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。蓝菌的次生代谢产物微囊藻毒素(Microcystin)有非常強的毒性,可能會嚴重损害肝脏[13],引致肝癌[14]。1996至1999年間,美國俄勒冈健康部門(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]节螺藻本身不产生这些毒物,但养殖环境经常会受到其他藍菌污染。
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