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microbiome

Your Gut May Be the Key to Chronic Fatigue, Long COVID

by Dr. Michael Lee – Health Editor July 27, 2025

written by Dr. Michael Lee – Health Editor

AI Detects ME/CFS Biomarkers with 90% Accuracy

Groundbreaking Study Links Gut, Immune System, and Metabolism to Chronic Fatigue Syndrome

Millions living with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) may finally see a path to personalized care. New research leverages artificial intelligence to pinpoint how the condition disrupts vital connections between the gut microbiome, immune system, and metabolism. The findings, highly relevant to long COVID due to symptom overlap, identified biological signatures that distinguish patients from healthy individuals with remarkable precision.

Unveiling Biological Signatures

A pioneering study has identified distinct biological markers capable of identifying ME/CFS patients with up to 90% accuracy. The research found that individuals with the condition exhibit altered metabolic pathways, including reduced beneficial fatty acids like butyrate, and disrupted immune cell activity. These biological discrepancies, linked to the gut microbiome and its byproducts, offer critical insights into the illness.

“Our study achieved 90% accuracy in distinguishing individuals with chronic fatigue syndrome, which is significant because doctors currently lack reliable biomarkers for diagnosis.”

—Dr. Derya Unutmaz, Professor in Immunology at The Jackson Laboratory

This diagnostic capability is a major step forward, as the absence of clear laboratory markers has sometimes led to skepticism from medical professionals, who may attribute symptoms to psychological factors.

AI Platform Maps Complex Interactions

The newly developed AI platform, BioMapAI, plays a crucial role in this advancement. It integrates thousands of data points, encompassing microbiome profiles, blood tests, immune markers, and reported symptoms, to identify unique patterns and disruptions characteristic of ME/CFS. This sophisticated approach makes precision medicine strategies for the condition more attainable.

Researchers aim to widely share their dataset and the BioMapAI platform, which is designed to support analyses across various symptoms and diseases, effectively integrating complex multi-omics data.

The platform successfully linked clinical symptoms with cutting-edge omics technologies, a critical step given ME/CFS’s variable nature.

“We integrated clinical symptoms with cutting-edge omics technologies to identify new biomarkers of ME/CFS. Linking symptoms at this level is crucial, because ME/CFS is highly variable. Patients experience a wide range of symptoms that differ in severity and duration, and current methods can’t fully capture that complexity.”

—Dr. Julia Oh, Microbiologist and Professor at Duke University

Data from 153 ME/CFS patients and 96 healthy controls were analyzed over four years. BioMapAI, developed by lead author Dr. Ruoyun Xiong, demonstrated strong predictive power, with immune cell analysis excelling at forecasting symptom severity and microbiome data proving most effective for gastrointestinal, emotional, and sleep disturbances.

Potential for Personalized Treatment

These findings hold significant promise for patients, not only by validating the biological basis of ME/CFS but also by offering personalized insights into symptom origins. This could pave the way for tailored dietary, lifestyle, and therapeutic interventions, particularly for individuals with long COVID who exhibit similar symptoms.

The study noted that biological disruptions appear to become more entrenched over time, with those ill for over ten years showing more complex network disruptions than those ill for less than four years. While this suggests potential challenges for long-standing ME/CFS, it does not preclude the possibility of reversal.

The research, detailed in Nature Medicine and led by Dr. Julia Oh (formerly at JAX, now at Duke University) in collaboration with ME/CFS experts Dr. Lucinda Bateman and Dr. Suzanne Vernon of the Bateman Horne Center, and Dr. Derya Unutmaz, establishes a clearer scientific foundation for understanding and treating this often-misunderstood illness. The study received funding from NIH grant 1U54NS105539.

July 27, 2025 0 comments

Health

Restricted diet triggers drop in microbial diversity without convergence

by Dr. Michael Lee – Health Editor July 22, 2025

written by Dr. Michael Lee – Health Editor

Oatmeal Diet Fails to Unify Gut Microbiomes

Radical dietary simplification reveals surprising individual responses

A six-day regimen of just oats, milk, and water, designed to homogenize gut bacteria, has yielded unexpected results. Researchers discovered that despite identical diets, participants’ gut microbiomes remained uniquely distinct, challenging the notion of a one-size-fits-all approach to gut health.

Dietary Monotony, Microbial Diversity

An exploratory study, dubbed the “Oatmeal Study,” tracked 18 healthy Belgian adults over 21 days. The intervention phase, lasting six days, saw participants consume only oat flakes, whole milk, and water. While this dramatically reduced dietary variety and caloric intake by over 31%, the microbial communities within their guts did not converge.

