Glossary¶

Every key term in this book, defined in plain words, with an example and a link to the chapter that teaches it.

A · B · C · D · E · F · G · H · I · J · K · L · M · N · O · P · Q · R · S · T · U · V · Z · 1 · 5

1¶

16S rRNA Sequencing¶

A method for identifying bacteria in a sample by reading the DNA of one marker gene, the 16S ribosomal RNA gene, which all bacteria have and which differs between groups.

Example: Like reading product barcodes, 16S rRNA sequencing shows roughly which bacteria are present, but not what each one can do.

See also: Metagenomic Sequencing

Taught in Chapter 3: Meet the Microbiome.

A written plan, developed by the school with the student and their parents or guardians, that lists the accommodations a student with a disability needs for equal access to education, under Section 504 of the Rehabilitation Act of 1973.

Example: A 504 plan for a student with Crohn's disease could include restroom access, rest breaks, and extra time.

See also: School Accommodation

Taught in Chapter 19: Culture, Food, Family, and Stigma.

A¶

Absolute vs Relative Risk¶

The difference between two ways of describing how much a treatment changes the chance of an outcome: absolute risk is the actual chance in a group, and relative risk compares the groups as a ratio, which can sound large even when the actual numbers are small.

Example: In the Vowst trial, recurrence was 12.4% versus 39.8% with placebo at 8 weeks, an absolute drop of about 27 percentage points, which sounds even bigger described as a relative reduction.

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Acetate¶

The two-carbon short-chain fatty acid, usually the most abundant one. It travels farthest, passing through the liver and reaching the rest of the body in the blood.

Example: Acetate is the short-chain fatty acid most likely to reach the brain's blood supply.

See also: Short-Chain Fatty Acid, Butyrate

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Acetylcholine¶

A neurotransmitter that activates muscles and many glands. In the gut it is the main "go" signal enteric motor neurons use to make smooth muscle contract, and it is the main chemical the vagus nerve releases onto its targets.

Example: An excitatory enteric motor neuron releases acetylcholine to start a contraction during peristalsis.

See also: Neurotransmitter, Vagus Nerve

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Acute Stress¶

Short-term stress from a single challenge, in which the stress response switches on and then returns to baseline within minutes to hours once the challenge ends.

Example: The nerves Sam feels at the starting line of a race are acute stress.

See also: Chronic Stress, Stress Response

Taught in Chapter 7: Stress and the Gut.

Adaptive Immunity¶

The slower but highly specific part of the immune system, run by T cells and B cells, that learns to recognize particular invaders and keeps a memory so it responds faster the next time.

Example: B cells in the gut that become plasma cells and make antibodies against a specific microbe are part of adaptive immunity.

See also: Innate Immunity, Regulatory T Cell

Taught in Chapter 4: The Immune System as a Sense Organ.

Adrenal Gland¶

A small gland on top of each kidney, with an outer cortex that makes steroid hormones like cortisol and an inner medulla that makes epinephrine and norepinephrine.

Example: The adrenal glands release cortisol when ACTH reaches them through the blood.

Taught in Chapter 7: Stress and the Gut.

Adrenocorticotropic Hormone (ACTH)¶

A hormone released by the anterior pituitary into the blood that travels to the adrenal glands and tells their outer layer to make cortisol.

Example: When the pituitary releases more ACTH during stress, the adrenal glands soon make more cortisol.

See also: Pituitary Gland, Cortisol

Taught in Chapter 7: Stress and the Gut.

Afferent Signal¶

A signal carried by nerve fibers toward the central nervous system, usually sensory information from the body. A memory trick: afferent arrives.

Example: A message that the stomach is stretched, traveling up the vagus nerve to the brainstem, is an afferent signal.

See also: Efferent Signal, Vagus Nerve

Taught in Chapter 2: The Vagus Highway.

Alarm Features¶

Symptoms, signs, or history that suggest a disease other than IBS, such as inflammation, bleeding, or cancer, and that call for further medical evaluation.

Example: Blood in the stool, unexplained weight loss, and anemia are alarm features.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Alpha-Synuclein¶

A protein found in neurons, especially at their signaling tips, that can misfold and clump together. These clumps are a hallmark of Parkinson's disease.

Example: Even healthy human appendixes have been found to contain clumped alpha-synuclein.

See also: Lewy Body, Prion-Like Spread

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Alzheimer's Disease¶

A progressive brain disease that slowly destroys memory and thinking skills and, eventually, the ability to carry out everyday tasks. It is the most common cause of dementia in older adults.

Example: More than 6 million Americans, most aged 65 or older, may have Alzheimer's disease.

See also: Amyloid Beta, Neurodegeneration

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Aminosalicylate¶

An anti-inflammatory medicine that works on the gut lining, used mainly for mild to moderate ulcerative colitis. It is also called a 5-ASA drug.

Example: Mesalamine is an aminosalicylate, a long-established medicine for ulcerative colitis.

See also: Ulcerative Colitis, Corticosteroid

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Amyloid Beta¶

A small protein fragment, cut from a larger protein in the brain, that can clump into sticky plaques between neurons. These plaques are one of the main signs of Alzheimer's disease.

Example: Amyloid beta plaques can begin forming a decade or more before memory problems appear.

See also: Alzheimer's Disease

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Animal Model¶

A non-human animal, such as a mouse or rat, used to study a biological process or disease because it shares key features with humans and can be studied in ways not possible in people.

Example: Researchers use a mouse animal model to test whether a gut bacterium changes behavior, because they can control the mouse's diet and genes.

Taught in Chapter 3: Meet the Microbiome.

Anterior Cingulate Cortex¶

A strip of cortex near the front of the brain, along the midline, that helps give pain its unpleasant, emotional "I need to do something" quality and helps focus attention on it. It is often shortened to ACC.

Example: Worrying about a cramp during class engages the anterior cingulate cortex, which makes the pain feel more urgent.

See also: Insula, Pain Perception

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Anti-TNF Therapy¶

A type of biologic treatment that blocks tumor necrosis factor, a cytokine that drives inflammation in IBD. Anti-TNF medicines were the first biologics approved for IBD.

Example: Infliximab and adalimumab are anti-TNF therapies.

See also: Tumor Necrosis Factor, Biologic Therapy

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Antibiotic Disruption¶

The change in the gut microbiota caused by antibiotics: a loss of bacterial numbers and diversity, shifts in which groups dominate, and a recovery afterward that is often fast but not always complete.

Example: After a course of antibiotics for strep throat, a person's gut diversity may drop and take weeks to recover.

Taught in Chapter 3: Meet the Microbiome.

Anxiety Disorder¶

A mental health condition in which worry, fear, or nervousness does not go away, shows up in many situations, and can get worse over time, interfering with daily life.

Example: Generalized anxiety disorder, panic disorder, and social anxiety disorder are types of anxiety disorder.

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Appendix and Parkinson's¶

The research question of whether removing the appendix changes a person's later risk of Parkinson's disease, based on the idea that the appendix might store misfolded alpha-synuclein that could seed the disease.

Example: One large study linked appendix removal to lower Parkinson's risk, while a Danish study of 265,758 people found slightly higher risk, so the question of the appendix and Parkinson's is still open.

See also: Braak Hypothesis, Gut-First Subtype

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Attention-Deficit/Hyperactivity Disorder (ADHD)¶

A neurodevelopmental condition involving ongoing patterns of inattention, hyperactivity, and/or impulsivity that show up in more than one setting and affect daily life.

Example: A student with ADHD may struggle to stay focused on homework at home and in class, not just in one setting.

See also: Neurodiversity, Autism

Taught in Chapter 13: Autism, ADHD, and the Gut.

Autism¶

A lifelong neurodevelopmental difference that affects how a person communicates and interacts with others, processes sensory information, and experiences the world, often including focused interests and repetitive behaviors.

Example: An autistic teen may find loud cafeterias overwhelming and have a deep, focused interest in trains.

Taught in Chapter 13: Autism, ADHD, and the Gut.

Autonomic Nervous System¶

The automatic, involuntary part of the nervous system that controls internal organs, glands, and smooth muscle. It has a sympathetic branch and a parasympathetic branch.

Example: Your heart rate rising during a race and your gut slowing down both happen through the autonomic nervous system, without you deciding.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

B¶

Bacteria-to-Human Cell Ratio¶

The number of bacterial cells in a person's body divided by the number of human cells. A typical adult has roughly 38 trillion bacterial cells and 30 trillion human cells, about 1.3 to 1.

Example: The old "10 to 1" figure for the bacteria-to-human cell ratio is wrong.

See also: Gut Microbiota

Taught in Chapter 3: Meet the Microbiome.

Bacterial Strain¶

A genetic variant within a single bacterial species. Strains of the same species share most of their genes but differ in some, which can change what they do.

Example: Most strains of E. coli are harmless, but a few strains can cause serious illness.

See also: Strain Specificity, Pathogen

Taught in Chapter 3: Meet the Microbiome.

Balloon Distension Test¶

A research and specialty test in which a thin, soft balloon in the rectum or colon is inflated with set volumes or pressures while the person reports when they first feel it, when it is uncomfortable, and when it hurts.

Example: A balloon distension test can show that a person with IBS feels pain at a lower volume than average.

See also: Visceral Hypersensitivity

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Behavior Change¶

The process of adopting and keeping a new health habit, usually by setting small, specific goals, tracking them, and adjusting based on what you learn.

Example: Moving bedtime 15 minutes earlier each week, rather than changing everything at once, is a realistic behavior change plan.

See also: Self-Monitoring, Sleep Hygiene

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Benefit-Risk Balance¶

The weighing of how much a treatment is likely to help against how likely and how serious its harms are, for a particular person and a particular condition.

Example: An implanted device that needs surgery has a better benefit-risk balance for severe, drug-resistant epilepsy than for mild stress.

See also: Shared Decision-Making, FDA Approval

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Bidirectional Relationship¶

A connection between two things in which each one can influence the other, so changes can flow in both directions.

Example: Gut symptoms can worsen mood, and anxiety can worsen gut symptoms, a bidirectional relationship.

See also: Gut-Brain Axis, Reverse Causation

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Bifidobacterium¶

A large group of bacteria that live naturally in the human gut and ferment sugars and some fibers.

Example: Human milk oligosaccharides feed Bifidobacterium, so this group often dominates a breastfed infant's gut.

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Bioelectronic Medicine¶

An approach to treatment that uses electrical stimulation of nerves, instead of or alongside drugs, to change how organs or the immune system work.

Example: The SetPoint System, the first approved device designed to treat an autoimmune disease by stimulating the vagus nerve, is a milestone for bioelectronic medicine.

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Biologic Therapy¶

Treatment with a medicine made by living cells, usually a lab-made antibody, that blocks one specific immune signal or cell pathway involved in inflammation.

Example: Riya takes biologic therapy by injection to keep her Crohn's in remission.

See also: Anti-TNF Therapy, JAK Inhibitor

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Birth Mode and Microbes¶

The way a baby's delivery, vaginal birth or cesarean section, shapes which microbes first colonize the newborn's gut.

Example: Babies born by C-section tend at first to carry more skin-type microbes than babies born vaginally.

See also: Microbiome Development

Taught in Chapter 3: Meet the Microbiome.

Blood-Brain Barrier¶

The specialized lining of the brain's blood vessels, made of tightly sealed endothelial cells supported by other cells, that tightly controls which ions, molecules, and cells pass from the blood into the brain. It is often shortened to BBB.

Example: Serotonin made in the gut does not cross the blood-brain barrier, but tryptophan can.

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Blood-Brain Barrier Permeability¶

How easily substances can pass from the blood into the brain across the blood-brain barrier. Higher permeability means a "leakier" barrier.

Example: In mice, germ-free animals had higher blood-brain barrier permeability than normal mice, and gut bacteria or butyrate helped tighten it.

See also: Blood-Brain Barrier, Germ-Free Mouse

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Braak Hypothesis¶

The proposal, published by Heiko Braak and colleagues in 2003, that Parkinson's pathology spreads through the nervous system in a predictable order, beginning low in the brainstem and in the smell system, and in some cases may start in the gut and travel up the vagus nerve.

Example: The Braak hypothesis predicts that cutting the vagus nerve might lower Parkinson's risk, which researchers tested in vagotomy studies.

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Brain-First Subtype¶

A proposed form of Parkinson's disease in which alpha-synuclein pathology starts inside the brain, reaches the dopamine system early, and spreads down to the brainstem and body nerves later.

Example: A person whose tremor appears first, with gut problems only later if at all, fits the brain-first subtype.

See also: Gut-First Subtype

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Brain-Gut Psychotherapy¶

The family of psychological treatments designed specifically for gut conditions, which target how the brain processes gut signals, how stress and worry change gut function, and how fear of symptoms leads to avoidance.

Example: Gut-focused CBT and gut-directed hypnotherapy are both forms of brain-gut psychotherapy.

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Brainstem¶

The stalk of brain tissue that connects the rest of the brain to the spinal cord, made of the midbrain, the pons, and the medulla.

Example: Signals from the vagus nerve arrive first in the medulla, the lowest part of the brainstem.

Taught in Chapter 2: The Vagus Highway.

Butyrate¶

The four-carbon short-chain fatty acid. Most of it never leaves the gut wall, because colonocytes use it as their fuel.

Example: Butyrate made by colon bacteria from fiber feeds the cells lining the colon.

See also: Colonocyte, Gene Regulation by Butyrate

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

C¶

C. difficile Infection¶

An infection of the colon by the bacterium Clostridioides difficile that causes diarrhea and colon inflammation and can be life-threatening. It most often follows antibiotics that wipe out the normal bacteria that keep it in check. It is often shortened to CDI.

Example: A person who develops severe diarrhea a week after taking antibiotics may be tested for C. difficile infection.

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Caregiver Role¶

The set of responsibilities family members take on for someone with a health condition, such as managing appointments and medicines, preparing food, giving emotional support, and advocating with schools, along with the stress that can come with it.

Example: As a teen grows older, the caregiver role often shifts from parents to the teen, who gradually manages their own medicine and appointments.

See also: Family Communication

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Celiac Disease¶

A lifelong, immune-driven disorder in which eating gluten triggers the immune system to damage the lining of the small intestine.

