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Santiago VF, Rosa-Fernandes L, Macedo-da-Silva J, Angeli CB, Mule SN, Marinho CRF, Torrecilhas AC, Marie SNK, Palmisano G. Isolation of Extracellular Vesicles Using Titanium Dioxide Microspheres. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1443:1-22. [PMID: 38409413 DOI: 10.1007/978-3-031-50624-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Extracellular vesicles (EVs) are bilayer membrane particles released from several cell types to the extracellular environment. EVs have a crucial role in cell-cell communication, involving different biological processes in health and diseases. Due to the potential of biomarkers for several diseases as diagnostic and therapeutic tools, it is relevant to understand the biology of the EVs and their content. One of the current challenges involving EVs is regarding the purification method, which is a critical step for EV's functional and characterization studies. Ultracentrifugation is the most used method for EV isolation, where the nanoparticles are separated in sequential centrifugation to isolate the EVs based on their size. However, for viscous biofluids such as plasma, there is a co-isolation of the most abundant proteins, which can impair the EV's protein identification due to the low abundance of these proteins and signal suppression by the most abundant plasma proteins. Emerging techniques have gained attention in recent years. Titanium dioxide (TiO2) is one of the most promising techniques due to its property for selective isolation based on the interaction with phospholipids in the EV membrane. Using a small amount of TiO2 beads and a low volume of plasma, it is possible to isolate EVs with reduced plasma protein co-isolation. This study describes a comprehensive workflow for the isolation and characterization of plasma extracellular vesicles (EVs) using mass spectrometry-based proteomics techniques. The aim of this chapter is describe the EV isolation using TiO2 beads enrichment and high-throughput mass spectrometry techniques to efficiently identify the protein composition of EVs in a fast and straightforward manner.
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Affiliation(s)
- Veronica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudia B Angeli
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Torrecilhas
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas; Departamento de Ciências Farmacêuticas; Laboratório de Imunologia Celular e Bioquímica de Fungos e Protozoários. Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Suely N K Marie
- Laboratory of Molecular and Cellular Biology (LIM15), Department of Neurology, Fac-uldade de Medicina FMUSP, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia.
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Kaisanlahti A, Salmi S, Kumpula S, Amatya SB, Turunen J, Tejesvi M, Byts N, Tapiainen T, Reunanen J. Bacterial extracellular vesicles - brain invaders? A systematic review. Front Mol Neurosci 2023; 16:1227655. [PMID: 37781094 PMCID: PMC10537964 DOI: 10.3389/fnmol.2023.1227655] [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: 05/23/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Knowledge on the human gut microbiota in health and disease continues to rapidly expand. In recent years, changes in the gut microbiota composition have been reported as a part of the pathology in numerous neurodegenerative diseases. Bacterial extracellular vesicles (EVs) have been suggested as a novel mechanism for the crosstalk between the brain and gut microbiota, physiologically connecting the observed changes in the brain to gut microbiota dysbiosis. Methods Publications reporting findings on bacterial EVs passage through the blood-brain barrier were identified in PubMed and Scopus databases. Results The literature search yielded 138 non-duplicate publications, from which 113 records were excluded in title and abstract screening step. From 25 publications subjected to full-text screening, 8 were excluded. The resulting 17 publications were considered for the review. Discussion Bacterial EVs have been described with capability to cross the blood-brain barrier, but the mechanisms behind the crossing remain largely unknown. Importantly, very little data exists in this context on EVs secreted by the human gut microbiota. This systematic review summarizes the present evidence of bacterial EVs crossing the blood-brain barrier and highlights the importance of future research on gut microbiota-derived EVs in the context of gut-brain communication across the blood-brain barrier.
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Affiliation(s)
- Anna Kaisanlahti
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Sonja Salmi
- Disease Networks Research Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Sohvi Kumpula
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Sajeen Bahadur Amatya
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Jenni Turunen
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Mysore Tejesvi
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Nadiya Byts
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
| | - Terhi Tapiainen
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
- Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Justus Reunanen
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland
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3
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Luo R, Chang Y, Liang H, Zhang W, Song Y, Li G, Yang C. Interactions between extracellular vesicles and microbiome in human diseases: New therapeutic opportunities. IMETA 2023; 2:e86. [PMID: 38868436 PMCID: PMC10989913 DOI: 10.1002/imt2.86] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 12/21/2022] [Accepted: 01/14/2023] [Indexed: 06/14/2024]
Abstract
In recent decades, accumulating research on the interactions between microbiome homeostasis and host health has broadened new frontiers in delineating the molecular mechanisms of disease pathogenesis and developing novel therapeutic strategies. By transporting proteins, nucleic acids, lipids, and metabolites in their versatile bioactive molecules, extracellular vesicles (EVs), natural bioactive cell-secreted nanoparticles, may be key mediators of microbiota-host communications. In addition to their positive and negative roles in diverse physiological and pathological processes, there is considerable evidence to implicate EVs secreted by bacteria (bacterial EVs [BEVs]) in the onset and progression of various diseases, including gastrointestinal, respiratory, dermatological, neurological, and musculoskeletal diseases, as well as in cancer. Moreover, an increasing number of studies have explored BEV-based platforms to design novel biomedical diagnostic and therapeutic strategies. Hence, in this review, we highlight the recent advances in BEV biogenesis, composition, biofunctions, and their potential involvement in disease pathologies. Furthermore, we introduce the current and emerging clinical applications of BEVs in diagnostic analytics, vaccine design, and novel therapeutic development.
