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

Sanjay Swarup, Abhishek Gupta, Marianne Chung, Vaishnavi Radhakrishnan, V. Davis, Michael D. J. Lynch, Trevor C. Charles, Jiu-Jun Cheng, Glenn Mendoza

BMC Complementary Medicine and Therapies February 13, 2025 DOI: 10.1186/s12906-025-04783-4 (opens in new tab)

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Study at a glance

AI-extracted from the abstract
Characteristics Single-arm pilot clinical trial Pilot study Peer reviewed
Sample size 24
Population Arhatic Yoga practitioners, including beginners and advanced practitioners, attending a 9-day meditation retreat
Interventions Arhatic Yoga meditation vegetarian diet
Duration 9-day intensive retreat; samples collected at Day 0, Day 3, and Day 9
Measures 16S rRNA gene amplicon sequencing, PICRUSt2, DESeq2, non-metric multidimensional scaling (NMDS), PERMANOVA
Topics Meditation
Key findings Arhatic Yoga meditation combined with a vegetarian diet during a 9-day retreat was associated with changes in oral and gut microbiome profiles, including enriched health-benefiting microbes and convergence between beginner and advanced practitioners. The authors suggest this implies strong selection pressure on beneficial gut microbes, though the single-arm pilot design cannot establish causation.

Abstract

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

Comparable studies

Other non-randomized and open-label trials on meditation, most cited first.

Study Year Design Participants
Mindfulness-Based Stress Reduction in Relation to Quality of Life, Mood, Symptoms of Stress, and Immune Parameters in Breast and Prostate Cancer Outpatients Early-stage breast and prostate cancer patients 2003 Pre-post intervention study n = 59
Exploring self‐compassion and empathy in the context of mindfulness‐based stress reduction (MBSR) Community sample 2010 Pre-post intervention study
Mindfulness-Based Stress Reduction Lowers Psychological Distress In Medical Students Second-year medical students 2003 Prospective nonrandomized cohort-controlled study n = 302
Intensive meditation training, immune cell telomerase activity, and psychological mediators. Retreat participants and matched controls 2011 Controlled trial with wait-list control group n = 60
The Effectiveness of Mindfulness Training for Children with ADHD and Mindful Parenting for their Parents Children aged 8-12 with ADHD and their parents 2011 Within-group waitlist controlled trial n = 22

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