Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota

Maria Stolaki, Mans Minekus, Koen Venema, Leo Lahti, Eddy J. Smid, Michiel Kleerebezem*, Erwin G. Zoetendal

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

The important role for the human small intestinal microbiota in health and disease has been widely acknowledged. However, the difficulties encountered in accessing the small intestine in a non-invasive way in healthy subjects have limited the possibilities to study its microbiota. In this study, a dynamic in vitro model that simulates the human ileum was developed, including its microbiota. Ileostomy effluent and fecal inocula were employed to cultivate microbial communities within the in vitro model. Microbial stability was repetitively achieved after 10 days of model operation with bacterial concentrations reaching on average 107 to 108 16S rRNA copy numbers/ml. High diversities similar to those observed in in vivo ileum samples were achieved at steady state using both fecal and ileostomy effluent inocula. Functional stability based on Short Chain Fatty Acid concentrations was reached after 10 days of operation using fecal inocula, but was not reached with ileostomy effluent as inoculum. Principal Components and cluster analysis of the phylogenetic profiles revealed that in vitro samples at steady state clustered closest to two samples obtained from the terminal ileum of healthy individuals, independent of the inoculum used, demonstrating that the in vitro microbiota at steady state resembles that of the human ileum.

Original languageEnglish
Article numberfiz096
JournalFEMS microbiology ecology
Volume95
Issue number8
DOIs
Publication statusPublished - 1 Aug 2019

Fingerprint

Microbiota
Ileum
Ileostomy
microbial community
effluent
health and disease
cluster analysis
Volatile Fatty Acids
principal component analysis
fatty acid
Principal Component Analysis
Small Intestine
phylogenetics
Cluster Analysis
Healthy Volunteers
In Vitro Techniques
Health

Keywords

  • in vitro model
  • gut health
  • ileum
  • microbial diversity
  • microbiota
  • short chain fatty acids

Cite this

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title = "Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota",
abstract = "The important role for the human small intestinal microbiota in health and disease has been widely acknowledged. However, the difficulties encountered in accessing the small intestine in a non-invasive way in healthy subjects have limited the possibilities to study its microbiota. In this study, a dynamic in vitro model that simulates the human ileum was developed, including its microbiota. Ileostomy effluent and fecal inocula were employed to cultivate microbial communities within the in vitro model. Microbial stability was repetitively achieved after 10 days of model operation with bacterial concentrations reaching on average 107 to 108 16S rRNA copy numbers/ml. High diversities similar to those observed in in vivo ileum samples were achieved at steady state using both fecal and ileostomy effluent inocula. Functional stability based on Short Chain Fatty Acid concentrations was reached after 10 days of operation using fecal inocula, but was not reached with ileostomy effluent as inoculum. Principal Components and cluster analysis of the phylogenetic profiles revealed that in vitro samples at steady state clustered closest to two samples obtained from the terminal ileum of healthy individuals, independent of the inoculum used, demonstrating that the in vitro microbiota at steady state resembles that of the human ileum.",
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author = "Maria Stolaki and Mans Minekus and Koen Venema and Leo Lahti and Smid, {Eddy J.} and Michiel Kleerebezem and Zoetendal, {Erwin G.}",
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Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota. / Stolaki, Maria; Minekus, Mans; Venema, Koen; Lahti, Leo; Smid, Eddy J.; Kleerebezem, Michiel; Zoetendal, Erwin G.

In: FEMS microbiology ecology, Vol. 95, No. 8, fiz096, 01.08.2019.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Minekus, Mans

AU - Venema, Koen

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AU - Smid, Eddy J.

AU - Kleerebezem, Michiel

AU - Zoetendal, Erwin G.

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AB - The important role for the human small intestinal microbiota in health and disease has been widely acknowledged. However, the difficulties encountered in accessing the small intestine in a non-invasive way in healthy subjects have limited the possibilities to study its microbiota. In this study, a dynamic in vitro model that simulates the human ileum was developed, including its microbiota. Ileostomy effluent and fecal inocula were employed to cultivate microbial communities within the in vitro model. Microbial stability was repetitively achieved after 10 days of model operation with bacterial concentrations reaching on average 107 to 108 16S rRNA copy numbers/ml. High diversities similar to those observed in in vivo ileum samples were achieved at steady state using both fecal and ileostomy effluent inocula. Functional stability based on Short Chain Fatty Acid concentrations was reached after 10 days of operation using fecal inocula, but was not reached with ileostomy effluent as inoculum. Principal Components and cluster analysis of the phylogenetic profiles revealed that in vitro samples at steady state clustered closest to two samples obtained from the terminal ileum of healthy individuals, independent of the inoculum used, demonstrating that the in vitro microbiota at steady state resembles that of the human ileum.

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