Nutrition Research
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Macronutrients
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Dietary Factors
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Food, Beverages,
and Supplements
Summary
The gut microbiota refers to the trillions of microbes — bacteria, yeast, archaea and viruses — that live inside the gastrointestinal tract, mostly in the colon. We provide a habitat for them; in return, they provide us with helpful compounds and functions.
Most research to date has focused on bacterial members of our fecal microbiota (see below). Our dietary choices directly impact the abundance of particular bacterial species and the compounds they produce. A diet rich in a variety of plant foods (fruit, vegetables, grains, beans, nuts, and seeds) will provide many substrates (soluble fiber, glycans, and phytochemicals) that escape digestion in the small intestine, make it to the colon, and cultivate the growth of beneficial bacteria. The daily inclusion of foods with live, active cultures (primarily from fermented foods) appears to benefit health, though the specific contribution of live microbes cannot be precisely determined.
Probiotics, prebiotics, and postbiotics are a family of constituents that are often found — although not exclusively — in foods or dietary supplements. They have been shown to promote health, in part through their interaction with the gut microbiota. Typically, when administered orally, the benefits from these substances are realized while ingested and shortly thereafter, though responses are highly individualized.
DEFINITIONS
Biota - a Greek root meaning ‘all life’
Microbiota - the collection of microorganisms that live on and within and individual
Gut microbiota - the collection of microorganisms that live in the gastrointestinal tract, mostly in the colon
Microbiome - all of the genes that comprise one’s microbiota
Microbe - a microscopic organism, such as bacteria, viruses, and fungi
Probiotic - live microorganisms that, when administered in adequate amounts, confer a health benefit on the host
Prebiotic - a substrate that is selectively utilized by host microorganisms conferring a health benefit
Postbiotic - a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host
Overview
The microorganisms that live in our digestive tract play a prominent role in health and well-being. Although they can be found throughout the digestive tract, the vast majority reside in our colon. The collection of microorganisms that inhabit the gastrointestinal tract (the gut) is referred to as the gut microbiota.
Some major functions of the gut microbiota are:
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Protection against pathogens and pathobionts. Pathogens are disease-causing organisms. Pathobionts are bacteria that can become harmful under certain conditions. Commensal bacteria in the gut employ several strategies to keep the numbers of disease-causing bacteria in check:
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limitation of space and nutrients
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production of antimicrobial substances
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changing pH and oxygen levels
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supporting the colonic mucus layer
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induction of the host immune response
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Production of beneficial compounds. As gut bacteria process substrates that reach the colon, they produce a variety of small molecules and metabolites. These compounds exert their influence inside the colon and in other parts of the body, since they can be absorbed into the blood and lymph and travel to other organs and tissues. Some examples of bacterial-produced compounds include
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vitamin K and several B vitamins
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fermentation products, such as short-chain fatty acids
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signaling molecules, such as hormones, peptides, and neurotransmitters
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gases
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antimicrobial compounds, such as bacteriocins
What we eat influences the abundance of specific bacterial species and what they produce. When thinking about our food choices, then, it is not only about energy and nutrients for our body but also about what is cultivating our gut microbiota.
DEFINITIONS
Pathogen - an organism that causes disease
Pathobionts - symbiotic bacteria that become pathogenic under certain conditions
Commensals - microbes living in a symbiotic (mutually beneficial) relationship with the host
Metabolites - small molecules produced as intermediates or end products of metabolism
HIGHLIGHT: FECAL SAMPLE ANALYSIS
Research on the gut microbiota has focused mainly on the analysis of fecal samples.
Notably, anatomy, ecology, and physiology differ along the length of the gastrointestinal tract, especially between the small and large intestines. For example, oxygen concentration, pH, redox potential, mucus thickness, tight junction permeability, and transit speed vary between these locations; all of these factors influence gut microbiota composition and function. Therefore, microbiota analysis from fecal samples alone has some limitations — it largely represents the luminal content of the large intestine and might under-represent the mucosal microbiota as well as other more proximal sites throughout the gut.
REFERENCES:
Jensen BAH, Heyndrickx M, Jonkers D, et.al. Small intestine vs. colon ecology and physiology: Why it matters in probiotic administration. Cell Rep Med. 2023;4(9):101190.
Zmora N, Suez J, Elinav E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol. 2019;16(1):35-56.
Nutrition Research
DEFINITIONS
Soluble fiber - fiber that dissolves in water
Fermentation - the anaerobic breakdown of organic substrates, resulting in the formation of smaller components and the energy molecule, adenosine triphosphate (ATP)
Anaerobic - in the absence of oxygen
Resistant starch - a type of carbohydrate that is sequestered in plant cell walls and therefore inaccessible to human digestive enzymes
Synbiotic - a mixture comprising live microorganisms and substrate(s) selectively utilized by the host microorganisms that confers a health benefit on the host
Antibiotic - a medication that kills microbes
Dietary Fiber
What it is
General
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Fiber is a diverse class of complex carbohydrates that cannot be digested by human enzymes in the small intestine.
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Dietary fibers can be classified according to their physical and chemical properties: soluble, insoluble, viscous, and fermentable.
