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Gut microbiome · your second genome
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In one pass Some of what you swallow is not yours to digest.
Educational content, not medical advice — consult a clinician.
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Chapter 1
What gut bacteria do for you
Some of what you swallow is not yours to digest.
Your large intestine is home to tens of trillions of microbes, weighing about 200-500 g together, roughly a small bag of rice. They form a whole working ecosystem, and their most important job is digesting the fiber you cannot break down yourself. Fiber slides through the small intestine to the colon, where the microbes ferment it into short-chain fatty acids. One of them, butyrate, is eaten directly by the cells of the colon wall: well-fed wall cells pack tightly together, and the barrier holds.
The microbes also give your immune system daily practice, and some of their products travel along the vagus nerve and through the blood to reach the brain, a route called the gut-brain axis. So building a healthy microbiome comes from feeding it fiber and many kinds of plants, not from a single supplement.
If you have bloody or black stools, or weight loss you cannot explain, see a doctor now; do not treat it as a microbiome that needs work.
Your large intestine is home to tens of trillions of microbes, weighing about 200-500 g together, roughly a small bag of rice. They form a whole working ecosystem, and their most important job is digesting the fiber you cannot break down yourself. Fiber slides through the small intestine to the colon, where the microbes ferment it into short-chain fatty acids. One of them, butyrate, is eaten directly by the cells of the colon wall: well-fed wall cells pack tightly together, and the barrier holds.
The microbes also give your immune system daily practice, and some of their products travel along the vagus nerve and through the blood to reach the brain, a route called the gut-brain axis. So building a healthy microbiome comes from feeding it fiber and many kinds of plants, not from a single supplement.
If you have bloody or black stools, or weight loss you cannot explain, see a doctor now; do not treat it as a microbiome that needs work.
Mechanism · What gut microbes make for you
If you remember only one thing the microbiome makes, make it short-chain fatty acids (, a group of small fatty acids that bacteria produce when they ferment fiber), and above all butyrate. Understanding them explains, almost in one go, why fiber matters, and why the microbiome is linked to both inflammation and metabolism.The human body lacks enzymes to digest most fiber. That fiber reaches the colon, the microbes ferment it, and three main short-chain fatty acids come out: acetate, propionate, and butyrate (Koh 2016 review). They are not waste but signaling molecules and fuel the body can use:
Butyrate is the preferred fuel of the cells lining the colon, feeding the gut wall directly. A well-fed, sturdy wall keeps the barrier intact, so fragments of bacterial outer walls (the endotoxin LPS) cannot easily seep into the blood. This is the starting point of the metabolic endotoxemia hypothesis of chronic low-grade inflammation.Propionate mostly goes to the liver, where it helps regulate sugar and fat metabolism.Acetate enters the general circulation and affects appetite and metabolism elsewhere in the body.Short-chain fatty acids also prompt L cells in the gut to release two fullness hormones, and PYY, which affect appetite and insulin sensitivity. This link connects eating more fiber with blood sugar and weight management.
So fiber is good for the gut is not an empty phrase. Its physical path is: fiber, then fermentation by the microbes, then butyrate and other short-chain fatty acids, which feed the gut wall, keep the barrier intact, and help regulate immunity and metabolism. Conversely, when fiber is almost absent for a long time, the microbes go hungry (the consequences are on the harms page of the chapter Diet · you feed what grows).
The microbes do a few other jobs on the side. They can make some B vitamins (including some B12, , and folate), with one discount: most B12 is made in the colon, downstream of the ileum where it is absorbed, so people get little use from it. A commonly quoted estimate is that about 70% of immune cells sit around the gut and deal with these microbes every day, and part of the immune system's sense of proportion is trained this way. A healthy microbiome fills the available niches and so helps keep disease-causing bacteria out.
This also explains why fermented foods and high-fiber foods have different value. High fiber sends raw material to your own microbes so they make short-chain fatty acids; fermented foods bring live microbes directly, plus beneficial substances those microbes have already made (postbiotics). The two paths run in parallel and do not replace each other.
