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Fall Foods – Seasonal Eating For Your Microbiome

As autumn rolls around and the leaves start to change, it’s time to take advantage of those last trips to the farmer’s market and stock up on late summer vegetables that bring with them a lot of color and add diversity to your seasonal diet. If you’ve ever heard me speak in an interview, you’ve heard me talk about the importance of a varied plant-rich diet for supporting a diverse, health-promoting gut microbiome.

Have you considered the influence of seasonal eating patterns on your own health? What happens if you widen your palette of vegetable choices? In fact, seasonal eating contributes to gut microbial diversity by introducing new foods that are in season, while transitioning off foods that are past their season.

When Tania came to see me, she was exhausted. It was fall, and she was distressed about her ever-expanding waistline. “I don’t get it!” she sighed, “I do everything right: I eat vegetables, eat lots of fruit, protein, healthy fats, and I don’t add sugar to anything. Rarely will I even touch dessert.” Yet, she kept packing on the pounds.

Turns out she was still adding a lot of fructose-rich fruit to her diet, way past the summer season. While she didn’t realize how much of a sugar-load that was, it was also breeding yeast overgrowth in her gut. She was bloated, moody and unhappy.

As food has become ubiquitously available world-wide year-round way past its seasons, the lines are blurred as to when it is appropriate to eat foods that are not locally sources and in-season. It has allowed a monotony to a diet, that ages ago would have been broken by the lack of transportation or refrigeration to keep foods fresh that were not in-season or local. In essence, it permits you to fall into patterns of eating that reduce the range and diversity of the foods you choose.  

If you’ve been following me, you know that you are in primary control of your health and the health of your microbiome through the foods you eat. In short, when you think of it this way, who are you really eating for?  Yourself?  Or your microbiome?  

Did you know that a balanced microbiome is protective against chronic illnesses like cardiovascular disease, irritable bowel disease (IBD), obesity, type 2 diabetes and even cancer? Yes, that’s right! Specific foods can greatly affect an individual’s overall health in terms of immune and metabolic function.1 That’s a mouth full! In other words, you feed your microbiome, and in turn it regulates all sorts of body functions, from your immune system to how you metabolize sugar.

By introducing seasonality to the way you eat, you help promote and maintain diversity within your gut flora. Ultimately, that is the goal! And that is where we started with Tania, by first cutting out all the summer fruit in her diet.   

Seasonal Foods

As foods are the freshest and lowest in carbon footprint when they come from your local farm-stand to your doorstep, eating seasonally results in more nutritious foods, less toxic load on our environment and better flavor. It should really be a no-brainer to eat seasonally as best you can!

Fall can be a beautiful time of year and a great time to incorporate diversity-promoting root vegetables, pumpkins, and squashes into your diet. In fact, this is a great time to enjoy various foods that will directly improve the health of your gut.

Allow me to explain the wonderful ways you can eat seasonally to feed your microbiome.

The Facts

Studies show that diet plays a major role in altering the gut microbiome. To some, this may not be a surprise. However, what is alarming is that within as little as 24 hours your microbiome can shift greatly, based only on what you eat. However, as scary as it may seem that a weekend of indulgence in pizza, wings, beer and dessert could drastically shift your gut flora into some frightening “halloween” creatures, there is comfort in knowing this, because in the reverse we can manipulate your diet to induce favorable changes in your microbiome.1    

In a systematic review, researchers showed that certain foods determine the predominant bacterial species within the gut. When shifts are favorable, it allows for greater growth of beneficial flora. However, when individuals eat a highly processed diet in added sugar and fat, a negative shift in gut bacteria has been found. This leads to unfavorable changes in the microbiome, which can manifest as leaky gut, autoimmunity and other disease states.1  

Eating For Your Gut

Fortunately, as mentioned above, positive changes can be made by eating the right, seasonal foods. Many seasonal, fall foods are rich in non-digestible carbohydrates or fibers called resistant starches, which act as prebiotic nutrients for the gut microbiome. Prebiotic foods are not digested in the small intestine; instead, passing through intact to the large intestine (or colon) where they undergo digestion and fermentation by the microflora.

