Human Gut Microbiome Response Induced by Fermented Dairy Product Intake
Authors: Volokh Olesya , Tyakht Alexander , Berezhnaya Yulia , Nesterova Polina , St. Peter John V. 
Published: November 2023

Accumulating data suggest that the gut microbiome can rapidly respond to changes in diet. Impact on gut microbe community structure after consumption of fermented foods is variable. We used metagenomic methods to evaluate changes in gut microbe composition after 30‐days of oral intake of a fermented dairy product (FDP) fortified with Bifidobacterium animalis subsp. lactis.

Metagenomic 16S rRNA gene sequencing identified gut microbial species modulated in association with consumption of FDP in healthy adults (n=150). Two daily portions (115 g/serving) were consumed during a 1‐month intervention study (no other fermented dairy or prebiotics/probiotics were allowed). Microbial strains contained in the FDP were: Bifidobacterium animalis subsp. lactis, Streptococcus thermophilus and Lactobacillus delbrueckii (107 CFU/g for each strain). DNA was extracted from stool samples collected before and after the test period.

Microbe community diversity dynamics analysis showed that FDP intake was not associated with changes in alpha‐diversity. However, significant shift in overall microbe community structure (PERMANOVA test, p < 0.05) & individual microbial taxa was seen. Paired comparison of the abundance of individual taxon pre & post FDP was performed using metagenomeSeq. Taxa relative abundance were both increased (n=30) & decreased (n=17). Significant increase of Bifidobacterium, Streptococcus and Lactobacillus genera abundance was seen. While this may be associated with FDP‐microbe intake, there was also an increase of endogenous bifidobacteria species (B. bifidum). Increased lactose fermenting taxa included Slackia isoflavoniconvertens and Adlercreutzia equolifaciens; bacteria with specific ability to metabolize isoflavone to equol, a compound potentially beneficial for human health via hormonal and cardiovascular functions.

We applied PICRUSt software to assess microbe community functions before and after FDP intake. Specifically, this software facilitates prediction of metabolic potential represented by relative abundance of KEGG metabolic pathways encoded in the genomes of the detected bacterial species. FDP intake was associated with increased capacity to metabolize lactose, starch and short‐chain sugars, as well as amino acid synthesis. These effects were accompanied by lowered synthesis of lipopolysaccharides suggesting decreased proinflammatory activity.

Significant shifts in microbe taxon and function suggest that a single month of FDP consumption may promote general positive effect on gut microbiota composition. Noteworthy, the increase of indigenous B. bifidum abundance indicates that this FDP could potentially affect the ecology of the gut microbiome. Further study is required to confirm any potential lasting impact on indigenous B. bifidum and other resident microbes after FDP discontinuation. Together with the interesting effect of increasing equol‐producing bacteria, the results suggest potential for multi‐faceted positive impact of FDP consumption on human gut health by promoting shifts in microbiota species that are associated with positive impact on biomarkers of inflammatory, hormonal, and cardiovascular function.

Support or Funding Information

Funding: PepsiCo Global R&D