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Numbers · how large this ecology is, and how personal
A healthy adult gut holds about 500-1000 species of microbes, 95% of them packed into the colon. By count, according to the newer estimate in Sender 2016, the body has about 30 trillion human cells, and its bacteria are of the same order of magnitude. The old line that there are 100 trillion bacteria, several times the number of human cells was too high.The real surprise is the number of genes: together these microbes carry 100-150 times as many genes as you do (Valdes 2018 review), which is why some people call them your second genome.
The microbiome is also more personal than your genes. Any two people's microbiomes are less than 50% alike, while human genomes are more than 99% identical. So a method that worked for someone else's microbes will not necessarily work for yours.
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Evidence · What counts as a healthy microbiome
What counts as a healthy microbiome? The key is not whether some star species is present but whether the community is diverse enough.The richer the species, the more stable it tends to be: healthy people have more diversity than people with chronic disease, who in turn have more than people who have just finished a course of antibiotics. Low diversity is associated with inflammatory bowel disease, diabetes, cardiovascular disease, and even depression, but most of these findings come from observational studies, and which comes first, and which causes which, has not been worked out. A person whose microbiome still looks like itself after a stretch of time (stability) is also in good shape.
Akkermansia and the butyrate producer Faecalibacterium, which are often singled out as beneficial, do track with quite a few diseases when their numbers are low. But sorting microbes into good and bad is an oversimplification: the same species can help or harm in a different host or a different environment. It is an ecosystem, not a list of friends and enemies. What matters is always the overall balance and diversity.
Background · How the microbiome changes over a lifetime
This ecosystem keeps changing throughout life.The way you are born opens the story: a baby born vaginally picks up microbes from the mother's birth canal, while a baby born by C-section first picks up skin microbes (which is loosely linked to a slightly higher risk of allergy and autoimmune disease). From ages 0-3, breast milk and first foods spread diversity out. In adulthood the microbiome is relatively stable, unless antibiotics, a major illness, or a move to a completely new environment intervene. In old age, diversity slowly slides again, and that is associated with frailty, dementia, and risk of death.
Chapter 2
Diet · you feed what grows
What you eat decides which microbes you feed, and which microbes you feed decides which ones grow (Sonnenburg 2014 review).
The microbes do not want expensive food. They want the kind of carbohydrate you cannot digest yourself, the kind that slips past absorption in the small intestine and arrives intact in the colon to become their meal. Its technical name is microbiota-accessible carbohydrate (MAC).
So when you ask whether something feeds your microbes, the question is not how nutritious it is. The question is: does it reach the colon intact? What is left after you chew it, after stomach acid soaks it, and after the small intestine's enzymes take it apart is the microbes' food. Sugars and starches that you absorb completely in the small intestine never reach them at all.
When the microbes get food, they ferment it; fermentation makes short-chain fatty acids; and those fatty acids feed your gut wall in return. That is the real physical path beneath the phrase fiber is good for the gut.
The microbes do not want expensive food. They want the kind of carbohydrate you cannot digest yourself, the kind that slips past absorption in the small intestine and arrives intact in the colon to become their meal. Its technical name is microbiota-accessible carbohydrate (MAC).
So when you ask whether something feeds your microbes, the question is not how nutritious it is. The question is: does it reach the colon intact? What is left after you chew it, after stomach acid soaks it, and after the small intestine's enzymes take it apart is the microbes' food. Sugars and starches that you absorb completely in the small intestine never reach them at all.
When the microbes get food, they ferment it; fermentation makes short-chain fatty acids; and those fatty acids feed your gut wall in return. That is the real physical path beneath the phrase fiber is good for the gut.
In practice · Which foods actually feed the microbes
Insoluble fiber: whole grains, vegetable skins, nuts, and seeds. Soluble fiber: oat beta-glucan, apple pectin, and legumes. Resistant starch (starch that escapes digestion in the small intestine): cooled rice and potatoes, green bananas, and legumes. These slip past absorption in the small intestine and go straight to the colon.Add the polyphenols in berries, green tea, dark chocolate, and olive oil; the microbes remake some of them into more usable forms.
Fermented foods (yogurt, kefir, kimchi, sauerkraut, kombucha, natto) take a different road. They do not deliver raw material; they deliver live microbes directly, plus beneficial substances those microbes have already made (postbiotics).
