1
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Nagayama M, Gogokhia L, Longman RS. Precision microbiota therapy for IBD: premise and promise. Gut Microbes 2025; 17:2489067. [PMID: 40190259 PMCID: PMC11980506 DOI: 10.1080/19490976.2025.2489067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 12/19/2024] [Accepted: 03/28/2025] [Indexed: 04/11/2025] Open
Abstract
Inflammatory Bowel Disease (IBD) is a spectrum of chronic inflammatory diseases of the intestine that includes subtypes of ulcerative colitis (UC) and Crohn's Disease (CD) and currently has no cure. While IBD results from a complex interplay between genetic, environmental, and immunological factors, sequencing advances over the last 10-15 years revealed signature changes in gut microbiota that contribute to the pathogenesis of IBD. These findings highlight IBD as a disease target for microbiome-based therapies, with the potential to treat the underlying microbial pathogenesis and provide adjuvant therapy to the emerging spectrum of advanced therapies for IBD. Building on the success of fecal microbiota transplantation (FMT) for Clostridioides difficile infection, therapies targeting gut microbiota have emerged as promising approaches for treating IBD; however, unique aspects of IBD pathogenesis highlight the need for more precision in the approach to microbiome therapeutics that leverage aspects of recipient and donor selection, diet and xenobiotics, and strain-specific interactions to enhance the efficacy and safety of IBD therapy. This review focuses on both pre-clinical and clinical studies that support the premise for microbial therapeutics for IBD and aims to provide a framework for the development of precision microbiome therapeutics to optimize clinical outcomes for patients with IBD.
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Affiliation(s)
- Manabu Nagayama
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
- Jill Roberts Center for Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lasha Gogokhia
- Jill Roberts Center for Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Randy S. Longman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
- Jill Roberts Center for Inflammatory Bowel Disease, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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2
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Jiang S, Huang S, Zhang Z, Ma W, Han Z, Song Y, Huo D, Cui W, Zhang J. Gut microbiota drives structural variation of exogenous probiotics to enhance colonization. Gut Microbes 2025; 17:2503371. [PMID: 40349120 PMCID: PMC12068336 DOI: 10.1080/19490976.2025.2503371] [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] [Received: 02/25/2025] [Revised: 04/26/2025] [Accepted: 05/02/2025] [Indexed: 05/14/2025] Open
Abstract
Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic Lactiplantibacillus plantarum HNU082 (Lp082) to test whether Lp082 gut-adapted mutants can resolve colonization resistance in a new gut environment. Relying on culture-based methods and metagenomics, two distinct evolutionary clades of Lp082 in mice gut were observed, where one clade, which acquired more mutations, exhibited a longer survival time. However, these Lp082 isolates carrying many single nucleotide variants (SNVs) still exhibited phenotypic inconsistencies, with 13 strains of enhanced acid resistance. Thus, nanopore sequencing was proposed to identify structural variations (SVs). Among them, 12 strains had the Cro/C1-type HTH DNA-binding domain insertion, which enhanced growth and reproduction under bile salt stress, thereby increasing colonization time and quantity in the gut. The gut domestication process can drive probiotics to undergo many SNVs and SVs, thereby enhancing their colonization ability, which provides new insights into the colonization mechanisms and offers an ecology-based strategy.
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Affiliation(s)
- Shuaiming Jiang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, SAR, China
| | - Zeng Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Wenyao Ma
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Zhe Han
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Yuan Song
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Dongxue Huo
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Weipeng Cui
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
| | - Jiachao Zhang
- School of Food Science and Engineering, Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Hainan University, Haikou, China
- Collaborative Innovation Center of One Health, Hainan University, Haikou, Hainan, China
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3
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Yao J, Ning B, Ding J. The gut microbiota: an emerging modulator of drug resistance in hepatocellular carcinoma. Gut Microbes 2025; 17:2473504. [PMID: 40042184 PMCID: PMC11901387 DOI: 10.1080/19490976.2025.2473504] [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] [Received: 06/12/2024] [Revised: 11/08/2024] [Accepted: 02/21/2025] [Indexed: 03/14/2025] Open
Abstract
Liver cancer is usually diagnosed at an advanced stage and is the third most common cause of cancer-related death worldwide. In addition to the lack of effective treatment options, resistance to therapeutic drugs is a major clinical challenge. The gut microbiota has recently been recognized as one of the key factors regulating host health. The microbiota and its metabolites can directly or indirectly regulate gene expression in the liver, leading to gut-liver axis dysregulation, which is closely related to liver cancer occurrence and the treatment response. Gut microbiota disturbance may participate in tumor progression and drug resistance through metabolite production, gene transfer, immune regulation, and other mechanisms. However, systematic reviews on the role of the gut microbiota in drug resistance in liver cancer are lacking. Herein, we review the relationships between the gut microbiota and the occurrence and drug resistance of hepatocellular carcinoma, summarize the emerging mechanisms underlying gut microbiota-mediated drug resistance, and propose new personalized treatment options to overcome this resistance.
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Affiliation(s)
- Jiali Yao
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Beifang Ning
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
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4
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Lee J, McClure S, Weichselbaum RR, Mimee M. Designing live bacterial therapeutics for cancer. Adv Drug Deliv Rev 2025; 221:115579. [PMID: 40228606 PMCID: PMC12067981 DOI: 10.1016/j.addr.2025.115579] [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: 01/31/2025] [Revised: 03/26/2025] [Accepted: 04/09/2025] [Indexed: 04/16/2025]
Abstract
Humans are home to a diverse community of bacteria, many of which form symbiotic relationships with their host. Notably, tumors can also harbor their own unique bacterial populations that can influence tumor growth and progression. These bacteria, which selectively colonize hypoxic and acidic tumor microenvironments, present a novel therapeutic strategy to combat cancer. Advancements in synthetic biology enable us to safely and efficiently program therapeutic drug production in bacteria, further enhancing their potential. This review provides a comprehensive guide to utilizing bacteria for cancer treatment. We discuss key considerations for selecting bacterial strains, emphasizing their colonization efficiency, the delicate balance between safety and anti-tumor efficacy, and the availability of tools for genetic engineering. We also delve into strategies for precise spatiotemporal control of drug delivery to minimize adverse effects and maximize therapeutic impact, exploring recent examples of engineered bacteria designed to combat tumors. Finally, we address the underlying challenges and future prospects of bacterial cancer therapy. This review underscores the versatility of bacterial therapies and outlines strategies to fully harness their potential in the fight against cancer.
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Affiliation(s)
- Jaehyun Lee
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Sandra McClure
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchoissois Family Institute, University of Chicago, Chicago, IL 60637, USA; Committee On Molecular Metabolism and Nutrition, University of Chicago, Chicago, IL 60637, USA
| | - Ralph R Weichselbaum
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago 60637, USA; The Ludwig Center for Metastasis Research, University of Chicago, Chicago 60637, USA
| | - Mark Mimee
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchoissois Family Institute, University of Chicago, Chicago, IL 60637, USA; Committee On Molecular Metabolism and Nutrition, University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA.
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5
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Zhang Z, Kong APS, Wong VWS, Hui HX. Intermittent fasting and metabolic dysfunction-associated steatotic liver disease: the potential role of the gut-liver axis. Cell Biosci 2025; 15:64. [PMID: 40410852 PMCID: PMC12102857 DOI: 10.1186/s13578-025-01406-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2025] [Accepted: 05/05/2025] [Indexed: 05/25/2025] Open
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing public health concern linked to the increasing prevalence of metabolic syndrome, including obesity and type 2 diabetes (T2D). MASLD remains a significant clinical challenge due to the absence of effective therapeutic interventions. Intermittent fasting (IF) has emerged as a promising non-pharmacological strategy for managing MASLD. Although the exact mechanisms underpinning the possible beneficial effects of IF on MASLD are not yet fully elucidated, the gut microbiota and its metabolic byproducts are increasingly recognized as potential mediators of these effects. The gut-liver axis may act as an important conduit through which IF exerts its beneficial influence on hepatic function. This review comprehensively examines the impact of various IF protocols on gut microbiota composition, investigating the resultant alterations in microbial diversity and metabolomic profiles, and their potential implications for liver health and the improvement of MASLD.
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Affiliation(s)
- Zhaoxi Zhang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Alice Pik-Shan Kong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Vincent Wai-Sun Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hannah Xiaoyan Hui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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6
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Liu D, Ton PM, Zong D, Zarrinpar A, Ding Y. Expression of Fluorescence Reporters and Natural Products in Native Gut Escherichia coli. ACS Synth Biol 2025; 14:1557-1566. [PMID: 40138712 DOI: 10.1021/acssynbio.4c00835] [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: 03/29/2025]
Abstract
Escherichia coli is a widely studied model organism and an integral component of the human gut microbiome, offering significant potential for bacteria-based therapeutic applications. Despite this promise, engineering native E. coli strains remains challenging. In this study, we employed the chassis-independent recombinase-assisted genome engineering (CRAGE) technique to genetically engineer the native gut strain E. coli EcAZ-1 and the probiotic strain E. coli Nissle 1917 (EcN). We successfully expressed a suite of heterologous genes, including the bioluminescent lux operon, green fluorescent protein (GFP), and oxygen-independent fluorescent protein IFP2.0, in both strains. Optimization of IFP2.0 fluorescence was achieved under both aerobic and anaerobic conditions by coexpressing a heme oxygenase gene and/or supplementing the chromophore biliverdin or hemin. Additionally, we engineered these strains to biosynthesize the bioactive compounds naringenin and mycosporine-like amino acids. This work highlights the potential of native E. coli strains as versatile platforms for synthetic biology, paving the way for innovative applications in biomedical research and therapeutic development.
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Affiliation(s)
- Dake Liu
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - Phuong M Ton
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
| | - David Zong
- Division of Gastroenterology, University of California, San Diego, La Jolla, California 92093, United States
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, California 92093, United States
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California 92093, United States
- Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, California 92093, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, Florida 32610, United States
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7
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Fields BD, Pascal DG, Rando OK, Huddleston ME, Ingram K, Hopton R, Grogg MW, Nelson MT, Voigt CA. Design of a Continuous GAA-Producing Probiotic as a Potential Mitigator of the Effects of Sleep Deprivation. ACS Synth Biol 2025. [PMID: 40378286 DOI: 10.1021/acssynbio.4c00690] [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: 05/18/2025]
Abstract
Creatine is a popular athletic supplement that has also been shown to improve cognitive performance upon sleep deprivation. However, it is rapidly cleared from the gastrointestinal tract a few hours after consumption. Toward providing a persistent creatine dose, we engineered the human probiotic Escherichia coli Nissle (EcN) to produce guanidinoacetic acid (GAA), which is converted to creatine in the liver. We find GAA-producing enzymes present in the human microbiome and compare their activities to known enzymes. Three copies of arginine:glycine amidinotransferase (AGAT) from Actinokineospora terrae are expressed from the genome, and native gcvP, argR, and argA are edited or deleted to improve substrate availability without negatively impacting cell viability. A standard EcN dose (1012 cells) produces 41 ± 7 mg GAA per hour under laboratory conditions. This work demonstrates that a probiotic bacterium can be engineered to produce sustained GAA titers known to impact cognitive performance.
