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This study aimed to analyze the effects of dietary supplementation with flaxseed （Linum usitatissimum） and Schizochytrium on rumen microorganisms and meat fatty acid profiles in yaks.Twenty-one 12-month-old male healthy yaks weighing （95.00±5.20） kg were selected and divided into 3 groups according to the test requirements， with 7 replicates in each group. Supplementary feeding group （S） served as the control group， and the 2 experimental groups were fed with flaxseed （Y） and Schizochytrium （L） respectively for 210 days to analyze the effects on the microbial community structure and differential metabolites in the rumen of housed yaks， in conjunction with 16S rRNA sequencing and non-target metabolomes. Flaxseed and Schizochytrium supplementation significantly affected growth performance， muscle fatty acid composition， and rumen microbiota. Both treatment groups showed significantly lower dry matter intake （P<0.05） but improved feed conversion ratio （P<0.05）. The Schizochytrium group exhibited significantly higher muscle docosahexaenoic acid （DHA） content （0.35% vs. control 0.04%， P<0.05） and lower n-6/n-3 PUFA ratio （5.42 vs. control 36.28）. The flaxseed group showed increased total fatty acids （1.44 g vs. control 0.85 g， P<0.05）. Rumen analysis revealed significantly higher Firmicutes phylum abundance （69% vs. control 57%， P<0.05） and significantly lower Bacteroidota abundance （21% vs. control 27%，P<0.05） in the flaxseed group. The Schizochytrium group demonstrated increased Prevotella genus abundance （7.5% vs. control 3.9%， P<0.05）. α-diversity decreased in treatment groups versus control， while β-diversity differed significantly among groups. Muscle metabolomics analysis results indicated the downregulated phospholipid and acylcarnitine metabolism （P<0.05） and upregulated fatty acid derivatives in both treatment groups. Rumen microbiota correlated significantly with muscle metabolism （e.g.， Patescibacteria positively correlated with succinic acid metabolism， P<0.05）. Flaxseed and Schizochytrium promote lipid deposition in yaks by affecting rumen microbes and muscle metabolism， providing a theoretical basis for precision feeding strategies in alpine regions.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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