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Zaccaria E, Klaassen T, Alleleyn AME, Boekhorst J, Smokvina T, Kleerebezem M, Troost FJ. Endogenous small intestinal microbiome determinants of transient colonisation efficiency by bacteria from fermented dairy products: a randomised controlled trial. Microbiome 2023; 11:43. [PMID: 36879297 PMCID: PMC9990280 DOI: 10.1186/s40168-023-01491-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND The effects of fermented food consumption on the small intestine microbiome and its role on host homeostasis are largely uncharacterised as our knowledge on intestinal microbiota relies mainly on faecal samples analysis. We investigated changes in small intestinal microbial composition and functionality, short chain fatty acid (SCFA) profiles, and on gastro-intestinal (GI) permeability in ileostomy subjects upon the consumption of fermented milk products. RESULTS We report the results from a randomised, cross-over, explorative study where 16 ileostomy subjects underwent 3, 2-week intervention periods. In each period, they consumed either milk fermented by Lacticaseibacillus rhamnosus CNCM I-3690, or milk fermented by Streptococcus thermophilus CNCM I-1630 and Lactobacillus delbrueckii subsp. bulgaricus CNCM I-1519, or a chemically acidified milk (placebo) daily. We performed metataxonomic, metatranscriptomic analysis, and SCFA profiling of ileostomy effluents as well as a sugar permeability test to investigate the microbiome impact of these interventions and their potential effect on mucosal barrier function. Consumption of the intervention products impacted the overall small intestinal microbiome composition and functionality, mainly due to the introduction of the product-derived bacteria that reach in several samples 50% of the total microbial community. The interventions did not affect the SCFA levels in ileostoma effluent, or gastro-intestinal permeability and the effects on the endogenous microbial community were negligible. The impact on microbiome composition was highly personalised, and we identified the poorly characterised bacterial family, Peptostreptococcaceae, to be positively associated with a low abundance of the ingested bacteria. Activity profiling of the microbiota revealed that carbon- versus amino acid-derived energy metabolism of the endogenous microbiome could be responsible for the individual-specific intervention effects on the small intestine microbiome composition and function, reflected also on urine microbial metabolites generated through proteolytic fermentation. CONCLUSIONS The ingested bacteria are the main drivers of the intervention effect on the small intestinal microbiota composition. Their transient abundance level is highly personalised and influenced by the energy metabolism of the ecosystem that is reflected by its microbial composition ( http://www. CLINICALTRIALS gov , ID NCT NCT02920294). Video Abstract.
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Affiliation(s)
- Edoardo Zaccaria
- Host Microbe Interactomics Group, Wageningen University & Research, De Elst 1, 6708WD, Wageningen, The Netherlands
- Food Innovation and Health, Center for Healthy Eating and Food Innovation, Maastricht University, Venlo, 5911AA, The Netherlands
| | - Tim Klaassen
- Food Innovation and Health, Center for Healthy Eating and Food Innovation, Maastricht University, Venlo, 5911AA, The Netherlands
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, P.O. Box 5800, 6202AZ, Maastricht, The Netherlands
| | - Annick M E Alleleyn
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, P.O. Box 5800, 6202AZ, Maastricht, The Netherlands
| | - Jos Boekhorst
- Host Microbe Interactomics Group, Wageningen University & Research, De Elst 1, 6708WD, Wageningen, The Netherlands
| | - Tamara Smokvina
- Danone Nutricia Research, Av. De la Vauve, 91767, Palaiseau, France
| | - Michiel Kleerebezem
- Host Microbe Interactomics Group, Wageningen University & Research, De Elst 1, 6708WD, Wageningen, The Netherlands.
| | - Freddy J Troost
- Food Innovation and Health, Center for Healthy Eating and Food Innovation, Maastricht University, Venlo, 5911AA, The Netherlands
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, P.O. Box 5800, 6202AZ, Maastricht, The Netherlands
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