Effect of Yoga and Meditation on Human Gut Microbiota: A Systematic Review

Abstract

The evidence from the clinical studies on the influence of yoga and meditation on gut microbiota in humans has been summarized in this systematic review. Searches were conducted until November 2023 in four electronic databases: SCOPUS, PubMed, Google Scholar, and Cochrane Controlled Registry of Trials (CENTRAL) to find relevant studies published in English. Studies on the influence of yoga and meditation on gut microbiome in human participants of any age or gender were included in the systematic review. The outcomes were modulations in the composition and function of gut microbiota and their metabolite levels. Due to the varied approaches used in the study designs and outcome measures of the included studies, a narrative synthesis was carried out. The database search resulted in 247 titles and abstracts, out of which four articles were included for qualitative synthesis. There was one nonrandomized controlled study and three observational studies. The studies were conducted on a healthy population (n = 440). The participants were followers of a vegan or vegetarian diet. The control group subjects were nonmeditators, i.e., who never received any meditation training. All the reviewed studies have shown a favorable change in the composition and function of gut microbiota and their metabolites with meditation practice when compared to controls. Yoga and meditation improved the composition and function of gut microbiota. However, all the subjects were following a vegetarian/vegan diet, so the beneficial changes demonstrated in the gut microbiota may be attributed to the combined effects of meditation and a vegetarian/vegan diet.

Introduction

Host–microbiota interactions have been linked to the pathophysiology of not only gastrointestinal and neurological disorders but also the cardiometabolic disorders and many other diseases through metabolic and inflammatory pathways. A bidirectional interaction occurs between the brain, gut, and its microbiome through neural, neuroendocrine, and immune communication pathways.[1] The human body consists of approximately 10¹³ cells and provides shelter to about 10¹⁴–10¹⁵ individual microorganisms. These microorganisms can be divided into two groups as normal habitats and acquired. Microorganisms are usually present in the skin, external ear, mouth, pharynx, tonsils, large intestine, external genitalia, anterior urethra, and vagina. However, around 99% of these microorganisms are nonpathogenic. They are helpful to humans as they are involved in food metabolism, the development of the immune system, the synthesis of certain vitamins, and protection against pathogens. Studies reveal that approximately 1,000 bacterial species reside in the human gut, with the dominant bacteria belonging to four major phyla: Firmicutes (Lactobacillus, Clostridium, Enterococcus, and Ruminococcus), Bacteroidetes (Prevotella and Bacteroides), Actinobacteria, and Proteobacteria.[2] The balance and composition of the human gut microbiota is influenced by a variety of endogenous and exogenous factors such as age, gender, genetics, geography, diet, lifestyle, and use of biotics and medications, particularly antibiotics.

The gut microbiome generates biologically active metabolites that impact many aspects of host physiology and can play an important role in the holistic development of an individual. However, the dysbiosis in the normal microbial community structure and function is associated with multiple disease states, including gastrointestinal disorders, dermatological conditions, musculoskeletal disorders, obesity, cardiovascular diseases (CVD), allergy, central nervous system (CNS)-related diseases, cancers, inflammatory diseases, and metabolic disorders.[3,4,5] Numerous animal studies have demonstrated the basic connection between dysbiosis and obesity.[6] It has also been shown that dysbiosis induces and promotes liver cancer by regulating the immune system.[7] Furthermore, it is interesting to note that irritable bowel syndrome and inflammatory bowel diseases have been effectively treated with fecal microbiota transplantation.[8]

The composition and function of the gut microbiome are influenced by several external factors. The two most important ones are diet and mental health. A growing body of evidence indicates that diet and stress can influence and modify the interactions between the brain, gut, and microbiota, which can have significant effects on mental health and neurological illnesses.[1,9] Indian ancient sciences (Ayurveda and Yoga) have always believed that all diseases begin either in the gut or mind for thousands of years, this principle holdsvery much true for ever inreasing lifestyle related diseases, even today.[10] Yoga and meditation are shown to reduce stress, improve physical, mental, and psychological well-being,[11] and thus may influence the gut microbiota composition and its functions through brain–gut interactions.

Since antiquity, meditation has been practiced for self-realization, inner awareness, and as a path to enlightenment in many religious traditions. The origin of meditation practices is thought to be from Hinduism and Buddhism, and the history of their practice dates as far back as 5000 BC. References to meditation can also be found in Christianity, Judaism, and Islam.

There are many different types of meditation that are practiced today. To name a few that have their roots in the ancient Indian Vedic tradition (Hinduism) include yoga and yoga-based meditations (OM, Transcendental, and Cyclic meditations). And those having their roots in Buddhist teachings include Zen, Vipassana, Mindfulness, Taoist, and Loving Kindness (Metta) meditations.[12] Meditation originated from Hinduism is also popularly known as yog or yoga. Among the existing four streams of yoga, Raj-yoga or Ashtanga (“Ashta” means eight and “anga” means parts) yoga is the most popular worldwide that includes a sequence of eight steps of meditative practices.[13] The first 6 steps of yoga are preparatory practices (Yama, Niyama, Asanas, Pranayama, Pratyahara, and Dharna) designed to purify the mind and energize and relax the joints and muscles of the body before engaging in meditation. Yama (means Do’s) and niyama (means don’ts) are the lifestyle principles that must be adhered to the daily routine.[14] Meditation (Dhyana) is the penultimate step of Ashtanga yoga prescribed to reach the ultimate stage of emancipation. Henceforth, in future discussions, yoga will be used for meditations originated from Hinduism or Vedic tradition of India.[12,13]

Currently, there is no evidence synthesized on the impact of yoga and meditation on the gut microbiome. Therefore, we have summarized the evidence from the clinical studies on the influence of yoga and meditation on gut microbiota in this systematic review. Further, the available methods for the assessment of gut microbiota are also discussed.

