We’re still understanding the important and complex role that the microbiome plays in human health, though we do know that the trillions of bacteria in the human body influence our immune function and digestion. But beyond what we know, there's simultaneously a fascinating field of research and a lot of hype and scaremongering.

One thing we're still working out is how antibiotics affect the gut microbiome and how well it's able to recover after the treatment is finished. A paper in Nature Microbiology this week finds that, after a course of broad-spectrum antibiotics, 12 men were able to recover to a mostly normal microbiome level within six months. Nine species of gut dwellers, though, never reappeared; instead, there were some undesirable species of bacteria that managed to take hold.

Albert Palleja and colleagues first collected stool samples from 12 healthy men to see what their microbiomes looked like at the start. The small and specific sample means that the results can’t be generalized, so the study is less a statement on what antibiotics do to people in general and more an exploration of what the possibilities look like.

Those 12 men then took a cocktail of different antibiotics used for a range of conditions from drug-resistant bacterial meningitis to chlamydia. The treatment was a modified version of antibiotic treatments used in ICUs, the researchers write, and “include[d] antibiotics given to patients with infections by multidrug-resistant bacteria.”

After a four-day treatment period, the researchers started tracking “process of eradication, partial survival, gradual regrowth and re-establishment of these gut microbial communities.” They checked in on the men’s microbiomes via their poop immediately after the antibiotics, after a few days, and again after six months.

Time passes...

Immediately after the treatment, the diversity of the men’s microbiomes was hugely reduced, but the bacteria were not entirely eradicated. After six months, they had bounced back, but there were some essential differences: the richness of the number of bacterial species that the researchers could detect was diminished, suggesting that “some microorganisms that were originally present may have been permanently lost or severely depleted due to the treatment,” write Palleja and his colleagues.

Follow-up analyses confirmed that some species had disappeared. And there were some bacteria that hadn’t been detected before the treatment but appeared in the samples afterward. These are from species that form spores—almost like seeds for bacteria—when conditions aren’t ideal, so they might have been lurking in the gut before the antibiotics and emerged only when the other species were wiped out. Learning more about this possibility could help us control some of the bacterial infections that commonly occur after broad-spectrum antibiotic treatments have hugely disrupted the normal gut microbiome, the authors suggest.

All of these results come from just one course of antibiotics, but Oluf Pedersen, the chief scientist on the project, pointed out that most people will see multiple rounds of exposure to antibiotics. “In this case, it is good that we can regenerate our gut microbiota which is important for our general health,” he said. “The concern, however, relates to the potentially permanent loss of beneficial bacteria after multiple exposures to antibiotics during our lifetime.” Antibiotic treatment in groups like children and the elderly is also likely to have different effects, and properly understanding all of this complexity is a matter of ongoing research.

Of course, this doesn’t mean antibiotics are a bad thing—they’re responsible for one of the most dramatic public-health miracles of human history. “Antibiotics can be a blessing for preserving human health,” says Pedersen, “but should only be used based upon clear evidence for a bacterial cause of infection.”

Nature Microbiology, 2018. DOI: 10.1038/s41564-018-0257-9 (About DOIs).