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Affiliation(s)
- Brandon D Fields
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel G Pascal
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Olivia K Rando
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mary E Huddleston
- Blue Halo Inc., 4401 Dayton-Xenia Rd, Dayton, Ohio 45432, United States
| | - Katherine Ingram
- Blue Halo Inc., 4401 Dayton-Xenia Rd, Dayton, Ohio 45432, United States
| | - Rachel Hopton
- Blue Halo Inc., 4401 Dayton-Xenia Rd, Dayton, Ohio 45432, United States
| | - Matthew W Grogg
- United States Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson AFB, Ohio 45433, United States
| | - M Tyler Nelson
- United States Air Force Research Laboratory, 711th Human Performance Wing, Wright-Patterson AFB, Ohio 45433, United States
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Dang S, Zhang X, Zhang Y, Zhang H. New thoughts on the intestinal microbiome-B cell-IgA axis and therapies in IgA nephropathy. Autoimmun Rev 2025; 24:103835. [PMID: 40360014 DOI: 10.1016/j.autrev.2025.103835] [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: 03/21/2025] [Revised: 05/08/2025] [Accepted: 05/08/2025] [Indexed: 05/15/2025]
Abstract
IgA nephropathy (IgAN), as the most common chronic glomerulonephritis worldwide, is often triggered by mucosal infections and follows a chronic progression, with the majority of patients ultimately progressing to end-stage renal disease (ESRD) during their lifetimes. Since the mystery of its complete pathogenesis has not been fully solved, the resulting lack of effective early diagnosis and treatment greatly affects the prognosis of patients. Given the well-defined pathological feature of IgA deposition in the mesangial region, the source and role of pathogenic IgA has been focused on. Starting from the microbiology and immunity of the gut, we systematically review both the physiological and the pathological process of microbiome-B cell-IgA axis, from microbial-induced IgA production to the role of IgA in the intestinal immune milieu, and ultimately end up with the various aspects of microbiome-B cell-IgA axis in the pathogenesis of IgAN as well as the corresponding therapeutic initiatives available. Our retrospective review helps researchers to systematically understand the complex role between intestinal flora dysbiosis and pathogenic IgA in IgAN. This understanding provides a foundation for in-depth explorations to uncover more detailed pathogenic mechanisms and to develop more precise and effective diagnostic and therapeutic approaches.
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Affiliation(s)
- Shaoqing Dang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China; Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangyu Zhang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China; Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China.
| | - Yuemiao Zhang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China; Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China.
| | - Hong Zhang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China; Institute of Nephrology, Peking University, Beijing, China; Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China; Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China.
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9
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Liu M, Blattman SB, Takahashi M, Mandayam N, Jiang W, Oikonomou P, Tavazoie SF, Tavazoie S. Conserved genetic basis for microbial colonization of the gut. Cell 2025; 188:2505-2520.e22. [PMID: 40187346 PMCID: PMC12048274 DOI: 10.1016/j.cell.2025.03.010] [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: 08/26/2024] [Revised: 12/02/2024] [Accepted: 03/06/2025] [Indexed: 04/07/2025]
Abstract
Despite the fundamental importance of gut microbes, the genetic basis of their colonization remains largely unexplored. Here, by applying cross-species genotype-habitat association at the tree-of-life scale, we identify conserved microbial gene modules associated with gut colonization. Across thousands of species, we discovered 79 taxonomically diverse putative colonization factors organized into operonic and non-operonic modules. They include previously characterized colonization pathways such as autoinducer-2 biosynthesis and novel processes including tRNA modification and translation. In vivo functional validation revealed YigZ (IMPACT family) and tRNA hydroxylation protein-P (TrhP) are required for E. coli intestinal colonization. Overexpressing YigZ alone is sufficient to enhance colonization of the poorly colonizing MG1655 E. coli by >100-fold. Moreover, natural allelic variations in YigZ impact inter-strain colonization efficiency. Our findings highlight the power of large-scale comparative genomics in revealing the genetic basis of microbial adaptations. These broadly conserved colonization factors may prove critical for understanding gastrointestinal (GI) dysbiosis and developing therapeutics.
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Affiliation(s)
- Menghan Liu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Sydney B Blattman
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Mai Takahashi
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Nandan Mandayam
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenyan Jiang
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Panos Oikonomou
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Saeed Tavazoie
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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10
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Park S, Jung S, Lee G, Lee E, Black R, Hong J, Jeong S. Self-Nourishing and Armored Probiotics via Egg-Inspired Encapsulation. Adv Healthc Mater 2025; 14:e2405219. [PMID: 40103525 PMCID: PMC12031648 DOI: 10.1002/adhm.202405219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 02/24/2025] [Indexed: 03/20/2025]
Abstract
The gut microbiota plays an essential role in regulating overall physiology, including metabolism and neurological and immune functions. Therefore, their dysregulation is closely associated with metabolic disorders, such as obesity and diabetes, as well as other pathological conditions, including inflammatory bowel diseases, cancer, and neurological disorders. Probiotics are commonly used to maintain a healthy gut microbiome, but their oral delivery is inefficient mainly due to their poor stability in the harsh gastrointestinal (GI) environment. This work presents an innovative encapsulation strategy, inspired by the natural structure of an egg, for the effective oral delivery of probiotics, termed PIE (Probiotics-In-Egg). The PIE technology is based upon encapsulating probiotics with phosvitin and ovalbumin derived from egg yolk and egg white, respectively. PIE exhibits significantly enhanced survival and proliferation in a simulated GI tract, as well as the ability to neutralize harmful reactive oxygen species (ROS) and sustain in nutrient-depleted conditions. Moreover, when administered orally in mouse models, PIE demonstrates excellent bioavailability and enhanced colonization in the GI tract. This egg-inspired encapsulation technology has great potential as a practical and effective platform for oral delivery of probiotics, which can significantly help maintain a healthy gut microbiome.
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Affiliation(s)
- Sohyeon Park
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sungwon Jung
- Department of Chemical & Biomolecular Engineering, College of Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Geonhui Lee
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Erin Lee
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rodger Black
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jinkee Hong
- Department of Chemical & Biomolecular Engineering, College of Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sangmoo Jeong
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
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11
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Gurung B, Courreges MC, Pollak J, Malgor R, Jiang L, Wang B, Wang S. Non-invasive treatment of Clostridioides difficile infection with a human-origin probiotic cocktail through gut microbiome-gut metabolome modulations. Front Microbiol 2025; 16:1555220. [PMID: 40078549 PMCID: PMC11897039 DOI: 10.3389/fmicb.2025.1555220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Accepted: 02/10/2025] [Indexed: 03/14/2025] Open
Abstract
Clostridioides difficile (C. difficile) is a leading cause of hospital-associated diarrhea, primarily due to gut dysbiosis following antibiotic use. Probiotics have been found to provide several benefits to hosts via modulation of the gut microbiota and their metabolites. However, till now, no conventional probiotics have been clearly proven to be an effective prophylactic option for CDI prevention. Therefore, more studies on developing specific probiotic candidates targeting CDI and improving diversity of probiotics administrated are needed. In this study, a human-origin highly diverse and highly targeted probiotic cocktail (Pro11) containing 11 various probiotic species was developed against C. difficile. Pro11 protected mice against CDI with lower clinical scores and higher survival rates, and inhibited C. difficile in vivo with less C. difficile burden and toxins production determined in colon. Histological analysis demonstrated that Pro11 strengthened gut barrier, reducing gut permeability (less secreted sCD14 in serum) and gut inflammation. In addition, gut microbiome analysis demonstrated that Pro11 increased gut microbiome diversity and beneficial species. Along with gut microbiome modulation, gut metabolites including butyrate, were significantly increased in the probiotics-fed group. Results from this study highlighted probiotics as a promising CDI therapy as gut microbiota modulators, which will lay the foundation for translating probiotics in mitigating CDI and other intestinal pathogens for clinical use.
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Affiliation(s)
- Bijay Gurung
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States
- Infectious and Tropical Disease Institute, Ohio University, Athens, OH, United States
| | - Maria C. Courreges
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States
| | - Julie Pollak
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, Melbourne, FL, United States
| | - Ramiro Malgor
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States
| | - Lin Jiang
- Division of Natural Sciences, New College of Florida, Sarasota, FL, United States
| | - Bo Wang
- Department of Chemistry and Chemical Engineering, Florida Institute of Technology, Melbourne, FL, United States
| | - Shaohua Wang
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, OH, United States
- Infectious and Tropical Disease Institute, Ohio University, Athens, OH, United States
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12
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Wang K, Yuan B, Zhang F, Li Z, Jia X, Hu Y, Chen Z, Hong J, Du L, Jin Y. A bioadhesive antioxidase-overexpressed probiotic prevents radiation enteritis by scavenging the excess reactive oxygen species. Free Radic Biol Med 2025; 227:485-498. [PMID: 39643134 DOI: 10.1016/j.freeradbiomed.2024.12.013] [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: 10/09/2024] [Revised: 11/26/2024] [Accepted: 12/03/2024] [Indexed: 12/09/2024]
Abstract
The scavenging of the excess reactive oxygen species (ROS) induced by radiation is fundamental for radiation protection. However, directly applying antioxidants results in low bioavailability and side effects. Superoxide dismutase (SOD) and catalase (CAT) have high ROS clearance efficiency, whereas their application is limited by the enzyme inactivation, making it difficult to exhibit significant therapeutic effects. Here, we engineered a probiotic Escherichia coli Nissle 1917 (EcN), i.e., AAEcN, serving as a SOD/CAT vehicle to scavenge ROS for the prevention and treatment of radiation enteritis (RE). The overexpressed Drsod and katE in AAEcN showed 5-fold ROS elimination efficiency compared to the wild EcN. Furthermore, the intestinal retention time of engineered EcN was prolonged through trefoil factor 3 gene (TFF3) modification of curli fibers on the bacterial surface, which contributed to the persistence of antioxidant enzyme activity. We found that AAEcN rapidly eliminated the intracellular ROS induced by radiation. Only a single oral dosing of AAEcN was satisfied to alleviate the radiation damage to the small intestine, colon, and spleen. Moreover, the homeostasis of pro-/anti-inflammatory cytokines was realized. The proliferation of the intestinal stem cells and spleen hematopoietic stem cells was enhanced, while the apoptosis of mucosal cells was inhibited. Our findings suggest valuable insights into the ROS scavenging way in RE, and establish an empirical basis for developing probiotics as an antioxidant enzyme vehicle for the bacteriotherapy of RE.
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Affiliation(s)
- Ke Wang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China; School of Pharmacy, Henan University, Kaifeng, 475004, China
| | - Bochuan Yuan
- Beijing Institute of Radiation Medicine, Beijing, 100850, China.
| | - Feng Zhang
- Beijing Institute of Radiation Medicine, Beijing, 100850, China; School of Pharmacy, Henan University, Kaifeng, 475004, China
| | - Zhangyu Li
- Beijing Institute of Radiation Medicine, Beijing, 100850, China; School of Pharmacy, Henan University, Kaifeng, 475004, China
| | - Xueli Jia
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yadan Hu
- Beijing Institute of Radiation Medicine, Beijing, 100850, China; School of Pharmacy, Henan University, Kaifeng, 475004, China
| | - Ziyuan Chen
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Jinyun Hong
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Lina Du
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | - Yiguang Jin
- Beijing Institute of Radiation Medicine, Beijing, 100850, China.
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13
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Siguenza N, Bailey S, Sadegi M, Gootin H, Tiu M, Price JD, Ramer-Tait A, Zarrinpar A. Gut Competition Dynamics of Live Bacterial Therapeutics Are Shaped by Microbiome Complexity, Diet, and Therapeutic Transgenes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.21.634159. [PMID: 39896492 PMCID: PMC11785071 DOI: 10.1101/2025.01.21.634159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
Abstract
Competitive exclusion is conventionally believed to prevent the establishment of a secondary strain of the same bacterial species in the gut microbiome, raising concerns for the deployment of live bacterial therapeutics (LBTs), especially if the bacterial chassis is a strain native to the gut. In this study, we investigated factors influencing competition dynamics in the murine gut using isogenic native Escherichia coli strains. We found that competition outcomes are context-dependent, modulated by microbiome complexity, LBT transgene expression, intestinal inflammation, and host diet. Furthermore, we demonstrated that native LBTs can establish long-term engraftment in the gut alongside a parental strain, with transgene-associated fitness effects influencing competition. We identified various interventions, including strategic dosing and dietary modulation, that significantly enhanced LBT colonization levels by 2 to 3 orders of magnitude. These insights provide a framework for optimizing LBT engraftment and efficacy, supporting their potential translation for human therapeutic applications.
