4.8. Microbial Profiling
SKIN, STERILE, LYSIS
Skin was swabbed for 10 s while constantly rotating using a sterile polyester-tipped applicator (Puritan, Guilford, ME, USA) soaked in 0.9% NaCl. Swabs were stored in DNA/RNA shield lysis buffer and beat beads (Zymo Research, Irvine, CA, USA) at −80 °C until analysis. Extraction, sequencing, and data generation were performed at Baseclear B.V. (Leiden, The Netherlands). Extraction was performed using a ZymoBIOMICS DNA Miniprep Kit (Zymo Research) according to the manufacturer’s instructions. The sample was split, and 16s RNA region v3–v4 or internal transcribed spacer region 2 (ITS2) sequencing was performed on a NovaSeq 6000 or MiSeq (Illumina, San Diego, CA, USA) after the appropriate sample quality control, for bacterial and fungal profiling, respectively. The reads were classified using the RDP database for bacterial [