- April 3, 2025
As recent research highlights the importance of the gut microbiome, fermented foods have gained immense popularity. Once rare in conventional grocery stores, items like kombucha, kimchi, kefir, and sauerkraut are now widely available. These foods contain beneficial byproducts of fermentation and live microbes that can boost gut diversity and support better mental and physical performance.
However, not everyone experiences the benefits of fermented foods. The reason lies in a compound called histamine, a byproduct of fermentation produced by certain bacteria. For some individuals, histamines can cause adverse reactions, making fermented foods less suitable for them.
Your gut biome, the collection of microorganisms in your digestive tract, plays a crucial role in your overall health. Keeping it balanced is essential for reducing disease and optimizing performance. Overused antibiotics, environmental toxins, and heavily processed foods can disrupt your microbiota, leading to various health issues such as diabetes, obesity, depression, eczema, and irritable bowel syndrome.
Fermented foods contain live microorganisms that provide a vital dose of diversity to your gut. Studies have linked these foods to improved immunity, better weight management, cardiovascular health, glucose metabolism, and even cognitive function. A healthy balance of gut bacteria also helps moderate inflammation, reducing the risk of chronic diseases like arthritis, fibrosis, and depression.
The fermentation process increases the nutritional value of many foods by breaking down anti-nutrients and enhancing the bioavailability of stored nutrients. The bacteria involved in fermentation produce beneficial compounds that give these foods their antioxidant, antimicrobial, antifungal, anti-inflammatory, antidiabetic, and anti-atherosclerotic properties.
While a diverse microbiome offers numerous benefits, some common microbes produce toxins that can cause discomfort for certain individuals. These toxins include “biogenic amines” such as histamine, which can affect some people’s guts more than others. If fermented foods leave you feeling nauseous, inflamed, bloated, or generally unwell, you may be sensitive to histamine-producing bacteria or foods.
Histamines are neurotransmitters that influence brain function and immune health. During an allergic response, mast cells release histamines, causing inflammation to increase blood flow and allow immune cells to react to an intruder. This leads to classic allergy symptoms like puffy eyes, headaches, skin rashes, and nasal congestion. Histamines also form when bacteria break down proteins during fermentation and digestion.
For most people, histamines are not problematic. However, genetics or a damaged gut can lead to low levels of the enzymes DAO and HNMT, which are needed to break down histamines. Histamine intolerance occurs when your body cannot metabolize the amount of histamine in your diet, leading to an accumulation in your bloodstream and triggering symptoms similar to allergies or food sensitivities.
Symptoms of histamine intolerance include skin irritation, hives, throat tightening, increased heart rate, nasal congestion, migraines, fatigue, heartburn, reflux, inflammation, and weight gain. Understanding which bacteria produce histamines can help you manage your diet better. Some bacteria convert the amino acid histidine into histamine, while others can break down histamine. This balance determines the histamine content of fermented foods and the amount produced during digestion.
Eating foods high in histamine-producing bacteria can exacerbate histamine intolerance by supplying histamines and increasing the population of these bacteria in the gut. Even those without chronic histamine intolerance can experience issues by consuming too many high-histamine foods.
It’s challenging to know which bacterial strains are present in fermented foods, especially homemade ones. If you’re histamine-intolerant, you may need to avoid fermented foods altogether. However, you might tolerate certain foods or strains better than others. Avoiding histamine-producing bacteria and seeking out foods made with histamine-degrading bacteria can help you enjoy fermented foods without adverse effects.
Histamine-producing bacteria: Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus (found in many yogurts and fermented foods).
Neutral bacteria: Streptococcus thermophiles (also in yogurt) and Lactobacillus rhamnosus (downregulates histamine receptors and reduces inflammation).
Histamine-degrading bacteria: Bifidobacterium infantis, Bifidobacterium longum, Lactobacillus plantarum, and Saccharomyces boulardii (a yeast that increases DAO activity).
Fermented foods like sauerkraut, kombucha, and pickles can increase microbial diversity and offer numerous benefits, but only if your body tolerates them. You might find that you tolerate some brands better than others, depending on how they’re made. Experiment with fermented products made with organic vegetables and avoid those with artificial additives.
If fermented foods don’t sit well with you, it’s okay to avoid them. If you’re curious about which ferments work for you, seek out foods made with histamine-reducing bacteria or try low-histamine foods.
Try These:
Biohacking Coffee: Coffee is a fermented food, and Biohacking coffee beans are designed to have the lowest levels of histamines.
Amasai: Inspired by a traditional fermented drink from Northern Tanzania and Kenya, made from grass-fed, antibiotic-free cow’s milk and histamine-reducing bacteria.
Avoid These:
Common store-bought yogurts and cheeses:Many are fermented with Lactobacillus casei, Lactobacillus reuteri, and Lactobacillus bulgaricus.
Fermented soy products:These contain very high levels of dietary histamine.
Apple Cider Vinegar:While beneficial for some, it is often high in histamines.
Home-fermented foods:It’s challenging to know which bacteria are present in homemade ferments.
Some individuals are sensitive to histamines, which are byproducts of fermentation produced by certain bacteria.
Symptoms include skin irritation, hives, throat tightening, increased heart rate, nasal congestion, migraines, fatigue, heartburn, reflux, inflammation, and weight gain.
Avoid high-histamine foods and seek out foods made with histamine-degrading bacteria. Consider getting a microbial analysis to understand your gut bacteria better.
Yes, some fermented foods are made with histamine-degrading bacteria and are better tolerated by those with histamine sensitivity.
Biohacking coffee and Amasai are examples of low-histamine foods that can be included in your diet.
Understanding the role of histamines in fermented foods can help you make informed choices about your diet. By identifying which foods and bacterial strains work best for you, you can enjoy the benefits of a diverse gut microbiome without the adverse effects.
nataly@bioupgraded.com
@bioupgraded
Dallas, TX, USA