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Affiliation(s)
- Nicole Siguenza
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Sharyl Bailey
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Mohammad Sadegi
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Hanna Gootin
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Maria Tiu
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
| | - Jeffrey D. Price
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amanda Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Amir Zarrinpar
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA
- Division of Gastroenterology, Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, CA, USA
- The Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA, USA
- Institute of Diabetes and Metabolic Health, University of California San Diego, La Jolla, CA, USA
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14
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Jin K, Huang Y, Che H, Wu Y. Engineered Bacteria for Disease Diagnosis and Treatment Using Synthetic Biology. Microb Biotechnol 2025; 18:e70080. [PMID: 39801378 PMCID: PMC11725985 DOI: 10.1111/1751-7915.70080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 12/18/2024] [Accepted: 12/26/2024] [Indexed: 01/16/2025] Open
Abstract
Using synthetic biology techniques, bacteria have been engineered to serve as microrobots for diagnosing diseases and delivering treatments. These engineered bacteria can be used individually or in combination as microbial consortia. The components within these consortia complement each other, enhancing diagnostic accuracy and providing synergistic effects that improve treatment efficacy. The application of microbial therapies in cancer, intestinal diseases, and metabolic disorders underscores their significant potential. The impact of these therapies on the host's native microbiota is crucial, as engineered microbes can modulate and interact with the host's microbial environment, influencing treatment outcomes and overall health. Despite numerous advancements, challenges remain. These include ensuring the long-term survival and safety of bacteria, developing new chassis microbes and gene editing techniques for non-model strains, minimising potential toxicity, and understanding bacterial interactions with the host microbiota. This mini-review examines the current state of engineered bacteria and microbial consortia in disease diagnosis and treatment, highlighting advancements, challenges, and future directions in this promising field.
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Affiliation(s)
- Kai Jin
- Department of Environmental and Chemical EngineeringShanghai UniversityShanghaiChina
| | - Yi Huang
- Department of Environmental and Chemical EngineeringShanghai UniversityShanghaiChina
| | - Hailong Che
- Department of Environmental and Chemical EngineeringShanghai UniversityShanghaiChina
| | - Yihan Wu
- Department of Environmental and Chemical EngineeringShanghai UniversityShanghaiChina
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15
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Vazquez-Uribe R, Hedin KA, Licht TR, Nieuwdorp M, Sommer MOA. Advanced microbiome therapeutics as a novel modality for oral delivery of peptides to manage metabolic diseases. Trends Endocrinol Metab 2025; 36:29-41. [PMID: 38782649 DOI: 10.1016/j.tem.2024.04.021] [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: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The rising prevalence of metabolic diseases calls for innovative treatments. Peptide-based drugs have transformed the management of conditions such as obesity and type 2 diabetes. Yet, challenges persist in oral delivery of these peptides. This review explores the potential of 'advanced microbiome therapeutics' (AMTs), which involve engineered microbes for delivery of peptides in situ, thereby enhancing their bioavailability. Preclinical work on AMTs has shown promise in treating animal models of metabolic diseases, including obesity, type 2 diabetes, and metabolic dysfunction-associated steatotic liver disease. Outstanding challenges toward realizing the potential of AMTs involve improving peptide expression, ensuring predictable colonization control, enhancing stability, and managing safety and biocontainment concerns. Still, AMTs have potential for revolutionizing the treatment of metabolic diseases, potentially offering dynamic and personalized novel therapeutic approaches.
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Affiliation(s)
- Ruben Vazquez-Uribe
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Karl Alex Hedin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Max Nieuwdorp
- Departments of Internal and Experimental Vascular Medicine, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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16
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Zou ZP, Zhang XP, Zhang Q, Yin BC, Zhou Y, Ye BC. Genetically engineered bacteria as inflammatory bowel disease therapeutics. ENGINEERING MICROBIOLOGY 2024; 4:100167. [PMID: 39628589 PMCID: PMC11611042 DOI: 10.1016/j.engmic.2024.100167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/24/2024] [Accepted: 08/26/2024] [Indexed: 12/06/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic and recurrent disease caused by immune response disorders that disrupt the intestinal lumen symbiotic ecosystem and dysregulate mucosal immune functions. Current therapies available for IBD primarily focus on symptom management, making early diagnosis and prompt intervention challenging. The development of genetically engineered bacteria using synthetic biology presents a new strategy for addressing these challenges. In this review, we present recent breakthroughs in the field of engineered bacteria for the treatment and detection of IBD and describe how bacteria can be genetically modified to produce therapeutic molecules or execute diagnostic functions. In particular, we discuss the challenges faced in translating live bacterial therapeutics from bacterial design to delivery strategies for further clinical applications.
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Affiliation(s)
| | | | - Qian Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Bin-Cheng Yin
- 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
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17
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Minami A, Asai T, Tachibana T, Tanaka Y, Nakajima M, Tamura S, Nakazawa M, Tsuru Y, Fujiyama Y, Tagawa YI, Kuzuyama T, Kakuta S, Ogawa T. Establishment of the improved colonization of Escherichia coli laboratory strain in the intestine mediated by single gene deletion. Biochem Biophys Res Commun 2024; 734:150448. [PMID: 39094368 DOI: 10.1016/j.bbrc.2024.150448] [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: 07/12/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
In light of the emerging importance of the gut microbiome in human health, there is a need to improve the colonization efficiency of therapeutic bacteria called probiotics. Despite their recognized potential, artificially administered bacteria exhibit poor colonization in the intestine, limiting their therapeutic efficacy. Addressing this challenge requires innovative strategies; however, reported examples are limited. In nature, including in the intestinal tract, bacteria live via biofilm formation. Recently, it has been reported that RNase I, a member of the RNase T2 family conserved among almost all species, including bacteria, inhibits biofilm formation in Escherichia coli. In this study, we focus on these results and investigate the relationship between high biofilm formation and intestinal attachment using a non-settling E. coli laboratory strain as a probiotic model. The intestinal colonization abilities were evaluated through a microfluidic device mimicking the intestinal tract and through oral administration to mice. The in vitro and in vivo experiments showed that the E. coli strain lacking RNase I exhibited remarkable stability in intestinal colonization. We investigated the observation of colonization using fluorescence in situ hybridization, and inoculated E. coli cells were aggregated with the gut microbiome in the cecum and colon. This study proposes a technique to improve the intestinal colonization of bacteria by simply manipulating a single gene disruption, and it is expected to contribute to future research on the colonization of useful bacteria.
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Affiliation(s)
- Atsushi Minami
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takehiro Asai
- Department of Veterinary Medical Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tsuyoshi Tachibana
- Department of Veterinary Medical Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yu Tanaka
- Department of Veterinary Medical Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mitsuyuki Nakajima
- Department of Veterinary Medical Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shiori Tamura
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Morihiro Nakazawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Yoshiharu Tsuru
- Life Science Laboratory, Primetech Corporation, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yoichi Fujiyama
- Technology Research Laboratory, Shimadzu Corporation, Hikaridai, Seika-cho, Soraku-gun, Kyoto, 619-0237, Japan
| | - Yoh-Ichi Tagawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
| | - Tomohisa Kuzuyama
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute of Innovative Microbiology, The University of Tokyo, Japan
| | - Shigeru Kakuta
- Department of Veterinary Medical Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute of Innovative Microbiology, The University of Tokyo, Japan; Research Center for Food Safety, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Tetsuhiro Ogawa
- Department of Biotechnology, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Collaborative Research Institute of Innovative Microbiology, The University of Tokyo, Japan.
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18
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Abstract
A global rise in pet ownership and an increasing tendency towards the humanisation of pets have resulted in a greater focus on improving animal health and longevity. These developments coincide with the increased recognition of the role of the gut microbiome in animal health. The gut microbiome has been shown to play a prominent role in gastrointestinal health, and it is becoming increasingly clear that these health benefits extend beyond the gut and into different physiological systems, such as the immune system. Dietary supplementation with products known as 'biotics', which include probiotics, prebiotics, synbiotics and postbiotics, is a strategy used to modify the gut microbiome and promote host health. Although biotics have been successfully used in companion animals, questions remain regarding appropriate biotic selection, mechanisms of action, optimum inclusion levels and safety. This review aims to summarise the effects of biotics on the gut microbiome of dogs and cats and assess their potential role in supporting gastrointestinal health.
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Affiliation(s)
- Sofia M Wilson
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Kelly S Swanson
- Department of Animal Sciences, Department of Veterinary Medicine and Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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19
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Wang J, Li Y, Sun D, Li J, Li L, Zhang X, Liu X, Feng Z, Xue H, Cui Y, Wang Y, Liu D, Wang H. Implementing Optogenetic-Controlled Bacterial Systems in Drosophila melanogaster for Alleviation of Heavy Metal Poisoning. ACS Synth Biol 2024; 13:3312-3325. [PMID: 39312764 DOI: 10.1021/acssynbio.4c00409] [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: 09/25/2024]
Abstract
Drosophila melanogaster (fruit fly) is an animal model chassis in biological and genetic research owing to its short life cycle, ease of cultivation, and acceptability to genetic modification. While the D. melanogaster chassis offers valuable insights into drug efficacy, toxicity, and mechanisms, several obvious challenges such as dosage control and drug resistance still limit its utility in pharmacological studies. Our research combines optogenetic control with engineered gut bacteria to facilitate the precise delivery of therapeutic substances in D. melanogaster for biomedical research. We have shown that the engineered bacteria can be orally administered to D. melanogaster to get a stable density of approximately 28,000 CFUs/per fly, leading to no detectable negative effects on the growth of D. melanogaster. In a model of D. melanogaster exposure to heavy metal, these orally administered bacteria uniformly express target genes under green light control to produce MtnB protein for binding and detoxifying lead, which significantly reduces the level of oxidative stress in the intestinal tract of Pb-treated flies. This pioneering study lays the groundwork for using optogenetic-controlled bacteria in the model chassis D. melanogaster to advance biomedical applications.
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Affiliation(s)
- Junyi Wang
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
| | - Ying Li
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China
| | - Dawei Sun
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
| | - Jingyi Li
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China
| | - Lianyue Li
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
| | - Xinyu Zhang
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
| | - Xinyu Liu
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
| | - Zhijie Feng
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
| | - Huimin Xue
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
| | - Yuhui Cui
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
| | - Yiwen Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China
| | - Duo Liu
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Hanjie Wang
- School of Life Sciences, Faculty of Medicine, Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin University, Tianjin 300072, China
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20
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Jin WY, Guo JX, Tang R, Wang J, Zhao H, Zhang M, Teng LZ, Sansonetti PJ, Gao YZ. In vivo detection of endogenous toxic phenolic compounds of intestine. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135526. [PMID: 39153300 DOI: 10.1016/j.jhazmat.2024.135526] [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: 06/03/2024] [Revised: 07/31/2024] [Accepted: 08/13/2024] [Indexed: 08/19/2024]
Abstract
Phenol and p-cresol are two common toxic small molecules related to various diseases. Existing reports confirmed that high L-tyrosine in the daily diet can increase the concentration of phenolic compounds in blood and urine. L-tyrosine is a common component of protein-rich foods. Some anaerobic bacteria in the gut can convert non-toxic l-tyrosine into these two toxic phenolic compounds, phenol and p-cresol. Existing methods have been constructed for measuring the concentration of phenolic compound in feces. However, there is still a lack of direct visual evidence to measure the phenolic compounds in the intestine. In this study, we aimed to construct a whole-cell biosensor for phenolic compounds detection based on the dmpR, the regulator from the phenol metabolism cluster. The commensal bacterium Citrobacter amalonaticus PS01 was selected and used as the chassis. Compared with the biosensor based on ECN1917, the biosensor PS01[dmpR] could better implant into the mouse gut through gavage and showed a higher sensitive to phenolic compound. And the concentration of phenolic compounds in the intestines could be observed with the help of in vivo imaging system using PS01[dmpR]. This paper demonstrated endogenous phenol synthesis in the gut and the strategy of using commensal bacteria to construct whole-cell biosensors for detecting small molecule compounds in the intestines.
