Additional file 6: Figure S5. of Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Taxonomic profile and relative abundance of the fungal core microbiome after aerobic exposure (14 days). OTUs were assigned at the genus level. (TIF 427 kb

Additional file 3: Figure S2. of Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

PCo analysis. Principal coordinates analysis for bacterial (left) and fungal (right) communities according to sampling time; fresh forage, terminal silage, aerobically exposed silage (A and B) and silage type (C and D). (TIF 822 kb

Additional file 2: Table S1. of Bacterial and fungal core microbiomes associated with small grain silages during ensiling and aerobic spoilage

Bacterial and Fungal Diversity Index. Table S2. Mapping File used for MOTHUR pipeline. (DOCX 18 kb

Biodegradation of Prions in Compost

Composting may serve as a practical and economical means of disposing of specified risk materials (SRM) or animal mortalities potentially infected with prion diseases (transmissible spongiform encephalopathies, TSE). Our study investigated the degradation of prions associated with scrapie (PrP^263K), chronic waste disease (PrP^CWD), and bovine spongiform encephalopathy (PrP^BSE) in lab-scale composters and PrP^263K in field-scale compost piles. Western blotting (WB) indicated that PrP^263K, PrP^CWD, and PrP^BSE were reduced by at least 2 log₁₀, 1–2 log₁₀, and 1 log₁₀ after 28 days of lab-scale composting, respectively. Further analysis using protein misfolding cyclic amplification (PMCA) confirmed a reduction of 2 log₁₀ in PrP^263K and 3 log₁₀ in PrP^CWD. Enrichment for proteolytic microorganisms through the addition of feather keratin to compost enhanced degradation of PrP^263K and PrP^CWD. For field-scale composting, stainless steel beads coated with PrP^263K were exposed to compost conditions and removed periodically for bioassays in Syrian hamsters. After 230 days of composting, only one in five hamsters succumbed to TSE disease, suggesting at least a 4.8 log₁₀ reduction in PrP^263K infectivity. Our findings show that composting reduces PrP^TSE, resulting in one 50% infectious dose (ID₅₀) remaining in every 5600 kg of final compost for land application. With these considerations, composting may be a viable method for SRM disposal