.2023.100543] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/07/2023] Open
Abstract
With the in-depth and comprehensive study of bacteria and their related ecosystems in the human body, bacterial-based drug delivery system has become an emerging biomimetic platform that can retain the innate biological functions. Benefiting from its good biocompatibility and ideal targeting ability as a biological carrier, Escherichia coli Nissle 1917 (ECN) has been focused on the treatment strategies of inflammatory bowel disease and tumor. The advantage of a bacterial carrier is that it can express exogenous protein while also acting as a natural capsule by releasing drug slowly as a result of its own colonization impact. In order to survive in harsh environments such as the digestive tract and tumor microenvironment, ECN can be modified or genetically engineered to enhance its function and host adaptability. The adoption of ECN carries or expresses drugs which are essential for accurate diagnosis and treatment. This review briefly describes the properties of ECN, the relationship between ECN and inflammation and tumor, and the strategy of using surface modification and genetic engineering to modify ECN as a delivery carrier for disease treatment.
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Affiliation(s)
- Haojie Chen
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China
| | - Pengyu Lei
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China
| | - Hao Ji
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China
| | - Qinsi Yang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325000, China
| | - Bo Peng
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325000, China
| | - Jiahui Ma
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China
| | - Yimeng Fang
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China
| | - Linkai Qu
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Hua Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, China
| | - Wei Wu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing, 400044, China
| | - Libo Jin
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China
- Wenzhou City and WenZhouOuTai Medical Laboratory Co.,Ltd Joint Doctoral Innovation Station, Wenzhou Association for Science and Technology, Wenzhou, 325000, China
| | - Da Sun
- Institute of Life Sciences & Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, China
- Wenzhou City and Kunlong Technology Co., Ltd., Joint Doctoral Innovation Station, Wenzhou Association for Science and Technology, Wenzhou, 325000, China
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80
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Zhang Y, Rodrigues LR, Cao Z, Li J. Editorial: Microorganisms and their derivatives for cancer therapy. Front Bioeng Biotechnol 2023; 11:1137341. [PMID: 36714005 PMCID: PMC9880520 DOI: 10.3389/fbioe.2023.1137341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Affiliation(s)
- Yunlei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China,Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China,*Correspondence: Yunlei Zhang,
| | - Lígia R. Rodrigues
- CEB—Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Zhenping Cao
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Juanjuan Li
- School of Life Sciences, Hainan University, Haikou, China
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81
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Aggarwal N, Kitano S, Puah GRY, Kittelmann S, Hwang IY, Chang MW. Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies. Chem Rev 2023; 123:31-72. [PMID: 36317983 PMCID: PMC9837825 DOI: 10.1021/acs.chemrev.2c00431] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 01/12/2023]
Abstract
The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.
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Affiliation(s)
- Nikhil Aggarwal
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Shohei Kitano
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ginette Ru Ying Puah
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - Sandra Kittelmann
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - In Young Hwang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Singapore
Institute of Technology, Singapore 138683, Singapore
| | - Matthew Wook Chang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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82
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Expression of phenylalanine ammonia lyase as an intracellularly free and extracellularly cell surface-immobilized enzyme on a gut microbe as a live biotherapeutic for phenylketonuria. SCIENCE CHINA. LIFE SCIENCES 2023; 66:127-136. [PMID: 35907113 PMCID: PMC9362719 DOI: 10.1007/s11427-021-2137-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023]
Abstract
Phenylketonuria (PKU), a disease resulting in the disability to degrade phenylalanine (Phe) is an inborn error with a 1 in 10,000 morbidity rate on average around the world which leads to neurotoxicity. As an potential alternative to a protein-restricted diet, oral intake of engineered probiotics degrading Phe inside the body is a promising treatment, currently at clinical stage II (Isabella, et al., 2018). However, limited transmembrane transport of Phe is a bottleneck to further improvement of the probiotic's activity. Here, we achieved simultaneous degradation of Phe both intracellularly and extracellularly by expressing genes encoding the Phe-metabolizing enzyme phenylalanine ammonia lyase (PAL) as an intracellularly free and a cell surface-immobilized enzyme in Escherichia coli Nissle 1917 (EcN) which overcomes the transportation problem. The metabolic engineering strategy was also combined with strengthening of Phe transportation, transportation of PAL-catalyzed trans-cinnamic acid and fixation of released ammonia. Administration of our final synthetic strain TYS8500 with PAL both displayed on the cell surface and expressed inside the cell to the PahF263S PKU mouse model reduced blood Phe concentration by 44.4% compared to the control EcN, independent of dietary protein intake. TYS8500 shows great potential in future applications for PKU therapy.
