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

## TL;DR

This study maps the gut bacteria of two desert-adapted chicken breeds and identifies potential probiotics that could help raise healthier poultry in dry regions.

## Contribution

The study provides a high-resolution map of gut microbiota and isolates novel probiotic strains from two indigenous chicken breeds in the Tarim Basin.

## Key findings

- Both chicken breeds share the Rikenellaceae RC9 gut group as the dominant microbe in the cecum.
- Eight probiotic strains with in vitro attributes were isolated, including Lactobacillus and Enterococcus species.
- The study reveals distinct microbial profiles in the duodenum, jejunum, and ileum between the two chicken breeds.

## Abstract

We mapped the gut bacteria of two desert-adapted chicken breeds from China’s Tarim Basin—Baicheng You Chicken and Hotan Black Chicken—to hunt for beneficial microbes they naturally carry. After sampling four intestinal sites and culturing bacteria from the cecum, we found that both breeds share the same dominant microbe in this section. From their intestinal contents, we isolated eight promising probiotic strains. Already thriving in an extremely arid climate, these home-grown bacteria could become low-cost, water-saving probiotics for poultry in other dry regions, helping farmers raise healthier flocks with fewer antibiotics and chemicals.

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, Lactobacillus dominated Hotan Black Chicken (43.16%), whereas Ligilactobacillus prevailed in Baicheng You Chicken (37.03%). This segregation persisted in the jejunum, with Lactobacillus accounting for 62.55% of Hotan Black Chicken reads and Ligilactobacillus accounting for 60.76% reads in Baicheng You Chicken. The ileal core of Hotan Black Chicken remained Lactobacillus (50.63%), while Baicheng You Chicken shifted to Enterococcus (32.37%). In the cecum, both breeds converged on the Rikenellaceae 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 Lactobacillus and Ligilactobacillus, whereas Baicheng You Chicken harbored a greater proportion of Enterococcus. Concurrently, eight strains with in vitro probiotic attributes were isolated, four from each breed, identified as Ligilactobacillus salivarius, Limosilactobacillus reuteri, Lactobacillus gallinarum, Enterococcus lactis, Enterococcus faecium, Enterococcus faecalis, and Bacillus velezensis. 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.