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Dasriya VL, Samtiya M, Ranveer S, Dhillon HS, Devi N, Sharma V, Nikam P, Puniya M, Chaudhary P, Chaudhary V, Behare PV, Dhewa T, Vemuri R, Raposo A, Puniya DV, Khedkar GD, Vishweswaraiah RH, Vij S, Alarifi SN, Han H, Puniya AK. Modulation of gut-microbiota through probiotics and dietary interventions to improve host health. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:6359-6375. [PMID: 38334314 DOI: 10.1002/jsfa.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
Dietary patterns play an important role in regards to the modulation and control of the gut microbiome composition and function. The interaction between diet and microbiota plays an important role in order to maintain intestinal homeostasis, which ultimately affect the host's health. Diet directly impacts the microbes that inhabit the gastrointestinal tract (GIT), which then contributes to the production of secondary metabolites, such as short-chain fatty acids, neurotransmitters, and antimicrobial peptides. Dietary consumption with genetically modified probiotics can be the best vaccine delivery vector and protect cells from various illnesses. A holistic approach to disease prevention, treatment, and management takes these intrinsically linked diet-microbes, microbe-microbe interactions, and microbe-host interactions into account. Dietary components, such as fiber can modulate beneficial gut microbiota, and they have resulting ameliorative effects against metabolic disorders. Medical interventions, such as antibiotic drugs can conversely have detrimental effects on gut microbiota by disputing the balance between Bacteroides and firmicute, which contribute to continuing disease states. We summarize the known effects of various dietary components, such as fibers, carbohydrates, fatty acids, vitamins, minerals, proteins, phenolic acids, and antibiotics on the composition of the gut microbiota in this article in addition to the beneficial effect of genetically modified probiotics and consequentially their role in regards to shaping human health. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
| | - Mrinal Samtiya
- Department of Nutrition Biology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, India
| | - Soniya Ranveer
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | | | - Nishu Devi
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Vikas Sharma
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Pranali Nikam
- College of Dairy Science and Food Technology, Dau Shri Vasudev Chandrakar, Kamdhenu University, Raipur, India
| | - Monica Puniya
- Science and Standards Division, Food Safety and Standards Authority of India, FDA Bhawan, New Delhi, India
| | - Priya Chaudhary
- Microbiology Department, VCSG Government Institute of Medical Science and Research, Srinagar, India
| | - Vishu Chaudhary
- University Institute of Biotechnology, Chandigarh University, Sahibzada Ajit Singh Nagar, India
| | - Pradip V Behare
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Tejpal Dhewa
- Department of Nutrition Biology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, India
| | - Ravichandra Vemuri
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Lisboa, Portugal
| | - Dharun Vijay Puniya
- Center of One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Gulab D Khedkar
- Paul Hebert Center for DNA Barcoding and Biodiversity Studies, Dr Babasaheb Ambedkar Marathwada University, Aurangabad, India
| | | | - Shilpa Vij
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Sehad N Alarifi
- Department of Food and Nutrition Science, Al-Quwayiyah College of Sciences and Humanities, Shaqra University, Shaqraa, Saudi Arabia
| | - Heesup Han
- College of Hospitality and Tourism Management, Sejong University, Seoul, South Korea
| | - Anil Kumar Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
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2
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Cao Z, Liu J. Surface nanocoating of bacteria as a versatile platform to develop living therapeutics. Nat Protoc 2024:10.1038/s41596-024-01019-6. [PMID: 39044001 DOI: 10.1038/s41596-024-01019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/01/2024] [Indexed: 07/25/2024]
Abstract
Bacteria have been extensively utilized as living therapeutics for disease treatment due to their unique characteristics, such as genetic manipulability, rapid proliferation and specificity to target disease sites. Various in vivo insults can, however, decrease the vitality of dosed bacteria, leading to low overall bioavailability. Additionally, the innate antigens on the bacterial surface and the released toxins and metabolites may cause undesired safety issues. These limitations inevitably result in inadequate treatment outcomes, thereby hindering the clinical transformation of living bacterial therapeutics. Recently, we have developed a versatile platform to prepare advanced living bacterial therapeutics by nanocoating bacteria individually via either chemical decoration or physical encapsulation, which can improve bioavailability and reduce side effects for enhanced microbial therapy. Here we use interfacial self-assembly to prepare lipid membrane-coated bacteria (LCB), exhibiting increased resistance against a variety of harsh environmental conditions owing to the nanocoating's protective capability. Meanwhile, we apply mechanical extrusion to generate cell membrane-coated bacteria (CMCB), displaying improved biocompatibility owing to the nanocoating's shielding effect. We describe their detailed preparation procedures and demonstrate the expected functions of the coated bacteria. We also show that following oral delivery and intravenous injection in mouse models, LCB and CMCB present appealing potential for treating colitis and tumors, respectively. Compared with bioengineering that lacks versatile molecular tools for heterogeneous expression, the surface nanocoating technique is convenient to introduce functional components without restriction on bacterial strain types. Excluding bacterial culture, the fabrication of LCB takes ~2 h, while the preparation of CMCB takes ~5 h.
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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 Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jinyao Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
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Durmusoglu D, Haller DJ, Al'Abri IS, Day K, Sands C, Clark A, San-Miguel A, Vazquez-Uribe R, Sommer MOA, Crook NC. Programming Probiotics: Diet-Responsive Gene Expression and Colonization Control in Engineered S. boulardii. ACS Synth Biol 2024; 13:1851-1865. [PMID: 38787439 DOI: 10.1021/acssynbio.4c00145] [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: 05/25/2024]
Abstract
Saccharomyces boulardii (Sb) is an emerging probiotic chassis for delivering biomolecules to the mammalian gut, offering unique advantages as the only eukaryotic probiotic. However, precise control over gene expression and gut residence time in Sb have remained challenging. To address this, we developed five ligand-responsive gene expression systems and repaired galactose metabolism in Sb, enabling inducible gene expression in this strain. Engineering these systems allowed us to construct AND logic gates, control the surface display of proteins, and turn on protein production in the mouse gut in response to dietary sugar. Additionally, repairing galactose metabolism expanded Sb's habitat within the intestines and resulted in galactose-responsive control over gut residence time. This work opens new avenues for precise dosing of therapeutics by Sb via control over its in vivo gene expression levels and localization within the gastrointestinal tract.
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Affiliation(s)
- Deniz Durmusoglu
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Daniel J Haller
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Ibrahim S Al'Abri
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Katie Day
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Carmen Sands
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andrew Clark
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Adriana San-Miguel
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
| | - Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nathan C Crook
- Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27606, United States
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Yang S, Qiao J, Zhang M, Kwok LY, Matijašić BB, Zhang H, Zhang W. Prevention and treatment of antibiotics-associated adverse effects through the use of probiotics: A review. J Adv Res 2024:S2090-1232(24)00230-3. [PMID: 38844120 DOI: 10.1016/j.jare.2024.06.006] [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: 01/22/2024] [Revised: 05/18/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND The human gut hosts a diverse microbial community, essential for maintaining overall health. However, antibiotics, commonly prescribed for infections, can disrupt this delicate balance, leading to antibiotic-associated diarrhea, inflammatory bowel disease, obesity, and even neurological disorders. Recognizing this, probiotics have emerged as a promising strategy to counteract these adverse effects. AIM OF REVIEW This review aims to offer a comprehensive overview of the latest evidence concerning the utilization of probiotics in managing antibiotic-associated side effects. KEY SCIENTIFIC CONCEPTS OF REVIEW Probiotics play a crucial role in preserving gut homeostasis, regulating intestinal function and metabolism, and modulating the host immune system. These mechanisms serve to effectively alleviate antibiotic-associated adverse effects and enhance overall well-being.
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Affiliation(s)
- Shuwei Yang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Jiaqi Qiao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | | | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Huhhot 010018, China.
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Zhang H, Chen B, Wang Z, Peng K, Liu Y, Wang Z. Resensitizing tigecycline- and colistin-resistant Escherichia coli using an engineered conjugative CRISPR/Cas9 system. Microbiol Spectr 2024; 12:e0388423. [PMID: 38385691 PMCID: PMC10986596 DOI: 10.1128/spectrum.03884-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
Tigecycline and colistin were referred to as the "last resort" antibiotics in defending against carbapenem-resistant, Gram-negative bacterial infections, and are currently widely used in clinical treatment. However, the emergence and prevalence of plasmid-mediated tet(X4) and mcr-1 genes pose a serious threat to the therapeutic application of tigecycline and colistin, respectively. In this research, a tigecycline- and colistin-resistant bacteria resensitization system was developed based on efficient and specific DNA damage caused by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Associated Protein 9 (Cas9) nucleases. A conjugation method was used to deliver the resensitization system, which harbors two single-guide RNAs targeting tet(X4) and mcr-1 genes and constitutively expressed Cas9. The conjugation efficiency was nearly 100% after conjugation condition optimization in vitro, and the resensitivity efficiency for clinical isolates was over 90%. In addition, when performing resensitization in vivo, the resistance marker was replaced with a glutamate-based, chromosomal, plasmid-balanced lethal system to prevent the introduction of additional resistance genes in clinical settings, making this strategy a therapeutic approach to combat the in vivo spread of antibiotic resistance genes (ARGs) among bacterial pathogens. As a proof of concept, this resensitive system can significantly decrease the counts of tigecycline- and colistin-resistant bacteria to 1% in vivo. Our study demonstrates the efficacy and adaptability of CRISPR-Cas systems as powerful and programmable antimicrobials in resensitizing tet(X4)- and mcr-1-mediated, tigecycline- and colistin-resistant strains, and opens up new pathways for the development of CRISPR-based tools for selective bacterial pathogen elimination and precise microbiome composition change. IMPORTANCE The emergence of plasmid-encoded tet(X4) and mcr-1 isolated from human and animal sources has affected the treatment of tigecycline and colistin, and has posed a significant threat to public health. Tigecycline and colistin are considered as the "last line of defense" for the treatment of multidrug-resistant (MDR) Gram-negative bacterial infections, so there is an urgent need to find a method that can resensitize tet(X4)-mediated tigecycline-resistant and mcr-1-mediated colistin-resistant bacteria. In this study, we developed a glutamate-based, chromosomal, plasmid-balanced lethal conjugative CRISPR/Cas9 system, which can simultaneously resensitize tet(X4)-mediated tigecycline-resistant and mcr-1-mediated colistin-resistant Escherichia coli. The counts of tigecycline- and colistin-resistant bacteria decreased to 1% in vivo after the resensitization system was administered. This study opens up new pathways for the development of CRISPR-based tools for selective bacterial pathogen elimination and precise microbiome composition change.
