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Zaragoza N, Anderson GI, Allison-Logan S, Monir K, Furst AL. Novel delivery systems for controlled release of bacterial therapeutics. Trends Biotechnol 2024; 42:929-937. [PMID: 38310020 DOI: 10.1016/j.tibtech.2024.01.002] [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: 11/13/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
As more is learned about the benefits of microbes, their potential to prevent and treat disease is expanding. Microbial therapeutics are less burdensome and costly to produce than traditional molecular drugs, often with superior efficacy. Yet, as with most medicines, controlled dosing and delivery to the area of need remain key challenges for microbes. Advances in materials to control small-molecule delivery are expected to translate to microbes, enabling similar control with equivalent benefits. In this perspective, recent advances in living biotherapeutics are discussed within the context of new methods for their controlled release. The integration of these advances provides a roadmap for the design, synthesis, and analysis of controlled microbial therapeutic delivery systems.
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Affiliation(s)
- Nadia Zaragoza
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grace I Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stephanie Allison-Logan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kirmina Monir
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ariel L Furst
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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2
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Li Z, Xiong W, Liang Z, Wang J, Zeng Z, Kołat D, Li X, Zhou D, Xu X, Zhao L. Critical role of the gut microbiota in immune responses and cancer immunotherapy. J Hematol Oncol 2024; 17:33. [PMID: 38745196 PMCID: PMC11094969 DOI: 10.1186/s13045-024-01541-w] [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: 10/25/2023] [Accepted: 04/03/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiota plays a critical role in the progression of human diseases, especially cancer. In recent decades, there has been accumulating evidence of the connections between the gut microbiota and cancer immunotherapy. Therefore, understanding the functional role of the gut microbiota in regulating immune responses to cancer immunotherapy is crucial for developing precision medicine. In this review, we extract insights from state-of-the-art research to decipher the complicated crosstalk among the gut microbiota, the systemic immune system, and immunotherapy in the context of cancer. Additionally, as the gut microbiota can account for immune-related adverse events, we discuss potential interventions to minimize these adverse effects and discuss the clinical application of five microbiota-targeted strategies that precisely increase the efficacy of cancer immunotherapy. Finally, as the gut microbiota holds promising potential as a target for precision cancer immunotherapeutics, we summarize current challenges and provide a general outlook on future directions in this field.
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Affiliation(s)
- Zehua Li
- Department of Plastic and Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
- Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, England
| | - Weixi Xiong
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Institute of Brain Science and Brain-Inspired Technology of West China Hospital, Sichuan University, Chengdu, China
| | - Zhu Liang
- Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, England
- Target Discovery Institute, Center for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, England
| | - Jinyu Wang
- Departments of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Ziyi Zeng
- Department of Neonatology, West China Second University Hospital of Sichuan University, Chengdu, China
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, Lodz, Poland
- Department of Biomedicine and Experimental Surgery, Medical University of Lodz, Lodz, Poland
| | - Xi Li
- Department of Urology, Churchill Hospital, Oxford University Hospitals NHS Foundation, Oxford, UK
| | - Dong Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Institute of Brain Science and Brain-Inspired Technology of West China Hospital, Sichuan University, Chengdu, China
| | - Xuewen Xu
- Department of Plastic and Burn Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Linyong Zhao
- Department of General Surgery and Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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3
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Wu YQ, Zou ZP, Zhou Y, Ye BC. Dual engineered bacteria improve inflammatory bowel disease in mice. Appl Microbiol Biotechnol 2024; 108:333. [PMID: 38739270 DOI: 10.1007/s00253-024-13163-w] [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: 08/09/2023] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/14/2024]
Abstract
Currently, there are many different therapies available for inflammatory bowel disease (IBD), including engineered live bacterial therapeutics. However, most of these studies focus on producing a single therapeutic drug using individual bacteria, which may cause inefficacy. The use of dual drugs can enhance therapeutic effects. However, expressing multiple therapeutic drugs in one bacterial chassis increases the burden on the bacterium and hinders good secretion and expression. Therefore, a dual-bacterial, dual-drug expression system allows for the introduction of two probiotic chassis and enhances both therapeutic and probiotic effects. In this study, we constructed a dual bacterial system to simultaneously neutralize pro-inflammatory factors and enhance the anti-inflammatory pathway. These bacteria for therapy consist of Escherichia coli Nissle 1917 that expressed and secreted anti-TNF-α nanobody and IL-10, respectively. The oral administration of genetically engineered bacteria led to a decrease in inflammatory cell infiltration in colon and a reduction in the levels of pro-inflammatory cytokines. Additionally, the administration of engineered bacteria did not markedly aggravate gut fibrosis and had a moderating effect on intestinal microbes. This system proposes a dual-engineered bacterial drug combination treatment therapy for inflammatory bowel disease, which provides a new approach to intervene and treat IBD. KEY POINTS: • The paper discusses the effects of using dual engineered bacteria on IBD • Prospects of engineered bacteria in the clinical treatment of IBD.
