Many people take probiotics in the belief that the probiotics will help their gut microbiome (microbial community) recover after taking antibiotics. This is because antibiotics kill both beneficial and pathogenic bacteria, and research shows it may take months for the gut to recover (it depends on the antibiotics taken). However, 2 studies (in both mice and healthy humans) conducted by a group of researchers at the Weizmann Institute of Science in Israel challenge that belief. The researchers used both mice and healthy humans in both well-done studies. They found that taking probiotics after a week of antibiotics actually delayed recovery of the gut microbial community in humans - months longer!
In summary: As expected, taking antibiotics had a big effect on the gut microbiome - the researchers wrote "a dramatic impact" and "profound microbial depletion" (after taking one week of standard doses of "broad-spectrum antibiotics"). However, they found large differences among the 3 groups in gut microbial recovery after antibiotics. The spontaneous recovery group (they did not take probiotics after antibiotics) showed recovery of gut microbes within 3 weeks. The fecal transplant group (of their own fecal microbes which was collected before they took antibiotics) showed gut microbial recovery within 1 day of the fecal microbial transplant. In contrast, the group taking daily probiotics for 28 days did not show full recovery (to where they were before antibiotics) by day 28, and the gut microbial community was still out of whack (dysbiosis) even 5 months after stopping probiotics (actually even at 180 days when the study ended).
What species were in the probiotics? Eleven species commonly found in ordinary probiotics: Lactobacillus acidophilus, L. casei, L. casei subsp. paracasei, L. plantarum, L. rhamnosus, Bifidobacterium longum, B. bifidum, B. breve, B. longum sbsp. infantism, Lactococcus lactis, and Streptococcus thermophilus. These are all considered beneficial species. But keep in mind that the human gut has hundreds of microbial species - not just the few found in probiotics.
Bottom line: Eat well after taking a course of antibiotics so as to feed beneficial microbes, and do not routinely take probiotics thinking it will help the microbes in the gut.
What was also interesting was that in the first study where healthy individuals took the probiotics (and no antibiotics), they found that the probiotic species did not colonize the gut in everyone - only some species and in some people. It's as if there is a "resistance to colonization". This resistance is perhaps what other studies show - that within one week of discontinuing probiotics, they are gone from the gut.
From Science Daily - Human gut study questions probiotic health benefits
Probiotics are found in everything from chocolate and pickles to hand lotion and baby formula, and millions of people buy probiotic supplements to boost digestive health. But new research suggests they might not be as effective as we think. Through a series of experiments looking inside the human gut, researchers show that many people's digestive tracts prevent standard probiotics from successfully colonizing them. Furthermore, taking probiotics to counterbalance antibiotics could delay the return of normal gut bacteria and gut gene expression to their naïve state. The research publishes as two back-to-back papers on September 6 in the journal Cell.
"People have thrown a lot of support to probiotics, even though the literature underlying our understanding of them is very controversial; we wanted to determine whether probiotics such as the ones you buy in the supermarket do colonize the gastrointestinal tract like they're supposed to, and then whether these probiotics are having any impact on the human host," says senior author Eran Elinav, an immunologist at the Weizmann Institute of Science in Israel. "Surprisingly, we saw that many healthy volunteers were actually resistant in that the probiotics couldn't colonize their GI tracts. This suggests that probiotics should not be universally given as a 'one-size-fits-all' supplement. Instead, they could be tailored to the needs of each individual."
In the first study, 25 human volunteers underwent upper endoscopies and colonoscopies to sample their baseline microbiome in regions of the gut. 15 of those volunteers were then divided into two groups. The first group consumed generic probiotic strains, while the second was administered a placebo. Both groups then underwent a second round of upper endoscopies and colonoscopies to assess their internal response before being followed for another 2 months.
The scientists discovered that the probiotics successfully colonized the GI tracts of some people, called the "persisters," while the gut microbiomes of "resisters" expelled them. Moreover, the persister and resister patterns would determine whether probiotics, in a given person, would impact their indigenous microbiome and human gene expression. The researchers could predict whether a person would be a persister or resister just by examining their baseline microbiome and gut gene expression profile. They also found that stool only partially correlates with the microbiome functioning inside the body, so relying on stool as was done in previous studies for many years could be misleading.
In the second study, the researchers questioned whether patients should be taking probiotics to counter the effects of antibiotics, as they are often told to do in order to repopulate the gut microbiota after it's cleared by antibiotic treatment. To look at this, 21 volunteers were given a course of antibiotics and then randomly assigned to one of three groups. The first was a "watch-and-wait" group that let their microbiome recover on its own. The second group was administered the same generic probiotics used in the first study. The third group was treated with an autologous fecal microbiome transplant (aFMT) made up of their own bacteria that had been collected before giving them the antibiotic.
After the antibiotics had cleared the way, the standard probiotics could easily colonize the gut of everyone in the second group, but to the team's surprise, this probiotic colonization prevented the host's normal microbiome and gut gene expression profile from returning to their normal state for months afterward. In contrast, the aFMT resulted in the third group's native gut microbiome and gene program returning to normal within days.
"Contrary to the current dogma that probiotics are harmless and benefit everyone, these results reveal a new potential adverse side effect of probiotic use with antibiotics that might even bring long-term consequences," Elinav says. "In contrast, replenishing the gut with one's own microbes is a personalized mother-nature-designed treatment that led to a full reversal of the antibiotics' effects."