Food Is Medicine

The Human Microbiome

The most influential “organ” in the human body might be made up of foreign cells—six pounds worth of microorganisms. Katherine Pollard discusses how her lab at the Gladstone Institutes uses big data and high-performance computing to study the human microbiome and learn how it influences health and disease.

The human microbiome plays a role in processes as diverse as metabolism, immune function, and mental health. Yet despite the importance of this system, scientists are just beginning to uncover which microorganisms reside in and on our bodies and determine what functions they perform. The development of innovative technology and analytical methods has enabled researchers like Dr. Pollard to decode the complex interactions between our human cells and microbial brethren, and infer meaning from the staggering amounts of data 10 trillion organisms create.

Your Microbiome: What Is It, and How Can It Help or Hurt You?

Your body hosts literally trillions of organisms—bacteria, fungi, viruses, and other tiny life forms—that collectively make up your microbiome. But what does your microbiome do, and how can it affect your health? Dr. Sonnenburg, bestselling author of The Good Gut, will explain the link between our Western diet and chronic illness. He’ll also suggest ways you can take back the reins and restore your health through diet and lifestyle. Presentation by Justin Sonnenburg, PhD, Associate Professor of Microbiology and Immunology

Rob Knight: How our microbes make us who we are

Rob Knight is a pioneer in studying human microbes, the community of tiny single-cell organisms living inside our bodies that have a huge — and largely unexplored — role in our health. “The three pounds of microbes that you carry around with you might be more important than every single gene you carry around in your genome,” he says. 

"Brain-Gut Axis: The Effect of Intestinal Microbiome on Mental Health" - Dr Emily Deans

The link between your gut health and autoimmune diseases.

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More than half your body is not human.

Dr. Robynne Chutkan | Revitalize | Why The Microbiome Is The Future Of Medicine

We've all heard about the microbiome, but what is it? Why should we care? And, most importantly, what should we do about it?

"Brain-Gut Axis: The Effect of Intestinal Microbiome on Mental Health" - Dr Emily Deans

Katherine Pollard: "Massive Data Sheds Light on Your Microbiome" | Talks at Google

How the Gut Microbiome affects the Brain and Mind

Sewage is an Information Superhighway

The Collective Microbiome: Rolf Halden 100 & Change MacArthur Foundation Submission.

Do our microbes affect our behavior? We've known for almost 200 years that trillions of microbes live on our skin and deep inside us, particularly in our gut. Until recently, we thought they were just freeloaders using our bodies to get food and shelter, causing us no trouble. However, we now know that the genes of these microbes (our microbiome) make many chemicals that affect our body and may influence our vulnerability to heart disease, diabetes, obesity, depression, anxiety, and several degenerative neurological diseases. Recent studies suggest the microbes within us may also influence our behavior. It is possible that the microbes within us not only influence our risk of various diseases but also influence our behavior. Scientists now even consider it conceivable that the microbes within us may influence things like intelligence, attitudes, empathy, who we are attracted to — in short, who we are. Harvard Health Publishing.

The Gut-Brain Axis: How Microbiota and Host Inflammasome Influence Brain Physiology and Pathology. The intestinal bacteria can affect the central nervous system (CNS) physiology and inflammation. The nervous system and the gastrointestinal tract are communicating through a bidirectional network of signaling pathways called the gut-brain axis, which consists of multiple connections, including the vagus nerve, the immune system, and bacterial metabolites and products. During dysbiosis, these pathways are dysregulated and associated with altered permeability of the blood-brain barrier (BBB) and neuroinflammation. PMCID: PMC7758428.

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The Microbiome and Aging.  In this review we present how the microbiota changes as the host ages, but also how the intricate relationship between host and indigenous bacteria impacts organismal aging and life span. We propose microbiome dysbiosis as an additional hallmark and biomarker of aging.

pubmed logoMicrobes and the Mind: How Bacteria Shape Affect, Neurological Processes, Cognition, Social Relationships, Development, and Pathology. This article reviews the ways in which bacteria shape affect, neurological processes, cognition, social relationships, development, and psychological pathology.

pubmed logoThe role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. Short-chain fatty acids (SCFAs), the end products of fermentation of dietary fibers by the anaerobic intestinal microbiota, have been shown to exert multiple beneficial effects on mammalian energy metabolism. The mechanisms underlying these effects are the subject of intensive research and encompass the complex interplay between diet, gut microbiota, and host energy metabolism. This review summarizes the role of SCFAs in host energy metabolism, starting from the production by the gut microbiota to the uptake by the host and ending with the effects on host metabolism.

