*5.6. Antibiotics*

Specific properties of antibiotics, as a mode of action and antimicrobial spectrum, might act as powerful forces for the selection of intestinal bacterial populations, especially if the infant is exposed to antibiotics too early and/or for long periods of time [3,15]. Antibiotics are able to alter the abundances of resident bacteria, significantly impact the growth of otherwise dominant bacterial phyla, and lead to an overall decrease in microbial diversity. A study by Fouhy and colleagues [36] showed that infants exposed to ampicillin and gentamicin shortly after birth harbored higher proportions of *Proteobacteria* and *Actinobacteria*, and the genus *Lactobacillus* for up to four weeks after concluding treatment. Another study reported an attenuation in colonization with *Bifidobacterium* and an increase of *Enterococcus* in subjects receiving oral or intravenous antibiotics during the first four days of life [37].

This variability among individuals suggests caution when including subjects who have been treated with antibiotics [38]. Indeed, the exclusion criteria from the NIH Human Microbiome Project (HMP, dbGAP, see the url https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study\_id= phs000228.v4.p1) include the use of systemic antibiotics, antifungals, antivirals, or antiparasitics within six months of sampling. However, this criterion, although optimal, may not be easily applicable with subjects in the pediatric age. For this reason, shorter time windows are often considered. In any case, it is mandatory to accurately document, within the metadata file, any history of antibiotics as well as other medication use.
