Intestinal Microbiota and Nutrient Metabolism

The intestinal microbiota is the dense community of micro-organisms in the gut, most numerous in the colon, that contributes to host nutrition by fermenting dietary components the host cannot digest. Through this fermentation it salvages energy from unabsorbed carbohydrate, produces short-chain fatty acids and certain vitamins, and participates in a mutualistic relationship with the host.

Definition

The intestinal microbiota is the community of micro-organisms inhabiting the gastrointestinal tract; its role in nutrient metabolism is the set of microbial activities — principally colonic fermentation of non-digestible substrates to short-chain fatty acids and synthesis of some vitamins — that contribute to the host's nutrient supply.

Scope

This topic covers the composition and scale of the gut microbial community, its metabolic contribution to nutrition — chiefly the fermentation of non-digestible carbohydrate to short-chain fatty acids — and the dietary modulation of the microbiota through prebiotics. It is reference physiology and nutrition and does not provide probiotic, prebiotic, or dietary prescriptions.

Core questions

• What is the composition and scale of the human gut microbiota?
• How does microbial fermentation contribute to host nutrient and energy supply?
• How does diet, including prebiotics, shape the microbiota and its metabolic output?

Key concepts

• Host-microbiota mutualism
• Colonic fermentation of non-digestible carbohydrate
• Short-chain fatty acids (acetate, propionate, butyrate)
• Energy salvage from unabsorbed substrate
• Microbial synthesis of vitamins
• Prebiotics and dietary modulation
• Community diversity, stability, and resilience

Mechanisms

The gut harbours a microbial community comparable in cell number to the host's own cells (Sender et al., 2016), engaged in a mutualistic relationship in which the microbes gain a nutrient-rich habitat and the host gains metabolic capacity it lacks (Bäckhed et al., 2005). Carbohydrate that escapes small-intestinal digestion reaches the colon, where the microbiota ferments it to short-chain fatty acids — acetate, propionate, and butyrate — which are absorbed and used by the host, recovering energy that would otherwise be lost (Cummings et al., 1987). The composition and metabolic output of this community vary between individuals yet show characteristic stability and resilience (Lozupone et al., 2012), and they can be shaped by diet: selectively fermented substrates termed prebiotics promote particular microbial activities (Gibson & Roberfroid, 1995; Gibson et al., 2017).

Clinical relevance

The microbiota's metabolic role informs how dietary fibre, fermentation, and host-microbe interactions are reasoned about in nutrition and the health sciences. This entry describes normal microbial nutrient metabolism for reference and education and is not a basis for individual probiotic, prebiotic, dietary, or treatment recommendations.

Debates

How should 'prebiotic' be defined?

The original concept of a selectively fermented ingredient that benefits the host has been revisited as microbiome science advanced; an international expert consensus updated and broadened the definition and scope of prebiotics, refining the criteria a substrate must meet.

Seminal works

• backhed-2005
• cummings-1987
• gibson-1995
• lozupone-2012

Frequently asked questions

How does the gut microbiota help with nutrition?

It ferments dietary components the host cannot digest, especially carbohydrate that reaches the colon, producing short-chain fatty acids that the host absorbs and uses for energy, and it also synthesises some vitamins.

What are prebiotics?

Prebiotics are dietary substrates that are selectively used by host micro-organisms to confer a health benefit; their definition has been refined over time by expert consensus as understanding of the microbiota has grown.