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Exploring the Gut Microbiome: A Beginner’s Guide

Written by Institute for Natural Medicine Staff

Medically Reviewed by Michelle Simon, PhD, ND

Published February 14, 2025
Last Updated February 25, 2025

The gut is one of the body’s most misunderstood and underappreciated parts. This intricate ecosystem does far more than digest food—it influences nearly every aspect of health. Hippocrates said it best: “All disease begins in the gut.”

Inside the GI tract is a garden of microorganisms (bacteria, viruses, and fungi). These microbes are in constant communication with cells and organs, sending and receiving signals that affect everything from digestion to immunity.¹ Scientists call gut connections “axes,” linking them to major organs like the brain, skin, and liver.

“The gut microbiome has been [connected] to almost every major diagnosis and treatment response,” says Heather Zwickey, PhD, professor and researcher at the National University of Natural Medicine. “We know that people who have a healthy gut microbiome not only have better health and respond better to medications, but they also tend to live longer.”

The gut microbiome is a health motherboard

Intestinal walls are colonized by gut microbes. When these microbes comprise beneficial bacteria, they protect the body from foreign invaders and uphold the intestinal lining (aka the epithelium) so nothing can escape its border.²

“Dysbiosis,” a weakened epithelium, can negatively affect the GI microbiome. Three issues precede dysbiosis³:

Loss of beneficial bacteria along the intestinal lining
Loss of bacterial diversity
Overgrowth of potentially harmful bacteria

Research shows dysbiosis may contribute to chronic conditions like diabetes, heart disease, and kidney disorders, as well as numerous other inflammatory conditions.³ A damaged intestinal barrier may also allow more endotoxins to enter the bloodstream, leading to impaired energy metabolism, insulin resistance, nonalcoholic fatty liver disease, and obesity.⁴

Good bacteria, a vital ally for wellness

The gut microbiome isn’t just a maze of microbes—it actively contributes to our well-being. One of the most incredible ways is its ability to produce beneficial compounds for our body. A healthy gut nourishes us from within, like a self-sustaining greenhouse.

Through a process called biosynthesis, gut bacteria create B vitamins required for energy production, brain function, and cell metabolism.⁵ Microbes generate key metabolites such as short-chain fatty acids and neurotransmitter precursors that positively influence mood.⁶

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Three pillars of GI health: diet, lifestyle, stress management

The microbiome is sensitive to diet, exercise, medications, and environmental factors. Healthy habits and mindful living support a happier gut and, in turn, a healthier body.

“A healthy microbiome has strong intestinal integrity characterized by microbial diversity,” explains Dr. Zwickey. “That diversity is influenced by a variety of factors, including a healthy diet and lifestyle.”

Why ‘metabolites’ matter

One of GI microorganisms’ central functions is converting food to chemicals used throughout the body.

When food is digested, the microbiome transforms it into useful metabolites—small molecules that serve as the body’s biochemical messengers. Metabolites can be primary, like amino acids and sugars essential for growth, or secondary, like antibiotics and plant alkaloids that boost immunity.

Metabolites serve vital purposes: fighting inflammation, strengthening the intestinal barrier, destroying harmful microbes, improving insulin sensitivity, and protecting the brain.¹ Many are beneficial, while others, like lipopolysaccharides (LPS), trigger inflammation.

“A person with a healthy, diverse microbiome will produce a broad array of metabolites—between 800 to 1,000,” says Dr. Zwickey. “A person who has an unhealthy microbiome may produce [fewer] metabolites and may be missing key microbes, [producing] metabolites that increase inflammation, or making metabolites that are toxic.”

Feeding the microbiome for optimal function

A diverse gut microbiome is essential for digestion, immunity, and even mental health. People who incorporate a greater variety of plant-based foods into their diets have more varied gut microbiomes than picky eaters. Specifically, eating 30 or more different plant types per week offers significantly higher microbial diversity than consuming 10 or fewer plant types weekly.⁷

According to Dr. Zwickey, foods containing prebiotics and polyphenols are even more beneficial for gut health than probiotics.

