Microbiome: The Garden Within

Illustration by Tom Rybarczyk
Illustration by Tom Rybarczyk

For every cell in the human body, there are about 10 nonhuman cells. These microbial residents of our gut, skin, eyes and nasal passages collectively are referred to as the “microbiome” — and research of its role in human health has revealed enough surprising discoveries that the National Institutes of Health has launched an international Human Microbiome Project.

The human microbiome refers specifically to the community of microorganisms that live in and on the human body (or any “host” animal) and their collective genome, which interacts with our host genes. The microbiota (formerly called “microflora”) refers to the microorganisms themselves. Our microbiota are affected by everything from how we entered the world to how much time we spend barefoot. Bacteria, yeasts, molds, dirt and the types of food we eat all impact microbiota, thereby influencing the microbiome.

Gut bacteria aid digestion by breaking down otherwise indigestible plant fibers into short-chain fatty acids that intestinal cells can access. Emerging research also suggests that gut bacteria influence many other metabolic functions, so much so that some experts now regard it as a “hidden” organ system, capable of interacting with its host down to DNA expression. As a result, the microbiome’s role in conditions as varied as irritable bowel diseases, obesity, Type 2 diabetes, depression, autoimmune disorders and Parkinson’s disease is under intense scientific scrutiny. The core questions remain: How does the microbiome become altered in a way that negatively affects the host, and how does a host build better microbiota?

Establishing the Colony

The bacteria that our immune systems recognize as “normal” (the bacteria that will prevail in our guts or the duration of our lives) is established by our first exposure to our mothers’ microbial mix. Babies born vaginally are colonized by microbes present in the birth canal, primarily by strains of Lactobacillus species that differ from non-pregnant women. By contrast, babies born via cesarean section are colonized by the microbiota of a mother’s skin and whatever other bacteria happen to be present at birth, predominantly Staphylococcus species.

First foods matter as well. Breast milk has its own microbiota that differ depending on whether the mother gave birth vaginally or via C-section, possibly due to the antibiotics women receive before and after C-section delivery. Breast milk contains oligosaccharides that act as prebiotics — food for the infant’s developing intestinal community. After birth, infants begin to cultivate their own bacterial mix until the developing microbiota reach a relatively stable state, shaped by environment and diet. By age 2, the child’s microbiota are believed to resemble an adult’s.

An Evolving System

Our microbiome co-evolves with us and influences our metabolism, physiology, nutrition and immune function. Once the microbiome is established, it is believed to be relatively stable throughout a person’s life, although short- and long-term changes can occur. Antibiotics dramatically affect the microbiome. The ability of the microbial residents to bounce back after a round of antibiotics varies greatly among individuals, and multiple rounds of antibiotics can significantly shift the types of microbes that survive. Often this kind of disruption leads to dysbiosis, an imbalance of beneficial and pathogenic bacteria and other microbes.

Dietary changes also significantly alter the microbiome, and preliminary human studies suggest that these changes can occur in as little as three days. Interestingly, while what we eat alters our microbiomes, the microbiota also appear to influence what we choose to eat, as microbes compete for space and nutrients. Researchers suspect that dominant gut microbes trigger cravings for foods that either benefit them or suppress their bacterial competitors.

Microbes may even create dysphoria in the host until the person succumbs to the craving. Researchers propose several possible mechanisms by which this works: Microbes may be able to influence taste receptors, making certain foods taste better; they may spark the release of hunger-triggering hormones; or they may influence eating habits by hijacking the vagus nerve that connects the gut and brain.

Altered microbiota and dysbiosis may be related to many chronic diseases and conditions, including obesity, diabetes, metabolic syndrome, depression and gut diseases. This link appears to be rooted in inflammation, endotoxemia and possibly changes to the immune system, which means treating the gut may be an effective way for registered dietitian nutritionists to address multiple conditions.

Digestive Health, IBS and IBD

Irritable Bowel Syndrome is an increasingly common functional gastrointestinal disorder, the hallmark symptoms of which include abdominal discomfort or pain, distension and bloating, and diarrhea, constipation or a combination of both. Low-grade inflammation and significant dysbiosis are prominent features of this syndrome. While normal gut microbiota prevent pathogenic bacteria from gaining a foothold on the intestinal lining, dysbiosis may allow the bacteria associated with IBS symptoms to thrive, triggering further inflammation by activating the immune system.