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Affiliation(s)
- Rongjin Luo
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Department of Spine Surgery, Honghui HospitalXi'an Jiaotong UniversityXi'anChina
| | - Yanmin Chang
- Department of Neurology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Huaizhen Liang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Weifeng Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yu Song
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Gaocai Li
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Cao Yang
- Department of Orthopaedics, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
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Hosseini-Giv N, Basas A, Hicks C, El-Omar E, El-Assaad F, Hosseini-Beheshti E. Bacterial extracellular vesicles and their novel therapeutic applications in health and cancer. Front Cell Infect Microbiol 2022; 12:962216. [PMID: 36439225 PMCID: PMC9691856 DOI: 10.3389/fcimb.2022.962216] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/20/2022] [Indexed: 10/03/2023] Open
Abstract
Bacterial cells communicate with host cells and other bacteria through the release of membrane vesicles known as bacterial extracellular vesicles (BEV). BEV are established mediators of intracellular signaling, stress tolerance, horizontal gene transfer, immune stimulation and pathogenicity. Both Gram-positive and Gram-negative bacteria produce extracellular vesicles through different mechanisms based on cell structure. BEV contain and transfer different types of cargo such as nucleic acids, proteins and lipids, which are used to interact with and affect host cells such as cytotoxicity and immunomodulation. The role of these membranous microvesicles in host communication, intra- and inter-species cell interaction and signaling, and contribution to various diseases have been well demonstrated. Due to their structure, these vesicles can be easily engineered to be utilized for clinical application, as shown with its role in vaccine therapy, and could be used as a diagnostic and cancer drug delivery tool in the future. However, like other novel therapeutic approaches, further investigation and standardization is imperative for BEV to become a routine vector or a conventional treatment method.
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Affiliation(s)
- Niloufar Hosseini-Giv
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Alyza Basas
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Chloe Hicks
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Emad El-Omar
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Fatima El-Assaad
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Elham Hosseini-Beheshti
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
- The Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
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Jing X, Gong Y, Pan H, Meng Y, Ren Y, Diao Z, Mu R, Xu T, Zhang J, Ji Y, Li Y, Wang C, Qu L, Cui L, Ma B, Xu J. Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature. ISME COMMUNICATIONS 2022; 2:106. [PMID: 37938284 PMCID: PMC9723661 DOI: 10.1038/s43705-022-00188-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 01/25/2023]
Abstract
Due to the challenges in detecting in situ activity and cultivating the not-yet-cultured, functional assessment and mining of living microbes from nature has typically followed a 'culture-first' paradigm. Here, employing phosphate-solubilizing microbes (PSM) as model, we introduce a 'screen-first' strategy that is underpinned by a precisely one-cell-resolution, complete workflow of single-cell Raman-activated Sorting and Cultivation (scRACS-Culture). Directly from domestic sewage, individual cells were screened for in-situ organic-phosphate-solubilizing activity via D2O intake rate, sorted by the function via Raman-activated Gravity-driven Encapsulation (RAGE), and then cultivated from precisely one cell. By scRACS-Culture, pure cultures of strong organic PSM including Comamonas spp., Acinetobacter spp., Enterobacter spp. and Citrobacter spp., were derived, whose phosphate-solubilizing activities in situ are 90-200% higher than in pure culture, underscoring the importance of 'screen-first' strategy. Moreover, employing scRACS-Seq for post-RACS cells that remain uncultured, we discovered a previously unknown, low-abundance, strong organic-PSM of Cutibacterium spp. that employs secretary metallophosphoesterase (MPP), cell-wall-anchored 5'-nucleotidase (encoded by ushA) and periplasmic-membrane located PstSCAB-PhoU transporter system for efficient solubilization and scavenging of extracellular phosphate in sewage. Therefore, scRACS-Culture and scRACS-Seq provide an in situ function-based, 'screen-first' approach for assessing and mining microbes directly from the environment.
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Affiliation(s)
- Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Huihui Pan
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Yishang Ren
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Zhidian Diao
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Runzhi Mu
- Qingdao Zhang Cun River Water Co., Ltd, Qingdao, Shandong, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
- Qingdao Single-Cell Biotechnology Co., Ltd, Qingdao, Shandong, China
| | - Yuandong Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Chen Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- Shandong Energy Institute, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China
| | - Lingyun Qu
- The First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian, China
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Shandong Energy Institute, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China.
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Shandong Energy Institute, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, China.
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Protein content of the Oenococcus oeni extracellular vesicles-enriched fraction. Food Microbiol 2022; 106:104038. [DOI: 10.1016/j.fm.2022.104038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/04/2022] [Accepted: 04/10/2022] [Indexed: 11/23/2022]
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7
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Gao J, Su Y, Wang Z. Engineering bacterial membrane nanovesicles for improved therapies in infectious diseases and cancer. Adv Drug Deliv Rev 2022; 186:114340. [PMID: 35569561 PMCID: PMC9899072 DOI: 10.1016/j.addr.2022.114340] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/08/2022] [Accepted: 05/08/2022] [Indexed: 02/06/2023]
Abstract
Research on bacterial membrane vesicles (BMVs) is an emerging topic, and the goal is to address whether BMVs can bring translational tools to improve current therapies. In this review, we provided the updated studies on BMVs including their production, their types, and therapeutic regimens for treating infectious diseases and cancers. We described several platforms of BMVs, such as outer membrane vesicles (OMVs), inner membrane vesicles (IMVs) and double membrane vesicles (DMVs), and those structures were produced from Gram-negative or Gram-positive bacteria. We also discussed how to engineer and formulate new and novel BMVs using chemical, physical, and genetic methods. For therapies, we analyzed current methods for loading drugs in BMVs and discussed their limitations. Finally, we reviewed several therapeutic platforms of BMVs that have been exploited in improving the treatments of infectious diseases and cancers. Although BMVs offer the promising biomedical applications, it is needed to develop rigorous approaches and methods to generate reproducible and scalable drug delivery systems for translation.
