Spatio-temporal dynamics of the human small intestinal microbiome and its response to a synbiotic
Ran An,
Ellen Wilms,
Jacoline Gerritsen,
Hye Kyong Kim,
Celia Seguí Pérez,
Isolde Besseling-van der Vaart,
Daisy M.A.E. Jonkers,
Ger T. Rijkers,
Willem M. de Vos,
Ad A.M. Masclee,
Erwin G. Zoetendal,
Freddy J. Troost,
Hauke Smidt
Affiliations
Ran An
Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
Ellen Wilms
Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
Jacoline Gerritsen
Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
Hye Kyong Kim
Institute of Biology, Leiden University, Leiden, The Netherlands
Celia Seguí Pérez
Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
Isolde Besseling-van der Vaart
Winclove Probiotics, Amsterdam, The Netherlands
Daisy M.A.E. Jonkers
Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
Ger T. Rijkers
Science Department, University College Roosevelt, Middelburg, The Netherlands
Willem M. de Vos
Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
Ad A.M. Masclee
Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
Erwin G. Zoetendal
Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
Freddy J. Troost
Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+, Maastricht, The Netherlands
Hauke Smidt
Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
ABSTRACTAlthough fecal microbiota composition is considered to preserve relevant and representative information for distal colonic content, it is evident that it does not represent microbial communities inhabiting the small intestine. Nevertheless, studies investigating the human small intestinal microbiome and its response to dietary intervention are still scarce. The current study investigated the spatio-temporal dynamics of the small intestinal microbiome within a day and over 20 days, as well as its responses to a 14-day synbiotic or placebo control supplementation in 20 healthy subjects. Microbial composition and metabolome of luminal content of duodenum, jejunum, proximal ileum and feces differed significantly from each other. Additionally, differences in microbiota composition along the small intestine were most pronounced in the morning after overnight fasting, whereas differences in composition were not always measurable around noon or in the afternoon. Although overall small intestinal microbiota composition did not change significantly within 1 day and during 20 days, remarkable, individual-specific temporal dynamics were observed in individual subjects. In response to the synbiotic supplementation, only the microbial diversity in jejunum changed significantly. Increased metabolic activity of probiotic strains during intestinal passage, as assessed by metatranscriptome analysis, was not observed. Nevertheless, synbiotic supplementation led to a short-term spike in the relative abundance of genera included in the product in the small intestine approximately 2 hours post-ingestion. Collectively, small intestinal microbiota are highly dynamic. Ingested probiotic bacteria could lead to a transient spike in the relative abundance of corresponding genera and ASVs, suggesting their passage through the entire gastrointestinal tract. This study was registered to http://www.clinicaltrials.gov, NCT02018900.
