Scientists have discovered that human health is strongly influenced by the millions of microbes that live within our intestinal tract, collectively known as the gut microbiome. Syndromes ranging from mental health disorders to chronic inflammation and chronic disease have been attributed to changes in this system.

What Does a Healthy Microbiome Look Like:

A healthy microbiome consists of a diverse population of bacteria, fungi, and viruses that are both helpful and potentially harmful. In a normal system, harmful bacteria are kept in check by beneficial bacteria, and the organisms coexist without problems.

What Happens to the Microbiome in a Disease State:

Certain disorders may have a “microbiome signature”–that is, a template of abnormal bacteria seen over and over again in a particular disease state. This concept is an area of active research because identifying a “microbiome signature” may help doctors diagnose and treat sooner, before damage is done. Here are some examples:

In systemic lupus erythematosus, a lower ratio of Firmicutes to Bacteroidetes (two types of gut bacteria) has been described.

Systemic sclerosis, sjögren’s syndrome and anti-phospholipid syndrome share modifications of the microbiome in both the intestinal tract and in the mouth ( a separate microbiome).

A population of patients with early rheumatoid arthritis had a large Prevotella Copri population present in their microbiomes, a bacteria normally seen only in small amounts.

Key Influencers of the Microbiome:

Diet- what you eat is the most important determinant of your microbiome structure and function. Adaptations are seen in as little as 24 hours after changing your diet.

Genetics- your genes are the second most important factor in shaping your microbiome.

Medications-not just antibiotics, but also proton pump inhibitors, methotrexate, biologics, metformin, selective serotonin reuptake inhibitors, and laxatives all change the composition of the gut microbiome

Environment- where you live, pets, soil quality

Cooked vs Raw:

What you eat is the biggest determinant in the health of your microbiome…but it turns out that how you prepare your food is equally important.

Carmondy et al published “Cooking Shapes the Structure and Function of the Gut Microbiome” in Nature Microbiology, and noticed the following in an animal study:

Rapid microbiome changes were seen in mice fed meat instead of tubers.

Cooked food led to more gut microbiome diversity, an important factor in microbiome health.

Many raw foods contained potent antimicrobial compounds that appeared to directly damage certain gut microbes.

Raw diets caused mice to lose weight, but when the team transplanted these altered microbiomes into mice consuming regular-diets, the normally fed animals then became obese.

Cooking: Ancient and Evolutionary

The debate between cooked versus raw food continues, but this study raises intriguing questions about how food preparation relates to the development of obesity and autoimmunity, as well as how the gut microbiome has evolved with us over millions of years to adapt to our cooking methods.

Kitchen-Prescription Recipe: Spring Minestrone

Spring Minestrone

¼ cup of olive oil
Two large leeks, white and light green part only, quartered and soaked to remove the grit
Two cloves of garlic, finally minced
One cup of dry white wine
1 quart of organic low sodium chicken stock
4 cups of water
1 inch piece of rind from a Parmigiano Reggiano cheese (optional)
4 sprigs of fresh thyme, leaves removed
Zest of one organic lemon
Two medium zucchinis sliced into half-moons, ¼ inch thick
One bunch of asparagus, woody stems removed, and sliced into 1-inch pieces
One cup of frozen peas
5 ounces of baby spinach
Kosher salt
Extra virgin olive oil for serving

Heat the olive oil in a large Dutch oven over medium heat. Finely slice the leeks, and sauté in the olive oil for five minutes, or until they are soft and fragrant. Add the garlic, and sauté for two more minutes. Turn off the heat. Poor in the white wine, turn the heat back on to a medium flame, and cook, stirring frequently, until the liquid is reduced by half. Pour in the stock, add 4 cups of water, the rind of the Parmigiano Reggiano cheese and the thyme leaves, and bring the mixture to a boil. Add the zucchini and asparagus, lower the heat to a simmer, and cook for 20 minutes, or until the vegetables are soft. Stir in the frozen peas and the baby spinach, and cook for another 10 minutes. Season to taste with kosher salt, and stir in the lemon zest. Serve hot, drizzled with extra virgin olive oil.

Medical Mentions:

If you do not eat dairy, substitute 1 tablespoon of white miso paste for the rind of the Parmigiano Reggiano cheese.