Methods

This systematic review was reported in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and has been registered in the PROSPERO (CRD42023433700).

Data sources and search strategy

Searches were conducted until November 2023 in four electronic databases: SCOPUS, PubMed, Google Scholar, and Cochrane Controlled Registry of Trials (CENTRAL) to find relevant studies[15] published in English. The keywords: “Yoga,” “Meditation,” “Pranayama,” “yogic breathing exercise,” “Yogasanas,” “asanas,” “Meditation,” “Mindfulness,” “Gut microbiota,” “Gut flora,” “Gut microbiome” “Metabolome,” “16S rRNA” “Short-chain fatty acids,” and “SCFA;” and to search and capture most relevant and related articles, the Boolean operators “AND,” and “OR” were used by two reviewers (RKM and PKJ). The complete database search strategy is provided in Supplementary Table 1. The references were also screened manually to find out articles for review by two reviewers (RKM and PKJ). Two reviewers (RKM and PKJ) independently examined the abstracts and titles in the databases in accordance with the eligibility requirements; in the case that there was a disagreement, a third reviewer (SGP) was consulted.

Supplementary Table 1.

Search strategy applied across databases

Database	Search string (with field tags/MeSH)	Limits/filters applied	Final search date (date month, and year)
Scopus	TITLE-ABS-KEY((“Yoga” OR “Meditation” OR “Pranayama” OR “Yogic breathing exercise” OR “Yogasanas” OR “Asanas” OR “Mindfulness”) AND (“Gut microbiota” OR “Gut flora” OR “Gut microbiome” OR “16S rRNA”) AND (“SCFA” OR “Short-chain fatty acids” OR “Metabolome”)	English (Human studies where applicable)	June 13, 2023
Cochrane central	(“Yoga”:ti, ab OR “Meditation”:ti, ab OR “Pranayama”:ti, ab OR “Yogic breathing exercise”:ti, ab OR “Yogasanas”:ti, ab OR “Asanas”:ti, ab OR “Mindfulness”:ti, ab) AND (“Gut microbiota”:ti, ab OR “Gut flora”:ti, ab OR “Gut microbiome”:ti, ab OR “16S rRNA”:ti, ab) AND (“SCFA”:ti, ab OR “Short-chain fatty acids”:ti, ab OR “Metabolome”:ti, ab)	Humans; English	June 23, 2023
PubMed	((“Yoga”[MeSH] OR “Meditation”[MeSH] OR “Mindfulness”[MeSH]) OR (“Pranayama”[Title/Abstract] OR “Yogic breathing exercise”[Title/Abstract] OR “Yogasanas”[Title/Abstract] OR “Asanas”[Title/Abstract])) AND (“Gastrointestinal Microbiome”[MeSH] OR “Gut microbiota”[Title/Abstract] OR “Gut flora”[Title/Abstract] OR “Gut microbiome”[Title/Abstract]) OR “16S rRNA”[Title/Abstract] AND (“Fatty Acids, Volatile”[MeSH] OR “SCFA”[Title/Abstract] OR “Short-chain fatty acids”[Title/Abstract] OR “Metabolome”[Title/Abstract])	English	June 25, 2023
Google scholar	“Yoga” OR “Meditation” OR “Pranayama” OR “Yogic breathing exercise” OR “Yogasanas” OR “Asanas” OR “Mindfulness” AND (“Gut microbiota” OR “Gut flora” OR “Gut microbiome” OR “16S rRNA”) AND (“SCFA” OR “Short-chain fatty acids” OR “Metabolome”)	First 200 results; relevance order; English	June 26, 2023

MeSH: Medical subject headings

Study selection

Studies on the influence of yoga and meditation on gut microbiome in human participants of any age or gender were included in the systematic review. Studies published by institutions/organizations/Universities, online and conference proceedings were also included. Language was not restricted when searching through or screening the studies. Studies without sufficient data and studies whose full text was not available or unable to retrieve the missing data from authors were excluded from the review [Figure 1].

Figure 1.

Schematic representation of the steps involved in the assessment and analysis of gut microbiome

The types of interventions included for this review were yoga meditation, OM meditation, Transcendental meditation, cyclic meditation, Vipassana meditation, Buddhist meditation, Zen meditation, Mindfulness meditation, and Loving-kindness meditation or Metta meditation, and Taoists meditation . Yoga is a lifestyle that includes several practices from dietary and behavioral modifications, physical activity, breathing modifications, relaxation, concentration, and meditation. Therefore, studies involving either single-component or combined techniques of yoga were all included in the review. Active or passive comparator, standard care, usual care, and without any comparator or no control group (single group) were included.

The primary outcome was changes in the composition of gut microbiota. The measures of the outcome were 16S rRNA diversity (alpha and beta diversity). Changes in the metabolites such as trimethylamine, trimethylamine N-oxide, short-chain fatty acids (SCFA), and bile acids were the secondary outcomes. However, other measures related to gut microbiota were also considered for the review.

Data extraction

Three investigators studied the full text of the selected articles. Two reviewers extracted the relevant data independently from the eligible studies. The following details were extracted: Type of yoga or meditation, type of comparator, details of intervention (duration of session, frequency, total duration of intervention), adherence to intervention (number of hours practiced in a week), study outcomes and their measures, results and conclusions, and adverse events. Author and study details (first author, published year, and country of study origin) were also extracted. If there was any discrepancy or no consensus between the two reviewers, it was resolved by group discussion with a third reviewer (SGP). Due to the diverse methodology of the selected studies (in study design, study quality, and measures of outcomes), narrative data were synthesized.

