Metagenomic Analysis of The Effect of Formula versus Blended Food on Gut Microbiota of Children, using an in vitro Gut Model

Background: Artificial nutrition is needed for many children with complex medical conditions who can no longer support their nutritional needs orally. Enteral nutrition in the home environment uses almost exclusively sterile commercial formulas, however, the use of blended tube feeds made from food liquidised at home is becoming more commonly used. Dietary patterns have been shown to impact the bacterial composition of the gut microbiota in real time. The gut microbiome affects virtually all aspects of human health and influences the development of chronic diseases. The aim of this study was to use a triple stage chemostat model to simulate the human gut and study the effects of blended tube feeds and commercial formula on the gut microbial population. Methodology: Pre-digested commercial formula and blended tube feed was added to an in vitro gut model seeded by pooled faecal samples of healthy children. Microbiota community profiles were evaluated through bacterial culture and long read Nanopore sequencing, and CZ-ID. Construction of metagenome assembled genomes (MAGs) identified microbial community structure and provided prevalence data. Alpha and beta diversity metrics were used to quantify microbial diversity and species richness. Results: Microbiota composition changed during the commercial formula feeding with increased prevalence of Bacteroides, Bifidobacterium, Lactobacillus, Lacrimispora, Megasphaera and Hungatella compared to the control model. Microbiota composition also changed during the blended tube feeding with increased prevalence of Lachnospiraceae, Bacteroides, Lactobacillus, Bifidobacterium and Faecalibacterium compared to the control model. Compositional changes within the gut microbial populations occurred with the introduction of both commercial formula and the blended recipe. More increases were seen in beneficial bacteria in response to the blended tube feed compared to the commercial formula. No increases in pathogenic bacteria were seen in response to the blended feed compared with the commercial formula. Conclusion: The blended tube feed promoted a greater prevalence of bacterial species that are considered beneficial within the gut microbiota compared with commercial formula. These changes in gut microbial composition are associated with a healthier state.