Example: Celiac disease affects about 1% of people worldwide and about 2 million people in the US.

See also: Gluten, Villous Atrophy, Gluten-Free Diet

Taught in Chapter 12: Celiac Disease and Food Reactions.

Central Nervous System¶

The brain and spinal cord, which together form the body's main processing center. It is often shortened to CNS.

Example: A signal from the gut that reaches the brainstem has entered the central nervous system.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Central Sensitization¶

An increase in the excitability of pain-processing neurons in the spinal cord and brain, so that normal or weak incoming signals produce stronger pain responses.

Example: After long-lasting gut pain, central sensitization can make ordinary digestion feel painful even when the gut tissue looks normal.

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Cholecystokinin¶

A gut hormone released by enteroendocrine cells in the small intestine, mainly after protein-rich and fat-rich food, that helps digest food and acts as a satiety signal partly by exciting vagal sensory nerves. It is often shortened to CCK.

Example: Cholecystokinin was named for making the gallbladder contract, which squeezes bile into the intestine to help digest fat.

See also: Gut Hormone, Satiety Signal

Taught in Chapter 2: The Vagus Highway.

Chronic Stress¶

Stress that lasts for weeks or months, or keeps returning before the body has recovered, so the stress systems stay switched on or are repeatedly reactivated.

Example: Months of ongoing family conflict or bullying can cause chronic stress.

See also: Acute Stress, Early-Life Stress

Taught in Chapter 7: Stress and the Gut.

Circadian Rhythm¶

A roughly 24-hour cycle in the body's functions, such as sleepiness, body temperature, hormone release, and digestion, driven by an internal clock and kept in step with the outside world, mostly by light.

Example: Feeling sleepy at night and alert in the morning reflects your circadian rhythm.

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Circumventricular Organ¶

One of several small brain regions around the fluid-filled ventricles that lack a complete blood-brain barrier, letting them sample the blood directly.

Example: Cytokines in the blood can be detected at a circumventricular organ even though they cannot cross the rest of the blood-brain barrier.

Taught in Chapter 4: The Immune System as a Sense Organ.

Claim-Checking Method¶

This book's step-by-step process for judging a health claim: state the exact claim, trace it to its original source, ask the six questions, check the numbers and the money, weigh it against the wider evidence, and assign a Hype Meter grade with a careful rewrite.

Example: Using the claim-checking method, a student traces a supplement ad to a small mouse study, checks who paid for it, and grades the claim Preliminary or Hype.

See also: Hype Meter, Reading an Abstract

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Clinical Trial Phases¶

A series of increasingly large studies in people that test a new treatment first for safety, then for whether it works, then how it compares at a large scale, with monitoring continuing after approval.

Example: A Phase 1 trial might include about 20 to 100 people, while a Phase 3 trial might include about 300 to 3,000.

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Cognitive Behavioral Therapy¶

A structured, skills-based form of talk therapy that helps people notice and change unhelpful thought patterns and behaviors, which can reduce symptoms and their impact. It is often shortened to CBT.

Example: In cognitive behavioral therapy for IBS, a teen practices replacing "I'll have an accident in class" with a more balanced thought.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Cohort Study¶

A study that follows a group of people over time, measuring things at the start and again later, to see which earlier factors predict later outcomes.

Example: In one cohort study, higher anxiety at the start predicted a new functional gut disorder 12 years later, evidence for a brain-to-gut direction.

See also: Observational Study, Reverse Causation

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Colonization Resistance¶

The ability of the normal gut microbiota to keep harmful microbes from settling in and multiplying, by competing for space and nutrients, making blocking substances, and stimulating the body's defenses.

Example: When antibiotics weaken colonization resistance, C. difficile can take over the colon.

Taught in Chapter 3: Meet the Microbiome.

Colonocyte¶

One of the epithelial cells lining the inside of the colon, which absorb water and salts and help form the barrier between gut contents and the body.

Example: Colonocytes get much of their energy from butyrate made by gut bacteria.

See also: Butyrate, Intestinal Epithelium

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Colonoscopy¶

A procedure in which a doctor passes a long, thin, flexible tube with a light and camera through the anus to look at the lining of the rectum and colon, and often the end of the small intestine, usually under sedation.

Example: During a colonoscopy, the doctor takes small tissue samples (biopsies) to confirm IBD.

See also: Mucosal Healing, Fecal Calprotectin

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Colony-Forming Unit¶

A count of how many microbes in a sample are alive and able to multiply, measured by growing a diluted sample on nutrient gel and counting the colonies. It is often shortened to CFU.

Example: A label that brags "50 billion colony-forming units" tells you how many live microbes it contains, not whether they help you.

See also: Probiotic

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Commensal Bacteria¶

Bacteria that normally live on or in the body without causing harm, and often provide benefits such as helping digest fiber or crowding out harmful microbes.

Example: Commensal bacteria in the colon ferment fiber you cannot digest into short-chain fatty acids.

See also: Colonization Resistance, Pathogen

Taught in Chapter 3: Meet the Microbiome.

Conflict of Interest¶

A situation in which a researcher, author, or organization has financial or personal ties, such as funding, a job, stock, or a patent, that could influence, or seem to influence, how research is designed, interpreted, or reported.

Example: A probiotic trial paid for and run by the company that sells the probiotic has a conflict of interest worth noting.

See also: Health Claim Marketing, Preregistration

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Confounding Variable¶

A third factor that affects both things being studied, creating a link between them even if neither causes the other.

Example: Poor sleep could worsen both mood and gut symptoms, making it a possible confounding variable in gut-mood research.

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Constipation¶

Having fewer bowel movements than usual (often fewer than three a week), or stools that are hard, dry, or difficult to pass.

Example: About 16 out of 100 adults have constipation symptoms, usually from ordinary causes like low fiber or too little fluid.

See also: Prodromal Symptoms, Dietary Fiber

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Consumer Wellness Device¶

A product sold directly to the public that claims to support general health or well-being, such as relaxation or stress relief, and is marketed without having to show the FDA that it treats any disease.

Example: An ear clip sold online to "tone your vagus nerve for calm" is a consumer wellness device, not an FDA-approved treatment.

See also: Noninvasive VNS, Health Claim Marketing

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Correlation vs Causation¶

The distinction between two things happening together (a correlation, or association) and one thing actually producing the other (causation).

Example: People with depression have different gut microbes on average, but that correlation alone does not show the microbes caused the depression.

See also: Reverse Causation, Confounding Variable

Taught in Chapter 3: Meet the Microbiome.

Corticosteroid¶

A powerful, fast-acting medicine related to the body's stress hormone cortisol that broadly calms the immune system. It is often just called a steroid.

Example: Riya had a course of a corticosteroid at diagnosis to calm her Crohn's quickly.

See also: Cortisol, Immunomodulator

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Corticotropin-Releasing Hormone¶

A hormone made by neurons in the hypothalamus that tells the pituitary gland to release ACTH. It is also made outside the HPA axis, including in the gut wall, and is also called corticotropin-releasing factor (CRF). It is often shortened to CRH.

Example: In animal studies, corticotropin-releasing hormone acting in the colon speeds up colon movement.

Taught in Chapter 7: Stress and the Gut.

Cortisol¶

The main stress hormone in humans, a steroid made by the adrenal cortex that helps the body handle longer-lasting stress by raising available fuel and calming inflammation, and that shuts down its own production through feedback.

Example: Cortisol levels rise during a stressful week of exams and fall again once the exams end.

Taught in Chapter 7: Stress and the Gut.

Cranial Nerve¶

One of the twelve nerves on each side of the head that connect directly to the brain rather than the spinal cord, numbered I through XII.

Example: The vagus nerve is cranial nerve X, the tenth cranial nerve.

See also: Vagus Nerve, Brainstem

Taught in Chapter 2: The Vagus Highway.

Crisis Resources¶

Services that give immediate, free support to someone in emotional distress or danger, such as suicide and crisis hotlines, text lines, and emergency rooms.

Example: In the US, you can call or text 988, or chat at 988lifeline.org, to reach the 988 Suicide & Crisis Lifeline, which is free, confidential, and available 24/7.

See also: Help-Seeking

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Crohn's Disease¶

A form of inflammatory bowel disease that can affect any part of the digestive tract, from mouth to anus, most often the end of the small intestine and the start of the colon, often in patches with healthy sections between.

Example: Riya's Crohn's disease affects the end of her small intestine and part of her colon, the most common pattern.

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Cytokine¶

A small protein that cells release to send signals to other cells, especially to coordinate immune responses and inflammation.

Example: Interleukin-6 and tumor necrosis factor are cytokines that turn inflammation up.

Taught in Chapter 4: The Immune System as a Sense Organ.

D¶

Defining a Healthy Microbiome¶

The scientific challenge of identifying which features of a gut microbial community reliably support health, and what their normal ranges are, given that healthy people's microbiomes differ greatly.

Example: A stool test claiming to compare your microbes to "the healthy microbiome" overlooks that scientists are still defining a healthy microbiome.

See also: Microbial Diversity, Dysbiosis

Taught in Chapter 3: Meet the Microbiome.

Descending Pain Modulation¶

The brain's ability to turn incoming pain signals down, or up, by sending signals from the brainstem down to the dorsal horn of the spinal cord.

Example: An athlete who does not notice an injury until after a game shows descending pain modulation turning pain down.

See also: Gate Control Theory, Pain Perception

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Diet as Confounder¶

The idea that differences in what people eat can create an apparent link between a condition and the gut microbiome, because diet shapes the microbiome and may also differ between groups for reasons related to the condition.

Example: If autistic children eat a narrower range of foods, their gut bacteria may differ because of diet, not autism, an example of diet as confounder.

See also: Confounding Variable, Selective Eating

Taught in Chapter 13: Autism, ADHD, and the Gut.

Dietary Fiber¶

The part of plant foods that human digestive enzymes cannot break down, so it reaches the large intestine mostly intact, where gut microbes can ferment some of it.

Example: Beans, lentils, oats, and vegetables are good sources of dietary fiber.

See also: Fermentation, Dietary Fiber Gap, Prebiotic

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Dietary Fiber Gap¶

The difference between how much fiber people actually eat and how much dietary guidelines suggest.

Example: Average US intake is about 16 grams a day, while the 2020 to 2025 guidelines suggested about 25 g for girls and 31 g for boys aged 14 to 18, a large dietary fiber gap.

See also: Dietary Fiber

Taught in Chapter 15: Food and Mood.

Dietary Pattern¶

The overall combination of foods and drinks a person usually eats over time, studied as a whole instead of one food or nutrient at a time.

Example: The Mediterranean diet is a dietary pattern, not a single food.

Taught in Chapter 15: Food and Mood.

Dietary Supplement Regulation¶

The set of US rules for products like vitamins, herbs, and most probiotics, which, unlike medicines, do not need FDA approval for safety or effectiveness before they are sold. The main law is the Dietary Supplement Health and Education Act of 1994 (DSHEA).

Example: Under dietary supplement regulation, a probiotic company can start selling its product without first proving to the FDA that it works.

See also: FDA Approval, Structure-Function Claim

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Digestive Tract¶

The continuous tube that food travels through, from the mouth through the throat, esophagus, stomach, small intestine, and large intestine to the anus. Doctors also call it the gastrointestinal (GI) tract.

Example: In a living adult, the digestive tract is about 7.6 meters (25 feet) long, coiled up inside the abdomen.

See also: Gut Wall Layers, Enteric Nervous System

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Disease Flare¶

A period when IBD becomes active, with increased inflammation and symptoms such as diarrhea, pain, bleeding, and tiredness.

Example: Riya is mostly in remission but has an occasional disease flare.

See also: Remission, Fecal Calprotectin

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Dopamine¶

A neurotransmitter the brain uses in movement, motivation, and learning from rewards, which also acts in other parts of the body, including the gut.

Example: In Parkinson's disease, the loss of neurons that make dopamine causes movement symptoms.

See also: Dopamine Neuron Loss, Neurotransmitter

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Dopamine Neuron Loss¶

The death of dopamine-making neurons in the substantia nigra, the main cause of the movement symptoms of Parkinson's disease.

Example: By the time movement symptoms appear, most people with Parkinson's have already lost 60 to 80% or more of these cells, so dopamine neuron loss starts long before diagnosis.

See also: Parkinson's Disease, Dopamine

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Dorsal Horn¶

The back part of the spinal cord's gray matter, where incoming sensory neurons form synapses with spinal neurons that carry signals on toward the brain. Signals can be boosted or dampened here.

Example: In gate control theory, the dorsal horn is where touch signals can partly block pain signals.

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Dorsal Motor Nucleus¶

A cluster of neurons in the medulla, next to the nucleus tractus solitarius, whose fibers travel down the vagus nerve to carry motor signals to the stomach and intestines, usually by connecting to enteric neurons.

Example: When you smell dinner, the dorsal motor nucleus can signal the stomach, through the vagus, to get ready.

Taught in Chapter 2: The Vagus Highway.

Dorsal Root Ganglion¶

A cluster of sensory neuron cell bodies just outside the spinal cord, on the nerve root that enters the back side of the cord.

Example: A spinal sensory neuron that detects colon stretch has its cell body in a dorsal root ganglion.

See also: Spinal Afferent Nerve, Dorsal Horn

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Dose-Response Relationship¶

A pattern in which more of an exposure goes with a steadily larger effect. It makes a causal story more believable but is not proof.

Example: If each extra serving of vegetables went with a slightly lower depression risk, that would be a dose-response relationship.

Taught in Chapter 15: Food and Mood.

Dysbiosis¶

A change in the gut microbiota away from its usual makeup that is thought to be harmful, such as lower diversity, loss of helpful groups, or overgrowth of potentially harmful ones. Scientists warn that the term is slippery.

Example: A study reporting "dysbiosis" in people with a disease usually shows a difference in microbes, not that the difference caused the disease.

Taught in Chapter 3: Meet the Microbiome.

E¶

Early-Life Stress¶

Serious or repeated stress before birth, in infancy, or in childhood, such as separation from caregivers, neglect, or trauma, that may change how the stress system and gut-brain axis respond later in life.