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The Effects of Stress and Meditation on the Immune System, Human Microbiota, and Epigenetics. Psychological stress typically triggers a fight-or-flight response, prompting corticotropin-releasing hormone and catecholamine production in various parts of the body, which ultimately disturbs the microbiota. In the absence of stress, a healthy microbiota produces short-chain fatty acids that exert anti-inflammatory and antitumor effects. During stress, an altered gut microbial population affects the regulation of neurotransmitters mediated by the microbiome and gut barrier function. Meditation helps regulate the stress response, thereby suppressing chronic inflammation states and maintaining a healthy gut-barrier function. The current research team recommends the integration of meditation into conventional health care and wellness models.

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Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans.

Our Microbiome - Health Matters

Gut Microbiota and Its Role in Anti-aging Phenomenon: Evidence-Based Review. The presence of abundant bacterial taxa is a common structure that determines the microbiota of human being. The presence of this microbiota greatly varies from geographic location, sex, food habits and age. Microbiota existing within the gut plays a significant role in nutrient absorption, development of immunity, curing of diseases and various developmental phases. With change in age, chronology diversification and variation of gut microbiota are observed within human being. But it has been observed that with the enhancement of age the richness of the microbial diversity has shown a sharp decline. The enhancement of age also results in the drift of the characteristic of the microbes associated with the microbiota from commensals to pathogenic. Various studies have shown that age associated gut-dysbiosis may result in decrease in tlongevity along with unhealthy aging. PMID: 36930406.

The Healer Within and Our Microbiome

Holistically working with the micobiome and energy medicine is a large part of future of Western medicine and will dominate in the latter 21st Century. Western medicine is just discovering the importance of the microbiome. Researchers are already finding connections between the immune response and disease. A major component of the body's immune response is generated by the microbiome. Autoimmune disorders (i.e. they can't figure it out so they use this term) are being traced to imbalances or dysfunction in the gut microbiome. He mentions the example of an incorrect mix (individualized for each person, just like holistic medicine) of microbiota species (e.g. bifidobacterium) leads to an incorrect or non-existent immune response (i.e. an "autoimmune disorder").

Note that the enteric nervous system which is the extension of the autonomic nervous system to and through the gut (i.e. it is the nervous system of the microbiota/gut) is connected to the central nervous system via the vagus nerve. Qigong directly affects the vagus nerve in a very positive way, and that's another reason why Qigong practice is so simple yet powerful.

Exposure to prescribed medication in early life and impacts on gut microbiota and disease development. PMCID: PMC10835216

Our Mental Health Is Determined by an Intrinsic Interplay between the Central Nervous System, Enteric Nerves, and Gut Microbiota.  Intercommunications between the gut and CNS regulate mood, cognitive behavior, and neuropsychiatric disorders such as autism, depression, and schizophrenia. The modulation, development, and renewal of nerves in the ENS and changes in the gut microbiome alter the synthesis and degradation of neurotransmitters, ultimately influencing our mental health. PMID: 38203207.

Monitoring in vivo neural activity to understand gut-brain signaling. This review emphasizes recent studies that have advanced our knowledge of gut-brain signaling and food intake control, with a focus on how gut signaling influences in vivo neural activity in animal models. Moving forward, dissecting the complex pathways and circuits that transmit nutritive signals from the gut to the brain will reveal fundamental principles of energy balance, ultimately enabling new treatment strategies for diseases rooted in body weight control [PMID: 33558881].

Human Body Microbes Make Antibiotics, Study Finds. Each of us has a microbiome which is a component of our 'healer within' and is a major beneficiary of Qigong practice. Our microbiome can be considered part of our internal "pharmacy" where we can get safe and natural personalized drugs. New microbiome pictureresearch, funded in part by NCCIH, suggests that some of the bacteria that share our human bodies manufacture antibiotics and that these substances may be capable of fighting infection. The researchers, from the University of California, San Francisco; the University of California, Santa Cruz; Indiana University; Washington University School of Medicine; and Harvard Medical School, published their findings in a recent issue of the journal Cell: 

pubmed logoA systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Our findings illustrate the widespread distribution of small-molecule-encoding biosynthetic gene clusters in the human microbiome, and they demonstrate the bacterial production of drug-like molecules in humans.