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Affiliation(s)
- Haijie Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Bo Chen
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Zeyu Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Kai Peng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Yuan Liu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Zhiqiang Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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6
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Wang Y, Shi Y, Peng X, Li T, Liang C, Wang W, Zhou M, Yang J, Cheng J, Zhang Z, Hou L. Biochemotaxis-Oriented Engineering Bacteria Expressing GLP-1 Enhance Diabetes Therapy by Regulating the Balance of Immune. Adv Healthc Mater 2024; 13:e2303958. [PMID: 38253022 DOI: 10.1002/adhm.202303958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Indexed: 01/24/2024]
Abstract
Glucagon like peptide-1 (GLP-1) is an effective hypoglycemic drug that can repair the pancreas β cells and promote insulin secretion. However, GLP-1 has poor stability and lacks of target ability, which makes it difficult to reach the site of action to exert its efficacy. Here, GLP-1-expressing plasmids are introduced into the Escherichia coli Nissle 1917 (EcN) and a lipid membrane is formed through simple self-assembly on its surface, resulting in an oral delivery system (LEG) capable of resisting the harsh environment of the gastrointestinal tract. The system utilizes the chemotactic properties of probiotics to achieve efficient enrichment at the pancreatic site, and protects islet β cells from destruction by regulating the balance of immune cells. More interestingly, LEG not only continuously produces GLP-1 to restore pancreatic islet β cell function and secrete insulin to control blood sugar levels, but also regulates the intestinal flora and increases the richness and diversity of probiotics. In mice diabetes models, oral administration of LEG only once every other day has good biosafety and compliance, and achieves long-term control of blood glucose. Therefore, this strategy not only provides an oral delivery platform for pancreatic targeting, but also opens up new avenues for reversing diabetes.
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Affiliation(s)
- Yifei Wang
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yupeng Shi
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xueyuan Peng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Tongtong Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Chenglin Liang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Wenhao Wang
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Mengyang Zhou
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jiali Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jingliang Cheng
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou, 450001, China
| | - Lin Hou
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou, 450001, China
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Liu J, Yuan S, Bremmer A, Hu Q. Convergence of Nanotechnology and Bacteriotherapy for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309295. [PMID: 38358998 PMCID: PMC11040386 DOI: 10.1002/advs.202309295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Bacteria have distinctive properties that make them ideal for biomedical applications. They can self-propel, sense their surroundings, and be externally detected. Using bacteria as medical therapeutic agents or delivery platforms opens new possibilities for advanced diagnosis and therapies. Nano-drug delivery platforms have numerous advantages over traditional ones, such as high loading capacity, controlled drug release, and adaptable functionalities. Combining bacteria and nanotechnologies to create therapeutic agents or delivery platforms has gained increasing attention in recent years and shows promise for improved diagnosis and treatment of diseases. In this review, design principles of integrating nanoparticles with bacteria, bacteria-derived nano-sized vesicles, and their applications and future in advanced diagnosis and therapeutics are summarized.
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Affiliation(s)
- Jun Liu
- Pharmaceutical Sciences Division, School of PharmacyUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
- Wisconsin Center for NanoBioSystemsUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
- Carbone Cancer Center, School of Medicine and Public HealthUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
| | - Sichen Yuan
- Pharmaceutical Sciences Division, School of PharmacyUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
- Wisconsin Center for NanoBioSystemsUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
- Carbone Cancer Center, School of Medicine and Public HealthUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
| | - Alexa Bremmer
- Pharmaceutical Sciences Division, School of PharmacyUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of PharmacyUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
- Wisconsin Center for NanoBioSystemsUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
- Carbone Cancer Center, School of Medicine and Public HealthUniversity of Wisconsin, Madison (UW‐Madison)MadisonWI53705USA
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8
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Mahdizade Ari M, Dadgar L, Elahi Z, Ghanavati R, Taheri B. Genetically Engineered Microorganisms and Their Impact on Human Health. Int J Clin Pract 2024; 2024:6638269. [PMID: 38495751 PMCID: PMC10944348 DOI: 10.1155/2024/6638269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 11/20/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
The emergence of antibiotic-resistant strains, the decreased effectiveness of conventional therapies, and the side effects have led researchers to seek a safer, more cost-effective, patient-friendly, and effective method that does not develop antibiotic resistance. With progress in synthetic biology and genetic engineering, genetically engineered microorganisms effective in treatment, prophylaxis, drug delivery, and diagnosis have been developed. The present study reviews the types of genetically engineered bacteria and phages, their impacts on diseases, cancer, and metabolic and inflammatory disorders, the biosynthesis of these modified strains, the route of administration, and their effects on the environment. We conclude that genetically engineered microorganisms can be considered promising candidates for adjunctive treatment of diseases and cancers.
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Affiliation(s)
- Marzie Mahdizade Ari
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Leila Dadgar
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Elahi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | | | - Behrouz Taheri
- Department of Biotechnology, School of Medicine, Ahvaz Jundishapour University of medical Sciences, Ahvaz, Iran
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Kolodkin-Gal I, Dash O, Rak R. Probiotic cultivated meat: bacterial-based scaffolds and products to improve cultivated meat. Trends Biotechnol 2024; 42:269-281. [PMID: 37805297 DOI: 10.1016/j.tibtech.2023.09.002] [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: 07/03/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/09/2023]
Abstract
Cultivated meat is emerging to replace traditional livestock industries, which have ecological costs, including land and water overuse and considerable carbon emissions. During cultivated meat production, mammalian cells can increase their numbers dramatically through self-renewal/proliferation and transform into mature cells, such as muscle or fat cells, through maturation/differentiation. Here, we address opportunities for introducing probiotic bacteria into the cultivated meat industry, including using them to produce renewable antimicrobials and scaffolding materials. We also offer solutions to challenges, including the growth of bacteria and mammalian cells, the effect of probiotic bacteria on production costs, and the effect of bacteria and their products on texture and taste. Our summary provides a promising framework for applying microbial composites in the cultivated meat industry.
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Affiliation(s)
- Ilana Kolodkin-Gal
- Scojen Institute for Synthetic Biology, Reichman University, Herzliya, Israel.
| | - Orit Dash
- Department of Animal Sciences, Faculty of Agriculture and Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel; Institute of Animal Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Roni Rak
- Institute of Animal Science, ARO, The Volcani Center, Rishon LeZion, Israel.
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10
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Parvin T, Sadras SR. Advanced probiotics: bioengineering and their therapeutic application. Mol Biol Rep 2024; 51:361. [PMID: 38403783 DOI: 10.1007/s11033-024-09309-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/01/2024] [Indexed: 02/27/2024]
Abstract
The role of gut bacteria in human health has long been acknowledged and dysbiosis of the gut microbiota has been correlated with a variety of disorders. Synthetic biology has rapidly grown over the past few years offering a variety of biological applications such as harnessing the relationship between bacteria and human health. Lactic acid bacteria (LAB) are thought to be appropriate chassis organisms for genetic modification with potential biomedical applications. A thorough understanding of the molecular mechanisms behind their beneficial qualities is essential to assist the multifunctional medicinal sectors. Effective genome editing will aid in the creation of next-generation designer probiotics with enhanced resilience and specialized capabilities, furthering our knowledge of the molecular mechanisms behind the physiological impacts of probiotics and their interactions with the host and microbiota. The goal of this review is to provide a brief overview of the methods used to create modified probiotics with the scientific rationale behind gene editing technology, the mechanism of action of engineered probiotics along with their application to treat conditions like inflammatory bowel disease, cancer, bacterial infections, and various metabolic diseases. In addition, application concerns and future directions are also presented.
