Effects of dietary energy restriction of ultra-processed foods compared to a generic energy restriction on the intestinal microbiota of individuals with obesity: a secondary analysis of a randomized clinical trial

Evidence suggests that the intake of ultra-processed foods (UPF) influences gut microbiota. The present study evaluated the impact of energy restriction of dietary UPF compared to a general energy restriction on the gut microbiota of individuals with obesity. This was a parallel, randomized clinical trial. Individuals with obesity were randomly allocated into two groups: control, with general energy restriction (ER-G), and intervention, with energy restriction associated with UPF restriction (ER-UPF), limited to 5% of total intake. Individuals were followed-up monthly for 6 months. Stool samples were collected at baseline and after 6 months for DNA extraction and sequencing of the 16S rRNA gene (V3-V4 region). Socioeconomic, clinical, anthropometric, and dietary intake data were also collected. Abundance of microbiota data was analyzed using the Linear Models for Microarray Data (limma-voom) and the Microbiome Multivariable Associations with Linear Models (MaAsLin2) packages, with the Benjamini-Hochberg correction method. Alpha-diversity was analyzed using the Shannon, Simpson and Simpson-inverse index, whereas beta-diversity was analyzed using the Bray-Curtis index with the PERMANOVA test. Other variables were analyzed using mixed ANOVA with an alpha level of 5%. A total of 43 individuals were included, and at the end of the study, 34 individuals (18 intervention and 16 control) had complete data and were analyzed. %UPF consumption significantly decreased in the group that restricted UPF (<i>p</i>-interaction = 0.01), whereas waist circumference and body fat decreased in both groups (<i>p</i>-moment < 0.01). It was observed an increase in phylum and family microbial alpha-diversity in both groups with a slight decrease at the genus level. The <i>Ruminococcaceae</i> family showed a significantly greater increase in the ER-UPF group compared to the control group (<i>p</i>-interaction = 0.03), as did the <i>Faecalibacterium</i> genus (<i>p</i> = 0.02). These findings highlight the complexity of interactions between diet, body composition, and gut microbiota, suggesting that UPF restriction may have positive but limited effects on microbiota modulation in the short to medium term. Registration number of Clinical Trial: RBR - 3q9vgk9.