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Neurotransmitter modulation by the gut microbiotaThe gut microbiota - the trillions of bacteria that reside within the gastrointestinal tract - has been found to not only be an essential component immune and metabolic health, but also seems to influence development and diseases of the enteric and central nervous system, including motility disorders, behavioral disorders, neurodegenerative disease, cerebrovascular accidents, and neuroimmune-mediated disorders. Accumulating evidence in animals suggests that manipulation of these neurotransmitters by bacteria may have an impact in host physiology, and preliminary human studies are showing that microbiota-based interventions can also alter neurotransmitter levels.

Gut Bacteria and Neurotransmitters. Gut bacteria play an important role in the digestion of food, immune activation, and regulation of entero-endocrine signaling pathways, but also communicate with the central nervous system (CNS) through the production of specific metabolic compounds, e.g., bile acids, short-chain fatty acids (SCFAs), glutamate (Glu), γ-aminobutyric acid (GABA), dopamine (DA), norepinephrine (NE), serotonin (5-HT) and histamine. Afferent vagus nerve (VN) fibers that transport signals from the gastro-intestinal tract (GIT) and gut microbiota to the brain are also linked to receptors in the esophagus, liver, and pancreas. In response to these stimuli, the brain sends signals back to entero-epithelial cells via efferent VN fibers. Fibers of the VN are not in direct contact with the gut wall or intestinal microbiota. Instead, signals reach the gut microbiota via 100 to 500 million neurons from the enteric nervous system (ENS) in the submucosa and myenteric plexus of the gut wall. The modulation, development, and renewal of ENS neurons are controlled by gut microbiota, especially those with the ability to produce and metabolize hormones. PMCID: PMC9504309.

pubmed logoThe role of the gut microbiome in the development of schizophrenia.  The development of the neural circuitry underlying social, cognitive and emotional domains requires precise regulation from molecular signalling pathways, especially during critical periods or "windows", when the brain is particularly sensitive to the influence of environmental input signalling. Many of the brain regions involved, and the molecular substrates sub-serving these domains are responsive to life-long microbiota-gut-brain (MGB) axis signalling. This intricate microbial signalling system communicates with the brain via the vagus nerve, immune system, enteric nervous system, enteroendocrine signalling and production of microbial metabolites, such as short-chain fatty acids. Preclinical data has demonstrated that MGB axis signalling influences neurotransmission, neurogenesis, myelination, dendrite formation and blood brain barrier development, and modulates cognitive function and behaviour patterns, such as, social interaction, stress management and locomotor activity.

The Human Microbiome, the Self You Never Knew

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The Living Organisms Sharing Your Body

Can a basic understanding of the Human Microbiome change the way we think of ourselves and provide substantial food for thought as we reflect on who and what we are as a species?We know that we are made of bones, blood, cells, muscle, etc. and we tend to think that these are what makes us human. However, we often overlook the Human Microbiome. This is a naturally occurring community microorganisms (microbes) in our body – including diverse viruses, fungi, and protozoa – that outnumber human cells almost two to one! While this might sound scary, this thriving community of microbes in our body is working in harmony with our human cells to create life as we know it. More...

Gut bacteria and mind control: to fix your brain, fix your gut!

Gut microbiota, pathogenic proteins and neurodegenerative diseases. As the world's population ages, neurodegenerative diseases (NDs) have brought a great burden to the world. However, effective treatment measures have not been found to alleviate the occurrence and development of NDs. Abnormal accumulation of pathogenic proteins is an important cause of NDs. Therefore, effective inhibition of the accumulation of pathogenic proteins has become a priority. As the second brain of human, the gut plays an important role in regulate emotion and cognition functions. PMCID: PMC9715766

The Microbiome Diet: Populating Friendly Bacteria For Optimal Health – Saturday Strategy

Fermentation; How To Get Healthy Bacteria To Your System

Probing the Link Between Gut Microbial Imbalance and Multiple Sclerosis

Mounting evidence suggests a deep connection between the gut microbiota and central nervous system. A hypothesis with important clinical implications generated from this concept is that an imbalance in the gut microbial community can lead to immune dysregulation and, in turn, autoimmune disease, including such neuroinflammatory conditions as multiple sclerosis (MS).

