Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles
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) an...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2023-12-01
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| Series: | Gut Microbes |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/19490976.2023.2288200 |
| _version_ | 1797320558289879040 |
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| author | Chih-Chi Li Wei-Fan Hsu Po-Chieh Chiang Ming-Che Kuo Andrew M. Wo Yufeng Jane Tseng |
| author_facet | Chih-Chi Li Wei-Fan Hsu Po-Chieh Chiang Ming-Che Kuo Andrew M. Wo Yufeng Jane Tseng |
| author_sort | Chih-Chi Li |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T04:40:55Z |
| format | Article |
| id | doaj.art-6e046f233cee4182a402b8b8170c7af3 |
| institution | Directory Open Access Journal |
| issn | 1949-0976 1949-0984 |
| language | English |
| last_indexed | 2024-03-08T04:40:55Z |
| publishDate | 2023-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Gut Microbes |
| spelling | doaj.art-6e046f233cee4182a402b8b8170c7af32024-02-08T12:02:08ZengTaylor & Francis GroupGut Microbes1949-09761949-09842023-12-0115210.1080/19490976.2023.2288200Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesiclesChih-Chi Li0Wei-Fan Hsu1Po-Chieh Chiang2Ming-Che Kuo3Andrew M. Wo4Yufeng Jane Tseng5Graduate Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering and Computer Science, National Taiwan University, Taipei, TaiwanInstitute of Applied Mechanics, National Taiwan University, Taipei, TaiwanDepartment of R&D, Reliance Biosciences Inc, New Taipei City, TaiwanDepartment of Medicine, National Taiwan University Cancer Center, Taipei, TaiwanInstitute of Applied Mechanics, National Taiwan University, Taipei, TaiwanGraduate Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering and Computer Science, National Taiwan University, Taipei, TaiwanABSTRACTPast 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.https://www.tandfonline.com/doi/10.1080/19490976.2023.2288200Bacterial extracellular vesicleextracellular vesiclestoolfecalseparationcharacterization |
| spellingShingle | Chih-Chi Li Wei-Fan Hsu Po-Chieh Chiang Ming-Che Kuo Andrew M. Wo Yufeng Jane Tseng Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles Gut Microbes Bacterial extracellular vesicle extracellular vesicle stool fecal separation characterization |
| title | Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles |
| title_full | Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles |
| title_fullStr | Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles |
| title_full_unstemmed | Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles |
| title_short | Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles |
| title_sort | characterization of markers functional properties and microbiome composition in human gut derived bacterial extracellular vesicles |
| topic | Bacterial extracellular vesicle extracellular vesicle stool fecal separation characterization |
| url | https://www.tandfonline.com/doi/10.1080/19490976.2023.2288200 |
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