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Affiliation(s)
| | | | - Zhenjia Wang
- Corresponding author at: 205 East Spokane Falls BLVD, Spokane, WA 99202, United States of America. (Z. Wang)
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8
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Different Cutibacterium acnes Phylotypes Release Distinct Extracellular Vesicles. Int J Mol Sci 2022; 23:ijms23105797. [PMID: 35628607 PMCID: PMC9147970 DOI: 10.3390/ijms23105797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial extracellular vesicles (EVs) perform various biological functions, including those that are critical to microbes. Determination of EVs composition allows for a deep understanding of their role in the bacterial community and communication among them. Cutibacterium acnes, formerly Propionibacterium acnes, are commensal bacteria responsible for various infections, e.g., prosthesis, sarcoidosis, soft-tissue infections, and the most known but still controversial—acnes lesion. In C. acnes, three major phylotypes represented variable disease associations. Herein, for the first time, we present a comparative analysis of EVs obtained from three C. acnes phylotypes (IA1, IB, and II) to demonstrate the existence of differences in their protein and lipid composition. In the following work, the morphological analysis of EVs was performed, and the SDS-PAGE protein profile and the lipid profile were presented using the TLC and MALDI-TOF MS methods. This study allowed us to show major differences between the protein and lipid composition of C. acnes EVs. This is a clear indication that EVs released by different phylotypes of the one species are not identical to each other in terms of composition and should be separately analyzed each time to obtain reliable results.
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Yang J, Shin TS, Kim JS, Jee YK, Kim YK. A new horizon of precision medicine: combination of the microbiome and extracellular vesicles. Exp Mol Med 2022; 54:466-482. [PMID: 35459887 PMCID: PMC9028892 DOI: 10.1038/s12276-022-00748-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/09/2021] [Accepted: 12/23/2021] [Indexed: 11/10/2022] Open
Abstract
Over several decades, the disease pattern of intractable disease has changed from acute infection to chronic disease accompanied by immune and metabolic dysfunction. In addition, scientific evidence has shown that humans are holobionts; of the DNA in humans, 1% is derived from the human genome, and 99% is derived from microbial genomes (the microbiome). Extracellular vesicles (EVs) are lipid bilayer-delimited nanoparticles and key messengers in cell-to-cell communication. Many publications indicate that microbial EVs are both positively and negatively involved in the pathogenesis of various intractable diseases, including inflammatory diseases, metabolic disorders, and cancers. Microbial EVs in feces, blood, and urine show significant differences in their profiles between patients with a particular disease and healthy subjects, demonstrating the potential of microbial EVs as biomarkers for disease diagnosis, especially for assessing disease risk. Furthermore, microbial EV therapy offers a variety of advantages over live biotherapeutics and human cell EV (or exosome) therapy for the treatment of intractable diseases. In summary, microbial EVs are a new tool in medicine, and microbial EV technology might provide us with innovative diagnostic and therapeutic solutions in precision medicine. The tiny membrane-bound vesicles containing various biomolecules that the organisms comprising our microbiome release could offer a powerful tool for precision medicine. Our bodies are home to trillions of microbes, which interact closely with our tissues to maintain a healthy physiological environment. Yoon-Keun Kim of the Institute of MD Healthcare, Seoul, South Korea, and colleagues have reviewed current research into the extracellular vesicles that these microbes use to communicate with other microbes and their human hosts. The authors note that these vesicles affect tissues throughout the body, and their activities have been linked to various disorders including asthma, Crohn’s disease and cancer. A deeper understanding of how these vesicles prevent or accelerate various conditions in different individuals could yield useful new diagnostic biomarkers and provide the foundation for interventions that are optimized for each patient.
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Affiliation(s)
- Jinho Yang
- Institute of MD Healthcare Inc., Seoul, Republic of Korea
| | - Tae-Seop Shin
- Institute of MD Healthcare Inc., Seoul, Republic of Korea
| | - Jong Seong Kim
- Institute of MD Healthcare Inc., Seoul, Republic of Korea
| | - Young-Koo Jee
- Department of Internal Medicine, Dankook University College of Medicine, Cheonan, Republic of Korea
| | - Yoon-Keun Kim
- Institute of MD Healthcare Inc., Seoul, Republic of Korea.
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Stødkilde K, Nielsen JT, Petersen SV, Paetzold B, Brüggemann H, Mulder FAA, Andersen CBF. Solution Structure of the Cutibacterium acnes-Specific Protein RoxP and Insights Into Its Antioxidant Activity. Front Cell Infect Microbiol 2022; 12:803004. [PMID: 35223541 PMCID: PMC8873378 DOI: 10.3389/fcimb.2022.803004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
Cutibacterium acnes is a predominant bacterium on human skin and is generally regarded as commensal. Recently, the abundantly secreted protein produced by C. acnes, RoxP, was shown to alleviate radical-induced cell damage, presumably via antioxidant activity, which could potentially be harnessed to fortify skin barrier function. The aim of this study was to determine the structure of RoxP and elucidate the mechanisms behind its antioxidative effect. Here, we present the solution structure of RoxP revealing a compact immunoglobulin-like domain containing a long flexible loop which, in concert with the core domain, forms a positively charged groove that could function as a binding site for cofactors or substrates. Although RoxP shares structural features with cell-adhesion proteins, we show that it does not appear to be responsible for adhesion of C. acnes bacteria to human keratinocytes. We identify two tyrosine-containing stretches located in the flexible loop of RoxP, which appear to be responsible for the antioxidant activity of RoxP.