Available methods for assessment of gut microbiome

In this section, an attempt has been made to describe the available methods for assessing gut microbiota. The steps followed in the assessment of gut microbes have been depicted in Figure 1. The study of microbiome is a contemporary development in the biological sciences, and its origin lies in microbiology and molecular genetics. However, the implications of microbiome studies are beyond traditional microbiology, where isolation of pure cultures of microorganisms is the focus. With rapid advancement in genome sequencing technologies and large-scale data analysis tools like bioinformatics, the emphasis has been shifted from single gene analysis (rRNA) to whole genome analysis and interpretation. In contrast to conventional microbiological methods, the advanced technologies/methodologies in combination with the ease of extracting genetic material directly from the virgin samples/environment enable the speedy analysis of the composition and functionality of the whole microbial community in a habitat.[16] In modern microbiology investigations, the primary focus is on the intricate microbial communities that interact with hosts and impact both health and disease processes.[17] Moreover, the microbiome is a composite of the genomes (metagenomes) and metabolites (gene products of the microbiota) found in the host or a specific environment. As a consequence, we now know that the imbalance or dysbiosis in the human microbiota, directly or indirectly, has a significant detrimental effect on human health. In recent decades, several advanced technologies are available to study the microbiota and microbiome; however, below are some fundamental techniques most commonly used to analyze the composite of human/host microbiome.

Ribosomal marker gene for diversity analysis

By sequencing the 16S rRNA gene of bacteria and the 18S rRNA gene of fungi from the total DNA extracted from fecal samples, the diversity of the human gut microbiota can be analyzed. These genes offer a distinctive signature or barcode that can be assigned to specific taxonomies and counted to determine the frequencies of each member within the community. They are highly conserved but have diverged throughout time. Assigning taxonomy can be done via machine learning methods like Ribosomal Database Project RDP Classifier[18] or mapping to reference databases like Greengenes[19] and SILVA[20] and standard microbiome analysis packages such as QIIME[21] and Mothur.[22]

Shotgun metagenomics for diversity analysis

Due to its focus on a small portion of microbial genomes, ribosomal marker gene analysis may introduce bias and limit access to complete genomic information. In contrast, untargeted sequencing techniques such as shotgun metagenomics can detect every microbial genome in a sample.[23,24] This approach enables the study of DNA viruses, bacteria, fungi, protozoa, and other microbes by capturing the full spectrum of genetic information from a microbiome sample; however, it relies heavily on reference genomes and empirical data. In addition, the amplicon sequencing method can be used to estimate the relative abundance and infer the functional potential of microbial communities. Sequence assembly is typically performed using a hybrid approach that combines whole-genome sequencing with short-read data, linked through overlapping reads to generate contigs. Alternatively, de novo genome assembly can be used. Popular software tools for de novo assembly include MEGAHIT,[25] MetaVelvet,[26] and IDBA-UD.[27]

Functional analysis by metatranscriptomics, metaproteomics, and metabolomics

Metatranscriptomics captures the RNA transcribed from microorganisms, which allows calculation of the expression activities of these microorganisms.[28] Typically, transcriptomics involves isolation of the total RNA from the sample, cDNA synthesis, RNA enrichment, and library preparation and sequencing using Illumina, HiSeq, or NovaSeq for short reads, and PacBio and Oxford Nanopore sequencing for longer read lengths. Further, these reads are mapped to genomes and KEGG pathways[29] to know transcriptionally active organisms along with the function of their expressed genes. Bioinformatics tools like SOAPdenovo have been applied to understand different health conditions.[30] Metabolomics and metaproteomics often utilize mass spectrometry to detect target and nontarget metabolites. Metabolomics measures small molecules like metabolic by-products/intermediates from the host and/or bacteria. Also, it reveals how these molecules interact with both host metabolism and microbiota.[31] Metaproteomics focuses on detecting and quantifying the proteins present in a microbiome.[32]

Quality assessment

The quality of the individual studies was assessed independently by two reviewers (RKM and PKJ) using the Newcastle-Ottawa Quality Assessment Scale. The third reviewer (SGP) was consulted for any discrepancy between the two authors or if there was no consensus between the two authors. The Newcastle–Ottawa Quality Assessment Scale includes selection, comparability, and outcomes. The quality of the studies was divided into good (7–8 points), satisfactory (5–6 points), and unsatisfactory (0–4 points).

Data extraction and analysis

The details of the selection criteria, sample size, participant information (age, sex, number, health, or related to any condition), type of meditation intervention, duration, and details of the intervention, type of comparison/control group, method of measuring outcome measures, results, and conclusion were all included in the data extraction form that was developed for this review. Two independent reviewers were assigned for data extraction and analysis. When there was no agreement between the two reviewers, the third reviewer was consulted. Due to the varied approaches used in the study designs and outcome measures of the included studies, a narrative synthesis was carried out. Quality of the studies was assessed using a Newcastle–Ottawa Quality Assessment Scale.

Results

Study selection process and search results

Figure 2 shows the selection process and results of the review. A total of 247 titles and abstracts were found through the database search; however, 238 papers were excluded according to our selection criteria. Nine studies were reviewed using their full text to determine their eligibility. Five studies were also eliminated because four of them lacked yoga or meditation basis, and one’s measurements were not accurate. Finally, four articles were included for qualitative synthesis.[33,34,35,36]

Figure 2.