“Foods that qualify as prebiotics have greatly expanded and now include polyphenols that stimulate the growth of particular taxa of microbes,” she notes. “Spices, teas, and other herbs contain polyphenols that are good for the gut microbiome.” Fermented foods such as kimchi, miso, and tempeh contain prebiotics and probiotics shown to diversify and support good GI bacteria.⁸

Foods that enhance microbiome diversity

Legumes and fiber-rich vegetables

Beans and pulses are excellent sources of fiber that promote good bacterial growth. Lentils, for example, contain 15 grams of fiber per serving.
Oats are a great source of soluble fiber, which helps nourish gut microbiota.
Cabbage is a fiber powerhouse that feeds and diversifies healthy gut bacteria.

Alliums

Full of prebiotic fiber that fuels gut microbes, alliums also provide vitamin C and selenium for immune and liver health.

Onions
Leeks
Garlic
Scallions

Leafy greens

High in fiber, vitamins A, C, E, and K, and nutrients for optimal bacterial diversity.

Spinach
Kale
Chard

Probiotics and vitamins restore balance

Probiotics have the potential to renew intestinal epithelial cells and tighten GI junctions, reducing dysbiosis risk.⁹ They can help repair a leaky stomach lining by competing with harmful bacteria for nutrients and living space along the gastrointestinal tract.⁷

Vitamins A, D, C, and E and other nutrients, like colostrum, also support GI health.¹⁰ Colostrum is the first milk produced by mammals after giving birth. While still early, colostrum research is promising, with nine studies demonstrating its ability to strengthen gut permeability.¹¹ Antibody-rich colostrum contains vital proteins and growth factors essential for newborn immunity and nourishment.

The importance of reducing antibiotic exposure

When the gut microbiome thrives in balance, it can help protect and optimize our health. But when it’s disturbed, the consequences can be serious.

Several factors negatively affect the microbiome early in life. Being born via C–section, not being breastfed, and taking antibiotics may all hinder the development of a robust gut microbiome.

Antibiotic use, in particular, is a major concern. Roughly one third of antibiotics prescribed in the United States might be unnecessary.¹² Many ear infections, for example, are viral and do not respond to antibiotics. The same is true for most colds. Yet, antibiotics continue to be overprescribed, often compromising the gut’s delicate microbial balance.

Antibiotic overuse is especially harmful for children. The microbiome takes about three years to fully develop, yet by that time, the average American child has already received four courses of antibiotics. This early GI disruption may have long-term consequences, including increased risk of asthma, allergic rhinitis, atopic dermatitis, celiac disease, obesity, and attention deficit hyperactivity disorder.¹³

One study found that children who received antibiotics in the first two years of life were at a specifically higher risk for health and cognitive conditions:

A 20% higher risk of obesity
A 21% increased risk of learning disabilities
A 90% greater risk of asthma
An 89% higher likelihood of celiac disease

The study also revealed a dose-dependent relationship—the more antibiotic courses a child received, the greater their risk of developing a chronic condition.¹⁴

“Eliminating things that kill beneficial microbes is equally important to repairing the gut microbiome,” explains Dr. Zwickey. “It’s important to reduce the number of antibiotics people take, as well as reduce preservatives and pesticides in foods and beverages, as we know these chemicals kill good gut microbes.”

While antibiotics are essential in certain situations, they should only be used when truly needed. One of the best ways to protect the gut microbiome is to decrease unnecessary antibiotic use, allowing the body to fight minor infections naturally.

Minimizing stress, maximizing resilience

Research is also confirming the long-suspected connection between gut health and stress. Effectively managing stress and anxiety fosters a healthier gut, and a healthy gut leads to more resilience.¹⁵^,¹⁶

The key to personalized medicine?

Health care is finally catching up to what naturopathic medicine has long recognized—the gut is at the core of our well-being. Some experts see the GI microbiome as a gateway to tailored treatment.

“From a research perspective, the gut microbiome may help us better predict individualized treatment responses,” says Dr. Zwickey. “For example, people who have more of a particular microbe with a specific enzyme may have a better response to a selected herbal or nutritional intervention.”