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Affiliation(s)
| | | | | | | | | | - Frans A A Mulder
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
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Gut Microbiota Extracellular Vesicles as Signaling Molecules Mediating Host-Microbiota Communications. Int J Mol Sci 2021; 22:ijms222313166. [PMID: 34884969 PMCID: PMC8658398 DOI: 10.3390/ijms222313166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
Over the past decade, gut microbiota dysbiosis has been linked to many health disorders; however, the detailed mechanism of this correlation remains unclear. Gut microbiota can communicate with the host through immunological or metabolic signalling. Recently, microbiota-released extracellular vesicles (MEVs) have emerged as significant mediators in the intercellular signalling mechanism that could be an integral part of microbiota-host communications. MEVs are small membrane-bound vesicles that encase a broad spectrum of biologically active compounds (i.e., proteins, mRNA, miRNA, DNA, carbohydrates, and lipids), thus mediating the horizontal transfer of their cargo across intra- and intercellular space. In this study, we provide a comprehensive and in-depth discussion of the biogenesis of microbial-derived EVs, their classification and routes of production, as well as their role in inter-bacterial and inter-kingdom signaling.
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Çelik P, Derkuş B, Erdoğan K, Barut D, Manga EB, Yıldırım Y, Pecha S, Çabuk A. Bacterial membrane vesicle functions, laboratory methods, and applications. Biotechnol Adv 2021; 54:107869. [PMID: 34793882 DOI: 10.1016/j.biotechadv.2021.107869] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022]
Abstract
Bacterial membrane vesicles are cupped-shaped structures formed by bacteria in response to environmental stress, genetic alteration, antibiotic exposure, and others. Due to the structural similarities shared with the producer organism, they can retain certain characteristics like stimulating immune responses. They are also able to carry molecules for long distances, without changes in the concentration and integrity of the molecule. Bacteria originally secrete membrane vesicles for gene transfer, excretion, cell to cell interaction, pathogenesis, and protection against phages. These functions are unique and have several innovative applications in the pharmaceutical industry that have attracted both scientific and commercial interest.This led to the development of efficient methods to artificially stimulate vesicle production, purification, and manipulation in the lab at nanoscales. Also, for specific applications, engineering methods to impart pathogen antigens against specific diseases or customization as cargo vehicles to deliver payloads to specific cells have been reported. Many applications of bacteria membrane vesicles are in cancer drugs, vaccines, and adjuvant development with several candidates in clinical trials showing promising results. Despite this, applications in therapy and commercialization stay timid probably due to some challenges one of which is the poor understanding of biogenesis mechanisms. Nevertheless, so far, bacterial membrane vesicles seem to be a reliable and cost-efficient technology with several therapeutic applications. Research toward characterizing more membrane vesicles, genetic engineering, and nanotechnology will enable the scope of applications to widen. This might include solutions to other currently faced medical and healthcare-related challenges.
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Affiliation(s)
- PınarAytar Çelik
- Environmental Protection and Control Program, Eskişehir Osmangazi University, Eskişehir 26110, Turkey; Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey.
| | - Burak Derkuş
- Department of Chemistry, Faculty of Science, Ankara University, 06560 Ankara, Turkey
| | - Kübra Erdoğan
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Dilan Barut
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Enuh Blaise Manga
- Department of Biotechnology and Biosafety, Graduate School of Natural and Applied Science, Eskisehir Osmangazi University, 26040 Eskisehir, Turkey
| | - Yalın Yıldırım
- Department of Cardiovascular Surgery, University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Simon Pecha
- Department of Cardiovascular Surgery, University Heart & Vascular Center Hamburg, Hamburg, Germany
| | - Ahmet Çabuk
- Department of Biology, Faculty of Science and Letter, Eskişehir Osmangazi University, Eskişehir 26040, Turkey
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Staudenmaier L, Focken J, Schlatterer K, Kretschmer D, Schittek B. Bacterial membrane vesicles shape Staphylococcus aureus skin colonization and induction of innate immune responses. Exp Dermatol 2021; 31:349-361. [PMID: 34679243 DOI: 10.1111/exd.14478] [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: 06/15/2021] [Revised: 09/10/2021] [Accepted: 10/17/2021] [Indexed: 11/30/2022]
Abstract
Staphylococcus aureus colonization is abundant on the skin of atopic dermatitis (AD) patients where it contributes to skin inflammation. S. aureus produces virulence factors that distinguish it from commensal skin bacteria such as S. epidermidis and S. lugdunensis. However, it has remained unclear, which of these virulence factors have the strongest impact on AD. Membrane vesicles (MVs) are released by pathogenic bacteria and might play an essential role in the long-distance delivery of bacterial effectors such as virulence factors. We show that MVs are also released by skin commensals in a similar quantity and membrane lipid amount as those from pathogenic S. aureus. Interestingly, MVs from skin commensals can protect against S. aureus skin colonization by conditioning human skin for enhanced defence. In contrast, MVs released by S. aureus are able to induce CXCL8 and TNF-α in primary human keratinocytes, recruit neutrophils and induce neutrophil extracellular traps, which enhance S. aureus skin colonization. CXCL8 induction is TLR2- and NFkB-dependent and the induction level correlates with the membrane lipid and protein A content of the MVs. Interestingly, MVs of S. aureus strains from the lesional skin of AD patients show an enhanced membrane lipid and protein A content compared to the strains from the non-lesional sites and have an enhanced proinflammatory potential. Our data underline the complex interplay in host- and bacterial derived factors in S. aureus skin colonization and the important role of bacterial derived MVs and their membrane lipid and protein A content in skin inflammatory disorders.
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Affiliation(s)
- Lena Staudenmaier
- Department of Dermatology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Jule Focken
- Department of Dermatology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Katja Schlatterer
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, Tübingen, Germany
| | - Dorothee Kretschmer
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.,Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology, University of Tübingen, Tübingen, Germany
| | - Birgit Schittek
- Department of Dermatology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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Abstract
Extracellular vesicles (EVs) are membrane-derived lipid bilayers secreted by bacteria and eukaryotic cells. Bacterial membrane vesicles were discovered over 60 years ago and have been extensively studied in Gram-negative bacteria. During their production, EVs are loaded with proteins, nucleic acids, and various compounds that are subsequently released into the environment. Depending on the packaged cargo, EVs have a broad spectrum of action and are involved in pathogenesis, antibiotic resistance, nutrient uptake, and nucleic acid transfer. Due to differences in cell wall structure, EVs in Gram-positive bacteria have been disregarded for decades, and our understanding of their biogenesis and host cell interaction is incomplete. Recently, studies on bacteria such as Staphylococcus aureus, Streptococcus spp., Bacillus subtilis, and Mycobacterium spp. have demonstrated EV production in Gram-positive bacteria and shown the great importance EVs have in Gram-positive bacterial physiology and disease progression. Here, we review the latest findings on the biogenesis and functions of EVs from Gram-positive bacteria and identify key areas for future research.