Example: In animals, early-life stress has long-lasting effects on the stress system and the gut; in people, links between early adversity and IBS are associations.

Taught in Chapter 7: Stress and the Gut.

Eating Disorder Risk¶

The chance of developing an eating disorder, a serious illness marked by severe disturbances in eating behaviors, thoughts, and feelings about food.

Example: Strict food rules and cutting out whole food groups to eat "perfectly" for gut health can be warning signs of eating disorder risk.

See also: Unneeded Restrictive Diet

Taught in Chapter 15: Food and Mood.

Effect Size¶

A number that describes how big a difference between groups is, often measured in standard deviations, so results from different scales can be compared. An effect size of 0 means no difference.

Example: Two trials using different depression questionnaires can be compared by converting each result into an effect size.

See also: Statistical Significance, Meta-Analysis

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Efferent Signal¶

A signal carried by nerve fibers away from the central nervous system, out to muscles, glands, or organs, usually a command. A memory trick: efferent exits.

Example: A command from the brainstem telling the stomach to relax and make room for food is an efferent signal.

See also: Afferent Signal, Dorsal Motor Nucleus

Taught in Chapter 2: The Vagus Highway.

Enteric Glia¶

Non-neuron cells of the enteric nervous system that surround and support enteric neurons and help regulate gut function. Much of the evidence for their roles in reflexes, the barrier, and immunity comes from animals.

Example: Scientists once thought enteric glia were just packing material, but that view has been refuted.

See also: Enteric Neuron, Microglia

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Enteric Nervous System¶

The network of neurons and support cells built into the wall of the digestive tract, from the esophagus to the anus. It can run gut reflexes without input from the brain or spinal cord.

Example: The enteric nervous system can still push food along a loop of intestine even after its connections to the brain are cut.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Enteric Nervous System Neuron Count¶

The estimated total number of neurons in the human enteric nervous system: hundreds of millions, about 400 to 600 million by common estimates, roughly as many as the spinal cord.

Example: The brain has about 86 billion neurons, so the enteric nervous system neuron count is far smaller than the brain's.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Enteric Neuron¶

A nerve cell whose cell body sits in one of the ganglia of the gut wall. Enteric neurons include sensory neurons, interneurons, and motor neurons, up to about 20 types in all.

Example: An excitatory enteric motor neuron releases acetylcholine to make gut smooth muscle contract.

See also: Enteric Nervous System, Enteric Glia

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Enterochromaffin Cell¶

A type of enteroendocrine cell in the gut lining that senses conditions inside the gut and releases serotonin, making most of the body's serotonin with the enzyme TPH1. It is often shortened to EC cell.

Example: When food stretches the intestine, enterochromaffin cells release serotonin that activates nearby nerve endings.

See also: Serotonin, Enteroendocrine Cell

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Enteroendocrine Cell¶

A hormone-releasing sensor cell scattered among the lining cells of the stomach and intestines that detects nutrients and other substances and responds by releasing hormones and other signals. These cells make up about 1% of intestinal lining cells.

Example: When fat reaches the small intestine, enteroendocrine cells release cholecystokinin.

Taught in Chapter 2: The Vagus Highway.

Evidence Grade¶

A rating that summarizes how strong and how direct the scientific support for a specific claim is, as the claim is actually stated.

Example: A claim backed mostly by small mouse studies earns an evidence grade of Preliminary.

See also: Hype Meter, Hierarchy of Evidence

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Exercise and Gut Transit¶

The way physical activity changes how quickly food and waste move through the digestive tract, along with related changes in blood flow and the gut lining. The effect depends heavily on how hard and how long a person exercises.

Example: Easy runs seem to settle Sam's stomach, while hard race-day efforts sometimes send him sprinting for a porta-potty, two sides of exercise and gut transit.

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Exercise and Mood¶

The effects of physical activity on emotional well-being, including symptoms of depression, anxiety, and stress.

Example: An umbrella review of 1,039 trials found that physical activity programs had medium-sized benefits for depression, strong evidence on exercise and mood.

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Extraintestinal Manifestation¶

A sign of IBD that shows up outside the intestines, such as joint pain, skin problems, eye inflammation, or liver problems.

Example: Painful, swollen knees during a Crohn's flare are an extraintestinal manifestation.

See also: Inflammatory Bowel Disease

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

F¶

Family Communication¶

How family members share information, feelings, and decisions with each other, including which topics are open for discussion, who speaks for whom, and how disagreements are handled.

Example: A family meeting where Riya explains what a flare feels like and her grandmother asks how to help is open family communication.

See also: Caregiver Role

Taught in Chapter 19: Culture, Food, Family, and Stigma.

FDA Approval¶

The US Food and Drug Administration's decision, based on evidence a company submits, that a drug, biologic, or high-risk device is safe and effective for a specific intended use, meaning its benefits outweigh its risks for that use.

Example: Rebyota received FDA approval on November 30, 2022, to prevent recurrent C. difficile infection in adults, which is not approval for any other condition.

See also: Clinical Trial Phases, Off-Label Use

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Fecal Calprotectin¶

A protein released mainly by neutrophils that can be measured in stool. High levels signal inflammation in the intestines.

Example: A high fecal calprotectin result helps a doctor tell a Crohn's flare from IBS symptoms without inflammation.

See also: Disease Flare, Colonoscopy

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Fecal Microbiota Transplant¶

A procedure in which stool from a carefully screened healthy donor, containing that person's gut microbes, is delivered into a patient's digestive tract to restore a healthier microbial community. It is often shortened to FMT.

Example: A fecal microbiota transplant can be given through a colonoscope, an enema, a nasal tube, or capsules.

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Fermentation¶

The process in which microbes break down carbohydrates without oxygen, releasing energy for themselves and leaving behind products such as gases and short-chain fatty acids.

Example: Bacteria in the colon carry out fermentation of the fiber in an apple, producing gas and short-chain fatty acids.

See also: Short-Chain Fatty Acid, Dietary Fiber

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Fermented Food¶

Food made by letting microbes such as bacteria or yeasts transform it.

Example: Yogurt, kefir, kimchi, sauerkraut, miso, and idli and dosa batter are fermented foods.

See also: Probiotic, Fermentation

Taught in Chapter 15: Food and Mood.

Fight-or-Flight Response¶

The fast, nerve-driven part of the stress response, in which the sympathetic nervous system and the hormones epinephrine and norepinephrine prepare the body for sudden physical effort within seconds.

Example: A near-miss on a bike makes your heart race and your gut slow down within seconds through the fight-or-flight response.

Taught in Chapter 7: Stress and the Gut.

FODMAP (Fermentable Oligo-, Di-, Monosaccharides and Polyols)¶

A type of short-chain carbohydrate that is poorly absorbed in the small intestine and quickly fermented by gut bacteria, which can draw water into the bowel and produce gas.

Example: Onions, garlic, wheat, and some fruits are high in FODMAPs.

See also: Low-FODMAP Diet, Fructan

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Food Allergy¶

A harmful reaction caused by a specific immune response that happens reliably every time a person is exposed to a particular food.

Example: Hives and a swollen lip within 10 minutes of eating shrimp are signs of a food allergy.

See also: Immunoglobulin E, Food Intolerance

Taught in Chapter 12: Celiac Disease and Food Reactions.

Food Insecurity¶

The condition of not having reliable access to enough food for an active, healthy life because of limited money or other resources.

Example: In 2024, 13.7% of US households experienced food insecurity, according to the US Department of Agriculture.

See also: Dietary Pattern

Taught in Chapter 15: Food and Mood.

Food Intolerance¶

A reliable, unpleasant reaction to a food that does not involve the immune system, often because the body cannot fully digest something.

Example: Lactose intolerance is a food intolerance, not a food allergy.

See also: Lactose Intolerance, Food Allergy

Taught in Chapter 12: Celiac Disease and Food Reactions.

Free Fatty Acid Receptor¶

A protein on the surface of a cell that detects fatty acids outside the cell and passes a signal inside. Two of them, FFAR2 and FFAR3, respond to short-chain fatty acids.

Example: Short-chain fatty acids binding to free fatty acid receptors on enteroendocrine cells can trigger the release of gut hormones.

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Fructan¶

A carbohydrate built from linked fructose units that the human small intestine cannot break down. It is a type of FODMAP found in wheat and some other foods.

Example: Someone who feels better off wheat may be reacting to its fructans rather than its gluten.

Taught in Chapter 12: Celiac Disease and Food Reactions.

Functional Dyspepsia¶

A disorder of gut-brain interaction of the upper gut, defined by bothersome fullness after meals, feeling full too early, or pain or burning in the upper belly, with no structural disease found to explain the symptoms.

Example: A person who feels painfully full after a few bites, with a normal upper endoscopy, may have functional dyspepsia.

See also: Gut-Brain Interaction Disorder

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

G¶

Gamma-Aminobutyric Acid (GABA)¶

The brain's main inhibitory neurotransmitter, which mostly makes receiving neurons less likely to fire, like a brake pedal.

Example: Some gut bacteria make GABA, but that does not show their GABA reaches or calms the brain.

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Gate Control Theory¶

The idea, proposed by Melzack and Wall in 1965, that the dorsal horn of the spinal cord works like a gate that can let pain signals through or partly block them, depending on other incoming signals and signals from the brain.

Example: Rubbing a bumped elbow eases the pain because touch signals help close the gate, as gate control theory predicts.

See also: Dorsal Horn, Descending Pain Modulation

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Gene Regulation by Butyrate¶

Butyrate's ability to block enzymes called histone deacetylases, which leaves more acetyl tags on histones and changes which genes a cell turns on.

Example: Gene regulation by butyrate is one of the three main ways short-chain fatty acids act, along with acting on receptors and serving as fuel.

See also: Butyrate, Regulatory T Cell

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Germ-Free Mouse¶

A mouse raised in a sterile isolator from birth so that it has no microorganisms in or on its body, which lets researchers add specific microbes and watch what changes.

Example: Germ-free mice showed an exaggerated stress hormone response, and giving them one bacterial species, Bifidobacterium infantis, reversed it.

See also: Animal Model, Germ-Free Stress Response

Taught in Chapter 3: Meet the Microbiome.

Germ-Free Stress Response¶

The larger-than-normal HPA axis response to stress seen in mice raised without any microbes, which suggests that gut microbes help tune the stress system as it develops.

Example: Germ-free mice placed in a mildly stressful tube released more stress hormones than normal mice, an example of the germ-free stress response.

Taught in Chapter 7: Stress and the Gut.

GI Symptoms in Autism¶

The higher rate of digestive problems, such as constipation, diarrhea, and belly pain, reported in autistic children compared with non-autistic children. These are real health issues that deserve diagnosis and treatment, separate from autism itself.

Example: An autistic child who becomes irritable and stops sleeping well may be in pain from constipation, one of the common GI symptoms in autism.

Taught in Chapter 13: Autism, ADHD, and the Gut.

GI-Specific Anxiety¶

Worry and fear focused specifically on gut sensations, gut symptoms, or situations where they might happen, such as fearing a cramp in class or avoiding trips where a restroom is hard to reach.

Example: Researchers measure GI-specific anxiety with tools such as the 15-question Visceral Sensitivity Index.

See also: Anxiety Disorder, Interoception

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Global IBD Rise¶

The spread of inflammatory bowel disease from a few early industrialized regions to countries around the world over the last century, with rising new cases in many newly industrialized countries.

Example: A 2017 review of 147 studies found IBD incidence rising in newly industrialized countries in Asia, Africa, and South America.

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Glucagon-Like Peptide-1 (GLP-1)¶

A gut hormone released after eating by L-cells in the intestinal lining that boosts insulin release when blood sugar is high, slows stomach emptying, and reduces food intake.

Example: Some diabetes and weight-loss medicines work by copying the action of GLP-1.

See also: Gut Hormone, Satiety Signal

Taught in Chapter 2: The Vagus Highway.

Gluten¶

A group of proteins found naturally in wheat, barley, and rye that gives bread dough its stretch.

Example: Gluten is found in bread and pasta, and also hides in processed foods that use malt or some starches.

Taught in Chapter 12: Celiac Disease and Food Reactions.

Gluten Ataxia¶

A problem with balance and coordination linked to gluten sensitivity, thought to involve immune damage to the cerebellum, the part of the brain that fine-tunes movement.

Example: A person with celiac disease who becomes unsteady on their feet may be checked for gluten ataxia.

See also: Celiac Disease, Peripheral Neuropathy

Taught in Chapter 12: Celiac Disease and Food Reactions.

Gluten-Free Diet¶

An eating plan that strictly avoids wheat, barley, rye, and ingredients made from them. For people with celiac disease, it is lifelong and is the only proven treatment.

Example: On a gluten-free diet, symptoms often improve within weeks, but the villi can take much longer to grow back.

Taught in Chapter 12: Celiac Disease and Food Reactions.

Gut Hormone¶

A chemical messenger made by cells of the digestive tract, mostly enteroendocrine cells, that travels through the blood or acts on nearby nerves to influence digestion, appetite, and blood sugar.

Example: Cholecystokinin and GLP-1 are two gut hormones that help you feel full.

Taught in Chapter 2: The Vagus Highway.

Gut Microbiota¶

The community of living microorganisms in the digestive tract: the bacteria, archaea, fungi, and other microbes themselves.

Example: Most of your gut microbiota lives in the colon, where food moves slowly and there is little oxygen.

See also: Microbiome, Microbial Diversity

Taught in Chapter 3: Meet the Microbiome.

Gut Serotonin Mood Myth¶

The popular but unsupported claim that because most of the body's serotonin is made in the gut, the gut directly controls mood, so "healing your gut" will raise brain serotonin and make you happier.

Example: A post saying "95% of your happy chemical is in your gut, so fix your gut to fix your mood" repeats the gut serotonin mood myth.

See also: Serotonin, Blood-Brain Barrier

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Gut Wall Layers¶

The four tissue layers of the digestive tract wall, from the inside out: the mucosa (inner lining), the submucosa (connective tissue), the muscularis (muscle), and the serosa (thin outer covering).

