Assessing the complex ecology of intestinal microbiome
Assessing the complex ecology of intestinal microbiome
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DOI：
10.3920/978-90-8686-893-3_16
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发表时间：
2019-01-01
期刊：
影响因子：
--
通讯作者：
Rinttila, T.
中科院分区：
文献类型：
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作者：
Apajalahti, J.;Rinttila, T.
温血动物的肠道微生物群是一个群落，其代谢活性高于宿主的许多组织。单胃动物小肠中的微生物群相对简单，主要包括特征良好的乳酸菌。在下段肠道（盲肠/结肠）中，大多数细菌分类群的特征很差，细菌群落的个体成员的作用也没有完全了解。作为一个物理化学环境，这两个肠段是高度不同的，因此，占主导地位的发酵分歧。微生物群落组成的研究可以通过不依赖于培养的DNA方法进行，但目前应用的许多方法都有其固有的缺陷，这很容易导致偏倚的结果。特别是，基于聚合酶链反应（PCR）的初始基因扩增的方法比不依赖PCR的方法更容易产生偏倚。虽然微生物组的大多数成员还没有作为纯培养物生长和表征，但可以在实验室条件下研究整个群落。当没有试图解构社区时，细菌间的交叉喂养和其他相互作用持续存在。这种方法论方法（称为离体）可用于研究社区层面的适应和具体活动。在微生物代谢中，产生具有发酵类型特征的化合物，并可用作特定指示剂。蛋白质在小肠中的消化率差导致肉鸡盲肠中蛋白质降解产物的浓度增加。上肠营养吸收不良会导致单糖从回肠绕过至盲肠，并通常导致盲肠酸中毒。为了更多地了解微生物群在动物健康和营养中的作用，详细研究细菌的功能而不是它们的分类地位非常重要。
The intestinal microbiota of warm-blooded animals is a community, with metabolic activity higher than in many tissues of the host. The microbiota in the small intestine of monogastric animals is relatively simple, mainly comprising well-characterised lactic acid bacteria. In the lower intestine (caecum/colon), the majority of bacterial taxa are poorly characterised and the role of individual members of the bacterial community is not fully understood. As a physicochemical environment, these two intestinal segments are highly different and, consequently, prevailing fermentation diverges. Microbial community composition can be studied by culture-independent DNA-based methods, but many of the methods currently applied have their inherent flaws, which can easily lead to biased results. In particular, methods based on initial gene amplification by polymerase chain reaction (PCR) are more prone to biases than PCR-independent methods. Although most members of the microbiome have not been grown as pure cultures and characterised, it is possible to study entire communities under laboratory conditions. When no attempt is made to deconstruct the community, interbacterial cross-feeding and other interactions persist. Such methodological approach, referred to as ex vivo, can be used to study adaptation and specific activities at community level. In microbial metabolism, compounds characteristic of a fermentation type are produced and can be used as specific indicators. Poor protein digestibility in the small intestine leads to increased concentration of protein degradation products in the caecum of broiler chickens. Poor nutrient uptake in the upper intestine leads to bypass of simple sugars from ileum to caecum and often to caecal acidosis. To learn more about the role of microbiota in animal health and nutrition, it is highly important to study in detail the functions of bacteria, rather than their taxonomic position.