As science continues to uncover the secrets of the gut microbiome, its inner workings are becoming clearer. But there’s still much more to learn about this powerful internal ecosystem and its profound impact on whole-body health.

Footnotes

1
Kho ZY, Lal SK. The human gut microbiome—potential controller of wellness and disease. Front Microbiol. 2018;9. https://doi.org/10.3389/fmicb.2018.01835
2
DeGruttola AK, Low D, Mizoguchi A, Mizoguchi E. Current understanding of dysbiosis in disease in human and animal models. Inflamm Bowel Dis. 2016;22(5):1137-1150. https://doi.org/10.1097/MIB.0000000000000750
3
Wilkins LJ, Monga M, Miller AW. Defining dysbiosis for a cluster of chronic diseases. Sci Reports. 2019;9. https://www.nature.com/articles/s41598-019-49452-y
4
Zhang Y, Zhu X, Yu X, et al. Enhancing intestinal barrier efficiency: a novel metabolic diseases therapy. Front Nutr. 2023;10. https://doi.org/10.3389/fnut.2023.1120168
5
Hossain KS, Amarasena S, Mayengbam S. B Vitamins and their roles in gut health. Microorganisms. 2022 Jun 7;10(6):1168. https://doi.org/10.3390/microorganisms10061168
6
Silva YP, Bernardi A, Frozza RL. The role of short-chain fatty acids from gut microbiota in gut-brain communication. Front Endocrinol (Lausanne). 2020 Jan 31;11:25. https://doi.org/10.3389/fendo.2020.00025
7
McDonald D, Hyde E, Debelius JW, et al. American gut: an open platform for citizen science microbiome research. mSystems. 2018 May 15;3(3):e00031-18. https://doi.org/10.1128/msystems.00031-18
8
Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 Aug 5;184(16):4137-4153.e14. https://doi.org/10.1016/j.cell.2021.06.019
9
Gou H, Zhang Y, Ren L, et al. How do intestinal probiotics restore the intestinal barrier? Front Microbiol. 2022;13. https://doi.org/10.3389/fmicb.2022.929346
10
Pham VT, Dold S, Rehman A, et al. Vitamins, the gut microbiome and gastrointestinal health in humans. Nutr Res. 2021;95:35-53. https://doi.org/10.1016/j.nutres.2021.09.001
11
Dziewiecka H, Buttar HS, Kasperska A, et al. A systematic review of the influence of bovine colostrum supplementation on leaky gut syndrome in athletes: diagnostic biomarkers and future directions. Nutrients. 2022;14(12). https://doi.org/10.3390/nu14122512
12
Hersh AL, King LM, Shapiro DJ, Hicks LA, Fleming-Dutra KE. Unnecessary antibiotic prescribing in US ambulatory care settings, 2010-2015. Clin Infect Dis. 2021 Jan 23;72(1):133-137. https://doi.org/10.1093/cid/ciaa667
13
Aversa Z, Atkinson EJ, Schafer MJ, Theiler RN, Rocca WA, Blaser MJ, LeBrasseur NK. Association of infant antibiotic exposure with childhood health outcomes. Mayo Clin Proc. 2021 Jan;96(1):66-77. https://doi.org/10.1016/j.mayocp.2020.07.019
14
Blaser MJ. Antibiotic use and its consequences for the normal microbiome. Science. 2016 Apr 29;352(6285):544-5. https://doi.org/10.1126/science.aad9358
15
Tofani G, Leigh S, Gheorghe CE, et al. Gut microbiota regulates stress responsivity via the circadian system. Cell Metab. 2024;37:1-16. https://doi.org/10.1016/j.cmet.2024.10.003
16
An E, Delgadillo DR, Yang J, et al. Stress-resilience impacts psychological wellbeing as evidenced by brain-gut microbiome interactions. Nat Mental Health. 2024;2. https://www.nature.com/articles/s44220-024-00266-6

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Exploring the Gut Microbiome: A Beginner’s Guide

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The gut microbiome is a health motherboard

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