Cystic Fibrosis-related gut dysbiosis (CFRGD) has become a recognised complication in children with this condition, and current evidence remains insufficient to guide the selection of probiotic strains for supplementation treatments. The aim of this study was to characterise the effect of three probiotic strains on CFRGD by means of a dynamic in vitro simulation of the colonic fermentation (SHIME^®). The configuration of the system included three bioreactors colonised with the faecal inoculum of a child with cystic fibrosis. For 20 days, each bioreactor was supplied daily with either Lacticaseibacillus rhamnosus GG (ATCC 53103 TM), Limosilactobacillus reuteri (DSM 17938) or Lactiplantibacillus plantarum (DSM 22266). The baseline microbiota was characterised by a high abundance of Prevotella, Faecalibacterium and Acidaminococcus genera. After 20 days of supplementation, L. rhamnosus and L. plantarum reduced Prevotella significantly, and the three strains led to increased Faecalibacterium and Bifidobacterium and decreased Acidaminococcus, with some of these changes being maintained 10 days after ceasing supplementation. The metabolic activity remained unaltered in terms of short-chain fatty acids, but branched-chain fatty acids showed a significant decrease, especially with L. plantarum. Additionally, ammonia decreased at 20 days of supplementation, and lactate continuously increased with the three strains. The effects on colonic microbiota of L. rhamnosus, L. reuteri or L. plantarum were established, including increased beneficial bacteria, such as Faecalibacterium, and beneficial metabolites such as lactate; and on the other hand, a reduction in pathogenic genera, including Prevotella or Acidaminococcus and branched-chain fatty acids, overall supported their use as probiotics in the context of CFRGD.

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.

The gut microbiota plays a crucial role in human health and is key to understanding how various factors modulate its composition in older adults, enabling targeted interventions. This study aims to identify how dietary and lifestyle patterns influence older adults’ gut microbiota profile, considering the plant-based or animal origin of the dietary protein. A cross-sectional observational study was conducted with older adults aged between 60 and 80. Faecal samples were analyzed to determine gut microbiota composition and assess short-chain fatty acid (SCFA) production. Associations between microbiota profiles, dietary patterns, and metabolic markers were conducted through correlation and t tests. The study revealed that a diet rich in plant-based protein was linked to a lower body mass index (BMI) and to a significantly higher relative abundance of Verrucomicrobiota (4.46%) compared to an animal protein diet (1.47%). Firmicutes was the predominant phylum (61.10% relative abundance), while Proteobacteria levels tended to be higher in individuals with high-fat diets and alcohol consumption. Regarding genera, some of them are directly related to gut microbiota diversity and inversely related to BMI, such as Christensenellaceae R-7 group and Akkermansia. Also, Roseburia was significantly associated with valeric acid levels (r = 0.43, p = 1.5 × 10⁻³). High fibre intake was associated with reduced branched-chain SCFA (bc-SCFA) production. Increasing plant-based protein and fibre intake may promote a more favourable gut microbiota composition and enhance resilience against dysbiosis and related age-related conditions. Also, the presence of beneficial genera can increase gut microbiota diversity and decrease BMI, as well as induce healthy gut metabolic profiles. These findings underscore the potential of personalized nutrition and dietary strategies tailored to protein origin and fibre intake to modulate the gut microbiota and improve metabolic health in older adults.