Rapid shift of gut microbiome and enrichment of beneficial microbes during arhatic yoga meditation retreat in a single-arm pilot study

Abstract

Background: The human microbiome plays a vital role in human health, mediated by the gut-brain axis, with a large diversity of functions and physiological benefits. The dynamics and mechanisms of meditations on oral and gut microbiome modulations are not well understood. This study investigates the short-term modulations of the gut and oral microbiome during an Arhatic Yoga meditation retreat as well as on the role of microbiome in improving well-being through a possible gut-brain axis.

Methods: A single-arm pilot clinical trial was conducted in a controlled environment during a 9-day intensive retreat of Arhatic Yoga meditation practices with vegetarian diet. Oral and fecal samples of 24 practitioners were collected at the start (Day0: T1), middle (Day3: T2), and end (Day9:T3) of the retreat. Targeted 16S rRNA gene amplicon sequencing was performed for both oral and gut samples. Functional pathway predictions was identified using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2). DESeq2 was used to identify the differential abundant taxa. Various statistical analyses were performed to assess the significant changes in the data.

Results: Our findings revealed that Arhatic Yoga meditation together with a vegetarian diet led to changes in the oral and gut microbiome profiles within the 9-day retreat. Oral microbiome profile showed a significant (p < 0.05) difference in the species richness and evenness at the end of study, while non-metric multidimensional scaling (NMDS) confirmed the shift in the gut microbiome profile of the practitioners by T2 timepoint, which was further supported by PERMANOVA analysis (p < 0.05). Health-benefiting microbes known to improve the gastrointestinal and gut-barrier functions, immune modulation, and gut-brain axis were enriched. Gut microbiome of both beginner and advanced Arhatic Yoga practitioners showed similar trends of convergence by the end of study. This implies a strong selection pressure by Arhatic Yoga meditation together with a vegetarian diet on the beneficial gut microbiome.

Conclusion: This pilot study demonstrates that Arhatic Yoga meditation practices combined with a vegetarian diet during a short intensive retreat resulted in enrichment of known health-promoting microbes. Such microbial consortia may be developed for potential health benefits and used as probiotics to improve the gastrointestinal and immune systems, as well as functions mediated by the gut-brain axis.

Trial registration: Study was submitted in https://clinicaltrials.gov/on28-02-2024 . Retrospective registered.

Keywords: Arhatic yoga; Beneficial microbes; Clinical trial; Gut-brain axis; Meditation; Oral and gut microbiome.

Fig. 1

Alpha diversity measures of the fecal and oral microbiome. Timepoint variations in the alpha diversity measures of (a) fecal and (b) saliva samples. Pairwise-Wilcoxon test was performed to assess the significant difference in the alpha diversity parameters over time

Fig. 2

Beta-diversity plot depicts difference in fecal and oral samples. (a) Non-metric dimensional scaling (NMDS) based on a Bray–Curtis dissimilarity matrix (Stress = 0.15) on microbiome profile of fecal and oral samples. (b) Distance to centroid is represented in box plot. Each dot represents the sample from each participant

Fig. 3

Changes in microbiome profile of fecal and oral samples over time. Principal coordinate analysis (PCoA) ordination plot based on a Bray–Curtis dissimilarity matrix of microbiome profile of fecal (a) and oral (b) samples with time

Fig. 4

Line graph representing the change in average abundance of major bacterial taxa (top 25) with time in fecal samples

Fig. 5

Line graph representing the change in average abundance of major bacterial taxa (top 25) with time in oral samples

Fig. 6

DESeq2 based identification of major microbial ASVs (p < 0.05) which are differentially abundant between timepoint T1 and T3 in fecal samples

Fig. 7

Differentially abundant KEGG derived metabolic pathways of fecal samples between. T1 and T3 timepoints

Fig. 8

DESeq2 based identification of major bacterial ASVs (p < 0.05) which are differentially abundant between practitioners with different Arhatic levels at timepoint T1 (a) and T3 (b) in fecal samples