Antibiotic treatment triggers gut dysbiosis in a chicken model of gastro-intestinal infection

Infection of the digestive track by gastro-intestinal pathogens results in the development of symptoms ranging from mild diarrhea to more severe clinical signs such as dysentery, severe dehydration and potentially death. Although, antibiotics are efficient to tackle infections, they also trigger gut dysbiosis. Here is the first study demonstrating the impact of infection by a gastro-intestinal pathogen (Brachyspira pilosicoli) and its resolution by antibiotic treatment (tiamulin) on chicken caecal microbiota composition using 16S rDNA next generation sequencing (NGS). We used three groups of 40 birds: a control groups, infected groups and infected and antibiotic treated group. All groups were followed for 4 weeks. Caecal samples were collected at three time points for all groups (n =8). Antibiotic treatment was followed by a significant reduction of caecal microbiota alpha diversity that was recovered 2 weeks after the end of the treatment periode. Infection and antibiotic treatment triggered shift in the gut microbiota composition that recovered over time for infection but not the antibiotic treatment group.