Discovering Rapid Microbiome Changes from Arhatic Yoga Practices

In just three days, our spiritual practices showed measurable biological impacts on both oral and gut microbiomes, revealing fascinating connections between ancient wisdom and modern science.

Published in Microbiology

Discovering Rapid Microbiome Changes from Arhatic Yoga Practices
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BioMed Central
BioMed Central BioMed Central

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

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.

Why This Research Matters

As both a life sciences researcher and practitioner of Pranic Healing, I've long sought to bridge these two worlds. For years, I wondered if we could scientifically document the physiological effects of spiritual practices like Arhatic Yoga—a higher spiritual form built on the foundation of Pranic Healing that integrates meditation, breathing exercises, and universal energy harnessing techniques.

This research question gained momentum through my collaboration with medical faculty colleagues at the National University Hospital in Singapore. We had previously studied microbiome shifts during pregnancy related to gestational diabetes and breast milk changes after delivery. Through this work, I realized that tens of thousands of microbiome members could serve as independent markers for tracking physiological responses to spiritual practices.

The opportunity to conduct this study came when Master Glenn Mendoza, MD, MPH, one of the senior disciples of Master Choa Kok Sui, suggested we collect data during a nine-day spiritual retreat in upstate New York. This setting was scientifically invaluable—participants followed identical routines, performed the same practices, followed identical dietary intake, and shared the same environment, effectively removing variables that might confound our results.

This represents the first study tracking human physiological responses to Arhatic Yoga practices over such a short timeframe. Previous meditation studies typically observed participants over several months, not days. Our study included 44 participants ranging from 18-70 years old, with varying levels of experience in Arhatic Yoga practices, making it a diverse cohort for investigating these effects.

Our Approach and Findings

We designed a single-arm pilot trial, where we tracked individuals at day zero, day three, and day nine of the retreat. Each participant served as their own control, allowing us to identify patterns emerging across different individuals over time. We collected both oral and fecal samples for microbiome analysis using 16S rRNA gene sequencing to identify bacterial taxonomic profiles.

Alpha diversity measures of the fecal and oral microbiome. Timepoint variations in

the alpha diversity measures of (a) fecal and (b) saliva samples. Pairwise-Wilcox test was

performed to assess the significant difference in the alpha diversity parameters over time

What surprised us most was how quickly significant changes appeared. Within just three days—a mere matter of hours of combined practices—we observed clear, statistically significant signatures of microbial shifts in both oral and gut samples. As researchers and practitioners, we were amazed that these biological changes manifested so rapidly, rather than requiring weeks or months of practice.

The data revealed significant increases in beneficial bacteria associated with anti-inflammatory properties and improved metabolic health. Particularly noteworthy was the enrichment of Faecalibacterium in the gut microbiome, which is known for its anti-inflammatory properties and production of butyrate, a short-chain fatty acid that supports gut barrier function. In the oral microbiome, we observed increases in genera like Streptococcus and Haemophilus, which have been associated with oral health when in proper balance. Most noteworthy Corynebacterium, Rothia, and Neisseria, also shifted which are known to promote cardiovascular and metabolic health through nitric oxide signaling molecules. 

Another unexpected finding was the fascinating linkages between oral and gut microbiome signatures. Our data suggested benefits for the gut-brain axis, as well as potential connections between oral and heart health. Network analysis revealed coordinated changes between specific oral and gut bacteria, suggesting a systemic response to the Arhatic Yoga practices that could potentially bring profound changes to core human functions in both brain and heart, key determinants of health and longevity.

Changes in microbiome profile of fecal and saliva samples over time. Principal

coordinate axis (PCoA) ordination plot based on a Bray-Curtis dissimilarity matrix on

microbiome profile of fecal (a) and oral (b) samples with time.

Broader Implications

This study offers several valuable insights. First, it demonstrates that even beginning practitioners can experience tangible benefits within a remarkably short timeframe. While experienced practitioners may perceive deeper emotional and mental benefits, newcomers can observe physical and physiological changes almost immediately. The practices performed during the retreat included specific meditation techniques, breathing exercises (pranayama), and gentle physical movements, all conducted within a structured daily routine. One limitation of this study was that the lifestyle effects of diet and exercise could not be separated, as Arhatic Yoga involves a combination of these factors.

Second, our work establishes microbiomes as reliable markers for both short-term and long-term studies of meditation and spiritual practices. This opens doors for more logistically manageable research designs that can further explore the scientific basis of yoga and other spiritual practices. The rapid changes we observed suggest that short-duration studies involving microbiome profiling could be viable for investigating many mind-body interventions, potentially reducing research costs and participant burden. 

Third, we found similar microbiome responses across participants with different ethnicities and varying levels of experience with Arhatic Yoga. Whether someone was an experienced practitioner or a beginner, the microbiome profiles we observed during the nine-day period were statistically very similar, suggesting that responses converge toward a common endpoint. This points to possible universal biological mechanisms that transcend individual differences.

Looking forward, this research could help identify beneficial microbes that might be developed into probiotics to enhance the combined effects of spiritual and healthy lifestyle practices on human health. The specific bacterial signatures we identified could potentially serve as biomarkers for wellness or as targets for therapeutic interventions. We're already planning further studies along these lines to deepen our understanding of how ancient wisdom practices transform our biology, including longer-term follow-up and investigation of functional outcomes related to immune function and stress response.

Connecting Ancient Wisdom with Modern Science

This journey from hypothesis to discovery has been both scientifically rewarding and personally inspiring. Our findings bridge ancient wisdom and modern science, demonstrating that practices developed thousands of years ago have measurable, rapid effects on our biology. As we continue to explore these connections, we hope our work encourages both scientific investigation of spiritual practices and informed integration of these practices into healthcare approaches. The microbiome may be just the beginning of understanding how these ancient techniques create profound changes in human physiology, potentially opening new pathways for enhancing health and well-being in our modern world.

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