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Sequencing library preparation and 16S rDNA amplicon sequencing
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The hypervariable regions V3 and V4 of the 16S rRNA gene were sequenced using the Illumina MiSeq platform in the DNA core facility of the University of Helsinki, as described in detail in the Supplementary information. The first-round PCR was done using primers 341 F and 785 R. Control and newborn samples were preamplified by 21 PCR cycles, 7-day and adult fecal samples by 15, and others by 18 to compensate for different quantities of 16S rDNA copies in the samples.
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