Instead of becoming more alike, the participants’ microbiomes often grew more divergent. The impact of the diet on genus-level microbial variation was a mere 3.4%, with significant individual differences ranging from 1.67% to 16.42%. This finding suggests that factors beyond diet, such as genetics and an individual’s baseline microbiome, play a dominant role in shaping gut microbial responses.

Shift Towards Potentially Unhealthy Gut Signatures

During the oat-only period, researchers observed a significant shift in microbial community structure. The prevalence of the Bacteroides2 (Bact2) enterotype, often linked to dysbiosis, increased. Simultaneously, a decline was noted in *Faecalibacterium*, a beneficial genus known for producing anti-inflammatory compounds.

This transient rise in Bact2, coupled with a reduction in beneficial bacteria, raises questions about the health implications of such restrictive diets. These microbial shifts reversed once normal eating patterns resumed.

Reduced Microbial Load and Diversity

Faecal microbial load decreased by more than 30% during the intervention. This reduction in bacterial biomass aligns with the lower caloric intake and caloric restriction observed in similar studies. Overall gut microbiome diversity, measured by the Shannon index, also dropped significantly.

Such a decrease in diversity is often associated with less mature and resilient microbial ecosystems. This suggests that while oats are nutritious, extreme dietary restriction can negatively impact the robustness of the gut flora.

Personalized Responses Underscore Complexity

Despite the consistent dietary input, individual responses to the intervention varied dramatically. Some participants exhibited substantial changes in their gut bacteria, while others remained largely unaffected. Efforts to identify predictive factors, such as gender or initial microbiome diversity, proved inconclusive after statistical corrections.

This unpredictability highlights the intricate interplay between hosts and their microbiomes. It suggests that personalized nutrition strategies, rather than universal dietary advice, may be crucial for effectively modulating gut health.

The study’s findings challenge the intuitive assumption that simplifying one’s diet will lead to a more uniform gut microbiome. They underscore the resilience of individual microbial communities and the profound influence of pre-existing host-microbiota dynamics. For instance, a 2023 study on the Western diet found that it significantly reduced gut microbial diversity compared to a Mediterranean diet, reinforcing the impact of diet on microbial richness (Nature Scientific Reports, 2023).

Ultimately, the “Oatmeal Study” demonstrates that even drastic dietary simplification does not guarantee microbial uniformity. The human microbiome’s resilience and individuality, driven by complex host-microbe interactions, remain paramount. These insights are vital for developing future interventions aimed at microbiome modulation, emphasizing the need to account for personal variability and ecological context.

July 22, 2025 0 comments

Health

Probiotics: Strain-Specific Effects on Gut Microbiome Recovery

by Dr. Michael Lee – Health Editor July 22, 2025

written by Dr. Michael Lee – Health Editor

Here’s a breakdown of the provided text,focusing on the research about probiotics and gut recovery after antibiotics:

The Problem:

The gut’s bacterial environment (microbiota) is not well understood.
A healthy microbiota provides “colonization resistance,” preventing pathogens from taking hold. Antibiotics can disrupt this healthy microbiota,making the gut vulnerable.

The Research Question:

How long does it take for colonization resistance against C.diff (a common gut pathogen) to return after antibiotic treatment?
What is the impact of two common commercial probiotic strains, Lactobacillus acidophilus (L. acidophilus) and Lactobacillus gasseri (L. gasseri), on this recovery?

The Study Design:

Mice were treated with cefoperazone, a broad-spectrum antibiotic. Three groups of mice were studied:
1. No probiotic treatment.
2. Treated with L. acidophilus.
3. Treated with L. gasseri.
Each group was exposed to C. diff weekly for four weeks.
The researchers measured bacterial load and C.diff resistance in the mice’s microbiota.

Key Findings:

No Probiotic Group: Showed decreased bacterial load and resistance to C. diff by four weeks after stopping antibiotics.
L. acidophilus Group: Had increased bacterial load in weeks two and three after stopping antibiotics.
L. gasseri group: Had no detectable C. diff after two weeks.Mechanisms of L. gasseri:

L. gasseri did not appear to colonize or remain in the gut long-term.
Instead, it seemed to work indirectly by:
Producing bacteriocins (antimicrobial peptides). Encouraging the growth of Muribaculaceae, another possibly beneficial bacteria.

Important Implications and Takeaways:

Strain-Specific Effects: The impact of probiotics is highly dependent on the specific strain used, the individual’s microbiome composition, and the disease being addressed.
Complexity of Probiotics: Probiotics can have transient or indirect effects on the microbiome, making their mechanisms more complex than initially thought.
Indirect Recovery: L. gasseri didn’t directly prevent infection but promoted recovery by supporting other beneficial bacteria (Muribaculaceae), which then provided resistance.
Functional Testing is Crucial: This study highlights the need for functional testing of probiotic resistance in the microbiome, not just measuring their presence.
* Potential for Complication: While probiotics can be beneficial, they can also have effects weeks after governance and, in certain specific cases, may prolong or complicate recovery.

