Relationships within Rumen Methanogens and Fungal Communities and response to changes in Alfalfa forms and starch in sheep diet

The AHHR diet reduced methanogens Chao 1 index compared to the AS diets (P < 0.05), and the Shannon index was lower than in the ASLR diet (P < 0.05). The fungi Chao 1 index was higher in the AH diets than in the ASHR diet (P < 0.05), and the fungi Shannon index was higher in the LR diets than in the HR diets (P < 0.05). The relative abundance of Aspergillus in the AHLR diet was significantly higher than in the AS diets (P < 0.01), and the relative abundance of Occultifur and Meyerozyma were decreased in the AH than in the AS diets (P < 0.05). The LEfSe analysis showed that Methanobrevibacter_sp_YE315 and Methanobrevibacter_sp_AbM4 were enriched in the ASLR diet, while Methanobrevibacter_millerae was enriched in the ASHR diet. For the fungal biomarkers, the AHLR diet included Aspergillus, Metschnikowia, unclassified_f__Stachybotryaceae, the AHHR diet included stachybotrys, Stemphylium and Cystobasidium, the ASLR diet included unclassified_k__Fungi, Trichothecium, and Psathyrella, and the ASHR diet included Alfaria. Correlation analysis results showed the relative abundance of Methanobrevibacter, Methanoculleus, Penicillium, Cladosporium, and Exophiala and the concentration of isobutyrate and isovalerate, which may provide deeper insights into the previously observed differences.