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Affiliation(s)
- Tamanna Parvin
- Department of Biochemistry and Molecular Biology, School of Life Science, Pondicherry University, Puducherry, India.
| | - Sudha Rani Sadras
- Department of Biochemistry and Molecular Biology, School of Life Science, Pondicherry University, Puducherry, India
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11
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Kim TH, Ju K, Kim SK, Woo SG, Lee JS, Lee CH, Rha E, Shin J, Kwon KK, Lee H, Kim H, Lee SG, Lee DH. Novel Signal Peptides and Episomal Plasmid System for Enhanced Protein Secretion in Engineered Bacteroides Species. ACS Synth Biol 2024; 13:648-657. [PMID: 38224571 DOI: 10.1021/acssynbio.3c00649] [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: 01/17/2024]
Abstract
The genus Bacteroides, a predominant group in the human gut microbiome, presents significant potential for microbiome engineering and the development of live biotherapeutics aimed at treating gut diseases. Despite its promising capabilities, tools for effectively engineering Bacteroides species have been limited. In our study, we have made a breakthrough by identifying novel signal peptides in Bacteroides thetaiotaomicron and Akkermansia muciniphila. These peptides facilitate efficient protein transport across cellular membranes in Bacteroides, a critical step for therapeutic applications. Additionally, we have developed an advanced episomal plasmid system. This system demonstrates superior protein secretion capabilities compared to traditional chromosomal integration plasmids, making it a vital tool for enhancing the delivery of therapeutic proteins in Bacteroides species. Initially, the stability of this episomal plasmid posed a challenge; however, we have overcome this by incorporating an essential gene-based selection system. This novel strategy not only ensures plasmid stability but also aligns with the growing need for antibiotic-free selection methods in clinical settings. Our work, therefore, not only provides a more robust secretion system for Bacteroides but also sets a new standard for the development of live biotherapeutics.
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Affiliation(s)
- Tae Hyun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Kowoon Ju
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seong Keun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Gyun Woo
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jung-Sook Lee
- Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si 56212, Republic of Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jonghyeok Shin
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Haseong Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
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12
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Hahn J, Ding S, Im J, Harimoto T, Leong KW, Danino T. Bacterial therapies at the interface of synthetic biology and nanomedicine. NATURE REVIEWS BIOENGINEERING 2024; 2:120-135. [PMID: 38962719 PMCID: PMC11218715 DOI: 10.1038/s44222-023-00119-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 07/05/2024]
Abstract
Bacteria are emerging as living drugs to treat a broad range of disease indications. However, the inherent advantages of these replicating and immunostimulatory therapies also carry the potential for toxicity. Advances in synthetic biology and the integration of nanomedicine can address this challenge through the engineering of controllable systems that regulate spatial and temporal activation for improved safety and efficacy. Here, we review recent progress in nanobiotechnology-driven engineering of bacteria-based therapies, highlighting limitations and opportunities that will facilitate clinical translation.
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Affiliation(s)
- Jaeseung Hahn
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Suwan Ding
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jongwon Im
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Tetsuhiro Harimoto
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
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13
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Li C, Wang ZX, Xiao H, Wu FG. Intestinal Delivery of Probiotics: Materials, Strategies, and Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2310174. [PMID: 38245861 DOI: 10.1002/adma.202310174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 01/04/2024] [Indexed: 01/22/2024]
Abstract
Probiotics with diverse and crucial properties and functions have attracted broad interest from many researchers, who adopt intestinal delivery of probiotics to modulate the gut microbiota. However, the major problems faced for the therapeutic applications of probiotics are the viability and colonization of probiotics during their processing, oral intake, and subsequent delivery to the gut. The challenges of simple oral delivery (stability, controllability, targeting, etc.) have greatly limited the use of probiotics in clinical therapies. Nanotechnology can endow the probiotics to be delivered to the intestine with improved survival rate and increased resistance to the adverse environment. Additionally, the progress in synthetic biology has created new opportunities for efficiently and purposefully designing and manipulating the probiotics. In this article, a brief overview of the types of probiotics for intestinal delivery, the current progress of different probiotic encapsulation strategies, including the chemical, physical, and genetic strategies and their combinations, and the emerging single-cell encapsulation strategies using nanocoating methods, is presented. The action mechanisms of probiotics that are responsible for eliciting beneficial effects are also briefly discussed. Finally, the therapeutic applications of engineered probiotics are discussed, and the future trends toward developing engineered probiotics with advanced features and improved health benefits are proposed.
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Affiliation(s)
- Chengcheng Li
- International Innovation Center for Forest Chemicals and Materials and Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing, 210037, China
| | - Zi-Xi Wang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, New Brunswick, E3B 5A3, Canada
| | - Fu-Gen Wu
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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14
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Reuter S, Raspe J, Taube C. Microbes little helpers and suppliers for therapeutic asthma approaches. Respir Res 2024; 25:29. [PMID: 38218816 PMCID: PMC10787474 DOI: 10.1186/s12931-023-02660-7] [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: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 01/15/2024] Open
Abstract
Bronchial asthma is a prevalent and increasingly chronic inflammatory lung disease affecting over 300 million people globally. Initially considered an allergic disorder driven by mast cells and eosinophils, asthma is now recognized as a complex syndrome with various clinical phenotypes and immunological endotypes. These encompass type 2 inflammatory endotypes characterized by interleukin (IL)-4, IL-5, and IL-13 dominance, alongside others featuring mixed or non-eosinophilic inflammation. Therapeutic success varies significantly based on asthma phenotypes, with inhaled corticosteroids and beta-2 agonists effective for milder forms, but limited in severe cases. Novel antibody-based therapies have shown promise, primarily for severe allergic and type 2-high asthma. To address this gap, novel treatment strategies are essential for better control of asthma pathology, prevention, and exacerbation reduction. One promising approach involves stimulating endogenous anti-inflammatory responses through regulatory T cells (Tregs). Tregs play a vital role in maintaining immune homeostasis, preventing autoimmunity, and mitigating excessive inflammation after pathogenic encounters. Tregs have demonstrated their ability to control both type 2-high and type 2-low inflammation in murine models and dampen human cell-dependent allergic airway inflammation. Furthermore, microbes, typically associated with disease development, have shown immune-dampening properties that could be harnessed for therapeutic benefits. Both commensal microbiota and pathogenic microbes have demonstrated potential in bacterial-host interactions for therapeutic purposes. This review explores microbe-associated approaches as potential treatments for inflammatory diseases, shedding light on current and future therapeutics.
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Affiliation(s)
- Sebastian Reuter
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany.
| | - Jonas Raspe
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany
| | - Christian Taube
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany
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15
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Knödlseder N, Fábrega MJ, Santos-Moreno J, Manils J, Toloza L, Marín Vilar M, Fernández C, Broadbent K, Maruotti J, Lemenager H, Carolis C, Zouboulis CC, Soler C, Lood R, Brüggemann H, Güell M. Delivery of a sebum modulator by an engineered skin microbe in mice. Nat Biotechnol 2024:10.1038/s41587-023-02072-4. [PMID: 38195987 DOI: 10.1038/s41587-023-02072-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 11/17/2023] [Indexed: 01/11/2024]
Abstract
Microorganisms can be equipped with synthetic genetic programs for the production of targeted therapeutic molecules. Cutibacterium acnes is the most abundant commensal of the human skin, making it an attractive chassis to create skin-delivered therapeutics. Here, we report the engineering of this bacterium to produce and secrete the therapeutic molecule neutrophil gelatinase-associated lipocalin, in vivo, for the modulation of cutaneous sebum production.
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Affiliation(s)
- Nastassia Knödlseder
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - María-José Fábrega
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Javier Santos-Moreno
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Joan Manils
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Lorena Toloza
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria Marín Vilar
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Cristina Fernández
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Katrina Broadbent
- Protein Technologies Facility, Center of Genomic Regulation, Barcelona, Spain
| | | | | | - Carlo Carolis
- Protein Technologies Facility, Center of Genomic Regulation, Barcelona, Spain
| | - Christos C Zouboulis
- Hochschulklinik für Dermatologie, Venerologie und Allergologie, Immunologisches Zentrum; Städtisches Klinikum Dessau; and Medizinische Hochschule Brandenburg Theodor Fontane und Fakultät für Gesundheitswissenschaften Brandenburg, Dessau-Roßlau, Germany
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Rolf Lood
- Department of Clinical Sciences, Division of Infection Medicine, Lund University, Lund, Sweden
| | | | - Marc Güell
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
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16
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Ungor I, Apidianakis Y. Bacterial synergies and antagonisms affecting Pseudomonas aeruginosa virulence in the human lung, skin and intestine. Future Microbiol 2024; 19:141-155. [PMID: 37843410 DOI: 10.2217/fmb-2022-0155] [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: 07/07/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Pseudomonas aeruginosa requires a significant breach in the host defense to cause an infection. While its virulence factors are well studied, its tropism cannot be explained only by studying its interaction with the host. Why are P. aeruginosa infections so rare in the intestine compared with the lung and skin? There is not enough evidence to claim specificity in virulence factors deployed by P. aeruginosa in each anatomical site, and host physiology differences between the lung and the intestine cannot easily explain the observed differences in virulence. This perspective highlights a relatively overlooked parameter in P. aeruginosa virulence, namely, potential synergies with bacteria found in the human skin and lung, as well as antagonisms with bacteria of the human intestine.
