Spatial Multi-Omics Analysis of the Qianqiu Goat Gut Microbiome and Metabolome

This study profiled the rumen (RM), small intestine (SI), and large intestine (LI) of 24 samples collected from eight 6-month-old Qianqiu goats (body weight 28.40 ± 1.80 kg), with the samples equally divided into three groups. A combination of methods was used, including 16S rRNA sequencing, untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics, Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and weighted gene co-expression network analysis-based module detection (WGCNA) with network integration. An uncommon composition of organisms dominated the SI: the hydrogenotrophic methanogens Methanobrevibacter (SI 24.51%; RM 1.92%; LI 2.19%) and Methanosphaera (SI 0.43%; RM 0.02%; LI 0.02%), together with the acetogen Acetitomaculum (SI 1.58%; RM 0.34%; LI 0.11%), were markedly more abundant compared to the RM or LI. Correlation and pathway analyses indicated that Methanobrevibacter was positively correlated with a steroid-type lipid metabolite (r = 0.52, p < 0.05) and with bile-acid-related metabolites. Acetitomaculum was positively correlated with several metabolites: 4-Hydroxyphenyl 4-hydroxybenzoate (r = 0.79, p < 0.05), 2-Aminoethyl dihydrogen phosphate (r = 0.76, p < 0.05), 1-Myristoyl-2-stearoyl-sn-glycero-3-phosphocholine (r = 0.76, p < 0.05), and 1,2-Dioleoyl-sn-Glycero-3-Phosphocholine (r = 0.74, p < 0.05). Together, these data define a small-intestinal microbial-metabolite module in Qianqiu goats characterized by elevated abundances of specific methanogens and acetogens in the SI. Specific positive correlations were identified between these taxa and metabolites associated with lipids and bile acids.