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Updated: May 24, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Link between ultra-processed foods and drinks intake, gut microbiota and inflammation: an exploratory analysis in
Laetitia Lengelé1, Manon Autuori1, Emilie Bosteels1
1Metabolism and Nutrition Research Group, Louvain Drug Research Institute, LDRI, Université catholique de Louvain, Brussels, Belgium.
Background:
Ultra-processed foods and drinks (UPFD) have been acknowledged to promote metabolic disturbances and inflammation. Knowing that both events can be associated with gut microbiota alterations, this observational longitudinal analysis aimed to explore the link between UPFD intake, faecal microbiota composition and activity, and inflammatory biomarkers.
Methods:
MICROBOOST-1 study included 20 adults for 3 study visits spaced at least 7 days apart. Dietary intakes were collected using three non-consecutive 24 h recalls, including a weekend day, and performed the week preceding each study visit. Foods and drinks were categorized in a double-blind manner as ultra-processed following the NOVA classification. Mean energy-adjusted UPFD consumption was then divided into quartiles. Stool samples were collected at most four days before each study visit. Faecal microbiota composition was analysed using 16S-rDNA Illumina sequencing, and exhaled breath hydrogen - reflecting gut microbial fermentation - was measured. Inflammatory cytokines were quantified in saliva. Mixed models were applied accounting for multiple time points per participant. Overall UPFD, "meat, fish, and cheese" (MFC) and "sugar-sweetened beverages" (SSB) categories were investigated.
Results:
In comparison with the lowest consumption quartile of UPFD categories, the highest quartile showed no change in α- and β-diversity, but a lower relative abundance of Faecalibacterium, Desulfovibrio, Veillonella and a higher relative abundance of Hominimerdicola and Phocaeicola for all UPFD (q-value < 0.05). A decrease in Agathobacter and Coprococcus and an increase in Actinomyces relative abundances characterized the MFC category, whereas higher Actinomyces and lower Flintibacter relative abundances were observed for SSB category (q-value < 0.05). SSB intake was also related to lower exhaled hydrogen and to higher salivary level of IL-6 (p-value < 0.05). Total UPFD intake was linked to increased salivary IL-1β (p-value < 0.05). This cytokine was positively associated with Flintibacter and negatively associated with Faecalibacterium. In addition, Phocaeicola, Desulfovibrio, Veillonella, Actinomyces and Coprococcus were positively associated with IL-6, while Desulfovibrio and Veillonella were positively and Actinomyces and Agathobacter negatively related to IL-8 (p-value < 0.05).
Conclusion:
In our study, using non-invasive tools, we observed associations between the level of UPFD intake and components of the gut microbiota and inflammation.
Clinical Trial Number:
The protocol is recorded at «clinicaltrials.gov» (NCT05949411).
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