Myth · Some fiber never feeds the microbes
Two points are especially easy to confuse, and each is worth pulling out.The first is wheat bran. It is fiber, but it is neither viscous nor easily fermented, and the microbes barely touch it (McRorie 2017). It eases constipation by adding bulk to stool in a purely physical way, not by feeding anyone.
The second is psyllium husk. It is soluble and intensely viscous, yet almost unfermented: its gel travels intact to the rectum and works as a lubricant (Marlett 2000). It works precisely because the microbes cannot eat it, which is also why it does not cause bloating the way inulin does.
So to judge what a fiber actually does, do not look at whether it is soluble or insoluble. Look at viscosity and fermentability, two independent axes (McRorie 2017). For how to use the two axes to read different fibers, see Carbs & Fiber.
Evidence · Where the fermented-food arm won
What exactly does fermented food do better than adding fiber alone? In 2021, Stanford's Sonnenburg team ran a randomized trial: 36 healthy adults in two groups, each eating its assigned diet for 10 weeks.In the high-fiber-only group, average diversity barely moved, and the inflammatory response split into 3 different patterns depending on what each person's microbiome looked like at the start. In the group that ate 6 servings of fermented food a day, diversity went up and 19 inflammatory proteins came down (that is a secondary analysis in the fermented-food group; the trial's pre-set primary outcome, a cytokine response score, did not change clearly in either group).
It suggests that fermented food may act more directly than simply piling on fiber. But this was a small trial of only 36 people over 10 weeks, measuring the microbiome and inflammatory markers in the blood rather than disease outcomes, and it needs larger trials to reproduce it.
Safety · What damages the microbiome
Emulsifiers in ultra-processed foods (carboxymethyl cellulose, polysorbate) damage the microbiome and the mucus layer; the evidence for this comes mainly from animal experiments. Artificial sweeteners such as sucralose and saccharin worsened glucose tolerance in mouse experiments and in a small number of volunteers, and only in some of them, with very large differences between individuals (Suez 2014). Antibiotics make the microbiome collapse in the short term; it mostly recovers afterward, but not completely, and antibiotic use in early childhood is also associated with a higher later risk of obesity and autoimmune disease.The easiest harm to miss is starving it. When fiber is almost absent for a long time (a typical Western diet), the hungry microbes turn to eating the gut's mucus layer, and the barrier is weakened (this link has been seen mainly in mice). That is not merely a lack of benefit; it may be actively harmful.
Heavy drinking, long-term stress, too little sleep, and sitting too much are also each associated with lower diversity.
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Evidence · Where the 30 plants a week comes from
Eat 30 different plants a week is a widely quoted rule that comes from the American Gut project (McDonald 2018). That project is a large data set in which members of the public volunteered stool samples and reported their own diets: people who ate more than 30 kinds of plants a week had clearly higher microbiome diversity than people who ate fewer than 10.How to count: fruit, vegetables, whole grains, legumes, nuts, seeds, spices, and tea all count. The trick may lie in the number of kinds, not in how much of each; a handful of mixed nuts or a serving of mixed beans already covers several.
Know its limits: these are cross-sectional data from volunteers who reported their own diets, so they show an association. People who eat a wide variety often differ in other habits too; 30 is a memorable cut-off, not a dose tested in a trial.
Myth · Colon cleanses and detox
Claims about toxins building up in stagnant stool have no medical basis.Enemas and heavy use of laxatives do empty the gut in the short term, but over the long term they damage the microbiome and disturb the body's electrolytes. A healthy liver, kidneys, and microbiome are already metabolizing and clearing waste for you all the time.
There is only one situation that truly calls for emptying the gut: before a colonoscopy, under a doctor's direction. It is not a daily wellness routine.
Chapter 3
Imbalance and which claims hold up
Gut microbiome is one of the scientific terms that marketing has borrowed most heavily in recent years. At one end is solid science; at the other are inflated or invented claims about leaky gut, detox, gut testing, and custom supplements. This chapter draws the line between them.
