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Solstice greetings: bugs and guts
June 21, 2022, 5:14am ET

Greetings on the Solstice. I hope that you and your loved ones have some annual traditions that you will enjoy in the coming months. I began looking forward to summer after my annual colonoscopy in May.

I was diagnosed with ulcerative colitis 37 years ago and have been in and out of hospitals since. On the day of my colonoscopy, I gave the medical team permission to take extra biopsies during the procedure and draw some extra blood for a research study about the link between genetics and inflammatory bowel disease. As an experienced nurse drew blood from one of my experienced veins, I asked my current doctor what he and his peers know now that they didn’t know ten years ago. “We understand much more about the microbiome,” he replied through his mask. He is my seventh gastroenterologist and the first to mention the microbiome.

A letter that starts with a colonoscopy might not seem promising, but I promise that what follows won’t be gross. I hope you’ll stay with me because the human digestive system and the earth’s natural systems depend on one another, and both are threatened by misapplied science and reasoning.

Don’t not eat your vitamins 

For a year or so in college, I worked at a store called the Vitamin Shoppe. Why it had the old-timey “Shoppe” in its name was one of many mysteries: What were all of these supplements for? Did they really work? Did our ancestors miss out on these things and suffer as a result? I took the job not because I was interested in vitamins but because it was an easy way to earn some money and didn’t require me to wear a referee’s uniform (unlike the job at Foot Locker that I quit after one miserable shift). Recently, however, I heard a podcast about the history of vitamins that resolved some of those mysteries, illuminated my health and public health, and offered insight into modern society’s approach to climate change. 

In the late 1800s, a new, gruesome, lethal disease called beriberi suddenly emerged in the Dutch colony of Indonesia. At the time, Western science was abuzz with its newfound understanding of bacteria. “We understand that bacteria cause illness! They must be the cause of every illness!” was the consensus of the day. So a Dutch scientist named Christiaan Eijkman began looking for the beriberi bacterium. He injected some chickens with human blood from sick people and watched for the disease to spread. No matter how he separated the chickens, however, the control and treatment groups kept having the same outcomes: Lots of chickens got beriberi. Then, one day, beriberi started disappearing from all of the chickens in both the control and treatment groups. Soon it was gone. Eijkman had cured beriberi but didn’t know how. The answer, it turned out, was to stop giving the chickens “more advanced” food, namely white rice.

People in China were eating rice at least 11,000 years ago, making it one of the first domesticated plants. Rice farming grew over the millennia along with Asian civilization. Indeed, the word for rice is the same as the word for food in Chinese and several other Asian languages. Rice kernels have a hard outer layer called a hull which must be removed for rice to be edible. Inside the hull is a brown layer of bran, and inside that bran is a light-colored kernel. Until the late 1800s, what people called “rice” was hulled but retained its bran. We now call that food “brown rice.” The invention of new, industrial milling machines enabled the removal of both the husk and the bran, revealing a light, almost white interior. White rice’s bright appearance made it seem more modern, its starchy sweetness appealed to people, and, most valuable of all, without its bran, rice could be stored almost indefinitely. 

Eijkman eventually figured out that beriberi wasn’t caused by the introduction of a new pathogen but rather by the loss of a critical nutrient. Among many other things, rice bran contains thiamin, which is involved in several basic cell functions and is necessary for the body to turn nutrients into energy. The new white rice diet left the people and chickens of Indonesia deficient. Eijkman’s chickens, it turned out, were saved because word got out that his chickens were being fed “superior” white rice, which was considered a relative luxury. When his assistants changed their diet back to brown rice, the chickens recovered.

Beriberi was among the first known “deficiency diseases.” It wouldn’t be the last. Vitamin C was discovered because sailors who ate no fruits or vegetables on long voyages got scurvy (Japanese sailors got beriberi in the 1880s from white rice), and other vitamin deficiencies were discovered after further agricultural and dietary innovations led to new illnesses. And as industrial diets moved toward purer starches and meat and away from plants, scientists discovered even more vitamins.

After the discovery of thiamin, a Polish scientist coined the term “vitamin,” putting together vita, Latin for “life,” and amine, a group of compounds that included thiamin. Successive deficiency diseases were not due to amines, but vitamin endured as a catch-all name for a growing list of molecules that science identified as critical to human health. They undoubtedly represent only a share of the micronutrients that benefit our bodies, but the other ones haven’t yet revealed themselves with a single, novel disease. Which brings me back to my gut. 