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Affiliation(s)
- Wen-Yu Jin
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Xin Guo
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rongkang Tang
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jielin Wang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huan Zhao
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng Zhang
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; Pasteurian College, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215123, China
| | - Lin-Zuo Teng
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China
| | - Philippe J Sansonetti
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Université de Paris, Paris, France.
| | - Yi-Zhou Gao
- Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; The Center for Microbes, Development, and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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21
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Jian C, Yinhang W, Jing Z, Zhanbo Q, Zefeng W, Shuwen H. Escherichia coli on colorectal cancer: A two-edged sword. Microb Biotechnol 2024; 17:e70029. [PMID: 39400440 PMCID: PMC11472651 DOI: 10.1111/1751-7915.70029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 09/26/2024] [Indexed: 10/15/2024] Open
Abstract
Escherichia coli (E. coli) is a ubiquitous symbiotic bacterium in the gut, and the diversity of E. coli genes determines the diversity of its functions. In this review, the two-edged sword theory was innovatively proposed. For the question 'how can we harness the ambivalent nature of E. coli to screen and treat CRC?', in terms of CRC screening, the variations in the abundance and subtypes of E. coli across different populations present an opportunity to utilise it as a biomarker, while in terms of CRC treatment, the natural beneficial effect of E. coli on CRC may be limited, and engineered E. coli, particularly certain subtypes with probiotic potential, can indeed play a significant role in CRC treatment. It seems that the favourable role of E. coli as a genetic tool lies not in its direct impact on CRC but its potential as a research platform that can be integrated with various technologies such as nanoparticles, imaging methods, and synthetic biology modification. The relationship between gut microflora and CRC remains unclear due to the complex diversity and interaction of gut microflora. Therefore, the application of E. coli should be based on the 'One Health' view and take the interactions between E. coli and other microorganisms, host, and environmental factors, as well as its own changes into account. In this paper, the two-edged sword role of E. coli in CRC is emphasised to realise the great potential of E. coli in CRC screening and treatment.
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Affiliation(s)
- Chu Jian
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityHuzhouZhejiangPeople's Republic of China
- Huzhou Central HospitalFifth Affiliated Clinical Medical College of Zhejiang Chinese Medical UniversityHuzhouZhejiangPeople's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of HuzhouHuzhouZhejiangPeople's Republic of China
| | - Wu Yinhang
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityHuzhouZhejiangPeople's Republic of China
- Huzhou Central HospitalFifth Affiliated Clinical Medical College of Zhejiang Chinese Medical UniversityHuzhouZhejiangPeople's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of HuzhouHuzhouZhejiangPeople's Republic of China
| | - Zhuang Jing
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityHuzhouZhejiangPeople's Republic of China
- Huzhou Central HospitalFifth Affiliated Clinical Medical College of Zhejiang Chinese Medical UniversityHuzhouZhejiangPeople's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of HuzhouHuzhouZhejiangPeople's Republic of China
| | - Qu Zhanbo
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityHuzhouZhejiangPeople's Republic of China
- Huzhou Central HospitalFifth Affiliated Clinical Medical College of Zhejiang Chinese Medical UniversityHuzhouZhejiangPeople's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of HuzhouHuzhouZhejiangPeople's Republic of China
| | - Wang Zefeng
- Huzhou UniversityHuzhouZhejiangPeople's Republic of China
| | - Han Shuwen
- Huzhou Central HospitalAffiliated Central Hospital Huzhou UniversityHuzhouZhejiangPeople's Republic of China
- Huzhou Central HospitalFifth Affiliated Clinical Medical College of Zhejiang Chinese Medical UniversityHuzhouZhejiangPeople's Republic of China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of HuzhouHuzhouZhejiangPeople's Republic of China
- ASIR (Institute ‐ Association of intelligent systems and robotics)Rueil‐MalmaisonFrance
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22
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Datta S, Pasham S, Inavolu S, Boini KM, Koka S. Role of Gut Microbial Metabolites in Cardiovascular Diseases-Current Insights and the Road Ahead. Int J Mol Sci 2024; 25:10208. [PMID: 39337693 PMCID: PMC11432476 DOI: 10.3390/ijms251810208] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/18/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Cardiovascular diseases (CVDs) are the leading cause of premature morbidity and mortality globally. The identification of novel risk factors contributing to CVD onset and progression has enabled an improved understanding of CVD pathophysiology. In addition to the conventional risk factors like high blood pressure, diabetes, obesity and smoking, the role of gut microbiome and intestinal microbe-derived metabolites in maintaining cardiovascular health has gained recent attention in the field of CVD pathophysiology. The human gastrointestinal tract caters to a highly diverse spectrum of microbes recognized as the gut microbiota, which are central to several physiologically significant cascades such as metabolism, nutrient absorption, and energy balance. The manipulation of the gut microbial subtleties potentially contributes to CVD, inflammation, neurodegeneration, obesity, and diabetic onset. The existing paradigm of studies suggests that the disruption of the gut microbial dynamics contributes towards CVD incidence. However, the exact mechanistic understanding of such a correlation from a signaling perspective remains elusive. This review has focused upon an in-depth characterization of gut microbial metabolites and their role in varied pathophysiological conditions, and highlights the potential molecular and signaling mechanisms governing the gut microbial metabolites in CVDs. In addition, it summarizes the existing courses of therapy in modulating the gut microbiome and its metabolites, limitations and scientific gaps in our current understanding, as well as future directions of studies involving the modulation of the gut microbiome and its metabolites, which can be undertaken to develop CVD-associated treatment options. Clarity in the understanding of the molecular interaction(s) and associations governing the gut microbiome and CVD shall potentially enable the development of novel druggable targets to ameliorate CVD in the years to come.
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Affiliation(s)
- Sayantap Datta
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Sindhura Pasham
- Department of Pharmaceutical Sciences, Irma Lerma College of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA
| | - Sriram Inavolu
- Department of Pharmaceutical Sciences, Irma Lerma College of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA
| | - Krishna M Boini
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA
| | - Saisudha Koka
- Department of Pharmaceutical Sciences, Irma Lerma College of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA
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23
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Srivastava R, González-Prieto C, Lynch JP, Muscolo ME, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF. In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli. PNAS NEXUS 2024; 3:pgae374. [PMID: 39262854 PMCID: PMC11388102 DOI: 10.1093/pnasnexus/pgae374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 08/15/2024] [Indexed: 09/13/2024]
Abstract
Engineered smart microbes that deliver therapeutic payloads are emerging as treatment modalities, particularly for diseases with links to the gastrointestinal tract. Enterohemorrhagic Escherichia coli (EHEC) is a causative agent of potentially lethal hemolytic uremic syndrome. Given concerns that antibiotic treatment increases EHEC production of Shiga toxin (Stx), which is responsible for systemic disease, novel remedies are needed. EHEC encodes a type III secretion system (T3SS) that injects Tir into enterocytes. Tir inserts into the host cell membrane, exposing an extracellular domain that subsequently binds intimin, one of its outer membrane proteins, triggering the formation of attaching and effacing (A/E) lesions that promote EHEC mucosal colonization. Citrobacter rodentium (Cr), a natural A/E mouse pathogen, similarly requires Tir and intimin for its pathogenesis. Mice infected with Cr(ΦStx2dact), a variant lysogenized with an EHEC-derived phage that produces Stx2dact, develop intestinal A/E lesions and toxin-dependent disease. Stx2a is more closely associated with human disease. By developing an efficient approach to seamlessly modify the C. rodentium genome, we generated Cr_Tir-MEHEC(ΦStx2a), a variant that expresses Stx2a and the EHEC extracellular Tir domain. We found that mouse precolonization with HS-PROT3EcT-TD4, a human commensal E. coli strain (E. coli HS) engineered to efficiently secrete an anti-EHEC Tir nanobody, delayed bacterial colonization and improved survival after challenge with Cr_Tir-MEHEC(ΦStx2a). This study suggests that commensal E. coli engineered to deliver payloads that block essential virulence determinants can be developed as a new means to prevent and potentially treat infections including those due to antibiotic resistant microbes.
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Affiliation(s)
- Rajkamal Srivastava
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Coral González-Prieto
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jason P Lynch
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Michele E Muscolo
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA
| | - Catherine Y Lin
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA
| | - Markus A Brown
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Luisa Lemos
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anishma Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Marcia S Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, 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
| | - Cammie F Lesser
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Ragon Institute of Harvard and MIT, Cambridge, MA 02139, USA
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24
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Xu M, Feng G, Fang J. Microcapsules based on biological macromolecules for intestinal health: A review. Int J Biol Macromol 2024; 276:133956. [PMID: 39029830 DOI: 10.1016/j.ijbiomac.2024.133956] [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: 04/03/2024] [Revised: 07/04/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
Intestinal dysfunction is becoming increasingly associated with neurological and endocrine issues, raising concerns about its impact on world health. With the introduction of several breakthrough technologies for detecting and treating intestinal illnesses, significant progress has been made in the previous few years. On the other hand, traditional intrusive diagnostic techniques are expensive and time-consuming. Furthermore, the efficacy of conventional drugs (not capsules) is reduced since they are more likely to degrade before reaching their target. In this context, microcapsules based on different types of biological macromolecules have been used to encapsulate active drugs and sensors to track intestinal ailments and address these issues. Several biomacromolecules/biomaterials (natural protein, alginate, chitosan, cellulose and RNA etc.) are widely used for make microcapsules for intestinal diseases, and can significantly improve the therapeutic effect and reduce adverse reactions. This article systematically summarizes microencapsulated based on biomacromolecules material for intestinal health control and efficacy enhancement. It also discusses the application and mechanism research of microencapsulated biomacromolecules drugs in reducing intestinal inflammation, in addition to covering the preparation techniques of microencapsulated drug delivery systems used for intestinal health. Microcapsule delivery systems' limits and potential applications for intestinal disease diagnosis, treatment, and surveillance were highlighted.
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Affiliation(s)
- Minhui Xu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha 410128, Hunan, China
| | - Guangfu Feng
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha 410128, Hunan, China.
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, Changsha 410128, Hunan, China
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25
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Safdar M, Ullah M, Hamayun S, Wahab A, Khan SU, Abdikakhorovich SA, Haq ZU, Mehreen A, Naeem M, Mustopa AZ, Hasan N. Microbiome miracles and their pioneering advances and future frontiers in cardiovascular disease. Curr Probl Cardiol 2024; 49:102686. [PMID: 38830479 DOI: 10.1016/j.cpcardiol.2024.102686] [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: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
Cardiovascular diseases (CVDs) represent a significant global health challenge, underscoring the need for innovative approaches to prevention and treatment. Recent years have seen a surge in interest in unraveling the complex relationship between the gut microbiome and cardiovascular health. This article delves into current research on the composition, diversity, and impact of the gut microbiome on CVD development. Recent advancements have elucidated the profound influence of the gut microbiome on disease progression, particularly through key mediators like Trimethylamine-N-oxide (TMAO) and other microbial metabolites. Understanding these mechanisms reveals promising therapeutic targets, including interventions aimed at modulating the gut microbiome's interaction with the immune system and its contribution to endothelial dysfunction. Harnessing this understanding, personalized medicine strategies tailored to individuals' gut microbiome profiles offer innovative avenues for reducing cardiovascular risk. As research in this field continues to evolve, there is vast potential for transformative advancements in cardiovascular medicine, paving the way for precision prevention and treatment strategies to address this global health challenge.