First, what is real. Dysbiosis is not having picked up some bad bugs; it is the whole ecosystem being out of balance: diversity falls, beneficial butyrate producers become fewer, and opportunistic microbes gain the upper hand. The drivers include a lot of ultra-processed food, too little fiber, overuse of antibiotics, chronic stress, and too little sleep.
One widely discussed chain goes like this: with fewer butyrate producers, the cells of the colon wall get less food; the wall thins and the cells loosen, fragments of bacterial outer walls (the endotoxin LPS) seep into the blood, and the immune system stays slightly switched on for a long time. That is low-grade inflammation. It lines up with inflammatory bowel disease, metabolic syndrome, and some mood problems.
But lining up with is not causing: the evidence for this chain comes mainly from animal experiments and observational studies, and many studies can only say that a microbiome pattern and a disease appear together, not that one causes the other.
First, what is real. Dysbiosis is not having picked up some bad bugs; it is the whole ecosystem being out of balance: diversity falls, beneficial butyrate producers become fewer, and opportunistic microbes gain the upper hand. The drivers include a lot of ultra-processed food, too little fiber, overuse of antibiotics, chronic stress, and too little sleep.
One widely discussed chain goes like this: with fewer butyrate producers, the cells of the colon wall get less food; the wall thins and the cells loosen, fragments of bacterial outer walls (the endotoxin LPS) seep into the blood, and the immune system stays slightly switched on for a long time. That is low-grade inflammation. It lines up with inflammatory bowel disease, metabolic syndrome, and some mood problems.
But lining up with is not causing: the evidence for this chain comes mainly from animal experiments and observational studies, and many studies can only say that a microbiome pattern and a disease appear together, not that one causes the other.
Mechanism · How much of the gut-brain axis is real
The gut and the brain talk in both directions, along three lines at once: the vagus nerve, immune signals, and microbial products (short-chain fatty acids and substances made from tryptophan) (Cryan 2019 review).The most quoted line is that about 90% of serotonin is made in the gut. That is true, but this serotonin mainly runs the gut's own movements; it does not travel straight to the brain to run your mood. Marketing often twists this point.
In animal experiments, swapping the microbiome can change behavior, and that is a real signal. But taking a particular probiotic treats depression still has weak evidence in people and cannot replace psychiatric care.
A fair reading: looking after the microbiome over the long term (fiber, many kinds of plants, fermented food, sleep) may give mood a mild, indirect lift. It is not a happiness bug. For how the axis itself works, The Gut-Brain Axis goes into more detail.
Myth · Four claims that are oversold or made up
Leaky gut syndrome: increased permeability of the gut barrier is a real physiological phenomenon (the endotoxin leak described above). But packaging it as a diagnosis that explains every chronic disease and can be repaired by buying supplements is a step no evidence supports. Mainstream medicine does not treat it as a stand-alone diagnosis.Detox and clearing stagnant stool: the idea of toxins building up in stagnant stool has no medical basis. Enemas and heavy use of laxatives end up damaging the microbiome and the body's electrolyte balance over the long term (in more detail in the chapter Diet · you feed what grows).
An alkaline diet changes gut pH to detox you: food barely changes the pH of the blood, and the body tightly controls the pH of each section of the gut. This claim does not hold.
Gut test, then custom probiotics: commercial microbiome tests (stool sequencing) can still tell a clinician very little, and the customized supplements sold on the back of them are mostly marketing. Do not make drastic decisions based on them.
In practice · How to spot a claim that goes too far
The gut microbiome is real science, but precisely because it is complex and sounds a little mysterious, it is especially easy to borrow for selling things.The test is simple: anything that says the microbiome can repair everything, flush out toxins, or deliver a customized effect has basically crossed the edge of the evidence.
What actually helps is still the plain list: many kinds of plants, fiber, fermented food, good sleep, and time.
Chapter 4
Probiotics and fecal transplants
Probiotics and fermented foods are not the same thing.
By the definition of the International Scientific Association for Probiotics and Prebiotics (ISAPP) (Hill 2014), a probiotic is a live microorganism that, when given in adequate amounts, benefits the host. Three words in that sentence carry weight: the dose must be enough, the strain must be specific, and the evidence must exist. The benefit follows the specific strain and dose; it is not a property of every fermented food. Few probiotic products on the shelf meet all three at once.