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Affiliation(s)
- Izel Ungor
- Department of Biological Sciences, University of Cyprus, Nicosia, 2109, Cyprus
| | - Yiorgos Apidianakis
- Department of Biological Sciences, University of Cyprus, Nicosia, 2109, Cyprus
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17
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Wu J, Huang H, Wang L, Gao M, Meng S, Zou S, Feng Y, Feng Z, Zhu Z, Cao X, Li B, Kang G. A tailored series of engineered yeasts for the cell-dependent treatment of inflammatory bowel disease by rational butyrate supplementation. Gut Microbes 2024; 16:2316575. [PMID: 38381494 PMCID: PMC10883098 DOI: 10.1080/19490976.2024.2316575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Intestinal microbiota dysbiosis and metabolic disruption are considered essential characteristics in inflammatory bowel disorders (IBD). Reasonable butyrate supplementation can help patients regulate intestinal flora structure and promote mucosal repair. Here, to restore microbiota homeostasis and butyrate levels in the patient's intestines, we modified the genome of Saccharomyces cerevisiae to produce butyrate. We precisely regulated the relevant metabolic pathways to enable the yeast to produce sufficient butyrate in the intestine with uneven oxygen distribution. A series of engineered strains with different butyrate synthesis abilities was constructed to meet the needs of different patients, and the strongest can reach 1.8 g/L title of butyrate. Next, this series of strains was used to co-cultivate with gut microbiota collected from patients with mild-to-moderate ulcerative colitis. After receiving treatment with engineered strains, the gut microbiota and the butyrate content have been regulated to varying degrees depending on the synthetic ability of the strain. The abundance of probiotics such as Bifidobacterium and Lactobacillus increased, while the abundance of harmful bacteria like Candidatus Bacilloplasma decreased. Meanwhile, the series of butyrate-producing yeast significantly improved trinitrobenzene sulfonic acid (TNBS)-induced colitis in mice by restoring butyrate content. Among the series of engineered yeasts, the strain with the second-highest butyrate synthesis ability showed the most significant regulatory and the best therapeutic effect on the gut microbiota from IBD patients and the colitis mouse model. This study confirmed the existence of a therapeutic window for IBD treatment by supplementing butyrate, and it is necessary to restore butyrate levels according to the actual situation of patients to restore intestinal flora.
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Affiliation(s)
- Jiahao Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - He Huang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Lina Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Mengxue Gao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Shuxian Meng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Shaolan Zou
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yuanhang Feng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zeling Feng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhixin Zhu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xiaocang Cao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Bingzhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
| | - Guangbo Kang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin, China
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18
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Amrofell MB, Rengarajan S, Vo ST, Ramirez Tovar ES, LoBello L, Dantas G, Moon TS. Engineering E. coli strains using antibiotic-resistance-gene-free plasmids. CELL REPORTS METHODS 2023; 3:100669. [PMID: 38086386 PMCID: PMC10753387 DOI: 10.1016/j.crmeth.2023.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/29/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
We created a generalizable pipeline for antibiotic-resistance-gene-free plasmid (ARGFP)-based cloning using a dual auxotrophic- and essential-gene-based selection strategy. We use auxotrophic selection to construct plasmids in engineered E. coli DH10B cloning strains and both auxotrophic- and essential-gene-based selection to (1) select for recombinant strains and (2) maintain a plasmid in E. coli Nissle 1917, a common chassis for engineered probiotic applications, and E. coli MG1655, the laboratory "wild-type" E. coli strain. We show that our approach has comparable efficiency to that of antibiotic-resistance-gene-based cloning. We also show that the double-knockout Nissle and MG1655 strains are simple to transform with plasmids of interest. Notably, we show that the engineered Nissle strains are amenable to long-term plasmid maintenance in repeated culturing as well as in the mouse gut, demonstrating the potential for broad applications while minimizing the risk of antibiotic resistance spread via horizontal gene transfer.
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Affiliation(s)
- Matthew B Amrofell
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Sunaina Rengarajan
- Department of Medicine, Division of Dermatology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven T Vo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Erick S Ramirez Tovar
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Larissa LoBello
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA.
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19
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Yeh YH, Kelly VW, Pour RR, Sirk SJ. A molecular toolkit for heterologous protein secretion across Bacteroides species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571725. [PMID: 38168418 PMCID: PMC10760143 DOI: 10.1101/2023.12.14.571725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Bacteroides species are abundant and prevalent stably colonizing members of the human gut microbiota, making them a promising chassis for developing long-term interventions for chronic diseases. Engineering these bacteria as on-site production and delivery vehicles for biologic drugs or diagnostics, however, requires efficient heterologous protein secretion tools, which are currently lacking. To address this limitation, we systematically investigated methods to enable heterologous protein secretion in Bacteroides using both endogenous and exogenous secretion systems. Here, we report a collection of secretion carriers that can export functional proteins across multiple Bacteroides species at high titers. To understand the mechanistic drivers of Bacteroides secretion, we characterized signal peptide sequence features as well as post-secretion extracellular fate and cargo size limit of protein cargo. To increase titers and enable flexible control of protein secretion, we developed a strong, self-contained, inducible expression circuit. Finally, we validated the functionality of our secretion carriers in vivo in a mouse model. This toolkit should enable expanded development of long-term living therapeutic interventions for chronic gastrointestinal disease.
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Affiliation(s)
- Yu-Hsuan Yeh
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Vince W. Kelly
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Rahman Rahman Pour
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Present address: Perlumi, Berkeley, CA 94704, USA
| | - Shannon J. Sirk
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801, USA
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Lead Contact
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20
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Li H, Jia M, Qi Q, Wang Q. Engineered probiotic Lactobacillus plantarum WCSF I for monitoring and treatment of Staphylococcus aureus infection. Microbiol Spectr 2023; 11:e0182923. [PMID: 37909791 PMCID: PMC10848683 DOI: 10.1128/spectrum.01829-23] [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: 05/03/2023] [Accepted: 09/23/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Bacterial infection and the emergence of drug-resistant strains are major problems in clinical treatment. Staphylococcus aureus, which typically infects the skin and blood of animals, is also a potential intestinal pathogen that needs to be addressed by the emergence of a new treatment approach. Probiotic therapy is the most likely alternative to antibiotic therapy to solve the problem of bacterial drug resistance in clinical practice. In this study, the engineered Lactobacillus plantarum can not only sense the signal AIP to detect S. aureus but also kill S. aureus by secreting the lysostaphin enzyme. Our strategy employed an Agr quorum-sensing genetic circuit to simultaneously detect and treat pathogenic bacteria, which provided a theoretical possibility for solving practical clinical bacterial infection cases in the future.
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Affiliation(s)
- Haoran Li
- National Glycoengineering Research Center, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Minjun Jia
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qian Wang
- National Glycoengineering Research Center, Shandong University, Qingdao, China
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21
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Fishbein SRS, Mahmud B, Dantas G. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol 2023; 21:772-788. [PMID: 37491458 DOI: 10.1038/s41579-023-00933-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.
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Affiliation(s)
- Skye R S Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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22
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Bartram E, Asai M, Gabant P, Wigneshweraraj S. Enhancing the antibacterial function of probiotic Escherichia coli Nissle: when less is more. Appl Environ Microbiol 2023; 89:e0097523. [PMID: 37930328 PMCID: PMC10686094 DOI: 10.1128/aem.00975-23] [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: 06/13/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023] Open
Abstract
Probiotic bacteria confer multiple health benefits, including preventing the growth, colonization, or carriage of harmful bacteria in the gut. Bacteriocins are antibacterial peptides produced by diverse bacteria, and their production is tightly regulated and coordinated at the transcriptional level. A popular strategy for enhancing the antibacterial properties of probiotic bacteria is to retrofit them with the ability to overproduce heterologous bacteriocins. This is often achieved from non-native constitutive promoters or in response to host or pathogen signal from synthetic promoters. How the dysregulated overproduction of heterologous bacteriocins affects the fitness and antibacterial efficacy of the retrofitted probiotic bacteria is often overlooked. We have conferred the prototypical probiotic Escherichia coli strain Nissle (EcN) the ability to produce microcin C (McC) from the wild-type promoter and two mutant promoters that allow, relative to the wild-type promoter, high and low amounts of McC production. This was done by introducing specific changes to the sequence of the wild-type promoter driving transcription of the McC operon while ensuring that the modified promoters respond to native regulation. By studying the transcriptomic responses and antibacterial efficacy of the retrofitted EcN bacteria in a Galleria mellonella infection model of enterohemorrhagic E. coli, we show that EcN bacteria that produce the lowest amount of McC display the highest antibacterial efficacy with little-to-none undesired collateral impact on their fitness. The results highlight considerations researchers may take into account when retrofitting probiotic bacteria with heterogenous gene products for therapeutic, prophylactic, or diagnostic applications. Bacteria that resist killing by antibiotics are a major risk to modern medicine. The use of beneficial "probiotic" bacteria to make antibiotic-like compounds at the site of infection in the body is emerging as a popular alternative to the use of conventional antibiotics. A potential drawback of engineering probiotic bacteria in this way is that producing antibiotic-like compounds could impart undesired side effects on the performance of such bacteria, thereby compromising their intended use. This study highlights considerations researchers may take into account when engineering probiotic bacteria for therapeutic, prophylactic, or diagnostic applications.