People with IBS often experience higher levels of anxiety, stress and depression, as well as higher rates of metabolic syndrome. While the exact cause of IBS remains unclear, some research points to dysbiosis along with dysregulation of the brain-gut axis and autonomic nervous system. IBS and inflammatory bowel disease — including ulcerative colitis and Crohn’s disease — are associated with increased intestinal permeability (sometimes referred to as “leaky gut syndrome”). IBS typically features low levels of beneficial Bifidobacterium bacteria; IBD, which also may be triggered by dysbiosis, features low bacterial diversity. Probiotics have shown to be effective therapeutic interventions for both IBS and IBD, shown to improve intestinal integrity, alleviate symptoms, reduce inflammation and strengthen the intestinal barrier.

Obesity, Type 2 Diabetes and Metabolic Syndrome

Obesity and its consequences are a complex set of syndromes. Lifestyle, diet and exercise habits contribute significantly to this “diabesity” epidemic, though changes to the microbiota also appear to play a role by influencing weight gain and metabolism. From animal studies, we’ve learned that transferring gut bacteria from obese animals to germ-free, lean animals induces obesity and metabolic disease, even when diets are unchanged.

While the relationship of microbiota and weight in humans is less clear, studies have consistently demonstrated dysbiosis in people with Type 2 diabetes. Healthy control subjects tend to have more bacteria that produce the shortchain fatty acid butyrate, and individuals with Type 2 diabetes tend to have higher levels of pathogens, such as Clostridium species, though research has not yet confirmed whether a difference in gut microbes is a contributing factor or an effect. In addition, when pathogen-free microbiota from lean, healthy donors are transferred to patients with metabolic disease, insulin sensitivity improves.

Microbiota and Mood

Lending credence to the gut’s reputation as a “second brain,” it’s been observed that stress and depression are linked with IBS and IBD, and the microbiome also may play a role. Psychological and physiological stress affects the gut in ways that alter the microbiota and foster dysbiosis, bacterial overgrowth and intestinal permeability. These changes trigger inflammation and affect the brain and central nervous system through increased toxic exposures (endotoxins from bacterial metabolites enter the bloodstream through a “leaky gut”) and neurotransmitter disruption. Gut microbes produce hormones and neurotransmitters that are taken up by the human brain.

Preliminary research indicates that changes to the microbiome may affect things such as mood, anxiety, memory and concentration. Rodent studies have found that manipulating the microbiome results in changed behavior. However, while an anti-inflammatory diet could provide some benefit, there aren’t any large-scale human studies that clarify the role of dietary intervention on the central nervous system with respect to changes to the microbiome.

Mind Your Microbes

Amid mounting interest in its influence on human health and disease, attention has turned to therapeutic approaches that target the gut. A diet high in fruit, vegetables and perhaps whole grains allows beneficial bacteria to dominate and inhibits the growth of more harmful strains. While researchers haven’t reached consensus about what constitutes an optimal microbiome, there is some general advice for tending our microbial gardens:


    • Fruit and Vegetables
      A plant-centric diet rich in vegetables, fruit and legumes, and high in dietary fiber and polyphenols, appears to benefit the microbiota. These foods offer intestinal bacteria fuel in the form of prebiotics.
    • Fermented Foods
      While beneficial bacterial strains found in fermented foods may not settle into the gut permanently, they may affect microbiota by influencing the gene expression of the bacteria already there. Naturally fermented foods, such as yogurt and kefir with “live, active cultures,” sauerkraut, kimchi, tempeh and raw vinegar, are high in beneficial Lactobacillus bacteria. To get the benefits, be sure the foods are “lactofermented” or naturally fermented and raw or unpasteurized, as pasteurization kills beneficial bacteria.


  • Garden Herbs
    Garlic and leeks contain natural sources of the prebiotic inulin. Garlic also has natural antimicrobial properties, which may help suppress pathogenic bacteria and foster beneficial bacteria growth.
  • Focus on Fresh
    Enjoy minimally processed foods and limit sugar and unhealthy fats, especially trans fats. Some studies have associated diets of highly-processed foods with dysbiosis and pro-inflammatory microbiota.
  • Probiotic Supplements
    Consider taking a high-quality probiotic supplement (with several different strains of Lactobacillus and Bifidobacterium species, such as L. acidophilus, L. reuteri, B. longum and B. bifidum), particularly during and after antibiotic use to recolonize the digestive tract and help manage antibiotic-induced diarrhea. Since antibiotics kill all bacteria, it is best to take probiotic supplements at least two hours before or after taking antibiotics.
Robin Foroutan
Robin Foroutan, MS, RDN, is a National Spokesperson for the Academy of Nutrition and Dietetics who specializes in integrative medicine, functional medicine and holistic healing. She practices privately and at the Morrison Center.