Can Gut Bacteria Resurrect from Antibiotics?

Some don’t and probiotics don’t help.

“We show that the gut bacterial community of healthy adults are resilient and able to recover after short-term simultaneous exposure to three different antibiotics,” says Professor Oluf Pedersen from the Novo Nordisk Foundation Center for Basic Metabolic Research, Denmark.

“In this case, it is good that we can regenerate our gut microbiota which is important for our general health. The concern, however, relates to the potentially permanent loss of beneficial bacteria after multiple exposures to antibiotics during our lifetime,” Pedersen adds.

A Permanent Loss

Pedersen led a team of 23 researchers to investigate how our gut microbiome recovers from antibiotics exposure. They published their findings in the prestigious Nature Microbiology journal in October 2018.

They showed that 4-day antibiotics (meropenem, gentamicin, and vancomycin) intake completely abolished the gut microbiota of healthy adults. Profound depletion in Bifidobacteria and other butyrate producers were observed. While pathogenic Clostridium species normally in low levels thrived.

Still, the gut microbiota slowly returns to baseline over 6 months. Some common and beneficial bacterial species, however, never made it back:

• Bifidobacterium species that compete with pathogens and modulate the immune system.
• Coprococcus eutactus and Eubacterium ventriosum that synthesize butyrate.
• Methanobrevibacter smithii that digest polysaccharides to produce methane.
• 6 out of 8 Faecalibacterium prausnitzii strains who are major butyrate producers.

“Antibiotics can be a blessing for preserving human health but should only be used based upon clear evidence for a bacterial cause of infection,” Pedersen advised.

Similar outcomes were previously shown by Stanford academicians where ciprofloxacin negatively affected a third of the gut microbiota composition of healthy adults. At 6-months post-antibiotic, several bacterial taxa never recovered. A follow-up study by the same team showed that the second round of ciprofloxacin yielded similar trends of microbiome shift and loss. Like what Pedersen et al. found, the majority of bacterial loss were those involved in the metabolism of polysaccharides and short-chain fatty acids.

“The antimicrobial agents that we deploy against pathogens also disrupt coevolved microbial communities that are integral to human health,” the Stanford authors wrote. “Antibiotic perturbation may cause a shift to an alternative stable state, the full consequences of which remain unknown.”

Infants are severely affected by antibiotics as well. Antibiotic exposure during the first year of life is a risk factor for asthma. Researchers then analyzed the gut microbiome of asthmatic children who previously received antibiotics. They found depletion of several key immunomodulatory species — Faecalibacterium, Lachnospira, Veillonella, and Rothia — in their gut.

Avoid These If Possible

Here are the classes of antibiotics known to alter the gut microbiome, based on a 2019 review in the Journal of Antimicrobial Chemotherapy:

• Penicillins (piperacillin/tazobactam)
• Cephalosporins (cefepime, ceftazidime, ceftriaxone)
• Carbapenems (meropenem, imipenem, ertapenem)
• Fluoroquinolones (ciprofloxacin, levofloxacin, moxifloxacin)

Contrary to what is expected, probiotics don’t compensate for the loss of gut microbial diversity from antibiotics. In 2018, a team of 26 researchers randomized antibiotics-treated people (who had depleted gut microbial diversity) into three groups: no intervention, probiotics, and faecal microbiome transplantation (FMT).

“We have found a potentially alarming adverse effect of probiotics,” says Prof. Eran Elinav from Weizmann Institute of Science, the principal investigator of the study. Probiotics actually delayed the self-restoration of the gut microbiome to baseline. Whereas the opposite was observed for faecal microbiome transplantation.

“Probiotics induced a markedly delayed and persistently incomplete indigenous stool/mucosal microbiome reconstitution and host transcriptome recovery toward homeostatic configuration, while autologous FMT induced a rapid and near-complete recovery within days of the administration,” they explained.