How to Increase Probiotics in Your Diet

Immunity Solution by Dr. Joel Fuhrman

How to prevent oxidation and inflammation

"Disease does not exist. It is the body adapting to deficiency or toxicity." Dr. John Bergman.

Cracking Brain Diseases from Gut Microbes-Mediated Metabolites for Precise Treatment. The gut-brain axis has been a subject of significant interest in recent years. Understanding the link between the gut and brain axis is crucial for the treatment of disorders. Here, the intricate components and unique relationship between gut microbiota-derived metabolites and the brain are explained in detail. Additionally, the association between gut microbiota-derived metabolites and the integrity of the blood-brain barrier and brain health is emphasized. Meanwhile, gut microbiota-derived metabolites with their recent applications, challenges and opportunities their pathways on different disease treatment are focus discussed. The prospective strategy of gut microbiota-derived metabolites potential applies to the brain disease treatments, such as Parkinson's disease and Alzheimer's disease, is proposed. This review provides a broad perspective on gut microbiota-derived metabolites characteristics facilitate understand the connection between gut and brain and pave the way for the development of a new medication delivery system for gut microbiota-derived metabolites. 

This review aims to summarize the intricate relationship between gut microbial metabolites and the brain. The types of gut microbial metabolites, gut-brain signaling pathways, the effects of metabolites on brain cells, and brain diseases and treatment measures related to metabolites are all thoroughly explained. The review also highlights the crucial role of gut microbial metabolites in brain diseases and their treatment, providing viable treatment strategies for non-invasive brain diseases and paving the way for the continuous development of related fields. PMCID: PMC10321288

Eisenberg - 05 The Potentials of Food as Medicine - Osher 20th Anniversary

As part of a special Osher Center 20th anniversary mini-series, we interview David Eisenberg, MD, Executive Director of the Teaching Kitchen Collaborative, Director of Culinary Nutrition at the Harvard T. H Chan School of Public Health and former Director of the Osher Center for Integrative Medicine at Harvard Medical School and Brigham and Women's Hospital (2000-2010).

Add These Fiber-Rich Foods to Your Diet to Fight Inflammation


Butyrate is a short-chain fatty acid. The richest source of butyrate is butter. But as it turns out, your intestinal cells fully rely on gut bacteria to produce butyrate. In fact, their very survival depends on it. Butyrate is an important source of energy for intestinal cells. Without butyrate—or with only a short supply—intestinal cells die. (1) This may explain why the highest concentration of butyrate in the human body is found in the gut. Butyrate does more than feed intestinal cells. It also controls inflammation.

Gut-Brain-Microbiota Axis: Antibiotics and Functional Gastrointestinal Disorders. There is a connection between gastrointestinal tract and central nervous system and this is mediated by neurotransmitters, inflammatory cytokines, the vagus nerve and the hypothalamic-pituitary-adrenal axis. Functional gastrointestinal disorders are prevalent diseases affecting more than one third of the population. The etiology of these disorders is not clarified. Visceral hyperalgesia is the main hypothesis for explaining clinical symptoms, however gut-brain axis disorder is a new terminology for functional disorders. In this review, microbiota-gut-brain axis connection pathways and related disorders are discussed. Antibiotics are widely used in developed countries and recent evidence indicates antibiotic-induced dysbiosis as an important factor for functional disorders. Antibiotics exert negative effects on gut microbiota composition and functions [PMID: 33513791].

