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High temporal and inter-individual variation detected in the human ileal microbiota

Authors

  • Carien C. G. M. Booijink,

    1. Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands.
    2. Top Institute Food and Nutrition (TIFN), PO Box 557, 6700 AN Wageningen, the Netherlands.
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  • Sahar El-Aidy,

    1. Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands.
    2. Top Institute Food and Nutrition (TIFN), PO Box 557, 6700 AN Wageningen, the Netherlands.
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  • Mirjana Rajilić-Stojanović,

    1. Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands.
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  • Hans G. H. J. Heilig,

    1. Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands.
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  • Freddy J. Troost,

    1. Top Institute Food and Nutrition (TIFN), PO Box 557, 6700 AN Wageningen, the Netherlands.
    2. Department of Internal Medicine, Division of Gastroenterology-Hepatology, Maastricht University Medical Center, PO Box 616, 6200 MD Maastricht, the Netherlands.
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  • Hauke Smidt,

    1. Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands.
    2. Top Institute Food and Nutrition (TIFN), PO Box 557, 6700 AN Wageningen, the Netherlands.
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  • Michiel Kleerebezem,

    1. Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands.
    2. Top Institute Food and Nutrition (TIFN), PO Box 557, 6700 AN Wageningen, the Netherlands.
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  • Willem M. De Vos,

    1. Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands.
    2. Top Institute Food and Nutrition (TIFN), PO Box 557, 6700 AN Wageningen, the Netherlands.
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  • Erwin G. Zoetendal

    Corresponding author
    1. Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, the Netherlands.
    2. Top Institute Food and Nutrition (TIFN), PO Box 557, 6700 AN Wageningen, the Netherlands.
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E-mail erwin.zoetendal@wur.nl; Tel. (+31) 317 483 111; Fax (+31) 317 483 829.

Summary

The diversity and temporal stability of the predominant bacteria in the human ileum was studied with the use of ileal effluent samples of seven individuals with Brooke ileostomies. The total number of bacteria within the ileal effluent was in the range of 107–108 bacteria per gram (wet weight). The diversity of the bacteria in the ileal effluent showed marked differences compared with that in faecal samples from age-matched healthy adults. The ileal effluent had a higher relative abundance of species within the orders Lactobacillales and Clostridiales, mainly Streptococcus bovis-related species, and the Veillonella group, and a lower proportion of species related to Ruminococcus gnavus, R. obeum and Bacteroides plebeius. In addition, inter-individual differences were found, indicative of a highly personal ileal microbiota profile. Furthermore, temporal profiles showed large fluctuations per individual over a period of 9–28 days (average similarity over a period of 9 days was as low as 44%), and differences between morning and afternoon profiles were observed. Parallel cloning and sequencing efforts revealed several phylotypes that were not identified in previous studies (12 out of 65 phylotypes showed less than 97% sequence similarity with previously reported sequences). Achaea were found to be below detection limit by quantitative PCR. Overall, the results indicate that the microbiota of the human ileum is relatively unstable, less complex and consisting of different dominating phylotypes when compared with the colonic microbiota.

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