The most obvious negative effects of probiotics that some people experience are that taking probiotics gives them gas and bloating. This usually wears off within a week or so. Best advice is to start slowly with small amounts until you know how your body is going to react.
Like many consumables, the most important point when considering safety is knowing who it is that will be taking the product. For example, if you're allergic to soy then you can't eat a soy product that would be completely safe for another person. A baby can not eat a product containing salt that would be completely safe for an adult to eat.
And so it is with probiotics - there are a few medical conditions that make a probiotic supplement that would be totally safe for most people to take, an unsafe choice for a few people.
A 2001 study concluded:"Humans live in close association with vast numbers of microorganism that are present on the skin, in the mouth, and in the gastrointestinal (GI) tract. These commensal microbes have coevolved with humans and demonstrate a high degree of interdependence with them."1
Over the course of evolution, bacteria have adapted to colonize every available niche. It would be a brave person to say that a bacteria that is helpful in one part of the body, might not become a danger when introduced to another area.
For example, Staphylococcus aureus (not a probiotic) lives happily in the nasal cavity of many of us. But let it loose on broken skin and you have a nasty staph infection.
Possibly the biggest potential danger of probiotics is the risk of transferring antibiotic resistance from probiotics to more deadly microorganisms. This is why scientists have strict rules on which bacteria can qualify as probiotic.
There has been some research that suggested that HOW a person took a probiotic might influence how safe it is. Reassuringly, taken probiotics by mouth was always the "safe" way in experiments with animals2 and was the recommended way for healthy people to take probiotics.
One desirable trait of a good probiotic is that it can stick to the surface of various organs such as our gastrointestinal tract or vagina but this same trait is also one of the "competitive advantages" that harmful bacteria have. This is just one reason why scientists take so much care in assessing whether any particular bacteria is a probiotic.
Anyone who is severely immunosuppressed should not take probiotics unless they are under the care of their health professional. Check out this research on HIV and probiotic safety which showed that some probiotics seemed suitable and some did not.
The safety of probiotics for patients with pancreatic dysfunction is also not clear.
Post cardiac surgery patients should also discuss this with their doctor to avoid any possible negative effects of probiotics.
Patients with blood in their stools also need to talk to their doctor before they start a course of probiotics.
Pregnant women should talk to their health care professional.
Probiotics have an impressive track record with diarrhea in toddlers, but remember that diarrhea causes dehydration that can kill particularly in babies and children so discuss the treatment with your doctor first.
As you can see, for most of us there are no negative effects of probiotics.
1. Alvarez-Olmos MI,Oberhelman RA. Probiotic agents and infectious diseases:a modern perspective on a traditional therapy. Clinical Infectious Diseases 2001;32:1567-1576
2. Mary Ellen Sanders, Louis MA Akkermans, Dirk Haller, Cathy Hammerman, James Heimbach, Gabriele Hörmannsperger, Geert Huys, Dan D Levy, Femke Lutgendorff, David Mack, Phoukham Phothirath, Gloria Solano-Aguilar, and Elaine Vaughan. Safety assessment of probiotics for human use. Gut Microbes. 2010 May-Jun; 1(3): 164–185.