Antibiotics may alter infant gut composition

Even a single course of antibiotics introduced during the development of the gut fungal microbiota (ie, mycobiota) in infants may alter fungal gut composition, a study from Finland suggests.

“The frequent use of antibiotics in infants and the many potential long-term effects … highlight the importance [of studying] the effects of antibiotics on the infant gut microbiota,” said the researchers.

“[A]ntibiotics increase the risk of developing chronic inflammatory diseases, such as inflammatory bowel disease (IBD), and they [may also] have a link to overweight,” said PhD student Rebeka Ventin-Holmberg from the University of Helsinki, Finland, in a press release. “[As such,] investigating the effects of antibiotics is important for the development of techniques that can be used to avoid chronic inflammatory diseases and other disruptions to the gut microbiota.”

Thirty-seven antibiotic-naïve children (median age 2 months) with respiratory syncytial virus were evaluated. Of these, 21 received one to four courses of antibiotics (amoxicillin and macrolides), while 16 remained antibiotic-naïve throughout the trial (controls). Faecal samples were collected before, during, and after treatment. Participants were followed for up to 9.5 months. [J Fungi 2022;8:328]

Infants on amoxicillin had significantly higher relative abundance of the fungal genus Candida than those in the control arm at 1–2 days (p_FDR<0.001) and >6 weeks after treatment initiation (end of study [EoS]; p_FDR=0.028). “When bacteria are disrupted by antibiotics, fungi, especially Candida, have the opportunity to grow,” the researchers explained. “[A]s the bacterial diversity decreased, the fungal diversity increased.”

Antibiotic recipients also had significantly higher relative abundance of Malassezia at 3–6 weeks after treatment initiation (p_FDR<0.001 for both).

The phylum Basidiomycota was more abundant in the antibiotic vs the control arm at EoS (p_FDR=0.009), and particularly among macrolide recipients at 3–6 weeks after treatment initiation (p_FDR=0.033). “Basidiomycota has been observed to be more abundant in IBD previously, suggesting a persisting fungal dysbiosis >6 weeks after antibiotics in these patients,” the researchers noted.

Those on antibiotics had significantly higher fungal diversity and richness than those in the control arm at 3–5 days (p=0.04 [diversity] and p=0.03 [richness]) and 1–2 weeks following treatment initiation (p=0.005 and p=0.03, respectively), as well as at EoS (p=0.03 for both). At EoS, the difference in diversity was more significant between macrolide recipients and controls (p=0.0027). These results align with evidence showing increased fungal diversity in adults after a single course of antibiotics. [Microbiome 2020;8:133]

The control arm only had an abundance of Saccharomyces at 1–2 weeks following treatment initiation (p_FDR<0.001).

Gut bacteria regulate fungi

In summary, the study showed that antibiotic use affected the gut mycobiota, characterized by an increased relative abundance of Candida and higher diversity and richness in antibiotic recipients. “This could indicate that aberrant gut mycobiota composition after antibiotic treatment could, together with bacterial microbiota, be a cause of the long-term effects that antibiotics have on human health,” said the researchers.

“Since antibiotics do not directly affect fungi, the observed changes in the gut mycobiota are likely mediated by the changing bacterial composition. Our results strongly suggest that commensal gut bacteria regulate the fungi, keeping them in check,” noted Ventin-Holmberg and colleagues.

“Consequently, future research should focus on all microorganisms in the gut together to better understand their interconnections and to obtain a better overview of the microbiome as a whole,” the researchers concluded.