In the past dozen years or so, there has been a revolution in medicine. New technologies have allowed scientists to identify and catalog the multitudes of microbes living in the human body—and especially, the gastrointestinal tract—with unprecedented speed and accuracy. Known as metagenomic sequencing, this technology has enabled scientists to understand, with far better accuracy and precision than ever before, which particular species of bacteria and other microorganisms live in the gut, in which particular locations, and in which relative amounts.

These communities of (ideally) friendly bacteria, formerly known as the microflora, are now referred to as the intestinal microbiome, or the microbiota. At up to one hundred trillion individual cells per person, these microbes outnumber human cells by ten-to-one. In one gram of stool there are one trillion bacteria! In a very real sense, humans can be thought of as “superorganisms,” composed of diverse communities of bacteria living in harmony with their human hosts, to the mutual benefit of each.

Some scientists have described the gut microbiome as “another organ,” because it produces substances, responds to its environment, and integrates with other systems. In the influential journal, Nature, Washington University researcher, George M. Weinstock wrote: “This amazingly complex and poorly understood group of communities has an enormous impact on humans.” Among other things, the gut microbiome produces compounds that aid the body’s immune system, and extracts nutrients from food that would otherwise remain unavailable to us. They even produce certain vitamins that are of benefit to their human hosts.

The Microbiome and IBD

Not surprisingly, experts in inflammatory bowel disease (IBD) are increasingly cognizant of the role of the gut microbiome in IBD. Studies have shown that people with IBD (Crohn’s disease and ulcerative colitis) tend to have different mixtures of bacterial species living in their guts, for instance, than in healthy people. They also tend to have far less diversity of microbes living in the gut. This suggests that certain species (or mixtures of species), in certain amounts, are necessary for optimal health.

IBD occurs when the immune system incorrectly identifies certain friendly bacteria as foreign invaders. The body mounts an inflammatory response, which does not resolve properly. Eventually, areas of the intestinal lining (the gut mucosa) may be damaged by this relentless inflammation. The exact cause of Crohn’s disease and/or ulcerative colitis is uncertain. But it probably involves interactions among multiple factors, including an individual’s genes and certain environmental factors.

Some scientists now believe that disturbances in the microbiome may also play an important role. The widespread use of broad-spectrum antibiotics, which can devastate the normal gut microflora, is a possible culprit. For decades, doctors have prescribed antibiotics more or less freely, with what now appears to have been inadequate consideration for the impact these drugs may have on the health of beneficial populations of resident bacteria. With the disturbing rise in antibiotic resistance, and the development of drug-resistant “superbugs,” doctors are presently prescribing antibiotics more judiciously.

Although occasionally medically necessary, tinkering with the normal microbiome may apparently have unintended consequences. But what about the opposite approach? If killing intestinal bacteria indiscriminately can be harmful, can it be beneficial to replace these microorganisms with known species of friendly microbes? In some instances, yes. And that’s the rationale behind the use of probiotics.


Probiotics are live “friendly” bacteria, capable of living in the gastrointestinal tract. They may be ingested in food, or in supplement form. The term prebiotics refers to non-digestible dietary fiber, primarily from plant foods, which provides “food” for beneficial colonic bacteria. Intake of prebiotics supports the health of the normal microbiome, and presumably, the gut itself. In recent years there’s been a huge increase in interest in probiotics. Yogurt is widely marketed on the basis of its live “active cultures,” which are reputed to boost health in vague ways. Similarly, oral probiotic dietary supplements are common on drugstore shelves in pill or powder form.

Unfortunately, controlled clinical trials have been relatively few and far between. While probiotics are beneficial in theory, people with IBD should consult with their physician(s) before beginning any new regimen of probiotic supplementation. Needless to say, patients should never start taking probiotics if it means they intend to stop taking prescribed medications against a doctor’s advice.

Generally, the use of probiotics in IBD appears to be a case of “probably can’t hurt, and might help.” But, again, it’s important to consult with your doctor before taking probiotics. Probiotic therapy is not inexpensive, and resources might be better spent elsewhere.

In theory, regular use of probiotics should encourage the establishment of known gut-friendly species of bacterial communities in the gastrointestinal tract, which in turn might help re-regulate the immune response in the gut, while also working to inhibit other, less friendly microbes from taking hold. But results from the limited number of controlled clinical trials presently available suggest that using probiotics to influence the course of IBD is very much a matter of taking the right probiotics, in the correct quantities, for the right amount of time.

Probiotics for Crohn’s Disease

Probiotics as a treatment for IBD is promising. Unfortunately, probiotics appear to have little benefit in the treatment of Crohn’s disease specifically.

  • A recent meta-analysis (a statistical analysis of data from all relevant clinical trials) determined that probiotics had little effect on the course of disease among patients with Crohn’s disease.
  • The same study found that the use of probiotics was not associated with any significant adverse events among Crohn’s disease patients, however.
  • There is some limited evidence that certain probiotics may help maintain remission of Crohn’s disease activity, once remission has been achieved through other therapies, such as surgery.
  • A probiotic product called VSL#3 (Sigma-Tau Pharmaceuticals, Inc.) has shown some promise in a clinical trial to reduce the risk of Crohn’s disease returning after surgery. It features the following probiotics: Bifidobacterium breve, Bifidobacterium longum, Bifidobacterium infantis, Lactobacillus acidophilus, Lactobacillus plantarum, Lactobacillus paracasei, Lactobacillus bulgaricus and Streptococcus thermophilus.