Precision Nutrition: Seven Dietary Guidelines for a Healthy Microbiota

The Physicians Committee

Precision Nutrition: Seven Dietary Guidelines for a Healthy Microbiota


The human microbiome remains a trending research topic for good reason: It’s now different than it was 100 years ago. The bacteria in our guts produce vitamins and amino acids. It helps its human host regulate the immune system, inflammation, hormones, mood, and behavior.1,2 While we share 99.9 percent of our genes with other people, we only share 10 percent of our microbiome, the collective genetic makeup of our bacterial populations.3 Why does this matter? We have a near 1:1 to 1:10 ratio of human cells to bacterial cells in our bodies.4 We’re the sum of all parts and we're biologically unique. We’ll continue to learn more about how the microbiome influences human health as the rise of metagenomics, the study of bacteria living inside our personal ecosystem, unfolds.

Current research includes the Human Food Project, an initiative to categorize what is in our intestinal tract, and federal initiatives, including the Human Microbiome Project and President Obama’s National Microbiome Initiative, which will reveal more about how the microbiome influences human health and chronic disease, climate change, and food security.

While the results are underway, the Physicians Committee recommends seven dietary guidelines to support a healthy microbiota, a term that describes colonies of microorganisms—or microbes—living in our bodies, starting in our gut.

Dietary Guidelines

The seven preliminary dietary guidelines to foster a healthy microbiota were released at the International Conference on Nutrition in Medicine (ICNM) on Friday, July 29, 2016, and updated on March 22, 2017.

The seven guidelines are as follows:

  1. Build meals around plant-based foods: vegetables, fruits, whole grains, and legumes.
  2. Aim to consume at least 50 to 55 grams of fiber daily.
  3. Include at least 5 to 8 grams of plant-based prebiotics per day. Aim for at least two servings of prebiotic foods outlined in the guidelines below.
  4. Add a small amount of fermented foods, or probiotics, to your diet.
  5. Avoid red meat, high-fat dairy products, fried foods, food additives, and advanced glycation end (AGE) products.*
  6. Limit fat from oils and high fat sauces or condiments, especially if you have or are at risk for type 2 diabetes.
  7. Use antibiotics only when necessary and avoid using for viral illnesses.

*AGE products are in foods and can cause oxidative stress, damaging the cells in the body.  A full description is pasted in the food additives and AGE section below.


What’s In? Plant-Based Eating Patterns

A Diet for Disease Prevention

Studies show plant-based eating patterns can prevent, treat, and in many cases, may even reverse obesity, diabetes, heart disease, and chronic pain, while providing a first-line defense against certain forms of cancer and dementia.5,6,7,8,9 People who follow a plant-based diet also have the healthiest intestinal bacteria, according to a study published in the journal Gut.10

University of Oxford researchers predict a plant-based diet, if adopted worldwide, could save 8.1 million lives, trim $1 trillion in health care costs, and reduce 70 percent of carbon-based emissions over the next 30 years.11

Plant-Based Foods and the Gut Flora

Whether the goal is to improve personal or population-wide health, the science behind this transformation starts in our gut. A diet rich in vegetables, fruits, whole grains, and legumes promotes a healthy and diverse gut flora and provides health benefits to its human host.12

Fiber, available exclusively from plant-based foods, is fermented by our bacteria in the large intestine and releases short-chain fatty acids (SCFA), which have been shown to promote satiety, reduce inflammation, improve blood sugar control, enhance nutrient absorption, and increase fatty acid metabolism, which, along with hormone regulation, reduces total fat storage.

Previous generations consumed at least 55 grams of daily fiber, more than three times today’s average of 16.13 

An example of a high-fiber diet includes three servings of whole grains, two servings of legumes, five servings of vegetables, four servings of fruits, and a 1-ounce serving of nuts or seeds. By increasing baseline fiber intake by at least 14 grams, net calorie consumption falls by 10 percent.14

Fiber: The Controlled Study

Steven O’Keefe, M.D., a nutrition researcher at the University of Pittsburgh, wanted to examine the link between fiber and chronic disease. He took 20 study participants in rural South Africa, who follow a low-fat, high-fiber diet, rich in maize, okra, tomatoes, spinach, pineapple, mangoes, and black-eyed peas, and asked them to follow a high-fat, low-fiber diet for 14 days. The South African study participants, ages 50 to 65, dined on sausage links, pancakes, hamburgers, meatloaf, and fries, foods that are common in Pittsburgh, where Dr. O’Keefe provided 20 African-American study participants the foods common in South Africa. After just two weeks, both groups exchanged their risk for colon cancer—which is 13 times higher in the United States.15

The South African group experienced inflammation in the bowel and a 400 percent increase in the secretion of carcinogenic secondary bile acids, due to high fat intake. The Pittsburgh study participants experienced an increase in butyrate production, an anti-inflammatory marker, reduced their levels of secondary bile in the colon by 70 percent, and nearly half eliminated intestinal polyps. The researchers find high fat intake increases the abundance of Bilophila wadsworthia, a bacteria species that increases inflammation. Alternatively, fiber increases the abundance of species that produce SCFA and reduces inflammation. 