Example: The submucosal plexus sits in the submucosa, while the myenteric plexus sits between the two muscle sheets of the muscularis.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Gut-Associated Lymphoid Tissue¶

The collection of immune tissue in the gut wall where immune cells sample what we swallow and organize responses, including the Peyer's patches, the appendix, and many small scattered clusters. It is often shortened to GALT.

Example: Peyer's patches in the ileum are part of the gut-associated lymphoid tissue.

See also: Adaptive Immunity, Regulatory T Cell

Taught in Chapter 4: The Immune System as a Sense Organ.

Gut-Brain Axis¶

The two-way communication system linking the gut (its nerves, hormones, immune cells, and microbes) with the brain. Signals travel through nerves, hormones, immune messengers, and microbial chemicals.

Example: Sam's belly cramping before a big test is one sign of the gut-brain axis carrying signals from brain to gut.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Gut-Brain Interaction Disorder¶

A condition in which gut symptoms come from problems in how the gut and brain communicate and process signals, such as increased gut sensitivity and altered gut movement, rather than from visible damage or inflammation. The plural is shortened to DGBI.

Example: Irritable bowel syndrome and functional dyspepsia are gut-brain interaction disorders.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Gut-Brain Neuromodulator¶

A medicine that acts on the nervous system's processing of gut signals, often a low dose of a medicine first developed as an antidepressant, used to reduce gut pain and change gut movement in disorders of gut-brain interaction.

Example: A low-dose tricyclic antidepressant prescribed for IBS pain acts as a gut-brain neuromodulator, not as a treatment for depression.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Gut-Directed Hypnotherapy¶

A type of hypnotherapy in which a trained therapist guides a person into a deeply relaxed, focused state and uses suggestions and imagery aimed at calming the gut and changing how gut sensations are processed.

Example: Sam has been learning gut-directed relaxation, and gut-directed hypnotherapy is a structured, therapist-led version of that idea.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Gut-First Subtype¶

A proposed form of Parkinson's disease in which alpha-synuclein pathology starts in the gut or other body nerves, reaches the brainstem through the vagus nerve, and climbs to the dopamine neurons later. It is also called "body-first."

Example: A person with years of constipation and dream-enactment before any tremor fits the predicted pattern of the gut-first subtype.

See also: Brain-First Subtype, Braak Hypothesis

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

H¶

Harmful Cure Claims¶

Promises that a product, diet, supplement, or procedure can cure or reverse autism or ADHD. They are unsupported by evidence and can cause harm through risky treatments, wasted money and time, missed care, and the message that neurodivergent people need fixing.

Example: A website promising that a supplement will "reverse autism" or "cure ADHD" is making harmful cure claims.

See also: Neurodiversity, Health Claim Marketing

Taught in Chapter 13: Autism, ADHD, and the Gut.

Health Claim Marketing¶

The use of health-related promises, such as "boosts immunity," "clinically proven," or "reduces stress," to sell products through labels, ads, websites, and influencer posts.

Example: An influencer post saying a gummy is "clinically proven to beat bloating" is health claim marketing.

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Health Literacy¶

The ability to find, understand, and use health information and services to make decisions for yourself and others.

Example: Reading a medicine label and knowing when to call the doctor are parts of health literacy.

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Healthy User Bias¶

A distortion in observational studies that happens because people who choose one health behavior often also have many other healthy habits and advantages, making that behavior look more beneficial than it really is.

Example: People who eat a lot of vegetables also tend to exercise more and smoke less, so healthy user bias can exaggerate the benefit of vegetables.

Taught in Chapter 15: Food and Mood.

Heart Rate Variability¶

The natural variation in the time between one heartbeat and the next. Part of it reflects the vagus nerve braking the heart during each exhale. It is often shortened to HRV.

Example: Your heart speeds up slightly when you breathe in and slows when you breathe out, which shows up as heart rate variability.

See also: Vagal Tone, Slow Breathing

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Help-Seeking¶

The process of recognizing that you are struggling and reaching out for support, whether to a friend, family member, school counselor, doctor, or mental health professional.

Example: Telling a school counselor that worry about flares is keeping you from sleeping is an act of help-seeking.

See also: Help-Seeking Barriers, Crisis Resources

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Help-Seeking Barriers¶

The obstacles that keep people from getting care when they need it, including stigma, cost, not knowing where to go, long waits, language differences, and worries about privacy or what family and community will think.

Example: Not having a ride to appointments and fearing what relatives will say are help-seeking barriers.

See also: Help-Seeking, Mental Health Stigma

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Hierarchy of Evidence¶

The idea that different kinds of studies give different levels of confidence about cause and effect, often drawn as a pyramid with the weakest kinds, such as anecdotes, at the bottom and the strongest, such as systematic reviews and meta-analyses, at the top.

Example: On the hierarchy of evidence, a well-done randomized controlled trial in people ranks above a single mouse study.

See also: Evidence Grade, Systematic Review

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Hirschsprung Disease¶

A condition present from birth in which enteric neurons are missing from the last part of the large intestine, so that segment cannot relax and push stool forward, causing a blockage.

Example: A newborn who does not pass stool in the first days of life may be checked for Hirschsprung disease.

See also: Neural Crest, Enteric Nervous System

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

HLA-DQ2 and HLA-DQ8¶

Versions of immune-system genes in the human leukocyte antigen (HLA) family that make proteins on certain immune cells. Nearly everyone with celiac disease carries one or both.

Example: About 30% of people carry HLA-DQ2 or HLA-DQ8, but only about 3% of those carriers develop celiac disease.

See also: Celiac Disease

Taught in Chapter 12: Celiac Disease and Food Reactions.

Human Milk Oligosaccharides¶

A family of complex sugar molecules found in large amounts in human milk that the baby cannot digest, which instead feed certain helpful gut bacteria such as Bifidobacterium. They are often shortened to HMOs.

Example: Human milk oligosaccharides were first discovered as a "bifidus factor," food for helpful bacteria.

Taught in Chapter 3: Meet the Microbiome.

Hype Meter¶

This book's four-level scale for grading how well the evidence supports a popular gut-brain claim: Strong, Moderate, Preliminary, or Hype.

Example: The claim that "70% of your immune system is in your gut" gets a Hype grade on the Hype Meter.

See also: Evidence Grade, Claim-Checking Method

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Hypothalamic-Pituitary-Adrenal (HPA) Axis¶

The hormone chain in which the hypothalamus signals the pituitary gland, the pituitary signals the adrenal glands, and the adrenal glands release cortisol.

Example: Before a big exam, Sam's HPA axis raises his cortisol level over minutes to hours.

Taught in Chapter 7: Stress and the Gut.

Hypothalamus¶

A small region at the base of the brain that links the nervous system to the hormone system and helps control body temperature, hunger, thirst, sleep, and the stress response.

Example: During stress, the hypothalamus releases corticotropin-releasing hormone, starting the hormone chain that ends in cortisol.

Taught in Chapter 7: Stress and the Gut.

I¶

IBD Risk Factors¶

The inherited and environmental factors that raise a person's chance of developing IBD without, on their own, causing it.

Example: Smoking is an IBD risk factor: research suggests it may double the chance of developing Crohn's disease.

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

IBD Surgery¶

An operation to remove a severely diseased section of bowel or to treat a complication of IBD, such as a stricture, fistula, abscess, severe bleeding, or precancerous changes.

Example: A person with Crohn's whose small intestine has a tight stricture may need IBD surgery to remove that segment.

See also: Crohn's Disease, Ulcerative Colitis

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

IBS Subtypes¶

Categories of IBS based on a person's main stool pattern on days with abnormal bowel movements: IBS with constipation, IBS with diarrhea, IBS with mixed bowel habits, and IBS that does not fit any of these.

Example: Sam has IBS with mixed bowel habits, one of the IBS subtypes.

See also: Irritable Bowel Syndrome

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Identity-First Language¶

A way of describing a group that puts the identity first, such as "autistic person" instead of "person with autism," often preferred because many autistic people see autism as a core part of who they are.

Example: This book uses identity-first language for autism by default.

See also: Autism, Neurodiversity

Taught in Chapter 13: Autism, ADHD, and the Gut.

Illness Burden¶

The total load a health condition places on a person's life, including symptoms such as pain, urgency, and fatigue, plus missed school, appointments, side effects, costs, worry, and effects on friendships and self-image.

Example: Planning every outing around restrooms is part of the illness burden of a gut condition.

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Illness Concealment¶

Keeping a health condition or its symptoms secret from others, such as by making up excuses for missed school or not telling a doctor about embarrassing symptoms.

Example: Skipping lunch to avoid bathroom trips so no one finds out about your IBS is illness concealment.

See also: Self-Stigma, Talking to Your Doctor

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Immune-Mediated Disease¶

A condition in which the body's own immune response, rather than an outside germ or a toxin, causes most of the damage.

Example: Inflammatory bowel disease, rheumatoid arthritis, and psoriasis are immune-mediated diseases.

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Immune-to-Brain Signaling¶

The set of pathways by which messages from the immune system, especially cytokines, reach the brain and change its activity, such as through the vagus nerve and leaky spots in the blood-brain barrier.

Example: Cytokines from a gut infection activating vagal sensory fibers is one route of immune-to-brain signaling.

Taught in Chapter 4: The Immune System as a Sense Organ.

Immunoglobulin E¶

A class of antibody that drives immediate allergic reactions. In food allergy, it sits on immune cells such as mast cells and triggers them to release chemicals within minutes when the food is eaten. It is often shortened to IgE.

Example: Immunoglobulin E against a food protein, sitting on mast cells, is why an allergic reaction can start within minutes of eating.

See also: Food Allergy, Mast Cell

Taught in Chapter 12: Celiac Disease and Food Reactions.

Immunomodulator¶

A medicine that dampens the immune system's activity more slowly and steadily, used mainly to maintain remission or help other medicines work better.

Example: Azathioprine is an immunomodulator that can take weeks to months to work fully.

See also: Corticosteroid, Biologic Therapy

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Implanted VNS Device¶

A small pulse generator placed under the skin by a surgeon and connected to the vagus nerve in the neck, which delivers programmed electrical pulses on a schedule.

Example: Implanted VNS devices are FDA approved for drug-resistant partial-onset epilepsy (1997), treatment-resistant depression in adults (2005), with the Vivistim System, arm-movement rehabilitation after stroke (2021), and, with the SetPoint System, moderate to severe rheumatoid arthritis in adults (July 30, 2025).

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Inflammation¶

The body's protective response to infection or injury, in which blood vessels widen and leak, immune cells rush in, and the area becomes warm, red, swollen, and painful.

Example: A scraped knee that turns red and puffy is showing inflammation.

See also: Cytokine, Neuroinflammation

Taught in Chapter 4: The Immune System as a Sense Organ.

Inflammatory Bowel Disease¶

A group of chronic conditions in which abnormal immune reactions cause long-lasting, recurring inflammation of the digestive tract. Its two main forms are ulcerative colitis and Crohn's disease. It is often shortened to IBD.

Example: In US claims data, about 721 per 100,000 people, roughly 2.39 million Americans, have inflammatory bowel disease.

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Inflammatory Depression Theory¶

The idea that ongoing inflammation in the body, signaled to the brain by cytokines and other immune messengers, can push brain circuits toward depression-like changes in mood, energy, and motivation, at least in some people.

Example: Higher depression symptom rates during active IBD than in remission fit, but do not prove, the inflammatory depression theory.

See also: Sickness Behavior, Cytokine

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Inflammatory Reflex¶

A nerve circuit in which the brain senses inflammation, partly through incoming vagus signals, and responds by sending signals back out, largely through the vagus nerve, that calm the immune system's release of inflammatory chemicals such as cytokines.

Example: The SetPoint System for rheumatoid arthritis is designed to use the inflammatory reflex by stimulating the vagus nerve.

See also: Vagus Nerve Stimulation, Cytokine

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Innate Immunity¶

The fast, general part of the immune system present from birth that responds within minutes to hours to broad signs of trouble and reacts the same way each time.

Example: Macrophages swallowing bacteria that slip past the gut lining are part of innate immunity.

Taught in Chapter 4: The Immune System as a Sense Organ.

Insula¶

A region of cortex folded deep inside each side of the brain that maps signals from inside the body, such as gut stretch, heartbeat, and breathing. It is a key area for interoception.

Example: In brain scans, gut stretch from a balloon consistently activated the thalamus, the insula, and part of the cingulate cortex.

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Integrated Care¶

An approach in which physical and mental health care are delivered together by a coordinated team, such as a gastroenterologist, nurse, dietitian, and psychologist who share information and plan care as one team.

Example: A clinic where an IBD patient sees the gastroenterologist and the psychologist in the same visit is offering integrated care.

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Interleukin-1 Beta¶

A pro-inflammatory cytokine released by activated innate immune cells, such as macrophages, early in an immune response. It helps coordinate local and body-wide inflammation and is strongly linked to sickness behavior.

Example: Interleukin-1 beta released during the flu is one reason you feel tired and lose your appetite.

See also: Cytokine, Sickness Behavior

Taught in Chapter 4: The Immune System as a Sense Organ.

Interleukin-6¶

A pro-inflammatory cytokine released during inflammation that travels in the blood and helps produce body-wide effects such as fever and the liver's acute phase response. It is often shortened to IL-6.

Example: Because it is easy to measure in blood, interleukin-6 appears in many human studies of inflammation and mood.

Taught in Chapter 4: The Immune System as a Sense Organ.

Interoception¶

The process by which the nervous system senses, interprets, and combines signals from inside the body, such as fullness, nausea, heartbeat, and breathing, building a moment-to-moment map of the body's internal state.

Example: Noticing that your heart is pounding and your stomach is fluttering before a speech is interoception.

See also: Interoceptive Differences, Insula

Taught in Chapter 2: The Vagus Highway.

Interoceptive Differences¶

Differences in how a person notices, interprets, or reports signals from inside the body, such as hunger, pain, or the need to use the bathroom.

Example: A child with interoceptive differences may not notice they need the bathroom until it is urgent.

See also: Interoception, GI Symptoms in Autism

Taught in Chapter 13: Autism, ADHD, and the Gut.

