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The Effect of Antibiotics on the Infant Gut Fungal Microbiota

Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
Folkhälsan Research Center, 00250 Helsinki, Finland
Children’s Hospital, Helsinki University, 00029 Helsinki, Finland
Department of Paediatrics and Adolescent Medicine, Turku University Hospital, University of Turku, 20014 Turku, Finland
Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands
Department of Pediatrics, Tampere University, 33520 Tampere, Finland
Author to whom correspondence should be addressed.
Academic Editors: Jürgen Löffler, Thomas Rogers and Agostinho Carvalho
J. Fungi 2022, 8(4), 328;
Received: 14 February 2022 / Revised: 15 March 2022 / Accepted: 18 March 2022 / Published: 22 March 2022
(This article belongs to the Special Issue New Insights into Current Understanding of Host–Fungal Interactions)
Antibiotics are commonly used drugs in infants, causing disruptions in the developing gut microbiota with possible detrimental long-term effects such as chronic inflammatory diseases. The focus has been on bacteria, but research shows that fungi might have an important role as well. There are only a few studies on the infant gut fungal microbiota, the mycobiota, in relation to antibiotic treatment. Here, the aim was to investigate the impact of antibiotics on the infant gut mycobiota, and the interkingdom associations between bacteria and fungi. We had 37 antibiotic-naïve patients suffering from respiratory syncytial virus, of which 21 received one to four courses of antibiotics due to complications, and 16 remained antibiotic-naïve throughout the study. Fecal samples were collected before, during and after antibiotic treatment with a follow-up period of up to 9.5 months. The gut mycobiota was studied by Illumina MiSeq sequencing of the ITS1 region. We found that antibiotic use affected the gut mycobiota, most prominently seen as a higher relative abundance of Candida (p < 0.001), and a higher fungal diversity (p = 0.005–0.04) and richness (p = 0.03) in the antibiotic-treated infants compared to the antibiotic-naïve ones at multiple timepoints. This indicates that the gut mycobiota could contribute to the long-term consequences of antibiotic treatments. View Full-Text
Keywords: amoxicillin; bacteria; Candida; children; macrolide; mycobiota amoxicillin; bacteria; Candida; children; macrolide; mycobiota
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MDPI and ACS Style

Ventin-Holmberg, R.; Saqib, S.; Korpela, K.; Nikkonen, A.; Peltola, V.; Salonen, A.; de Vos, W.M.; Kolho, K.-L. The Effect of Antibiotics on the Infant Gut Fungal Microbiota. J. Fungi 2022, 8, 328.

AMA Style

Ventin-Holmberg R, Saqib S, Korpela K, Nikkonen A, Peltola V, Salonen A, de Vos WM, Kolho K-L. The Effect of Antibiotics on the Infant Gut Fungal Microbiota. Journal of Fungi. 2022; 8(4):328.

Chicago/Turabian Style

Ventin-Holmberg, Rebecka, Schahzad Saqib, Katri Korpela, Anne Nikkonen, Ville Peltola, Anne Salonen, Willem M. de Vos, and Kaija-Leena Kolho. 2022. "The Effect of Antibiotics on the Infant Gut Fungal Microbiota" Journal of Fungi 8, no. 4: 328.

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