Why Do I Feel Worse After Taking Probiotics?

Michael Eisenwasser 3 min read

Probiotics are supposed to help your gut. So it's frustrating when you start taking them and actually feel worse.

If you have histamine intolerance or MCAS, this isn't in your head. Certain probiotic strains produce histamine, and taking them is like adding fuel to a fire you're trying to put out.

Not all bacteria are created equal

Here's what most people don't realize: some bacterial strains break down histamine, while others produce it. When you take a probiotic loaded with histamine-producing bacteria, you're adding to your histamine burden from the inside out.

And unlike eating a high-histamine meal, the effects can persist while you're taking it. Many probiotics don't permanently colonize, but they can still affect what's happening in your gut as long as you keep taking them.

The usual suspects

Some strains of the following have been reported to produce histamine or biogenic amines:

• Lactobacillus casei (some strains)
• Lactobacillus bulgaricus (a subspecies of L. delbrueckii)
• Lactobacillus reuteri (some strains)
• Streptococcus thermophilus (some strains)
• Enterococcus faecalis (some strains)

Check your probiotic label. L. bulgaricus and S. thermophilus are standard yogurt starter cultures, which is why yogurt can be such a problem.

Better options

These strains are generally considered less likely to produce histamine:

• Bifidobacterium infantis
• Bifidobacterium longum
• Bifidobacterium breve
• Lactobacillus rhamnosus (some strains)
• Lactobacillus plantarum (some strains)

You'll sometimes see these marketed as "histamine-friendly" probiotics. Some companies now make formulas specifically for histamine intolerance. Histamine X by Seeking Health is one example.

That said, individual responses vary. What works for one person might not work for you.

Why it takes a while to figure out

Some people react to a new probiotic right away. Others don't notice issues for days or weeks. By then, you might not connect your worsening symptoms to the probiotic you started three weeks ago.

If you've recently added a probiotic and things have gotten worse or more unpredictable, it's worth investigating.

What to look for

Probiotic-triggered histamine problems often show up as:

• More digestive issues than usual (bloating, gas, diarrhea)
• Skin flushing or itching
• Headaches
• Feeling anxious or wired
• Worse sleep
• Reacting to foods that used to be fine

See common symptoms of histamine intolerance for more.

What to do about it

If you suspect your probiotic:

1. Stop taking it and wait 1-2 weeks to see if things improve
2. Check the label for histamine-producing strains
3. If you want to try again, look for one with only histamine-friendly strains
4. Introduce it slowly and pay attention to how you feel

Don't expect immediate improvement. It takes time for bacteria to clear out.

Same goes for fermented foods

This isn't just about supplements. Yogurt, kefir, sauerkraut, kombucha: these fermented foods often contain significant amounts of histamine and other biogenic amines from the fermentation process. If you've been loading up on fermented foods for gut health and feeling worse, now you know why.

More on problematic foods: foods with high histamine levels.

You don't have to avoid all probiotics

Gut health still matters when you have histamine intolerance. The trick is being selective. Some people do really well once they find the right strains. It just takes some trial and error.

Tracking symptoms before and after starting a new probiotic helps you see what's actually happening, including the delayed reactions that make this stuff so hard to figure out on your own.

Track your symptoms and discover patterns with Histamine Tracker. Includes a database of 1,000+ foods with histamine ratings.