MOESM2 of Clostridium difficile colonization and antibiotics response in PolyFermS continuous model mimicking elderly intestinal fermentation

Additional file 2. Daily mean metabolites concentrations in ceftriaxone (=CRO) treated TR3 compared to CR during period A (CRO I) and B (CRO II)

Set-up of the continuous fermentation models with immobilized gut microbiota.

<p><b>(A) Model 1.</b> 3-stage model consisting of a proximal, transverse and distal colon reactor <b>(B) Model 2.</b> 2-stage model with an inoculum reactor connected to two parallel test systems consisting of a proximal and distal colon reactor <b>(C) Model 3.</b> 2-stage model with an inoculum reactor (proximal colon conditions) feeding 5 distal colon reactors connected in parallel; RT: Retention time, V: Volume.</p

Correlations between genus-level phylogenetic groups and metabolites (SCFA, BCFA) of three last days at the end of stabilization period of model 2.

<p>The correlations, assessed by Spearman are indicated by either red (positive) and blue (negative), the significant correlations (q < 0.05) are indicated by ‘+’. Only genus related phylotypes > 0.1% and with at least one significant correlation with metabolites are depicted. Parentheses indicate an unknown genus belonging to a family or order.</p

Metabolites concentration (mM) and ratios (%) measured by HPLC in effluent samples of models’ reactors at the end of the stabilization period.

<p>PC, proximal colon reactor; DC, distal colon reactor; IR, inoculum reactor; CR, control reactor; TR, test reactor</p><p>Data are means ± SD of three last days at the end of the stabilization period; samples were analyzed in duplicate. ND, not detected</p><p>Values with different letters are significantly different within one model (P < 0.05)</p><p>Metabolites concentration (mM) and ratios (%) measured by HPLC in effluent samples of models’ reactors at the end of the stabilization period.</p

Shannon diversity index of fecal samples and reactors of PolyFermS models.

<p>The Shannon index was assessed in fecal donors 2 and 3, all reactors of model 2 and reactors IR, CR, TR3 and TR4 of model 3 of three last days at the end of stabilization phase. A higher Shannon index reflects a more diverse community (in abundance and evenness).</p

PCoA analysis of PolyFermS models based on weighted and unweighted UniFrac analysis.

<p>Each symbol is representing a different reactor. <b>(A)</b> Three last days at the end of the stabilization period of all reactors of model 2 (IR, PC1, DC1, PC2 and DC2) and <b>(B)</b> three last days at the end of the stabilization period of model 3 (IR, CR, TR3 and TR4).</p

Daily mean SCFA concentrations in fermentation effluents of IR of PolyFermS models measured by HPLC.

<p>Initial stabilization: stabilization period in continuous mode to reach pseudo steady-state.; stabilized operation mode: continuous operation mode during pseudo steady-state conditions. <b>(A)</b> Model 2 and <b>(B)</b> model 3; (♦) acetate, (●) butyrate, and (■) propionate.</p

Microbial composition of fecal samples and reactors of PolyFermS models measured by 454 pyrosequencing.

<p>Relative abundance at <b>(A)</b> phylum level of fecal samples of donors 2 and 3, IR and DCI of model 2 and IR and CR of model 3 <b>(B)</b> family level and <b>(C)</b> genus level of fecal samples of donors 2 and 3, all reactors of model 2 and reactors IR, CR, TR3 and TR4 of model 3 identified by pyrosequencing of the V5-V6 hypervariable regions of the 16S rRNA gene. Effluent samples are average values of three last days at the end of the stabilization period. Parentheses indicate an unknown family belonging to an order or an unknown genus belonging to a family or order. Values < 1% are summarized in the group “others”.</p

qPCR enumeration of bacterial groups in fecal inocula and effluent samples of models’ reactors at the end of the stabilization period.

<p>PC, proximal colon reactor; DC, distal colon reactor; IR, inoculum reactor; CR, control reactor; TR, test reactor; ND, not detected</p><p>¹Data are mean log₁₀ copies 16S rRNA gene g^-1 feces; samples were analyzed in duplicate.</p><p>²Data are mean log₁₀ copies 16S rRNA gene g^-1 fermentation effluent ± SD of three last days at the end of the stabilization period; samples were analyzed in duplicate. Values with different letters are significantly different within one model (P < 0.05)</p><p>qPCR enumeration of bacterial groups in fecal inocula and effluent samples of models’ reactors at the end of the stabilization period.</p