Journal Article

Single-cell transcriptomic atlas of the chicken cecum reveals cellular responses and state shifts during Eimeria tenella infection

Liu, Bo-Gong, Lin, Bing-Jin, Guo, Song-Chang, He, Xi, Ouyang, Qing-Yuan, Fang, Ling-Zhao, Song, Ze-He, Zhang, Hai-Han, Liu, Hui-Chao, Tu, Jun-Hao

2025

Overview

Eimeria tenella ( E. tenella ) infection is a major cause of coccidiosis in chickens, leading to significant economic losses in the poultry industry due to its impact on the cecum. This study presents a comprehensive single-cell atlas of the chicken cecal epithelium by generating 7,394 cells using 10X Genomics single-cell RNA sequencing (scRNA-seq). We identified 13 distinct cell types, including key immune and epithelial populations, and characterized their gene expression profiles and cell–cell communication networks. Integration of this single-cell data with bulk RNA-seq data from E. tenella -infected chickens revealed significant alterations in cell type composition and state, particularly a marked decrease in APOB + enterocytes and an increase in cycling T cells during infection. Trajectory analysis of APOB + enterocytes uncovered shifts toward cellular states associated with cell death and a reduction in those linked to mitochondrial and cytoplasmic protection when infected with E. tenella . These findings highlight the substantial impact of E. tenella on epithelial integrity and immune responses, emphasizing the parasite’s role in disrupting nutrient absorption and energy metabolism. Our single-cell atlas serves as a critical resource for understanding the cellular architecture of the chicken cecum and provides a valuable framework for future investigations into cecal diseases and metabolic functions, with potential applications in enhancing poultry health and productivity.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Analysis / Animal Genetics and Genomics / Animals / Annotations / Anopheles / APOB + enterocytes / B cells / Biomedical and Life Sciences / Causes of / Cecum / Cecum - cytology / Cecum - metabolism / Cecum - parasitology / Cecum - pathology / Cell death / Cell interaction / Cell interactions / Cells / Chicken cecum / Chickens / Chickens - genetics / Chickens - parasitology / Coccidiosis / Coccidiosis - genetics / Coccidiosis - parasitology / Coccidiosis - veterinary / Communication / Communication networks / Complications and side effects / Data processing / Development and progression / Diseases / Economic impact / Eimeria tenella / Eimeria tenella - physiology / Energy metabolism / Enterocytes / Epithelium / Gene expression / Gene Expression Profiling / Gene sequencing / Genes / Genetic aspects / Genomics / Health aspects / Infection / Infections / Intestine, Large / Life Sciences / Lymphocytes / Lymphocytes T / Microarrays / Microbial Genetics and Genomics / Parasites / Physiological aspects / Plant Genetics and Genomics / Poultry / Poultry Diseases - genetics / Poultry Diseases - parasitology / Poultry industry / Proteomics / Quality control / Ribonucleic acid / RNA / RNA sequencing / Single-Cell Analysis / Single-cell RNA sequencing (scRNA-seq) / Software / Sporozoa / T cells / Trajectory analysis / Transcriptome / Transcriptomics / Variance analysis