Fig. 1

Overview of study design. Of the 106 included infants, 56 were fed formula with prebiotics (prebiotic group; blue), and 50 were fed the same prebiotic formula with Lactobacillus paracasei ssp. paracasei F19 (synbiotic group; orange) from 1 to 6 months of age. Follow-up continued until 12 months of age. We used 16S rRNA gene amplicon sequencing of 324 fecal samples collected at ages 1, 4, 6, and 12 months for the analysis of gut microbial composition. The fecal metabolome at these ages was investigated in 54 infants (193 samples) using a combination of untargeted gas chromatography-mass spectrometry/liquid chromatography-mass spectrometry (GC–MS/LC–MS). Eleven infants were diagnosed with lower respiratory tract infection (LRTI) by a physician in the first year of life. These and eleven matched controls were selected for deep metagenomic sequencing. In the final analyses, the metagenome and antibiotic resistome in fecal samples of 9 infants with LRTI and 10 matched controls were examined