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Affiliation(s)
- Yong-Qi Wu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Zhen-Ping Zou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ying Zhou
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China.
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4
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Roux AE, Langella P, Martin R. Overview on biotics development. Curr Opin Biotechnol 2024; 86:103073. [PMID: 38335705 DOI: 10.1016/j.copbio.2024.103073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024]
Abstract
Although probiotics have been used in food products and supplements for decades, there has been a considerable increase in their use more recently. Recent technological advances have thus led to major advances in knowledge of the gut microbiota, enabling a significant development of biotics. In this review, we discuss the uses of traditional probiotics but also the discovery of next-generation probiotics that could be used as live biotherapeutics. These novel preventive and therapeutic strategies hold promise for the treatment of numerous diseases such as inflammatory bowel diseases such as Crohn's disease and ulcerative colitis. Probiotic bacteria can be consumed alone, or in combination with prebiotics as synbiotics, or mixed with other probiotic strains to form a consortium for enhanced effects. We also discuss the benefits of using postbiotics.
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Affiliation(s)
- Anne-Emmanuelle Roux
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Philippe Langella
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Rebeca Martin
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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Zhou T, Wu J, Tang H, Liu D, Jeon BH, Jin W, Wang Y, Zheng Y, Khan A, Han H, Li X. Enhancing tumor-specific recognition of programmable synthetic bacterial consortium for precision therapy of colorectal cancer. NPJ Biofilms Microbiomes 2024; 10:6. [PMID: 38245564 PMCID: PMC10799920 DOI: 10.1038/s41522-024-00479-8] [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: 08/01/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024] Open
Abstract
Probiotics hold promise as a potential therapy for colorectal cancer (CRC), but encounter obstacles related to tumor specificity, drug penetration, and dosage adjustability. In this study, genetic circuits based on the E. coli Nissle 1917 (EcN) chassis were developed to sense indicators of tumor microenvironment and control the expression of therapeutic payloads. Integration of XOR gate amplify gene switch into EcN biosensors resulted in a 1.8-2.3-fold increase in signal output, as confirmed by mathematical model fitting. Co-culturing programmable EcNs with CRC cells demonstrated a significant reduction in cellular viability ranging from 30% to 50%. This approach was further validated in a mouse subcutaneous tumor model, revealing 47%-52% inhibition of tumor growth upon administration of therapeutic strains. Additionally, in a mouse tumorigenesis model induced by AOM and DSS, the use of synthetic bacterial consortium (SynCon) equipped with multiple sensing modules led to approximately 1.2-fold increased colon length and 2.4-fold decreased polyp count. Gut microbiota analysis suggested that SynCon maintained the abundance of butyrate-producing bacteria Lactobacillaceae NK4A136, whereas reducing the level of gut inflammation-related bacteria Bacteroides. Taken together, engineered EcNs confer the advantage of specific recognition of CRC, while SynCon serves to augment the synergistic effect of this approach.
