Polysorbate 80-fed, carboxymethylcellulose-fed and control microbiota DataSet

[Description of methods used for collection/generation of data] The three colon reactors (R1, R2 and R3) of the BFBL gut simulator were inoculated (1%) with child (5-7 years old) pooled fecal sample. After the microbiota stabilization, polysorbate 80 or carboxymethylcellulose were added into the BFBL simulator at increasing concentrations (1, 3 and 5 g/L in case of polysobrbate 80 or 0.3, 1, 3 and 5 g/L in case of carboxymethylcellulose), three times per day during 1 week for each concentration. In addition, another run without additives feeding (control) was carried out for the same period of time to assess changes due to the experimental conditions. During the experimental set up, samples were collected every day from the three colon reactors and centrifuged (11,200 ×g during 10 min at 4 °C), and the pellet and supernatant were stored separately. Bacterial genomic DNA from the pellet was extracted according to the manufacturer’s instruction of the EZNA® Bacterial DNA Kit (Omega Biotek) and using a FastPrep equipment for mechanical lysis (Bio 101 FastPrep FP120, Savant Instruments). DNA samples were sent to Novogene Europe (Cambridge, UK) for sequencing the V3-V4 region of the 16S rRNA gene amplified by using 341F (5′- CCTAYGGGRBGCASCAG-3′) and 806R (5′-GGA CTACNNGGGTATCTAAT-3′) primers. The PCR products were sequenced on a paired-end Illumina platform (NovaSeq 6000, Illumina) to generate 250 bp paired-end raw reads.