Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles

References

• Hand TW, Vujkovic-Cvijin I, Ridaura VK, Belkaid Y. Linking the microbiota, chronic disease, and the immune system. Trends Endocrinol Metab. 2016;27(12):831–25. doi:10.1016/j.tem.2016.08.003.
   PubMed Web of Science ®Google Scholar
• Moos WH, Faller DV, Harpp DN, Kanara I, Pernokas J, Powers WR, Steliou K. Microbiota and neurological disorders: a gut feeling. Biores Open Access. 2016;5(1):137–145. doi:10.1089/biores.2016.0010.
   PubMedGoogle Scholar
• Vlasova AN, Takanashi S, Miyazaki A, Rajashekara G, Saif LJ. How the gut microbiome regulates host immune responses to viral vaccines. Curr Opin Virol. 2019;37:16–25. doi:10.1016/j.coviro.2019.05.001.
   PubMed Web of Science ®Google Scholar
• Liang X, Dai N, Sheng K, Lu H, Wang J, Chen L, Wang Y. Gut bacterial extracellular vesicles: important players in regulating intestinal microenvironment. Gut Microbes. 2022;14(1):2134689. doi:10.1080/19490976.2022.2134689.
   PubMed Web of Science ®Google Scholar
• Zeng MY, Inohara N, Nunez G. Mechanisms of inflammation-driven bacterial dysbiosis in the gut. Mucosal Immunol. 2017;10(1):18–26. doi:10.1038/mi.2016.75.
   PubMed Web of Science ®Google Scholar
• Turunen J, Tejesvi MV, Suokas M, Virtanen N, Paalanne N, Kaisanlahti A, Reunanen J, Tapiainen T. Bacterial extracellular vesicles in the microbiome of first-pass meconium in newborn infants. Pediatr Res. 2023;93(4):887–896. doi:10.1038/s41390-022-02242-1.
   PubMed Web of Science ®Google Scholar
• Liu L, Liang L, Yang C, Zhou Y, Chen Y. Extracellular vesicles of Fusobacterium nucleatum compromise intestinal barrier through targeting RIPK1-mediated cell death pathway. Gut Microbes. 2021;13(1):1–20. doi:10.1080/19490976.2021.1902718.
   Web of Science ®Google Scholar
• Castillo DJ, Rifkin RF, Cowan DA, Potgieter M. The healthy human blood microbiome: fact or fiction? Front Cell Infect Microbiol. 2019;9:148. doi:10.3389/fcimb.2019.00148.
   PubMed Web of Science ®Google Scholar
• Jones EJ, Booth C, Fonseca S, Parker A, Cross K, Miquel-Clopés A, Hautefort I, Mayer U, Wileman T, Stentz R, et al. The uptake, trafficking, and biodistribution of Bacteroides thetaiotaomicron generated outer membrane vesicles. Front Microbiol. 2020;11(57). doi:10.3389/fmicb.2020.00057.
   Google Scholar
• Brennan K, Martin K, FitzGerald SP, O’Sullivan J, Wu Y, Blanco A, Richardson C, Mc Gee MM. A comparison of methods for the isolation and separation of extracellular vesicles from protein and lipid particles in human serum. Sci Rep. 2020;10(1):1039. doi:10.1038/s41598-020-57497-7.
   PubMed Web of Science ®Google Scholar
• Doyle LM, Wang MZ. Overview of extracellular vesicles, their origin, composition, purpose, and methods for exosome isolation and analysis. Cells. 2019;8(7):727. doi:10.3390/cells8070727.
   PubMed Web of Science ®Google Scholar
• Toyofuku M, Nomura N, Eberl L. Types and origins of bacterial membrane vesicles. Nat Rev Microbiol. 2019;17(1):13–24. doi:10.1038/s41579-018-0112-2.
   PubMed Web of Science ®Google Scholar
• Lee EY, Bang JY, Park GW, Choi D-S, Kang JS, Kim H-J, Park K-S, Lee J-O, Kim Y-K, Kwon K-H, et al. Global proteomic profiling of native outer membrane vesicles derived from Escherichia coli. Proteomics. 2007;7(17):3143–3153. doi:10.1002/pmic.200700196.
   PubMed Web of Science ®Google Scholar
• Tulkens J, De Wever O, Hendrix A. Analyzing bacterial extracellular vesicles in human body fluids by orthogonal biophysical separation and biochemical characterization. Nat Protoc. 2020;15(1):40–67. doi:10.1038/s41596-019-0236-5.
   PubMed Web of Science ®Google Scholar
• Brown L, Wolf JM, Prados-Rosales R, Casadevall A. Through the wall: extracellular vesicles in gram-positive bacteria, mycobacteria and fungi. Nat Rev Microbiol. 2015;13(10):620–630. doi:10.1038/nrmicro3480.