Be sure to remember these foods are rich in fiber — the reason they are so important for gut health! Common resistant starch foods include sunchokes, garlic, leeks and onions.1,2,3

Resistant starches are absorbed in the large intestines at a much different rate than traditional carbs. Due to this, they show positive changes in metabolism. Resistant starches are associated with a decrease in blood sugar levels and insulin responses after meals due to the difference in type of carbohydrates, as compared to other commonly eaten carb-rich foods (like bread, white rice, and pasta). This is beneficial in reducing risk of chronic diseases, along with improving the metabolism of an individual.2

Resistant starches are fermented in the gut, with the result being short chain fatty acids (SCFA) like butyrate, propionate, and acetate. SCFAs (specifically butyrate) have anti-inflammatory effects on the gut and may reduce the risk of chronic diseases like cancer, type 2 diabetes, IBD and cardiovascular disease.3


Among the many reasons fall eating is so satisfying to our senses is because of the warming spices used. Spices like star anise and cinnamon along with many other fall picks contain polyphenols. These phytochemicals are popular in the natural health world for their abundance in antioxidants. Studies also show that polyphenols promote favorable changes in beneficial probiotic bacteria within the microbiome, such as Bifidobacterium and Lactobacillus.1

Change Your Diet Today!

We know that eating foods that feed favorable bacterial strains is imperative for total wellness. Start making changes today as we enter autumn, and enjoy the beautiful and delicious foods we have this season.

Seasonal Food List4

Check out a list of seasonal foods below. These foods are rich in phytonutrients and fiber, along with a pick of delicious resistant-starch options.

Acorn Squash





Brussel Sprouts

Butternut Squash


Delicata Squash








Spaghetti Squash

Sweet Potatoes

Sunchokes/Jerusalem Artichokes


How to Eat These Foods

To get the most bang for your bite, you want to prepare or eat these foods differently. For instance, try your best to consume onions, leeks and garlic as raw (or close to raw) as tolerated. However, avoid raw onions if you have a sensitivity to sulfur-rich foods. Eaten raw, they may provoke a headache or migraine. A great recipe to follow is my Scallion Vinaigrette, which uses raw, crushed scallions to give the salad dressing a distinct flavor, while promoting the growth of your probiotic flora.

In general, other resistant starch foods like sunchokes, squashes and sweet potatoes are digested best when cooked, then cooled before eating.

We had Tania incorporate more of these foods into her diet, while cutting out fruit and increasing the ratio of healthy fats. With this approach, we were able to stop the vicious cycle of insulin resistance and abdominal fat gain. We successfully reversed it by supporting her body’s ability to burn fat for energy. Incorporating seasonal eating into Tania’s diet plan helped improve her nutrient quality and resulted in the weight loss she was ultimately looking for.   

Creating A Happy Gut This Season

It is so important that you address your gut health from all aspects, including seasonal eating to promote a happy gut. If you’re looking to enhance your gut health, be sure to check out my Quick Start to a Happy Gut, your complimentary guide to total wellness through a healthy gut!

Happy Gut Recipes

Be sure try out the recipes at the Happy Gut Kitchen and stay tuned for upcoming new recipes we’ll be featuring this fall!

The Cure is in The Kitchen! (Where The Chef and the Doctor Meet!)

Dr. Pedre-David-Bouley

Question: What defines the meeting place between your plate and your health?  Where do the chef and the doctor meet on common ground?

Answer: Bouley Botanical.

David-Bouley-Dr. Pedre-Happy-Gut

On a Spring evening, April 19th, Dr. Pedre was invited to present at a special Happy Gut dinner at master chef David Bouley‘s Bouley Botanical restaurant space in Tribeca, New York City.

The event was part of Bouley Botanical’s Doctor and the Chef Series.  The evening featured a multi-course tasting menu, along with talks by Dr. Pedre and Chef David Bouley on healing through food.  The evening was a memorable, extraordinary culinary journey through multiple Happy-Gut-Approved dishes which we’ll recap here!

First, the space….


Elegant and open…filled with the scent of the live herbs growing happily!  Chef Bouley explained the special fans and environment cultivated for the health of these herbs.  Sixty diners came to the event.