Angry guts

Ulcerative colitis is an autoimmune disease. “Autoimmune” is a scientific way of describing a body attacking itself. Cells in my colon wrongly identify neighboring cells as threatening and summon my immune system to kill them. The result is a pointless war on the surface of my large intestine. When I became sick as a teen in the mid-1980s, the medical establishment didn’t know why people got ulcerative colitis, and there was very little promising research into it. Mostly it was treated by taking oral steroids, which curb the entire immune system, with severe consequences all over the body.

In the ensuing decades, a lot of research was done on ulcerative colitis and its sibling, Crohn’s disease, which together are known as inflammatory bowel disease (IBD). This research has overwhelmingly followed the conventions of Western science: Look for a single treatment that will inhibit the disease or look for a discrete cause of the disease. My blood and tissues were collected for a study looking for a combination of genes that incite war in my belly, in hopes of developing a treatment that would lead to peace. 

I hope the study is successful, as many people would benefit from better treatment. Still, I can’t get over a couple of facts: 1) Until the 1880s, no one in the world had IBD before it started appearing in Britain, the leading industrial country at the time, and 2) It remained a Western disease until it appeared in Asia and the Middle East in recent decades. 

A 2016 article in the journal Nature, titled “Epidemiology: Rising in the East,” quotes a Hong Kong gastroenterologist who says, “I can hardly keep up with all the [IBD] patients I have; the number of cases is basically exploding.” The article begins: “Inflammatory bowel disease is a growing problem in Asia. But that increase presents a golden opportunity for research.” The quoted doctors (including my own gastroenterologist) are looking for a combination of genetics and environmental factors that are causing so many people to have these problems. When I was first diagnosed, I was told that one in every few thousand American adults had IBD. Today, more than 1% of adults in the US have either ulcerative colitis or Crohn’s, and the number keeps rising. One thing is clear: The rise of colitis follows the rise of the industrial diet, especially refined starch, sugar, and meat. In other words, it’s great that there’s an opportunity for research, but we already know the main cause of people’s immune systems going haywire. 

Not too much

I have taught a basic data literacy and statistics course to colleagues and other adults a few times in the past 15 years. A 1997 article called “Unhappy Meals” by Michael Pollan is always on the syllabus. Pollan starts the article with seven words that the students don’t expect: “Eat food. Not too much. Mostly plants.” 

I assign this article because while superficially its subject is food, the real subject is classifying outcomes, determining causality, and identifying treatments: the process for which we use data. In the first paragraph, Pollan starts clarifying his terms, noting that it was once obvious what the word food meant, but it’s become increasingly less so as supermarkets have been filled with “food-like substances” that come in heavily branded containers, bearing data-loaded labels and promising health benefits. Pollan is interested in how we got here and thinks a series of events in 1977 were likely important:

Responding to an alarming increase in chronic diseases linked to diet — including heart disease, cancer and diabetes — a Senate Select Committee on Nutrition, headed by George McGovern, held hearings on the problem and prepared what by all rights should have been an uncontroversial document called “Dietary Goals for the United States.” The committee learned that while rates of coronary heart disease had soared in America since World War II, other cultures that consumed traditional diets based largely on plants had strikingly low rates of chronic disease. Epidemiologists also had observed that in America during the war years, when meat and dairy products were strictly rationed, the rate of heart disease temporarily plummeted.

Note the similarity with beriberi and scurvy: Rare chronic heart disease, cancers, and diabetes were becoming endemic, and there was extremely strong evidence that the increase was connected with a big dietary change. How did the committee react? 

Naïvely putting two and two together, the committee drafted a straightforward set of dietary guidelines calling on Americans to cut down on red meat and dairy products. Within weeks a firestorm, emanating from the red-meat and dairy industries, engulfed the committee, and Senator McGovern (who had a great many cattle ranchers among his South Dakota constituents) was forced to beat a retreat. The committee’s recommendations were hastily rewritten. Plain talk about food — the committee had advised Americans to actually “reduce consumption of meat” — was replaced by artful compromise: “Choose meats, poultry and fish that will reduce saturated-fat intake.”

