3 Tips for a Healthy Gut Biome (Hint: Yogurt is Not One of Them)
Your gut biome (the bacteria living in your intestines) is crucial to your health. The overuse of antibiotics, diets high in processed foods, and foods containing histamines are your gut biome’s worst nightmare. When your gut bacteria get thrown off, you can develop something called histamine intolerance, which leads to increased inflammation, congestion, hives, migraines, and fatigue — just to name a few symptoms. Even if you have a lot of DAO enzymes (the molecule that breaks down histamines) you may not be able to keep up with the amount of histamines in the foods you eat, especially if you eat lots of aged and fermented foods, or microbiologically produced foods, like the standard American diet’s favorite “health food” — yogurt.
If you’re already concerned about your gut bacteria, and you take probiotics to help those bacteria flourish, you may be doing the exact opposite of what you want, depending on the specific bacteria that you’re supplementing. For example, if you’re taking a histamine-producing bacteria in yogurt like Lactobaccillus casei, you’ll be doing more harm than good. That’s why it’s important to be aware of which bacteria produce histamines, which degrade them, and which don’t affect them at all.
Yes, you read the title of this post correctly. You’re about to read how yogurt and some probiotics negatively affect our gut bacteria. Both can be unknown culprits in making people fat and foggy headed.
For the past 30 years, obesity and autoimmune disease rates have been on a steady rise. At the same time, a little-known condition called histamine intolerance has become much more common. It’s a challenge to figure out the root causes and common denominators for these three seemingly unrelated health trends.
Lots of research shows that an unhealthy gut contributes to obesity, diabetes, rheumatoid arthritis, autism, depression, and chronic fatigue. The gut biome (intestinal bacteria), your diet, and the gut lining determine gut health. Modern lifestyle factors like the overuse of antibiotics, and diets high in processed, preserved, and histamine producing foods (i.e. most conventional yogurt), all contribute to an unhealthy gut biome. To repair an unhealthy gut and decrease histamine intolerance you need to eat an anti-inflammation diet, minimizing histamine producing bacteria and maximizing histaminedegrading bacteria.
This isn’t just science to me — it’s personal. My history of 15 years of heavy antibiotic use for chronic sinus infections as a young man set me up to have a histamine intolerance. Biohacking that problem helped me to discover the histamine connection years ago, but the link to the gut biome was quite elusive.
Why Your Gut Biome has Changed and Why Probiotics Have Become So Important
The human gut biome (microbiome) consists of about 100 trillion bacteria cells — more than 10 times more than there are human cells in your body. You could even start to think of your gut biome as a significant organ in your body, so keeping it healthy and balanced is essential to reduce disease and optimize performance. As we learn more about the makeup of good and bad bacteria in the gut biome, researchers are also doing cutting edge DNA microbiome sequencing to show how people’s gut biomes are changing on a population level.
Gut biomes are becoming imbalanced because there are less good bacteria and more bad bacteria available in modern lifestyles and the standard American diet. When microbiota balance is out of whack, your body develops chronic inflammation, which can become autoimmune disease or other serious health problems. New research even suggests that diabetes may be an autoimmune disease triggered by poor gut health.
By now, most people know that one contributor to a broken microbiome is overuse of antibiotics. Antibiotics may wipe out whatever bad bacteria you were hoping they would, but they can also clear your system of the really good bacteria that promote a healthy gut. A number of studies show that even a single course of antibiotics can permanently alter the gut flora.[2,3]
Aside from antibiotics overuse, poor diets and environmental toxins also wreak havoc on the gut by wearing down the protective barriers of the intestinal walls, eventually creating a leaky gut. As I’ve written previously, foods that are heavily processed, preserved, and filled with chemicals and toxins, damage gut health. Common types of these gut-damaging foods include: gluten, processed meats, sugar, most alcohol, mold toxins from coffee and chocolate, and more. These foods increase histamine levels, which in part is due to bad bacteria. I will go into more detail about histamine inducing bacteria in foods later in this post.
One of the reasons I’m such a fan of fresh, organic, local meat and vegetables is that our gut bacteria ultimately are related to our soil bacteria. Soil bacteria are the microbiome of the planet. Industrial agriculture has permanently modified soil organisms — molds and bacteria — so that they produce more toxins than ever before in history. The genes that form those toxins get shared with the bacteria growing in your gut.