The venue is filled with life, here is the stairwell column, which is covered in black felt pocket “homes” for each herb!

Bouley-Botanical-staris-Dr. Pedre

The juxtaposition of herbs and urban shows us we can find balance in the worlds which stimulate us and create health.


Below, is the “herb wall” separating the dining space from the kitchen.

Dr. Pedre-Bouley-Botanical

The room filled with guests and Chef Bouley spoke about his background working with the freshest produce and re-visiting heritage methods to create purees and oils of garlic.

Bouley-Botanical-Dr. Pedre

Chef Bouley calls these “basic tools” to have on hand as “building blocks’ in your kitchen that are anti-cancer and anti-inflammatory.

garlic puree

Chef Bouley next introduced Dr. Pedre, who spoke about the pillars of his Happy Gut Program.  Dr. Pedre aptly explained his analogy of a garden wall to illustrate what makes a healthy gut, as he explained on his Good Morning America segment, here.

Dr. Pedre-GMA

Our gut lining is one cell thick with cells tightly compacted like the stones of a wall.  Many factors change the permability and thus the immunity defenses of our gut lining which in turn compromise our health.  These include pesticides; GMO foods, which now range from potatoes to fish; stress; gluten; acid and sugar imbalances…such a long list!

Thankfully, a happy gut is obtainable as outlined in Dr. Pedre’s book HAPPY GUT, The Cleansing Program to Help You Lose Weight, Gain Energy, and Eliminate Pain, and his cleanse program.

After Dr. Pedre’s talk, the most amazing appetizers began to appear.

Happy-Gut-appetizer-Dr. Pedre

This delicate crisp is made of kuzu, a low-glycemic, high-fiber Japanese root vegetable which will not bump your blood sugar.  Topped with black truffle.

Caviar=Dr. Pedre

Caviar was also served like this!


To cleanse the palate, a carrot and tumeric soup with prebiotic sunchokes was next served.  Turmeric is an anti-inflammatory spice that has far-reaching benefits, including reducing inflammation in the gastrointestinal tract as well as the brain, making it a potent superfood for preventing Alzheimer’s.  Then another prebiotic-rich vegetable, a delicate salad of fresh baby greens with asparagus appeared to continue to feed the friendly bacteria in the gut!

Asparagus-Dr. Pedre-Happy-Gut

This was a concert of French Provence White, Jumbo Green and Pencil Asparagus swimming in Bouley Botanical Chlorophyll Blast and Fresh Passion Fruit.

Wild-Salmon-Dr. Pedre

As a first course, this moon-shaped dish appeared next with the first of the season, Wild Salmon with Organic Quinoa, Celery Root, Porcini Mushrooms and Ginger Yuzu Botanical Herbs Dashi.

Chicken-Dr. Pedre

The second main course was organic chicken, here opened so you can see all the delicious ingredients.  This was Pennsylvania Chicken with Wild New England Ramps, Wild French Blue Foot Mushrooms and Colorado Morels!

Dessert-Dr. Pedre

Dessert was another trip to a culinary flavor explosion, without the guilt of a high-sugar treat.  This sculptured beauty arrived.  Hibiscus Granite, when opened…

Dessert-Happy-Gut-Dr. Pedre

…revealed natural New York State Cascade Grape Sorbet, with Tahitian Vanilla ice.

So much inspiration, information and delicious tastes all evening, showing that eating for a happy gut is far from bland.  It is rich in colors, flavors, and textures. We thank Bouley Botanical, all the guests, and all our readers for their enthusiasm.  This kind of collaborative evening happily moves the realms of health and food closer.  We see that tending to our health (and our desire for delicious food!) can contribute to the health of the planet and even our LOCAL environment as seen by Chef Bouley’s example of housing a botanical within the confines of concrete Manhattan.  Ultimately, the doctor of the future will bring out a recipe pad, instead of the prescription pad, directing their patients to join them in the kitchen to cook up healing recipes.

The cure is in the kitchen!

Stay tuned for future events with Chef David Bouley.  Dr. Pedre’s Happy Gut Dinner was so popular, he has already been asked to return for a Fall event at the Botanical.

Best regards,

The Happy Gut Team