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

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

Gut Microbes. 2023 Dec;15(2):2288200. doi: 10.1080/19490976.2023.2288200. Epub 2023 Dec 1.

Authors

Chih-Chi Li¹, Wei-Fan Hsu^{2

3}, Po-Chieh Chiang³, Ming-Che Kuo^{4

5}, Andrew M Wo^{2

3}, Yufeng Jane Tseng^{1

6

7}

Affiliations

¹ Graduate Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering and Computer Science, National Taiwan University, Taipei, Taiwan.
² Institute of Applied Mechanics, National Taiwan University, Taipei, Taiwan.
³ Department of R&D, Reliance Biosciences Inc, New Taipei City, Taiwan.
⁴ Department of Medicine, National Taiwan University Cancer Center, Taipei, Taiwan.
⁵ Department of Neurology, National Taiwan University Hospital, Taipei, Taiwan.
⁶ Department of Computer Science and Information Engineering, College of Electrical Engineering and Computer Science, National Taiwan University, Taipei, Taiwan.
⁷ Master's Program in Smart Medicine and Health Informatics, National Taiwan University, Taipei, Taiwan.

Abstract

Past 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.

Keywords: 16S rRNA; Bacterial extracellular vesicle; characterization; extracellular vesicle; fecal; metagenomics; microbiome; personalized medicine; separation; stool.

MeSH terms

Bacteria / genetics
DNA
Extracellular Vesicles*
Feces / microbiology
Gastrointestinal Microbiome* / genetics
Humans
Microbiota* / genetics
RNA, Ribosomal, 16S / genetics

Substances

RNA, Ribosomal, 16S
DNA

Grants and funding

This work was supported by the Taiwan Food and Drug Administration (TFDA) under project number MOHW112-FDA-D-114-000611, the Higher Education Sprout Project by the Ministry of Education (MOE) in Taiwan under project number NTU-112L900703, the National Science and Technology Council (NSTC) in Taiwan under project number most-111-2320-B-002-043-MY2, the National Taiwan University Cancer Center under project number NTUCCS-112-13, and Reliance Biosciences Inc. under project number RB2019-2022-001 .