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83
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Tseng YC, Xue C, Ng IS. Symbiosis culture of probiotic Escherichia coli Nissle 1917 and Lactobacillus rhamnosus GG using lactate utilization protein YkgG. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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84
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van ‘t Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA. High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinformatics 2022; 23:566. [PMID: 36585633 PMCID: PMC9801561 DOI: 10.1186/s12859-022-05108-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Escherichia coli Nissle 1917 (EcN) is a probiotic bacterium used to treat various gastrointestinal diseases. EcN is increasingly being used as a chassis for the engineering of advanced microbiome therapeutics. To aid in future engineering efforts, our aim was to construct an updated metabolic model of EcN with extended secondary metabolite representation. RESULTS An updated high-quality genome-scale metabolic model of EcN, iHM1533, was developed based on comparison with 55 E. coli/Shigella reference GEMs and manual curation, including expanded secondary metabolite pathways (enterobactin, salmochelins, aerobactin, yersiniabactin, and colibactin). The model was validated and improved using phenotype microarray data, resulting in an 82.3% accuracy in predicting growth phenotypes on various nutrition sources. Flux variability analysis with previously published 13C fluxomics data validated prediction of the internal central carbon fluxes. A standardised test suite called Memote assessed the quality of iHM1533 to have an overall score of 89%. The model was applied by using constraint-based flux analysis to predict targets for optimisation of secondary metabolite production. Modelling predicted design targets from across amino acid metabolism, carbon metabolism, and other subsystems that are common or unique for influencing the production of various secondary metabolites. CONCLUSION iHM1533 represents a well-annotated metabolic model of EcN with extended secondary metabolite representation. Phenotype characterisation and the iHM1533 model provide a better understanding of the metabolic capabilities of EcN and will help future metabolic engineering efforts.
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Affiliation(s)
- Max van ‘t Hof
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Omkar S. Mohite
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jonathan M. Monk
- grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Tilmann Weber
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Bernhard O. Palsson
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark ,grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Morten O. A. Sommer
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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85
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Wang S, Cui J, Jiang S, Zheng C, Zhao J, Zhang H, Zhai Q. Early life gut microbiota: Consequences for health and opportunities for prevention. Crit Rev Food Sci Nutr 2022; 64:5793-5817. [PMID: 36537331 DOI: 10.1080/10408398.2022.2158451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The gut microbiota influences many aspects of the host, including immune system maturation, nutrient absorption and metabolism, and protection from pathogens. Increasing evidences from cohort and animal studies indicate that changes in the gut microbiota early in life increases the risk of developing specific diseases early and later in life. Therefore, it is becoming increasingly important to identify specific disease prevention or therapeutic solutions targeting the gut microbiota, especially during infancy, which is the window of the human gut microbiota establishment process. In this review, we provide an overview of current knowledge concerning the relationship between disturbances in the gut microbiota early in life and health consequences later in life (e.g., necrotizing enterocolitis, celiac disease, asthma, allergies, autism spectrum disorders, overweight/obesity, diabetes and growth retardation), with a focus on changes in the gut microbiota prior to disease onset. In addition, we summarize and discuss potential microbiota-based interventions early in life (e.g., diet adjustments, probiotics, prebiotics, fecal microbiota transplantation, environmental changes) to promote health or prevent the development of specific diseases. This knowledge should aid the understanding of early life microbiology and inform the development of prediction and prevention measures for short- and long-term health disorders based on the gut microbiota.