So when you judge whether a probiotic is worth buying, do not look at what it claims to fix. Look at whether it shows the strain number, the daily count of live microbes, and the matching study together. The uses with real evidence behind them make a short list.
By the definition of the International Scientific Association for Probiotics and Prebiotics (ISAPP) (Hill 2014), a probiotic is a live microorganism that, when given in adequate amounts, benefits the host. Three words in that sentence carry weight: the dose must be enough, the strain must be specific, and the evidence must exist. The benefit follows the specific strain and dose; it is not a property of every fermented food. Few probiotic products on the shelf meet all three at once.
So when you judge whether a probiotic is worth buying, do not look at what it claims to fix. Look at whether it shows the strain number, the daily count of live microbes, and the matching study together. The uses with real evidence behind them make a short list.
Evidence · which uses are actually supported, which are not
Uses with evidence behind them (ordered by how much evidence there is):Preventing antibiotic-associated diarrhea (diarrhea that starts while taking antibiotics): the best-supported use. Multiple randomized trials support multi-strain combinations (Lactobacillus, Bifidobacterium, and the yeast Saccharomyces boulardii), and the effect varies by strain and population.Preventing C. difficile infection while taking antibiotics: the American Gastroenterological Association (AGA) 2020 guideline gives a conditional suggestion (a weak recommendation) for some specific strains.Some symptoms of irritable bowel syndrome (): some specific strains show signals of improvement in trials, with large individual differences. But AGA 2020 makes no recommendation for IBS and advises using probiotics only within clinical trials.
Uses or claims where the evidence does not hold up or is weak:
Acute infectious diarrhea in children (for example, rotavirus): this was once treated as strong evidence and no longer stands. When the Cochrane 2020 review pooled the trials, the for the difference in diarrhea duration crossed zero, and the certainty of the evidence was very low; AGA 2020 suggests against probiotics for children with acute infectious gastroenteritis. Probiotics takes this apart in more detail.A short course after antibiotics, and travelers' diarrhea: the first is a common practice you can discuss with a doctor; the second has no strong evidence.General wellness and everyday immune boosting: no strong evidence in healthy people.Clearer skin or anti-aging: only early data.Weight loss and metabolic syndrome: limited evidence, with signals for only some strains.Depression and anxiety (so-called psychobiotics): early data, and no substitute for psychiatric care.
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In practice · How to pick a probiotic or a yogurt
What to look for in a probiotic:The specific strain name (for example, Lactobacillus rhamnosus GG or Bifidobacterium lactis BB-12, names that include a strain code), not just a generic lactic acid bacteria.Live count (CFU, colony-forming units): the usual range is 1-10 × 10⁹ CFU a day, and more is not necessarily better.Cold storage, unless the label says it can be kept at room temperature.Past the expiry date, most of the microbes are dead.Healthy people have no need to take the same product long term.
Is yogurt a probiotic?
Not necessarily. Yogurt that is heat-treated after fermentation (commonly the kind sold for room-temperature storage) contains dead microbes.A truly live yogurt says on the label that it contains live cultures, is kept in the cold chain, and ideally states the live count.Kefir and genuinely fermented kimchi and sauerkraut usually carry more live microbes, of more kinds.
Prebiotics:
They are food for microbes, not microbes themselves.Common ones include inulin, fructo-oligosaccharides (FOS), galacto-oligosaccharides (GOS), and resistant starch.Natural sources are plentiful: garlic, onion, leek, asparagus, banana, oats, and legumes.A probiotic combined with a prebiotic is called a synbiotic: there is more marketing than evidence so far.
Clinical · Where fecal transplants are used
Fecal microbiota transplant (FMT):It moves the whole microbial community from a healthy donor's stool into a patient's colon. What moves is an entire community, not one or two species, which makes it a different thing from taking a bottle of probiotics.The best-supported use: recurrent C. difficile infection, supported by randomized trials, with clearance rates of 80–90%.Still under study: inducing remission in inflammatory bowel disease, metabolic syndrome, autism, and depression, with mixed results.Do not do it yourself: donors must be screened for disease-causing bacteria and parasites, and it should be done at a proper medical institution.