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Affiliation(s)
- Emma Bartram
- Section of Molecular Microbiology, Imperial College London, London, United Kingdom
- Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
| | - Masanori Asai
- Section of Molecular Microbiology, Imperial College London, London, United Kingdom
- Section of Paediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | | | - Sivaramesh Wigneshweraraj
- Section of Molecular Microbiology, Imperial College London, London, United Kingdom
- Centre for Bacterial Resistance Biology, Imperial College London, London, United Kingdom
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Sun Y, Liu M, Tang X, Zhou Y, Zhang J, Yang B. Culture-Delivery Live Probiotics Dressing for Accelerated Infected Wound Healing. ACS APPLIED MATERIALS & INTERFACES 2023; 15:53283-53296. [PMID: 37948751 DOI: 10.1021/acsami.3c12845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Probiotic therapy in infected wound healing is hindered by its low viability and colonization efficiency during treatments. Developing dressings that maintain metabolic activity and prevent the potential leakage of probiotics is imperative. Herein, a culture-delivery live probiotics hydrogel dressing is designed and synthesized, formed by gelatin modified with norbornene (GelNB) and sulfhydryl (GelSH), distributing Lactobacillus reuteri (L. reuteri)-laden alginate microspheres (AlgMPs). GelNB-GelSH hydrogel (GelNBSH) incorporating AlgMPs embedding L. reuteri (GelNBSH-L) possesses bioprintability and efficient polymerization that can maintain the activity of L. reuteri in situ, promote its proliferation, and limit its leakage. Thereby, GelNBSH-L achieved a sustainable antimicrobial effect against both S. aureus and E. coli (>90%). Above all, the results show that GelNBSH-L could ensure propitious viability and efficient antibacterial properties of probiotics, effectively inhibit the further development of bacterial infectious wounds and shorten the repair cycle, aiding in ameliorating future clinical probiotic biotherapy.
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Affiliation(s)
- Yihan Sun
- State Key Laboratory of Supramolecular Structure and Material, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun 130012, China
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun 130021, China
| | - Manxuan Liu
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun 130021, China
| | - Xiaoduo Tang
- State Key Laboratory of Supramolecular Structure and Material, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun 130012, China
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun 130021, China
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun 130021, China
| | - Yanmin Zhou
- Jilin Provincial Key Laboratory of Tooth Development and Bone Remodeling, Hospital of Stomatology, Jilin University, Changchun 130021, China
| | - Junhu Zhang
- State Key Laboratory of Supramolecular Structure and Material, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun 130012, China
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun 130021, China
| | - Bai Yang
- State Key Laboratory of Supramolecular Structure and Material, Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun 130012, China
- Joint Laboratory of Opto-Functional Theranostics in Medicine and Chemistry, The First Hospital of Jilin University, Changchun 130021, China
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24
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Wang XG, Zou ZP, Du Y, Ye BC, Zhou Y. Construction of an Engineered Escherichia coli with Efficient Chemotactic and Metabolizing Ability toward Tetrathionate. ACS Synth Biol 2023; 12:3414-3423. [PMID: 37939253 DOI: 10.1021/acssynbio.3c00445] [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: 11/10/2023]
Abstract
The emergence of genetically engineered bacteria has provided a new means for the diagnosis and treatment of diseases. However, in vivo applications of these engineered bacteria are hindered by their inefficient accumulation in areas of inflammation. In this study, we constructed an engineered Escherichia coli (E. coli) for directional migration toward tetrathionate (a biomarker of gut inflammation), which is regulated by the TtrSR two-component system (TCS) from Shewanella baltica OS195 (S. baltica). Specifically, we removed endogenous cheZ to control the motility of E. coli. Moreover, we introduced the reductase gene cluster (ttrBCA) from Salmonella enterica serotype typhimurium (S. typhimurium), a major pathogen causing gut inflammation, into E. coli to metabolize tetrathionate. The resulting strain was tested for its motility along the gradients of tetrathionate; the engineered strain exhibits tropism to tetrathionate compared with the original strain. Furthermore, the engineered E. coli could only restore its smooth swimming ability when tetrathionate existed. With these modifications enabling tetrathionate-mediated chemotactic and metabolizing activity, this strategy with therapeutic elements will provide a great potential opportunity for target treatment of various diseases by swapping the corresponding genetic circuits.
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Affiliation(s)
- Xin-Ge Wang
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Zhen-Ping Zou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Yue Du
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
| | - Ying Zhou
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai 200237, China
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25
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Yang J, Yang H, Li Y. The triple interactions between gut microbiota, mycobiota and host immunity. Crit Rev Food Sci Nutr 2023; 63:11604-11624. [PMID: 35776086 DOI: 10.1080/10408398.2022.2094888] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The gut microbiome is mainly composed of microbiota and mycobiota, both of which play important roles in the development of the host immune system, metabolic regulation, and maintenance of intestinal homeostasis. With the increasing awareness of the pathogenic essence of infectious, immunodeficiency, and tumor-related diseases, the interactions between gut bacteria, fungi, and host immunity have been shown to directly influence the disease process or final therapeutic outcome, and collaborative and antagonistic relationships are commonly found between bacteria and fungi. Interventions represented by probiotics, prebiotics, engineered probiotics, fecal microbiota transplantation (FMT), and drugs can effectively modulate the triple interactions. In particular, traditional probiotics represented by Bifidobacterium and Lactobacillus and next-generation probiotics represented by Akkermansia muciniphila and Faecalibacterium prausnitzii showed a high enrichment trend in the gut of patients with a high response to inflammation remission and tumor immunotherapy, which predicts the potential medicinal value of these beneficial microbial formulations. However, there are bottlenecks in all these interventions that need to be broken. Meanwhile, further unraveling the underlying mechanisms of the "triple interactions" model can guide precise interventions and ultimately improve the efficiency of interventions on the host gut microbiome and immune modulation, thus directly or indirectly improving anti-inflammatory and tumor immunotherapy effects.
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Affiliation(s)
- Jingpeng Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Hong Yang
- State Key Laboratory of Microbial Metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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26
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González-Prieto C, Lynch JP, Lesser CF. PROT 3EcT, engineered Escherichia coli for the targeted delivery of therapeutics. Trends Mol Med 2023; 29:968-969. [PMID: 37574350 PMCID: PMC10592157 DOI: 10.1016/j.molmed.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023]
Affiliation(s)
- 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
| | - 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
| | - 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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27
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Tanniche I, Behkam B. Engineered live bacteria as disease detection and diagnosis tools. J Biol Eng 2023; 17:65. [PMID: 37875910 PMCID: PMC10598922 DOI: 10.1186/s13036-023-00379-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/18/2023] [Indexed: 10/26/2023] Open
Abstract
Sensitive and minimally invasive medical diagnostics are essential to the early detection of diseases, monitoring their progression and response to treatment. Engineered bacteria as live sensors are being developed as a new class of biosensors for sensitive, robust, noninvasive, and in situ detection of disease onset at low cost. Akin to microrobotic systems, a combination of simple genetic rules, basic logic gates, and complex synthetic bioengineering principles are used to program bacterial vectors as living machines for detecting biomarkers of diseases, some of which cannot be detected with other sensing technologies. Bacterial whole-cell biosensors (BWCBs) can have wide-ranging functions from detection only, to detection and recording, to closed-loop detection-regulated treatment. In this review article, we first summarize the unique benefits of bacteria as living sensors. We then describe the different bacteria-based diagnosis approaches and provide examples of diagnosing various diseases and disorders. We also discuss the use of bacteria as imaging vectors for disease detection and image-guided surgery. We conclude by highlighting current challenges and opportunities for further exploration toward clinical translation of these bacteria-based systems.
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Affiliation(s)
- Imen Tanniche
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Bahareh Behkam
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
- School of Biomedical Engineered and Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
- Center for Engineered Health, Institute for Critical Technology and Applied Science, Virginia Tech, Blacksburg, VA, 24061, USA.
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28
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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: 0] [Impact Index Per Article: 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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29
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Mehboudi N, Rahimi HR, Bakhtiari HA, Alimardani M, Jalili A. The impact of probiotic cell-free metabolites in MDR Pseudomonas aeruginosa: antibacterial properties and effect on antibiotic resistance genes expression. Lett Appl Microbiol 2023; 76:ovad111. [PMID: 37742315 DOI: 10.1093/lambio/ovad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/04/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
There is a significant demand for novel antibacterial agents against multidrug-resistant (MDR) gram-negative bacteria. Recently, probiotics have been noted for their antibacterial properties against various pathogens. This study aimed to investigate the effects of probiotic cell-free supernatants on MDR Pseudomonas aeruginosa. Clinical isolates demonstrating the highest degree of antibiotic resistance were chosen, and the antibacterial effect of probiotic metabolites was evaluated using an agar-well diffusion assay. In addition, the effect of probiotics on the expression of resistance genes was evaluated using real-time PCR. The CFS was assessed using GC-MS to determine the antibacterial compounds. The supernatants inhibited the growth of the isolates (P < 0.0001); however, there was no noticeable difference in the effectiveness of the probiotics. In addition, the supernatants decreased the expression levels of mexD, mexB, mexF, and ampC, and an increase in oprD was observed in some groups. After the assessment of Lactobacillus acidophilus by GC-MS, antibacterial compounds, such as acetamide, nonadecane, 9-methyl, and tetradecane, were determined. Our findings showed that probiotic metabolites can effectively inhibit the growth of MDR P. aeruginosa. Gene expression analysis also revealed that the mechanism of antibacterial action was most likely related to the regulation of efflux pumps.
