Fine-Tuning the Digestive Symphony

I like to think of digestion as a magnificent symphony in which a diverse array of organs, bacteria, and biochemicals work in concert to transform the foods we eat into the nutrients and energy we need. If any instrument is out of tune, the music suffers.

This notion of the digestive system as an orchestra is an easy metaphor to help patients understand how digestion takes place, why symptoms arise, and how our various therapeutic interventions help restore the proper rhythm and harmony. 

The Overture: Eyes, Nose, and Mouth

Many people don’t realize it, but digestion actually begins with the eyes and nose. Seeing and smelling food in anticipation of eating send signals from the brain to the gut about what to expect. It’s something chefs, restauranteurs, and food marketers certainly understand, which is why they go to such great lengths to present food in the most visually appealing and aromatic ways.

As food enters the mouth, it encounters the teeth and saliva. The act of chewing is very important for mechanically breaking down the food. Saliva contains amylase and other enzymes that begin to break down complex carbohydrates into smaller starches and sugars, and lingual lipase that begins to break down dietary fats. That process gets truncated when people wolf down their food without much chewing.

As peristaltic waves move the food to the end of the esophagus, the lower esophageal sphincter relaxes and lets the food pass into the stomach—a muscular reservoir of strong acid–before squeezing shut to prevent backflow. Gastroesophageal reflux (GERD) results when the sphincter is playing out of tune with the rest of the digestive orchestra, and fails to close properly.

First Movement: Stomach & Small Intestine

In the stomach, the food gets churned with stomach acid and digestive enzymes such as pepsin which breaks down proteins. The resultant chyme is slowly emptied into the small intestine where the bulk of digestion occurs.

Once in the small intestine, the chyme triggers secretion of bile and pancreatic enzymes. Combined, these alkaline secretions break down carbohydrates, fats, and proteins into their smallest components. At least that’s what’s supposed to happen. As any clinician knows, the process is impaired in many people.

Further peristaltic waves through the intestinal smooth muscle tissue move the chyme through the small intestine, where the digested nutrients are absorbed into the bloodstream.

Second Movement: The Large Intestine

The mixture passes through the ileocecal valve into the large intestine, which extracts and absorbs water. The remaining residue of undigestible material, remnants of the digestive juices, and sloughed epithelial cells from the intestinal lining is moved forward into the rectum for storage and eventual elimination as stool.

It is here in the large intestine that we find the largest bacterial ecosystem of the human body. The intestinal microbiome has many functions, including: further digestion of food and breakdown of harmful toxins; synthesis of certain vitamins and neurochemical signals; generation of energy for the gut mucosa itself; protection against pathogens; and “training” of the immune system.

Researchers are still making new discoveries about the gut microbiome, and our understanding of it is far from complete. Suffice it to say that a healthy population of gut bacteria is necessary for optimum health.

Fine-Tuning the Instruments

Let’s face it: in the GI tract, things easily go out of tune and the digestive symphony becomes discordant. GI problems are among the most common reasons people seek medical care. There are several things we can recommend to help patients keep their digestive instruments in tune and operating properly:

Herbal Bitters: Starting in the mouth, the use of digestive herbal bitters can stimulate salivary production and jump-start the whole digestive system. Taking a dose of bitters before a meal is—or was—customary in many parts of the world with longstanding herbal medicine traditions.

There are many different formulas for “Bitters,” using a wide range of herbs. Among the common ones are: Angelica (Angelica archangelica), Fennel (Foeniculum vulgare), Ginger (Zingiber officinale), Dandelion (Taraxicum officinale), and Burdock (Arctium lappa). A few drops of a standardized Bitters formula before eating provides a host of phytochemicals that bind to bitter taste receptors, which then send signals for saliva production, and secretion of cholecystokinin, ghrelin, and motilin. All of these play key roles in the digestive symphony. 

