ITS MiSeq sequencing data: antibiotics in infants. The effect of antibiotics on the infant gut fungal microbiota

Antibiotics are commonly used drugs in infants, causing disruption in the developing gut mi-crobiota with possible detrimental long-term effects such as chronic inflammatory diseases. The focus has been on bacteria, but research show that fungi might have an important role as well. There are only few studies on the infant gut fungal microbiota in relation to antibiotic treatment. Therefore, we focused on the impact of antibiotics on the infant gut fungal microbiota, and further on 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 to > 9 months. The gut fungal microbiota was studied by MiSeq sequencing of the ITS1 region. We found that antibiotics did affect the gut fungal microbiota, with a higher abundance of Candida, and a higher fungal diversity and richness in the antibiotic-treated infants compared to the antibiotic-naïve. This could indicate that the fungal gut microbiota also has a role in the outcome of antibiotic treatment.