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Moldy forage can contribute to a range of disorders in the horse. Inhaled fungal and actinomycete spores can cause primary allergic and inflammatory respiratory disease, as well as influencing the incidence, severity, and duration of episodes of infectious respiratory disease. However, molds may also produce toxic secondary metabolites called mycotoxins. Mycotoxins may contribute to reproductive, immunological, respiratory, gastrointestinal, and other disorders in livestock including the horse. Mycotoxins can behave as immunosuppressants, thus having the possibility to contribute to secondary disorders. Mold and subsequent mycotoxin contamination of a forage can increase during extreme environmental conditions such as high humidity at the time of baling or from mechanical damage to the forage.

Fusarium mycotoxins include vomitoxin (deoxynivalenol or DON), zearalenone, fumonisins, moniliformin, and fusarin C. There is evidence of synergism between mycotoxins, one example being between vomitoxin and fusaric acid (a phytotoxin). Signs of toxicity are induced at much lower levels of exposure when these two toxins are ingested together than when ingested separately.

Fumonisin B1 is associated with moldy corn poisoning in horses (equine leukoencephalomalacia, or ELEM). Animals must consume a feed which contains at least 10 ppm fumonisin B1 for ELEM to occur. Fumonisin B1 can also cause liver damage and pulmonary edema in horses and swine. Combined levels of fumonisin B1 and fumonisin B2 as low as 5 ppm have been associated with ELEM in horses, whereas swine were unaffected at those levels. Zearalenone, an estrogenic toxin, can lead to reproductive problems including hyperestrogenism. Disorders seen in swine and horses include uterine enlargement and inflammation and atrophy of the ovaries. It has not been shown to cause abortions.

Vomitoxin, one of the most frequent tricothecene contaminants found on cereal crops, has been  associated with loss of appetite, vomiting, lesions of the intestinal tract, immunosuppression, lethargy, and ataxia in domestic animals and man. Studies have shown the presence of potentially significant levels of vomitoxin in hay being fed to horses. This was in hay that owners were happy with, based on visual inspection. The levels found in this study could potentially have an influence on the health of horses consuming such hay. The threshold of significant biological activity is unknown for the horse; however, chronic exposure to lower levels rather than acute exposure to high levels may contribute to a wide range of disorders.

To minimize problems with moldy hay, buy from a reputable producer, store hay so that it is protected from moisture, allow air circulation around stored hay, and check each bale for visible mold before feeding.

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