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Affiliation(s)
- Nastaran Mehboudi
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran
| | - Hamid R Rahimi
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran
| | - H Aghaee Bakhtiari
- Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran
| | - Maliheh Alimardani
- Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran
| | - Amin Jalili
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad 9177948564, Iran
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30
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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: 9] [Impact Index Per Article: 9.0] [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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31
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Liu L, Helal SE, Peng N. CRISPR-Cas-Based Engineering of Probiotics. BIODESIGN RESEARCH 2023; 5:0017. [PMID: 37849462 PMCID: PMC10541000 DOI: 10.34133/bdr.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Probiotics are the treasure of the microbiology fields. They have been widely used in the food industry, clinical treatment, and other fields. The equivocal health-promoting effects and the unknown action mechanism were the largest obstacles for further probiotic's developed applications. In recent years, various genome editing techniques have been developed and applied to explore the mechanisms and functional modifications of probiotics. As important genome editing tools, CRISPR-Cas systems that have opened new improvements in genome editing dedicated to probiotics. The high efficiency, flexibility, and specificity are the advantages of using CRISPR-Cas systems. Here, we summarize the classification and distribution of CRISPR-Cas systems in probiotics, as well as the editing tools developed on the basis of them. Then, we discuss the genome editing of probiotics based on CRISPR-Cas systems and the applications of the engineered probiotics through CRISPR-Cas systems. Finally, we proposed a design route for CRISPR systems that related to the genetically engineered probiotics.
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Affiliation(s)
- Ling Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan, China
| | - Shimaa Elsayed Helal
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Nan Peng
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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Li J, Sun M, Liu L, Yang W, Sun A, Yu J, Liu D, Zhao W, Cheng M, He Z, Gu Z, Sun J. Nanoprobiotics for Remolding the Pro-inflammatory Microenvironment and Microbiome in the Treatment of Colitis. NANO LETTERS 2023; 23:8593-8601. [PMID: 37625135 DOI: 10.1021/acs.nanolett.3c02408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Despite the great progress of current bacterially based biotherapeutics, their unsatisfying efficacy and underlying safety problems have limited their clinical application. Herein, inspired by probiotic Escherichia coli strain Nissle 1917, probiotic-derived outer membrane vesicles (OMVs) are found to serve as an effective therapeutic platform for the treatment of inflammatory bowel disease (IBD). To further enhance the therapeutic effect, the probiotic-derived OMV-encapsulating manganese dioxide nanozymes are constructed, named nanoprobiotics, which can adhere to inflamed colonic epithelium and eliminate intestinal excess reactive oxygen species in the murine IBD model. Moreover, combined with the anti-inflammatory medicine metformin, nanoprobiotics could further remold the pro-inflammatory microenvironment, improve the overall richness and diversity of the gut microbiota, and exhibit better therapeutic efficacy than commercial IBD chemotherapeutics. Importantly, insignificant overt systemic toxicity in this treatment was observed. By integrating cytokine storm calm with biotherapy, we develop a safe and effective bionanoplatform for the effective treatment of inflammation-mediated intestinal diseases.
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Affiliation(s)
- Jiwei Li
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, Liaoning 110016, China
| | - Mengchi Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, Liaoning 110016, China
| | - Linlin Liu
- Department of Nephrology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Weiguang Yang
- Department of Nephrology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Ao Sun
- Department of Nephrology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110001, China
| | - Jicheng Yu
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang 311121, China
| | - Dongchun Liu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, Liaoning 110016, China
| | - Wutong Zhao
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, Liaoning 110016, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang, Liaoning 110016, China
| | - Zhonggui He
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, Liaoning 110016, China
| | - Zhen Gu
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang 311121, China
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310016, China
- Jinhua Institute of Zhejiang University, Jinhua, Zhejiang 321299, China
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Jin Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Wenhua Road 103, Shenyang, Liaoning 110016, China
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Kim H, Jang JH, Jung IY, Kim HR, Cho JH. Novel Genetically Engineered Probiotics for Targeted Elimination of Pseudomonas aeruginosa in Intestinal Colonization. Biomedicines 2023; 11:2645. [PMID: 37893018 PMCID: PMC10604247 DOI: 10.3390/biomedicines11102645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
The intestinal carriage rates of Pseudomonas aeruginosa are notably elevated in immunosuppressed individuals and hospitalized patients, increasing the risk of infection and antibiotic-associated diarrhea. A potential solution to this issue lies in autonomous antibacterial therapy, remaining inactive until a pathogen is detected, and releasing antibacterial compounds on demand to eliminate the pathogen. This study focuses on the development of genetically engineered probiotics capable of detecting and eradicating P. aeruginosa by producing and secreting PA2-GNU7, a P. aeruginosa-selective antimicrobial peptide (AMP), triggered by the presence of P. aeruginosa quorum-sensing molecule N-(3-oxododecanoyl)-L-homoserine lactone (3OC12HSL). To achieve this goal, plasmid-based systems were constructed to produce AMPs in response to 3OC12HSL and secrete them into the extracellular medium using either the microcin V secretion system or YebF as a carrier protein. Following the transfer of these plasmid-based systems to Escherichia coli Nissle 1917 (EcN), we successfully demonstrated the ability of the engineered EcN to express and secrete PA2-GNU7, leading to the inhibition of P. aeruginosa growth in vitro. In addition, in a mouse model of intestinal P. aeruginosa colonization, the administration of engineered EcN resulted in reduced levels of P. aeruginosa in both the feces and the colon. These findings suggest that engineered EcN holds promise as a potential option for combating intestinal P. aeruginosa colonization, thus mitigating the risk of future endogenous infections in vulnerable patients.
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Affiliation(s)
- Hyun Kim
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea; (H.K.); (J.H.J.)
| | - Ju Hye Jang
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea; (H.K.); (J.H.J.)
| | - In Young Jung
- Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (I.Y.J.); (H.R.K.)
| | - Ha Rang Kim
- Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (I.Y.J.); (H.R.K.)
| | - Ju Hyun Cho
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea; (H.K.); (J.H.J.)
- Division of Applied Life Science (BK21Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (I.Y.J.); (H.R.K.)
- Division of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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Chen S, He X, Qin Z, Li G, Wang W, Nai Z, Tian Y, Liu D, Jiang X. Loss in the Antibacterial Ability of a PyrR Gene Regulating Pyrimidine Biosynthesis after Using CRISPR/Cas9-Mediated Knockout for Metabolic Engineering in Lactobacillus casei. Microorganisms 2023; 11:2371. [PMID: 37894029 PMCID: PMC10609543 DOI: 10.3390/microorganisms11102371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Lactobacillus casei (L. casei) has four possible mechanisms: antimicrobial antagonism, competitional adhesion, immunoregulation, and the inhibition of bacterial toxins. To delineate the metabolic reactions of nucleotides from L. casei that are associated with mechanisms of inhibiting pathogens and immunoregulation, we report that a PyrR-deficient L. casei strain was constructed using the CRISPR-Cas9D10A tool. Furthermore, there were some changes in its basic biological characterization, such as its growth curve, auxotroph, and morphological damage. The metabolic profiles of the supernatant between the PyrR-deficient and wild strains revealed the regulation of the synthesis of genetic material and of certain targeting pathways and metabolites. In addition, the characteristics of the PyrR-deficient strain were significantly altered as it lost the ability to inhibit the growth of pathogens. Moreover, we identified PyrR-regulating pyrimidine biosynthesis, which further improved its internalization and colocalization with macrophages. Evidence shows that the PyrR gene is a key active component in L. casei supernatants for the regulation of pyrimidine biosynthesis against a wide range of pathogens.
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Affiliation(s)
- Shaojun Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Xinmiao He
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Ziliang Qin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Gang Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Wentao Wang
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Zida Nai
- College of Agriculture, Yanbian University, Yanji 133002, China
| | - Yaguang Tian
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Di Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Xinpeng Jiang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
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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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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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Goodson M. ACS Biomaterials Science and Engineering Special Issue Editorial: Design and Evaluation of Engineered Probiotics. ACS Biomater Sci Eng 2023; 9:5098-5100. [PMID: 37691547 DOI: 10.1021/acsbiomaterials.3c00779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
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Yuan S, Wang KS, Meng H, Hou XT, Xue JC, Liu BH, Cheng WW, Li J, Zhang HM, Nan JX, Zhang QG. The gut microbes in inflammatory bowel disease: Future novel target option for pharmacotherapy. Biomed Pharmacother 2023; 165:114893. [PMID: 37352702 DOI: 10.1016/j.biopha.2023.114893] [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: 03/16/2023] [Revised: 05/09/2023] [Accepted: 05/13/2023] [Indexed: 06/25/2023] Open
Abstract
Gut microbes constitute the main microbiota in the human body, which can regulate biological processes such as immunity, cell proliferation, and differentiation, hence playing a specific function in intestinal diseases. In recent years, gut microbes have become a research hotspot in the pharmaceutical field. Because of their enormous number, diversity, and functional complexity, gut microbes have essential functions in the development of many digestive diseases. Inflammatory bowel disease (IBD) is a chronic non-specific inflammatory disease with a complex etiology, the exact cause and pathogenesis are unclear. There are no medicines that can cure IBD, and more research on therapeutic drugs is urgently needed. It has been reported that gut microbes play a critical role in pathogenesis, and there is a tight and complex association between gut microbes and IBD. The dysregulation of gut microbes may be a predisposing factor for IBD, and at the same time, IBD may exacerbate gut microbes' disorders, but the mechanism of interaction between the two is still not well defined. The study of the relationship between gut microbes and IBD is not only important to elucidate the pathogenesis but also has a positive effect on the treatment based on the regimen of regulating gut microbes. This review describes the latest research progress on the functions of gut microbes and their relationship with IBD, which can provide reference and assistance for further research. It may provide a theoretical basis for the application of probiotics, fecal microbiota transplantation, and other therapeutic methods to regulate gut microbes in IBD.
