happy probiotic pills floating through a red gut on a blue background

6 Signs Your Probiotics Are Working, According to a Gut Health Doctor

Gut feelings and beyond.

Everyone and their mom is taking a probiotic supplement, and we’re here for it. A balanced gut microbiome—the collection of microorganisms that live in your digestive tract—is good for way more than healthy digestion. It’s been linked to everything from brain health and weight loss, to heart health and athletic performance (1, 2, 3, 4). The downside: Since the potential impact of a healthy gut is so widespread, it can be hard to spot signs that probiotics are working.

Dr. Niel Paulvin, D.O., an optimization-focused functional medicine doctor, says that there’s a science behind which probiotics you need, which signs indicate your probiotic is doing its job, and how to test your microbiome to track changes.

About the Expert

Dr. Neil Paulvin, D.O., is a longevity expert and regenerative medicine specialist. He specializes in gut health, autoimmune and inflammation-based conditions, and hormone imbalances.

Signs Probiotics Are Working

The signs probiotics are working depends on the reason you’re taking them and which probiotic you’re taking. .

“The gut-brain connection is complicated, so not everyone will respond the same way to a probiotic,” explains Paulvin. Complicating matters further, there are thousands of probiotic strains, each with its own unique function. But if you’re taking a probiotic for general gut health, there are some common indicators that they might be working.

1. A stronger immune system

A growing body of research suggests probiotics can enhance immune function and response, and reduce inflammation—which may improve your ability to fight off a common cold and reduce your risk of developing chronic inflammatory diseases like Crohn’s disease (5, 6).

2. Improved digestion

Unwanted digestive symptoms like bloating and constipation are a sign of poor gut health. One review suggests probiotic supplementation may be an effective means of relieving gas, constipation, bloating, and diarrhea by improving the balance of good gut flora (7). In particular, different combinations of Lactobacillus and Bifidobacterium strains have been shown to reduce constipation, increasing the frequency and consistency of bowel movements (8).

3. Better cognition, memory, and mood

You might associate neurotransmitters like serotonin, dopamine, and GABA with your brain but your gut produces vast amounts of these chemicals, which regulate mood, focus, and more. And we mean vast amounts: around 95 percent of serotonin is produced in your gut (9). When your gut microbiome is out of whack, your thinking skills, mental health, stress, and mood take a hit. While human studies are limited, some emerging research has linked probiotics with:


4. Improved sleep

Your gut microbiome regulates the production of melatonin, glutamate, GABA, and serotonin which play an important role in sleep quality. While studies in humans are relatively new and scarce, experts suggest that probiotics may improve sleep by helping to reduce the risk of sleep disorders and optimize the sleep-wake cycle (13, 14).

5. Increased energy

A balanced gut microbiome is better equipped to absorb essential vitamins and minerals which play a key role in energy production such as vitamin B12, iron, and zinc. One review concluded that certain probiotic strains like Lactobacillus acidophilus and Lactobacillus plantarum may improve micronutrient levels (15).

Exactly how it improves nutrient absorption depends on the species. For example, some species of bacteria (Lactobacillus and Bifidobacterium) can produce vitamins (particularly, B vitamins and vitamin K). While other bacteria may make a bigger impact by improving gut microbiota composition or the surface of the gut wall for better nutrient absorption.

6. Clearer skin

While there are many potential causes of unexplained skin issues, an imbalanced gut may manifest as acne, eczema, or rosacea. If your gut is the issue, studies suggest probiotics may help clear up skin problems by reducing allergic reactions and inflammation, increasing vitamin and mineral absorption, enhancing lactose tolerance, strengthening the gut wall, and squashing the incidence of gut infections (16, 17).

How to Test if Your Probiotics Are Working

While any of the above can serve as a signal that your probiotics are working, a stool test can confirm that it’s actually making an impact, Paulvin adds. He typically uses a GI-MAP (Gastrointestinal Microbial Assay Plus), or Genova GI Effects Comprehensive Profile test to diagnose gut issues, choose the right medication or supplements, and track changes over time. “These tests can see if the amount of bacteria is increasing in the right proportion,” he explains.

“The GI-MAP test analyzes the composition of the gut microbiome from a 360-degree view, identifying various bacteria, parasites, viruses, and fungi present in the GI tract. It also assesses inflammatory markers and immune function,” says Paulvin.

The Genova GI test, however, might be even more comprehensive. In addition to the above, it also tests the absorption of nutrients, and provides information about intestinal health—including mucosal integrity and the presence of potential irritants in the gut.

Stool tests aren’t cheap. You can get a GI-MAP test for $360, and a Genova GI test can run up to $400 (without insurance).


How Long Does it Take a Probiotic to Work?

It depends. “If you’re targeting a short-term condition (like bloating, constipation, or diarrhea), a probiotic may work in a few days. For chronic conditions (like SIBO or IBS), it could take up to a few months,” explains Paulvin.

