Exposure of gut microbiota to antibiotics can promote antibiotic resistance and development of diseases caused by multi-drug-resistant organisms. Here we present a case of a 54-year-old male patient with a diagnosis of acute cholecystitis with significant biliary duct leakage, admitted to Intensive Care Unit (ICU) due to a septic syndrome after surgery. Fecal microbial population was analyzed by DGGE and Real Time PCR during and after a combined antibiotic therapy and enteral nutritional feeding. Gut microbiota dysbiosis was demonstrated during ICU recovery. After antibiotic therapy discontinuation and the switch to normal diet, microbial gut population gradually increased up to values comparable with those of a healthy subject. Bifidobacterium spp. took longer to re-stabilize, reaching normal value after two weeks. Our case report corroborates the resilient nature of gut microbiota, but points out the long time needed to recover after antibiotic treatment, paving the way to supplementation with key probiotic species.