PacBio Full-length 16S Sequencing data

This is the data from our study "<b>Associations Between Gut Microbiota Characteristics and Non-Motor Symptoms Following Pharmacological and Surgical Treatments in Parkinson's Disease Patients</b>".<br>DNA was amplified using dual-unique barcoded primers targeting 16S-ITS-23S, the so-called StrainID kit from Shoreline Biome using StrainID Set A, 96 Barcodes (Shoreline Biome, Shoreline Wave StrainID set A Kit, WAVESID-A). Briefly, this approach involves a single-step PCR, made up of primers that contain the barcode and target-specific primers, and generates amplicons ready for PacBioSMRTbell template prep and subsequent sequencing on the PacBio Sequel Systems. The whole protocol, from input DNA to amplicon purification and pooling, followed the Shoreline Wave for PacBio Technical Manual. The pooled amplicons (83-96 amplicons including controls) were quantified using fluorometry as described above, and their length was verified using an Advanced Analytical Fragment Analyzer System with the Fragment Analyzer NGS Fragment Kit (Agilent, DNF-473-1000). As well as the input DNA of interest, five controls were included: a no template control, ZymoBIOMICSMicrobial Community DNA Standard, ZymoBIOMICS Microbial Community DNA Standard II, ZymoBIOMICS Fecal Reference with TruMatrix™ Technology, and ZymoBIOMICS Gut Microbiome Standard (Zymo Research; D6305, D6311, D6323, and D6331, respectively).Thereafter, barcoded SMRTbell libraries were constructed using an Express TPK 2.0 (PacBio, 100-938-900) in conjunction with the Barcoded Overhang Adapter Kit 8A &amp; 8B (PacBio, 101-628-400 &amp; 101-628-500) and according to the Shoreline Protocol for High-Density Multiplexing on PacBio Sequel Systems. The quantity and size of each SMRTbell library were selected as detailed above using Qubit and a Fragment Analyzer. Two barcoded SMRTbell libraries were sequenced using the PacBio SMRT cell 8M. A PacBio Sequel II 2.1 binding kit (PacBio, 101-843-000) was used for polymerase binding, and a Sequel II 2.0 sequencing kit along with the Sequel II DNA Internal Control (PacBio 101-820-200), CCS sequencing mode and a 10h movie time for sequencing. After each run, reads were sorted into the original sample pools by demultiplexing theSMRTbell barcodes using PacBio SMRTLink v9.0 software. After SMRTbell demultiplexing and primer removal, the resulting pooled amplicon files were further demultiplexed into individual samples, and taxonomic identification was assigned to all reads using the Shoreline Biome SBanalyzer 3.1 (CentOS command line installation (https://shorelinebiome.com/resources) and Athena Microbial Reference Database (v2.2) by running the pipeline StrainID_OR_NanoID_Kit.txt with default settings. The Interfaculty Bioinformatics Unit at the University of Bern performed this step.