Signs Probiotics Aren’t Working

Picking up a random probiotic supplement and hoping for the best is not a one-way ticket to better health. Because different probiotic strains affect the body differently, if you’re taking the wrong strain you may not notice any changes; or worse, if a specific strain isn’t well-suited to your individual microbiome new symptoms like bloating, diarrhea, constipation, and/or brain fog could crop up, per Paulvin. “If you don’t see any changes in your digestion or gut health after taking the probiotics for a few months, this may be a sign that they aren’t working for you,” he says.

Why Isn’t My Probiotic Working?

According to Paulvin, a string of individual factors can affect a probiotics functionality, including your age, genetic makeup, health, diet, and whether you take your probiotic on an empty stomach or with food. (Pro tip: consume probiotics with food to avoid nausea.)

It could also be the probiotic that’s the problem: “The dose or strain may be incorrect [for your symptoms], or the product quality might be poor,” says Paulvin.

How to Choose the Right Probiotic

Eating more probiotic-rich foods like sauerkraut, kimchi, and fermented dairy like yogurt, along with prebiotic fiber (which feeds probiotics) like high fiber veggies and legumes is square one for healing your gut. When you have targeted needs, however, that’s when probiotic supplements can come in handy.

“General probiotics should have four to five basic strains in the right amount,” says Paulvin. A brand that packs a combo of Bifidobacterium (including Bifidobacterium bifidum), Lactobacillus (including Lactobacillus acidophilus), and Akkermansia is ideal.

If using a probiotic for a specific issue, you’ll need a specific probiotic for that issue. For example, L. bulgaricus (the probiotic in Activia yogurt) is effective for IBS; while, L. rhamnosus GG (LGG) is effective for diarrhea sparked by taking an antibiotic (18). “Taking a stool test is the quickest and most effective way to determine which probiotics your body needs,” Paulvin says.

If you can’t swing a test, start with a general probiotic that hits the key strains mentioned above and reevaluate your symptoms in two to three months. If your symptoms haven’t improved (or gotten worse) check with your doctor.

  1. Labarre, A. et al. (2022) Fatty Acids Derived From the Probiotic Lacticaseibacillus rhamnosus HA-114 Suppress Age-Dependent Neurodegeneration.
  2. Shoaie, S. et al. (2015) Quantifying Diet-Induced Metabolic Change of the Human Gut Microbiome.
  3. Rahman, M. et al. (2022) The Gut Microbiota (Microbiome) in Cardiovascular Disease and Its Therapeutic Regulation.
  4. O’ Brien, M. et al. (2022) The Athlete Gut Microbiome and its Relevance to Health and Performance: A Review.
  5. Mazziotta, C. et al. (2023) Probiotics Mechanism of Action on Immune Cells and Beneficial Effects on Human Health.
  6. Nour, G. et al. (2023) Effect of Probiotics on Common Cold, Influenza, and Influenza-Like Illness: A Systematic Review and Meta-Analysis. 
  7. Hungin, A. et al. (2018) Systematic Review: Probiotics in the Management of Lower Gastrointestinal Symptoms—An Updated Evidence-Based International Consensus.
  8. Mitelmao, F. et al. (2022) The Effect of Probiotics on Functional Constipation in Adults: A Randomized, Double-Blind Controlled Trial.
  9. Appleton, J. et al. (2018) The Gut-Brain Axis: Influence of Microbiota on mood and Mental Health.
  10. Schaub, A. et al. (2022) Clinical, Gut Microbial and Neural Effects of a Probiotic Add-On Therapy in Depressed Patients: A Randomized Controlled Trial.
  11. Marotta, A. et al. (2019) Effects of Probiotics on Cognitive Reactivity, Mood, and Sleep Quality.
  12. Bagga, D. et al. (2018) Probiotics Drive Gut Microbiota Triggering Emotional Brain Signatures.
  13. Neroni, B. et al. (2021) Relationship Between Sleep Disorders and Gut Dysbiosis: What Affects What?
  14. Sgro, M. et al. (2022) Synchronizing Our Clocks as we Age: the Influence of the Brain-Gut-Immune Axis on the Sleep-Wake Cycle Across the Lifespan.
  15. Barkhidarian, B. et al. (2021) Probiotic Supplementation and Micronutrient Status in Healthy Subjects: A Systematic Review of Clinical Trials.
  16. Gao, T. et al. (2023) The Role of Probiotics in Skin Health and Related Gut-Skin Axis: A Review.
  17. Reunka, S. et al. (2023) Probiotics: A Review on Microbiome That Helps for Better Health—A Dermatologist’s Perspective.
  18. Ciorba, M. et al. (2013) A Gastroenterologist’s Guide to Probiotics.