The rumen is divided into multiple rumen sacs based on anatomical structure, and each has its unique physiological environment. Tarim wapiti preserved roughage tolerance after domestication, and adaptation to the desertified environment led to the development of a unique rumen shape and intraruminal environment. In this work, six Tarim wapiti were chosen and tested for fermentation parameters, microbes, and histomorphology in four rumen areas (Dorsal sac, DS; Ventral sac, VS; Caudodorsal blind sac, CDBS; Caudoventral blind sac, CVBS). Tarim wapiti’s rumen blind sac had better developed rumen histomorphology, the ventral sac was richer in VFAs, and the dominant bacteria varied most notably in the phylum Firmicutes, which was enriched in the caudoventral blind sac. The ventral sac biomarkers focused on carbohydrate fermentation-associated bacteria, the dorsal sac focused on N recycling, and the caudoventral blind sac identified the only phylum-level bacterium, Firmicutes; we were surprised to find a probiotic bacterium, Bacillus clausii, identified as a biomarker in the ventral sac. This research provides a better understanding of rumen fermentation parameters, microorganisms, and histomorphology in the Tarim wapiti rumen within a unique ecological habitat, laying the groundwork for future regulation targeting the rumen microbiota and subsequent animal production improvement.

Background: The rumen epithelium, liver, and muscle tissues are key metabolic organs in ruminants, each performing distinct yet interconnected roles in energy metabolism and growth. However, how these tissues coordinate their gene expression to meet metabolic demands in Hu sheep remains poorly understood. Results: RNA sequencing of 48 tissue samples (rumen epithelium, liver, and muscle tissues from 16 male Hu sheep) identified 30,171 transcripts, including 7,403 commonly expressed and 3,414 uniquely expressed genes. The rumen epithelium displayed the highest number of uniquely expressed genes but lower functional enrichment compared to the liver and muscle, emphasizing its specialized yet limited metabolic pathways. Functional enrichment analysis showed that the rumen epithelium was enriched in pathways related to epithelial renewal. Differential gene expression analysis of commonly expressed genes further distinguished these tissues, reinforcing the metabolic specialization of the rumen epithelium. Weighted Gene Co-expression Network Analysis (WGCNA) revealed distinct tissue-specific modules associated with tissues. Key hub genes from different co-expression modules included histone deacetylase 1 ( HDAC1 , MEblue module, rumen epithelium), alpha-1-microglobulin/bikunin precursor ( AMBP , MEdarkslateblue module, liver), and SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily d member 3 ( SMARCD3 , MEbrown module, muscle), which regulate epithelial renewal, metabolic detoxification, and growth, respectively. Modules correlated with dry matter intake (DMI) were mainly found in the rumen epithelium and liver, while average daily gain (ADG)-related modules were enriched in the liver and muscle, indicating tissue-dependent regulatory mechanisms linking metabolic networks to performance. Conclusions: This study reveals transcriptional specialization and inter-tissue coordination in Hu sheep metabolic organs, identifies tissue-specific gene modules associated with DMI and ADG, and highlights hub genes as potential targets for precision breeding and feeding strategies to improve feed efficiency and growth in Hu sheep.

Under long-term ecological stress, the Tarim wapiti (Cervus elaphus yarkandensis) has evolved unique adaptations in digestive physiology and energy metabolism. A multi-omics comparison of three Tarim wapiti and five Karakul sheep was used to examine the synergistic mechanism between rumen bacteria, short-chain fatty acids, and host epithelial regulation in order to clarify the mechanism of high roughage digestion efficiency in Tarim wapiti. Metagenomic sequencing (Illumina NovaSeq 6000) and gas chromatography revealed that Tarim wapiti exhibited significantly higher acetate and total VFA (TVFA) concentrations compared to Karakul sheep (p < 0.01), accompanied by lower ruminal pH and propionate levels. Core microbiota analysis identified Bacteroidetes (relative abundance: 52.3% vs. 48.1%), Prevotellaceae (22.7% vs. 19.4%), and Prevotella (18.9% vs. 15.6%) as dominant taxa in both species, with significant enrichment of Bacteroidetes in wapiti (p < 0.01). Functional annotation (PICRUSt2) demonstrated enhanced glycan biosynthesis (KEGG ko00511), DNA replication/repair (ko03430), and glycoside hydrolases (GH20, GH33, GH92, GH97) in wapiti (FDR < 0.05). Transcriptomic profiling (RNA-Seq) of rumen epithelium showed upregulated expression of SCFA transporters (PAT1: 2.1-fold, DRA: 1.8-fold, AE2: 2.3-fold; p < 0.01) and pH regulators (Na⁺/K⁺ ATPase: 1.7-fold; p < 0.05) in wapiti. Integrated analysis revealed coordinated microbial–host interactions through three key modules: (1) Bacteroidetes-driven polysaccharide degradation, (2) GHs-mediated fiber fermentation, and (3) epithelial transporters facilitating short-chain fatty acids absorption. These evolutionary adaptations, particularly the Bacteroidetes–short-chain fatty acids–transporter axis, likely underpin the wapiti’s superior roughage utilization efficiency, providing molecular insights for improving ruminant feeding strategies in an arid environment.

Rumen microbiota is pivotal for nutrient metabolism and physiological adaptation in ruminants. This study investigated the rumen microbial community, fermentation parameters, and serum biochemistry of three Cervid species—Sika deer (Cervus nippon), Reindeer (Rangifer tarandus), and Milu deer (Elaphurus davidianus) (n = 5/group)—fed an identical diet. Using 16S rRNA sequencing and biochemical analyses, we found that while Bacteroidota, Firmicutes, and Proteobacteria were dominant phyla across species. Sika deer and Milu deer exhibited significantly higher microbial diversity and abundance of carbohydrate-digesting genera (e.g., Butyrivibrio, Saccharofermentans), and pathways of carbohydrate digestion and absorption, starch and sucrose metabolism compared to Reindeer. Conversely, Reindeer showed increased abundances of Lachnospiraceae ND3007 and butyrate metabolism pathway, and significantly elevated rumen volatile fatty acid concentrations, particularly acetate and butyrate. Serum profiling revealed that Milu deer had significantly higher lipid levels (CHO, TG, LDL-C) but lower total protein and AST levels compared to other species. Notably, WGCNA linked these blood lipid traits to host genes enriched in PI3K-Akt, MAPK, and bile secretion pathways. These findings demonstrate distinct species-specific rumen fermentation patterns and host metabolic adaptations, suggesting a coordinated regulation between the rumen microbiome and host genetics in Cervid.