After sequencing, demultiplexing of samples was performed using Illumina's BCL2FASTQ algorithm. Reads were filtered using an average Q-score > 30. Forward and reverse reads were appended together after removal of primers and any leading bases, and clustered using version 2.1.5 of the Swarm algorithm  using a distance of 1 nucleotide and the “fastidious” and “usearch-abundance” flags. The most abundant sequence per cluster was considered the real biological sequence and was assigned the count of all reads in the cluster. The remainder of the reads in a cluster were considered to contain errors as a product of sequencing. The representative reads from all clusters were subjected to chimera removal using the VSEARCH algorithm . Reads passing all above filters (filtered reads) were aligned using 100% identity over 100% of the length against a hand-curated database of target 16S rRNA gene sequences and taxonomic annotations derived from version 123 of the SILVA database . The hand-curated databases for each taxa were created by selectively removing sequences with amplicons that were ambiguously annotated to more than one taxonomic group, while still maximizing the performance metrics sensitivity, specificity, precision, and negative predictive value of identification for the remaining amplicons in each taxa (S1 Doc). In total 28 taxonomic groups of clinical relevance passed our criteria of over 90% for each performance metric (S1 Table). Raw FASTQ reads mapping to the samples and the taxa in the reference databases used in this study were uploaded to EBI’s ENA under accession code PRJEB20022. The relative abundance of each taxa was determined by dividing the count linked to that taxa by the total number of filtered reads.