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Suzuki I, Shimizu T, Senpuku H. Short chain fatty acids induced the type 1 and type 2 fimbrillin-dependent and fimbrillin-independent initial attachment and colonization of Actinomyces oris monoculture but not coculture with streptococci. BMC Microbiol 2020; 20:329. [PMID: 33129273 PMCID: PMC7603776 DOI: 10.1186/s12866-020-01976-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Actinomyces oris is an early colonizer and has two types of fimbriae on its cell surface, type 1 fimbriae (FimP and FimQ) and type 2 fimbriae (FimA and FimB), which contribute to the attachment and coaggregation with other bacteria and the formation of biofilm on the tooth surface, respectively. Short-chain fatty acids (SCFAs) are metabolic products of oral bacteria including A. oris and regulate pH in dental plaques. To clarify the relationship between SCFAs and fimbrillins, effects of SCFAs on the initial attachment and colonization (INAC) assay using A. oris wild type and fimbriae mutants was investigated. INAC assays using A. oris MG1 strain cells were performed with SCFAs (acetic, butyric, propionic, valeric and lactic acids) or a mixture of them on human saliva-coated 6-well plates incubated in TSB with 0.25% sucrose for 1 h. The INAC was assessed by staining live and dead cells that were visualized with a confocal microscope. RESULTS Among the SCFAs, acetic, butyric and propionic acids and a mixture of acetic, butyric and propionic acids induced the type 1 and type 2 fimbriae-dependent and independent INAC by live A. oris, but these cells did not interact with streptococci. The main effects might be dependent on the levels of the non-ionized acid forms of the SCFAs in acidic stress conditions. GroEL was also found to be a contributor to the FimA-independent INAC by live A. oris cells stimulated with non-ionized acid. CONCLUSION SCFAs affect the INAC-associated activities of the A. oris fimbrillins and non-fimbrillins during ionized and non-ionized acid formations in the form of co-culturing with other bacteria in the dental plaque but not impact the interaction of A. oris with streptococci.
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Affiliation(s)
- Itaru Suzuki
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.,Department of Pediatric Dentistry, Nihon University Graduate School of Dentistry at Matsudo, Chiba, Japan
| | - Takehiko Shimizu
- Department of Pediatric Dentistry, Nihon University Graduate School of Dentistry at Matsudo, Chiba, Japan
| | - Hidenobu Senpuku
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan.
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Proteomic and metabolic characterization of membrane vesicles derived from Streptococcus mutans at different pH values. Appl Microbiol Biotechnol 2020; 104:9733-9748. [DOI: 10.1007/s00253-020-10563-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/12/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
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17
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Bose S, Aggarwal S, Singh DV, Acharya N. Extracellular vesicles: An emerging platform in gram-positive bacteria. MICROBIAL CELL (GRAZ, AUSTRIA) 2020; 7:312-322. [PMID: 33335921 PMCID: PMC7713254 DOI: 10.15698/mic2020.12.737] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/07/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022]
Abstract
Extracellular vesicles (EV), also known as membrane vesicles, are produced as an end product of secretion by both pathogenic and non-pathogenic bacteria. Several reports suggest that archaea, gram-negative bacteria, and eukaryotic cells secrete membrane vesicles as a means for cell-free intercellular communication. EVs influence intercellular communication by transferring a myriad of biomolecules including genetic information. Also, EVs have been implicated in many phenomena such as stress response, intercellular competition, lateral gene transfer, and pathogenicity. However, the cellular process of secreting EVs in gram-positive bacteria is less studied. A notion with the thick cell-walled microbes such as gram-positive bacteria is that the EV release is impossible among them. The role of gram-positive EVs in health and diseases is being studied gradually. Being nano-sized, the EVs from gram-positive bacteria carry a diversity of cargo compounds that have a role in bacterial competition, survival, invasion, host immune evasion, and infection. In this review, we summarise the current understanding of the EVs produced by gram-positive bacteria. Also, we discuss the functional aspects of these components while comparing them with gram-negative bacteria.
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Affiliation(s)
- Swagata Bose
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India
| | - Shifu Aggarwal
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India
| | - Durg Vijai Singh
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India
- Department of Biotechnology, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya-824236, India
| | - Narottam Acharya
- Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar-751023, India
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18
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Dagnelie MA, Corvec S, Khammari A, Dréno B. Bacterial extracellular vesicles: A new way to decipher host-microbiota communications in inflammatory dermatoses. Exp Dermatol 2019; 29:22-28. [PMID: 31633842 DOI: 10.1111/exd.14050] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/19/2019] [Accepted: 10/04/2019] [Indexed: 01/18/2023]
Abstract
Bacterial extracellular vesicles (EVs) are bilayered lipid membrane structures, bearing integral proteins and able to carry diverse cargo outside the cell to distant sites. In microorganisms, EVs carry several types of molecules: proteins, glycoproteins, mRNAs and small RNA species, as mammalian EVs do, but also carbohydrates. Studying EVs opens a whole new world of possibilities to better understand the interplay between host and bacteria crosstalks, although there are still many questions to be answered in the field, especially when it comes to microbiota-derived EVs. In this review, we propose to summarize and analyse the current literature about bacterial EVs and possible clinical applications, through answering three main questions: (a) What are bacterial EVs? (b) What are EV impacts on skin inflammatory disease physiopathology? (iii) What are the possible and expected clinical applications of EVs to treat inflammatory skin diseases?