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Affiliation(s)
- Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jingyuan Wu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Haibo Tang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, Korea
| | - Weilin Jin
- Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yiqing Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | | | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Huawen Han
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, China.
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China.
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Kumbhare SV, Pedroso I, Ugalde JA, Márquez-Miranda V, Sinha R, Almonacid DE. Drug and gut microbe relationships: Moving beyond antibiotics. Drug Discov Today 2023; 28:103797. [PMID: 37806386 DOI: 10.1016/j.drudis.2023.103797] [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: 05/17/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
Our understanding of drug-microbe relationships has evolved from viewing microbes as mere drug producers to a dynamic, modifiable system where they can serve as drugs or targets of precision pharmacology. This review highlights recent findings on the gut microbiome, particularly focusing on four aspects of research: (i) drugs for bugs, covering recent strategies for targeting gut pathogens; (ii) bugs as drugs, including probiotics; (iii) drugs from bugs, including postbiotics; and (iv) bugs and drugs, discussing additional types of drug-microbe interactions. This review provides a perspective on future translational research, including efficient companion diagnostics in pharmaceutical interventions.
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Affiliation(s)
| | | | - Juan A Ugalde
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
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Effendi SSW, Ng IS. Prospective and challenges of live bacterial therapeutics from a superhero Escherichia coli Nissle 1917. Crit Rev Microbiol 2023; 49:611-627. [PMID: 35947523 DOI: 10.1080/1040841x.2022.2109405] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/02/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022]
Abstract
Escherichia coli Nissle 1917 (EcN), the active component of Mutaflor(R), is a notable probiotic from Gram-negative to treat Crohn's disease and irritable bowel syndrome. Therefore, a comprehensive genomic database maximizes the systemic probiotic assessment to discover EcN's role in human health. Recently, advanced synthetic and genetic tools have opened up a rich area to execute EcN as "living medicines" with controllable functions. Incorporating unique biomarkers allows the engineered EcN to switch genes on and off in response to environmental cues. Since EcN holds promise as a safe nature vehicle, more studies are desired to fully realize a wide range of probiotic potential for disease treatment. This review aims to deliver a historical origin of EcN, discuss the recent promising genetic toolbox in the rational design of probiotics, and pinpoint the clinical translation and evaluation of engineered EcN in vitro and in vivo. The summary of safety concerns, strategies of biotherapeutics development, and the challenges and prospects of engineered EcN is also concluded.
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
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8
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Hu S, Fei M, Fu B, Yu M, Yuan P, Tang B, Yang H, Sun D. Development of probiotic E. coli Nissle 1917 for β-alanine production by using protein and metabolic engineering. Appl Microbiol Biotechnol 2023; 107:2277-2288. [PMID: 36929190 DOI: 10.1007/s00253-023-12477-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023]
Abstract
β-alanine has been used in food and pharmaceutical industries. Although Escherichia coli Nissle 1917 (EcN) is generally considered safe and engineered as living therapeutics, engineering EcN for producing industrial metabolites has rarely been explored. Here, by protein and metabolic engineering, EcN was engineered for producing β-alanine from glucose. First, an aspartate-α-decarboxylase variant ADCK43Y with improved activity was identified and over-expressed in EcN, promoting the titer of β-alanine from an undetectable level to 0.46 g/L. Second, directing the metabolic flux towards L-aspartate increased the titer of β-alanine to 0.92 g/L. Third, the yield of β-alanine was elevated to 1.19 g/L by blocking conversion of phosphoenolpyruvate to pyruvate, and further increased to 2.14 g/L through optimizing culture medium. Finally, the engineered EcN produced 11.9 g/L β-alanine in fed-batch fermentation. Our work not only shows the potential of EcN as a valuable industrial platform, but also facilitates production of β-alanine via fermentation. KEY POINTS: • Escherichia coli Nissle 1917 (EcN) was engineered as a β-alanine producing cell factory • Identification of a decarboxylase variant ADCK43Y with improved activity • Directing the metabolic flux to L-ASP and expressing ADCK43Y elevated the titer of β-alanine to 11.9 g/L.