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Affiliation(s)
- Shumin Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jingjing Cui
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Shilong Jiang
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd, Beijing, China
- PKUHSC-China Feihe Joint Research Institute of Nutrition and Healthy Lifespan Development, Beijing, China
| | - Chengdong Zheng
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd, Beijing, China
- PKUHSC-China Feihe Joint Research Institute of Nutrition and Healthy Lifespan Development, Beijing, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Heng Zhang
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
- Department of Child Health Care, Wuxi Maternity and Child Health Care Hospital, Wuxi, Jiangsu, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
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86
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Luo H, Chen Y, Kuang X, Wang X, Yang F, Cao Z, Wang L, Lin S, Wu F, Liu J. Chemical reaction-mediated covalent localization of bacteria. Nat Commun 2022; 13:7808. [PMID: 36528693 PMCID: PMC9759558 DOI: 10.1038/s41467-022-35579-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Methods capable of manipulating bacterial colonization are of great significance for modulating host-microbiota relationships. Here, we describe a strategy of in-situ chemical reaction-mediated covalent localization of bacteria. Through a simple one-step imidoester reaction, primary amino groups on bacterial surface can be converted to free thiols under cytocompatible conditions. Surface thiolation is applicable to modify diverse strains and the number of introduced thiols per bacterium can be easily tuned by varying feed ratios. These chemically reactive bacteria are able to spontaneously bond with mucous layer by catalyst-free thiol-disulfide exchange between mucin-associated disulfides and newly converted thiols on bacterial surface and show thiolation level-dependent attachment. Bacteria optimized with 9.3 × 107 thiols per cell achieve 170-fold higher attachment in mucin-enriched jejunum, a challenging location for gut microbiota to colonize. As a proof-of-concept application for microbiota transplantation, covalent bonding-assisted localization of an oral probiotic in the jejunum generates an improved remission of jejunal mucositis. Our findings demonstrate that transforming bacteria with a reactive surface provides an approach to chemically control bacterial localization, which is highly desirable for developing next-generation bacterial living bioagents.
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Affiliation(s)
- Huilong Luo
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Yanmei Chen
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Xiao Kuang
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Xinyue Wang
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Fengmin Yang
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Zhenping Cao
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Lu Wang
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Sisi Lin
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Feng Wu
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
| | - Jinyao Liu
- grid.16821.3c0000 0004 0368 8293Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127 Shanghai, China
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87
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Fecal Microbiota Transplantation and Other Gut Microbiota Manipulation Strategies. Microorganisms 2022; 10:microorganisms10122424. [PMID: 36557677 PMCID: PMC9781458 DOI: 10.3390/microorganisms10122424] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota is composed of bacteria, archaea, phages, and protozoa. It is now well known that their mutual interactions and metabolism influence host organism pathophysiology. Over the years, there has been growing interest in the composition of the gut microbiota and intervention strategies in order to modulate it. Characterizing the gut microbial populations represents the first step to clarifying the impact on the health/illness equilibrium, and then developing potential tools suited for each clinical disorder. In this review, we discuss the current gut microbiota manipulation strategies available and their clinical applications in personalized medicine. Among them, FMT represents the most widely explored therapeutic tools as recent guidelines and standardization protocols, not only for intestinal disorders. On the other hand, the use of prebiotics and probiotics has evidence of encouraging findings on their safety, patient compliance, and inter-individual effectiveness. In recent years, avant-garde approaches have emerged, including engineered bacterial strains, phage therapy, and genome editing (CRISPR-Cas9), which require further investigation through clinical trials.
