Microbial nutrient niches in the gut

Abstract

SummaryThe composition and function of the mammalian gut microbiota has been the subject of much research in recent years, but the principles underlying the assembly and structure of this complex community remain incompletely understood. Processes that shape the gut microbiota are thought to be mostly niche‐driven, with environmental factors such as the composition of available nutrients largely determining whether or not an organism can establish. The concept that the nutrient landscape dictates which organisms can successfully colonize and persist in the gut was first proposed in Rolf Freter's nutrient niche theory. In a situation where nutrients are perfectly mixed and there is balanced microbial growth, Freter postulated that an organism can only survive if it is able to utilize one or a few limiting nutrients more efficiently than its competitors. Recent experimental work indicates, however, that nutrients in the gut vary in space and time. We propose that in such a scenario, Freter's nutrient niche theory must be expanded to account for the co‐existence of microorganisms utilizing the same nutrients but in distinct sites or at different times, and that metabolic flexibility and mixed‐substrate utilization are common strategies for survival in the face of ever‐present nutrient fluctuations.

Enterotypes in the landscape of gut microbial community composition

“…Such characteristics are relevant from an ecological perspective, where theory predicts a higher diversity in dynamic systems like the gut, with nutrient availability and type fluctuating over time 56 . Using 16S amplicon sequencing, richness differences between three enterotypes were first shown in an Amish population 29 , with a cluster similar to ET B having the lowest richness, as has been recently confirmed in a large population-wide study 7 .…”

Age‐related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus)

“…During metamorphosis, the gastrointestinal tract experiences compartmentalization and completely divides into the stomach, duodenum, ileum, and rectum from ages 1 to 4, and each section serves a unique biological function. This compartmentalization, in addition to producing specialized microbial assemblages, may facilitate the extraction of nutrients (Pereira & Berry, ). Our study demonstrated that different microbial assemblages are present in each of these subcompartments, which appeared to agree with previous studies in other vertebrates; therefore, these subcompartments contain distinct physiochemical environments that develop diverse microbial assemblages along their total length (Keenan & Elsey, ).…”

The bioelements, the elementome, and the biogeochemical niche

“…). In microbial communities, genotype‐niches have also been described in function of the different availabilities of different nutrients (Pereira and Berry ) or as a function of the values of diverse functional traits (Lennon et al. ) thus describing multivariant spaces with a determined combination of nutrients availability or functional traits where a determined genotype can exist.…”