Careful Food Choices: Food choices have tremendous impact on digestive health. Processed foods, high glycemic foods, and foods laden with additives hinder good digestion. Choose a wide variety of predominantly whole foods, preferably organically or biodynamically grown. Patients should focus on plant-based “life-ly” foods: fresh or lightly steamed vegetables and fruits, lightly toasted nuts and seeds, sprouts of grains and beans, fermented foods, sea vegetables, herbs and edible flowers, freshly squeezed fruit juices, and vegetable juices. These retain active enzymes that enhance digestion.

Of course, food choices are highly individualized. It’s important to keep in mind that some people have sensitivities, allergies, or just simple aversions to particular foods that are healthy and enjoyable for others. Delayed hypersensitivity tests can help identify hidden sensitivities to foods, additives, heavy metals and environmental toxins.

Take Time to Chew: I recommend that people chew their food 15-20 times per mouthful. The maxim is, “drink your solids and sip your liquids.” It’s also a good idea to eat half of what one feels one needs, then stop and take a few deep breaths to give the body a chance to register what’s been eaten and whether one needs to eat more.

B Vitamins: The lower esophageal sphincter benefits from vitamins B6, B12, and folate. A good way to get these B vitamins is via sublingual lozenges. In many cases, this simple natural intervention will relieve GERD.

Hydrate, hydrate, hydrate: Our bodies are 50-75% water by weight, depending on age and health status.  Every biological system is dependent upon water. It flushes toxins from vital organs, transports nutrients to cells, regulates body temperature, and keeps tissues moist. I recommend drinking at least 8 glasses of water a day, more if one lives in a dry climate or exercises heavily. Vegetable broth and wet foods are also good ways to hydrate. For those who enjoy them, aperitifs like Campari, organic or biodynamic beer, cider, and wine are permissible in moderation. Physical activity is also important for good digestion. We need to move those fluids around!

Probiotics & Prebiotics: Daily supplementation with a good combination of Lactobacillus and Bifidobacteria strains ensures that helpful organisms predominate in the intestinal microenvironment, and harmful bugs are kept in check. Certain probiotic species also aid in clearing pesticide residues, hormones in foods, and toxic metals like lead and mercury.

Probiotics are especially important after someone has taken antibiotics, which tend to kill off helpful bacteria along with the targeted pathogen(s). Antibiotics are sometimes necessary, but they can definitely throw a lot of sour notes into the digestive symphony.

Healthy bacteria need to eat, and the fiber in our diets is their main source of nourishment. People on plant-rich diets may get enough fiber from what they eat, but many other people will benefit from a prebiotic supplement. Prebiotic fibers also bind toxins and accelerate their safer removal from the body.

L-Glutamine & Pyridoxal Alpha-Ketoglutarate (PAK): The cells of the intestinal mucosa are the body’s main consumers of the amino acid glutamine. This nutrient is especially important for repairing damaged intestinal mucosa. While some people get enough glutamine from their diets, others benefit from supplementation. The problem is that increased intake of glutamine can result in build-up of glutamate, which is an excitatory neurotoxin.

That’s where Pyridoxal Alpha-Ketoglutarate (PAK) comes in handy. This compound is a patented combination of pyridoxine and alpha-ketoglutarate. A fixed combination of L-glutamine and PAK (1,500 mg glutamine plus 500 mg PAK), aids in the recycling of glutamine, increasing its availability to the gut mucosa, the brain, and the muscles while preventing harmful accumulations of glutamate.

L-Histidine: This amino acid is a good source of stomach acid protons, which paradoxically are often lacking in people with stomach symptoms, and those with acute or delayed allergies. A 600 mg dose of L-Histidine prior to each meal can be helpful.


Russell Jaffe received his MD and PhD from Boston University School of Medicine in 1972. He is a founding chairman of the Scientific Committee of the American Holistic Medical Association. Dr. Jaffe developed the lymphocyte response assays (LRA) that enable physicians to rule in/out 491 common allergenic substances based on delayed hypersensitivity by functional LRA by ELISA/ACT. He is also founder of PERQUE, a practitioner-only nutraceuticals company (

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