Multi-Species Transcriptomics of the Mammalian Stomach Reveals Conserved Programs and Ruminant Chamber Specialization.
- 1Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory of Animal Biotech Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- 2Key Laboratory of Innovative Utilization of Local Cattle and Sheep Germplasm Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Zhengzhou University, Zhengzhou 450001, China.
- 3Institute of Livestock Breeding and Reproduction, Henan University, Zhengzhou 450046, China.
Abstract
The mammalian stomach has conserved digestive functions but also shows major anatomical and physiological differences among species. However, broad comparative transcriptomic analyses across mammals and across ruminant stomach chambers remain limited. Here, we collected and integrated 111 bulk RNA-seq datasets from 11 mammalian species (humans, mice, monkeys, dogs, horses, donkeys, pigs, cattle, deer, goats, and sheep) and analyzed 12,048 shared one-to-one orthologous genes. We identified 56 conserved genes mainly involved in translation, ribosome biogenesis, protein homeostasis, and mitochondrial function. Pairwise comparisons revealed extensive transcriptional differences, with 2070-7110 differentially expressed genes across species pairs, together with distinct species-associated transcription-factor activity patterns. We also identified 25 ruminant-enriched genes associated with epithelial differentiation, ion transport, mucosal defense, and metabolism. Analysis of 69 samples from the rumen, reticulum, omasum, and abomasum of sheep, goats, cattle, and deer showed clear chamber-associated transcriptomic differences. The abomasum had a distinct expression program, with 235 enriched genes related to hormone regulation, secretion, transport, and digestion. Weighted gene co-expression network analysis further identified different gene programs in the forestomach and abomasum. Together, these findings reveal conserved, species-associated, and chamber-associated transcriptional features of the mammalian stomach and provide a useful framework for understanding its molecular diversity.
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BibTeX
@article{huang2026multispecies,
title = {{Multi-Species Transcriptomics of the Mammalian Stomach Reveals Conserved Programs and Ruminant Chamber Specialization.}},
author = {Qi-Xuan Huang and Zhi-Hui Wang and Wen-Tian Wei and Si-Rui Liu and Yi-Lin Bai and Yue-Yu Bai and Meng-Hua Li and Song-Song Xu},
journal = {Biology},
year = {2026},
month = sep,
doi = {10.3390/biology15191677},
url = {https://europepmc.org/article/MED/42883350},
note = {CC BY},
}
RIS
TY - JOUR
TI - Multi-Species Transcriptomics of the Mammalian Stomach Reveals Conserved Programs and Ruminant Chamber Specialization.
AU - Qi-Xuan Huang
AU - Zhi-Hui Wang
AU - Wen-Tian Wei
AU - Si-Rui Liu
AU - Yi-Lin Bai
AU - Yue-Yu Bai
AU - Meng-Hua Li
AU - Song-Song Xu
PY - 2026
DA - 2026/09/22
JO - Biology
DO - 10.3390/biology15191677
UR - https://europepmc.org/article/MED/42883350
AB - The mammalian stomach has conserved digestive functions but also shows major anatomical and physiological differences among species. However, broad comparative transcriptomic analyses across mammals and across ruminant stomach chambers remain limited. Here, we collected and integrated 111 bulk RNA-seq datasets from 11 mammalian species (humans, mice, monkeys, dogs, horses, donkeys, pigs, cattle, deer, goats, and sheep) and analyzed 12,048 shared one-to-one orthologous genes. We identified 56 conserved genes mainly involved in translation, ribosome biogenesis, protein homeostasis, and mitochondrial function. Pairwise comparisons revealed extensive transcriptional differences, with 2070-7110 differentially expressed genes across species pairs, together with distinct species-associated transcription-factor activity patterns. We also identified 25 ruminant-enriched genes associated with epithelial differentiation, ion transport, mucosal defense, and metabolism. Analysis of 69 samples from the rumen, reticulum, omasum, and abomasum of sheep, goats, cattle, and deer showed clear chamber-associated transcriptomic differences. The abomasum had a distinct expression program, with 235 enriched genes related to hormone regulation, secretion, transport, and digestion. Weighted gene co-expression network analysis further identified different gene programs in the forestomach and abomasum. Together, these findings reveal conserved, species-associated, and chamber-associated transcriptional features of the mammalian stomach and provide a useful framework for understanding its molecular diversity.
SN - 2079-7737
ER -