Flow diagram showing the results of database search

Study characteristics and participants

Table 1 shows a descriptive summary, study design, sample size, participant characteristics, and intervention received. There was one non-randomized controlled study[35] and three observational studies.[33,34,36] One study investigated the effect of yoga[35] while the other three studied the influence of Buddhist meditation (Buddhist meditation) on gut microbiota.[33,34,36] Three studies originated in China[33,34,36] while one study was from the USA.[35] All the studies were conducted on a healthy population. The total number of participants in four studies was 440 (ranging from 24 to 288 subjects in each study). Raman et al.’s study included participants of both genders,[35] while Sun et al., and Qiao et al., included only males,[34,36] and Jia et al. had only female participants.[33] The study participants’ ages ranged from 24 to 55 years.

Table 1.

General characteristics of included studies

Author, year, Country of origin	Design of study	Condition	Sample size	Male/female	Groups, type and number of participants	Characteristics of participants	Experimental/study group intervention	Control group intervention
Jia et al., 2020[33] China	Cross-sectional study	Healthy	24	Male: 0 Female: 24	Meditation group included healthy vegan-long term meditators (n=12) Control group included healthy omniverous nonmeditators (n=12)	Meditation group Age: 39.17±6.658 years BMI: 22.35±2.79 Control group Age: 40.5±6.142 years BMI: 22.41±2.39	Long term Meditation with vegan diet for more than 3 years Duration of meditation practice: 5.83±2.368 years (mean±SD), practiced 30 min/day	Omnivores who never received any meditation training
Qiao et al., 2022[34] China	Cross-sectional study	Healthy	72	Male: 72 Female: 0	Meditation group included healthy monks (n=24) Control group included healthy omniverous nonmeditators (n=48)	Meditation group Age: 35.5 (26–55) years BW: 58 (50–78) kg BMI: 19.9 (17.13–27.64) Control group Age: 26 (24–43) BW: 50 (44–71) kg BMI: 19.63 (16.96–24.22)	Long term meditation with vegetarian diet Duration of meditation practice: 7.5 (1–27) years (median [range])	Subjects never received any meditation training
Raman et al., 2023[35] USA	Non-RCT, Open label	Healthy	288	Male: 139 Female: 149	Meditators group (n=265) Control group included spouses or other house hold members (n=23)	Meditation group Age: 40.7±10.9 years BMI: 22.9±3.83 Control group Age: 42±1.41 years BMI: 26.2±3.24	Isha yoga and advanced meditation program (Samyama) with a vegan diet including 50% raw food Duration of program: Pre-Samyama program during which subjects practiced Isha yoga for 1 h daily for 2 months. Samyama program for 8 days, entire day meditation sessions	No intervention
Sun et al., 2023[36] China	Cross-sectional study	Healthy	56	Male: 56 Female: 0	Meditation group included Buddhist monks (n=37) Control group included local age-matched residents (n=19)	Meditation group Age: NA BMI: NA Control group Age: NA BMI: NA	Long-term Samantha and Vipassana meditation Duration of meditation practice: 18.94±7.56 years (mean±SD), for at least 2 h a day for 3–30 years	Subjects never received any meditation training

Age is given as mean±SD. RCT: Randomized controlled trial, BW: Body weight, BMI: Body mass index, SD: Standard deviation, NA: Not available

Details of intervention

Table 2 provides detailed information of the intervention received by the study participants. The total duration of yoga intervention received by the study group participants in Raman et al. study was 5 weeks or 68 days.[35] The intervention program was divided into two parts: (1) premeditation program included preparatory practices for 60 days and (2) meditation (Samyama) program included a residential full-day training for 8 days. The Isha yoga group participants underwent training in preparatory practices for 60 days (premeditation or Samyama program) before enrolling for 8 days of full-day training on meditation or the Samyama program. Before beginning the Samyama program, the participants had to mentally and physically prepare themselves by adhering to a yogic lifestyle, diet, and practices for a period of sixty days. The pre-Samyama program training included asanas (stretching and maintenance of postures), kriyas (cleansing techniques), and pranayama (controlled breathing practices) [Table 3]. The Samyama program included concentration and meditation. During the Samyama program, participants spend the entire day in complete silence with long hours of meditation. The details of the Isha yoga intervention are available at https://isha.sadhguru.org/in/en/yoga-meditation/yoga-program-advanced/samyama. The study group participants followed a vegan diet during the entire program of 68 days. The control group participants were passive, and there was no dietary restriction to them.[35]

Table 2.

Details of yoga or meditation program

Author, year	Details of intervention
Jia et al., 2020[33]	Participants in the meditation group received long-term meditation training for 30 min per day with vegan diet for more than 3 years. The meditation instructions were as follows Sit cross-legged on a comfortable cushion; place your right hand on your left hand, with the thumbs facing each other; and place both hands in front of the navel; the spine should be straight and should not bend in any direction; both shoulders should be balanced with slight adduction; the jaw should be slightly open; the tongue should rest on the roof of the mouth; the eyes should gaze downward at the tip of the nose; and breathing should be uniform and natural
Qiao et al., 2022[34]	Practiced long-term meditation with vegetarian diet for 1–27 years (Meditators recruited for the study was from Zhengfa Temple of Wuxi City, Jiangsu Province) The detailed type of meditation practiced has not been mentioned
Raman et al., 2023[35]	Practices before Samyama: Samyama participants (meditators) were required to take several prerequisite meditation programs before enrolling in Samyama. These included Inner Engineering, Bhava Spandana, Shoonya, and Yogasanas. They were asked to perform multiple practices (learned in prerequisite programs) daily for the 60-day preparation period. These include kriya yoga practices (Shakti Chalana Kriya and Shambhavi Mahamudra Kriya), hata yoga (Surya Kriya and Yogasanas), Shoonya meditation twice a day, Sukha Kriya and Arda Siddhasana for at least one hour per day. Kriya yoga practices are combinations of posture, breath, and sound. Hata yoga practices consist of physical postures. Shoonya meditation is a process of conscious nondoing. Sukha Kriya consists of alternate nostril breathing, which leads to regulation of breath. Ardha Siddhasana is a posture in which one sits cross-legged with the heel of the left foot placed at the perineum During the Samyama program, meditators were to remain silent for the entire 8-day duration of the program. They took part in all-day meditation sessions with intermittent breaks. The program hall was closed to external influences. No specific instructions or programs were given to the controls. Upon completing the Samyama program, there were no further restrictions on meditators. Meditators were able to return to their previous lifestyle
Sun et al., 2023[36]	Participants in the meditation group practiced Samatha and Vipassana for at least 2 h a day for 3–30 years. Samatha is the Buddhist practice of calm abiding, which steadies and concentrates the mind by resting the individual’s attention on a single object or mantra. Vipassana is an insightful meditation practice that enables one to enquire into the true nature of all phenomena