When to see a doctor or dietitian:
Bloating, diarrhea, or constipation that lasts ≥ 4 weeks, plus weight loss or bloody stool: see a doctor immediately.Symptoms that have not settled > 8 weeks after a course of antibiotics: get the microbiome's recovery assessed.A chronic condition and a wish to improve your microbiome: a dietitian can guide an individualized diet (for example, low-, Mediterranean, or DASH).Microbiome testing services: commercial tests (uBiome, Viome, and others) have limited clinical value; do not make drastic decisions based on them.
Chapter 5
How to build a healthy microbiome
Building a healthy microbiome is plain work, and it does not have to cost much. The most effective move has never been buying probiotics; it is feeding the right food, then giving it time.
First priority · variety of plants. Aim for ≥ 30 different plant foods a week (fruit, vegetables, whole grains, legumes, nuts, seeds, spices, and tea all count). In the large American Gut data set, people who ate > 30 kinds had clearly higher microbiome diversity than people who ate < 10 (McDonald 2018; this is an observed association). You do not need much of each: a handful of mixed nuts or a serving of mixed beans covers several.
Second priority · fiber and fermented food, side by side. Fiber (especially resistant starch: cooled rice, cooled potatoes, legumes, green bananas) delivers raw material to your own microbes so they make short-chain fatty acids. Fermented food (genuinely live yogurt, kefir, real kimchi, natto) delivers live microbes directly, along with substances they have already made. The two paths run in parallel and do not replace each other.
First priority · variety of plants. Aim for ≥ 30 different plant foods a week (fruit, vegetables, whole grains, legumes, nuts, seeds, spices, and tea all count). In the large American Gut data set, people who ate > 30 kinds had clearly higher microbiome diversity than people who ate < 10 (McDonald 2018; this is an observed association). You do not need much of each: a handful of mixed nuts or a serving of mixed beans covers several.
Second priority · fiber and fermented food, side by side. Fiber (especially resistant starch: cooled rice, cooled potatoes, legumes, green bananas) delivers raw material to your own microbes so they make short-chain fatty acids. Fermented food (genuinely live yogurt, kefir, real kimchi, natto) delivers live microbes directly, along with substances they have already made. The two paths run in parallel and do not replace each other.
In practice · Add fiber slowly, avoid what harms it
Someone who has eaten little fiber for years and suddenly eats a lot of it mostly gets gas and diarrhea, something like an irritable bowel syndrome () flare. The steady way is to add only 5-10 g a week and give the microbes 4-6 weeks to adapt. Low-fermentation fiber (wheat bran, psyllium) produces almost no gas, so it is the easiest to add; high-fermentation fiber (inulin, fructo-oligosaccharides) is where the bloating comes from, so add it a little at a time.The other half is doing fewer things that harm it: use antibiotics only when truly needed (antibiotics for a viral cold do nothing for the cold and harm the microbiome); eat less ultra-processed food (in animal experiments its emulsifiers damage the mucus layer); and drink fewer artificial sweeteners (glucose tolerance may worsen in some people).
Enough sleep, regular exercise, and managing stress are also associated with microbiome diversity. They are not extras on top; they are the other half, alongside food.
In practice · Where probiotics and low-FODMAP fit
Probiotics are a tool, not a daily supplement. In the settings with evidence, antibiotic-associated diarrhea and specific symptoms of irritable bowel syndrome (), they can be used short term. For everyday immune boosting in healthy people there is no strong evidence, so there is no need to take them long term. If you do take one, check the specific strain, the live count, and cold-chain storage (see the chapter Probiotics and fecal transplants).If bloating, diarrhea, or constipation keeps coming back and already affects your life, do not tinker on your own; see a gastroenterologist or a dietitian.
The low- diet (temporarily cutting a group of short-chain carbohydrates that are easily fermented in the gut and produce gas) is a structured, diagnostic diet. It should be done short term under a dietitian's guidance, with foods then reintroduced systematically one at a time, not followed strictly for the long term, because long-term strict use may end up starving the microbiome. Irritable Bowel Syndrome covers it in detail.