   PubMed Web of Science ®Google Scholar
• Vlasova AN, Shao L, Kandasamy S, Fischer DD, Rauf A, Langel SN, Chattha KS, Kumar A, Huang H-C, Rajashekara G, et al. Escherichia coli nissle 1917 protects gnotobiotic pigs against human rotavirus by modulating pDC and NK-cell responses. Eur J Immunol. 2016;46(10):2426–2437. doi:10.1002/eji.201646498.
   PubMed Web of Science ®Google Scholar
• Vlasova AN, Kandasamy S, Chattha KS, Rajashekara G, Saif LJ. Comparison of probiotic lactobacilli and bifidobacteria effects, immune responses and rotavirus vaccines and infection in different host species. Vet Immunol Immunopathol. 2016;172:72–84. doi:10.1016/j.vetimm.2016.01.003.
   PubMed Web of Science ®Google Scholar
• Ferrandon D, Imler JL, Hoffmann JA. Sensing infection in Drosophila: toll and beyond. Semin Immunol. 2004;16(1):43–53. doi:10.1016/j.smim.2003.10.008.
   PubMed Web of Science ®Google Scholar
• Chaturvedi A, Pierce SK. How location governs toll-like receptor signaling. Traffic. 2009;10(6):621–628. doi:10.1111/j.1600-0854.2009.00899.x.
   PubMed Web of Science ®Google Scholar
• Kameli N, Borman R, Lpez-Iglesias C, Savelkoul P, Stassen FRM. Characterization of feces-derived bacterial membrane vesicles and the impact of their origin on the inflammatory response. Front Cell Infect Microbiol. 2021;11:667987. doi:10.3389/fcimb.2021.667987.
   PubMed Web of Science ®Google Scholar
• Meganathan V, Moyana R, Natarajan K, Kujur W, Kusampudi S, Mulik S, Boggaram V. Bacterial extracellular vesicles isolated from organic dust induce neutrophilic inflammation in the lung. Am J Physiol Lung Cell Mol Physiol. 2020;319(6):L893–L907. doi:10.1152/ajplung.00107.2020.
   PubMed Web of Science ®Google Scholar
• Hong J, Dauros‐Singorenko P, Whitcombe A, Payne L, Blenkiron C, Phillips A, Swift S. Analysis of the Escherichia coli extracellular vesicle proteome identifies markers of purity and culture conditions. J Extracell Vesicles. 2019;8(1):1632099. doi:10.1080/20013078.2019.1632099.
   PubMed Web of Science ®Google Scholar
• Clarridge JE. 3rd. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev. 2004;17(4):840–862. table of contents doi:10.1128/CMR.17.4.840-862.2004.
   PubMed Web of Science ®Google Scholar
• Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14(8):e1002533. doi:10.1371/journal.pbio.1002533.
   PubMed Web of Science ®Google Scholar
• Ravi RK, Walton K, Khosroheidari M. MiSeq: a next Generation sequencing platform for genomic analysis. Methods Mol Biol. 2018;1706:223–232. doi:10.1007/978-1-4939-7471-9_12.
   PubMedGoogle Scholar
• Kuczynski J, Lauber CL, Walters WA, Parfrey LW, Clemente JC, Gevers D, Knight R. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet. 2011;13(1):47–58. doi:10.1038/nrg3129.
   PubMed Web of Science ®Google Scholar
• Harm S, Schildbock C, Strobl K, Hartmann J. An in vitro study on factors affecting endotoxin neutralization in human plasma using the Limulus amebocyte lysate test. Sci Rep. 2021;11(1):4192. doi:10.1038/s41598-021-83487-4.
   PubMed Web of Science ®Google Scholar
• Tulkens J, Vergauwen G, Van Deun J, Geeurickx E, Dhondt B, Lippens L, De Scheerder M-A, Miinalainen I, Rappu P, De Geest BG. Increased levels of systemic LPS-positive bacterial extracellular vesicles in patients with intestinal barrier dysfunction. Gut. 2018;69(1):191–193. doi:10.1136/gutjnl-2018-317726.
   PubMed Web of Science ®Google Scholar
• Cecil JD, Sirisaengtaksin N, O’Brien-Simpson NM, Krachler AM, Sandkvist M, Cascales E, Christie PJ. Outer Membrane Vesicle-Host Cell Interactions. Microbiol Spectr. 2019;7(1). doi:10.1128/microbiolspec.PSIB-0001-2018.
   PubMed Web of Science ®Google Scholar
• Macia L, Nanan R, Hosseini-Beheshti E, Grau GE. Host- and Microbiota-Derived Extracellular Vesicles, Immune Function, and Disease Development. Int J Mol Sci. 2019;21(1):107. doi:10.3390/ijms21010107.
