Microbiome samples
Tecan
PLAQUE
Participants provided fecal samples using an OMNIgene-Gut stool collection kit (DNA Genotek), and subgingival plaque samples were collected by a dentist using the same collection kit. Genomic DNA was purified using PowerMag Soil DNA isolation kit (MoBio) optimized for Tecan automated platform, and shotgun sequenced on Illumina NextSeq 500 as single-end 75 base pairs (bp) reads, or on NovaSeq 6000 platform as single-end 100 bp reads. Reads were then processed with Trimmomatic0.38 to remove adapters and filtered by quality (parameters: -phred33 ILLUMINACLIP:<adapter file > :2:30:10 SLIDINGWINDOW:6:20 CROP:75 MINLEN:65 for 75 bp and CROP:100 MINLEN:90 for 100 bp)Species composition was calculated by two steps. In the first step non-human reads were mapped to a subset of Pasolli et al. representative genomes using Bowtie2No PCs were reduced from the gut compositional data, three were reduced from the oral compositional data, we ended up with 378 gut samples with 605 features, and 328 oral samples with 336 features. 77% of gut species and 59% of the oral species could not be classified at the species level since no reference genome was present in the bin.Shanon alpha diversity and richness were calculated before the data processing stages listed above. Human cell shedding was computed as the percentage of human reads filtered out of all reads that passed quality control.Microbial functions were calculated using MetaCyc24 pathways by HUMAnN3, Bowtie2, DIAMOND2 and MetaPhlAn4