A “high-fat, high-energy diet” is commonly recommended for children with cystic fibrosis (CF), leading to negative consequences on dietary patterns that could contribute to altered colonic microbiota. The aim of this study was to assess dietary intake and to identify possible associations with the composition of faecal microbiota in a cohort of children with CF. A cross-sectional observational study was conducted, including a 3-day food record simultaneously with the collection of faecal samples. The results showed a high fat intake (43.9% of total energy intake) and a mean dietary fibre intake of 10.6 g/day. The faecal microbiota was characterised at the phylum level as 54.5% Firmicutes and revealed an altered proportion between Proteobacteria (32%) and Bacteroidota (2.2%). Significant associations were found, including a negative association between protein, meat, and fish intake and Bifidobacterium, a positive association between lipids and Escherichia/Shigella and Streptococcus, a negative association between carbohydrates and Veillonella and Klebsiella, and a positive association between total dietary fibre and Bacteroides and Roseburia. The results reveal that a “high-fat, high-energy” diet does not satisfy dietary fibre intake from healthy food sources in children with CF. Further interventional studies are encouraged to explore the potential of shifting to a high-fibre or standard healthy diet to improve colonic microbiota.

Children with Cystic Fibrosis (CF) are more likely to have intestinal dysbiosis due to recurrent antibiotic therapy and the conventional hypercaloric diet administered to them. This study aimed at evaluating the effect of isolated prebiotic components and probiotic strains, and their combinations as potential synbiotics, on the intestinal microbiota of CF children. A static in vitro colonic fermentation model was used by colonizing vials with faecal inoculum, a culture medium, and the substrates to be tested. Post treatment, aliquots were taken to determine ammonium, lactate, and short-chain fatty acids production and to profile the microbiota composition by 16s rRNA sequencing. At genus level, Escherichia-Shigella decreased (15.8%) with the treatment pectin + L. rhamnosus, followed by the beta-glucan + L. salivarius (15.5%). Inversely, the most increase in Bacteroides (44%) was obtained by the treatment with Pectin + L. reuteri. Lactate and acetic acid production was significantly increased with prebiotics and their combinations with L. rhamnosus and L. salivarius. In conclusion, the use of beta-glucan and pectin in combination with probiotic strains from the Lactobacillaceae family suggest potential to modulate dysbiosis and metabolic activity on CF colonic microbiota, encouraging further studies in animal studies or clinical settings to confirm the findings in vivo.

Background: Cystic fibrosis (CF) is a genetic disorder that disrupts gut microbiota composition, promoting dysbiosis associated with chronic inflammation, impaired nutrient absorption, and poor clinical outcomes. While modulation of the intestinal microbiota through prebiotics, probiotics, and synbiotics has been proposed as a therapeutic strategy, clinical evidence remains limited, especially in children. Objective: This study aimed to evaluate the impact of three supplementation strategies (a prebiotic (β-glucan), a probiotic (Lacticaseibacillus rhamnosus GG), and their synbiotic combination) on the gut microbiota and metabolic activity of a CF child faecal donor using a dynamic in vitro colonic fermentation model (SHIME®). Methods: Microbial composition (16S rRNA gene sequencing), and metabolic activity (quantification of short-chain fatty acids (SCFAs), ammonia, and lactate) were analysed. Results: Results showed that the prebiotic increased alpha diversity; while both the prebiotic and probiotic treatments significantly reduced Bacillota and increased Bacteroidota, modulating the Bacillota/Bacteroidota ratio. The synbiotic treatment showed the most beneficial overall profile, including enhanced production of SCFAs, particularly butyrate and propionate, and increased abundance of Faecalibacterium and Agathobacter, which are two bacterial genera generally associated with gut health. Notably, the synbiotic also reduced the relative abundance of potentially pathogenic genera such as Veillonella, Megasphaera, and Stenotrophomonas, but paralleled with an increase in Clostridium ss 1. Although the probiotic alone showed some positive effects, it was less effective overall compared to the prebiotic and synbiotic approaches. Conclusions: These findings support the potential of synbiotic supplementation as a promising strategy to modulate gut dysbiosis in CF, though in vivo studies are needed to confirm the translational relevance of these results.