Assessing the Complex Ecology of Intestinal Microbiome

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.

Presented at the International Fibre Summit 2019 (https://internationalfibre.com/). Reproduced with permission from the organizers.