藍菌生物含有神經毒素BMAA(β-N-methylamino-L-alanine),BMAA已證實會對動物產生強烈的毒性,加速動物腦神經退化、四肢肌肉萎縮等等,小量BMAA積累已能選擇性殺死從老鼠的神經元。藍菌的次生代謝產物微囊藻毒素(Microcystin)有非常強的毒性,可能會嚴重損害肝臟[13],引致肝癌[14]。1996至1999年間,美國俄勒岡健康部門(Oregon Health Division)曾對市面上87種藍菌及螺旋藻保健食品進行測試,發現其中有85種保健食品含有微囊藻毒素。[15]節螺藻本身不產生這些毒物,但養殖環境經常會受到其他藍菌污染。
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