Interstitial Cells of Cajal¶

Specialized cells in the gut's muscle layers that generate rhythmic electrical signals, called slow waves, which set the timing of smooth muscle contractions. They are neither neurons nor muscle cells.

Example: Interstitial cells of Cajal act like a pacemaker, setting the beat that the gut's smooth muscle contracts to.

See also: Smooth Muscle, Peristalsis

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Intestinal Epithelium¶

The single layer of cells that lines the inside of the intestine and forms the barrier between the gut's contents and the body.

Example: Most cells of the intestinal epithelium absorb nutrients, while goblet cells in the same layer make mucus.

See also: Mucus Layer, Tight Junction

Taught in Chapter 4: The Immune System as a Sense Organ.

Intestinal Permeability¶

How easily substances pass across the gut lining from inside the intestine into the body, either through the cells or through the gaps between them. Some permeability is normal and necessary.

Example: Endurance exercise and common pain relievers such as ibuprofen can raise intestinal permeability for a while.

See also: Tight Junction, Leaky Gut Claim

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Intestinal Villi¶

Tiny, finger-like projections of the small intestine's lining that greatly increase its surface area for absorbing nutrients.

Example: Each of the intestinal villi is only about 0.5 to 1 millimeter long.

See also: Villous Atrophy, Small Bowel Biopsy

Taught in Chapter 12: Celiac Disease and Food Reactions.

Irritable Bowel Syndrome¶

A common disorder of gut-brain interaction marked by recurring belly pain linked to bowel movements and changes in how often stool happens or how it looks, without visible damage or disease in the digestive tract. It is often shortened to IBS.

Example: By Rome IV criteria, 6.1% of US adults had irritable bowel syndrome in a 2020 online survey.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

J¶

JAK Inhibitor¶

A pill, a small molecule rather than an antibody, that blocks Janus kinase (JAK) enzymes inside immune cells, which relay signals from many cytokines at once.

Example: Tofacitinib and upadacitinib are JAK inhibitors used for some people with IBD.

See also: Biologic Therapy, Cytokine

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

K¶

Kynurenine Pathway¶

The main chemical route for breaking down tryptophan, mostly in the liver, producing kynurenine and a series of other products, some of which can act on brain cells.

Example: More than 95% of dietary tryptophan is broken down through the kynurenine pathway, and only a small part becomes serotonin.

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

L¶

Lactobacillus¶

A group of bacteria known for turning sugars into lactic acid, used to make yogurt and other fermented foods. In 2020 the old genus was split into 25 genera, so many species now have new names.

Example: The species once called Lactobacillus rhamnosus is now named Lacticaseibacillus rhamnosus.

See also: Bifidobacterium, Bacterial Strain

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Lactose Intolerance¶

Digestive symptoms such as bloating, gas, and diarrhea after eating or drinking lactose (milk sugar), because the small intestine makes too little of the enzyme lactase to break it all down.

Example: A teen with lactose intolerance may have bloating, gas, and diarrhea for an afternoon after drinking a milkshake.

See also: Food Intolerance

Taught in Chapter 12: Celiac Disease and Food Reactions.

Leaky Gut Claim¶

The popular idea that "leaky gut syndrome" is a common hidden cause of many symptoms and diseases and can be diagnosed with consumer tests and cured with diets or supplements. "Leaky gut syndrome" is not a recognized medical diagnosis.

Example: An ad selling a supplement to "seal your leaky gut and cure your fatigue" is making the leaky gut claim.

See also: Intestinal Permeability, Hype Meter

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Levodopa Absorption¶

The process by which levodopa taken by mouth passes from the gut into the bloodstream. In Parkinson's it can be delayed or uneven because of slow stomach emptying, constipation, and competition from protein in meals.

Example: Delayed stomach emptying in Parkinson's can slow levodopa absorption and lead to more "off" periods, when symptoms come back.

See also: Parkinson's Disease, Constipation

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Lewy Body¶

An abnormal round clump, made mostly of misfolded alpha-synuclein, found inside nerve cells in Parkinson's disease and some related conditions.

Example: At autopsy, pathologists see Lewy bodies in the damaged brain cells of most people who had Parkinson's.

See also: Alpha-Synuclein, Parkinson's Disease

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Lipopolysaccharide¶

A large molecule made of fat and sugar parts that forms much of the outer membrane of gram-negative bacteria. Immune cells detect it through pattern recognition receptors and respond with inflammation. It is also called endotoxin, or LPS.

Example: In a serious infection, large amounts of lipopolysaccharide in the blood can trigger a dangerous body-wide reaction.

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Live Biotherapeutic Product¶

A medicine that contains live microorganisms and is meant to prevent, treat, or cure a disease, reviewed by the FDA like other drugs rather than sold as a supplement. It is often shortened to LBP.

Example: Vowst, oral capsules approved April 26, 2023, is a live biotherapeutic product used to prevent C. difficile infection from coming back in adults.

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Low-FODMAP Diet¶

A structured, short-term eating plan, best done with a dietitian, in which a person cuts back on high-FODMAP foods for a few weeks and then adds them back one group at a time to find triggers, so the long-term diet can stay as broad as possible.

Example: Working with a dietitian, a teen with IBS on a low-FODMAP diet finds that onions trigger symptoms but wheat does not.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

M¶

Major Depressive Disorder¶

A mental health condition marked by at least two weeks of depressed mood or loss of interest or pleasure in daily activities, along with other symptoms such as changes in sleep, appetite, energy, concentration, or self-worth. It is often just called depression.

Example: A teen who has felt hopeless, lost interest in friends, and slept poorly for most of a month should be checked for major depressive disorder.

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Mast Cell¶

An immune cell that lives in tissues, including the gut lining, and stores chemical signals such as histamine and tryptase that it can release quickly, causing inflammation, changing nerve signaling, and loosening the barrier.

Example: Stress signals can activate mast cells in the gut wall, which then irritate nearby nerve endings.

Taught in Chapter 7: Stress and the Gut.

Maternal Immune Activation¶

A strong immune response in a pregnant animal or person, such as from an infection. In research, it is usually triggered on purpose in pregnant mice to study effects on the offspring. It is often shortened to MIA.

Example: Offspring of mice exposed to maternal immune activation showed behaviors researchers label "autism-like," a mouse finding that does not show the same happens in people.

Taught in Chapter 13: Autism, ADHD, and the Gut.

Mediator Variable¶

A factor that lies on the causal path between a cause and an outcome and helps explain how the cause produces its effect.

Example: If fiber improved mood by changing gut microbes, the microbes would be a mediator variable.

See also: Confounding Variable

Taught in Chapter 15: Food and Mood.

Mediterranean Diet¶

A dietary pattern based on traditional eating habits of countries around the Mediterranean Sea, rich in vegetables, fruits, whole grains, legumes, nuts, olive oil, and fish, with fewer highly processed foods.

Example: In the SMILES trial, dietitians coached people toward a Mediterranean-style diet built from 12 food groups.

See also: Dietary Pattern, SMILES Trial

Taught in Chapter 15: Food and Mood.

Mental Health Stigma¶

Stigma directed at people with mental health conditions or at the act of seeking mental health care.

Example: Believing that seeing a therapist means you are "crazy" is mental health stigma.

See also: Stigma, Help-Seeking Barriers

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Meta-Analysis¶

A study that uses statistics to combine the results of many earlier studies on the same question into a single pooled estimate, usually more reliable than any one study, but only as good as the studies it includes.

Example: The estimate that 39.1% of people with IBS have anxiety symptoms comes from a meta-analysis.

See also: Systematic Review, Publication Bias

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Metabolic Endotoxemia¶

A small, long-lasting increase in blood lipopolysaccharide, linked to diet and gut microbes, that may promote low-grade inflammation and metabolic problems such as insulin resistance.

Example: Mice fed a high-fat diet developed metabolic endotoxemia, with a low but chronic rise in blood LPS.

See also: Lipopolysaccharide, Inflammation

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Metagenomic Sequencing¶

A method that reads fragments of all the DNA in a sample, from every organism present, so researchers can identify microbes in more detail and see which genes, and so which possible functions, are present. It is also called shotgun metagenomics.

Example: Metagenomic sequencing of a stool sample can show whether the community carries genes for making butyrate.

See also: 16S rRNA Sequencing, Microbiome

Taught in Chapter 3: Meet the Microbiome.

Microbe-Made Neurotransmitter¶

A chemical produced by bacteria or other microbes that is the same molecule the human body uses as a neurotransmitter, such as GABA, dopamine, or serotonin.

Example: A gut bacterium that produces GABA in a lab dish is making a microbe-made neurotransmitter, though that alone does not show an effect on the brain.

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Microbial Diversity¶

A measure of how many different kinds of microbes live in a community (richness) and how evenly their numbers are spread (evenness).

Example: A gut community with 300 kinds of bacteria in balanced numbers has higher microbial diversity than one dominated by a single kind.

Taught in Chapter 3: Meet the Microbiome.

Microbiome¶

The gut microbiota plus its "theater of activity": the microbes' genes, the molecules they make, and the environment they live in. In everyday talk, the word often means just the microbes.

Example: When researchers study which vitamins gut bacteria can make, they are studying the microbiome, not just a list of species.

See also: Gut Microbiota, Metagenomic Sequencing

Taught in Chapter 3: Meet the Microbiome.

Microbiome Daily Rhythm¶

The repeating, roughly 24-hour change in which gut microbes are most abundant, where they sit in the gut, and what chemicals they make, shaped largely by when the host eats.

Example: A 2014 study found that gut bacteria in mice and people rise and fall over the day, driven largely by feeding rhythms, showing a microbiome daily rhythm.

See also: Circadian Rhythm, Microbiome

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Microbiome Development¶

The process by which a newborn's gut, which starts with very few microbes, is colonized and changes over the first years of life toward a more stable, adult-like community.

Example: Like a cleared field where pioneer plants arrive first, microbiome development starts with a few fast-growing microbes and becomes richer over time.

Taught in Chapter 3: Meet the Microbiome.

Microbiota Transfer Study¶

An experiment in which gut microbes, usually from stool, from one group of people or animals are moved into animals whose own gut microbes have been removed or depleted, to see whether traits move along with the microbes.

Example: In a microbiota transfer study, rats given gut microbes from people with depression showed behaviors researchers read as depression-like.

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Microbiota Transfer Therapy¶

An experimental treatment protocol in which a person receives antibiotics, a bowel cleanse, and stomach-acid medicine, followed by repeated doses of processed stool from healthy donors to try to replace their gut microbes. It is often shortened to MTT.

Example: The 2017 Kang study of microbiota transfer therapy in 18 autistic children aged 7 to 16 was open-label with no placebo group, so it does not prove a treatment.

Taught in Chapter 13: Autism, ADHD, and the Gut.

Microglia¶

The brain's resident immune cells, a type of macrophage that lives permanently in the brain and spinal cord, surveying its surroundings, clearing debris, pruning connections, and responding to injury or infection.

Example: When an infection signals the brain, microglia switch to an active state and release cytokines.

See also: Neuroinflammation, Microglia Maturation

Taught in Chapter 4: The Immune System as a Sense Organ.

Microglia Maturation¶

The process by which young microglia develop into fully functional immune cells that can watch over brain tissue and respond to infection or injury.

Example: Germ-free mice had immature microglia, and giving them a mixture of acetate, propionate, and butyrate drove microglia maturation forward.

See also: Microglia, Germ-Free Mouse

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Microorganism¶

A living thing too small to see without a microscope, such as a bacterium, an archaeon, a yeast, or a single-celled parasite. It is also called a microbe.

Example: The yeast that makes bread rise is a microorganism.

See also: Gut Microbiota, Pathogen

Taught in Chapter 3: Meet the Microbiome.

Migrating Motor Complex¶

A repeating pattern of strong contractions that sweeps slowly along the stomach and small intestine during fasting, between meals. It is often shortened to MMC.

Example: Like a street sweeper on a schedule, the migrating motor complex clears leftover debris toward the large intestine overnight.

See also: Peristalsis

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Migration and IBD Risk¶

How the risk of developing IBD changes when people move from one country or environment to another, and what those changes suggest about the roles of genes and environment.

Example: In Leicestershire, England, South Asians had a higher relative risk of ulcerative colitis than Europeans in a 1992 study, a classic finding on migration and IBD risk.

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Mindfulness¶

The practice of paying attention to the present moment, including thoughts and body sensations, on purpose and without judging them.

Example: Noticing a cramp as "tightness, lower left, about a 4 out of 10" instead of spiraling into worry is mindfulness.

See also: Slow Breathing, Pain Catastrophizing

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Mouse-to-Human Translation¶

The process of testing whether a finding in mice or other animals holds true in people, along with the frequent failure of animal results to carry over.

Example: About one in three highly cited animal studies were later confirmed in human trials, showing how often mouse-to-human translation fails.

See also: Animal Model, Replication Failure

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Mucosal Healing¶

Healing of the gut's inner lining, so that ulcers and visible inflammation are gone when doctors look with an endoscope. It is also called endoscopic healing.

Example: Even though Riya feels well, her doctor checks for mucosal healing because hidden inflammation can damage the bowel over time.

See also: Remission, Colonoscopy

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Mucus Layer¶

The slippery gel, made mostly of large proteins called mucins, that coats the intestinal epithelium and keeps most microbes at a distance.

Example: In mice, the colon's mucus layer has a dense inner part that bacteria cannot enter and a looser outer part where they live.

See also: Intestinal Epithelium, Tight Junction

Taught in Chapter 4: The Immune System as a Sense Organ.

Myenteric Plexus¶

The outer network of enteric ganglia, lying between the circular and longitudinal muscle layers along the whole gut, that mainly controls the rhythm and strength of gut contractions. It is also called Auerbach's plexus.

Example: When the myenteric plexus signals the muscle behind a lump of food to squeeze, the food moves forward.

See also: Submucosal Plexus, Peristalsis

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

N¶

Negative Feedback¶

A control loop in which the product of a process acts back on the process to slow or stop it, keeping a body system near a set level.

Example: Rising cortisol tells the hypothalamus and pituitary to release less CRH and ACTH, a classic case of negative feedback.

