Effects of selection on production parameters and intestinal microbiota in heritage and modern broiler chickens

Authors: Kpodo, Kouassi; Miska, Katarzyna; SCHEIER, LORI - Retired ARS Employee; Proszkowiec-Wegla, Monika

Submitted to: Journal of Animal Science and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/15/2026
Publication Date: 3/7/2026
Citation: Kpodo, K. R., Miska, K. B., Scheier, L. L., & Proszkowiec-Wegla, M. K. (2026). Effects of selection on production parameters and intestinal microbiota in heritage and modern broiler chickens. Journal of Animal Science and Biotechnology, 17, Article 40. https://doi.org/10.1186/s40104-026-01360-8
DOI: https://doi.org/10.1186/s40104-026-01360-8

Interpretive Summary: Intestinal microbiota play an important role in gut homeostasis and function, and can partly affect chicken growth and performance. Modern broiler chickens have been selected for improved feed efficiency and growth rate, but how genetic selection affected intestinal microbiota is unknown. To better understand the effects of genetic selection on intestinal microbiota in meat-type chickens, heritage and modern (slow and fast growing) chicken breeds were hatched and raised under similar conditions for 35 days to determine growth performance. Next-generation sequencing was used to study changes in intestinal microbiota and metabolic pathways. The results showed that slow and fast-growing birds grew faster than heritage birds from days 13-35 during the post-hatch period and intestinal microbiota among the different breeds were affected. Gastrointestinal bacterial diversity was increased in modern chickens compared to the heritage chicken breeds mostly on days 14 and 35 post-hatch. The relative abundance of Lactobacillus salivarius was higher in fast-growing than in heritage chicken breeds. These results suggest that Lactobacillus species may be important in improving growth performance and could be a promising probiotic candidate. However, fast-growing breeds were also characterized by a higher level of the genus Streptococcus. Predicted metabolic pathways related to biosynthesis of nucleotides and biotin, which are important to maintain bacterial proliferation and growth were increased in fast-growing breeds. It appears that genetic selection has introduced some changes in intestinal microbiota in modern breeds. These results can help the poultry industry refine the use of bacteria as probiotics for growth performance in modern meat-type birds.

Technical Abstract: Background. Genetic selection has improved feed efficiency and growth in broiler chickens. Intestinal microbiota plays an important role in gut functions and host metabolism; however, it is unclear whether selection for rapid growth has affected intestinal microbiota. The objective of the study was to determine the effects of genetic selection on intestinal microbiota in broiler chickens. Methods. Heritage (Athens Canadian Random Bred: ACRB), slow- and fast-growing (SG, FG) chickens were raised under similar conditions for 35 days. 16S rRNA sequencing were performed on ileal and cecal luminal and mucosal bacterial populations, and data were analyzed using the qiime2 platform, differential abundance, and metabolic pathways. Results. The relative abundance of the genus Turicibacter was elevated (P<0.05) at hatch compared to 48 before hatch while at species level, Clostridium celatum was increased (P<0.05) at hatch. During the post-hatch period, body weight increased in SG, FG compared to ACRB and SG and FG at each timepoint from days 13 to 35. In IL-L, richness (day 14) was lower (P<0.05) in ACRB compared to FG and SG lines, respectively. In Ce-L, richness and Shannon index were reduced (P<0.05) in ACRB compared to FG lines only on day 35. The Shannon index was significantly (P<0.05) lower in ACRB birds compared to FG birds on day 35. The relative abundance of genera Escherichia was higher (P<0.05) in SG compared to other lines. FG birds were characterized by the highest (P<0.05) Streptococcus level. Relative abundance of most of the identified species were affected only by time post-hatch and only the relative abundance of a single species Lactobacillus salivarius was higher (P<0.05) in FG compared to ACRB birds. Predicted metabolic pathways related to biosynthesis of nucleotides and biotin, especially in the cecum, were increased in FG lines. Conclusion. These results indicate that selection for growth has affected intestinal microbiota as bacterial diversity was different in the ileum and cecum which could partly explain growth rate differences among heritage and modern lines. In addition, the increased predicted metabolic pathways in the cecum of FG birds could positively affect growth rate, and further research is needed to elucidate this hypothesis.