Table 3.

Results and conclusions

Author, year	Measures of Gut microbiota/metabolome	Bioinformatics tools used for data analysis	Results	Conclusion
Jia et al., 2020[33]	16S rDNA sequencing technology and bioinformatics analysis to detect the differences in intestinal microbiota composition Prediction of function of intestinal microbial flora	Sequencing: Illumina MiSeq platform (Illumina, San Diego, USA) Microbiota composition analysis: UPARSE software (version 7.1); RDP classifier; Silva database (SSU123) for for microbiota composition analysis	A significant change in the structure of the intestinal flora within meditators. Three beneficial bacteria genera (Bifidobacterium, Roseburia and Subdoligranulum) were significantly enriched in the meditation group compared with controls The prediction of differentially enriched intestinal microbial function showed a significant reduction in the metabolism of propionate, niacin, tyrosine, and nicotinamide in the intestinal microbiota and a significant enhancement in the biosynthesis of flavones, flavone alcohols, butosin, and neomycin; flavonoid-mediated oocyte maturation; cytoskeleton protein pathways; and antigen processing and presentation in the meditation group when compared with those in the control group	Long-term meditation with vegan diet improved the structure and function of intestinal flora when compared with controls
Qiao et al., 2022[34]	Gut microbiota diversity using 16SrRNA gene sequencing Relationship between gut microbiota and fecal metabolites Metabolomes were examined by nontargeted LC-MS metabolomics	Sequencing: Illumina MiSeq platform (Illumina, San Diego, USA) Microbiota composition and functional analysis: Majorbio Cloud Platform	A significant difference in the gut microbial structure between two groups. Intestinal microbial communities and metabolites were decreased in meditators than controls Bacteroidetes was increased while the Actinobacteria, Firmicutes, and Firmicutes/Bacteroidetes ratios were decreased in meditators than controls A significant increase in 26 metabolites (such as L-dopa and berberine), and a decrease in 8 metabolites (such as indoleacrylic acid, valyl−valine, and cadaverine) in meditators than controls DG, which is involved in immune related pathways, was more expressed in meditators practicing for more than 7.5 years than lesser ones	Long-term meditation with vegetarianism can modulate gut microbiota composition and metabolites
Raman et al., 2023[35]	Microbial diversity was studied using16SrRNA sequencing Levels of SCFA and other fecal metabolites composition Metabolomes were examined using mass spectrometer coupled to a UHLPC system and analyzed by El-MAVEN software Samples were collected three times: At baseline (T1), after 2 months of Isha Yoga as pre-Samayama preparatory practices (T2) and after 3 months of Samayama Meditation (T3)	Sequencing: Illumina MiSeq platform (Illumina, San Diego, USA) Microbiota composition analysis: idTaxa classifier from Decipher R package using SILVA (v 132 database)	No significant difference in Alpha diversity between meditation and control groups Significant difference in Beta diversity between T2 and T3 within meditators group while no change within control group Significant changes in a branched short-chain fatty acids, higher levels of iso-valerate and iso-buytrate within meditators at T2 when compared to T1 No difference in the abundance between meditation and control groups. Within meditation group, an altered abundance was showed at T3 compared to T1	Preparatory practice of Isha yoga and Samyama meditation program increased the beneficial bacteria, SCFA and other metabolites
Sun et al., 2023[36]	Microbial diversity was studied using16SrRNA sequencing Alpha and beta diversity indices to assess the gut bacterial diversity KEGG pathway analysis to explore function of fecal microbiota Prediction of function of intestinal microbial flora using PICRUSt analysis Plasma total cholesterol and apolipoprotein-B	Sequencing: Illumina HiSeq PE250 sequencing instrument (Illumina, California, USA) Microbiota composition analysis: UPARSE, RDP Classifier, Python scripts of QIIME (version 1.9.1)	A significant difference in alpha diversity between meditation and control groups A significant increase in Prevotella and Bacteroides (at genus level) within meditation group Predictive functional analysis showed significant differences in the abundance of KEGG pathways between the meditation and control groups A significant increase in glycan biosynthesis, metabolism, and lipopolysaccharide biosynthesis within the meditation group Total cholesterol and apolipoprotein-B levels were significantly reduced in the meditators group compared to controls	The long-term deep meditation may have a beneficial effect on the structure and function of gut microbiota. The microbiota enriched in meditators was associated with a reduced risk of anxiety, depression and cardiovascular disease

PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, RDP: Ribosomal Database Project, SCFA: Short chain fatty acid, SCFA: Short chain fatty acid, KEGG: Kyoto encyclopedia of genes and genomes, LC-MS: Liquid Chromatography-mass spectroscopy

The subjects of the three observational studies were regular long-term meditators with meditation experience ranging from 1 to 30 years.[33,34,36] The duration of daily yoga and meditation practice ranged from 30 min to 2 h. The participants were followers of the vegan[33] or vegetarian diet.[34] The control group subjects of these studies were non-meditators, i.e. who never received any meditation training.