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Affiliation(s)
- Mishal Safdar
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Muneeb Ullah
- College of Pharmacy, Pusan National University, Busandaehak-ro 63 beon-gil 2, Geumjeong-gu, Busan 46241, Republic of Korea; Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shah Hamayun
- Department of Cardiology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, 04485 Punjab, Pakistan
| | - Abdul Wahab
- Department of Pharmacy, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Shahid Ullah Khan
- Department of Biochemistry, Women Medical and Dental College, Khyber Medical University, Abbottabad, 22080, Khyber Pakhtunkhwa, Pakistan
| | | | - Zia Ul Haq
- Department of Public Health, Institute of Public Health Sciences, Khyber Medical University, Peshawar 25120, Pakistan
| | - Aqsa Mehreen
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Muhammad Naeem
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Punjab, Pakistan
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, National Research, and Innovation Agency (BRIN), Bogor 16911, Indonesia
| | - Nurhasni Hasan
- Faculty of Pharmacy, Universitas Hasanuddin, Jl. Perintis Kemerdekaan Km 10, Makassar 90245, Republic of Indonesia.
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26
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Radford GA, Vrbanac L, de Nys RT, Worthley DL, Wright JA, Hasty J, Woods SL. Towards Understanding Tumour Colonisation by Probiotic Bacterium E. coli Nissle 1917. Cancers (Basel) 2024; 16:2971. [PMID: 39272829 PMCID: PMC11394440 DOI: 10.3390/cancers16172971] [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: 08/06/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
The last decade has seen a rapid increase in studies utilising a genetically modified probiotic, Escherichia coli Nissle 1917 (EcN), as a chassis for cancer treatment and detection. This approach relies on the ability of EcN to home to and selectively colonise tumours over normal tissue, a characteristic common to some bacteria that is thought to result from the low-oxygen, nutrient-rich and immune-privileged niche the tumour provides. Pre-clinical studies have used genetically modified EcN to deliver therapeutic payloads that show efficacy in reducing tumour burden as a result of high-tumour and low off-target colonisation. Most recently, the EcN chassis has been expanded into an effective tumour-detection tool. These advances provide strong justification for the movement of genetically modified EcN into clinical oncology trials. What is currently unknown in the field is a deep mechanistic understanding of how EcN distributes to and localises within tumours. This review summarises the existing EcN literature, with the inclusion of research undertaken with other tumour-homing and pathogenic bacteria, to provide insights into possible mechanisms of EcN tumour homing for future validation. Understanding exactly how and why EcN colonises neoplastic tissue will inform the design and testing of the next generation of EcN chassis strains to address biosafety and containment concerns and optimise the detection and treatment of cancer.
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Affiliation(s)
| | - Laura Vrbanac
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
| | - Rebekah T. de Nys
- Precision Cancer Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia
| | | | - Josephine A. Wright
- Precision Cancer Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia
| | - Jeff Hasty
- Synthetic Biology Institute, University of California, San Diego, CA 92093, USA
- Department of Bioengineering, University of California, San Diego, CA 92093, USA
- Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, CA 92093, USA
- Center for Microbiome Innovation, University of California, San Diego, CA 92093, USA
| | - Susan L. Woods
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia
- Precision Cancer Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA 5000, Australia
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27
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Lin X, Jiao R, Cui H, Yan X, Zhang K. Physiochemically and Genetically Engineered Bacteria: Instructive Design Principles and Diverse Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2403156. [PMID: 38864372 PMCID: PMC11321697 DOI: 10.1002/advs.202403156] [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: 03/26/2024] [Revised: 04/18/2024] [Indexed: 06/13/2024]
Abstract
With the comprehensive understanding of microorganisms and the rapid advances of physiochemical engineering and bioengineering technologies, scientists are advancing rationally-engineered bacteria as emerging drugs for treating various diseases in clinical disease management. Engineered bacteria specifically refer to advanced physiochemical or genetic technologies in combination with cutting edge nanotechnology or physical technologies, which have been validated to play significant roles in lysing tumors, regulating immunity, influencing the metabolic pathways, etc. However, there has no specific reviews that concurrently cover physiochemically- and genetically-engineered bacteria and their derivatives yet, let alone their distinctive design principles and various functions and applications. Herein, the applications of physiochemically and genetically-engineered bacteria, and classify and discuss significant breakthroughs with an emphasis on their specific design principles and engineering methods objective to different specific uses and diseases beyond cancer is described. The combined strategies for developing in vivo biotherapeutic agents based on these physiochemically- and genetically-engineered bacteria or bacterial derivatives, and elucidated how they repress cancer and other diseases is also underlined. Additionally, the challenges faced by clinical translation and the future development directions are discussed. This review is expected to provide an overall impression on physiochemically- and genetically-engineered bacteria and enlighten more researchers.
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Affiliation(s)
- Xia Lin
- Central Laboratory and Department of UltrasoundSichuan Academy of Medical SciencesSichuan Provincial People's HospitalSchool of MedicineUniversity of Electronic Science and Technology of ChinaNo. 32, West Second Section, First Ring RoadChengduSichuan610072China
| | - Rong Jiao
- Central Laboratory and Department of UltrasoundSichuan Academy of Medical SciencesSichuan Provincial People's HospitalSchool of MedicineUniversity of Electronic Science and Technology of ChinaNo. 32, West Second Section, First Ring RoadChengduSichuan610072China
| | - Haowen Cui
- Central Laboratory and Department of UltrasoundSichuan Academy of Medical SciencesSichuan Provincial People's HospitalSchool of MedicineUniversity of Electronic Science and Technology of ChinaNo. 32, West Second Section, First Ring RoadChengduSichuan610072China
| | - Xuebing Yan
- Department of OncologyAffiliated Hospital of Yangzhou University. No.368Hanjiang Road, Hanjiang DistrictYangzhouJiangsu Province225012China
| | - Kun Zhang
- Central Laboratory and Department of UltrasoundSichuan Academy of Medical SciencesSichuan Provincial People's HospitalSchool of MedicineUniversity of Electronic Science and Technology of ChinaNo. 32, West Second Section, First Ring RoadChengduSichuan610072China
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28
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Kwon SY, Thi-Thu Ngo H, Son J, Hong Y, Min JJ. Exploiting bacteria for cancer immunotherapy. Nat Rev Clin Oncol 2024; 21:569-589. [PMID: 38840029 DOI: 10.1038/s41571-024-00908-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2024] [Indexed: 06/07/2024]
Abstract
Immunotherapy has revolutionized the treatment of cancer but continues to be constrained by limited response rates, acquired resistance, toxicities and high costs, which necessitates the development of new, innovative strategies. The discovery of a connection between the human microbiota and cancer dates back 4,000 years, when local infection was observed to result in tumour eradication in some individuals. However, the true oncological relevance of the intratumoural microbiota was not recognized until the turn of the twentieth century. The intratumoural microbiota can have pivotal roles in both the pathogenesis and treatment of cancer. In particular, intratumoural bacteria can either promote or inhibit cancer growth via remodelling of the tumour microenvironment. Over the past two decades, remarkable progress has been made preclinically in engineering bacteria as agents for cancer immunotherapy; some of these bacterial products have successfully reached the clinical stages of development. In this Review, we discuss the characteristics of intratumoural bacteria and their intricate interactions with the tumour microenvironment. We also describe the many strategies used to engineer bacteria for use in the treatment of cancer, summarizing contemporary data from completed and ongoing clinical trials. The work described herein highlights the potential of bacteria to transform the landscape of cancer therapy, bridging ancient wisdom with modern scientific innovation.
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Affiliation(s)
- Seong-Young Kwon
- Institute for Molecular Imaging and Theranostics, Chonnam National University Medical School, Jeonnam, Republic of Korea
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Jeonnam, Republic of Korea
| | - Hien Thi-Thu Ngo
- Institute for Molecular Imaging and Theranostics, Chonnam National University Medical School, Jeonnam, Republic of Korea
- Department of Biomedical Sciences, Chonnam National University Medical School, Jeonnam, Republic of Korea
- Department of Biochemistry, Hanoi Medical University, Hanoi, Vietnam
| | - Jinbae Son
- CNCure Biotech, Jeonnam, Republic of Korea
| | - Yeongjin Hong
- Institute for Molecular Imaging and Theranostics, Chonnam National University Medical School, Jeonnam, Republic of Korea
- CNCure Biotech, Jeonnam, Republic of Korea
- Department of Microbiology and Immunology, Chonnam National University Medical School, Jeonnam, Republic of Korea
- National Immunotherapy Innovation Center, Chonnam National University, Jeonnam, Republic of Korea
| | - Jung-Joon Min
- Institute for Molecular Imaging and Theranostics, Chonnam National University Medical School, Jeonnam, Republic of Korea.
- Department of Nuclear Medicine, Chonnam National University Medical School and Hwasun Hospital, Jeonnam, Republic of Korea.
- Department of Biomedical Sciences, Chonnam National University Medical School, Jeonnam, Republic of Korea.
- CNCure Biotech, Jeonnam, Republic of Korea.
- Department of Microbiology and Immunology, Chonnam National University Medical School, Jeonnam, Republic of Korea.
- National Immunotherapy Innovation Center, Chonnam National University, Jeonnam, Republic of Korea.
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29
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Srivastava R, González-Prieto C, Lynch JP, Muscolo M, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF. In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605899. [PMID: 39131305 PMCID: PMC11312530 DOI: 10.1101/2024.07.30.605899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Engineered smart microbes that deliver therapeutic payloads are emerging as treatment modalities, particularly for diseases with links to the gastrointestinal tract. Enterohemorrhagic E coli (EHEC) is a causative agent of potentially lethal hemolytic uremic syndrome. Given concerns that antibiotic treatment increases EHEC production of Shiga toxin (Stx), which is responsible for systemic disease, novel remedies are needed. EHEC encodes a type III secretion system (T3SS) that injects Tir into enterocytes. Tir inserts into the host cell membrane, exposing an extracellular domain that subsequently binds intimin, one of its outer membrane proteins, triggering the formation of attaching and effacing (A/E) lesions that promote EHEC mucosal colonization. Citrobacter rodentium (Cr), a natural A/E mouse pathogen, similarly requires Tir and intimin for its pathogenesis. Mice infected with Cr(ΦStx2dact), a variant lysogenized with an EHEC-derived phage that produces Stx2dact, develop intestinal A/E lesions and toxin-dependent disease. Stx2a is more closely associated with human disease. By developing an efficient approach to seamlessly modify the C. rodentium genome, we generated Cr_Tir-MEHEC(ΦStx2a), a variant that expresses Stx2a and the EHEC extracellular Tir domain. We found that mouse pre-colonization with HS-PROT3EcT-TD4, a human commensal E. coli strain (E. coli HS) engineered to efficiently secrete- an anti-EHEC Tir nanobody, delayed bacterial colonization and improved survival after challenge with Cr_Tir-MEHEC(ΦStx2a). This study provides the first evidence to support the efficacy of engineered commensal E. coli to intestinally deliver therapeutic payloads that block essential enteric pathogen virulence determinants, a strategy that may serve as an antibiotic-independent antibacterial therapeutic modality.
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Affiliation(s)
- Rajkamal Srivastava
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA, 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Coral González-Prieto
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA, 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jason P Lynch
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA, 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Michele Muscolo
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA, 02115, USA
| | - Catherine Y Lin
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA, 02115, USA
| | - Markus A Brown
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA, 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Luisa Lemos
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA, 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Anishma Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Marcia S Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, 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
| | - Cammie F Lesser
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, MA, 02115, USA
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Ragon Institute of Harvard and MIT, Cambridge, MA, 02139, USA
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30
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Siguenza N, Brevi A, Zhang JT, Pabani A, Bhushan A, Das M, Ding Y, Hasty J, Ghosh P, Zarrinpar A. Engineered bacterial therapeutics for detecting and treating CRC. Trends Cancer 2024; 10:588-597. [PMID: 38693003 PMCID: PMC11392429 DOI: 10.1016/j.trecan.2024.04.001] [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: 01/16/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024]
Abstract
Despite an overall decrease in occurrence, colorectal cancer (CRC) remains the third most common cause of cancer deaths in the USA. Detection of CRC is difficult in high-risk groups, including those with genetic predispositions, with disease traits, or from certain demographics. There is emerging interest in using engineered bacteria to identify early CRC development, monitor changes in the adenoma and CRC microenvironment, and prevent cancer progression. Novel genetic circuits for cancer therapeutics or functions to enhance existing treatment modalities have been tested and verified in vitro and in vivo. Inclusion of biocontainment measures would prepare strains to meet therapeutic standards. Thus, engineered bacteria present an opportunity for detection and treatment of CRC lesions in a highly sensitive and specific manner.