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88
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Huang Y, Lin X, Yu S, Chen R, Chen W. Intestinal Engineered Probiotics as Living Therapeutics: Chassis Selection, Colonization Enhancement, Gene Circuit Design, and Biocontainment. ACS Synth Biol 2022; 11:3134-3153. [PMID: 36094344 DOI: 10.1021/acssynbio.2c00314] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Intestinal probiotics are often used for the in situ treatment of diseases, such as metabolic disorders, tumors, and chronic inflammatory infections. Recently, there has been an increased emphasis on intelligent, customized treatments with a focus on long-term efficacy; however, traditional probiotic therapy has not kept up with this trend. The use of synthetic biology to construct gut-engineered probiotics as live therapeutics is a promising avenue in the treatment of specific diseases, such as phenylketonuria and inflammatory bowel disease. These studies generally involve a series of fundamental design issues: choosing an engineered chassis, improving the colonization ability of engineered probiotics, designing functional gene circuits, and ensuring the safety of engineered probiotics. In this review, we summarize the relevant past research, the progress of current research, and discuss the key issues that restrict the widespread application of intestinal engineered probiotic living therapeutics.
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Affiliation(s)
- Yan Huang
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiaojun Lin
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Siyang Yu
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Ruiyue Chen
- Team SZU-China at iGEM 2021, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Weizhao Chen
- Team SZU-China at iGEM 2021, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.,Shenzhen Key Laboratory for Microbial Gene Engineering, Shenzhen University, Shenzhen 518060, China
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89
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Li B, Li M, Luo Y, Li R, Li W, Liu Z. Engineered 5-HT producing gut probiotic improves gastrointestinal motility and behavior disorder. Front Cell Infect Microbiol 2022; 12:1013952. [PMID: 36339343 PMCID: PMC9630942 DOI: 10.3389/fcimb.2022.1013952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 12/03/2022] Open
Abstract
Slow transit constipation is an intractable constipation with unknown aetiology and uncertain pathogenesis. The gut microbiota maintains a symbiotic relationship with the host and has an impact on host metabolism. Previous studies have reported that some gut microbes have the ability to produce 5-hydroxytryptamine (5-HT), an important neurotransmitter. However, there are scarce data exploiting the effects of gut microbiota-derived 5-HT in constipation-related disease. We genetically engineered the probiotic Escherichia coli Nissle 1917 (EcN-5-HT) for synthesizing 5-HT in situ. The ability of EcN-5-HT to secrete 5-HT in vitro and in vivo was confirmed. Then, we examined the effects of EcN-5-HT on intestinal motility in a loperamide-induced constipation mouse model. After two weeks of EcN-5-HT oral gavage, the constipation-related symptoms were relieved and gastrointestinal motility were enhanced. Meanwhile, administration of EcN-5-HT alleviated the constipation related depressive-like behaviors. We also observed improved microbiota composition during EcN-5-HT treatment. This work suggests that gut microbiota-derived 5-HT might promise a potential therapeutic strategy for constipation and related behavioral disorders.
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Affiliation(s)
- Bei Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, China
| | - Min Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, China
| | - Yanan Luo
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, China
| | - Rong Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, China
| | - Wei Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, China
- *Correspondence: Wei Li, ; Zhi Liu,
| | - Zhi Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Molecular Biophysics, Ministry of Education, Wuhan, China
- *Correspondence: Wei Li, ; Zhi Liu,
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90
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Qi W, Ge Y, Wang X, Li Z, Li X, Wang N, He H, Luo X, Ma W, Chen L, Liu Y, Zhang T. Ameliorative Effect of Chitosan Oligosaccharides on Hepatic Encephalopathy by Reshaping Gut Microbiota and Gut-Liver Axis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:13186-13199. [PMID: 36194761 DOI: 10.1021/acs.jafc.2c01330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This study investigated the influence of chitosan oligosaccharides (COSs) on a thioacetamide-induced hepatic encephalopathy (HE) Wistar rat model. COS treatment statistically reduced the false neurotransmitters and blood ammonia in HE rats, along with the suppression of oxidative stress and inflammation. The disbalanced gut microbiota was detected in HE rats by 16S rDNA sequencing, but the abundance alterations of some intestinal bacteria at either the phylum or genus level were at least partly restored by COS treatment. According to metabolomics analysis of rat feces, six metabolism pathways with the greatest response to HE were screened, several of which were remarkably reversed by COS. The altered metabolites might serve as a bridge for the alleviated HE rats treated with COS and the enhanced intestinal bacterial structure. This study provides novel guidance to develop novel food or dietary supplements to improve HE diseases due to the potential beneficial effect of COS on gut-liver axis.