In essence, the research suggests that while probiotics can aid gut recovery after antibiotics, their effectiveness and mechanisms vary greatly by strain, and some may work indirectly by fostering the growth of other beneficial bacteria.

July 22, 2025 0 comments

Health

Self-Care Begins In The Gut: Why You Should Rethink Your Wellness Routine | Health and Fitness News

by Dr. Michael Lee – Health Editor July 19, 2025

written by Dr. Michael Lee – Health Editor

Nurture Your Inner Ecosystem: Gut Health as Self-Care

Expert Guide to Prioritizing Your Microbiome

Beyond surface-level wellness rituals, true self-care is deeply rooted within. An often-overlooked cornerstone of our physical and mental state is the health of our gut. This internal universe of microbes influences everything from digestion and mood to our immune defenses.

The Microbiome’s Mighty Influence

Our gut is host to trillions of microorganisms, forming a complex ecosystem vital for nutrient absorption, immune system regulation, and hormonal balance. Disruptions to this delicate environment, often caused by poor diet, stress, lack of sleep, or inactivity, can lead to a cascade of health issues.

Pariksha Rao, Director of Nutrition and Medical Affairs at The Good Bug, highlights the far-reaching impact of gut health. “An imbalanced microbiome is linked to conditions such as obesity, type 2 diabetes, inflammatory bowel disease, anxiety, depression, autoimmune disorders, and chronic inflammation,” she explains. “What affects the gut affects the body and mind.”

Regular exercise, nutrient-rich foods, and stress management are key to a healthy gut.

Fueling Your Gut: The Power of Food

Dietary choices directly sculpt the well-being of your gut microbiome. Incorporating a variety of plant-based foods is a straightforward way to foster beneficial bacteria. Fruits, vegetables, legumes, nuts, and whole grains provide essential fibers that nourish gut flora.

“Fermented foods such as yogurt, kefir, kimchi, sauerkraut, and miso contain live cultures that can support microbial diversity,” advises **Rao**. “These should be consumed regularly but in moderation. Every person’s gut is unique, so it’s important to notice how your body responds and make adjustments accordingly.”

Equally important is minimizing processed foods, artificial sweeteners, and excessive sugar, which can disrupt the gut’s delicate balance.

Movement Enhances More Than Fitness

Physical activity benefits more than just cardiovascular health and weight management; it significantly aids digestion and gut equilibrium. Gentle to moderate exercises like walking, yoga, cycling, or swimming help the digestive system function more smoothly.

“There’s no need for an intense workout plan. Even 30 minutes of mindful movement a few times a week can support gut health over time,” **Rao** notes.

Stress Management and Sleep: Crucial Pillars

The gut-brain connection is undeniable, with stress manifesting physically as digestive discomfort. Techniques like journaling, deep breathing exercises, or establishing calming daily rituals can alleviate strain on the digestive system.

Adequate sleep is also paramount for internal repair and restoration, supporting immune function, metabolic regulation, and the gut microbiome. A consistent sleep schedule is integral to overall well-being.

Personalize Your Path to Gut Wellness

There’s no one-size-fits-all approach to gut health. Observing how your body reacts to different foods and lifestyle changes is key. Keeping a food and lifestyle journal can help identify patterns and understand what promotes positive changes and comfort.

A study published in the journal *Nature Medicine* in 2023 found that personalized dietary interventions, based on an individual’s gut microbiome composition, led to improved metabolic markers and a better understanding of food responses (Nature Medicine, 2023). Consulting a nutritionist or healthcare professional can further refine your approach for optimal results.

July 19, 2025 0 comments

Health

Agricultural Dust Linked to Gut Health Problems in Farmworkers

by Dr. Michael Lee – Health Editor July 19, 2025

written by Dr. Michael Lee – Health Editor

Here’s a breakdown of the provided text, focusing on the key findings and implications:

Main Finding:

Inhaling dust from hog farms not only causes airway inflammation but also disrupts the gut microbiome and impairs intestinal function, leading to increased “leaky gut.”

