短链脂肪酸是主要在结肠中通过膳食可发酵纤维和抗性淀粉的肠道微生物发酵产生的有机酸，其次是膳食和内源性蛋白质。短链脂肪酸是一元羧酸盐，在健康结肠腔中的浓度比约为 60:25:15 醋酸盐 (C2):丙酸盐 (C3):丁酸盐 (C4)。结肠中这些弱酸的存在降低了腔内的 pH 值，这有利于产生丁酸盐的细菌的生长。宏基因组靶向方法的使用已将产生丁酸盐的细菌鉴定为功能组而不是连贯的系统发育组。在梭菌簇 IV 和 XIVa 的厚壁菌门内占优势，丁酸盐生产者是革兰氏阳性、严格厌氧和氧敏感的糖分解细菌。梭菌簇 IV 和 XIVa 的数量在新生儿期较低，到 2 岁时略有增加，然后在儿童后期和青春期急剧上升，但随后在成年期，特别是在老年人中再次开始下降。
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