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Affiliation(s)
- Wei Qi
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Yanyan Ge
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Xinyue Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Zihan Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Xiaoxue Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Nan Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Hongpeng He
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Xuegang Luo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Wenjian Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Liehuan Chen
- New Youlan Healthy Technology Co., Ltd., Guangzhou 510530, Guangdong, P. R. China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Tongcun Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
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91
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Liu Y, Feng J, Pan H, Zhang X, Zhang Y. Genetically engineered bacterium: Principles, practices, and prospects. Front Microbiol 2022; 13:997587. [PMID: 36312915 PMCID: PMC9606703 DOI: 10.3389/fmicb.2022.997587] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
Advances in synthetic biology and the clinical application of bacteriotherapy enable the use of genetically engineered bacteria (GEB) to combat various diseases. GEB act as a small 'machine factory' in the intestine or other tissues to continuously produce heterologous proteins or molecular compounds and, thus, diagnose or cure disease or work as an adjuvant reagent for disease treatment by regulating the immune system. Although the achievements of GEBs in the treatment or adjuvant therapy of diseases are promising, the practical implementation of this new therapeutic modality remains a grand challenge, especially at the initial stage. In this review, we introduce the development of GEBs and their advantages in disease management, summarize the latest research advances in microbial genetic techniques, and discuss their administration routes, performance indicators and the limitations of GEBs used as platforms for disease management. We also present several examples of GEB applications in the treatment of cancers and metabolic diseases and further highlight their great potential for clinical application in the near future.
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Affiliation(s)
- Yiting Liu
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Jing Feng
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Hangcheng Pan
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Xiuwei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Yunlei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
- Central Laboratory, Translational Medicine Research Center, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
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92
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Kobayashi T, Iwaki M, Nakajima A, Nogami A, Yoneda M. Current Research on the Pathogenesis of NAFLD/NASH and the Gut-Liver Axis: Gut Microbiota, Dysbiosis, and Leaky-Gut Syndrome. Int J Mol Sci 2022; 23:ijms231911689. [PMID: 36232990 PMCID: PMC9570241 DOI: 10.3390/ijms231911689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022] Open
Abstract
Global lifestyle changes have led to an increased incidence of non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), requiring further in-depth research to understand the mechanisms and develop new therapeutic strategies. In particular, high-fat and high-fructose diets have been shown to increase intestinal permeability, which can expose the liver to endotoxins. Indeed, accumulating evidence points to a link between these liver diseases and the intestinal axis, including dysbiosis of the gut microbiome and leaky-gut syndrome. Here, we review the mechanisms contributing to these links between the liver and small intestine in the pathogenesis of NAFLD/NASH, focusing on the roles of intestinal microbiota and their metabolites to influence enzymes essential for proper liver metabolism and function. Advances in next-generation sequencing technology have facilitated analyses of the metagenome, providing new insights into the roles of the intestinal microbiota and their functions in physiological and pathological mechanisms. This review summarizes recent research linking the gut microbiome to liver diseases, offering new research directions to elucidate the detailed mechanisms and novel targets for treatment and prevention.