Key Details:

Study lead: Declan McCole, a professor of biomedical sciences at UCR School of Medicine.
publication: Journal of Applied Toxicology. Mechanism: Hog farm dust contains high levels of bacteria and endotoxins.
Experimental Model: Mice were exposed intranasally to hog dust extract for three weeks.
Gut microbiome Impact:
critically important drop in beneficial bacterial species like Akkermansia muciniphila, Clostridium sp. ASF356, and Lachnospiraceae bacterium.
Decreased levels of crucial gut compounds like riboflavin, nicotinic acid, inosine, and leucine, which are significant for energy metabolism, immune regulation, and gut barrier maintenance.
intestinal Function Impact: increased “leaky gut” (intestinal permeability), which is linked to chronic diseases such as inflammatory bowel disease, celiac disease, and type 1 diabetes. Systemic Consequences: The study highlights that inhaled pollutants can have effects beyond the respiratory system, impacting the gut. This emphasizes the “gut-lung axis.”
Implications for Farmworkers: The findings underscore the need for improved workplace protections for agricultural workers due to the complex threat posed by agricultural dust (fine particulate matter and resistant bacteria).

Quote highlights:

Declan McCole: Emphasizes that inhaled pollutants have systemic consequences and the importance of considering the gut-lung axis in assessing health risks of agricultural bioaerosol exposure.
* Meli’sa Crawford: Notes the striking impact on the gut microbiome and metabolism, in addition to airway inflammation and increased passage of gut bacterial products into the bloodstream.

Overall Importance:

This research expands on previous knowledge by demonstrating a direct link between hog farm dust inhalation and negative impacts on the gut microbiome and intestinal health. It calls for greater attention to the systemic health risks associated with agricultural dust exposure, notably for farmworkers.

July 19, 2025 0 comments

Health

Early antibiotic exposure weakens infant immune development

by Dr. Michael Lee – Health Editor July 14, 2025

written by Dr. Michael Lee – Health Editor

Antibiotics May Harm Infant Immunity, Study Finds Potential Reversal

Key Molecule Inosine Shows Promise in Restoring Immune Defenses

New research suggests early-life antibiotic exposure can significantly impact a baby’s developing immune system, potentially leaving them vulnerable to respiratory infections. Scientists have identified a naturally occurring metabolite, inosine, that may offer a way to mend this damage.

Disrupting Immune Signals

A University of Rochester Medical Center (URMC) study, published in the journal *Cell*, discovered that antibiotics given during pregnancy and infancy can weaken the immune system’s ability to fight off illnesses like the flu. Researchers observed that these drugs disrupt the gut microbiome’s production of inosine, a crucial molecule for immune cell maturation.

“Think of inosine as a molecular messenger. It travels from the gut to developing immune cells, telling them how to mature properly and prepare for future infections.”

—Hitesh Deshmukh, MD, PhD, Senior Author and Chief of Neonatology at UR Medicine Golisano Children’s Hospital

This disruption affects the formation of tissue-resident memory T cells, specialized immune cells that reside in the lungs and offer long-term protection against viral threats. The study’s findings are part of a larger NIH initiative examining how early-life exposures influence lifelong disease risks.

Restoring Immune Function in Mice

The research team found that supplementing inosine in mice exposed to antibiotics helped correct the immune system deficiencies. This breakthrough opens avenues for developing therapies to strengthen immune memory in infants at risk.

Insights from Human and Animal Models

The study utilized both mouse models and human infant lung tissue. Researchers compared infant mice given common antibiotics (ampicillin, gentamicin, and vancomycin) with those with natural gut bacteria. The antibiotic-exposed mice showed fewer protective CD8+ T cells in their lungs and impaired ability to form memory cells.

These immune deficits persisted into adulthood, indicating potentially permanent changes in immune development. Crucially, the team analyzed lung samples from human infants in an NIH-funded biobank, confirming similar immune deficits in those exposed to antibiotics.

Dr. Gloria Pryhuber, a neonatologist at GCH, was instrumental in the research, providing access to her BRINDL biobank of infant lung samples collected over 15 years through NIH funding. This biobank enabled the team to validate their findings in human cells.

Dr. Deshmukh stated, “We’ve discovered that the gut microbiome acts as a teacher for the developing immune system. When antibiotics disrupt this natural education process, it’s like removing key chapters from a textbook: the immune system never learns crucial lessons about fighting respiratory infections.”

The study’s results could guide future research into interventions like dietary supplements or metabolite therapies aimed at bolstering newborn immunity without solely relying on antibiotics or potentially risky probiotics. A 2023 report noted that antibiotic resistance is a growing global health threat, underscoring the need for careful antibiotic stewardship, especially in vulnerable populations (WHO).

Future Therapeutic Possibilities

“This suggests we might be able to protect at-risk infants through targeted supplementation,” Dr. Deshmukh added. “While much more research is needed before this approach could be applied clinically, it gives us a path forward.”

July 14, 2025 0 comments

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