The study shows that microbiota, which contains 1,000 different species, reacts fast to dietary changes. Foods can influence the internal ecosystem in just 24 hours.16


For optimal gut health, quality and quantity both count when it comes to tracking fiber intake. While all prebiotics contain fiber, not all fiber counts as a prebiotic. Prebiotics, available in plant-based foods, resist digestion until they reach the colon. They then provide fuel for probiotic organisms, the “beneficial” gut bugs that live in the intestinal tract and decimate harmful bacteria.17 The human host experiences benefits from this transaction, including improvements in intestinal function, mineral absorption, hunger regulation, and a reduction in gut barrier impermeability, which enhances immune function.

To reap these rewards, consume at least 5 to 8 grams of prebiotics, the equivalent of two cups of raw leafy greens or a half-cup of beans each day.18 Oats, whole grains, bananas, beans, garlic, onions, artichokes, flax seeds, and raw dandelion greens are other common sources.


Probiotics, mentioned above, are living microorganisms and rely on prebiotics for fuel. They modulate our microbiota to help crowd out bad bacteria, kill pathogenic strands, and sustain beneficial varieties. These are the bugs you want to keep around. Their role is to maintain microbial order. They aide digestion, enhance immune function, and balance pH levels. This reduces the risk for type 2 diabetes, irritable bowel syndrome, diarrhea, high cholesterol, hypertension, heart disease, and cancer.19,20,21,22 The best sources are tempeh (a fermented soybean product), miso, and water kefir.23

 What’s Out? Western-Style Diets

The Dangers of Red Meat, High-Fat Dairy Products, and Fried Foods

What we don’t eat may be just as important as what we consume. Red meat, especially liver, high-fat dairy products, including milk fat and cheese, eggs, and fried foods are associated with dysbiosis, a microbial imbalance.24,25 This results in a higher ratio of harmful bacteria, and lower levels of healthful bacteria, making it harder for our bodies to function at optimal speed. These foods can negatively affect gut barrier function, allowing components of bacteria to enter the body, starting in the bloodstream. This produces an inflammatory response, increasing insulin resistance and the risk for type 2 diabetes.

Milk fat also causes the liver to secrete more bile, which then promotes the growth of Bilophila wadsworthia, the sulphite-reducing pathobiont mentioned above, and has been linked to ulcerative colitis and inflammatory bowel disease, and may promote liver cancer.26 Liver, eggs, and red meat are also high in L-carnitine, which is metabolized by bacteria in the gut to trimethylamine (TMA). This metabolite is absorbed, goes to the liver and releases trimethylamine-N-oxide (TMAO), which is known to promote atherosclerotic lesions.27,28 This phenomenon may explain why those who eat more meat and eggs have higher rates of cardiovascular disease.

Total Fat Intake and the Glycemic Index

It’s wise to limit total fat intake, which increases gut barrier permeability, or function, and increases insulin resistance, a risk factor for type 2 diabetes.29,30,31  Choose healthful varieties, including an ounce of nuts or seeds or a small amount of avocado. When it comes to carbohydrates, opt for those with a low glycemic index. Good options include steel-cut oats, sweet potatoes with skins, beans, whole grains, and most fruits and vegetables.

Food Additives and Advanced Glycation End Products

Food additives and advanced glycation end products (AGEs) can also disrupt internal gut health.32 AGEs include animal-derived foods that are high in fat and protein, including meats, especially red and seared meats. AGEs also include sugar-packed and highly processed foods. While the body can naturally expose itself of AGEs, it has a hard time eliminating them effectively if too many are consumed through food. Long-term risk factors include an increased risk of diabetes complications and cardiovascular, liver, and Alzheimer’s disease.33

Other Considerations

Antibiotic Use

The last guideline to create harmony among colonies of good and bad bacteria is to limit antibiotic use, specifically during the first several months of birth.34 In addition to decreasing the effectiveness of antibiotics, consuming antibiotics when we don’t need them modifies our microbiota and increases the risk for obesity and new infectious diseases, including C. diff, Clostridium difficile, which affects nearly half a million Americans—and takes close to 30,000 lives each year.35,36

Environmental Considerations

Outside of dietary factors and limiting antibiotic use, it’s best for mothers to choose natural birth over caesarian sections, unless medically necessary, and breastfeed, when possible.37 Everyone should limit excessive hygiene, which is easy to achieve by spending more time in nature.38,39 Other lifestyle factors for optimal gut health include stress management, regular exercise, and adequate sleep.40,41,42,43,44


To fuel healthy diversity and symbiosis in the microbiome, build meals around plant-based foods, especially natural sources of prebiotics and probiotics, and consume at least 50 to 55 grams of fiber each day. Avoid red meat, high-fat dairy products, fried foods, food additives, AGEs, and limit fat intake and unnecessary antibiotic use.45


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