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Affiliation(s)
- Shuo Yuan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin Province 133002, China
| | - Ke-Si Wang
- Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China
| | - Huan Meng
- Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China
| | - Xiao-Ting Hou
- Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China
| | - Jia-Chen Xue
- Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China; Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, 116001, China
| | - Bao-Hong Liu
- Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China
| | - Wen-Wen Cheng
- Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China
| | - Jiao Li
- Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China
| | - Hua-Min Zhang
- Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China
| | - Ji-Xing Nan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin Province 133002, China.
| | - Qing-Gao Zhang
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin Province 133002, China; Chronic diseases research center, Dalian University College of Medicine, Dalian, Liaoning, 116622, China.
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Tchesnokova V, Larson L, Basova I, Sledneva Y, Choudhury D, Solyanik T, Heng J, Bonilla TC, Pham S, Schartz EM, Madziwa LT, Holden E, Weissman SJ, Ralston JD, Sokurenko EV. Increase in the community circulation of ciprofloxacin-resistant Escherichia coli despite reduction in antibiotic prescriptions. COMMUNICATIONS MEDICINE 2023; 3:110. [PMID: 37567971 PMCID: PMC10421857 DOI: 10.1038/s43856-023-00337-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Community circulating gut microbiota is the main reservoir for uropathogenic Escherichia coli, including those resistant to antibiotics. Ciprofloxacin had been the primary antibiotic prescribed for urinary tract infections, but its broad use has been discouraged and steadily declined since 2015. How this change in prescriptions affected the community circulation of ciprofloxacin-resistant E. coli is unknown. METHODS We determined the frequency of isolation and other characteristics of E. coli resistant to ciprofloxacin in 515 and 1604 E. coli-positive fecal samples collected in 2015 and 2021, respectively. The samples were obtained from non-antibiotic-taking women of age 50+ receiving care in the Kaiser Permanente Washington healthcare system. RESULTS Here we show that despite a nearly three-fold drop in the prescription of ciprofloxacin between 2015 and 2021, the rates of gut carriage of ciprofloxacin-resistant E. coli increased from 14.2 % to 19.8% (P = .004). This is driven by a significant increase of isolates from the pandemic multi-drug resistant clonal group ST1193 (1.7% to 4.2%; P = .009) and isolates with relatively few ciprofloxacin-resistance determining chromosomal mutations (2.3% to 7.4%; P = .00003). Though prevalence of isolates with the plasmid-associated ciprofloxacin resistance dropped (59.0% to 30.9%; P = 2.7E-06), the isolates co-resistance to third generation cephalosporins has increased from 14.1% to 31.5% (P = .002). CONCLUSIONS Despite reduction in ciprofloxacin prescriptions, community circulation of the resistant uropathogenic E. coli increased with a rise of co-resistance to third generation cephalosporins. Thus, to reduce the rates of urinary tract infections refractory to antibiotic treatment, greater focus should be on controlling the resistant bacteria in gut microbiota.
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Affiliation(s)
- Veronika Tchesnokova
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Lydia Larson
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Irina Basova
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Yulia Sledneva
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Debarati Choudhury
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Thalia Solyanik
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Jennifer Heng
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Teresa Christina Bonilla
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Sophia Pham
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA
| | - Ellen M Schartz
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA, 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA
| | - Lawrence T Madziwa
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA, 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA
| | - Erika Holden
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA, 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA
| | - Scott J Weissman
- Department of Laboratory Medicine, Seattle Children's Hospital, 1100 Olive Way Tutor Center, Seattle, WA, 98101, USA
| | - James D Ralston
- Kaiser Permanente Washington, 2715 Naches Ave. SW, Renton, WA, 98057, USA
- Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA
| | - Evgeni V Sokurenko
- Department of Microbiology, University of Washington School of Medicine, 1705 NE Pacific St., Seattle, WA, 98195, USA.
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40
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Arnold J, Glazier J, Mimee M. Genetic Engineering of Resident Bacteria in the Gut Microbiome. J Bacteriol 2023; 205:e0012723. [PMID: 37382533 PMCID: PMC10367592 DOI: 10.1128/jb.00127-23] [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] [Indexed: 06/30/2023] Open
Abstract
Techniques by which to genetically manipulate members of the microbiota enable both the evaluation of host-microbe interactions and an avenue by which to monitor and modulate human physiology. Genetic engineering applications have traditionally focused on model gut residents, such as Escherichia coli and lactic acid bacteria. However, emerging efforts by which to develop synthetic biology toolsets for "nonmodel" resident gut microbes could provide an improved foundation for microbiome engineering. As genome engineering tools come online, so too have novel applications for engineered gut microbes. Engineered resident gut bacteria facilitate investigations of the roles of microbes and their metabolites on host health and allow for potential live microbial biotherapeutics. Due to the rapid pace of discovery in this burgeoning field, this minireview highlights advancements in the genetic engineering of all resident gut microbes.
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Affiliation(s)
- Jack Arnold
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Joshua Glazier
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
| | - Mark Mimee
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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41
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Gao Y, Wei J, Pu L, Fu S, Xing X, Zhang R, Jin F. Remotely Controllable Engineered Bacteria for Targeted Therapy of Pseudomonas aeruginosa Infection. ACS Synth Biol 2023. [PMID: 37418677 DOI: 10.1021/acssynbio.2c00655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) infection has become an intractable problem worldwide due to the decreasing efficacy of the mainstay therapy, antibiotic treatment. Hence, exploring new drugs and therapies to address this issue is crucial. Here, we construct a chimeric pyocin (ChPy) to specifically kill P. aeruginosa and engineer a near-infrared (NIR) light-responsive strain to produce and deliver this drug. Our engineered bacterial strain can continuously produce ChPy in the absence of light and release it to kill P. aeruginosa via remotely and precisely controlled bacterial lysis induced by NIR light. We demonstrate that our engineered bacterial strain is effective in P. aeruginosa-infected wound therapy in the mouse model, as it eradicated PAO1 in mouse wounds and shortened the wound healing time. Our work presents a potentially spatiotemporal and noninvasively controlled therapeutic strategy of engineered bacteria for the targeted treatment of P. aeruginosa infections.
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Affiliation(s)
- Yanmei Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, No. 96, JinZhai Road, Baohe District, Hefei, Anhui 230026, P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Jingjing Wei
- Department of Fine Chemical Engineering, Shenzhen Polytechnic, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Lu Pu
- West China School of Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan 610065, China
| | - Shengwei Fu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, No. 96, JinZhai Road, Baohe District, Hefei, Anhui 230026, P. R. China
| | - Xiaochen Xing
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Rongrong Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Fan Jin
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, No. 96, JinZhai Road, Baohe District, Hefei, Anhui 230026, P. R. China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
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Espinal P, Fusté E, Sierra JM, Jiménez-Galisteo G, Vinuesa T, Viñas M. Progress towards the clinical use of antimicrobial peptides: challenges and opportunities. Expert Opin Biol Ther 2023:1-10. [PMID: 37366927 DOI: 10.1080/14712598.2023.2226796] [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: 03/22/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
INTRODUCTION To overcome the challenge of multidrug resistance, natural and synthetic peptides are candidates to become the basis of innovative therapeutics, featuring diverse mechanisms of action. Traditionally, the time elapsed from medical discoveries to their application is long. The urgency derived from the emergence of antibiotic resistance recommends an acceleration of research to put the new weapons in the hands of clinicians. AREAS COVERED This narrative review introduces ideas and suggestions of new strategies that may be used as a basis upon which to recommend reduced development times and to facilitate the arrival of new molecules in the fight against microbes. EXPERT OPINION Although studies on new innovative antimicrobial treatments are being conducted, sooner rather than later, more clinical trials, preclinical and translational research are needed to promote the development of innovative antimicrobial treatments for multidrug resistant infections. The situation is worrying, no less than that generated by pandemics such as the ones we have just experienced and conflicts such as world wars. Although from the point of view of human perception, resistance to antibiotics may not seem as serious as these other situations, it is possibly the hidden pandemic that most jeopardizes the future of medicine.