Study outcomes and their measures

The study outcomes and their measures are shown in Table 3. The composition and microbial diversity were studied using 16S rDNA[33] or 16S rRNA gene sequencing.[34,35,36] Further, bioinformatics analysis was done to detect the differences in gut microbiota composition (alpha and beta diversity) and to predict their functions.[33,34,35,36] Raman et al. collected stool samples from the participants at baseline (T1) before starting the pre-meditation program, immediately before the meditation or Samyama program (T2), and after 3 months following Samyama.[35]

The metabolomes/metabolites were examined in two studies. Qiao et al. estimated metabolomes using nontargeted LC-MS (Qiao) with SIMCA software (V16.0.2, Sartorius Stedim Data Analytics AB, Umea, Sweden)[34] while Raman et al. measured SCFA levels and other fecal metabolite composition using UHLPC.[35] Biochemical examination of total cholesterol and apolipoprotein-B in plasma was done in one study.[36] The bioinformatics tools used by each study for sequencing, microbiota composition analysis, and predicting functional pathways are also given in Table 3.

Effect of yoga and meditation on gut microbiota

All four reviewed studies have shown a favorable change in the structure and function of gut microbiota with yoga and Buddhist meditation training when compared to controls [Table 4]. There was an increase in beneficial bacteria in the meditators compared to controls. The beneficial bacteria enriched in meditators in comparison with non-meditators were Bacteroides,[34,36] Bacteroidetes,[34] Faecalibacterium,[34,36] Lachnospira,[34] Roseburia,[33,34] Prevotella,[34,36] Lachnospiraceae,[33,34] Lactobacillus,[35] Ruminococcaceae,[35] Subdoligranulum,[33] ventriosum_group,[33] Erysipelortrichaceae,[33] Butyricicoccus,[33] and Collinsella.[35] In contrary, the nonbeneficial bacteria such as Firmicutes,[34] actinobacteria,[33,34] Blautia,[34] eubacterium,[34] Bifidobacteria,[34] Dorea,[34] Streptococcus,[34] Proteobacteria,[33] and Saccharibacteria[33] were found increased in the nonmeditators compared to the meditators. One of the studies assessed the relation between changes induced by Buddhist meditation in gut microbiota and cardiovascular risk. They demonstrated a correlation between a meditator’s enriched microbiota and a decreased risk of anxiety, depression, and CVD.[36]

Table 4.

Changes in the beneficial bacteria, nonbeneficial bacteria, metabolites, and functional pathways

Variables	Groups	Jia et al., 2020[33]	Qiao et al., 2022[34]	Raman et al., 2023[35]	Sun et al., 2023[36]
Beneficial bacteria ↑	Yoga/meditation group	Genus level: ↑Subdoligranulum, Roseburia, Lachnospiraceae, ventriosum_group, Erysipelortrichaceae, Lachospiraceae, Butyricicoccus, Bifidobacterium	Bacteroides ↑, Faecalibacterium, ↑ Lachnospira, Roseburia, ↑ Norank_f_Lachonospiraceae ↑, Prevotella, ↑ Bacteroidetes	↑ Lachnospiraceae, Lactobacillus, Bifidobacterium, Ruminococcaceae, Streptococcus and Collinsella	Genus level: ↑ Prevotella, Bacteroides (Megamonas and Faecalibacterium)
	Control group	-	-	-	-
Nonbeneficial bacteria	Yoga/meditation group	-	-	-	-
	Control group	↑ Geneus level: Actinobacteria, Proteobacteria, Saccharibacteria	Phylum: Firmicutes, actinobacteria ↑ Genera: ↑ Blautia, eubacterium, Bifidobacteria, Dorea, Streptococcus	-	-
Functional and metabolic changes	Yoga/Meditation group	↑ Biosynthesis of flavones, flavone alcohols, butosin and neomycin; flavonoid-mediated oocyte maturation; cytoskeleton protein pathway; and antigen processing and presentation	Carbohydrate metabolism, energy metabolism, glycan biosynthesis, TCA cycle, carbon fixation pathways, glycande gradation and lipopolysaccharide biosynthesis Minor changes related membrane transport	-	↑ glycan biosynthesis, metabolism and lipopolysaccharide biosynthesis
	Control group	-	ABC transporters and phosphotransferase	-	-
Metabolites	Yoga/meditation group	-	Lipid and lipid like molecules, L-dopa and berberine	↑ SCFA like, iso-butyrate, iso-valerate	-
	Control group	-	Indoleacrylic acid, valyl-valine and cadaverine	-
Biochemical investigation	Yoga/meditation group	-	-	-	↓ cholesterol and apolipoprotein B
	Control group	-	-	-	-

SCFA: Short chain fatty acid, TCA: Tricarboxylic Acid Cycle, ABC: ATP-binding cassette transporter, ↑: Increased

The effect of yoga and Buddhist meditation on metabolites was also studied and reported. Among the four reviewed studies, two assessed the metabolite levels,[34,35] while the other two did a functional pathway prediction analysis to predict the enriched metabolites.[33,36] Practice of yoga had raised plasma levels of SCFAs.[35] The metabolites like lipid and lipid-like molecules, L-dopa and berberine were increased, while Indoleacrylic acid, valyl–valine, and cadaverine were decreased in Buddhist meditators when compared to nonmeditators.[34]

Quality of studies

Table 5 shows the quality of individual studies assessed using Newcastle–Ottawa quality scale. The quality of three studies was good[33,35,36] while one study was found satisfactory.[34]

Table 5.