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Affiliation(s)
- Nicole Siguenza
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA; Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Arianna Brevi
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Joanna T Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Arman Pabani
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Abhinav Bhushan
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA; Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Amir Zarrinpar
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA; Jennifer Moreno Department of Veterans Affairs, La Jolla, CA, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA; Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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31
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Parthasarathy G, Malhi H, Bajaj JS. Therapeutic manipulation of the microbiome in liver disease. Hepatology 2024:01515467-990000000-00932. [PMID: 38922826 DOI: 10.1097/hep.0000000000000987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Myriad associations between the microbiome and various facets of liver physiology and pathology have been described in the literature. Building on descriptive and correlative sequencing studies, metagenomic studies are expanding our collective understanding of the functional and mechanistic role of the microbiome as mediators of the gut-liver axis. Based on these mechanisms, the functional activity of the microbiome represents an attractive, tractable, and precision medicine therapeutic target in several liver diseases. Indeed, several therapeutics have been used in liver disease even before their description as a microbiome-dependent approach. To bring successful microbiome-targeted and microbiome-inspired therapies to the clinic, a comprehensive appreciation of the different approaches to influence, collaborate with, or engineer the gut microbiome to coopt a disease-relevant function of interest in the right patient is key. Herein, we describe the various levels at which the microbiome can be targeted-from prebiotics, probiotics, synbiotics, and antibiotics to microbiome reconstitution and precision microbiome engineering. Assimilating data from preclinical animal models, human studies as well as clinical trials, we describe the potential for and rationale behind studying such therapies across several liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cirrhosis, HE as well as liver cancer. Lastly, we discuss lessons learned from previous attempts at developing such therapies, the regulatory framework that needs to be navigated, and the challenges that remain.
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Affiliation(s)
| | - Harmeet Malhi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University and Central Virginia Veterans Healthcare System, Richmond, Virginia, USA
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32
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Joshi SHN, Jenkins C, Ulaeto D, Gorochowski TE. Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology. BIODESIGN RESEARCH 2024; 6:0037. [PMID: 38919711 PMCID: PMC11197468 DOI: 10.34133/bdr.0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 06/27/2024] Open
Abstract
Living cells are exquisitely tuned to sense and respond to changes in their environment. Repurposing these systems to create engineered biosensors has seen growing interest in the field of synthetic biology and provides a foundation for many innovative applications spanning environmental monitoring to improved biobased production. In this review, we present a detailed overview of currently available biosensors and the methods that have supported their development, scale-up, and deployment. We focus on genetic sensors in living cells whose outputs affect gene expression. We find that emerging high-throughput experimental assays and evolutionary approaches combined with advanced bioinformatics and machine learning are establishing pipelines to produce genetic sensors for virtually any small molecule, protein, or nucleic acid. However, more complex sensing tasks based on classifying compositions of many stimuli and the reliable deployment of these systems into real-world settings remain challenges. We suggest that recent advances in our ability to precisely modify nonmodel organisms and the integration of proven control engineering principles (e.g., feedback) into the broader design of genetic sensing systems will be necessary to overcome these hurdles and realize the immense potential of the field.
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Affiliation(s)
| | - Christopher Jenkins
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - David Ulaeto
- CBR Division, Defence Science and Technology Laboratory, Porton Down, Wiltshire SP4 0JQ, UK
| | - Thomas E. Gorochowski
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
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33
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Yang M, Hutchinson N, Ye N, Yin J, Guan M, Wang Z, Chen P, Yang S, Crane JD, Zhang K, He X, Li J. Engineered Bacillus subtilis as oral probiotics to enhance clearance of blood lactate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.30.569300. [PMID: 38076834 PMCID: PMC10705430 DOI: 10.1101/2023.11.30.569300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Elevated lactate concentrations are implicated in various acute and chronic diseases such as sepsis and mitochondrial dysfunction, respectively. Conversely, ineffective lactate clearance is associated with poor clinical prognoses and high mortality in these diseases. While several groups have proposed using small molecule inhibitors and enzyme replacement to reduce circulating lactate, there are few practical and effective ways to manage this condition. Recent evidence suggests that lactate is exchanged between systemic circulation and the gut, allowing bidirectional modulation between the gut microbiota and peripheral tissues. Inspired by these findings, this work seeks to engineer spore-forming probiotic B. subtilis strains to enable intestinal delivery of lactate oxidase as a therapeutic enzyme. After strain optimization, we showed that oral administration of engineered B. subtilis spores to the gut of mice reduced elevations in blood lactate in two different mouse models involving exogenous challenge or pharmacologic perturbation without disrupting gut microbiota composition, liver function, or immune homeostasis. Taken together, through the oral delivery of engineered probiotic spores to the gastrointestinal tract, our proof-of-concept study offers a practical strategy to aid in the management of disease states with elevated blood lactate and provides a new approach to 'knocking down' circulating metabolites to help understand their roles in host physiological and pathological processes.
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Affiliation(s)
- Mengdi Yang
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Noah Hutchinson
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Ningyuan Ye
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Jianing Yin
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Ming Guan
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Zongqi Wang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, United States
| | - Peiru Chen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, United States
| | - Shaobo Yang
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
| | - Justin D. Crane
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA 02139
| | - Ke Zhang
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, United States
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, 02142, United States
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, 02115, United States
| | - Jiahe Li
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, United States
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34
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Zhang J, Hasty J, Zarrinpar A. Live bacterial therapeutics for detection and treatment of colorectal cancer. Nat Rev Gastroenterol Hepatol 2024; 21:295-296. [PMID: 38355755 PMCID: PMC11062807 DOI: 10.1038/s41575-024-00901-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Live microorganisms can be manipulated and engineered for colorectal cancer detection and treatment through methods such as faecal microbiota transplantation, native bacteria engineering and synthetic circuit engineering. Although promising, substantial effort is required to translate these approaches for clinical use.
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Affiliation(s)
- Joanna Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Biodynamics Laboratory, University of California, San Diego, La Jolla, CA, USA
- Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Biodynamics Laboratory, University of California, San Diego, La Jolla, CA, USA
- Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
| | - Amir Zarrinpar
- Synthetic Biology Institute, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Jennifer Moreno Department of Veterans Affairs, La Jolla, CA, USA.
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
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35
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Schöler D, Schnabl B. The role of the microbiome in liver disease. Curr Opin Gastroenterol 2024; 40:134-142. [PMID: 38362864 PMCID: PMC10990783 DOI: 10.1097/mog.0000000000001013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
PURPOSE OF REVIEW The intestinal microbiome and the gut-liver axis play a major role in health and disease. The human gut harbors trillions of microbes and a disruption of the gut homeostasis can contribute to liver disease. In this review, the progress in the field within the last 3 years is summarized, focusing on metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD), autoimmune liver disease (AILD), and hepatocellular carcinoma (HCC). RECENT FINDINGS Changes in the fecal virome and fungal mycobiome have been described in patients with various liver diseases. Several microbial derived metabolites including endogenous ethanol produced by bacteria, have been mechanistically linked to liver disease such as MASLD. Virulence factors encoded by gut bacteria contribute to ALD, AILD and HCC. Novel therapeutic approaches focused on the microbiome including phages, pre- and postbiotics have been successfully used in preclinical models. Fecal microbiota transplantation has been effective in attenuating liver disease. Probiotics are safe in patients with alcohol-associated hepatitis and improve liver disease and alcohol addiction. SUMMARY The gut-liver axis plays a key role in the pathophysiology of liver diseases. Understanding the microbiota in liver disease can help to develop precise microbiota centered therapies.
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Affiliation(s)
- David Schöler
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
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36
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Ratiner K, Ciocan D, Abdeen SK, Elinav E. Utilization of the microbiome in personalized medicine. Nat Rev Microbiol 2024; 22:291-308. [PMID: 38110694 DOI: 10.1038/s41579-023-00998-9] [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: 11/17/2023] [Indexed: 12/20/2023]
Abstract
Inter-individual human variability, driven by various genetic and environmental factors, complicates the ability to develop effective population-based early disease detection, treatment and prognostic assessment. The microbiome, consisting of diverse microorganism communities including viruses, bacteria, fungi and eukaryotes colonizing human body surfaces, has recently been identified as a contributor to inter-individual variation, through its person-specific signatures. As such, the microbiome may modulate disease manifestations, even among individuals with similar genetic disease susceptibility risks. Information stored within microbiomes may therefore enable early detection and prognostic assessment of disease in at-risk populations, whereas microbiome modulation may constitute an effective and safe treatment tailored to the individual. In this Review, we explore recent advances in the application of microbiome data in precision medicine across a growing number of human diseases. We also discuss the challenges, limitations and prospects of analysing microbiome data for personalized patient care.
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Affiliation(s)
- Karina Ratiner
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Dragos Ciocan
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Suhaib K Abdeen
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
- Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany.
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37
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Junaid M, Lu H, Din AU, Yu B, Liu Y, Li Y, Liu K, Yan J, Qi Z. Deciphering Microbiome, Transcriptome, and Metabolic Interactions in the Presence of Probiotic Lactobacillus acidophilus against Salmonella Typhimurium in a Murine Model. Antibiotics (Basel) 2024; 13:352. [PMID: 38667028 PMCID: PMC11047355 DOI: 10.3390/antibiotics13040352] [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: 02/19/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium), a foodborne pathogen that poses significant public health risks to humans and animals, presents a formidable challenge due to its antibiotic resistance. This study explores the potential of Lactobacillus acidophilus (L. acidophilus 1.3251) probiotics as an alternative strategy to combat antibiotic resistance associated with S. Typhimurium infection. In this investigation, twenty-four BALB/c mice were assigned to four groups: a non-infected, non-treated group (CNG); an infected, non-treated group (CPG); a group fed with L. acidophilus but not infected (LAG); and a group fed with L. acidophilus and challenged with Salmonella (LAST). The results revealed a reduction in Salmonella levels in the feces of mice, along with restored weight and improved overall health in the LAST compared to the CPG. The feeding of L. acidophilus was found to downregulate pro-inflammatory cytokine mRNA induced by Salmonella while upregulating anti-inflammatory cytokines. Additionally, it influenced the expression of mRNA transcript, encoding tight junction protein, oxidative stress-induced enzymes, and apoptosis-related mRNA expression. Furthermore, the LEfSe analysis demonstrated a significant shift in the abundance of critical commensal genera in the LAST, essential for maintaining gut homeostasis, metabolic reactions, anti-inflammatory responses, and butyrate production. Transcriptomic analysis revealed 2173 upregulated and 506 downregulated differentially expressed genes (DEGs) in the LAST vs. the CPG. Functional analysis of these DEGs highlighted their involvement in immunity, metabolism, and cellular development. Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis indicated their role in tumor necrosis factor (TNF), mitogen-activated protein kinase (MAPK), chemokine, Forkhead box O (FOXO), and transforming growth factor (TGF-β) signaling pathway. Moreover, the fecal metabolomic analysis identified 929 differential metabolites, with enrichment observed in valine, leucine, isoleucine, taurine, glycine, and other metabolites. These findings suggest that supplementation with L. acidophilus promotes the growth of beneficial commensal genera while mitigating Salmonella-induced intestinal disruption by modulating immunity, gut homeostasis, gut barrier integrity, and metabolism.
