Multi-centre study to assess the intestinal microbiota of ICU patients upon admission and follow-up of those with a sepsis diagnosis.

This study aimed at the assessment of the intestinal microbiota in critically ill patients with and without sepsis as well as determine its impact on outcome variables such as medical complications, ICU stay time, and mortality. A multi-centre study was conducted with a total of 250 peri-rectal swabs obtained from 155 patients upon admission and during the ICU stay in five fourth-level hospitals located in Medellín and Rionegro cities, Colombia. Microbiota analysis was conducted by amplifying and sequencing the V3-V4 hypervariable regions of the 16S rRNA bacterial gene. Linear mixed models were used to integrate microbiota data at OTUs level with more than 40 clinical and demographic variables to detect covariates and minimise the effect of confounding factors. Note: the raw fastq data associated with this study was obtained by pre-processing of the original six paired-end files (three PE libraries run in one MiSeq lane and containing 250 samples) and merging them into three major fastq files with "flash" tool. Sample demultiplexing was done by using "seqkit (grep)" algorithm. Therefore, barcode and primers information are still present in all sample fastq files, so, it is recommended to trim sequences at least 30 nt at 5' and 3' ends for all reads before any downstream process.