Taught in Chapter 7: Stress and the Gut.

Neural Crest¶

A group of embryonic cells that forms at the edge of the developing neural tube and migrates through the embryo, giving rise to many cell types, including the neurons and glia of the enteric nervous system.

Example: If neural crest cells stop migrating before they reach the end of the colon, that segment has no enteric neurons.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Neurodegeneration¶

The slow, progressive loss of the structure and function of neurons, ending in their death, in particular parts of the nervous system.

Example: Parkinson's disease and Alzheimer's disease are the two most common diseases of neurodegeneration.

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Neurodiversity¶

The idea that natural variation in how human brains develop and work, including autism and ADHD, is part of normal human diversity, so the goal is understanding, support, and accommodation rather than cure.

Example: Like left-handedness, which was once treated as a defect, neurodiversity treats brain differences as differences that need the right tools.

See also: Autism, Identity-First Language

Taught in Chapter 13: Autism, ADHD, and the Gut.

Neuroinflammation¶

Inflammation within the brain or spinal cord, involving activated microglia and other glia releasing cytokines and other inflammatory chemicals. It ranges from a brief, helpful response to a long-lasting state.

Example: Multiple sclerosis involves long-lasting neuroinflammation.

See also: Microglia, Inflammation

Taught in Chapter 4: The Immune System as a Sense Organ.

Neuropod Cell¶

An enteroendocrine cell that forms synapse-like connections with nerve fibers and signals to them quickly, so far described mostly in mice.

Example: In lab dishes, vagal neurons connected to neuropod cells responded to gut nutrients within milliseconds.

See also: Enteroendocrine Cell, Synapse

Taught in Chapter 2: The Vagus Highway.

Neurotransmitter¶

A chemical messenger that a neuron releases at a synapse, which crosses the gap and binds to receptors on the receiving cell, making it more or less likely to fire or changing how it works.

Example: Acetylcholine is the neurotransmitter the vagus nerve releases onto its targets.

See also: Synapse, Serotonin, Dopamine

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Nociceptor¶

A sensory nerve ending that responds to stimuli that could damage tissue, such as strong pressure, extreme heat, harsh chemicals, or chemicals released during inflammation. Nociceptors detect possible harm; they are not the same as pain.

Example: Nociceptors in your fingertip fire when you touch a hot pan.

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Nodose Ganglion¶

The cluster of cell bodies of vagal sensory neurons, located on the vagus nerve just below the skull. It is also called the inferior vagal ganglion.

Example: A stretch signal from the stomach passes through a neuron in the nodose ganglion on its way to the brainstem.

See also: Vagus Nerve, Nucleus Tractus Solitarius

Taught in Chapter 2: The Vagus Highway.

Non-Celiac Gluten Sensitivity¶

A condition in which people without celiac disease or wheat allergy report gut or other symptoms after eating gluten-containing foods that improve when they avoid them. It does not damage the villi and has no biomarker.

Example: A person with negative celiac tests who still feels bloated after bread may be evaluated for non-celiac gluten sensitivity, though fructans may be the real trigger.

See also: Celiac Disease, Fructan

Taught in Chapter 12: Celiac Disease and Food Reactions.

Noninvasive VNS¶

Vagus nerve stimulation delivered through the skin, without surgery, using a handheld or wearable device placed on the neck or ear.

Example: gammaCore, a handheld noninvasive VNS device, is FDA authorized for cluster headache (2017) and migraine (2018) in adults.

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Nucleus Tractus Solitarius¶

A cluster of neurons in the medulla that receives incoming sensory signals from the vagus nerve and passes them on to other brain areas. It is also called the nucleus of the solitary tract (NTS).

Example: Fullness signals from the gut reach the nucleus tractus solitarius before being relayed to areas that control appetite.

See also: Nodose Ganglion, Brainstem

Taught in Chapter 2: The Vagus Highway.

Nutritional Psychiatry¶

The young research field that studies how diet and nutrition relate to mental health, including whether changing diet can help prevent or treat conditions like depression and anxiety.

Example: The SMILES trial is a key study in nutritional psychiatry.

See also: SMILES Trial, Dietary Pattern

Taught in Chapter 15: Food and Mood.

O¶

Observational Study¶

A study in which researchers measure what people already do and their health, without assigning anyone to change anything, and then look for links.

Example: A study that surveys thousands of people about their diets and moods is an observational study.

Taught in Chapter 15: Food and Mood.

Off-Label Use¶

The use of an FDA-approved drug for a condition, dose, or form that is not listed in its official labeling.

Example: Prescribing a low-dose antidepressant for gut pain in IBS is an example of off-label use.

See also: FDA Approval, Tricyclic Antidepressant

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Open-Label Trial¶

A study in which participants, families, and researchers all know who is getting the treatment. There is usually no placebo group, so improvements may come from expectations, extra attention, or time passing.

Example: The 2017 microbiota transfer study in 18 autistic children was an open-label trial with no placebo group.

Taught in Chapter 13: Autism, ADHD, and the Gut.

P¶

Pain Catastrophizing¶

A pattern of thinking about pain in which a person tends to dwell on it, expect the worst from it, and feel helpless to do anything about it.

Example: Thinking "this cramp means something terrible is happening and I can't do anything" is an example of pain catastrophizing.

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Pain Perception¶

The brain's construction of the conscious experience of pain from incoming nerve signals, shaped by attention, emotion, memory, and context. It is separate from nociception, the nerve activity caused by a harmful stimulus.

Example: The same cramp can feel worse during a stressful test than during a fun movie because pain perception depends on context.

See also: Nociceptor, Descending Pain Modulation

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Parasympathetic Nervous System¶

The branch of the autonomic nervous system that supports "rest and digest" activities, such as slowing the heart and speeding up digestion. Its nerves leave from the brainstem and the lowest part of the spinal cord.

Example: After a calm meal, the parasympathetic nervous system, mainly through the vagus nerve, helps the stomach and intestines get to work.

See also: Sympathetic Nervous System, Vagus Nerve

Taught in Chapter 2: The Vagus Highway.

Parkinson's Disease¶

A progressive disorder of the nervous system that mainly affects movement, caused by the gradual damage and death of nerve cells in certain parts of the brain. It is often shortened to PD.

Example: Tremor, rigidity, slowness of movement, and balance problems are the four common movement symptoms of Parkinson's disease.

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Pathogen¶

A microorganism that can cause disease. Some cause disease in almost anyone; others, called opportunists, cause trouble mainly when the normal community or the body's defenses are weakened.

Example: Clostridioides difficile is an opportunistic pathogen that often takes hold after antibiotics.

Taught in Chapter 3: Meet the Microbiome.

Pattern Recognition Receptor¶

A protein on or inside an immune cell (and some other cells, such as gut lining cells) that recognizes molecular patterns shared by many microbes, or molecules released by stressed or damaged cells. It is often shortened to PRR.

Example: A pattern recognition receptor on a macrophage detects lipopolysaccharide from bacterial walls and starts inflammation.

See also: Innate Immunity, Lipopolysaccharide

Taught in Chapter 4: The Immune System as a Sense Organ.

Pediatric IBD¶

Inflammatory bowel disease that begins in childhood or the teen years, before adulthood. It can slow growth, lower weight gain, and delay puberty.

Example: Riya, diagnosed with Crohn's at 14, has pediatric IBD.

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Peer Review¶

The process in which a journal sends a submitted paper to independent experts in the same field, who check its methods, reasoning, and conclusions and recommend whether it should be published, revised, or rejected.

Example: Like a building inspector, peer review catches many problems but cannot check every detail of a study.

See also: Preprint

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Peer Support¶

Help and understanding from people who share a similar experience, offered through friendships, support groups, online communities, or camps.

Example: Camp Oasis, a summer camp for kids and teens with IBD, offers peer support.

See also: Stigma, Help-Seeking

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Peppermint Oil¶

An oil from the peppermint plant, usually taken in coated capsules that release it in the intestine, that relaxes gut smooth muscle and is used to ease IBS symptoms such as pain and cramping.

Example: A meta-analysis of 10 randomized trials found peppermint oil did better than placebo for overall IBS symptoms.

See also: Irritable Bowel Syndrome, Smooth Muscle

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Peripheral Nervous System¶

All the nerves and nerve-cell clusters (ganglia) outside the brain and spinal cord, which connect the central nervous system to the skin, muscles, and organs. It is often shortened to PNS.

Example: The vagus nerve running from the brainstem to the gut is part of the peripheral nervous system.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Peripheral Neuropathy¶

Damage to the nerves outside the brain and spinal cord, often causing numbness, tingling, burning, or weakness, usually starting in the hands and feet.

Example: Tingling feet in a person with untreated celiac disease may be a sign of peripheral neuropathy.

Taught in Chapter 12: Celiac Disease and Food Reactions.

Peripheral Sensitization¶

An increase in how strongly sensory nerve endings in a tissue respond, with a drop in the stimulus needed to make them fire, usually caused by inflammation or injury in that tissue.

Example: Inflammation in the gut wall can make its nerve endings fire at a gentler stretch than usual, a form of peripheral sensitization.

See also: Central Sensitization, Nociceptor

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Peristalsis¶

A wave of muscle contraction that travels along the digestive tract and pushes its contents forward, toward the anus.

Example: Peristalsis is why food still reaches your stomach if you swallow while lying down.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Peristaltic Reflex¶

A local reflex of the enteric nervous system in which stretch of the gut wall makes the muscle behind the stretched spot contract and the muscle ahead of it relax.

Example: A lump of food stretches the intestine, so the muscle above it squeezes and the muscle below it relaxes, moving the lump along.

See also: Peristalsis, Enteric Nervous System

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Physical Activity¶

Any body movement produced by skeletal muscles that uses energy. Exercise is the planned, repeated kind.

Example: The CDC says children and teens ages 6 to 17 should get 60 minutes or more of moderate-to-vigorous physical activity every day.

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Pituitary Gland¶

A pea-sized gland hanging just below the hypothalamus that releases hormones controlling many other glands. Its front part, the anterior pituitary, releases ACTH in the stress response.

Example: The pituitary gland responds to corticotropin-releasing hormone by releasing ACTH into the blood.

Taught in Chapter 7: Stress and the Gut.

Placebo Response¶

The improvement in symptoms people experience after receiving an inactive treatment, caused by expectations, attention and care, natural ups and downs of symptoms, and changes in how the brain processes body signals.

Example: In IBS trials, many people in the placebo group report feeling better, which is the placebo response, not faking.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Placebo-Controlled Trial¶

A study that compares a real treatment with a look-alike dummy treatment, ideally with assignment by chance and with neither participants nor researchers knowing who got which (double-blind), so expectation effects are the same in both groups.

Example: A placebo-controlled trial of a probiotic gives half the group identical-looking empty capsules.

Taught in Chapter 13: Autism, ADHD, and the Gut.

Polyphenol¶

One of a large family of natural chemical compounds made by plants that may affect the body partly through the gut microbes that break them down.

Example: Berries, grapes, tea, and turmeric contain polyphenols, and most of the polyphenols people eat reach the large intestine.

See also: Gut Microbiota

Taught in Chapter 15: Food and Mood.

Positive Diagnosis Strategy¶

An approach in which a clinician diagnoses IBS confidently from its typical symptom pattern, a careful history and exam, the absence of alarm features, and a few targeted tests, instead of first ordering every possible test.

Example: Using a positive diagnosis strategy, a doctor diagnoses IBS with diarrhea from the typical symptom pattern plus a celiac blood test and a fecal calprotectin test, without a long list of scans.

See also: Rome IV Criteria, Alarm Features

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Post-Infection IBS¶

IBS that develops after a bout of infectious gastroenteritis, such as food poisoning, in a person who did not have IBS before.

Example: In a meta-analysis of 45 studies, about 10.1% of people had IBS 12 months after infectious enteritis, an example of post-infection IBS.

See also: Irritable Bowel Syndrome

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Postbiotic¶

A preparation of inanimate (no longer alive) microorganisms and/or their components that confers a health benefit on the host (ISAPP, 2021).

Example: Heat-killed bacterial cells with a shown health benefit can be a postbiotic, but a purified chemical made by microbes, on its own, does not count.

See also: Probiotic, Synbiotic

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Prebiotic¶

A substrate that is selectively utilized by host microorganisms conferring a health benefit (ISAPP, 2017). In plain words, food that feeds certain microbes more than others and produces a health benefit.

Example: Many prebiotics are types of fiber that certain gut bacteria ferment more readily than others.

See also: Probiotic, Synbiotic, Dietary Fiber

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Precision Medicine¶

An emerging approach to disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person, instead of a one-size-fits-all approach.

Example: Choosing an IBS treatment someday based on a person's microbiome or genes would be precision medicine.

See also: Shared Decision-Making

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Preprint¶

A complete scientific paper shared publicly online before it has been checked by peer review.

Example: A news story based on a preprint posted on medRxiv is reporting preliminary results.

See also: Peer Review

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Preregistration¶

Publicly recording a study's question, main outcome, and analysis plan before collecting or looking at the results, so readers can check that researchers tested what they said they would.

Example: Clinical trials preregistered on ClinicalTrials.gov get an ID number starting with "NCT."

See also: Primary Outcome, Publication Bias

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Primary Outcome¶

The one main measurement a study commits to in advance, before results are known, as the test of whether the treatment works. Other measurements are secondary outcomes.

Example: If a trial's primary outcome shows no benefit but one of ten secondary measures does, the result is much weaker than the headline may suggest.

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Prion-Like Spread¶

The idea that a misfolded protein, such as alpha-synuclein, can pass from one neuron to a connected neuron and make normal copies of the protein misfold, so the damage moves along nerve pathways. It does not mean the disease is contagious between people.

Example: In mice, seeds of misfolded alpha-synuclein injected into the gut wall spread to the brain, but not when the vagus nerve was cut, consistent with prion-like spread.

See also: Alpha-Synuclein, Braak Hypothesis

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Probiotic¶

Live microorganisms that, when given in adequate amounts, confer a health benefit on the host (ISAPP, 2014).

Example: A capsule of a specific Lactobacillus strain that has been shown in trials to help a particular condition fits the definition of a probiotic; a yogurt with no tested benefit does not automatically count.