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Affiliation(s)
| | - Hongyu Lu
- Medical College, Guangxi University, Nanning 530004, China
| | - Ahmad Ud Din
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Kannapolis, NC 28081, USA
| | - Bin Yu
- Medical College, Guangxi University, Nanning 530004, China
| | - Yu Liu
- Medical College, Guangxi University, Nanning 530004, China
| | - Yixiang Li
- Medical College, Guangxi University, Nanning 530004, China
| | - Kefei Liu
- Tianjin Shengji Group., Co., Ltd., No. 2, Hai Tai Development 2nd Road, Huayuan Industrial Zone, Tianjin 300384, China
| | - Jianhua Yan
- Medical College, Guangxi University, Nanning 530004, China
| | - Zhongquan Qi
- Medical College, Guangxi University, Nanning 530004, China
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38
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMSF, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe 2024; 32:506-526.e9. [PMID: 38479397 PMCID: PMC11022754 DOI: 10.1016/j.chom.2024.02.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.
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Affiliation(s)
- Xin Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Xiaotao Shen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Jethro S Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Oxford Centre for Microbiome Studies, Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK
| | - Daniel J Spakowicz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Division of Medical Oncology, Ohio State University Wexner Medical Center, James Cancer Hospital and Solove Research Institute, Columbus, OH 43210, USA
| | | | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA
| | - Monica Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander Honkala
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Faye Chleilat
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirley Jingyi Chen
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kexin Cha
- Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shana Leopold
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lei Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Lin Lyu
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, Shanghai 200240, PRC
| | - Daniel Hornburg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Si Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyue Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chao Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Liuyiqi Jiang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, PRC
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew W Brooks
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Meng Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kévin Contrepois
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peng Gao
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | - Hoan Nguyen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Alessandra Celli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo-Young Hong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Woody L Hunt School of Dental Medicine, Texas Tech University Health Science Center, El Paso, TX 79905, USA
| | - Eddy J Bautista
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Corporación Colombiana de Investigación Agropecuaria (Agrosavia), Headquarters-Mosquera, Cundinamarca 250047, Colombia
| | - Yair Dorsett
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Paula B Kavathas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yanjiao Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
| | - Erica Sodergren
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Center for Genomics and Personalized Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford, CA 94305, USA; Stanford Healthcare Innovation Labs, Stanford University School of Medicine, Stanford, CA 94305, USA.
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39
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Brennan C, Chan K, Kumar T, Maissy E, Brubaker L, Dothard MI, Gilbert JA, Gilbert KE, Lewis AL, Thackray VG, Zarrinpar A, Knight R. Harnessing the power within: engineering the microbiome for enhanced gynecologic health. REPRODUCTION AND FERTILITY 2024; 5:e230060. [PMID: 38513356 PMCID: PMC11046331 DOI: 10.1530/raf-23-0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
Abstract Although numerous studies have demonstrated the impact of microbiome manipulation on human health, research on the microbiome's influence on female health remains relatively limited despite substantial disease burden. In light of this, we present a selected review of clinical trials and preclinical studies targeting both the vaginal and gut microbiomes for the prevention or treatment of various gynecologic conditions. Specifically, we explore studies that leverage microbiota transplants, probiotics, prebiotics, diet modifications, and engineered microbial strains. A healthy vaginal microbiome for females of reproductive age consists of lactic acid-producing bacteria predominantly of the Lactobacillus genus, which serves as a protective barrier against pathogens and maintains a balanced ecosystem. The gut microbiota's production of short-chain fatty acids, metabolism of primary bile acids, and modulation of sex steroid levels have significant implications for the interplay between host and microbes throughout the body, ultimately impacting reproductive health. By harnessing interventions that modulate both the vaginal and gut microbiomes, it becomes possible to not only maintain homeostasis but also mitigate pathological conditions. While the field is still working toward making broad clinical recommendations, the current studies demonstrate that manipulating the microbiome holds great potential for addressing diverse gynecologic conditions. Lay summary Manipulating the microbiome has recently entered popular culture, with various diets thought to aid the microbes that live within us. These microbes live in different locations of our body and accordingly help us digest food, modulate our immune system, and influence reproductive health. The role of the microbes living in and influencing the female reproductive tract remains understudied despite known roles in common conditions such as vulvovaginal candidiasis (affecting 75% of females in their lifetime), bacterial vaginosis (25% of females in their lifetime), cervical HPV infection (80% of females in their lifetime), endometriosis (6-10% of females of reproductive age), and polycystic ovary syndrome (10-12% of females of reproductive age). Here, we review four different approaches used to manipulate the female reproductive tract and gastrointestinal system microbiomes: microbiota transplants, probiotics, prebiotics, and dietary interventions, and the use of engineered microbial strains. In doing so, we aim to stimulate discussion on new ways to understand and treat female reproductive health conditions.
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Affiliation(s)
- Caitriona Brennan
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Kristina Chan
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Tanya Kumar
- Medical Scientist Training Program, University of California San Diego, La Jolla, California, USA
| | - Erica Maissy
- Division of Gastroenterology, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Linda Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Marisol I Dothard
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Katharine E Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amanda L Lewis
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Varykina G Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Amir Zarrinpar
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, California, USA
- Division of Gastroenterology, University of California San Diego, La Jolla, California, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, California, USA
- Institute of Diabetes and Metabolic Health, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California, USA
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40
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Liu C, Du MX, Xie LS, Wang WZ, Chen BS, Yun CY, Sun XW, Luo X, Jiang Y, Wang K, Jiang MZ, Qiao SS, Sun M, Cui BJ, Huang HJ, Qu SP, Li CK, Wu D, Wang LS, Jiang C, Liu HW, Liu SJ. Gut commensal Christensenella minuta modulates host metabolism via acylated secondary bile acids. Nat Microbiol 2024; 9:434-450. [PMID: 38233647 DOI: 10.1038/s41564-023-01570-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 11/29/2023] [Indexed: 01/19/2024]
Abstract
A strong correlation between gut microbes and host health has been observed in numerous gut metagenomic cohort studies. However, the underlying mechanisms governing host-microbe interactions in the gut remain largely unknown. Here we report that the gut commensal Christensenella minuta modulates host metabolism by generating a previously undescribed class of secondary bile acids with 3-O-acylation substitution that inhibit the intestinal farnesoid X receptor. Administration of C. minuta alleviated features of metabolic disease in high fat diet-induced obese mice associated with a significant increase in these acylated bile acids, which we refer to as 3-O-acyl-cholic acids. Specific knockout of intestinal farnesoid X receptor in mice counteracted the beneficial effects observed in their wild-type counterparts. Finally, we showed that 3-O-acyl-CAs were prevalent in healthy humans but significantly depleted in patients with type 2 diabetes. Our findings indicate a role for C. minuta and acylated bile acids in metabolic diseases.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Meng-Xuan Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Li-Sheng Xie
- College of Life Science, Hebei University, Baoding, P. R. China
| | - Wen-Zhao Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Bao-Song Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Chu-Yu Yun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Xi Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Yu Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Kai Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Shan-Shan Qiao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Min Sun
- The Second Hospital of Shandong University, Jinan, P. R. China
| | - Bao-Juan Cui
- The Second Hospital of Shandong University, Jinan, P. R. China
| | - Hao-Jie Huang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | | | | | - Dalei Wu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Lu-Shan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, P. R. China.
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Third Hospital, Peking University, Beijing, P. R. China.
| | - Hong-Wei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, P. R. China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China.
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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: 14] [Impact Index Per Article: 14.0] [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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42
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Cao Z, Pang Y, Pu J, Liu J. Bacteria-based drug delivery for treating non-oncological diseases. J Control Release 2024; 366:668-683. [PMID: 38219912 DOI: 10.1016/j.jconrel.2024.01.020] [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: 11/19/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
Bacteria inhabit all over the human body, especially the skin, gastrointestinal tract, respiratory tract, urogenital tract, as well as specific lesion sites, such as wound and tumor. By leveraging their distinctive attributes including rapid proliferation, inherent abilities to colonize various biointerfaces in vivo and produce diverse biomolecules, and the flexibility to be functionalized via genetic engineering or surface modification, bacteria have been widely developed as living therapeutic agents, showing promising potential to make a great impact on the exploration of advanced drug delivery systems. In this review, we present an overview of bacteria-based drug delivery and its applications in treating non-oncological diseases. We systematically summarize the physiological positions where living bacterial therapeutic agents can be delivered to, including the skin, gastrointestinal tract, respiratory tract, and female genital tract. We discuss the success of using bacteria-based drug delivery systems in the treatment of diseases that occur in specific locations, such as skin wound healing/infection, inflammatory bowel disease, respiratory diseases, and vaginitis. We also discuss the advantages as well as the limitations of these living therapeutics and bacteria-based drug delivery, highlighting the key points that need to be considered for further translation. This review article may provide unique insights for designing next-generation bacteria-based therapeutics and developing advanced drug delivery systems.
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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 200127, China
| | - Yan Pang
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
| | - Jun Pu
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, 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 200127, China.
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43
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Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.577565. [PMID: 38352363 PMCID: PMC10862915 DOI: 10.1101/2024.02.01.577565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease. Study Highlights The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.
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Gurbatri CR, Radford GA, Vrbanac L, Im J, Thomas EM, Coker C, Taylor SR, Jang Y, Sivan A, Rhee K, Saleh AA, Chien T, Zandkarimi F, Lia I, Lannagan TRM, Wang T, Wright JA, Kobayashi H, Ng JQ, Lawrence M, Sammour T, Thomas M, Lewis M, Papanicolas L, Perry J, Fitzsimmons T, Kaazan P, Lim A, Stavropoulos AM, Gouskos DA, Marker J, Ostroff C, Rogers G, Arpaia N, Worthley DL, Woods SL, Danino T. Engineering tumor-colonizing E. coli Nissle 1917 for detection and treatment of colorectal neoplasia. Nat Commun 2024; 15:646. [PMID: 38245513 PMCID: PMC10799955 DOI: 10.1038/s41467-024-44776-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024] Open
Abstract
Bioengineered probiotics enable new opportunities to improve colorectal cancer (CRC) screening, prevention and treatment. Here, first, we demonstrate selective colonization of colorectal adenomas after oral delivery of probiotic E. coli Nissle 1917 (EcN) to a genetically-engineered murine model of CRC predisposition and orthotopic models of CRC. We next undertake an interventional, double-blind, dual-centre, prospective clinical trial, in which CRC patients take either placebo or EcN for two weeks prior to resection of neoplastic and adjacent normal colorectal tissue (ACTRN12619000210178). We detect enrichment of EcN in tumor samples over normal tissue from probiotic-treated patients (primary outcome of the trial). Next, we develop early CRC intervention strategies. To detect lesions, we engineer EcN to produce a small molecule, salicylate. Oral delivery of this strain results in increased levels of salicylate in the urine of adenoma-bearing mice, in comparison to healthy controls. To assess therapeutic potential, we engineer EcN to locally release a cytokine, GM-CSF, and blocking nanobodies against PD-L1 and CTLA-4 at the neoplastic site, and demonstrate that oral delivery of this strain reduces adenoma burden by ~50%. Together, these results support the use of EcN as an orally-deliverable platform to detect disease and treat CRC through the production of screening and therapeutic molecules.