Newcastle–Ottawa quality assessment of included studies (***Grading Intensity)

Study, year	Selection	Comparability	Outcome	Overall score
Jia et al., 2020[33]	***	**	***	8
Qiao et al., 2022[34]	**	**	**	6
Raman et al., 2023[35]	***	**	***	8
Sun et al., 2023[36]	***	**	***	8

Note: One star was awarded for each numbered item within each domain of assessment scale. Overall score of 9-10 points indicates low risk of bias; 4-6 points indicate medium risk of bias

Adverse events

No adverse effects were reported in the reviewed studies.

Discussion

We think that this is the first comprehensive analysis of how yoga and meditation affect gut microbiome. Among the four reviewed studies, one was a non-randomized controlled trial (RCT) and three were observational studies. The type of meditation investigated was yoga and Buddhist meditation. The interventional study assessed the effect of yoga on gut microbiota, while the observational studies compared the changes in the gut microbiota between the long-term meditators and non-meditators. The long-term meditators were exposed to Buddhist meditation from 1 to 30 years. Reviewed studies involving a total of 440 healthy individuals have shown that either practicing yoga or Buddhist meditation with vegetarian/vegan diet can enhance the composition and functionality of gut microbiota and metabolites.

It is essential to understand the difference in the practices of different types of meditation for analyzing their effects. Several types of meditative practices, which have been discussed in the introduction, can be broadly classified into two groups, based on traditional texts and modern neuroscientific conceptions: (1) focused attention and (2) open monitoring meditation. The “focused attention” category includes meditative practices that entail voluntary focusing of attention on a chosen object, breathing, image, words (chanting mantra), or phrases. Yoga-based meditations such as OM meditation, cyclic meditation, chanting (mantra) meditation, transcendental meditation, and loving kindness meditation are examples of focused attention. Open monitoring meditation includes meditative practices that involve nonreactive monitoring of the content of experience from moment to moment. Here, instead of focusing on one object (like in focused attention), an individual strives to be in the present moment with open monitoring of all aspects of our experience, which may be internal (thoughts, feelings, and memory) or external (smell and sound) without becoming engrossed in or distracted by them. Vipassana meditation and mindful meditations are examples of open-monitoring meditation.[12] Among the reviewed studies, the influence of focused attention on gut microbiota has been assessed by one study[35] while open monitoring by another three studies.[33,34,36]

A favorable change in the structure and function of gut microbiota with yoga and Buddhist meditation training when compared to controls has been demonstrated in all the four reviewed studies. The common enriched beneficial bacteria (demonstrated in two or more studies) in the meditators are Bacteroides, Faecalibacterium, Roseburia, Prevotella, and Lachnospiraceae. One of the most significant functions of these beneficial bacteria is the production of SCFAs, which are vital for numerous physiological processes. SCFAs, primarily acetate, propionate, and butyrate, are produced when gut bacteria ferment dietary fibers. This fermentation mainly occurs in the colon, where a variety of anaerobic bacteria thrive. The types and amounts of SCFAs produced depend on the dietary intake of fibers and the specific microbial composition of the gut.[37] Butyrate is a primary energy source for colonocytes, the cells lining the colon. It promotes cell proliferation, enhances barrier function, and has anti-inflammatory properties, reducing the risk of colorectal cancer and inflammatory bowel diseases.[38] Acetate and propionate enter the bloodstream and have systemic effects. Acetate can influence appetite regulation and energy balance, while propionate is involved in gluconeogenesis and lipid metabolism. Both play roles in reducing the risk of metabolic disorders such as obesity and type 2 diabetes. SCFAs modulate the immune system by influencing the differentiation and function of various immune cells. They help maintain the integrity of the gut barrier, preventing pathogenic bacteria from triggering systemic inflammation.[37,38] Emerging evidence suggests that SCFAs can influence brain function and behavior through the gut–brain axis. They may impact neurotransmitter production and have been implicated in conditions such as depression and anxiety.[39] Enriched bacteria (Bacteroides, Faecalibacterium, Roseburia, Prevotella, and Lachnospiraceae) with meditation might have improved the production of SCFAs. Among the included studies, only Raman et al. evaluated SCFAs and demonstrated an enhancement in iso-butyrate and iso-valerate.[35]

The gut microbiota is an integral part to numerous metabolic functions and biosynthesis of vitamins that are essential for maintaining homeostasis and overall health. It is involved in metabolism of tyrosine, tryptophan, propionate, niacin, lipopolysaccharide and nicotinamide, and biosynthesis of glycan, lipopolysaccharide, flavonoids, butosinas as well as antigenprocessingand presention, etc.[40,41,42] Its influence extends from metabolism to immune modulation and hormonal regulation. It aids in the breakdown of complex carbohydrates, proteins, and fats.[40,42] Specific bacteria, such as those from the Bacteroidetes and Firmicutes phyla, produce enzymes that humans lack, allowing the digestion of dietary fibers into SCFAs. Gut microbes influence lipid metabolism through the modulation of bile acids (conversion of primary bile acids to secondary bile acids), which are crucial for fat digestion and absorption, and through the production of SCFAs, which can influence fat storage and lipolysis.[42] The studies included in this review demonstrated favorable changes in metabolism with meditation and vegetarian/vegan diet such as carbohydrate metabolism, energy metabolism, TCA cycle, carbon fixation pathways, glycan degradation,[34] glycan biosynthesis, and lipopolysaccharide biosynthesis.[34,36] Furthermore, the study conducted by Jia et al. (2022) showed increased biosynthesis of flavonoids, flavone alcohols, butosin and neomycin; and improvement in the flavonoid-mediatedoocyte maturation; cytoskeleton proteinpathway; and antigen processing and presentation.[33] However, asignificantincrease in severalmetabolites such as L-dopa and berberine; and, a decrease in metabolites such as indoleacrylic acid, valyl − valine, and cadaverine were reported in meditators than controls.[34] L-dopa is a neurotransmitter that is involved in happiness and is the most common drug used to treat Parkinson’s disease.[43] One study examined the relationship between gut microbiome modifications induced by Buddhist meditation and cardiovascular risk. They demonstrated the association between a meditator’s richer microbiota and a lower risk of anxiety, depression, and CVD.[36]

