There is so much information out there about which foods harm the gut and should be eliminated in order to heal from chronic gut conditions that I just had to write this article. I just couldn’t sit back any longer and allow the actual science to be ignored by the echo chamber of people parroting popular diet gurus who manage to get a lot of mainstream media attention on TV, magazines, and podcasts. So here you have it — a short, readable article on two main categories of foods that damage the gut microbiome and contribute to chronic gut conditions such as irritable bowel syndrome, Crohn’s, ulcerative colitis, colon cancer, the kind of bloating that can make you look (or feel) 9 months pregnant when all you did was eat your breakfast, and intestinal gas that is not only humiliating but could quite possibly cause an emergency aircraft landing. So keep reading, and please share this with the people you care about!

Foods & Supplements Containing Heme Iron

The food with the highest heme iron content is any type of animal liver, but red meat (beef, lamb, and pork) is likely the main source of heme iron in most people’s diets. Many multivitamin formulations and some other dietary supplements also contain heme iron or ferrous sulfate, another form of iron that is toxic to the gut. Heme iron is also present in poultry, fish, and shellfish. Heme iron is not found in plant sources of dietary iron, such as beans, blackstrap molasses, and leafy green veggies. However, some new plant-based “meats” allegedly contain a plant-based type of heme iron (which looks like blood). Whether these products are safe for individuals with gut issues is questionable without any research or clinical studies on how these new products affect the gut and gut microbiome.

High protein diets in general and diets high in beef and pork in particular have long been associated with an increased risk for developing a wide variety of conditions, from type 2 diabetes and heart disease to autoimmune diseases, cancers, and inflammatory bowel diseases. There are multiple components of animal meats and therefore multiple mechanisms involved in their contribution to the development of chronic, degenerative diseases. A discussion of all of the harmful components of meats, including non-human sialic acid Neu5Gc, advanced glycation end products, cancer-feeding amino acids, saturated fats, etc. will require a separate article. For the purposes of this article, right now I’m only focusing in on one component of animal meats — heme iron — and how it affects the intestinal microbiota and contributes to inflammatory bowel disease. (We’ll discuss some of the amino acid components in the next section of this article.)

The fate of dietary heme iron in the digestive tract and the way that dietary iron affects our microbiome is one key factor in the red meat-gut disorder connection. Iron doesn’t even get metabolized until it reaches the colon (the final section of our intestines), where it feeds gut pathogens. Dietary heme iron (the form of iron found in red meat, poultry, and fish) has been shown to induce gut dysbiosis and inflammatory bowel disease in animals. In addition, a randomized, controlled trial conducted on children in Africa found that iron supplements induce dysbiosis (an increase in Enterobacteria) and gut inflammation (evidenced by an increase in fecal calprotectin, a marker for inflammatory bowel disease).

When we eat heme iron or take heme iron or ferrous sulfate iron supplements, the Firmicutes phylum of bacteria (the category of bacteria associated with leanness) decreases and the Proteobacteria phylum of bacteria increases (with an emphasis on the Enterobacteria family). Proteobacteria and Enterobacteria are considered to be pathogenic categories of bacteria that include a wide range of different species, including Escherichia coli (the bacteria that causes food poisoning and urinary tract infections), Salmonella (another bacteria that causes food poisoning), Helicobacter (the bacteria infamous for causing stomach ulcers), Yersinia (the bacteria that has been associated with the development of Hashimoto’s thyroiditis and Graves’ disease), and Legionella (the bacteria that causes Legionaire’s disease).