Since the advent of antibiotics, scientists have been all over fighting bad bacteria. Now they are beginning to understand the importance of good bacteria and microorganisms in our guts. This “good bacteria” theory led to taking supplemental probiotics as the go-to way to help re-populate our guts after courses of antibiotics or other stressors. Although some probiotics are good for you, sadly (for yogurt companies especially), most manufactured probiotics are only minimally effective at re-populating the gut biome. It is becoming apparent that not all strains of probiotics interact with the gut in the same way.
Histamine Intolerance and Which Bacteria to Avoid
Disturbance in gut biome also plays a significant role in creating the recent rise in histamine intolerance. Histamine intolerance is the result of an imbalance between the breakdown of histamine and its buildup in the gut. This is generally caused by a deficiency in the DAO enzymes (found in intestinal mucosa) that helps metabolize and breakdown dietary sources of histamine.
A histamine overload leads to increased inflammation and many other symptoms including: skin irritation, hives, throat tightening, increased heart rate, nasal congestion, migraines, fatigue, heartburn, reflux, and weight gain. Unlike other food allergies and sensitivities, the response from histamine intolerance is cumulative and not always immediate, so it is harder to pin point right away. [5,6]
This is personal — I’m histamine intolerant but have been able to reduce my intolerance dramatically following the advice I’m sharing in this post.
Although there are some genetic causes for a decrease in the production of DAO enzymes, the change in people’s gut biome is also responsible for histamine intolerance. Even if someone has a normal production of DAO enzymes, the levels may still be insufficient when placed against high concentrations of histamine-rich foods and histamine producing bacteria.
Some common sources of histamine-producing foods are surprising. The following foods often have higher histamine contents or help release stored histamine:
- Matured or fermented foods (depending on the bacteria and yeasts that are involved in the process): Sauerkraut, Kombucha, pickles, fermented SOY products, soy sauce, fish sauce, fermented coffee (Upgraded Coffee is safe). Some fermented foods are acceptable as long as it does not cause a negative reaction.
- Microbiologically produced foods: Most yogurt, buttermilk, kefir, mature cheese, sauerkraut, wine (especially reds)
- Processed, smoked, and fermented meats: Lunchmeat, crappy bacon, sausage, pepperoni, salami, etc.
- Alcohol: Red wine, white wine, champagne, beer
- Yeasty Foods: breads made with yeast
- Certain Vegetables, Fruit, and Nuts: tomato, canned vegetables, strawberries, kiwi, pineapple, peanuts, cashews, walnuts, and more.
Different types of bacteria and probiotics also play a part in histamine regulation. Some probiotics are necessary for proper gut function (where histamine lowering enzymes DAO form), but some strains actually raise histamine levels. The different strains of studied probiotics are categorized as (1) histamine producing bacteria, (2) neutral bacteria, or (3) histamine degrading bacteria.[7–1]
- Histamine producing bacteria: Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus (Found in most yogurts and fermented foods).
- Neutral bacteria: Streptococcus thermophiles (also in yogurt) and Lactobacillus rhamnosus (shown to down regulate histamine receptors and up-regulate anti-inflammatory agents)
- Histamine degrading bacteria: Bifidobacterium infantis (found in breast milk), Bifidobacterium longum, Lactobacillus plantarum, and some soil-based organisms.
Some of these bacteria form histamine when they break down protein in foods, even vegetables, whether the food is in your gut or fermenting in your kitchen. Now you know why I’m skeptical about throwing a bunch of cabbage into a bucket to let it ferment. You just don’t know what you’re getting.
The Probiotic Bulletproof® Coffee Failed Experiment
At one point, I had a brilliant idea to add a prebiotic (food for probiotics) called fructooligosaccharide to my Bulletproof® Coffee in the morning, and take a probiotic with it. Over the last decade, I estimate I’ve spent around $25,000-$50,000 on various strains of probiotics to fix my gut, including the time I took pig whipworm eggs. Anyway, I took an “acidophilus pearl” capsule because those were convenient and I was out of my normal probiotic. The one I took had lactobacillus casei, a histamine producing bacteria in it.
The result? I gained 10 pounds in seven days, with a noticeable inflammation in the gut. I stopped the probiotics and it took 7 days to lose the weight.