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Probiotic Safety¶

The risks of taking live microbes, which are low for most healthy people but higher for people who are very sick, have weakened immune systems, or were born very early, because the microbes can occasionally cause infections.

Example: In October 2023, the FDA warned that probiotics given to preterm infants have caused serious infections, including a death.

See also: Probiotic, Benefit-Risk Balance

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Prodromal Symptoms¶

Early signs that can appear years before the main symptoms of a disease and before it can be diagnosed.

Example: In Parkinson's, constipation, loss of smell, acting out dreams during sleep, and mood changes can be prodromal symptoms.

See also: Constipation, Gut-First Subtype

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Propionate¶

The three-carbon short-chain fatty acid. Much of it is taken up by the liver before it can reach the rest of the body.

Example: After a high-fiber meal, propionate made in the colon travels in the blood to the liver.

See also: Short-Chain Fatty Acid, Acetate

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Psychiatric Comorbidity¶

The presence of a mental health condition, such as anxiety or depression, in a person who also has another health condition, such as IBD or IBS.

Example: Pooled studies found anxiety symptoms in 32.1% and depression symptoms in 25.2% of adults with IBD, showing how common psychiatric comorbidity is.

See also: Symptom Questionnaire, Integrated Care

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Psychobiotic¶

In its original 2013 definition by Dinan, Stanton, and Cryan, a live organism that, when taken in adequate amounts, produces a health benefit in patients with psychiatric illness. It is a research term, not an approved product category.

Example: A supplement labeled "psychobiotic" has not been approved by the FDA to treat depression or anxiety.

See also: Probiotic, Replication Failure

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Psychotherapy¶

Treatment that uses structured conversations and practice with a trained professional, such as a psychologist or licensed counselor, to change patterns of thinking, feeling, behavior, and body responses. It is often called talk therapy.

Example: Cognitive behavioral therapy is one type of psychotherapy.

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Publication Bias¶

The tendency for studies with exciting, positive results to be published more often and faster than studies that found nothing, so published research makes a treatment look better than it really is.

Example: If five probiotic trials found nothing and stayed unpublished while one positive trial was published, publication bias would mislead readers.

See also: Systematic Review, Preregistration

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Q¶

Quality of Life¶

A person's overall sense of well-being across the parts of life that matter to them, including physical health, emotions, relationships, school or work, and daily activities.

Example: In one study of adults with IBD, perceived stigma explained 10% to 22% of differences in health-related quality of life scores.

See also: Illness Burden, Stigma

Taught in Chapter 19: Culture, Food, Family, and Stigma.

R¶

Randomized Controlled Trial¶

An experiment in which participants are randomly assigned to a treatment or a comparison condition, so the groups start out alike on average and any difference at the end can be credited to the treatment. It is often shortened to RCT.

Example: The SMILES trial was a small randomized controlled trial of dietary support for depression.

Taught in Chapter 15: Food and Mood.

Reading an Abstract¶

The skill of pulling a study's question, methods, main results, and limits out of the short summary at the top of a scientific paper, and comparing what it actually found with how others describe it.

Example: Reading an abstract can reveal that a "probiotic beats depression" headline was based on a mouse study.

See also: Claim-Checking Method, Peer Review

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Referred Pain¶

Pain from an internal organ that is felt at a different spot on the body surface, usually skin or muscle supplied by nerves entering the same part of the spinal cord.

Example: In a 1973 study, the same balloon in the lower colon was felt in the lower middle belly by some people and in the sides, rectum, or back by others, showing referred pain.

See also: Visceral Pain, Dorsal Horn

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Regulatory T Cell¶

A type of T cell that calms or suppresses other immune responses, helping keep the immune system from attacking the body's own tissues or harmless things like food and friendly microbes. It is often shortened to Treg.

Example: Regulatory T cells in the gut help prevent an immune attack on the bacteria in yogurt or the protein in milk.

Taught in Chapter 4: The Immune System as a Sense Organ.

Remission¶

A period when IBD is quiet: symptoms fade or disappear, and ideally the inflammation settles too. Remission can last for weeks or years.

Example: The goal of Riya's biologic medicine is to keep her in remission long term.

See also: Disease Flare, Mucosal Healing

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Replication Failure¶

A situation in which a later study tests the same idea and does not find the original result. It does not automatically mean the first study was wrong.

Example: The strain JB-1 lowered anxiety-like behavior in mice in 2011, but a later trial in 29 healthy men found no such benefit, a replication failure.

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Reverse Causation¶

A situation in which the cause-and-effect arrow points the opposite way from the one assumed.

Example: If depression changes diet and sleep, which then change gut bacteria, a "bacteria cause depression" headline may have reverse causation.

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Rome IV Criteria¶

The 2016 set of symptom-based diagnostic rules from the Rome Foundation for disorders of gut-brain interaction. For IBS, they require recurrent belly pain on average at least 1 day a week in the last 3 months, linked to two or more of: bowel movements, a change in stool frequency, or a change in stool form, with symptoms starting at least 6 months before diagnosis.

Example: Most published IBS research used the Rome IV criteria, although Rome V, published in May 2026, is now the current version.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

S¶

Sample Size¶

The number of participants in a study. Small samples give results that swing more by chance and cannot detect uncommon side effects.

Example: A finding in 18 people is a hint, while the same finding in thousands is much more reliable, because sample size matters.

See also: Effect Size, Statistical Significance

Taught in Chapter 13: Autism, ADHD, and the Gut.

Satiety Signal¶

Any signal from the gut or body that tells the brain enough food has been eaten, producing a feeling of fullness and reducing the urge to keep eating.

Example: Stomach stretch and the release of cholecystokinin during a meal are both satiety signals.

Taught in Chapter 2: The Vagus Highway.

School Accommodation¶

A change in how a student learns, is tested, or participates in school that removes a barrier caused by a health condition or disability, without lowering what the student is expected to learn.

Example: A pass to use the restroom without asking is a common school accommodation for students with IBD.

See also: 504 Plan, Pediatric IBD

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Science Communication¶

The practice of explaining scientific findings to non-experts accurately, clearly, and with the right level of certainty, without hiding uncertainty or exaggerating results.

Example: Writing "in a study of 67 adults, a diet program helped some people with depression" instead of "diet cures depression" is good science communication.

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Second Brain Metaphor¶

The comparison of the enteric nervous system to a brain, which highlights that it is large, complex, and able to work independently, but can mislead people into thinking the gut thinks, feels, or decides.

Example: A post saying "your gut has feelings" stretches the second brain metaphor past what the evidence supports.

See also: Enteric Nervous System, Hype Meter

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Selective Eating¶

Eating a limited range of foods, often because of sensitivity to taste, texture, smell, or appearance, or a strong need for sameness. It is more common in autistic children.

Example: A child who eats only plain pasta and crackers shows selective eating.

Taught in Chapter 13: Autism, ADHD, and the Gut.

Selective Serotonin Reuptake Inhibitor (SSRI)¶

A type of medicine that blocks the serotonin transporter, so serotonin stays outside cells longer after release. SSRIs such as fluoxetine are prescribed for depression, anxiety disorders, and other conditions.

Example: Because SSRIs also block the transporter in the gut, they can cause side effects such as nausea or loose stools.

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Self-Monitoring¶

Regularly recording your own symptoms, behaviors, and circumstances, such as sleep, stress, food, activity, and bowel habits, to notice patterns and share accurate information with your care team.

Example: Keeping a two-week diary of sleep, stress, food, and symptoms to bring to an appointment is self-monitoring.

See also: Behavior Change, Talking to Your Doctor

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Self-Stigma¶

Turning society's negative beliefs about a condition on oneself, such as thinking "I'm disgusting" or "I'm a burden," which can lower self-esteem and confidence.

Example: A teen with IBD who thinks "no one would want to be friends with someone like me" is experiencing self-stigma.

See also: Stigma, Illness Concealment

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Serotonin¶

A chemical messenger made from the amino acid tryptophan. It acts as a neurotransmitter in the brain, controls movement, secretion, and sensations like nausea in the gut, and is carried in the blood by platelets. It is also called 5-HT.

Example: More than 90% of the body's serotonin is made in the gut, mostly by enterochromaffin cells.

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Serotonin Transporter¶

A protein pump in cell membranes that moves serotonin from outside a cell back inside, ending its signal. It is often shortened to SERT.

Example: In the gut, the serotonin transporter on lining cells clears away serotonin after enterochromaffin cells release it.

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Shared Decision-Making¶

A process in which a patient (and, for a teen, often their family) and their clinician decide on a treatment together, combining the clinician's knowledge of the evidence with the patient's own values, goals, and preferences.

Example: A doctor laying out the options, including waiting, while the teen and family explain what matters most to them, is shared decision-making.

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Short-Chain Fatty Acid¶

A small fatty acid, with a chain of no more than six carbon atoms, made mainly when gut microbes ferment fiber and resistant starch. It is often shortened to SCFA.

Example: Acetate, propionate, and butyrate are the three main short-chain fatty acids.

See also: Butyrate, Propionate, Acetate

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Sickness Behavior¶

The coordinated set of mood and behavior changes during infection or inflammation, such as tiredness, sleepiness, loss of appetite, low interest, poor concentration, and low mood, driven by immune signals acting on the brain.

Example: Wanting to stay in bed and skip meals when you have the flu is sickness behavior.

Taught in Chapter 4: The Immune System as a Sense Organ.

Sleep and Inflammation¶

The two-way link between sleep and the immune system: disturbed sleep is associated with higher inflammatory signals in the blood, and inflammation, such as during an infection or flare, can change sleep.

Example: Riya notices she sleeps worse during flares, and poor sleep may in turn feed inflammation, an example of sleep and inflammation.

See also: Teen Sleep Need, Cytokine

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Sleep Architecture¶

The structure of a night's sleep: the pattern of stages (light non-REM, deep non-REM, and REM sleep) and how they cycle and change across the night.

Example: Deep sleep is more common early in the night and REM sleep later, part of normal sleep architecture.

See also: Circadian Rhythm, Teen Sleep Need

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Sleep Hygiene¶

The set of everyday habits and bedroom conditions that make good sleep more likely, such as a regular schedule, a dark and cool room, and limiting caffeine and screens before bed.

Example: Charging your phone outside the bedroom is a sleep hygiene habit.

See also: Teen Sleep Need, Behavior Change

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Slow Breathing¶

Deliberately breathing at a slower-than-usual pace, often around six breaths per minute, with longer, steady exhales.

Example: Breathing in for about four seconds and out for about six is a simple slow breathing exercise.

See also: Heart Rate Variability, Vagal Tone

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Small Bowel Biopsy¶

The removal of tiny pieces of tissue from the small intestine, usually the duodenum, during an upper endoscopy, so a pathologist can look for villous atrophy and immune cells under a microscope.

Example: After a high tTG antibody result, a small bowel biopsy can confirm celiac disease.

Taught in Chapter 12: Celiac Disease and Food Reactions.

SMILES Trial¶

A 12-week randomized controlled trial, published in 2017 by Felice Jacka and colleagues, that tested whether dietitian support toward a Mediterranean-style diet improved symptoms in adults with major depression.

Example: In the SMILES trial, 67 adults took part; 32.3% in the diet-support group reached remission versus 8.0% in the social-support group, but the trial was small, short, and participants knew their group.

Taught in Chapter 15: Food and Mood.

Smooth Muscle¶

Muscle made of small, spindle-shaped cells that contract slowly, can stay partly contracted for a long time, and work without conscious control.

Example: You can choose to bend your elbow, but you cannot choose to squeeze your small intestine, because its wall is smooth muscle.

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Somatic Pain¶

Pain that comes from the skin, muscles, bones, and joints. It is usually sharp or aching and easy to point to.

Example: A paper cut on your finger causes somatic pain you can locate exactly.

See also: Visceral Pain, Referred Pain

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

South Asian Health Context¶

The cultural, family, migration, and health-system factors that can shape how people with roots in South Asia understand illness, talk about it, and seek care. South Asian communities are enormously diverse.

Example: Understanding the South Asian health context can help a doctor talk with Riya's family about diet and food traditions without stereotyping them.

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Spinal Afferent Nerve¶

A sensory nerve fiber that carries signals from an organ such as the gut to the spinal cord rather than straight to the brainstem, with its cell body in a ganglion beside the spinal cord.

Example: Pain from an inflamed colon travels largely through spinal afferent nerves, so it can still reach the brain if the vagus is cut.

See also: Afferent Signal, Dorsal Root Ganglion

Taught in Chapter 2: The Vagus Highway.

Spore-Forming Bacteria¶

Bacteria that can survive harsh conditions by forming tough, dormant spores. In the gut, a mix of them dominated by Clostridia has been shown in mice to boost serotonin production by the gut lining.

Example: When germ-free mice received spore-forming bacteria, serotonin in their colon and blood rose toward normal.

See also: Enterochromaffin Cell, Germ-Free Mouse

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Statistical Significance¶

A label given to a result that would be unlikely to occur by chance alone if there were truly no effect, usually judged by a p-value below a cutoff such as 0.05. It does not show how big or useful an effect is.

Example: In the ATLANTIS trial, amitriptyline's 27-point benefit in IBS scores was statistically significant but smaller than the 35-point difference often considered meaningful to patients.

See also: Effect Size, Sample Size

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Stigma¶

A set of negative beliefs and reactions that leads people to label, judge, and treat others as less worthy because of a trait, such as a health condition.

Example: Classmates joking about someone who often leaves for the bathroom is a form of stigma.

See also: Self-Stigma, Mental Health Stigma

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Strain Specificity¶

The finding that a probiotic's effects belong to a particular strain used for a particular condition, so a result from one strain cannot be assumed to apply to another, even in the same species.

Example: Because of strain specificity, a study showing one Lactobacillus strain helps diarrhea says nothing about a different strain sold for mood.

See also: Bacterial Strain, Probiotic

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Stress and Gut Motility¶

The way stress signals change the speed and pattern of muscle contractions in the digestive tract. In animal studies and small human experiments, stress hormones such as CRH speed up movement in the colon.

