Study of the interaction between STEC and human gut microbiota using the ARtificial COLon model (ARCOL)

Young children are at highest risk to develop STEC infection with potentially life-threatening complications. Among the risk factors explaining the sensitivity of this age group, the gut microbiota might play a crucial role, but this has been so far poorly investigated. Infant exhibits specific digestive physiology including an immature gut microbiota characterized by a lower diversity in terms of bacterial commensal species. For the first time, we investigated the effect of STEC infection on the human gut microbiota using the Mucosal ARtificial COLon (M-ARCOL) model inoculated either with fecal samples from one adult (38 years old) or the Toddler Mucosal ARCOL (Tm ARCOL) inoculated with fecal sample from one infant (18 months old). M- and Tm-ARCOL are one-stage fermentation systems which simulate the physicochemical, nutritional and microbial parameters of the human colon under adult or toddler conditions, respectively. Different bioreactors from M- and Tm-ARCOL were inoculated in parallel with two STEC strains (serotypes O113:H21 and O26:H11) and the commensal E. coli strain ECOR-1 (serotype O144:H4) used as non-pathogenic control. Gut microbiota composition and presence of Stx2-coding genes were monitored throughout the total fermentation process (14 days). The screening of stx2 gene was performed on both the total bacterial DNA as well as the DNA extracted from purified phages, in order to evaluate the amplification of the STEC strains and the free Stx2-phage. The presence of the stx2 gene was evidenced until the end of the fermentations in the Tm- ARCOL models infected with the 2 STEC strains. On the contrary, the stx2 gene was detected only until day 8 and day 9 in M-ARCOL infected with the STEC O113:H21 and O26:H11 strains, respectively. The Tm-ARCOL model infected with the STEC O26 strain showed an increase of the signals related with the stx2-gene in the preparation of the phage DNA, producing a peak at day 12 suggesting that the amplification of the phage occurred. The alpha-diversity analysis showed an increase in the microbial diversity following the inoculation of the 2 STEC strains in M-ARCOL, especially 24h post-infection with the strain O26:H11. The opposite tendency was observed in Tm-ARCOL. No significant variation of the gut microbiota composition was observed whatever the strains tested under infant conditions, while in M-ARCOL inoculated with the 2 STEC strains, we observed differences in gut microbiota composition between pre- and post- infection. Of note, a significant increase in the abundance of Prevotella, Dialister and Oscillibacter genera was observed after infection with STEC O113 while Clostridium, Ruminococcus, Prevotella, Subdoligranulum and Murdochiella populations increased following infection with STEC O26. These results showed that the microbiota of adult and young children respond differently to the STEC infection. The longer persistence of STEC strains in the toddler model compared to the adult one suggests that changes in composition of adult gut microbiota could be more efficient in clearing the infection. Finally, the peak of the stx2-gene in the phage DNA suggests that some of the microorganisms composing the infant microbiota may be involved in the amplification cycle of the Stx2-bacteriophages. Both these observations may explain, at least in part, the higher susceptibility of children to the more severe outcome of the STEC infection.