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Affiliation(s)
- Shilong Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Mingyue Fei
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Beibei Fu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Mingjing Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Panhong Yuan
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, 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, 310014, Zhejiang, China.
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Rutter JW, Dekker L, Owen KA, Barnes CP. Microbiome engineering: engineered live biotherapeutic products for treating human disease. Front Bioeng Biotechnol 2022; 10:1000873. [PMID: 36185459 PMCID: PMC9523163 DOI: 10.3389/fbioe.2022.1000873] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
The human microbiota is implicated in many disease states, including neurological disorders, cancer, and inflammatory diseases. This potentially huge impact on human health has prompted the development of microbiome engineering methods, which attempt to adapt the composition and function of the human host-microbiota system for a therapeutic purpose. One promising method is the use of engineered microorganisms that have been modified to perform a therapeutic function. The majority of these products have only been demonstrated in laboratory models; however, in recent years more concepts have reached the translational stage. This has led to an increase in the number of clinical trials, which are designed to assess the safety and efficacy of these treatments in humans. Within this review, we highlight the progress of some of these microbiome engineering clinical studies, with a focus on engineered live biotherapeutic products.
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Affiliation(s)
- Jack W. Rutter
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
- *Correspondence: Jack W. Rutter,
| | - Linda Dekker
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
| | - Kimberley A. Owen
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
| | - Chris P. Barnes
- Department of Cell & Developmental Biology, University College London, London, United Kingdom
- Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
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Shi Y, Cui H, Wang F, Zhang Y, Xu Q, Liu D, Wang K, Hou S. Role of gut microbiota in postoperative complications and prognosis of gastrointestinal surgery: A narrative review. Medicine (Baltimore) 2022; 101:e29826. [PMID: 35866808 PMCID: PMC9302249 DOI: 10.1097/md.0000000000029826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Gastrointestinal surgery is often challenging because of unexpected postoperative complications such as pouchitis, malabsorption, anastomotic leak, diarrhea, inflammatory responses, and life-threatening infections. Moreover, the gut microbiota has been shown to be associated with the complications described above. Major intestinal reconstruction, such as Roux-en-Y gastric bypass (RYGB) and ileal pouch-anal anastomosis surgery, could result in altered gut microbiota, which might lead to some of the benefits of these procedures but could also contribute to the development of postsurgical complications. Moreover, postsurgical reestablishment of the gut microbiota population is still poorly understood. Here, we review evidence outlining the role of gut microbiota in complications of gastrointestinal surgery, especially malabsorption, anastomotic leak, pouchitis, and infections. In addition, this review will evaluate the risks and benefits of live biotherapeutics in the complications of gastrointestinal surgery.