Example: Needing to rush to the bathroom before a big performance is an everyday sign of stress and gut motility at work.

Taught in Chapter 7: Stress and the Gut.

Stress Response¶

The set of changes in the brain, nerves, hormones, and immune system that helps the body deal with a challenge, real or perceived, and then return to balance.

Example: A fight with a friend and being out in the cold without a coat can both trigger the stress response.

Taught in Chapter 7: Stress and the Gut.

Structural vs Functional Disease¶

The distinction between conditions in which tests show a physical abnormality, such as inflammation, ulcers, a tumor, or a blockage (structural), and conditions in which the organ looks normal on standard tests but does not work normally (functional).

Example: IBD is a structural disease, while IBS has been called a functional disease.

Taught in Chapter 10: IBS and Disorders of Gut-Brain Interaction.

Structure-Function Claim¶

A statement that a supplement or food supports the normal structure or function of the body without claiming to diagnose, treat, cure, or prevent a disease. Such claims are not preapproved by the FDA.

Example: "Fiber maintains bowel regularity" is a structure-function claim, while "cures IBS" would be a disease claim.

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Student Research Project¶

A structured investigation in which a student picks one health claim, finds and evaluates the original evidence, assigns a Hype Meter grade, and explains the result in plain language for a real audience.

Example: A science fair poster that grades the claim "kombucha cures anxiety" after reading the original studies is a student research project.

Taught in Chapter 20: Be Your Own Scientist: Reading Health Claims.

Submucosal Plexus¶

The inner network of enteric ganglia, lying in the submucosa just under the lining, mainly in the small and large intestines. It mostly controls what the lining does, such as releasing fluid and mucus, and helps sense gut contents. It is also called Meissner's plexus.

Example: The submucosal plexus helps trigger fluid release into the intestine when the lining detects an irritant.

See also: Myenteric Plexus, Gut Wall Layers

Taught in Chapter 1: The Brain in Your Belly (and Why That Phrase Is Misleading).

Sympathetic Nervous System¶

The branch of the autonomic nervous system that prepares the body for action or stress, often called "fight or flight." It speeds the heart and slows digestion.

Example: When a runner sprints at the end of a race, the sympathetic nervous system holds back gut movement and fluid release.

Taught in Chapter 2: The Vagus Highway.

Symptom Questionnaire¶

A standard set of questions, scored with fixed rules, that measures how many symptoms of a condition a person reports and how strong they are. A score above a cutoff "screens positive," but it cannot diagnose.

Example: Many IBD mood studies used a symptom questionnaire, so their numbers describe symptoms, not diagnosed disorders.

See also: Psychiatric Comorbidity, Meta-Analysis

Taught in Chapter 11: Anxiety, Depression, and the Gut.

Synapse¶

The junction where a neuron passes a signal to another cell, such as another neuron, a muscle cell, or a gland cell, usually across a tiny gap called the synaptic cleft.

Example: An enteric motor neuron passes a "contract" message to smooth muscle at a synapse.

See also: Neurotransmitter

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Synbiotic¶

A mixture of live microorganisms and substrates selectively utilized by host microorganisms that confers a health benefit on the host (ISAPP, 2020).

Example: A product combining a probiotic strain with a fiber chosen to feed that same strain is a synergistic synbiotic.

See also: Probiotic, Prebiotic

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

Systematic Review¶

A study of studies that follows a written plan to search for every relevant study on a question, judge each one's quality, and summarize the results, so the conclusion does not depend on which studies an author happened to pick.

Example: A systematic review of probiotics and depression searches several databases with fixed rules rather than citing a few favorite trials.

See also: Meta-Analysis, Publication Bias

Taught in Chapter 16: Probiotics, Prebiotics, and "Psychobiotics".

T¶

Talking to Your Doctor¶

The skill of preparing for and taking an active part in medical visits: sharing accurate information, asking questions, and making decisions with your care team.

Example: Writing down your symptoms and three questions before an appointment is part of talking to your doctor.

See also: Shared Decision-Making, Self-Monitoring

Taught in Chapter 19: Culture, Food, Family, and Stigma.

Teen Sleep Need¶

The amount of sleep recommended for adolescents to support health, learning, and mood: 8 to 10 hours per 24 hours for ages 13 to 18, according to the American Academy of Sleep Medicine.

Example: A teen who sleeps 6 hours on school nights is falling well short of teen sleep need.

See also: Sleep Hygiene, Sleep and Inflammation

Taught in Chapter 18: Sleep, Exercise, and Therapy.

Thalamus¶

A pair of egg-shaped structures deep in the middle of the brain that relays most incoming sensory information, including pain signals, to the cortex.

Example: A pain signal from the gut passes through the thalamus on its way to the insula.

See also: Insula, Anterior Cingulate Cortex

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Tight Junction¶

A protein seal that links neighboring epithelial cells near their top edge and controls what can slip through the gaps between them.

Example: Tight junctions let water and some small molecules pass between gut cells but block most larger molecules.

See also: Intestinal Permeability, Zonulin

Taught in Chapter 4: The Immune System as a Sense Organ.

Tissue Transglutaminase Antibody¶

A blood test that measures antibodies against tissue transglutaminase (tTG), one of the body's own intestinal enzymes; high levels suggest active celiac disease.

Example: A doctor orders a tissue transglutaminase antibody test as a first screen for celiac disease, before the person stops eating gluten.

See also: Celiac Disease, Small Bowel Biopsy

Taught in Chapter 12: Celiac Disease and Food Reactions.

Transmural Inflammation¶

Inflammation that extends through the entire thickness of the gut wall, from the inner lining to the outer layer.

Example: Crohn's disease causes transmural inflammation, which is why it can lead to fistulas, while ulcerative colitis usually does not.

See also: Crohn's Disease, Gut Wall Layers

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Tricyclic Antidepressant¶

One of an older class of medicines, named for their three-ring chemical structure, first used for depression and now also prescribed, usually at much lower doses, to reduce chronic pain, including gut pain in disorders of gut-brain interaction. It is often shortened to TCA.

Example: Amitriptyline is a tricyclic antidepressant sometimes used at low doses for IBS pain.

See also: Gut-Brain Neuromodulator, Off-Label Use

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Truncal Vagotomy Studies¶

Large health-record studies that compare people who had their main vagus nerve trunks surgically cut, usually for ulcers, with people who did not, to test whether cutting the gut-to-brain vagus route lowers later Parkinson's risk.

Example: Truncal vagotomy studies compare full vagotomy with selective vagotomy, which cuts only some branches.

See also: Vagotomy, Braak Hypothesis

Taught in Chapter 14: Parkinson's, Alzheimer's, and the Gut.

Tryptophan¶

An essential amino acid, meaning the body cannot make it and must get it from protein in food. It is the raw material for serotonin and can cross the blood-brain barrier.

Example: Eggs, milk, seeds, and meat all supply tryptophan.

See also: Serotonin, Kynurenine Pathway

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Tryptophan Hydroxylase¶

The enzyme that performs the first and key step in making serotonin from tryptophan. It comes in two versions: TPH1, mainly in gut enterochromaffin cells, and TPH2, mainly in neurons.

Example: Because the brain uses its own tryptophan hydroxylase (TPH2), it makes its own serotonin separately from the gut.

See also: Serotonin, Enterochromaffin Cell

Taught in Chapter 5: Chemical Messengers and the Serotonin Myth.

Tumor Necrosis Factor¶

A pro-inflammatory cytokine, made by immune cells such as macrophages, that drives and sustains inflammation in tissues. It is often written TNF or TNF-alpha.

Example: Anti-TNF medicines block tumor necrosis factor to calm inflammation in Crohn's disease.

See also: Cytokine, Anti-TNF Therapy

Taught in Chapter 4: The Immune System as a Sense Organ.

U¶

Ulcerative Colitis¶

A form of inflammatory bowel disease in which inflammation affects only the colon and rectum, starting at the rectum and spreading upward in one continuous stretch, and stays in the inner layers of the gut wall. It is often shortened to UC.

Example: A person whose colonoscopy shows continuous inflammation from the rectum partway up the colon may have ulcerative colitis.

Taught in Chapter 9: Inflammatory Bowel Disease: Ulcerative Colitis and Crohn's.

Ultra-Processed Food¶

A food made by industrial formulation, mostly from substances extracted or derived from foods, often with additives such as flavors, colors, or emulsifiers not used in home kitchens. The term comes from the NOVA classification system.

Example: Many packaged snacks and sugary soft drinks count as ultra-processed food.

See also: Dietary Pattern, Observational Study

Taught in Chapter 15: Food and Mood.

Unneeded Restrictive Diet¶

Cutting out foods or whole food groups without a diagnosed medical reason, which can bring costs such as nutrient gaps, missed or delayed diagnoses, extra expense, and social stress, without a proven benefit.

Example: Going gluten-free "just in case" before a celiac test is an unneeded restrictive diet that can also make the test unreliable.

See also: Gluten-Free Diet, Eating Disorder Risk

Taught in Chapter 12: Celiac Disease and Food Reactions.

V¶

Vagal Tone¶

The ongoing, background level of activity in the vagus nerve's motor fibers, most often estimated through its calming effect on the heart.

Example: Even at rest, vagal tone gently brakes your heart, keeping it slower than it would otherwise beat.

See also: Heart Rate Variability, Vagus Nerve

Taught in Chapter 2: The Vagus Highway.

Vagotomy¶

Surgery that cuts all or part of the vagus nerve to the stomach, historically done to reduce stomach acid in people with ulcers.

Example: Surgeons performed many vagotomies for peptic ulcers starting in the 1940s.

See also: Vagus Nerve, Truncal Vagotomy Studies

Taught in Chapter 2: The Vagus Highway.

Vagus Nerve¶

A long, mixed nerve (cranial nerve X) that runs from the medulla through the neck and chest into the abdomen, carrying sensory and motor fibers to and from organs such as the heart, lungs, and digestive tract.

Example: Most vagus nerve fibers carry signals from the body to the brain; classic fiber counts in animals put the figure at about 80%.

Taught in Chapter 2: The Vagus Highway.

Vagus Nerve Stimulation¶

A treatment that delivers mild electrical pulses to the vagus nerve, through a device implanted under the skin or a handheld device placed on the skin, to change nerve signaling to the brain or body. It is often shortened to VNS.

Example: Vagus nerve stimulation is FDA approved for some kinds of epilepsy and depression but is not approved for Crohn's disease, IBS, or anxiety.

Taught in Chapter 17: Medicine for the Gut-Brain Axis.

Villous Atrophy¶

The shortening and flattening of the intestinal villi, seen under a microscope, that is the hallmark damage of celiac disease.

Example: A biopsy showing villous atrophy in the duodenum supports a diagnosis of celiac disease.

See also: Intestinal Villi, Small Bowel Biopsy

Taught in Chapter 12: Celiac Disease and Food Reactions.

Visceral Hypersensitivity¶

A lowered threshold for feeling sensations from internal organs, so that normal amounts of gut stretch or activity are felt as uncomfortable or painful.

Example: In balloon tests, many people with IBS report pain at lower balloon volumes than other people, a sign of visceral hypersensitivity.

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Visceral Pain¶

Pain that comes from internal organs such as the stomach, intestines, bladder, or heart. It tends to feel dull, crampy, or deep, and is hard to pinpoint.

Example: The vague, crampy ache of gas trapped in the intestines is visceral pain.

See also: Somatic Pain, Visceral Hypersensitivity

Taught in Chapter 8: Pain, Sensitivity, and the Gut.

Z¶

Zonulin¶

A protein that some researchers propose loosens tight junctions in the small intestine. It has been reported to be the same molecule as a blood protein called pre-haptoglobin 2, and its role is still debated.

Example: Widely used commercial zonulin tests detect other blood proteins, so a "high zonulin" result does not show that a gut is leaky.

See also: Tight Junction, Leaky Gut Claim

Taught in Chapter 6: Fiber, Fatty Acids, and the Blood-Brain Barrier.

Glossary¶

1¶

16S rRNA Sequencing¶

5¶

504 Plan¶

A¶

Absolute vs Relative Risk¶

Acetate¶

Acetylcholine¶

Acute Stress¶

Adaptive Immunity¶

Adrenal Gland¶

Adrenocorticotropic Hormone (ACTH)¶

Afferent Signal¶

Alarm Features¶

Alpha-Synuclein¶

Alzheimer's Disease¶

Aminosalicylate¶

Amyloid Beta¶

Animal Model¶

Anterior Cingulate Cortex¶

Anti-TNF Therapy¶

Antibiotic Disruption¶

Anxiety Disorder¶

Appendix and Parkinson's¶

Attention-Deficit/Hyperactivity Disorder (ADHD)¶

Autism¶

Autonomic Nervous System¶

B¶

Bacteria-to-Human Cell Ratio¶

Bacterial Strain¶

Balloon Distension Test¶

Behavior Change¶

Benefit-Risk Balance¶

Bidirectional Relationship¶

Bifidobacterium¶

Bioelectronic Medicine¶

Biologic Therapy¶

Birth Mode and Microbes¶

Blood-Brain Barrier¶

Blood-Brain Barrier Permeability¶

Braak Hypothesis¶

Brain-First Subtype¶

Brain-Gut Psychotherapy¶

Brainstem¶

Butyrate¶

C¶

C. difficile Infection¶

Caregiver Role¶

Celiac Disease¶

Central Nervous System¶

Central Sensitization¶

Cholecystokinin¶

Chronic Stress¶

Circadian Rhythm¶

Circumventricular Organ¶

Claim-Checking Method¶

Clinical Trial Phases¶

Cognitive Behavioral Therapy¶

Cohort Study¶

Colonization Resistance¶

Colonocyte¶

Colonoscopy¶

Colony-Forming Unit¶

Commensal Bacteria¶

Conflict of Interest¶

Confounding Variable¶

Constipation¶

Consumer Wellness Device¶

Correlation vs Causation¶

Corticosteroid¶

Corticotropin-Releasing Hormone¶

Cortisol¶

Cranial Nerve¶

Crisis Resources¶

Crohn's Disease¶

Cytokine¶

D¶

Defining a Healthy Microbiome¶

Descending Pain Modulation¶