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Most commonly, Penicillium moulds and some Aspergillus moulds survive in silage and produce mycotoxins. Fusarium moulds usually die in the process of being ensiled. Many silage mycotoxins have antimicrobial effects on the microbes found in the rumen. These mycotoxins negatively affect the fermentation process, causes various effects such as reduced milk yield. Silage mycotoxins can also be neurotoxic and tremorgenic. Examples include penicillic acid, PR toxin and mycophenolic acid.

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