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Affiliation(s)
- Paula Espinal
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, Campus Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ester Fusté
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, Campus Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
- Department of Public Health, Mental Health, And Maternal and Child Health Nursing, University of Barcelona and IDIBELL, Campus Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Josep M Sierra
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, Campus Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Guadalupe Jiménez-Galisteo
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, Campus Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Teresa Vinuesa
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, Campus Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Miguel Viñas
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, Campus Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
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Koehle AP, Brumwell SL, Seto EP, Lynch AM, Urbaniak C. Microbial applications for sustainable space exploration beyond low Earth orbit. NPJ Microgravity 2023; 9:47. [PMID: 37344487 DOI: 10.1038/s41526-023-00285-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/25/2023] [Indexed: 06/23/2023] Open
Abstract
With the construction of the International Space Station, humans have been continuously living and working in space for 22 years. Microbial studies in space and other extreme environments on Earth have shown the ability for bacteria and fungi to adapt and change compared to "normal" conditions. Some of these changes, like biofilm formation, can impact astronaut health and spacecraft integrity in a negative way, while others, such as a propensity for plastic degradation, can promote self-sufficiency and sustainability in space. With the next era of space exploration upon us, which will see crewed missions to the Moon and Mars in the next 10 years, incorporating microbiology research into planning, decision-making, and mission design will be paramount to ensuring success of these long-duration missions. These can include astronaut microbiome studies to protect against infections, immune system dysfunction and bone deterioration, or biological in situ resource utilization (bISRU) studies that incorporate microbes to act as radiation shields, create electricity and establish robust plant habitats for fresh food and recycling of waste. In this review, information will be presented on the beneficial use of microbes in bioregenerative life support systems, their applicability to bISRU, and their capability to be genetically engineered for biotechnological space applications. In addition, we discuss the negative effect microbes and microbial communities may have on long-duration space travel and provide mitigation strategies to reduce their impact. Utilizing the benefits of microbes, while understanding their limitations, will help us explore deeper into space and develop sustainable human habitats on the Moon, Mars and beyond.
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Affiliation(s)
- Allison P Koehle
- Department of Plant Science, Pennsylvania State University, University Park, PA, USA
| | - Stephanie L Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
| | | | - Anne M Lynch
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Graduate Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Camilla Urbaniak
- ZIN Technologies Inc, Middleburg Heights, OH, USA.
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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Triassi AJ, Fields BD, Monahan CE, Means JM, Park Y, Doosthosseini H, Padmakumar JP, Isabella VM, Voigt CA. Redesign of an Escherichia coli Nissle treatment for phenylketonuria using insulated genomic landing pads and genetic circuits to reduce burden. Cell Syst 2023; 14:512-524.e12. [PMID: 37348465 DOI: 10.1016/j.cels.2023.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 01/18/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
To build therapeutic strains, Escherichia coli Nissle (EcN) have been engineered to express antibiotics, toxin-degrading enzymes, immunoregulators, and anti-cancer chemotherapies. For efficacy, the recombinant genes need to be highly expressed, but this imposes a burden on the cell, and plasmids are difficult to maintain in the body. To address these problems, we have developed landing pads in the EcN genome and genetic circuits to control therapeutic gene expression. These tools were applied to EcN SYNB1618, undergoing clinical trials as a phenylketonuria treatment. The pathway for converting phenylalanine to trans-cinnamic acid was moved to a landing pad under the control of a circuit that keeps the pathway off during storage. The resulting strain (EcN SYN8784) achieved higher activity than EcN SYNB1618, reaching levels near when the pathway is carried on a plasmid. This work demonstrates a simple system for engineering EcN that aids quantitative strain design for therapeutics.
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Affiliation(s)
- Alexander J Triassi
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brandon D Fields
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Yongjin Park
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hamid Doosthosseini
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jai P Padmakumar
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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45
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Zhu YX, You Y, Chen Z, Xu D, Yue W, Ma X, Jiang J, Wu W, Lin H, Shi J. Inorganic Nanosheet-Shielded Probiotics: A Self-Adaptable Oral Delivery System for Intestinal Disease Treatment. NANO LETTERS 2023; 23:4683-4692. [PMID: 36912868 DOI: 10.1021/acs.nanolett.3c00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The oral delivery of probiotics is commonly adopted for intestinal disease treatments in clinical settings; however, the probiotics suffer from a strong acidic attack in the gastric area and the low-efficiency intestinal colonization of naked probiotics. Coating living probiotics with synthetic materials has proven effective in enabling the adaption of bacteria to gastrointestinal environments, which, unfortunately, may shield the probiotics from initiating therapeutic responses. In this study, we report a copolymer-modified two-dimensional H-silicene nanomaterial (termed SiH@TPGS-PEI) that can facilitate probiotics to adapt to diverse gastrointestinal microenvironments on-demand. Briefly, SiH@TPGS-PEI electrostatically coated on the surface of probiotic bacteria helps to resist erosive destruction in the acidic stomach and spontaneously degrades by reacting with water to generate hydrogen, an anti-inflammatory gas in response to the neutral/weakly alkaline intestinal environment, thus exposing the probiotic bacteria for colitis amelioration. This strategy may shed new light on the development of intelligent self-adaptive materials.
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Affiliation(s)
- Ya-Xuan Zhu
- Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai 200331, P. R. China
| | - Yanling You
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai 200050, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhixin Chen
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai 200050, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Deliang Xu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai 200050, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wenwen Yue
- Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai 200331, P. R. China
| | - Xinxin Ma
- Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai Jiao Tong University, Shanghai 200233, P. R. China
| | - Junjie Jiang
- Shanghai University of Traditional Chinese Medicine, Shanghai 201203, P. R. China
| | - Wencheng Wu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai 200050, P. R. China
| | - Han Lin
- Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai 200331, P. R. China
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai 200050, P. R. China
| | - Jianlin Shi
- Shanghai Tenth People's Hospital, Shanghai Frontiers Science Center of Nanocatalytic Medicine, School of Medicine, Tongji University, Shanghai 200331, P. R. China
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics Chinese Academy of Sciences, Research Unit of Nanocatalytic Medicine in Specific Therapy for Serious Disease, Chinese Academy of Medical Sciences (2021RU012), Shanghai 200050, P. R. China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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46
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Gencer G, Mancuso C, Chua KJ, Ling H, Costello CM, Chang MW, March JC. Engineering Escherichia coli for diagnosis and management of hyperuricemia. Front Bioeng Biotechnol 2023; 11:1191162. [PMID: 37288353 PMCID: PMC10242094 DOI: 10.3389/fbioe.2023.1191162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Uric acid disequilibrium is implicated in chronic hyperuricemia-related diseases. Long-term monitoring and lowering of serum uric acid levels may be crucial for diagnosis and effective management of these conditions. However, current strategies are not sufficient for accurate diagnosis and successful long-term management of hyperuricemia. Moreover, drug-based therapeutics can cause side effects in patients. The intestinal tract plays an important role in maintaining healthy serum acid levels. Hence, we investigated the engineered human commensal Escherichia coli as a novel method for diagnosis and long-term management of hyperuricemia. To monitor changes in uric acid concentration in the intestinal lumen, we developed a bioreporter using the uric acid responsive synthetic promoter, pucpro, and uric acid binding Bacillus subtilis PucR protein. Results demonstrated that the bioreporter module in commensal E. coli can detect changes in uric acid concentration in a dose-dependent manner. To eliminate the excess uric acid, we designed a uric acid degradation module, which overexpresses an E. coli uric acid transporter and a B. subtilis urate oxidase. Strains engineered with this module degraded all the uric acid (250 µM) found in the environment within 24 h, which is significantly lower (p < 0.001) compared to wild type E. coli. Finally, we designed an in vitro model using human intestinal cell line, Caco-2, which provided a versatile tool to study the uric acid transport and degradation in an environment mimicking the human intestinal tract. Results showed that engineered commensal E. coli reduced (p < 0.01) the apical uric acid concentration by 40.35% compared to wild type E. coli. This study shows that reprogramming E. coli holds promise as a valid alternative synthetic biology therapy to monitor and maintain healthy serum uric acid levels.
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Affiliation(s)
- Gozde Gencer
- Biological and Environmental Engineering Department, Cornell University, Ithaca, NY, United States
| | - Christopher Mancuso
- Biomedical Engineering Department, Boston University, Boston, MA, United States
| | - Koon Jiew Chua
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Lin School of Medicine and NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Hua Ling
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Lin School of Medicine and NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - Cait M. Costello
- Biological and Environmental Engineering Department, Cornell University, Ithaca, NY, United States
| | - Matthew Wook Chang
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Lin School of Medicine and NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, Singapore
| | - John C. March
- Biological and Environmental Engineering Department, Cornell University, Ithaca, NY, United States
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47
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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: 15] [Impact Index Per Article: 15.0] [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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48
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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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49
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Synthetic biology-inspired cell engineering in diagnosis, treatment, and drug development. Signal Transduct Target Ther 2023; 8:112. [PMID: 36906608 PMCID: PMC10007681 DOI: 10.1038/s41392-023-01375-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 03/13/2023] Open
Abstract
The fast-developing synthetic biology (SB) has provided many genetic tools to reprogram and engineer cells for improved performance, novel functions, and diverse applications. Such cell engineering resources can play a critical role in the research and development of novel therapeutics. However, there are certain limitations and challenges in applying genetically engineered cells in clinical practice. This literature review updates the recent advances in biomedical applications, including diagnosis, treatment, and drug development, of SB-inspired cell engineering. It describes technologies and relevant examples in a clinical and experimental setup that may significantly impact the biomedicine field. At last, this review concludes the results with future directions to optimize the performances of synthetic gene circuits to regulate the therapeutic activities of cell-based tools in specific diseases.
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50
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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 Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Wei Tang
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China
| | - Ling Huang
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Wei Zhou
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Shaojia Huang
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Linxuan Zou
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Lisha Yuan
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences Beijing China
| | - Dong Men
- State Key Laboratory of Virology Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China
| | - Shiyun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China
| | - Yangbo Hu
- State Key Laboratory of Virology Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan China.,Hubei Jiangxia Laboratory Wuhan China
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