Shotgun metagenomic sequencing of gut and respiratory microbiota in cystic fibrosis patients before and after CFTR modulator therapy
This study investigates the impact of highly effective CFTR modulator therapy with elexacaftor/tezacaftor/ivacaftor (ETI) on the gut and respiratory microbiota of people with cystic fibrosis (CF). CF is characterised by chronic lung infection, altered gut microbiota and systemic chronic inflammation, which together shape the composition and function of host-associated microbial communities. ETI has led to major clinical improvements, but its effects on the microbiota and microbial functions remain incompletely understood.  We conducted a longitudinal shotgun metagenomic study in individuals with CF attending our centre (Hospital Universitario Ramón y Cajal, Madrid, Spain). Faecal and sputum samples were collected at baseline immediately before ETI initiation (T0) and after 12 months of continuous ETI therapy (T12). In total, 35 patients and 140 samples are included in this dataset. Total DNA was obtained with the Speedtools DNA Extraction Kit (Biotools, Madrid, Spain). Library preparation was carried out at the UCA-GTB department (Instituto de Investigación Sanitaria Hospital Ramón y Cajal, Madrid, Spain). Libraries were constructed using the Illumina ADN Prep Tagmentation Kit (Cat. 20060059, Illumina, USA) and a short unique identifier for each sequencing library using IDT for Illumina DNA/RNA UD Indexes Set A, Tagmentation (96 Indexes–96 Samples, Cat. 20091654). Library quantity and quality were evaluated using QUBIT 1x dsDNA HS 500rx (ThermoFisher, Cat. Q33231) on a Qubit 2.0 Fluorometer (Invitrogen, ThermoFisher, USA), and size distribution was assessed on a High Sensitivity D1000 ScreenTape (Agilent Technologies, Cat. 5067-5584) and High Sensitivity D1000 ScreenTape Buffer (Agilent Technologies, Cat. 5067-5585) using a TapeStation 4150 system (Agilent Technologies, USA). Sequencing was performed on an Illumina NovaSeq 6000 system using a NovaSeq 6000 S1 Reagent Kit v1.5 (300 cycles) to generate 2×150 bp paired-end reads at HealthinCode (Valencia, Spain). Sequencing data were converted into raw data and demultiplexed into FASTQ files.  Raw Illumina® reads were processed using a custom Snakemake workflow for HUManN v3.9 (MMB-BioIT, University Medical Center Utrecht; https://gitlab.com/mmb-umcu/humann.git). Within this workflow, low-quality bases, adapters and host-derived reads were removed. Read cleaning and host decontamination were performed with KneadData, using a human reference database (HumanDB) and Bowtie2 to identify and discard human reads. The resulting decontaminated paired-end reads (_paired_1.fastq.gz and _paired_2.fastq.gz) are deposited in this study. The dataset is intended to support re-use by the research community for comparative analyses of pre- versus post-ETI microbiota.