Industrialization began the transformation of food away from its literal roots. After World War II, America reinvented eating through industry. Over the past 70 years, industrial farming, industrial food processing, and industrial food delivery and preparation have transformed diets around the world. In the process, they have transformed at least two microbiomes: the ones in our bellies and the ones in which plants grow. They have also transformed forests, fields, and the atmosphere. Along the way, autoimmune diseases have spread well beyond the gut, and other forms of poor health have emerged and surged. 

The point I’m here to make is one that you almost certainly know: If we could stick to eating food, mostly plants, and not too much, we would be far healthier, and our climate would be in less peril. In other words, we could stop doing things that we know are making us sick. Our kids would have healthier bodies and better attention, cognition, and emotional health. They would also have a less challenging future ahead. Instead, however, the dominant reaction to both the health crisis and climate change is to ask scientists and industry to come up with therapies for diseases we could avoid, vitamins to replace biodiversity we could sustain, and magical machines to capture carbon we could stop releasing.

Mostly plants

The “gold standard” in Western science is the randomized controlled trial (RCT), like the one Eijkman ran on the sick chickens. Such science requires the ability to isolate. Add or remove a single factor from a controlled population and try to determine the effects. The problem is that human nutrition and soil health will almost never fit in such experiments. For one thing, food comes from plants, and plants are complex. In his “Unhappy Meals” article, Pollan offers an example of a food that is commonly added in many cuisines: thyme.

Here’s a list of just the antioxidants that have been identified in garden-variety thyme: 4-Terpineol, alanine, anethole, apigenin, ascorbic acid, beta carotene, caffeic acid, camphene, carvacrol, chlorogenic acid, chrysoeriol, eriodictyol, eugenol, ferulic acid, gallic acid, gamma-terpinene isochlorogenic acid, isoeugenol, isothymonin, kaempferol, labiatic acid, lauric acid, linalyl acetate, luteolin, methionine, myrcene, myristic acid, naringenin, oleanolic acid, p-coumoric acid, p-hydroxy-benzoic acid, palmitic acid, rosmarinic acid, selenium, tannin, thymol, tryptophan, ursolic acid, vanillic acid.

This is what you’re ingesting when you eat food flavored with thyme. Some of these chemicals are broken down by your digestion, but others are going on to do undetermined things to your body: turning some gene’s expression on or off, perhaps, or heading off a free radical before it disturbs a strand of DNA deep in some cell. It would be great to know how this all works, but in the meantime we can enjoy thyme in the knowledge that it probably doesn’t do any harm (since people have been eating it forever) and that it may actually do some good (since people have been eating it forever) and that even if it does nothing, we like the way it tastes.

We can also know that if we aren’t eating bright green things like herbs, none of the things on that long list are entering our systems. I think of the short list of nutrients we call vitamins as the exceptions discovered by accidental experimentation: A community experienced a radical, isolated change in their diets; they got really sick in a novel way; and scientists were able to isolate the specific deficiency. Eijkman eventually won a Nobel Prize, but he discovered beriberi not because he created a treatment group and a control group but because people didn’t want to give chickens “superior” white rice. 

If there are that many things going on in thyme, imagine what is going on in healthy soil in which fragrant thyme grows. It turns out that just one gram (~1 teaspoon) of soil contains billions of living things.


Later this year, Probable Futures will release its next volume: Land. My collaborators and I have been happily digging through traditions, research, and stories about soil for the past couple of years. Some of what we have learned has been surprising, but mostly it has been similar to learning that stripping grains of all of their nutrients leads to bad consequences and that “fortifying” foods made of those depleted ingredients with the short list of “nutrients” on the side of a cereal box will probably still leave our bodies lacking and confused. On the one hand, it’s complex, and on the other, it’s simple and obvious. 

The human microbiome and the microbiome of soil have been with us all along. Before there was a scientific method, there were cultures of foraging, farming, cooking, and eating. These cultures learned the value of diversity and the connectedness of living systems. Farmers knew that soil was not a resource to be used up but rather a diverse culture to be studied, attended to, nurtured, and fed. As Wendell Berry puts it:

Out of the random grammar and lexicon of possibilities–geological, topographical, climatological, biological–the soil of any one place makes its own peculiar and inevitable sense… By its permeability and absorbency, for example, the healthy soil corrects the irregularities of rainfall; by the diversity of its vegetation it protects against both disease and erosion. Good farmers have always known this and have used the land accordingly… They are not appliers of generalizations, theoretical or methodological or mechanical… They are responsive partners in an intimate and mutual relationship.

