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Li H, Hong L, Szymczak W, Orner E, Garber AI, Cooper VS, Chen W, De A, Tang JX, Mani S. Protocol for isolating single species of bacteria with swarming ability from human feces. STAR Protoc 2024; 5:102961. [PMID: 38573864 PMCID: PMC10999858 DOI: 10.1016/j.xpro.2024.102961] [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: 09/18/2023] [Revised: 11/20/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024] Open
Abstract
Understanding the specific movements of bacteria isolated from human feces can serve as a novel diagnostic and therapeutic tool for inflammatory bowel disease. Here, we present a protocol for a microbial swarming assay and to isolate the bacteria responsible for swarming activity. We describe steps for identifying bacteria using MALDI-TOF mass spectrometry and whole-genome sequencing. We then detail procedures for validating findings by observing the same swarming phenotype upon reperforming the swarming assay. For complete details on the use and execution of this protocol, please refer to De et al.1.
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Affiliation(s)
- Hao Li
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lilli Hong
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wendy Szymczak
- Montefiore Medical Center, Bronx, NY 10467, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Orner
- Montefiore Medical Center, Bronx, NY 10467, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA; Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Weijie Chen
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Intelligent Medicine Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Arpan De
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jay X Tang
- Brown University, Physics Department, Providence, RI 02912, USA
| | - Sridhar Mani
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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2
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Jing R, Zhang L, Li R, Yang Z, Song J, Wang Q, Cao N, Han G, Yin H. Milk-derived extracellular vesicles functionalized with anti-tumour necrosis factor-α nanobody and anti-microbial peptide alleviate ulcerative colitis in mice. J Extracell Vesicles 2024; 13:e12462. [PMID: 38840457 PMCID: PMC11154809 DOI: 10.1002/jev2.12462] [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: 01/08/2024] [Revised: 04/16/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024] Open
Abstract
Ulcerative colitis (UC) manifests clinically with chronic intestinal inflammation and microflora dysbiosis. Although biologics can effectively control inflammation, efficient delivery to the colon and colon epithelial cells remains challenging. Milk-derived extracellular vesicles (EV) show promise as an oral delivery tool, however, the ability to load biologics into EV presents challenges to therapeutic applications. Here, we demonstrate that fusing cell-penetrating peptide (TAT) to green fluorescent protein (GFP) enabled biologics loading into EV and protected against degradation in the gastrointestinal environment in vitro and in vivo after oral delivery. Oral administration of EV loaded with anti-tumour necrosis factor-α (TNF-α) nanobody (VHHm3F) (EVVHH) via TAT significantly reduced tissue TNF-α levels and alleviated pathologies in mice with acute UC, compared to VHH alone. In mice with chronic UC, simultaneously introducing VHH and an antimicrobial peptide LL37 into EV (EVLV), then administering orally improved intestinal barrier, inflammation and microbiota balance, resulted in relief of UC-induced depression and anxiety. Collectively, we demonstrated that oral delivery of EVLV effectively alleviated UC in mice and TAT efficiently loaded biologics into EV to confer protection from degradation in the gastrointestinal tract. This therapeutic strategy is promising for UC and is a simple and generalizable approach towards drug-loaded orally-administrable EV treatment for other diseases.
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Affiliation(s)
- Renwei Jing
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
| | - Leijie Zhang
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
| | - Ruibin Li
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
| | - Zhongqiu Yang
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
| | - Jun Song
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
| | - Qian Wang
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
| | - Nan Cao
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
| | - Gang Han
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
| | - HaiFang Yin
- State Key Laboratory of Experimental Hematology & The Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical Epigenetics & Key Laboratory of Immune Microenvironment and Disease (Ministry of Education) & School of Basic Medical Sciences & School of Medical TechnologyTianjin Medical UniversityTianjinChina
- Department of Clinical LaboratoryTianjin Medical University General HospitalTianjinChina
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3
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Lin C, Lin Y, Wang S, Wang J, Mao X, Zhou Y, Zhang H, Chen W, Wang G. Bifidobacterium animalis subsp. lactis boosts neonatal immunity: unravelling systemic defences against Salmonella. Food Funct 2024; 15:236-254. [PMID: 38054827 DOI: 10.1039/d3fo03686c] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Bifidobacterium animalis subsp. lactis may be a useful probiotic intervention for regulating neonatal intestinal immune responses and counteracting Salmonella infection. However, recent research has focused on intestinal immunity, leaving uncertainties regarding the central, peripheral, and neural immune responses in neonates. Therefore, this study investigated the role and mechanisms of B. animalis subsp. lactis in the systemic immune responses of neonatal rats following Salmonella infection. Through extremely early pretreatment with B. animalis subsp. lactis (6 hours postnatal), the neonatal rat gut microbiota was effectively reshaped, especially the Bifidobacterium community. In the rats pretreated with B. animalis subsp. lactis, Salmonella was less prevalent in the blood, liver, spleen, and intestines following infection. The intervention promoted T lymphocyte subset balance in the spleen and thymus and fostered neurodevelopment and neuroimmune balance in the brain. Furthermore, metabolic profiling showed a strong correlation between the metabolites in the serum and colon, supporting the view that B. animalis subsp. lactis pretreatment influences the systemic immune response by modifying the composition and metabolism of the gut microbiota. Overall, the results imply that B. animalis subsp. lactis pretreatment, through the coordinated regulation of colonic and serum metabolites, influences the systemic immune responses of neonatal rats against Salmonella infection.
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Affiliation(s)
- Chunxiu Lin
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Yugui Lin
- Microbiology Laboratory, Zhongshan Bo'ai Hospital, Southern Medical University, Zhongshan 528400, P. R. China
| | - Shunhe Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, P. R. China
| | - Jialiang Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi 214200, P. R. China
| | - Yonghua Zhou
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi 214064, P. R. China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, P. R. China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, P. R. China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, P. R. China
| | - Gang Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, P. R. China.
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, P. R. China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, P. R. China
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