Long‐term monitoring of the human intestinal microbiota composition

Abstract

The microbiota that colonizes the human intestinal tract is complex and its structure is specific for each of us. In this study we expand the knowledge about the stability of the subject-specific microbiota and show that this ecosystem is stable in short-term intervals (< 1 year) but also during long periods of time (> 10 years). The faecal microbiota composition of five unrelated and healthy subjects was analysed using a comprehensive and highly reproducible phylogenetic microarray, the HITChip. The results show that the use of antibiotics, application of specific dietary regimes and distant travelling have limited impact on the microbiota composition. Several anaerobic genera, including Bifidobacterium and a number of genera within the Bacteroidetes and the Firmicutes phylum, exhibit significantly higher similarity than the total microbiota. Although the gut microbiota contains subject-specific species, the presence of which is preserved throughout the years, their relative abundance changes considerably. Consequently, the recently proposed enterotype status appears to be a varying characteristic of the microbiota. Our data show that the intestinal microbiota contains a core community of permanent colonizers, and that environmentally introduced changes of the microbiota throughout adulthood are primarily affecting the abundance but not the presence of specific microbial species.

Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children

“…However, the microbiota similarities, both in short and long term, were still remarkably lower than previously observed for western adults by using the same microarray technique for microbiota assessment (JalankaTuovinen et al, 2011;Rajilić-Stojanović et al, 2013;Fuentes et al, 2014;Satokari et al, 2014). Furthermore, we found that the most predominant Figure 6 The development of core microbiota # .…”

“…In contrast, the gut microbiota of healthy adults is individual specific and relatively stable in time (Claesson et al, 2011;Jalanka-Tuovinen et al, 2011;Rajilić-Stojanović et al, 2013). Two main phyla, Firmicutes and Bacteroidetes, constitute over 90% of the microbiota in healthy adults, followed by Actinobacteria, Proteobacteria and Verrucomicrobia (Claesson et al, 2011;Jalanka-Tuovinen et al, 2011;RingelKulka et al, 2013;Voreades et al, 2014).…”

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

“…While there is some debate on the discrete and permanent nature of enterotypes within the human literature (Arumugam et al, 2011;Wu et al, 2011;Huse et al, 2012;Rajilić-Stojanović et al, 2013), our functional predictions of metagenome content suggest that differing community types in the guppy system have inherent functional differences. For instance, guppies categorized to enterotype 1 were estimated to have the greatest relative proportion of their metagenomes devoted to vitamin biosynthesis.…”

Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection

“…The complexity of the intestinal microbial communities requires the application of highthroughput techniques, including metagenomics and 16S rRNA-based approaches. The microbiota composition fluctuates around a stable individual core, and the homoeostasis of this intestinal ecosystem has been shown to be a key factor in the maintenance of health and development of disease (Jalanka-Tuovinen et al, 2011;Rajilic-Stojanovic et al, 2012;Faith et al, 2013). Recently, a metagenomics analysis of European subjects showed that the intestinal microbiota of individuals can be assigned to one of three groups, named enterotypes, based on composition and relative abundance of certain key bacterial groups (Arumugam et al, 2011), which can fluctuate over time (Wu et al, 2011;Rajilic-Stojanovic et al, 2012).…”

“…The microbiota composition fluctuates around a stable individual core, and the homoeostasis of this intestinal ecosystem has been shown to be a key factor in the maintenance of health and development of disease (Jalanka-Tuovinen et al, 2011;Rajilic-Stojanovic et al, 2012;Faith et al, 2013). Recently, a metagenomics analysis of European subjects showed that the intestinal microbiota of individuals can be assigned to one of three groups, named enterotypes, based on composition and relative abundance of certain key bacterial groups (Arumugam et al, 2011), which can fluctuate over time (Wu et al, 2011;Rajilic-Stojanovic et al, 2012). Currently, however, this concept is under extensive debate, where researchers rather favour a continuous gradient as opposed to separate enterotypes (Huse et al, 2012;Jeffery et al, 2012;Yong, 2012).…”