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Affiliation(s)
- Yong Shi
- Department of General Surgery, Xuchang Central Hospital, Xuchang City, Henan Province, China
| | - Huxiao Cui
- Department of General Surgery, Xuchang Central Hospital, Xuchang City, Henan Province, China
| | - Fangjie Wang
- Department of General Surgery, Xuchang Central Hospital, Xuchang City, Henan Province, China
| | - Yanxia Zhang
- Department of General Surgery, Xuchang Central Hospital, Xuchang City, Henan Province, China
| | - Qingbin Xu
- Department of General Surgery, Xuchang Central Hospital, Xuchang City, Henan Province, China
| | - Dan Liu
- Department of General Surgery, Xuchang Central Hospital, Xuchang City, Henan Province, China
| | - Kunhui Wang
- Department of General Surgery, Xuchang Central Hospital, Xuchang City, Henan Province, China
| | - Sen Hou
- Department of General Surgery, Xuchang Central Hospital, Xuchang City, Henan Province, China
- *Correspondence: Sen Hou, Department of General Surgery, Xuchang Central Hospital, No. 30, Huatuo Road, Weidu District, Xuchang City, Henan Province, China (e-mail: )
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Construction of a sustainable 3-hydroxybutyrate-producing probiotic Escherichia coli for treatment of colitis. Cell Mol Immunol 2021; 18:2344-2357. [PMID: 34480146 PMCID: PMC8484604 DOI: 10.1038/s41423-021-00760-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/08/2021] [Indexed: 02/07/2023] Open
Abstract
Colitis is a common disease of the colon that is very difficult to treat. Probiotic bacteria could be an effective treatment. The probiotic Escherichia coli Nissle 1917 (EcN) was engineered to synthesize the ketone body (R)-3-hydroxybutyrate (3HB) for sustainable production in the gut lumen of mice suffering from colitis. Components of heterologous 3HB synthesis routes were constructed, expressed, optimized, and inserted into the EcN genome, combined with deletions in competitive branch pathways. The genome-engineered EcN produced the highest 3HB level of 0.6 g/L under microaerobic conditions. The live therapeutic was found to colonize the mouse gastrointestinal tract over 14 days, elevating gut 3HB and short-chain-length fatty acid (SCFA) levels 8.7- and 3.1-fold compared to those of wild-type EcN, respectively. The sustainable presence of 3HB in mouse guts promoted the growth of probiotic bacteria, especially Akkermansia spp., to over 31% from the initial 2% of all the microbiome. As a result, the engineered EcN termed EcNL4 ameliorated colitis induced via dextran sulfate sodium (DSS) in mice. Compared to wild-type EcN or oral administration of 3HB, oral EcNL4 uptake demonstrated better effects on mouse weights, colon lengths, occult blood levels, gut tissue myeloperoxidase activity and proinflammatory cytokine concentrations. Thus, a promising live bacterium was developed to improve colonic microenvironments and further treat colitis. This proof-of-concept design can be employed to treat other diseases of the colon.
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12
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Yang F, Zou Q, Gao B. GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed. Brief Bioinform 2021; 22:6123951. [PMID: 33515036 DOI: 10.1093/bib/bbaa436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/17/2020] [Accepted: 12/26/2020] [Indexed: 02/07/2023] Open
Abstract
The compositionality of the microbiome data is well-known but often neglected. The compositional transformation pertains to the supervised learning of microbiome data and is a critical step that decides the performance and reliability of the disease classifiers. We value the excellent performance of the distal discriminative balance analysis (DBA) method, which selects distal balances of pairs and trios of bacteria, in addressing the classification of high-dimensional microbiome data. By applying this method to the species-level abundances of all the disease phenotypes in the GMrepo database, we build a balance-based model repository for the classification of human gut microbiome-related diseases. The model repository supports the prediction of disease risks for new sample(s). More importantly, we highlight the concept of balance-disease associations rather than the conventional microbe-disease associations and develop the human Gut Balance-Disease Association Database (GBDAD). Each predictable balance for each disease model indicates a potential biomarker-disease relationship and can be interpreted as a bacteria ratio positively or negatively correlated with the disease. Furthermore, by linking the balance-disease associations to the evidenced microbe-disease associations in MicroPhenoDB, we surprisingly found that most species-disease associations inferred from the shotgun metagenomic datasets can be validated by external evidence beyond MicroPhenoDB. The balance-based species-disease association inference will accelerate the generation of new microbe-disease association hypotheses in gastrointestinal microecology research and clinical trials. The model repository and the GBDAD database are deployed on the GutBalance server, which supports interactive visualization and systematic interrogation of the disease models, disease-related balances and disease-related species of interest.
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Affiliation(s)
- Fenglong Yang
- University of Electronic Science and Technology of China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China
- Hainan Key Laboratory for Computational Science and Application, Hainan Normal University, Haikou 571158, China
| | - Bo Gao
- Department of Radiology, The Second Affiliated Hospital, Harbin Medical University, Harbin 150001, China
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