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Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

(2013) ISME JOURNAL. 7(5). p.949-961
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The human gut is colonized by a complex microbiota with multiple benefits. Although the surface-attached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease.
Keywords
16S RIBOSOMAL-RNA, SP-NOV., FECAL MICROBIOTA, bowel, Lachnospiraceae, Ruminococcaceae, Anaerostipes caccae, Faecalibacterium prausnitzii, mucus, INFLAMMATORY-BOWEL-DISEASE, PHYLOGENETIC MICROARRAY ANALYSIS, GEL-ELECTROPHORESIS ANALYSIS, HUMAN LARGE-INTESTINE, MUCOSA-ASSOCIATED MICROBIOTA, GASTROINTESTINAL-TRACT, SPATIAL-ORGANIZATION

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Citation

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MLA
Van den Abbeele, Pieter, Clara Belzer, Margot Goossens, et al. “Butyrate-producing Clostridium Cluster XIVa Species Specifically Colonize Mucins in an in Vitro Gut Model.” ISME JOURNAL 7.5 (2013): 949–961. Print.
APA
Van den Abbeele, P., Belzer, C., Goossens, M., Kleerebezem, M., De Vos, W. M., Thas, O., De Weirdt, R., et al. (2013). Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model. ISME JOURNAL, 7(5), 949–961.
Chicago author-date
Van den Abbeele, Pieter, Clara Belzer, Margot Goossens, Michiel Kleerebezem, Willem M De Vos, Olivier Thas, Rosemarie De Weirdt, Frederiek-Maarten Kerckhof, and Tom Van de Wiele. 2013. “Butyrate-producing Clostridium Cluster XIVa Species Specifically Colonize Mucins in an in Vitro Gut Model.” Isme Journal 7 (5): 949–961.
Chicago author-date (all authors)
Van den Abbeele, Pieter, Clara Belzer, Margot Goossens, Michiel Kleerebezem, Willem M De Vos, Olivier Thas, Rosemarie De Weirdt, Frederiek-Maarten Kerckhof, and Tom Van de Wiele. 2013. “Butyrate-producing Clostridium Cluster XIVa Species Specifically Colonize Mucins in an in Vitro Gut Model.” Isme Journal 7 (5): 949–961.
Vancouver
1.
Van den Abbeele P, Belzer C, Goossens M, Kleerebezem M, De Vos WM, Thas O, et al. Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model. ISME JOURNAL. 2013;7(5):949–61.
IEEE
[1]
P. Van den Abbeele et al., “Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model,” ISME JOURNAL, vol. 7, no. 5, pp. 949–961, 2013.
@article{3228107,
  abstract     = {The human gut is colonized by a complex microbiota with multiple benefits. Although the surface-attached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease.},
  author       = {Van den Abbeele, Pieter and Belzer, Clara and Goossens, Margot and Kleerebezem, Michiel and De Vos, Willem M and Thas, Olivier and De Weirdt, Rosemarie and Kerckhof, Frederiek-Maarten and Van de Wiele, Tom},
  issn         = {1751-7362},
  journal      = {ISME JOURNAL},
  keywords     = {16S RIBOSOMAL-RNA,SP-NOV.,FECAL MICROBIOTA,bowel,Lachnospiraceae,Ruminococcaceae,Anaerostipes caccae,Faecalibacterium prausnitzii,mucus,INFLAMMATORY-BOWEL-DISEASE,PHYLOGENETIC MICROARRAY ANALYSIS,GEL-ELECTROPHORESIS ANALYSIS,HUMAN LARGE-INTESTINE,MUCOSA-ASSOCIATED MICROBIOTA,GASTROINTESTINAL-TRACT,SPATIAL-ORGANIZATION},
  language     = {eng},
  number       = {5},
  pages        = {949--961},
  title        = {Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model},
  url          = {http://dx.doi.org/10.1038/ismej.2012.158},
  volume       = {7},
  year         = {2013},
}

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