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Affiliation(s)
- Candice R Gurbatri
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Georgette A Radford
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Laura Vrbanac
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Jongwon Im
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Elaine M Thomas
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Courtney Coker
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Samuel R Taylor
- Weill Cornell-Rockefeller-Sloan Kettering Tri-Institutional MD-PhD program, New York, NY, USA
| | - YoungUk Jang
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Ayelet Sivan
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Kyu Rhee
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Anas A Saleh
- Division of Infectious Diseases, Weill Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tiffany Chien
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | | | - Ioana Lia
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Tamsin R M Lannagan
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Tongtong Wang
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Josephine A Wright
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Hiroki Kobayashi
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
| | - Jia Q Ng
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Matt Lawrence
- Colorectal Unit, Department of Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Tarik Sammour
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
- Colorectal Unit, Department of Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Michelle Thomas
- Colorectal Unit, Department of Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Mark Lewis
- Colorectal Unit, Department of Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Lito Papanicolas
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - Joanne Perry
- Colorectal Unit, Department of Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Tracy Fitzsimmons
- Colorectal Unit, Department of Surgery, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Patricia Kaazan
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Amanda Lim
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
| | | | - Dion A Gouskos
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Julie Marker
- Cancer Voices SA, Adelaide, South Australia, Australia
| | - Cheri Ostroff
- University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Geraint Rogers
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - Nicholas Arpaia
- Department of Microbiology & Immunology, Vagelos College of Physicians and Surgeons of Columbia University, New York, NY, 10032, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10027, USA
| | - Daniel L Worthley
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia
- Colonoscopy Clinic, Spring Hill, 4000, Queensland, Australia
| | - Susan L Woods
- Adelaide Medical School, University of Adelaide, Adelaide, SA, 5000, Australia.
- South Australian Health and Medical Research Institute (SAHMRI), Adelaide, SA, 5000, Australia.
| | - Tal Danino
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10027, USA.
- Data Science Institute, Columbia University, New York, NY, 10027, USA.
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Ding Y, Gao Y, Chen R, Zhang Z, Li Q, Jia T, Zhang T, Xu R, Shi W, Chen L, Song Y, Han Q, Xia X, Song J, Zhang J. Development of a novel multi-epitope oral DNA vaccine for rabies based on a food-borne microbial vector. Int J Biol Macromol 2024; 255:128085. [PMID: 37977454 DOI: 10.1016/j.ijbiomac.2023.128085] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/19/2023]
Abstract
Rabies has been with humans for a long time, and its special transmission route and almost 100 % lethality rate made it once a nightmare for humans. In this study, by predicting the rabies virus glycoprotein outer membrane region and nucleoprotein B-cell antigenic epitopes, the coding sequence of the predicted highly antigenic polypeptide region obtained was assembled using the eukaryotic expression vector pcDNA3.1(-), and then E. coli was used as the delivery vector. The immunogenicity and protective properties of the vaccine were verified by in vivo and in vitro experiments, which demonstrated that the vaccine could produce antibodies in mice and prolong the survival time of mice exposed to the strong virus without any side effects. This study demonstrated that the preparation of an oral rabies DNA vaccine using food-borne microorganisms as a transport vehicle is feasible and could be a new strategy to eradicate rabies starting with wild animals.
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Affiliation(s)
- Yi Ding
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China; Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Yuanyuan Gao
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Rui Chen
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Zhenxing Zhang
- Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Qiang Li
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Ting Jia
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Taoping Zhang
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Ruixian Xu
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Wengang Shi
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Lu Chen
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Yuzhu Song
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Qinqin Han
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Xueshan Xia
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China
| | - Jianling Song
- Yunnan Tropical and Subtropical Animal Virus Disease Laboratory, Yunnan Animal Science and Veterinary Institute, Kunming 650224, China.
| | - Jinyang Zhang
- Molecular Medicine Research Centre of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jingming South Road, Kunming 650500, China.
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Garrido-Romero M, Pazos F, Sánchez-Martínez E, Benito C, Gómez-Ruiz JÁ, Borrego-Yaniz G, Bowes C, Broll H, Caminero A, Caro E, Chagoyen M, Chemaly M, Fernández-Dumont A, Gisavi H, Gkrintzali G, Khare S, Margolles A, Márquez A, Martín J, Merten C, Montilla A, Muñoz-Labrador A, Novoa J, Paraskevopoulos K, Payen C, Withers H, Ruas-Madiedo P, Ruiz L, Sanz Y, Jiménez-Saiz R, Moreno FJ. Relevance of gut microbiome research in food safety assessment. Gut Microbes 2024; 16:2410476. [PMID: 39360551 PMCID: PMC11451283 DOI: 10.1080/19490976.2024.2410476] [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: 05/08/2024] [Revised: 07/31/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024] Open
Abstract
The gut microbiome is indispensable for the host physiological functioning. Yet, the impact of non-nutritious dietary compounds on the human gut microbiota and the role of the gut microbes in their metabolism and potential adverse biological effects have been overlooked. Identifying potential hazards and benefits would contribute to protecting and harnessing the gut microbiome's role in supporting human health. We discuss the evidence on the potential detrimental impact of certain food additives and microplastics on the gut microbiome and human health, with a focus on underlying mechanisms and causality. We provide recommendations for the incorporation of gut microbiome science in food risk assessment and identify the knowledge and tools needed to fill these gaps. The incorporation of gut microbiome endpoints to safety assessments, together with well-established toxicity and mutagenicity studies, might better inform the risk assessment of certain contaminants in food, and/or food additives.
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Affiliation(s)
- Manuel Garrido-Romero
- Department of Bioactivity and Food Analysis, Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, CEI (UAM+CSIC), Madrid, Spain
| | - Florencio Pazos
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Elisa Sánchez-Martínez
- Department of Immunology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Carlos Benito
- Instituto de Gestión de la Innovación y del Conocimiento, INGENIO (CSIC and U. Politécnica de Valencia), Valencia, Spain
| | | | | | | | - Hermann Broll
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Alberto Caminero
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster Immunology Research Centre (MIRC), Schroeder Allergy and Immunology Research Institute (SAIRI), McMaster University, Hamilton, ON, Canada
| | | | - Mónica Chagoyen
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Marianne Chemaly
- French Agency for Food, Environmental and Occupational Health and Safety, ANSES, Hygiene and Quality of Poultry, Pig Products Unit, Ploufragan, France
| | | | | | | | - Sangeeta Khare
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Abelardo Margolles
- Group of Functionality and Ecology of Beneficial Microorganisms (MicroHealth), Instituto de Productos Lácteos (IPLA-CSIC), Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Ana Márquez
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | - Caroline Merten
- Administration luxembourgeoise vétérinaire et alimentaire (ALVA), Strassen, Luxembourg
| | - Antonia Montilla
- Department of Bioactivity and Food Analysis, Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, CEI (UAM+CSIC), Madrid, Spain
| | - Ana Muñoz-Labrador
- Department of Bioactivity and Food Analysis, Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, CEI (UAM+CSIC), Madrid, Spain
| | - Jorge Novoa
- Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | | | - Cyrielle Payen
- French Agency for Food, Environmental and Occupational Health and Safety, ANSES, Hygiene and Quality of Poultry, Pig Products Unit, Ploufragan, France
| | - Helen Withers
- Food Safety and Microbiology, Food Standards Australia New Zealand, Wellington, New Zealand
| | - Patricia Ruas-Madiedo
- Group of Functionality and Ecology of Beneficial Microorganisms (MicroHealth), Instituto de Productos Lácteos (IPLA-CSIC), Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Lorena Ruiz
- Group of Functionality and Ecology of Beneficial Microorganisms (MicroHealth), Instituto de Productos Lácteos (IPLA-CSIC), Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Asturias, Spain
| | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Centre Severo Ochoa, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Rodrigo Jiménez-Saiz
- Department of Immunology, Instituto de Investigación Sanitaria Hospital Universitario de La Princesa (IIS-Princesa), Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Department of Medicine, McMaster Immunology Research Centre (MIRC), Schroeder Allergy and Immunology Research Institute (SAIRI), McMaster University, Hamilton, ON, Canada
- Department of Immunology and Oncology, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria (UFV), Madrid, Spain
| | - F. Javier Moreno
- Department of Bioactivity and Food Analysis, Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, CEI (UAM+CSIC), Madrid, Spain
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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: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [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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Zhao Q, Wu J, Ding Y, Pang Y, Jiang C. Gut microbiota, immunity, and bile acid metabolism: decoding metabolic disease interactions. LIFE METABOLISM 2023; 2:load032. [PMID: 39872860 PMCID: PMC11749371 DOI: 10.1093/lifemeta/load032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 01/03/2025]
Abstract
In recent decades, the global prevalence of metabolic syndrome has surged, posing a significant public health challenge. Metabolic disorders, encompassing diabetes, obesity, nonalcoholic fatty liver disease, and polycystic ovarian syndrome, have been linked to alterations in the gut microbiota. Nonetheless, the connection between gut microbiota and host metabolic diseases warrants further investigation. In this review, we delve into the associations between various metabolic disorders and the gut microbiota, focusing on immune responses and bile acid (BA) metabolism. Notably, T helper cells, innate lymphoid cells, macrophages, and dendritic cells have been shown to modulate host metabolism through interactions with intestinal microorganisms and the release of cytokines. Furthermore, secondary BA metabolites, derived from the microbiota, are involved in the pathogenesis of metabolic diseases via the farnesoid X receptor and Takeda G protein-coupled receptor 5. By covering both aspects of this immune system-microorganism axis, we present a comprehensive overview of the roles played by the gut microbiota, microbiota-derived BA metabolites, and immune responses in metabolic diseases, as well as the interplay between these systems.
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Affiliation(s)
- Qixiang Zhao
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Jiayu Wu
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yong Ding
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Yanli Pang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
| | - Changtao Jiang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
- Center for Obesity and Metabolic Disease Research, School of Basic Medical Sciences, Peking University, Beijing 100191, China
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de Wit DF, Hanssen NMJ, Wortelboer K, Herrema H, Rampanelli E, Nieuwdorp M. Evidence for the contribution of the gut microbiome to obesity and its reversal. Sci Transl Med 2023; 15:eadg2773. [PMID: 37992156 DOI: 10.1126/scitranslmed.adg2773] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 09/27/2023] [Indexed: 11/24/2023]
Abstract
Obesity has become a worldwide pandemic affecting more than 650 million people and is associated with a high burden of morbidity. Alongside traditional risk factors for obesity, the gut microbiome has been identified as a potential factor in weight regulation. Although rodent studies suggest a link between the gut microbiome and body weight, human evidence for causality remains scarce. In this Review, we postulate that existing evidence remains to establish a contribution of the gut microbiome to the development of obesity in humans but that modified probiotic strains and supraphysiological dosages of microbial metabolites may be beneficial in combatting obesity.
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Affiliation(s)
- Douwe F de Wit
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
| | - Nordin M J Hanssen
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
| | - Koen Wortelboer
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
| | - Hilde Herrema
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, 1105AZ Amsterdam, Netherlands
| | - Elena Rampanelli
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, Netherlands
| | - Max Nieuwdorp
- Amsterdam UMC location University of Amsterdam, Experimental Vascular Medicine, 1105AZ Amsterdam, Netherlands
- Amsterdam Cardiovascular Sciences, Diabetes and Metabolism, 1105AZ Amsterdam, Netherlands
- Amsterdam UMC location Vrije Universiteit Medical Center, Department of Internal Medicine, Diabetes Center, 1105AZ Amsterdam, Netherlands
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Hsu CL, Schnabl B. The gut-liver axis and gut microbiota in health and liver disease. Nat Rev Microbiol 2023; 21:719-733. [PMID: 37316582 PMCID: PMC10794111 DOI: 10.1038/s41579-023-00904-3] [Citation(s) in RCA: 206] [Impact Index Per Article: 103.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 06/16/2023]
Abstract
The trillions of microorganisms in the human intestine are important regulators of health, and disruptions in the gut microbial communities can cause disease. The gut, liver and immune system have a symbiotic relationship with these microorganisms. Environmental factors, such as high-fat diets and alcohol consumption, can disrupt and alter microbial communities. This dysbiosis can lead to dysfunction of the intestinal barrier, translocation of microbial components to the liver and development or progression of liver disease. Changes in metabolites produced by gut microorganisms can also contribute to liver disease. In this Review, we discuss the importance of the gut microbiota in maintenance of health and the alterations in microbial mediators that contribute to liver disease. We present strategies for modulation of the intestinal microbiota and/or their metabolites as potential treatments for liver disease.
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Affiliation(s)
- Cynthia L Hsu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA.
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