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Affiliation(s)
- Marie-Ange Dagnelie
- Dermatology Department, CHU Nantes, CIC 1413, CRCINA, University Nantes, Nantes, France
| | - Stéphane Corvec
- Bacteriology Department, CHU Nantes, CRCINA, University Nantes, Nantes, France
| | - Amir Khammari
- Dermatology Department, CHU Nantes, CIC 1413, CRCINA, University Nantes, Nantes, France
| | - Brigitte Dréno
- Dermatology Department, CHU Nantes, CIC 1413, CRCINA, University Nantes, Nantes, France
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19
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Dagnelie MA, Corvec S, Saint-Jean M, Nguyen JM, Khammari A, Dréno B. Cutibacterium acnes phylotypes diversity loss: a trigger for skin inflammatory process. J Eur Acad Dermatol Venereol 2019; 33:2340-2348. [PMID: 31299116 DOI: 10.1111/jdv.15795] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 05/24/2019] [Indexed: 12/27/2022]
Abstract
BACKGROUND Acne has long been understood as a multifactorial chronic inflammatory disease of the pilosebaceous follicle, where Cutibacterium acnes (subdivided into six main phylotypes) is a crucial factor. In parallel, the loss of microbial diversity among the skin commensal communities has recently been shown as often accompanied by inflammatory skin disorders. OBJECTIVE This study investigated the association of C. acnes phylotype diversity loss and the impact on Innate Immune System (IIS) activation. METHODS The IIS response of skin after incubation with phylotypes IA1, II or III individually and with the combination of IA1 + II + III phylotypes, was studied in an in vitro skin explant system. The inflammatory response was monitored by immunohistochemistry and ELISA assays, targeting a selection of Innate Immune Markers (IIMs) (IL-6, IL-8, IL-10, IL-17, TGF-β). RESULTS IIMs were significantly upregulated in skin when being incubated with phylotype IA1 alone compared with the combination IA1 + II + III. In parallel, ELISA assays confirmed these results in supernatants for IL-17, IL-8 and IL-10. CONCLUSION We identify the loss of C. acnes phylotype diversity as a trigger for IIS activation, leading to cutaneous inflammation. These innovative data underline the possibility to set up new approaches to treat acne. Indeed, maintaining the balance between the different phylotypes of C. acnes may be an interesting target for the development of drugs.
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Affiliation(s)
- M-A Dagnelie
- Dermatology Department, CHU Nantes, CIC 1413, CRCINA, University Nantes, Nantes, France
| | - S Corvec
- Bacteriology Department, CHU Nantes, CRCINA, University Nantes, Nantes, France
| | - M Saint-Jean
- Dermatology Department, CHU Nantes, CIC 1413, CRCINA, University Nantes, Nantes, France
| | - J-M Nguyen
- Biostatistical Department, CHU Nantes, CIC 1413, CRCINA, University Nantes, Nantes, France
| | - A Khammari
- Dermatology Department, CHU Nantes, CIC 1413, CRCINA, University Nantes, Nantes, France
| | - B Dréno
- Dermatology Department, CHU Nantes, CIC 1413, CRCINA, University Nantes, Nantes, France
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Hou R, Li Y, Sui Z, Yuan H, Yang K, Liang Z, Zhang L, Zhang Y. Advances in exosome isolation methods and their applications in proteomic analysis of biological samples. Anal Bioanal Chem 2019; 411:5351-5361. [PMID: 31267193 DOI: 10.1007/s00216-019-01982-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/02/2019] [Accepted: 06/14/2019] [Indexed: 12/20/2022]
Abstract
Exosomes are membrane-bound vesicles secreted by cells, and contain various important biological molecules, such as lipids, proteins, messenger RNAs, microRNAs, and noncoding RNAs. Emerging evidence demonstrates that proteomic analysis of exosomes is of great significance in studying metabolic diseases, tumor metastasis, immune regulation, and so forth. However, exosome proteomic analysis has high requirements with regard to the purity of collected exosomes. Here recent advances in the methods for isolating exosomes and their applications in proteomic analysis are summarized. Graphical abstract.
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Affiliation(s)
- Rui Hou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
| | - Yilan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
| | - Huiming Yuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China.
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, Liaoning, China
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Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies. Microorganisms 2019; 7:microorganisms7050128. [PMID: 31086023 PMCID: PMC6560440 DOI: 10.3390/microorganisms7050128] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/25/2022] Open
Abstract
The anaerobic bacterium Propionibacterium acnes is believed to play an important role in the pathophysiology of the common skin disease acne vulgaris. Over the last 10 years our understanding of the taxonomic and intraspecies diversity of this bacterium has increased tremendously, and with it the realisation that particular strains are associated with skin health while others appear related to disease. This extensive review will cover our current knowledge regarding the association of P. acnes phylogroups, clonal complexes and sequence types with acne vulgaris based on multilocus sequence typing of isolates, and direct ribotyping of the P. acnes strain population in skin microbiome samples based on 16S rDNA metagenomic data. We will also consider how multi-omic and biochemical studies have facilitated our understanding of P. acnes pathogenicity and interactions with the host, thus providing insights into why certain lineages appear to have a heightened capacity to contribute to acne vulgaris development, while others are positively associated with skin health. We conclude with a discussion of new therapeutic strategies that are currently under investigation for acne vulgaris, including vaccination, and consider the potential of these treatments to also perturb beneficial lineages of P. acnes on the skin.