Around the world, farmers learned nearly identical lessons: Mix crops, livestock, field, forest, forage, and fruit; see the farm as a closed system, turning waste from one area into food for another; and, most of all, nurture the soil because it turns decay into health, death into life. Faraway people often arrived at startlingly similar diets: Grow beans with grains, and both are more productive; eat beans with whole grains and you get full nutrition. Feed what humans can’t eat to livestock whose own teeming guts quickly turn waste into soil, and treat meat as a modest portion of your diet. Include some live cultures, whether in fermented beans, pickled roots and greens, yogurt and cheese, or other funky things, and you’ll have food in less fertile months and a happier gut. Leave space for trees and other native plants to buffer wind blowing away topsoil and house pollinators.

I have a strong emotional affinity for the state of Iowa. My wife grew up there, detasseling corn as a summer job. I vividly recall the long, rolling hills on my first drive there to meet her family. Americans of European descent were eager to control this land because it was covered in some of the most abundant, vibrant, deep soil in the world. For thousands of years, deep-rooted perennial grasses had held the soil, grazing animals had aerated and fertilized it, and migrating birds had stopped in the marshy lowlands that covered much of the area and dropped seeds into fields, giving new plant species chances to try the local climate. Humans first appeared in Iowa around 13,000 years ago, shortly before Earth’s climate stabilized. Over millennia, their descendents sorted into many different tribes whose cultures integrated nature. American settlers named the state for the Ioway people who, along with communities from many other tribes, lived there until they were forced off the land by various means, including war, disease, finance, and governmental policy. 

For several generations after taking over the land, the new state residents practiced traditional methods: Everything that lived on the farm was turned back into soil. Then the US government began to drain the swampy, low-lying parts that didn’t naturally drain, and the agricultural industry took over from the farmers. 

Industrial farms dedicate giant stretches of land to a single crop whose seeds must be purchased from an agribusiness each year, with scarcely any non-crop plants anywhere. The primary residents of Iowa are livestock: In 2020, the state was home to 3 million people, 3.6 million cows, 11 million turkeys, 25 million hogs, and 80 million chickens. Corn or soybeans cover roughly two thirds of all land. Half of the corn is turned into ethanol, an inefficient, unnatural, and unsustainable “biofuel” that is combined with petroleum to power automobiles. The rest is fed to the animals who, instead of grazing on their natural diet of diverse plants and bugs, live indoors and are fed manufactured corn and soy meal. The animals’ guts no longer produce what could be called manure, but rather antibiotic-filled waste, which, instead of fertilizing the soil, is pumped into an immense sewage system that ends in lagoons and rivers. The soil on most fields is tilled every year and sprayed with a pesticide that only the cash crop has been bred to survive. Before planting, the cash crop is bathed in fossil-fuel-derived fertilizer. It’s simpler to grow at scale if you use hydrocarbons as feed to grow carbohydrates and kill and dispose of everything that isn’t “productive.”

… The wheel of life became an industrial metaphor; rather than turning in place, revolving in order to dwell, it began to roll on the highway of progress toward an ever-receding horizon. —Wendell Berry

If you haven’t explored the Water volume on, I strongly encourage you to. It is fascinating and beautiful. There is a section about changes in precipitation and its effect on Iowa. One consequence of industrial farming and more intense rainfall is flooding that spreads the pesticides and massive amounts of nitrogen fertilizer that Iowan farmers use into biomes as far away as the growing dead zone in the Gulf of Mexico. They are also certainly affecting the microbiomes of the people of Iowa. I recently talked with a meteorologist in Des Moines who told me that his family filters all of its tap water because there are so many chemicals in it. They replace the filters every month.

Doesn’t taste like chicken

Flavor is very difficult to measure. As agribusiness built a food system that could work well with massive finance and government regulation, it prioritized metrics that could be easily captured: yield, pest resistance, and color. The Red Delicious apple is neither delicious nor particularly nutritious, but it is reliably red and hard to kill. The “Chicken of Tomorrow” competition was sponsored by a large grocery store chain in 1945. Its criteria were uniformity of size, volume of breast, hatchability, and feed efficiency. 