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93
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Song WF, Yao WQ, Chen QW, Zheng D, Han ZY, Zhang XZ. In Situ Bioorthogonal Conjugation of Delivered Bacteria with Gut Inhabitants for Enhancing Probiotics Colonization. ACS CENTRAL SCIENCE 2022; 8:1306-1317. [PMID: 36188344 PMCID: PMC9523781 DOI: 10.1021/acscentsci.2c00533] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Indexed: 06/16/2023]
Abstract
Clinical treatment efficacy of oral bacterial therapy has been largely limited by insufficient gut retention of probiotics. Here, we developed a bioorthogonal-mediated bacterial delivery strategy for enhancing probiotics colonization by modulating bacterial adhesion between probiotics and gut inhabitants. Metabolic amino acid engineering was applied to metabolically incorporate azido-decorated d-alanine into peptidoglycans of gut inhabitants, which could enable in situ bioorthogonal conjugation with dibenzocyclooctyne (DBCO)-modified probiotics. Both in vitro and in vivo studies demonstrated that the occurrence of the bioorthogonal reaction between azido- and DBCO-modified bacteria could result in obvious bacterial adhesion even in a complex physiological environment. DBCO-modified Clostridium butyricum (C. butyricum) also showed more efficient reservation in the gut and led to obvious disease relief in dextran sodium sulfate-induced colitis mice. This strategy highlights metabolically modified gut inhabitants as artificial reaction sites to bind with DBCO-decorated probiotics via bioorthogonal reactions, which shows great potential for enhancing bacterial colonization.
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94
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Rutter JW, Dekker L, Owen KA, Barnes CP. Microbiome engineering: engineered live biotherapeutic products for treating human disease. Front Bioeng Biotechnol 2022; 10:1000873. [PMID: 36185459 PMCID: PMC9523163 DOI: 10.3389/fbioe.2022.1000873] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
The human microbiota is implicated in many disease states, including neurological disorders, cancer, and inflammatory diseases. This potentially huge impact on human health has prompted the development of microbiome engineering methods, which attempt to adapt the composition and function of the human host-microbiota system for a therapeutic purpose. One promising method is the use of engineered microorganisms that have been modified to perform a therapeutic function. The majority of these products have only been demonstrated in laboratory models; however, in recent years more concepts have reached the translational stage. This has led to an increase in the number of clinical trials, which are designed to assess the safety and efficacy of these treatments in humans. Within this review, we highlight the progress of some of these microbiome engineering clinical studies, with a focus on engineered live biotherapeutic products.
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Affiliation(s)
- Jack W. Rutter
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
- *Correspondence: Jack W. Rutter,
| | - Linda Dekker
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
| | - Kimberley A. Owen
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
| | - Chris P. Barnes
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
- Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
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95
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Griffin ME, Hang HC. Microbial mechanisms to improve immune checkpoint blockade responsiveness. Neoplasia 2022; 31:100818. [PMID: 35816968 PMCID: PMC9284443 DOI: 10.1016/j.neo.2022.100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/02/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022]
Abstract
The human microbiota acts as a diverse source of molecular cues that influence the development and homeostasis of the immune system. Beyond endogenous roles in the human holobiont, host-microbial interactions also alter outcomes for immune-related diseases and treatment regimens. Over the past decade, sequencing analyses of cancer patients have revealed correlations between microbiota composition and the efficacy of cancer immunotherapies such as checkpoint inhibitors. However, very little is known about the exact mechanisms that link specific microbiota with patient responses, limiting our ability to exploit these microbial agents for improved oncology care. Here, we summarize current progress towards a molecular understanding of host-microbial interactions in the context of checkpoint inhibitor immunotherapies. By highlighting the successes of a limited number of studies focused on identifying specific, causal molecules, we underscore how the exploration of specific microbial features such as proteins, enzymes, and metabolites may translate into precise and actionable therapies for personalized patient care in the clinic.
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Affiliation(s)
- Matthew E Griffin
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037.
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037; Department of Chemistry, Scripps Research, La Jolla, CA 92037.
