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Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX

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Abstract
Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e. g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e. g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.
Keywords
HUMAN INTESTINAL BACTERIA, 8-PRENYLNARINGENIN IN-VITRO, CONTINUOUS-CULTURE SYSTEM, ECOSYSTEM, SIMULATOR, FERMENTATION, INNATE IMMUNITY, RETENTION TIME, HUMULUS-LUPULUS L., GASTROINTESTINAL-TRACT

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Citation

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Chicago
Van den Abbeele, Pieter, Charlotte Grootaert, Massimo Marzorati, Sam Possemiers, Willy Verstraete, Philippe Gerard, Sylvie Rabot, et al. 2010. “Microbial Community Development in a Dynamic Gut Model Is Reproducible, Colon Region Specific, and Selective for Bacteroidetes and Clostridium Cluster IX.” Applied and Environmental Microbiology 76 (15): 5237–5246.
APA
Van den Abbeele, P., Grootaert, C., Marzorati, M., Possemiers, S., Verstraete, W., Gerard, P., Rabot, S., et al. (2010). Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 76(15), 5237–5246.
Vancouver
1.
Van den Abbeele P, Grootaert C, Marzorati M, Possemiers S, Verstraete W, Gerard P, et al. Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 2010;76(15):5237–46.
MLA
Van den Abbeele, Pieter, Charlotte Grootaert, Massimo Marzorati, et al. “Microbial Community Development in a Dynamic Gut Model Is Reproducible, Colon Region Specific, and Selective for Bacteroidetes and Clostridium Cluster IX.” APPLIED AND ENVIRONMENTAL MICROBIOLOGY 76.15 (2010): 5237–5246. Print.
@article{1107099,
  abstract     = {Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e. g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e. g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.},
  author       = {Van den Abbeele, Pieter and Grootaert, Charlotte and Marzorati, Massimo and Possemiers, Sam and Verstraete, Willy and Gerard, Philippe and Rabot, Sylvie and Bruneau, Aurelia and El Aidy, Sahar and Derrien, Muriel and Zoetendal, Erwin and Kleerebezem, Michiel and Smidt, Hauke and Van de Wiele, Tom},
  issn         = {0099-2240},
  journal      = {APPLIED AND ENVIRONMENTAL MICROBIOLOGY},
  keyword      = {HUMAN INTESTINAL BACTERIA,8-PRENYLNARINGENIN IN-VITRO,CONTINUOUS-CULTURE SYSTEM,ECOSYSTEM,SIMULATOR,FERMENTATION,INNATE IMMUNITY,RETENTION TIME,HUMULUS-LUPULUS L.,GASTROINTESTINAL-TRACT},
  language     = {eng},
  number       = {15},
  pages        = {5237--5246},
  title        = {Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX},
  url          = {http://dx.doi.org/10.1128/AEM.00759-10},
  volume       = {76},
  year         = {2010},
}

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