From an article in the Annual Review of Animal Biosciences in 2013:

Although the chicken was domesticated during the Neolithic period, the development of the modern broiler is a recent event that has occurred within the past 100 years. The chicken’s adaptability has allowed it to be grown globally under a range of husbandry conditions. That is, the same genetic stock may be found in a range of environments…. Under good husbandry and a high-energy diet, at 35 days of age a 1.40-kg broiler required 3.22 kg of feed in 1985. Twenty-five years later, we have a 2.44-kg broiler produced on 3.66 kg of feed.

Modern industry subjects cows to conditions that combine our experience and the chicken’s. It must be awful for them. Their noses are incredibly attuned to distinctive plants, undoubtedly informed by millennia of evolution. When grazing, they stop eating naturally. In feedlots, where they are fed a mix of corn, antibiotics, and—yes—vitamins, they are always hungry even though most of them have severe digestive problems. The modern steer reaches the average slaughter weight of 1,100 pounds in about 14 months.

Our ancestors followed their senses to foods that nourished them, and they ate a wide range of leafy greens, herbs, grains, meats, fungi, tubers, legumes, and all manner of other living things. They would likely be baffled by the blandness of the chicken of today. As the inheritors of this sensory legacy, why do we keep eating food that is losing its flavor? Food science.

In Mark Schatzker’s 2012 book The Dorito Effect, he explains that children who try many things develop a kind of vocabulary that their bodies then express as cravings. They seek out flavors to remedy deficiencies. Since developing ulcerative colitis, I have often craved pickled, fermented things, sour things, and crunchy, fibrous things. Only recently did I learn that these seem to be the foods that feed our guts’ microbiome. It undoubtedly helped that, worried about my gut, I stayed away from packaged and processed food. Otherwise, I might have been fooled.

Schatzker documents how, through testing in laboratories and focus groups, scientists figured out how to chemically simulate the flavors that we crave. The nutrition and complexity aren’t there, but our mouths don’t know. The best part for the food companies is that not long after your mouth is delighted with what it has sent down to the gut, the gut sends a signal back to the brain that says, “We are still craving the same thing,” so back you go to the snacks.

The forest for the trees

Peter Wohlleben managed a forest in Germany whose owners used it for lumber. He was trained to maximize the value of trees. Then some professors and students from a nearby university started conducting investigations and projects in his forest. Wohlleben’s interactions with them helped him become more observant of the trees and the soil around him. He came to a new, wonder-filled understanding of the forest, which he shares in his book The Hidden Life of Trees

The gist of The Hidden Life of Trees is that a forest is not a bunch of trees. It is a complex, diverse community that works through sharing, signaling, coordinating, experimenting, and many other interactions that we would call social. 

There turns out to be an incredibly dense network of fungi called mycelium, whose little tubes carry sugars, minerals, and other things between trees in various forms of exchange. This network was unknown to scientists until the last decade or so. Big, old trees are the most connected and, in a sense, anchor the forest. This corresponds with the finding in recent years that old-growth temperate forests, like the one Wohlleben works in, contain more carbon—that is, more life—below ground than above it. 

I particularly enjoyed Wohlleben’s book because it is from the perspective of someone who begins to realize—through interacting with scientists—that his professional mindset had distorted his vision so much that he ignored not just intuition and wisdom but things that were right in front of him. That is how I feel. I studied engineering, languages, economics, finance, and other topics. I worked in many places and often had the freedom to choose my own projects. I was looking for patterns in the world that could help reveal the future, improve the lives of people who were suffering, and increase prosperity. I often looked to what I thought of as distant history, including the late 19th century, for insight. Yet I never once really paid attention to the physical world. Compared with most of my colleagues and contemporaries, I was a wide-ranging generalist, but my approach to questions and problems was modern: Look for the one or two things, the hidden clue, the trick, the insight, the epiphany, the vitamin.

Working on climate change made me look around, look down, look up, and look way back to gain useful perspectives on the world we live in. I came to realize that the most important systems in the world rarely yield to this modern, controlled mode of analysis. And yet that isn’t the same as saying that we don’t have an understanding of them, and it certainly isn’t the same as saying that just because we can’t isolate them, we can’t recognize their importance in our actions. My current gastroenterologist has a much wider awareness than his predecessors did, but even he hasn’t asked me about my diet.


