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Human consumption of fermented millet (Kunun zaki) reduces the prevalence of selected antimicrobial resistance genes in human fecal samples

bioinformatics
microbiology
molecular-biology
clinical-trials
global-health

Abstract

Background : Antimicrobial resistance (AMR) poses a major global health challenge, with the human gut microbiota acting as a key reservoir for resistance genes. Traditional fermented foods may influence microbial gut dynamics and AMR gene carriage.

Objective: This study evaluated the impact of two Nigerian fermented beverages Kunun aya and Kunun zaki on the prevalence and distribution of selected AMR genes in the human gut microbiota.

Methods: We performed a pre/post experiment in 36 healthy volunteers from Abuja, North Central Nigeria in three groups: Kunun aya, Kunun zaki, and water (control). Participants consumed their assigned beverage daily for two weeks, followed by a two-week washout phase. Fecal samples collected at the three timepoints were tested for 11 AMR genes using PCR. Treatment effects were expressed as percentage point changes with 95% confidence intervals. Fisher’s exact test and Pearson correlation coefficients were used to assess prevalence differences and co-occurrence patterns, with multiple testing corrections applied (FDR and Bonferroni).

Results: At baseline, dfrA was the most prevalent gene (77.8%), followed by blaTEM (41.7%), mefA/E (38.9%), ermB (33.3%), qnrA (30.6%), and blaCTX-M (13.9%). Intervention effects varied by beverage: Kunun zaki reduced prevalence in four of six genes (mean change –11.7 percentage points), with the largest decreases observed for qnrA (–66.7 percentage points) and dfrA (–23.3 percentage points), In contrast, Kunun aya increased prevalence in five of six genes (mean change +18.1 percentage points), including blaTEM (+38.9 percentage points) and ermB (+30.6 percentage points) though no increase was significant. The control group showed minimal changes (mean –0.8 percentage points). No statistically significant sex-based differences in gene prevalence were observed.

Conclusions: Consumption of Kunun zaki was associated with reduced prevalence of specific AMR genes, particularly dfrA and qnrA, suggesting a potential microbiota-modulating effect. These findings support the exploration of culturally accepted fermented foods as complementary strategies to combat AMR threat. Larger studies are needed to confirm these preliminary results.


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