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Dietary fibers are found in a wide-range of plant-based foods, such as legumes, vegetables, nuts, seeds, fruits, and whole grains.
Microbiota-specific
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Fermentation of fiber and resistant starch is one function of the gut microbiota.
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sources of fermentable fiber: whole grains (wheat, oats, barley), nuts, seeds, legumes (beans, peas, and lentils), fruit (apples), and vegetables (avocados, onions, garlic)
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sources of resistant starch: green bananas and legumes (beans, peas, and lentils)
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Bacterial fermentation of soluble fiber yields short-chain fatty acids (SCFAs). SCFAs mediate numerous beneficial effects inside the colon and in other parts of the body.
What we know
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Certain bacteria have the ability to break down different dietary fibers and produce different metabolites.
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Microbial fermentation of fiber yields short-chain fatty acids (SCFAs).
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The most studied SCFAs are butyrate, acetate, and propionate, but many other SCFAs are produced by the gut microbiota.
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Butyrate has a main role in nourishing colonic cells and creating an environment that helps beneficial bacterial thrive.
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A myriad of cellular effects have been observed for SCFAs:
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Acetate can be converted into butyrate and used inside the colon.
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Acetate and propionate are absorbed into the bloodstream and incorporated into glucose or lipid metabolic pathways.
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Various SCFAs interact with cellular receptors in a wide range of body tissues, influencing insulin secretion, appetite, intestinal transit, and blood pressure.
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When fermentable dietary fiber is limited, bacteria can turn to alternative substrates from the diet or host glycans present in the colonic mucus layer. This may result in the production of harmful metabolites or degradation of the protective mucus layer.
For references and more information, see the articles on Fiber and Gut Health In Depth.
Glycans
What they are
General
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Glycans are a type of complex carbohydrate consisting of a large number of simple sugars linked by β-glycosidic bonds. Humans lack the enzymes required to break apart this type of bond; thus, glycans resist digestion in the small intestine.
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Glycans have a different structural composition than most known fibers.
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Glycans come from many sources:
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plants: cell walls and intracellular compartments
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animals: tissue and cartilage
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endogenous sources: colonic mucus and breast milk
Microbiota-specific
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Individual bacteria prefer different glycans. Some gut bacteria are ‘generalists’ and can degrade dozens of different types of glycans; others are ‘specialists’ and can degrade only one or a few different glycans.
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Endogenous glycans present in the colonic mucus layer are an important source of energy for the gut microbiota. Genetic factors (e.g., the chemical composition of mucin) and bacterial composition of the gut microbiota can influence the interaction between microbes and the mucus layer.
What we know
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Human milk oligosaccharides (HMOs) are a family of diverse and complex glycans that are abundant in human breast milk.
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HMOs and endogenous glycans shape the development of the infant’s gut microbiota, selecting for pioneer bacterial species (such as species of Bifidobacterium) that pave the way for successive colonization events.
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The addition of HMOs to infant formulas helps support bacteria, like Bifidobacterium, which are typically in greater abundance in breastfed infants than in infants receiving infant formula.
For references and more information, see the article on Gut Health In Depth.
Phytochemicals
What they are
General
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Phytochemicals are a large, diverse group of chemical compounds from plants that may exert a health benefit.
Microbiota-specific
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Many phytochemicals escape digestion in the small intestine, reach the colon and can be modified by gut microbes.
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Phytochemicals may influence gut health through:
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The generation of metabolites that interact with cellular receptors in the colon and possibly in other parts of the body.
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Influencing the abundance of certain bacterial species through prebiotic or antimicrobial effects.
What we know
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One class of phytochemicals, polyphenols, is thought to exert several beneficial effects in the gut:
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The polyphenol class of phytochemicals includes flavonoids, phenolic acids, lignans, stilbenes, curcuminoids, coumarins, and tannins.
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Observations are based mainly from in vitro and animal studies. Polyphenols may benefit gut health by:
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selectively encouraging the growth of beneficial bacteria (i.e., having a prebiotic effect)
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exerting an antimicrobial effect specifically against pathogenic microbes
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interacting with cellular factors to reduce inflammation
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Large variation among individuals significantly influences the potential impact obtained from the consumption of different phytochemicals:
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Personal differences in gut microbiota composition
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Particular bacterial species possessing the enzymes necessary to metabolize the phytochemical must be present; the presence of these species can vary widely between individuals.
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Genetic variability in the CYP family of enzymes
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Inside intestinal, colonic, and liver cells, the CYP family of enzymes further transform phytochemicals into various breakdown products.
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Genetic variability can influence the efficiency of the CYP enzymatic reaction, from nonfunctional to increased functional capacity, further influencing the form and amount of phytochemical that reaches a target tissue.
For references and more information, see the articles on Phytochemicals and Gut Health In Depth.
Fermented Foods
What they are
General
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Fermented foods and beverages are foods made through desired microbial growth and enzymatic conversions of food components.
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Fermented foods are not the same as probiotics. They are a broad category of foods that may contain and deliver ‘biotic’ substances, including probiotics, prebiotics, synbiotics, and postbiotics.