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The Potential Effects of Radiation on the Gut-Brain Axis. The gastrointestinal microbiota can communicate with the brain via various pathways and molecules, such as the enteric nervous system, the vagus nerve, microbial metabolites and the immune system. This relationship has been termed the "gut-brain axis". Alterations to the composition of the GI microbiome can lead to alterations in its functional metabolic output and means of communication, therefore potentially causing downstream cognitive effects. Consequently, studying how radiation can affect this important network of communication could lead to new and critical interventions, as well as prevention strategies. Herein, we review the evidence supporting a relationship between radiation exposure and disruption of the gut-brain axis as well as summarize strategies that may be used to counter the effects of radiation exposure on the GI microbiome.

pubmed logoMaking Sense of… the Microbiome in Psychiatry. "The human gut microbiome has been shown to influence many aspects of host health including more recently the brain. Several modes of interaction between the gut and the brain have been discovered, including via the synthesis of metabolites and neurotransmitters, activation of the vagus nerve and activation of the immune system. A growing body of work is implicating the microbiome in a variety of psychological processes and neuropsychiatric disorders. These include mood and anxiety disorders, neurodevelopmental disorders such as autism spectrum disorder and schizophrenia, and even neurodegenerative disorders such as Alzheimer's and Parkinson's Disease. Moreover, it is probable that most psychotropic medications have an impact on the microbiome." Note that the vagus nerve is affected by both the microbiome and the practice of Qigong. 

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Connection between Systemic Inflammation and Neuroinflammation Underlies Neuroprotective Mechanism of Several Phytochemicals in Neurodegenerative Diseases. phytochemicals may modulate and suppress neuroinflammation of the brain by several approaches: (1) reducing systemic inflammation and infiltration via the blood-brain barrier (BBB), (2) direct permeation into the brain parenchyma leading to neuroprotection, (3) enhancing integrity of disrupted BBB, and (4) vagal reflex-mediated nutrition and protection by gastrointestinal function signaling to the brain. Therefore, many phytochemicals have multiple potential neuroprotective approaches contributing to therapeutic benefit for pathogenesis of neurodegenerative diseases, and development of strategies for preventing these diseases represents a considerable public health concern and socioeconomic burden. 

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Gut thinking: the gut microbiome and mental health beyond the head. Mental health is not narrowly located in the head but is assimilated by the physical body and intermingled with the natural world, requiring different methods of research to unfold the meanings and implications of gut thinking for conceptions of human selfhood.


Metabolomics and the Microbiome

Metabolomics is the chemical fingerprint of your body. Your genome and genetic profile are simply a blueprint of the raw material or ingredients (proteins) of your body. The blueprint does not give an idea of how the (expressed) genes interact and how the environment affects the genes. Metabolomics is concerned with what is occurring in your body moment to moment (the set of active metabolites) as a result of factors such as nutrition and lifestyle with the ultimate goal of understanding how metabolism is regulated and identifying the metaboloic signatures of disease.

The gut microbiome is the body's main generator of metabolites. One main way that Qigong practice positively affects the microbiome is via stress reduction.

Exploring the Gut Microbiome’s Connection to Human Behavior – Lecture by Dr. John Cryan. A healthy life-style (in Daoist terms, Yang Sheng) includes the mind-body practice of Qigong, western-style exercise, proper nutrition, and healthy living habits. One of the most important notions in living a healthy life-style is understanding the key relationship between the gut microbiome and health. John F. Cryan, Ph.D., Professor and Chair of the Department of Anatomy and Neuroscience at University College Cork, in Ireland, gave a lecture, “Towards Psychobiotics: The Microbiome as a Key Regulator of Brain and Behavior,” as part of the National Center for Complementary and Integrative Health’s (NCCIH) Integrative Medicine Research Lecture Series. Dr. Cryan is an internationally recognized scientist in the exciting area of the interactions between gut microbes and the brain. He works closely with gastroenterologists, microbiologists, ecologists, and behavioral scientists in studying the various interactions and biological effects of the gut microbiome on human behavior. One way that the practice of Qigong directly affects the gut microbiome is through the reduction of stress.

It's a Gut Feeling - how the gut microbiota affects the state of mind. The gut microbiota is a dynamic and diverse ecosystem and forms a symbiotic relationship with the host. This research describes the components of the gut microbiota and mechanisms by which it can influence neural development, complex behaviours and nociception. Furthermore, the authors propose the novel concept of a "state of gut" rather than a state of mind.

Biological Magnetic Resonance Data Bank. A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules.

"There is no drug more powerful than good nutrition and exercise."

Tom Rogers
President. Qigong Institute