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96
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Gelfat I, Aqeel Y, Tremblay JM, Jaskiewicz JJ, Shrestha A, Lee JN, Hu S, Qian X, Magoun L, Sheoran A, Bedenice D, Giem C, Manjula-Basavanna A, Pulsifer AR, Tu HX, Li X, Minus ML, Osburne MS, Tzipori S, Shoemaker CB, Leong JM, Joshi NS. Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917. PLoS Pathog 2022; 18:e1010713. [PMID: 36107831 PMCID: PMC9477280 DOI: 10.1371/journal.ppat.1010713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
Enteric microbial pathogens, including Escherichia coli, Shigella and Cryptosporidium species, take a particularly heavy toll in low-income countries and are highly associated with infant mortality. We describe here a means to display anti-infective agents on the surface of a probiotic bacterium. Because of their stability and versatility, VHHs, the variable domains of camelid heavy-chain-only antibodies, have potential as components of novel agents to treat or prevent enteric infectious disease. We isolated and characterized VHHs targeting several enteropathogenic E. coli (EPEC) virulence factors: flagellin (Fla), which is required for bacterial motility and promotes colonization; both intimin and the translocated intimin receptor (Tir), which together play key roles in attachment to enterocytes; and E. coli secreted protein A (EspA), an essential component of the type III secretion system (T3SS) that is required for virulence. Several VHHs that recognize Fla, intimin, or Tir blocked function in vitro. The probiotic strain E. coli Nissle 1917 (EcN) produces on the bacterial surface curli fibers, which are the major proteinaceous component of E. coli biofilms. A subset of Fla-, intimin-, or Tir-binding VHHs, as well as VHHs that recognize either a T3SS of another important bacterial pathogen (Shigella flexneri), a soluble bacterial toxin (Shiga toxin or Clostridioides difficile toxin TcdA), or a major surface antigen of an important eukaryotic pathogen (Cryptosporidium parvum) were fused to CsgA, the major curli fiber subunit. Scanning electron micrographs indicated CsgA-VHH fusions were assembled into curli fibers on the EcN surface, and Congo Red binding indicated that these recombinant curli fibers were produced at high levels. Ectopic production of these VHHs conferred on EcN the cognate binding activity and, in the case of anti-Shiga toxin, was neutralizing. Taken together, these results demonstrate the potential of the curli-based pathogen sequestration strategy described herein and contribute to the development of novel VHH-based gut therapeutics.
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Affiliation(s)
- Ilia Gelfat
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Allston, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yousuf Aqeel
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Jacqueline M. Tremblay
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Justyna J. Jaskiewicz
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Anishma Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - James N. Lee
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shenglan Hu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Xi Qian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Loranne Magoun
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Abhineet Sheoran
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Daniela Bedenice
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Colter Giem
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Avinash Manjula-Basavanna
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Amanda R. Pulsifer
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hann X. Tu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Xiaoli Li
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Marilyn L. Minus
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Marcia S. Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Charles B. Shoemaker
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - John M. Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Medford, Massachusetts, United States of America
| | - Neel S. Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
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97
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Lynch JP, Goers L, Lesser CF. Emerging strategies for engineering Escherichia coli Nissle 1917-based therapeutics. Trends Pharmacol Sci 2022; 43:772-786. [PMID: 35232591 PMCID: PMC9378478 DOI: 10.1016/j.tips.2022.02.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/11/2022]
Abstract
Engineered microbes are rapidly being developed for the delivery of therapeutic modalities to sites of disease. Escherichia coli Nissle 1917 (EcN), a genetically tractable probiotic with a well-established human safety record, is emerging as a favored chassis. Here, we summarize the latest progress in rationally engineered variants of EcN for the treatment of infectious diseases, metabolic disorders, and inflammatory bowel diseases (IBDs) when administered orally, as well as cancers when injected directly into tumors or the systemic circulation. We also discuss emerging studies that raise potential safety concerns regarding these EcN-based strains as therapeutics due to their secretion of a genotoxic colibactin that can promote the formation of DNA double-stranded breaks in mammalian DNA.