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O’Neill AM, Gallo RL. Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris. MICROBIOME 2018; 6:177. [PMID: 30285861 PMCID: PMC6169095 DOI: 10.1186/s40168-018-0558-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/11/2018] [Indexed: 05/07/2023]
Abstract
Acne is one of the most common skin diseases worldwide and results in major health care costs and significant morbidity to severely affected individuals. However, the pathophysiology of this disorder is not well understood. Host-microbiome interactions that affect both innate and adaptive immune homeostasis appear to be a central factor in this disease, with recent observations suggesting that the composition and activities of the microbiota in acne is perturbed. Staphylococcus epidermidis and Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes) are two major inhabitants of the skin that are thought to contribute to the disease but are also known to promote health by inhibiting the growth and invasion of pathogens. Because C. acnes is ubiquitous in sebaceous-rich skin, it is typically labeled as the etiological agent of acne yet it fails to fulfill all of Koch's postulates. The outdated model of acne progression proposes that increased sebum production promotes over-proliferation of C. acnes in a plugged hair follicle, thereby driving inflammation. In contrast, growing evidence indicates that C. acnes is equally abundant in both unaffected and acne-affected follicles. Moreover, recent advances in metagenomic sequencing of the acne microbiome have revealed a diverse population structure distinct from healthy individuals, uncovering new lineage-specific virulence determinants. In this article, we review recent developments in the interactions of skin microbes with host immunity, discussing the contribution of dysbiosis to the immunobiology of acne and newly emerging skin microbiome-based therapeutics to treat acne.
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Affiliation(s)
- Alan M. O’Neill
- Department of Dermatology, University of California San Diego, La Jolla, CA 92037 USA
| | - Richard L. Gallo
- Department of Dermatology, University of California San Diego, La Jolla, CA 92037 USA
- Department of Dermatology, University of California San Diego, 9500 Gillman Dr., #0869, La Jolla, CA 92093 USA
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Bhardwaj N, Verma VK, Chaturvedi V, Verma P. GH10 XynF1 and Xyn11A: the predominant xylanase identified in the profiling of extracellular proteome of Aspergillus oryzae LC1. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1378-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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24
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do Carmo FLR, Silva WM, Tavares GC, Ibraim IC, Cordeiro BF, Oliveira ER, Rabah H, Cauty C, da Silva SH, Canário Viana MV, Caetano ACB, Dos Santos RG, de Oliveira Carvalho RD, Jardin J, Pereira FL, Folador EL, Le Loir Y, Figueiredo HCP, Jan G, Azevedo V. Mutation of the Surface Layer Protein SlpB Has Pleiotropic Effects in the Probiotic Propionibacterium freudenreichii CIRM-BIA 129. Front Microbiol 2018; 9:1807. [PMID: 30174657 PMCID: PMC6107788 DOI: 10.3389/fmicb.2018.01807] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/18/2018] [Indexed: 01/19/2023] Open
Abstract
Propionibacterium freudenreichii is a beneficial Gram-positive bacterium, traditionally used as a cheese-ripening starter, and currently considered as an emerging probiotic. As an example, the P. freudenreichii CIRM-BIA 129 strain recently revealed promising immunomodulatory properties. Its consumption accordingly exerts healing effects in different animal models of colitis, suggesting a potent role in the context of inflammatory bowel diseases. This anti-inflammatory effect depends on surface layer proteins (SLPs). SLPs may be involved in key functions in probiotics, such as persistence within the gut, adhesion to host cells and mucus, or immunomodulation. Several SLPs coexist in P. freudenreichii CIRM-BIA 129 and mediate immunomodulation and adhesion. A mutant P. freudenreichii CIRM-BIA 129ΔslpB (CB129ΔslpB) strain was shown to exhibit decreased adhesion to intestinal epithelial cells. In the present study, we thoroughly analyzed the impact of this mutation on cellular properties. Firstly, we investigated alterations of surface properties in CB129ΔslpB. Surface extractable proteins, surface charges (ζ-potential) and surface hydrophobicity were affected by the mutation. Whole-cell proteomics, using high definition mass spectrometry, identified 1,288 quantifiable proteins in the wild-type strain, i.e., 53% of the theoretical proteome predicted according to P. freudenreichii CIRM-BIA 129 genome sequence. In the mutant strain, we detected 1,252 proteins, including 1,227 proteins in common with the wild-type strain. Comparative quantitative analysis revealed 97 proteins with significant differences between wild-type and mutant strains. These proteins are involved in various cellular process like signaling, metabolism, and DNA repair and replication. Finally, in silico analysis predicted that slpB gene is not part of an operon, thus not affecting the downstream genes after gene knockout. This study, in accordance with the various roles attributed in the literature to SLPs, revealed a pleiotropic effect of a single slpB mutation, in the probiotic P. freudenreichii. This suggests that SlpB may be at a central node of cellular processes and confirms that both nature and amount of SLPs, which are highly variable within the P. freudenreichii species, determine the probiotic abilities of strains.