Diet also plays a crucial role in the maintenance of balance and composition of gut microbiota. Among the various dietary patterns, a vegetarian or vegan diet, which excludes all animal products, has gained attention for its impact on gut microbiota and overall health. A diet rich in diverse fibers from fruits, vegetables, whole grains, and legumes supports a healthy microbiota and optimal SCFA production. A systematic review suggested that a vegetarian/vegan diet rich in diverse fibers from fruits, vegetables, whole grains, and legumes is effective in promoting a diverse ecosystem of beneficial bacteria and optimal SCFA production.[44,45] As the study participants of all the included studies for this review were either vegetarians or vegans, the beneficial changes in the diversity and richness of beneficial bacteria and its metabolites like SCFA production may be attributed to the combined effect of vegetarian/vegan diet and meditation.[33,34,35,36]

As mentioned above, the brain exerts a dynamic influence over gut function and metabolite production, including SCFAs, through the gut–brain axis – a complex, bidirectional communication network involving neural, hormonal, and immune pathways. During periods of rest (parasympathetic dominance), vagal nerve activity promotes a balanced gut environment, supporting healthy microbial communities that efficiently ferment dietary fibers to produce SCFAs. In contrast, during stress (sympathetic dominance), brain signals activate the hypothalamic–pituitary–adrenal (HPA) axis, releasing cortisol and other stress mediators. These changes can alter gut motility, reduce mucus secretion, and impair blood flow to the gut, disrupting the microbial environment.[46,47] Stress-induced shifts in microbiota composition (dysbiosis) often lead to a decrease in SCFA production and an increase in potentially harmful metabolites.[48] Reduced SCFA production can further exacerbate inflammation and impair gut barrier function, creating a vicious cycle. Conversely, practices like yoga and meditation have been shown to downregulate the HPA axis and sympathetic activity, while enhancing parasympathetic (vagal) tone.[49,50,51] Enhanced vagal activity can favorably modulate gut motility, immune signaling, and microbiota composition, promoting an environment conducive to SCFA production.

Limitations

This review has few limitations. We acknowledge the limited number of studies included in this review. Despite an extensive and systematic database search, only four human studies met the predefined eligibility criteria focusing specifically on yoga or meditation and their influence on gut microbiota. This highlights both the novelty of this emerging research area and the current scarcity of high-quality clinical evidence. While this limitation restricts the generalizability of our findings, it also underscores the urgent need for well-designed RCTs to further explore and validate the gut microbiota-modulating effects of mind–body interventions such as yoga and meditation.

Another important limitation is the potential confounding effect of diet. All participants across the included studies were either vegetarians or vegans, and dietary patterns are known to significantly influence gut microbiota composition. While our review focused on the effects of yoga and meditation, it is likely that the observed microbial changes were the result of synergistic effects of both mind–body practices and plant-based dietary habits. This limitation has been explicitly acknowledged in both the Discussion and Conclusion sections, and we emphasize the need for future studies to control for dietary variables when examining the independent effects of yoga or meditation on gut microbiota.

We may have missed studies published in other languages because the literature search approach was limited to studies published in the English language. Further, unpublished studies were not searched. Only those studies that evaluated how yoga and meditation influenced metabolites and the human gut microbiota were included. There was only one interventional study out of the four reviewed studies; therefore, a meta-analysis of the effects of yoga and meditation on human gut microbiota was not feasible. Since the study protocols for the included studies in the review were not registered or published prospectively, it is not possible to completely rule out the possibility of publication bias. The generalizability of our results globally may be limited, since all the evidence found originated from the USA and China.

Implication for research and clinical practice

The findings of this review are compelling, as yoga and meditation were associated with an increase in beneficial microbiota and metabolites in healthy individuals. However, only one intervention (non-RCT) study compared the effects of yoga meditation between meditators and controls. This study is limited by the absence of testing in any disease conditions. Therefore, further clinical research is needed to evaluate the impact of yoga and meditation on various health conditions. Evidence on yoga- and meditation-induced changes in gut microbiota and their clinical outcomes remains limited. More RCTs are needed to verify the association between improved beneficial microbiota and metabolites with clinical outcomes. In addition, future research should aim to unravel the mechanisms behind gut microbiota interactions, the production of beneficial metabolites, and their implications for human health. Though are only four studies in thisreview, the qualitative methods employed adequately validate the significant increase in beneficial microbiota and metabolites with the practice of yoga and meditation.

Conclusion

Among the four studies reviewed, none were RCTs; one was a non-RCT and three were observational studies. These studies suggest that yoga and Buddhist meditation may positively influence the composition and function of the gut microbiota. However, since all participants adhered to a vegetarian or vegan diet, the observed benefits could be due to the combined or synergistic effects of meditation and plant-based dietary patterns. To better understand the specific role of meditation in modulating gut microbiota and its functions and to support future clinical recommendations, well-designed RCTs are essential.

PROSPERO Registration Number: CRD42023433700.

Conflicts of interest

There are no conflicts of interest.

Funding Statement

Nil.