FIG 1.

Experimental overview and microbial stress response. (A) Experimental design. Fecal matter from a healthy individual was used to inoculate triplicate fermentations in the presence of alcohol (EtOH) or antibiotics (48-h treatment) and compared to that of a control without intervention. In the second phase of the experiment, recovery after alcohol or antibiotic treatment was assessed. Colonic suspensions from both interventions were incubated for an additional 48 h in the absence of synbiotics (Antibiotics w/o synbiotic and Alcohol w/o synbiotic) or the presence of synbiotics (Antibiotics w synbiotic and Alcohol w synbiotic), while the control fermentation continued. To simulate the backup function of the mucosal environment, mucin-coated carriers from the control in phase 1 of the experiment were transferred to all colon reactors in phase 2. This is represented by the dotted gray lines. (B) Changes in SCFA concentrations as a function of antibiotic and EtOH treatment (test 1 in panel A). (C) Top statistically significant phylum- and genus-level changes (compared to the controls) in average microbial relative abundances for reactors exposed to stressors (test 1 in panel A). Gray cells in either of the columns describing relative abundance shifts indicate a non-statistically significant association (i.e., P value of >0.05). Green indicates enrichment relative to the control, while blue/orange indicates depletion relative to the control.