mixed sample
Protocols: Study participants received a sample collection kit with instructions (manuscript supplementary section 2) and a collection tube with >99% ethanol for fixed faecal sample collection and storage. Sample collection kit provided by Oxford Centre for Microbiome Studies Faecal samples were extracted manually using the QIAamp PowerFecal Pro DNA kit (Qiagen, 51804) according to the manufacturer's instructions. Sample homogenization in PowerBead tubes was performed using a Qiagen Vortex adapter coupled to a Vortex Genie 2 for 20 minutes at maximum speed. Initial DNA quantification was performed on a NanoDrop (Thermo Scientific) and DNA concentration was adjusted to within the desired mass range for sequencing and plated on a 96 well, low profile, skirted PCR plate (4titude) for sequencing submission For bacterial 16S rRNA gene amplicon sequencing, the variable V3 and V4 regions of the 16S rRNA gene were amplified from genomic DNA using the primers (standard IUPAC nucleotide nomenclature): Forward Primer = 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG, Reverse Primer = 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC The amplicons were then attached with indices and Illumina sequencing adapters using the Nextera XT index kit. The 16S amplicon libraries were pooled and sequenced in an Illumina MiSeq v3 flowcell as 300 paired end reads
isolate
not applicable
disease
organism
mixed sample
organism
mixed sample
collection date
not collected
participant id
PBS_neg
sequencing id
WTCHG_946783_71635139
scientific_name
mixed sample
organism part
geographic location (country and/or sea)
not collected