Most healthy adults can take probiotics without problems, but several groups of people face real and sometimes serious risks. These include people with weakened immune systems, premature infants, anyone with a central venous catheter, people with heart valve abnormalities, and those with certain digestive conditions. For these populations, the live bacteria or yeast in probiotics can escape the gut, enter the bloodstream, and cause infections that are difficult to treat.
People With Weakened Immune Systems
Probiotics are live organisms, and a healthy immune system keeps them confined to the digestive tract. When that immune defense is compromised, probiotic bacteria can cross the intestinal wall and reach the bloodstream, causing bacteremia (bacteria in the blood) or fungemia (fungi in the blood). The FDA specifically flags the following immunocompromised populations as being at risk: people taking anti-rejection medications after organ or stem cell transplants, those on injectable immunosuppressive drugs for autoimmune diseases, patients receiving chemotherapy or radiation, and anyone taking high-dose corticosteroids.
This doesn’t mean every person with an autoimmune condition needs to avoid probiotics. The concern is proportional to how suppressed your immune system actually is. Someone managing mild psoriasis with a topical cream is in a very different situation than someone on heavy immunosuppressants after a kidney transplant. If you’re unsure where you fall on that spectrum, the specifics of your medication regimen matter more than the diagnosis itself.
Premature and Very Low Birthweight Infants
The FDA issued a direct warning to healthcare providers about giving probiotics to preterm infants after a case in which a premature baby developed sepsis from the probiotic bacterium Bifidobacterium longum and died. Very preterm and very low birthweight infants have immature immune systems and fragile intestinal linings, making it easier for probiotic organisms to invade the bloodstream.
The American Academy of Pediatrics does not support routine probiotic use in preterm infants, particularly those born weighing less than 1,000 grams (about 2.2 pounds). No probiotic product has been approved by the FDA as a drug or biological product for use in infants of any age. This is a space where the gap between marketing claims and clinical evidence is wide, and the stakes for this vulnerable population are high.
ICU Patients and Those With Central Lines
A central venous catheter, the type of IV line placed in a large vein near the heart for long-term medication delivery, creates a direct pathway from the outside world into the bloodstream. In ICU patients with these lines, probiotics pose a measurable danger. A large study of over 23,000 ICU patients who received probiotics found that 86 developed bloodstream infections directly caused by the probiotic organisms. Zero such infections occurred in the comparison group that didn’t receive probiotics. The number needed to harm was 270, meaning roughly 1 in every 270 ICU patients given probiotics developed a probiotic-caused bloodstream infection.
Patients who contracted these infections had more than double the odds of dying compared to those who didn’t. Powder formulations were twice as likely to cause bloodstream infections as capsules or other forms, possibly because powder particles can contaminate catheter sites during handling. Research published in Nature Medicine confirmed this wasn’t coincidental: whole-genome sequencing showed that the bacteria found in patients’ blood were genetically identical to the strains in the probiotic capsules they were given. In some cases, the bacteria even developed new antibiotic resistance mutations while inside the patient.
People With Heart Valve Disease
Endocarditis, an infection of the heart’s inner lining or valves, is the most frequently reported serious probiotic-related infection in adults. It’s rare overall, but the people it affects almost always have an underlying heart condition. Those at highest risk include people with artificial heart valves, structural valve abnormalities, a history of cardiac surgery, or significant valve regurgitation (leaking). Intravenous drug users with valve damage are also at elevated risk.
Reported cases typically involve Lactobacillus species, one of the most common bacteria in probiotic supplements. In one documented case, a 71-year-old woman who was both immunocompromised from chronic steroid use and had underlying heart failure developed Lactobacillus endocarditis after months of probiotic use. The combination of immune suppression and heart disease made her particularly vulnerable. If you have a known heart valve problem, especially a prosthetic valve, the risk of probiotic-associated endocarditis is small but the consequences are severe enough to warrant caution.
People With Digestive Motility Problems or on Acid-Suppressing Drugs
Probiotics are designed to colonize the large intestine, but in some people they end up setting up camp in the small intestine instead. This is a problem. When probiotic bacteria like Lactobacillus and Bifidobacterium species ferment carbohydrates in the small intestine, they produce D-lactic acid, a compound that can accumulate and cause brain fogginess, severe bloating, and gas. In more significant cases, this leads to D-lactic acidosis, a condition where excess acid disrupts normal brain function.
This is most likely to happen in people with conditions that slow the movement of food through the small intestine (dysmotility), those with short bowel syndrome, and people who take proton pump inhibitors (PPIs) or opioids long-term. PPIs reduce stomach acid, and opioids slow gut motility, both of which create a more hospitable environment for bacteria to overgrow in the small intestine. Researchers have specifically cautioned against “excessive and indiscriminate use of probiotics” in these groups, particularly when there’s no well-defined medical reason to take them. If you experience worsening brain fog, bloating, or abdominal discomfort after starting a probiotic, the supplement itself could be contributing to small intestinal bacterial overgrowth rather than helping your gut.
Warning Signs of a Serious Reaction
For anyone in the groups above who is currently taking probiotics, certain symptoms should prompt immediate medical attention. A new or unexplained fever is the most common early sign of a probiotic-related bloodstream infection. Other red flags include chills, rapid heart rate, confusion, a drop in blood pressure, or feeling suddenly and significantly worse in a way that’s hard to pinpoint. These can signal bacteremia or early sepsis.
The challenge is that these symptoms overlap with many other conditions, so they’re easy to dismiss. Clinicians themselves sometimes don’t consider probiotics as a potential source of infection. If you’re immunocompromised, have a central line, or have heart valve disease and develop signs of infection while taking probiotics, make sure whoever is evaluating you knows about the supplement. Probiotic organisms don’t always show up on standard cultures, and identifying them as the cause requires knowing to look.
Probiotics Are Not Universally Helpful
Beyond the groups facing serious safety risks, it’s worth noting that major medical guidelines have pulled back on some previously popular uses of probiotics. The American College of Gastroenterology now recommends against using probiotics to prevent C. difficile infection in people taking antibiotics, a practice that was widely promoted for years. They also recommend against probiotics for preventing C. difficile recurrence. The evidence simply didn’t hold up.
For healthy people, probiotics are generally low-risk, but “low-risk” and “helpful” aren’t the same thing. Many people take probiotics as a general wellness supplement without a specific condition they’re trying to address. If you’re healthy, have no digestive complaints, and aren’t in any of the risk groups outlined above, probiotics are unlikely to harm you. But they may not be doing much for you either.