Red flag · When to stop adjusting on your own
Red flags — see a doctor now; do not treat these as a microbiome that needs building up:Bloating, diarrhea, or constipation that lasts ≥ 4 weeks, plus weight loss, bloody stool, or black stoolA sudden change in bowel habits (especially over age 45)These may signal an organic disease and need to be checked promptly.
The gut microbiome is an ecosystem inside you that diet can change quickly and that stays with you for life. Building it up does not depend on a miracle pill or a superfood; it depends on the plainest things: many kinds of plants, enough fiber, a little fermented food, less ultra-processed food, good sleep, and time. Once you understand the mechanism of short-chain fatty acids feeding the gut wall, you know why these habits work, and you are harder to carry off with talk of detox and custom microbes.
To keep reading: for how the digestive tract itself works, see Digestive System; for specific digestive problems, see Irritable Bowel Syndrome and ; for how the microbiome relates to inflammation, see Chronic low-grade inflammation; for what the microbes eat, see Carbs & Fiber and Fruit & vegetables; for what harms them, see Ultra-processed Foods and Artificial & Non-nutritive Sweeteners; for probiotic supplements themselves, see Probiotics.
References · 8
- Valdes, A. M., Walter, J., Segal, E., & Spector, T. D. (2018). Role of the gut microbiota in nutrition and health. BMJ, 361, k2179. 10.1136/bmj.k2179
- McDonald, D., Hyde, E., Debelius, J. W., Morton, J. T., Gonzalez, A., Ackermann, G., et al. (2018). American Gut: an open platform for citizen science microbiome research. mSystems, 3(3), e00031-18. Citizen-science cohort of more than 10,000 participants (mainly US, UK, Australia), samples mailed at room temperature. Reports that the number of distinct plant types eaten related to microbiome and metabolome features, while categorical labels such as veganism had little explanatory power. The abstract gives no count of plants per week (abstract, PMID 29795809). 10.1128/mSystems.00031-18
- Sonnenburg, E. D., & Sonnenburg, J. L. (2014). Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metabolism, 20(5), 779-786. 10.1016/j.cmet.2014.07.003
- McRorie, J. W., & McKeown, N. M. (2017). Understanding the physics of functional fibers in the gastrointestinal tract: an evidence-based approach to resolving enduring misconceptions about insoluble and soluble fiber. Journal of the Academy of Nutrition and Dietetics, 117(2), 251-264. 10.1016/j.jand.2016.09.021
- Marlett, J. A., Kajs, T. M., & Fischer, M. H. (2000). An unfermented gel component of psyllium seed husk promotes laxation as a lubricant in humans. The American Journal of Clinical Nutrition, 72(3), 784-789. 10.1093/ajcn/72.3.784
- Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., et al. (2019). The microbiota-gut-brain axis. Physiological Reviews, 99(4), 1877-2013. 10.1152/physrev.00018.2018
- Hill, C., Guarner, F., Reid, G., et al. (2014). The ISAPP consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology, 11, 506-514. A probiotic benefit is strain- and dose-specific, not a property of all fermented foods. 10.1038/nrgastro.2014.66
- Wastyk, H. C., Fragiadakis, G. K., Perelman, D., Dahan, D., Merrill, B. D., Yu, F. B., Topf, M., Gonzalez, C. G., Van Treuren, W., Han, S., Robinson, J. L., Elias, J. E., Sonnenburg, E. D., Gardner, C. D., & Sonnenburg, J. L. (2021). Gut-microbiota-targeted diets modulate human immune status. Cell, 184(16), 4137–4153.e14. 10-week diet intervention within a 17-week protocol: generally healthy adults randomized to a high-fiber or a high-fermented-food diet (n = 18 per arm per the summary; 39 assigned in all). The primary outcome, the cytokine response score, did not change significantly in either arm. The fermented-food arm rose from 0.4 to 6.3 ± 2.9 servings/day and showed increased microbiota diversity and decreased inflammatory markers; the high-fiber arm increased glycan-degrading CAZymes while community diversity stayed stable (full text, PMC9020749). 10.1016/j.cell.2021.06.019