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Examples of fermented foods with live microorganisms present: yogurt, sour cream, kefir, most cheeses, miso, natto, tempeh, most kombuchas, non-heated fermented vegetables (ex. kimchi, sauerkraut).
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Examples of fermented foods with live microorganisms absent: sourdough bread, heat-treated or pasteurized fermented vegetables, sausage, soy sauce, vinegar, and some kombuchas; wine, most beers and distilled spirits; coffee and chocolate beans (after roasting).
Microbiota-specific
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In addition to their nutritive function, fermented foods could benefit health through the modulation of the host immune system, the provision of bioactive compounds, or by modulating gut microbiota composition and activity.
What we know
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Higher dietary intake of foods containing live microbes (including fermented foods) is associated with modest health benefits.
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Identifying the specific component responsible for a health benefit is challenging. Fermented foods are a complex mixture. Macronutrients and micronutrients, the food matrix, and the possible presence of probiotics, prebiotics, and postbiotics may all contribute to the observed health benefit.
For references and more information, see the article on Gut Health In Depth.
Probiotics
What they are
General
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Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.
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Commonly available probiotic strains are lactobacilli and bifidobacteria.
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Probiotics are most commonly added to cultured dairy products (e.g., yogurt, kefir) or found as dietary supplements.
Microbiota-specific
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Specific bacterial strains have been identified that produce certain metabolites and beneficial functions.
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If individuals are lacking these strains or their associated functions (due to illness, medication use, or absence, for example), a probiotic may help fill a gap.
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Some ways by which probiotics may benefit health include
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an influence on resident gut microbes
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enhancement of intestinal barrier functions
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modulation of local and systemic immune responses
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modulation of systemic metabolic responses
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provision of enzymatic functions
What we know
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Benefits of probiotics are strain and dose dependent. Because of this strain specificity, products should be labeled with the genus, species, strain, and effective dose of any probiotic contained in the product.
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Because most probiotic strains studied to date stay in the colon only temporarily, regular consumption is necessary.
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Evidence from systematic reviews and meta-analyses of clinical trials supports the use of probiotics in several conditions, for example treating acute diarrhea, reducing the incidence of antibiotic-associated and C. difficile diarrhea, treating colic in breastfed infants, and managing symptoms of lactose intolerance, among others.
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Moderate scientific evidence exists for the use of probiotics along with antibiotic therapy to reduce the duration of antibiotic associated diarrhea in adults and children.
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The impact of a probiotic is highly individualized. Many variables influence the probiotic response, including host factors (such as health status, genetic background, and lifestyle factors) and the presence or absence of cooperative bacterial species that may work together.
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Safety in at-risk populations should be considered before adding a probiotic. At-risk populations include those with chronic diseases or critical illness, the immunocompromised, and preterm infants.
For references and more information, see the section on Probiotics in the article, Gut Health In Depth.
Prebiotics
What they are
General
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A prebiotic is a substrate that is selectively utilized by host microorganisms conferring a health benefit.
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Prebiotics are non-digestible substrates that promote the growth of specific beneficial bacteria.
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Typically, they are fermentable dietary fibers, but other types of compounds, such as polyphenols, polyunsaturated fatty acids (PUFAs), conjugated fatty acids, and other oligosaccharides are being investigated for their prebiotic potential.
Microbiota-specific
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A prebiotic may increase the abundance of specific beneficial bacteria.
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A prebiotic may influence metabolite production even when there is no change in bacterial composition.
What we know
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The influence of a prebiotic lasts only as long as it is consumed. Thus, continued consumption is necessary to sustain the prebiotic’s effect.
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Inulin, fructooligosaccharides (FOS), and galactooligosaccharides (GOS) are the most extensively studied prebiotics; in general, they increase the abundance of Bifidobacterium and Lactobacillus.
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These bacterial taxa are known to produce lactic and acetic acids, which reduce luminal pH and discourage pathogen growth.
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Both genera are also a source of commercialized probiotic strains.
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The response to a prebiotic is highly individualized.
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Host-specific factors (health status, genetic background) and the initial gut microbiota composition influence the impact of a prebiotic.
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Individuals may be classified as responders or non-responders depending on the presence of specific bacterial species that metabolize a given prebiotic.
For references and more information, see the section on Prebiotics in the article, Gut Health In Depth.
Postbiotics
What they are
General
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A postbiotic is a preparation of inanimate microorganisms and/or their components that confers a health benefit on the host.
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They must contain inactivated microbial cells or cell components, with or without metabolites, that contribute to their observed health benefits.
Microbiota-specific
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It is not only live, active cultures that exert beneficial health effects in the gut.
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Non-viable microbial cells and their components also reach the colon, and can act locally or travel to other parts of the body.
What we know
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Overall, postbiotics seem to mimic some of the beneficial effects of probiotics, while avoiding the risk of administering live microorganisms to at-risk populations.
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Physical interaction with host intestinal and immune cells seems an important mechanism of action.
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Research into the efficacy of these products is only just beginning.
For references and more information, see the section on Postbiotics in the article, Gut Health In Depth.
This article was underwritten, in part, by a grant from Amway.