Intestinal Microbiota and Probiotic Characteristics of Two Indigenous Chicken Breeds (Hotan Black Chicken and Baicheng You Chicken) from the Tarim Basin

Drawing on two indigenous chicken breeds that have adapted for centuries to the hyper-arid Tarim Basin, namely the Baicheng You Chicken and Hotan Black Chicken, this study provides a high-resolution map of their gut microbiota across the duodenum, jejunum, ileum and cecum and subsequently isolates putative probiotic strains from cecal contents using conventional culture techniques. In the duodenum, <i>Lactobacillus</i> dominated Hotan Black Chicken (43.16%), whereas <i>Ligilactobacillus</i> prevailed in Baicheng You Chicken (37.03%). This segregation persisted in the jejunum, with <i>Lactobacillus</i> accounting for 62.55% of Hotan Black Chicken reads and <i>Ligilactobacillus</i> accounting for 60.76% reads in Baicheng You Chicken. The ileal core of Hotan Black Chicken remained <i>Lactobacillus</i> (50.63%), while Baicheng You Chicken shifted to <i>Enterococcus</i> (32.37%). In the cecum, both breeds converged on the <i>Rikenellaceae</i> RC9 gut group as the single dominant lineage (Hotan Black Chicken, 46.87%; Baicheng You Chicken, 46.23%). At the genus level, Hotan Black Chicken was enriched in <i>Lactobacillus</i> and <i>Ligilactobacillus</i>, whereas Baicheng You Chicken harbored a greater proportion of <i>Enterococcus</i>. Concurrently, eight strains with in vitro probiotic attributes were isolated, four from each breed, identified as <i>Ligilactobacillus salivarius</i>, <i>Limosilactobacillus reuteri</i>, <i>Lactobacillus gallinarum</i>, <i>Enterococcus lactis</i>, <i>Enterococcus faecium</i>, <i>Enterococcus faecalis</i>, and <i>Bacillus velezensis</i>. This study deciphers the intestinal microbiome of two native Tarim Basin chicken breeds, Hotan Black Chicken and Baicheng You Chicken, and mines them for autochthonous probiotic strains. The obtained dataset has established a foundational resource for poultry-related probiotics adapted to extremely arid environments, providing theoretical insights and practical value for poultry nutritionists in water-scarce regions in the future.