Now obviously not everyone who takes iron supplements or consumes heme iron will develop inflammatory bowel disease. There are multiple — potentially hundreds — of gene loci involved in susceptibility to developing inflammatory bowel disease and other chronic conditions involving the gut. However, studies have shown that a heme-iron free diet (and avoidance of ferrous sulfate iron supplements) does prevent inflammatory bowel disease. Additionally, a plant-based diet has been shown to induce disease remission in Crohn’s disease patients with conditions that were unresponsive to medications. Plant-based sources of iron (such as pea protein and spirulina) do not feed pathogenic Enterobacteria and instead encourage the growth of beneficial bacteria that protect the gut from disease. It should be noted that IBD is a known side effect of low carb diets (which tend to be high in animal protein and heme iron), and the inflammatory condition can be reversed by a plant-based diet.

Foods High in Sulfur-Containing Amino Acids & Foods Containing Sulphites

Eggs, milk, cheese, shellfish, fish, most shelf-stable bottled juices including lemon, lime, and grape juice, many pickled and canned foods, some salad bar ingredients, many dried fruits, and wine are the worst offenders in this category. Eggs, milk, cheese, and shellfish usually need to be strictly avoided. For the other items, always check ingredient labels for the presence of sulphite, bisulphite, metabisulfite, or sulfur dioxide.

These foods can initiate or worsen symptoms associated with inflammatory bowel disease (IBD) such as Crohn’s and colitis, irritable bowel syndrome (IBS), small intestinal bacterial overgrowth (SIBO), or even just the occasional gas and bloating, as well as increase risk of developing colorectal cancer. Studies show that individuals with chronic gut problems do tend to eat more sulfur-containing amino acids than people who don’t have chronic gut problems, and the removal of foods high in these components alleviates symptoms.

But why exactly do these foods exacerbate gut problems, and why does the removal of these foods often bring relief? When we consume foods that are extremely high in these nutrients (such as eggs, cheese, milk, and shellfish), the metabolites of cysteine, methionine, and taurine increase the proliferation of pathogenic sulphate-reducing bacteria such as the well-studied species Desulfovibrio piger. These sulphate reducing bacteria produce hydrogen sulfide gas, which is toxic to the gut.

Sulphate-reducing bacteria are known as conditional anaerobes, meaning they can live with or without oxygen, and they are categorized as opportunistic pathogens. This means they become pathogenic when given the opportunity, such as a steady supply of their favorite foods (concentrated sources of methionine, cysteine, taurine, and sulphites). One way to tell whether you have an overgrowth of sulphate-reducing bacteria is if you have extremely smelly gas and bowel movements that smell like rotten eggs.

The solution to this is to completely eliminate the foods discussed here that are extremely concentrated sources of sulphur-containing amino acids and any foods or beverages that contain sulphites. Please note that you should not eliminate all food sources of sulfur-containing amino acids and organic sulfur. Methionine and cysteine are both essential amino acids, meaning we need to eat them in order to replace proteins in the body that are used for cellular growth, maintenance, and repair. These amino acids also combine to make taurine, which is an amino acid that is necessary for cardiovascular health. We also need organic sulfur, which is important for healthy hair, nails, skin, and joints. Plant-based sources of methionine and cysteine — such as beans & lentils, whole grains, nuts & seeds, and spirulina  — contain these essential amino acids in moderate amounts that are balanced with other essential amino acids, so they do not provide a concentrated food source for sulphate-reducing bacteria. Nutritional yeast is a moderate source of taurine. Plant-based sources of organic sulfur include cabbage, cauliflower, onions, and garlic, which have an overall beneficial effect on the gut microbiome by promoting the growth of butyrate-producing bacteria, which benefit gut health by providing food for colonocytes (the cells of your large intestine).

To learn about other foods that benefit your microbiome and overall gut health, please read the previous article in this series on the microbiome. Also make sure you’re signed up for my free newsletter to be notified when the next article in this series is posted, in which I’ll discuss what the scientific evidence says about how adding fats & oils to your food affects your gut microbiome and your brain. There will be an overview of the connection between the brain and the gut, and whether different fats and oils such as butter, coconut oil, olive oil, MCT oil, soybean oil, and canola oil are beneficial or detrimental to your gut and brain health. You don’t want to miss this one, which will surely be controversial!