Novel taxonomic and functional diversity of bacteria from the upper digestive tract of chicken

Abstract

AbstractStrategies to increase the production rate of chicken for human consumption alter the natural process of microbial colonisation and the nutritional performance of the animal. The lack of sufficient reference genomes limits the interpretation of sequencing data and restrain the study of complex functions. In this study, 43 strains obtained from crop, jejunum and ileum of chicken were isolated, characterised and genome analysed to observe their metabolic profiles, adaptive strategies and to serve as future references. Eight isolates represent new species that colonise the upper gut intestinal tract and present consistent adaptations that enable us to predict their ecological role, expanding our knowledge on the adaptive functions. Molecular characterisation confirmed the classification ofClostridium anaeroviscerissp. nov. (DSM 113860= LMG 32675),Clostridium butanolproducens(DSM 115076= LMG 32878),Ligilactobacillus hohenheimiussp. nov. (DSM 113870= LMG 32876),Limosilactobacillus gallussp. nov. (DSM 113833 =LMG 32623),Limosilactobacillus aviumsp. nov. (DSM 113849= LMG 32671), Limosilactobacillus pullumsp. nov. (DSM 115077 =LMG 32877),Limosilactobacillus digestussp. nov. (DSM113835= LMG 32625) andLimosilactobacillus difficilesp. nov. (DSM 114195= LMG 32875). Strains ofLimosilactobacilluswere found to be more abundant in the crop, whileLigilactobacillusdominated the ileal digesta. Isolates from crop encode a high number of glycosidases specialized in complex polysaccharides compared to strains isolated from jejunum and ileum. These results represent the first approach for the isolation and detection of bacteria from the chicken’s upper digestive tract and describe the functional diversity of bacteria inhabiting these regions, improving the potential handling of chicken microbiota with biotechnological applications.