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Affiliation(s)
- Jason P Lynch
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Lisa Goers
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Cammie F Lesser
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA; Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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98
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Effect of Probiotics on Host-Microbiota in Bacterial Infections. Pathogens 2022; 11:pathogens11090986. [PMID: 36145418 PMCID: PMC9500725 DOI: 10.3390/pathogens11090986] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
Diseases caused by bacteria cause millions of deaths every year. In addition, the problem of resistance to antibiotics is so serious that it threatens the achievements of modern medicine. This is a very important global problem as some bacteria can also develop persistence. Indeed, the persistence of pathogenic bacteria has evolved as a potent survival strategy to overcome host organisms’ defense mechanisms. Additionally, chronic or persistent infections may be caused by persisters which could facilitate antibiotic resistance. Probiotics are considered good bacteria. It has been described that the modulation of gut microbiota by probiotics could have a great potential to counteract the deleterious impact and/or regulate gut microbiota after bacterial infection. Probiotics might provide health benefits through the inhibition of pathogen growth or the replacement of pathogenic bacteria. Bearing in mind that current strategies to avoid bacterial persistence and prevent antibiotic resistance are not effective, other strategies need to be assessed. We have carried out a comprehensive review, which included the reported literature between 2016 and 2021, highlighting the clinical trials that reported the probiotics’ potential to regulate gut microbiota after bacterial infection and focusing in particular on the context of antibiotic resistance and persister cells.
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99
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Dicks LMT, Vermeulen W. Do Bacteria Provide an Alternative to Cancer Treatment and What Role Does Lactic Acid Bacteria Play? Microorganisms 2022; 10:microorganisms10091733. [PMID: 36144335 PMCID: PMC9501580 DOI: 10.3390/microorganisms10091733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/17/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is one of the leading causes of mortality and morbidity worldwide. According to 2022 statistics from the World Health Organization (WHO), close to 10 million deaths have been reported in 2020 and it is estimated that the number of cancer cases world-wide could increase to 21.6 million by 2030. Breast, lung, thyroid, pancreatic, liver, prostate, bladder, kidney, pelvis, colon, and rectum cancers are the most prevalent. Each year, approximately 400,000 children develop cancer. Treatment between countries vary, but usually includes either surgery, radiotherapy, or chemotherapy. Modern treatments such as hormone-, immuno- and antibody-based therapies are becoming increasingly popular. Several recent reports have been published on toxins, antibiotics, bacteriocins, non-ribosomal peptides, polyketides, phenylpropanoids, phenylflavonoids, purine nucleosides, short chain fatty acids (SCFAs) and enzymes with anticancer properties. Most of these molecules target cancer cells in a selective manner, either directly or indirectly through specific pathways. This review discusses the role of bacteria, including lactic acid bacteria, and their metabolites in the treatment of cancer.
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100
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Li YG, Yu ZJ, Li A, Ren ZG. Gut microbiota alteration and modulation in hepatitis B virus-related fibrosis and complications: Molecular mechanisms and therapeutic inventions. World J Gastroenterol 2022; 28:3555-3572. [PMID: 36161048 PMCID: PMC9372803 DOI: 10.3748/wjg.v28.i28.3555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/06/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) has posed a threat to public health, mainly resulting in liver damage. With long-term accumulation of extracellular matrix, patients with chronic hepatitis B are at high risk of developing into liver fibrosis and cirrhosis and even life-threatening hepatic carcinoma. The occurrence of complications such as spontaneous bacterial peritonitis and hepatic encephalopathy greatly increases disability and mortality. With deeper understanding of the bidirectional interaction between the liver and the gut (gut-liver axis), there is a growing consensus that the human health closely relates to the gut microbiota. Supported by animal and human studies, the gut microbiota alters as the HBV-related liver fibrosis initials and progresses, characterized as the decrease of the ratio between “good” and “potentially pathogenic” microbes. When the primary disease is controlled via antiviral treatment, the gut microbiota dysfunction tends to be improved. Conversely, the recovery of gut microbiota can promote the regression of liver fibrosis. Therapeutic strategies targeted on gut microbiota (rifaximin, probiotics, engineered probiotics and fecal microbiota transplantation) have been applied to animal models and patients, obtaining satisfactory results.
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Affiliation(s)
- Yao-Guang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Zu-Jiang Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Ang Li
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
| | - Zhi-Gang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan Province, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan 250000, Shandong Province, China
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