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

Chih-Chi Li; Wei-Fan Hsu; Po-Chieh Chiang; Ming-Che Kuo; Andrew M. Wo; Yufeng Jane Tseng

doi:10.1080/19490976.2023.2288200

Gut Microbes (Dec 2023)

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

Chih-Chi Li,
Wei-Fan Hsu,
Po-Chieh Chiang,
Ming-Che Kuo,
Andrew M. Wo,
Yufeng Jane Tseng

Affiliations

Chih-Chi Li: Graduate Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering and Computer Science, National Taiwan University, Taipei, Taiwan
Wei-Fan Hsu: Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
Po-Chieh Chiang: Department of R&D, Reliance Biosciences Inc, New Taipei City, Taiwan
Ming-Che Kuo: Department of Medicine, National Taiwan University Cancer Center, Taipei, Taiwan
Andrew M. Wo: Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan
Yufeng Jane Tseng: Graduate Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering and Computer Science, National Taiwan University, Taipei, Taiwan

DOI: https://doi.org/10.1080/19490976.2023.2288200
Journal volume & issue: Vol. 15, no. 2

Abstract

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ABSTRACTPast studies have confirmed the etiologies of bacterial extracellular vesicles (BEVs) in various diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC). This study aimed to investigate the characteristics of stool-derived bacterial extracellular vesicles (stBEVs) and discuss their association with stool bacteria. First, three culture models – gram-positive (G+)BcBEVs (from B.coagulans), gram-negative (G-)EcBEVs (from E.coli), and eukaryotic cell-derived EVs (EEV, from Colo205 cell line) – were used to benchmark various fractions of stEVs separated from optimized density gradient approach (DG). As such, WB, TEM, NTA, and functional assays, were utilized to analyze properties and distribution of EVs in cultured and stool samples. Stool samples from healthy individuals were interrogated using the approaches developed. Results demonstrated successful separation of most stBEVs (within DG fractions 8&9) from stEEVs (within DG fractions 5&6). Data also suggest the presence of stBEV DNA within vesicles after extraction of BEV DNA and DNase treatment. Metagenomic analysis from full-length (FL) region sequencing results confirmed significant differences between stool bacteria and stBEVs. Significantly, F8&9 and the pooled sample (F5-F9) exhibited a similar microbial composition, indicating that F8&9 were enriched in most stBEV species, primarily dominated by Firmicutes (89.6%). However, F5&6 and F7 still held low-density BEVs with a significantly higher proportion of Proteobacteria (20.5% and 40.7%, respectively) and Bacteroidetes (24% and 13.7%, respectively), considerably exceeding the proportions in stool and F8&9. Importantly, among five healthy individuals, significant variations were observed in the gut microbiota composition of their respective stBEVs, indicating the potential of stBEVs as a target for personalized medicine and research.

Published in Gut Microbes

ISSN: 1949-0976 (Print); 1949-0984 (Online)
Publisher: Taylor & Francis Group
Country of publisher: United States
LCC subjects: Medicine: Internal medicine: Specialties of internal medicine: Diseases of the digestive system. Gastroenterology
Website: https://www.tandfonline.com/journals/kgmi

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