Determine the  L. rhamnosus CNCM I-3690 survival, adaptation and small bowel microbiome impact in human in response to dietary interventions
Fermented foods and beverages are one of the major sources of environmental bacteria entering the gastrointestinal tract. However, little is known about the fate, survival and adaptation of those microbes to the new environment, especially when they enter in contact with the small intestinal conditions as our knowledge of microbiota relies mainly on faecal sample analysis.  In this study, we investigate, over a 12 hours period, the population size and viability of Lacticaseibacillus rhamnosus CNCM I-3690 in the ilea effluent and the corresponding effects on SI microbiota composition after ingestion. We also report the transcriptional adaptation of L. rhamnosus CNCM I-3690 in the SI by analysing strain-specific transcriptional profiles using effluent metatranscriptome data in comparison to in vitro cultivation transcriptomes. We report the results from an intervention study where 10 ileostomy subjects consumed milk fermented by L. rhamnosus CNCM I-3690 together with a standardized breakfast. Following this, ilea effluents were collected every 4 hours for 12 hours used for metataxonomic, metatranscriptomic and survival analyses of the ingested bacteria via both CFU enumeration and viability-qPCR. We demonstrate that L. rhamnosus CNCM I-3690 is able to effectively survive the passage of the human small intestine albeit in quite variable numbers in different participating volunteers. Despite the strain being consistently detected alive in the samples collected during the first 12 hours post-ingestion, we could not detect a conserved and appreciable effect of L. rhamnosus CNCM I-3690 consumption on the SI microbial composition, confirming previous results. In contrast, the ingested bacteria made a significant contribution to the ecosystem activity profile. In fact, the in situ transcriptome analysis of L. rhamnosus CNCM I-3690 indicates that this strain is active during SI passage and drastically adjusts its gene expression profile in comparison to in vitro culturing conditions. The metabolic adaptations of L. rhamnosus reflected the diverse and dynamic environmental and nutritional conditions in the SI environment of individuals, modulating especially the carbohydrate metabolism and the expression of surface-proteins.