Robin Wall Kimmerer is both an academic botanist and a citizen of the Potawatomi Nation. In the beginning of her wonderful book Braiding Sweetgrass, she writes about asking her university students to cite a positive relationship between people and other species. They are unable to. They think of humans as either a menace to nature or of nature as a thankless giver to humans. 

At the end of her book, Kimmerer quotes her father, who teaches children to build fires at a Native youth science camp: 

Fires help out lots of plants and animals. We’re told that’s why the Creator gave people the fire stick–to bring good things to the land. A lot of the time you hear people say that the best thing to do for nature is leave it alone and let it be. There are places where that’s absolutely true and our people respected that. But we were also given the responsibility to care for land. What people forget is that means participating–that the natural world relies on us to do good things… You have to contribute to the wellbeing of the world.

We are now running a global experiment: moving everyone to a meat-heavy, refined carbohydrate, sugary, industrial diet, accelerated by a food science industry that has figured out how to trick our taste buds into believing they are getting nourishment. The results of the experiment are clear: This food system generates roughly 20% of the carbon emissions that are altering the atmosphere. It is destroying soil that developed over millennia. It is making us chronically ill. In some perverse way, it might be profitable for giant agribusinesses to keep on this morbid trajectory while scientists feverishly chase spreading diseases with “silver bullets,” or we could declare an end to the experiment. 


As an undergraduate, I focused on what would now be called systems engineering. In a factory, a systems approach illuminates waste, excess, and vulnerability. The discipline’s keywords are quality, maintenance, and culture. This training helped me understand many of the things that were wrong with American industry in the late 1980s, but changing that culture felt like it would take a long time. Economics offered me an alluring option: Don’t worry about limits; focus on growth. Unlike a systems approach, modern economics is unbounded. The belief that infinite growth will lead to a better life, or better lives, was implicit in my work and life for two decades.

Reading Wendell Berry’s words from 1973 this spring, I felt foolish and a little sick to my stomach. “We have become guilty of the monstrous pride of thinking ourselves somehow entitled to undertake infinite destruction,” he wrote. His words hadn’t taught me anything factual that I hadn’t already known from my earlier education and basic understanding of ecology, but I saw more clearly how a rejection of limits had simplified my outlook and actions in the world. 

A couple of days after I finished Berry’s book, a big box painted with flowers and plants appeared in the park next to our neighborhood public library. I spotted it on my way to the grocery store and checked it out. It’s a compost receptacle. Lisa and I went over a couple of evenings later with a paper bag of banana peels, apple cores, onion and garlic skins, coffee grounds, and egg shells that we would have otherwise sent to a landfill in a plastic bag. We met some folks whose compost was tied neatly in green compostable bags they had bought online. They kindly gave us a roll of them. The next day, I asked Al at the corner store if he could stock compost bags. He replied that a few people had been asking recently, and he’d order some.

The Drawdown project is the most comprehensive assessment of actions we could take to reduce, eliminate, and even reverse greenhouse gas emissions. It ranks 101 solutions by their impact. Eliminate food waste is #1. Health and education is #2. Plant-rich diets is #3. Silvopasture, managed grazing, perennial staple crops, tree intercropping, regenerative annual cropping, conservation agriculture, and abandoned farmland restoration are 11, 17, 19, 20, 21, 22, and 23, respectively. There is a lot of well-deserved excitement about electric cars, and they will be a great help in lowering carbon emissions, but they come in at #24. We don’t need new science or technological breakthroughs to move in hopeful, healthy, tasty directions. But we do need to rebuild a true agri-culture, and we can all participate. 

A new season

In the Northern Hemisphere, the air is warm, and the sun is shining longer today than any other day of the year. Plants are magically combining the sun’s energy with CO2 captured from the air. Forests and fields are full of life. Even our small, slightly unkempt, urban backyard provided us a big bunch of delicious dandelion leaves, which I sautéed with olive oil and garlic. I hope that you and the people you love have ways to savor the bounty of the season and that you try some new things. 

The team at Probable Futures continues to work on the platform. We are also beginning to collaborate with a variety of educators and professionals, from television meteorologists to supply chain managers. If you see an opportunity to collaborate, want to say hello, or have a great recipe you would like to share, please write to us at

Thank you for being a part of our community.