Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model
The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its inter...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1054061/full |
| _version_ | 1797868246866591744 |
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| author | Stef Deyaert Frédéric Moens Walter Pirovano Bartholomeus van den Bogert Eline Suzanne Klaassens Massimo Marzorati Massimo Marzorati Tom Van de Wiele Tom Van de Wiele Michiel Kleerebezem Pieter Van den Abbeele |
| author_facet | Stef Deyaert Frédéric Moens Walter Pirovano Bartholomeus van den Bogert Eline Suzanne Klaassens Massimo Marzorati Massimo Marzorati Tom Van de Wiele Tom Van de Wiele Michiel Kleerebezem Pieter Van den Abbeele |
| author_sort | Stef Deyaert |
| collection | DOAJ |
| description | The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region in vivo. This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME®-technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera Streptococcus, Veillonella, Enterococcus, Lactobacillus, and Clostridium (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as in vivo, bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME® where it further increased the compositional relevance of the colonic community. This long-term in vitro model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present in vitro simulation increases the biological relevance of the current M-SHIME® technology. |
| first_indexed | 2024-04-09T23:52:58Z |
| format | Article |
| id | doaj.art-d7e2aae6c29b47939189f0fd2fe4f772 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-09T23:52:58Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-d7e2aae6c29b47939189f0fd2fe4f7722023-03-17T05:21:55ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-03-011310.3389/fmicb.2022.10540611054061Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut modelStef Deyaert0Frédéric Moens1Walter Pirovano2Bartholomeus van den Bogert3Eline Suzanne Klaassens4Massimo Marzorati5Massimo Marzorati6Tom Van de Wiele7Tom Van de Wiele8Michiel Kleerebezem9Pieter Van den Abbeele10ProDigest BV, Gent, BelgiumProDigest BV, Gent, BelgiumBaseclear, Leiden, NetherlandsBaseclear, Leiden, NetherlandsBaseclear, Leiden, NetherlandsProDigest BV, Gent, BelgiumCenter of Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Gent, BelgiumProDigest BV, Gent, BelgiumCenter of Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Gent, BelgiumDepartment of Animal Sciences, Wageningen University, Wageningen, NetherlandsProDigest BV, Gent, BelgiumThe human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region in vivo. This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME®-technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera Streptococcus, Veillonella, Enterococcus, Lactobacillus, and Clostridium (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as in vivo, bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME® where it further increased the compositional relevance of the colonic community. This long-term in vitro model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present in vitro simulation increases the biological relevance of the current M-SHIME® technology.https://www.frontiersin.org/articles/10.3389/fmicb.2022.1054061/fullileummicrobiotain vitro modelshort-chain fatty acidsmall intestinesimulator of the human intestinal microbial ecosystem |
| spellingShingle | Stef Deyaert Frédéric Moens Walter Pirovano Bartholomeus van den Bogert Eline Suzanne Klaassens Massimo Marzorati Massimo Marzorati Tom Van de Wiele Tom Van de Wiele Michiel Kleerebezem Pieter Van den Abbeele Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model Frontiers in Microbiology ileum microbiota in vitro model short-chain fatty acid small intestine simulator of the human intestinal microbial ecosystem |
| title | Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model |
| title_full | Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model |
| title_fullStr | Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model |
| title_full_unstemmed | Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model |
| title_short | Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model |
| title_sort | development of a reproducible small intestinal microbiota model and its integration into the shime r system a dynamic in vitro gut model |
| topic | ileum microbiota in vitro model short-chain fatty acid small intestine simulator of the human intestinal microbial ecosystem |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2022.1054061/full |
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