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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 cond, 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 cond

Fermented foods and beverages are a significant source of dietary bacteria that enter the gastrointestinal (GI) tract. However, little is known about how these microbes survive and adapt to the small intestinal environment. Colony-forming units (CFU) enumeration and viability qPCR of Lacticaseibacillus rhamnosus CNCM I-3690 in the ileal effluent of 10 ileostomy subjects during 12-h post consumption of a dairy product fermented with this strain demonstrated the high level of survival of this strain during human small intestine passage. Metatranscriptome analyses revealed the in situ transcriptome of L. rhamnosus in the small intestine, which was contrasted with transcriptome data obtained from in vitro cultivation. These comparative analyses revealed substantial metabolic adaptations of L. rhamnosus during small intestine transit, including adjustments of carbohydrate metabolism, surface-protein expression, and translation machinery. The prominent presence of L. rhamnosus in the effluent samples did not elicit an appreciable effect on the composition of the endogenous small intestine microbiome, but significantly altered the ecosystem’s overall activity profile, particularly of pathways associated with carbohydrate metabolism. Strikingly, two of the previously recognized gut-brain metabolic modules expressed in situ by L. rhamnosus (inositol degradation and glutamate synthesis II) are among the most dominantly enriched activities in the ecosystem’s activity profile. This study establishes the survival capacity of L. rhamnosus in the human small intestine and highlights its functional adjustment in situ, which we postulate to play a role in the probiotic effects associated with this strain.

Metabolites profiling of urine samples. The samples were collected for the INSIDE explorative dietary study. The study was aimed to characterize the impact of fermented food may have on the small intestinal microbiota and systematically.

Immunophenotyping of whole blood after ex-vivo stimulus. The samples were collected for the INSIDE explorative dietary study. The study was aimed to characterize the impact of fermented food may have on the small intestinal microbiota and systematically.

Metabolites profiling of blood samples. The samples were collected for the INSIDE explorative dietary study. The study was aimed to characterize the impact of fermented food may have on the small intestinal microbiota and systematically.

Biomarkers profiling of human blood serum. The samples were collected for the INSIDE explorative dietary study. The study was aimed to characterize the impact of fermented food may have on the small intestinal microbiota and systematically.

survival and adaptation of rhamnosus in the human GI tract, survival and adaptation of rhamnosus in the human GI tract

Metataxonomic profiling (16S) of ileostomy samples. The samples were collected for the INSIDE double-blinded, placebo controlled explorative dietary study. The study was aimed to characterize the impact of fermented food may have on the small intestinal microbiota and systematically. Subjects participated in an approximately 100 days long trial with 3 intervention periods. 27 ileal effluent samples were collected per subject allowing a longitudinal analysis of the impact that consumpion of milk fermented products may have on the small intestinal microbial composition.

Short chain fatty acid profiling of ileostomy samples. 16 volunteers received yogurt, L. rhamnosus or placebo in different orders. Ileostomy samples were collected in the morning after breakfast at the beginning and at the end of the 2 weeks intervention period. The samples were collected for the INSIDE explorative dietary study. The study was aimed to characterize the impact of fermented food may have on the small intestinal environment and systematically.

Sugar permeability test in urine samples. 16 volunteers received treatments in different orders (Placebo, L. rhamnosus, Yogurt) and urine was collected after 2 and 5 hours. The samples were collected for the INSIDE explorative dietary study. The study was aimed to characterize the impact of fermented food may have on the small intestinal microbiota and systematically. Sucrose and Lactulose content in the urine was measured. Sucrose is hydrolyzed in the duodenum, and is therefore a good marker for gastroduodenal permeability, measured in 0-5h urine. Lactulose can permeate through the paracellular route and rhamnose through the transcellular route in the small intestine. The ratio in 0-5h urine is mainly used for general assessment of the SI permeability.

Bifidobacteria are among the first colonisers of the gastrointestinal tract of breast-fed newborns due to, among other things, their ability to metabolise oligosaccharides naturally occurring in human milk. The presence of bifidobacteria in the infant gut has been shown to promote intestinal health and homeostasis as well as to preserve a functional gut barrier, thus positively influencing host health and well-being. Among human-associated gut commensals, Bifidobacterium bifidum has been described as the only species capable of the extracellular degradation of both mucin-type glycans and HMOs, thereby giving this species a special role as a commensal gut forager of both host and diet-derived glycans. In the present study, we assess the possible beneficial properties and probiotic potential of B. bifidum strain CNCM I-4319. In silico genome analysis and growth experiments confirmed the expected ability of this strain to consume HMOs and mucin. By employing various animal models, we were also able to assess the ability of B. bifidum CNCM I-4319 to preserve gut integrity and functionality from stress-induced and inflammatory damage, thereby enforcing its potential as an effective probiotic strain.

Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes ( core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer ( variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total ( the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides ( EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat ( CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core ( shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.

Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence–absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains’ core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification

The core genome of the Lactobacillus rhamnosus species was previously described (Douillard et. al, 2013). We are here adding a set of 40 genomes of the species L. rhamnosus that were analized in order to characterize the variable genome of this industrially relevant species., The core genome of the Lactobacillus rhamnosus species was previously described (Douillard et. al, 2013). We are here adding a set of 40 genomes of the species L. rhamnosus that were analized in order to characterize the variable genome of this industrially relevant species.