Can you restore your gut microbiome after a course of antibiotics?

Antibiotics cause major damage to the gut microbiome. Ciprofloxacin significantly reduces diversity within just three to four days. With a heavier combination of three broad-spectrum antibiotics, potentially harmful bacterial species temporarily disappear in the immediate aftermath, but at the same time beneficial species such as bifidobacteria and butyrate-producing bacteria decline sharply.

Recovery does occur, but is rarely complete. After a course of ciprofloxacin, the composition of the gut microbiome in all study participants still differed from its baseline ten months later. After the heavier triple course, the microbiome had largely returned after six weeks, but nine species that had been present in everyone before the course were still undetectable in most participants after six months. How much you recover varies considerably: there is no single recovery pattern, and even in the same person a second course plays out differently from the first.

Taking probiotics after a course of antibiotics sounds logical, but the opposite has been shown. Compared with people who took nothing extra, gut microbiome recovery in the gut lining was actually slower and incomplete in the group that took probiotics (a multi-strain product). Probiotics can reduce antibiotic-associated diarrhoea, but that is separate from actual restoration of the microbiome.

The fastest and most complete return was achieved with an autologous faecal transplant: stool that a person had frozen before the course and then had reintroduced afterwards. Within a few days the microbiome was almost entirely back, clearly faster than spontaneous recovery or recovery with probiotics. However, this is not a method that is readily available or applicable to everyone; it has so far been studied in a small group of participants.