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

Eight anaerobic strains obtained from crop, jejunum and ileum of chicken were isolated, characterized and genome ana-lysed to observe their metabolic profiles, adaptive strategies and to serve as novel future references. The novel species Ligilactobacillus hohenheimensis sp. nov. (DSM 113870^T =LMG 32876^T), Limosilactobacillus galli sp. nov. (DSM 113833^T =LMG 32623^T), Limosilactobacillus avium sp. nov. (DSM 113849^T =LMG 32671^T), Limosilactobacillus pulli sp. nov. (DSM 115077^T =LMG 32877^T), Limosilactobacillus viscerum sp. nov. (DSM 113835^T =LMG 32625^T), Limosilactobacillus difficilis sp. nov. (DSM 114195^T =LMG 32875^T) and Clostridium butanoliproducens (DSM 115076^T =LMG 32878^T) are found in the upper gastrointestinal tract and present consistent adaptations that enable us to predict their ecological role. Molecular characterization using 16S rRNA gene analysis and long-read whole genome sequencing, confirmed the description of the novel genus Fae-calispora gen. nov. with Faecalispora anaeroviscerum gen. nov. sp. nov. (DSM 113860^T =LMG 32675^T) as genus type species. After phylogenetic and taxonomic analysis, we recommend the reclassification of the species Clostridium jeddahense and Clostridium sporosphaeroides to the genus Faecalispora. Exploration of the microbiome from crop and small intestine of chicken expands our knowledge on the taxonomic diversity and adaptive functions of the inhabiting bacteria. The novel species identified in this project are part of a wider cultivation effort that represents the first repository of bacteria obtained from the crop and small intestine of chicken using culturomics, improving the potential handling of chicken microorganisms with biotechnological applications.