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

Strategies 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 of Clostridium anaerovisceris sp. nov. (DSM 113860= LMG 32675), Clostridium butanolproducens (DSM 115076= LMG 32878), Ligilactobacillus hohenheimius sp. nov. (DSM 113870= LMG 32876), Limosilactobacillus gallus sp. nov. (DSM 113833 =LMG 32623), Limosilactobacillus avium sp. nov. (DSM 113849= LMG 32671) , Limosilactobacillus pullum sp. nov. (DSM 115077 =LMG 32877), Limosilactobacillus digestus sp. nov. (DSM113835= LMG 32625) and Limosilactobacillus difficile sp. nov. (DSM 114195= LMG 32875). Strains of Limosilactobacillus were found to be more abundant in the crop, while Ligilactobacillus dominated 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.