Probiotic supplementation is a catch-22 and you should not just grab whatever has the best label on the shelf. If you have histamine intolerance, or you want to avoid developing it, experiment with avoiding histamine producing bacteria and focus on histamine degrading or neutral bacteria.
So just toss out the Lactobaccillus casei from your cupboards and fill your refrigerator with Bifidobacterium longum, right?! Uh… yeah… The good news is there are protocols, diets, and product already developed to help you reduce histamine-rich foods, avoid histamine producing bacteria, andconsume more histamine degrading bacteria.
3 Ways to a Healthy Gut Biome and Reduce Histamine Intolerance
#1) Heal your gut with an anti-inflammatory diet:
Eat a low histamine, anti-inflammatory diet (like the Bulletproof® Diet) as the primary way to protect your gut and reduce histamine intolerance. Eating prebiotic foods that selectively stimulate the growth of good bacteria in your gut is also helpful. Prebiotic foods include: Jerusalem artichoke, avocados, and vegetables high in soluble fiber like sweet potatoes, Brussels sprouts, asparagus, and turnips. Onions are in the yellow zone because of what they do to alpha brain waves, but they also have prebiotics in them.
#2) Reduce histamine producing bacteria
Avoid histamine producing bacteria like Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus that are mostly commonly found in the majority of yogurts and fermented foods, especially when they are not balanced by other species. Rampant unbalanced focus on lactobacillus in yogurt has led to this problem.
#3) Increase histamine degrading bacteria
Finding ways to get more histamine degrading bacteria into your diet can be difficult, but is great for gut health and key to reducing histamine intolerance. High phenol foods like blueberries, coffee, and chocolate can feed a type of gut bacteria called firmacutes.
My favorite (best tasting) source of balanced bacteria is a yogurt-like product, called Amasi, that contains 30 carefully controlled strains of bacteria. Traditionally, Amasi is the renowned drink of the Masai warrior tribes in Northern Tanzania and Kenya and is known for its rich variety of beneficial bacteria and highly bioavailable nutrients.
As you might have heard on podcast episode #47 with Jordan Rubin, founder of Beyond Organic and creator of Amasi, he replicated the Masai tribes’ production system to produce Amasi from grass fed, antibiotic free, cow’s milk. Rubin even went to the extent to make sure he used the same genetic breed of the Masai’s cows to assure they have non-inflammatory kind of casein (Beta casein A2).
The fermentation of the Amasi is influenced by key histamine degrading bacteria: Lactobacillus plantarum, Bifdocaterium lactis, and Bifidobacterium longum.13,14 These particular strains not only lower histamine levels, reduce inflammation, and improve digestion, but Amasi as a whole food helps improve absorption of specific nutrients such as vitamin B6, B2, and K, folic acid, niacon, and zinc.
Have you tried any of these hacks? What has/hasn’t worked for you?
Photo by: Diego
- Endotoxemia is Associated with an Increased Risk of Incident DiabetesHistamine intolerance-like symptoms in healthy volunteers after oral provocation with liquid histamine
- The influence of single dose intravenous antibiotics on faecal flora and emergence of Clostridium difficile
- The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing.
- Microbial ecology: Human gut microbes associated with obesity
- Histamine and Histamine Intolerance
- Histamine Intolerance by Dr. Janice Joneja
- Histamine Derived from Probiotic Lactobaccillus reuteri Supresses TNF via Modulation of PKA and ERK Signaling
- Evidence for a reduced histamine degradation capacity in a subgroup of patients with atopic eczema, by Maintz et al.
- Exogenous histamine aggravates eczema in a subgroup of patients with atopic dermatitis, by Worm et al.
- Bacterial Production and Destruction of Histamine in Foods, and Food Poisoning Caused by Histamine, by Dr. C. Lenistea
- The Production of Amines by Bacteria. The Decarboxylation of Amino-Acids by Strains of Bacterium Coli, by Ernest Fredrick Gale
- Therapeutical use of probiotic formulations in clinical practice, by T. Lannitti
- Bacterion production by Lactobacillus plantarum AMA-K isolated from Amasi, a Zimbabwean fermented milk product and study of absorption of bacterion AMA-K to Listera sp.
- Use of traditional African fermented beverages as delivery vehicles for Bifidobacterium lactis DSM 10140.