   PubMed Web of Science ®Google Scholar
• Wei S, Jiao D, Xing W. A rapid method for isolation of bacterial extracellular vesicles from culture media using epsilon-poly-L-lysine that enables immunological function research. Front Immunol. 2022;13:930510. doi:10.3389/fimmu.2022.930510.
   PubMed Web of Science ®Google Scholar
• Schneider M, Huber J, Hadaschik B, Siegers GM, Fiebig H-H, Schüler J. Characterization of colon cancer cells: a functional approach characterizing CD133 as a potential stem cell marker. BMC Cancer. 2012;12(1). doi:10.1186/1471-2407-12-96.
   Google Scholar
• Northrop-Albrecht EJ, Taylor WR, Huang BQ, Kisiel JB, Lucien F. Assessment of extracellular vesicle isolation methods from human stool supernatant. J Extracell Vesicles. 2022;11(4):e12208. doi:10.1002/jev2.12208.
   PubMed Web of Science ®Google Scholar
• Schulz E, Karagianni A, Koch M, Fuhrmann G. Hot EVs - How temperature affects extracellular vesicles. Eur J Pharm Biopharm. 2020;146:55–63. doi:10.1016/j.ejpb.2019.11.010.
   PubMed Web of Science ®Google Scholar
• Juan T, Furthauer M. Biogenesis and function of ESCRT-dependent extracellular vesicles. Semin Cell Dev Biol. 2018;74:66–77. doi:10.1016/j.semcdb.2017.08.022.
   PubMed Web of Science ®Google Scholar
• Quin C, Estaki M, Vollman DM, Barnett JA, Gill SK, Gibson DL. Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison. Sci Rep. 2018;8(1):8283. doi:10.1038/s41598-018-26423-3.
   PubMed Web of Science ®Google Scholar
• Hiergeist A, Glasner J, Reischl U, Gessner A. Analyses of Intestinal Microbiota: Culture versus Sequencing: Figure 1. ILAR J. 2015;56(2):228–240. doi:10.1093/ilar/ilv017.
   PubMed Web of Science ®Google Scholar
• Matsuo Y, Komiya S, Yasumizu Y, Yasuoka Y, Mizushima K, Takagi T, Kryukov K, Fukuda A, Morimoto Y, Naito Y, et al. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution. BMC Microbiol. 2021;21(1). doi:10.1186/s12866-021-02094-5.
   PubMed Web of Science ®Google Scholar
• Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019;37(10):1155–1162. doi:10.1038/s41587-019-0217-9.
   PubMed Web of Science ®Google Scholar
• Park J, Kim N-E, Yoon H, Shin CM, Kim N, Lee DH, Park JY, Choi CH, Kim JG, Kim Y-K, et al. Fecal Microbiota and Gut Microbe-Derived Extracellular Vesicles in Colorectal Cancer. Front Oncol. 2021;11:650026. doi:10.3389/fonc.2021.650026.
   PubMed Web of Science ®Google Scholar
• Yang J, McDowell A, Kim EK, Seo H, Yum K, Lee WH, Jee Y-K, Kim Y-K. Consumption of a Leuconostoc holzapfelii-enriched synbiotic beverage alters the composition of the microbiota and microbial extracellular vesicles. Experimental & Molecular Medicine. 2019;51(8):1–11. doi:10.1038/s12276-019-0288-1.
   Google Scholar
• Kim DJ, Yang J, Seo H, Lee WH, Ho Lee D, Kym S, Park YS, Kim JG, Jang I-J, Kim Y-K, et al. Colorectal cancer diagnostic model utilizing metagenomic and metabolomic data of stool microbial extracellular vesicles. Sci Rep. 2020;10(1):2860. doi:10.1038/s41598-020-59529-8.
   PubMed Web of Science ®Google Scholar
• Park JY, Kang C-S, Seo H-C, Shin J-C, Kym S-M, Park Y-S, Shin T-S, Kim J-G, Kim Y-K. Bacteria-derived extracellular vesicles in urine as a novel biomarker for gastric cancer: Integration of Liquid Biopsy and metagenome analysis. Cancers Basel. 2021;13(18):4687. doi:10.3390/cancers13184687.
   PubMed Web of Science ®Google Scholar
• Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6(1). doi:10.1186/s40168-018-0470-z.
   PubMedGoogle Scholar
• Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37(8):852–857. doi:10.1038/s41587-019-0209-9.
   PubMed Web of Science ®Google Scholar
• Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–780. doi:10.1093/molbev/mst010.
   PubMed Web of Science ®Google Scholar
• Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641–1650. doi:10.1093/molbev/msp077.
   PubMed Web of Science ®Google Scholar
• Price MN, Dehal PS, Arkin AP, Poon AFY. FastTree 2–approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5(3):e9490. doi:10.1371/journal.pone.0009490.
   PubMed Web of Science ®Google Scholar