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Affiliation(s)
- Fillipe L R do Carmo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France.,Agrocampus Ouest, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Wanderson M Silva
- Instituto de Biotecnología, CICVyA - Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Guilherme C Tavares
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Izabela C Ibraim
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Barbara F Cordeiro
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Emiliano R Oliveira
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Houem Rabah
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France.,Agrocampus Ouest, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Chantal Cauty
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Sara H da Silva
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcus V Canário Viana
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana C B Caetano
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Roselane G Dos Santos
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Julien Jardin
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Felipe L Pereira
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Edson L Folador
- Centro de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Yves Le Loir
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France.,Agrocampus Ouest, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Henrique C P Figueiredo
- AQUACEN, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Gwénaël Jan
- Institut National de la Recherche Agronomique, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France.,Agrocampus Ouest, UMR1253 Science & Technologie du Lait & de l'Oeuf, Rennes, France
| | - Vasco Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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25
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Liu Y, Defourny KAY, Smid EJ, Abee T. Gram-Positive Bacterial Extracellular Vesicles and Their Impact on Health and Disease. Front Microbiol 2018; 9:1502. [PMID: 30038605 PMCID: PMC6046439 DOI: 10.3389/fmicb.2018.01502] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/18/2018] [Indexed: 01/17/2023] Open
Abstract
During recent years it has become increasingly clear that the release of extracellular vesicles (EVs) is a feature inherent to all cellular life forms. These lipid bilayer-enclosed particles are secreted by members of all domains of life: Eukarya, Bacteria and Archaea, being similar in size, general composition, and potency as a functional entity. Noticeably, the recent discovery of EVs derived from bacteria belonging to the Gram-positive phyla Actinobacteria and Firmicutes has added a new layer of complexity to our understanding of bacterial physiology, host interactions, and pathogenesis. Being nano-sized structures, Gram-positive EVs carry a large diversity of cargo compounds, including nucleic acids, viral particles, enzymes, and effector proteins. The diversity in cargo molecules may point to roles of EVs in bacterial competition, survival, material exchange, host immune evasion and modulation, as well as infection and invasion. Consequently, the impact of Gram-positive EVs on health and disease are being revealed gradually. These findings have opened up new leads for the development of medical advances, including strategies for vaccination and anti-bacterial treatment. The rapidly advancing research into Gram-positive EVs is currently in a crucial phase, therefore this review aims to give an overview of the groundwork that has been laid at present and to discuss implications and future challenges of this new research field.
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Affiliation(s)
- Yue Liu
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Kyra A Y Defourny
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University & Research, Wageningen, Netherlands
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26
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Frohnmeyer E, Deptula P, Nyman TA, Laine PKS, Vihinen H, Paulin L, Auvinen P, Jokitalo E, Piironen V, Varmanen P, Savijoki K. Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains. Microb Biotechnol 2018; 11:510-526. [PMID: 29488359 PMCID: PMC5902329 DOI: 10.1111/1751-7915.13254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 01/19/2018] [Indexed: 12/20/2022] Open
Abstract
This study compared the secretomes (proteins exported out of the cell) of Propionibacterium freudenreichii of different origin to identify plausible adaptation factors. Phylosecretomics indicated strain‐specific variation in secretion of adhesins/invasins (SlpA, InlA), cell‐wall hydrolysing (NlpC60 peptidase, transglycosylase), protective (RpfB) and moonlighting (DnaK, GroEL, GaPDH, IDH, ENO, ClpB) enzymes and/or proteins. Detailed secretome comparison suggested that one of the cereal strains (JS14) released a tip fimbrillin (FimB) in to the extracellular milieu, which was in line with the electron microscopy and genomic analyses, indicating the lack of surface‐associated fimbrial‐like structures, predicting a mutated type‐2 fimbrial gene cluster (fimB‐fimA‐srtC2) and production of anchorless FimB. Instead, the cereal strain produced high amounts of SlpB that tentatively mediated adherent growth on hydrophilic surface and adherence to hydrophobic material. One of the dairy strains (JS22), producing non‐covalently bound surface‐proteins (LspA, ClpB, AraI) and releasing SlpA and InlA into the culture medium, was found to form clumps under physiological conditions. The JS22 strain lacked SlpB and displayed a non‐clumping and biofilm‐forming phenotype only under conditions of increased ionic strength (300 mM NaCl). However, this strain cultured under the same conditions was not adherent to hydrophobic support, which supports the contributory role of SlpB in mediating hydrophobic interactions. Thus, this study reports significant secretome variation in P. freudenreichii and suggests that strain‐specific differences in protein export, modification and protein–protein interactions have been the driving forces behind the adaptation of this bacterial species.
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Affiliation(s)
- Esther Frohnmeyer
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Paulina Deptula
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Tuula A Nyman
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, 0424 Oslo, Norway
| | - Pia K S Laine
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Helena Vihinen
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Lab, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Eija Jokitalo
- Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Vieno Piironen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Pekka Varmanen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Kirsi Savijoki
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
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27
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Dauros-Singorenko P, Blenkiron C, Phillips A, Swift S. The functional RNA cargo of bacterial membrane vesicles. FEMS Microbiol Lett 2018; 365:4830096. [DOI: 10.1093/femsle/fny023] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 01/25/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Priscila Dauros-Singorenko
- Department of Molecular Medicine and Pathology, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Department of Obstetrics and Gynaecology, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Anthony Phillips
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Department of Surgery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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28
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Liu Y, Alexeeva S, Defourny KA, Smid EJ, Abee T. Tiny but mighty: bacterial membrane vesicles in food biotechnological applications. Curr Opin Biotechnol 2017; 49:179-184. [PMID: 28985542 DOI: 10.1016/j.copbio.2017.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/15/2017] [Accepted: 09/03/2017] [Indexed: 12/15/2022]
Abstract
Membrane vesicle (MV) production is observed in all domains of life. Evidence of MV production accumulated in recent years among bacterial species involved in fermentation processes. These studies revealed MV composition, biological functions and properties, which made us recognize the potential of MVs in food applications as delivery vehicles of various compounds to other bacteria or the human host. Moreover, MV producing strains can deliver benefits as probiotics or starters in fermentation processes. Next to the natural production of MVs, we also highlight possible methods for artificial generation of bacterial MVs and cargo loading to enhance their applicability. We believe that a more in-depth understanding of bacterial MVs opens new avenues for their exploitation in biotechnological applications.
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Affiliation(s)
- Yue Liu
- Wageningen University, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Svetlana Alexeeva
- Wageningen University, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Kyra Ay Defourny
- Wageningen University, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - Eddy J Smid
- Wageningen University, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, The Netherlands.
| | - Tjakko Abee
- Wageningen University, Laboratory of Food Microbiology, P.O. Box 17, 6700 AA Wageningen, The Netherlands
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