Abstract
BackgroundThe human gastrointestinal tract harbors a diverse microbial community, in which metabolic phenotypes play important roles for the human host. Recent developments in meta-omics attempt to unravel metabolic roles of microbes by linking genotypic and phenotypic characteristics. This connection, however, still remains poorly understood with respect to its evolutionary and ecological context.ResultsWe generated automatically refined draft genome-scale metabolic models of 301 representative intestinal microbes in silico. We applied a combination of unsupervised machine-learning and systems biology techniques to study individual and global differences in genomic content and inferred metabolic capabilities. Based on the global metabolic differences, we found that energy metabolism and membrane synthesis play important roles in delineating different taxonomic groups. Furthermore, we found an exponential relationship between phylogeny and the reaction composition, meaning that closely related microbes of the same genus can exhibit pronounced differences with respect to their metabolic capabilities while at the family level only marginal metabolic differences can be observed. This finding was further substantiated by the metabolic divergence within different genera. In particular, we could distinguish three sub-type clusters based on membrane and energy metabolism within the Lactobacilli as well as two clusters within the Bifidobacteria and Bacteroides.ConclusionsWe demonstrate that phenotypic differentiation within closely related species could be explained by their metabolic repertoire rather than their phylogenetic relationships. These results have important implications in our understanding of the ecological and evolutionary complexity of the human gastrointestinal microbiome.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-015-0121-6) contains supplementary material, which is available to authorized users.
Highlights
The human gastrointestinal tract harbors a diverse microbial community, in which metabolic phenotypes play important roles for the human host
A large proportion of probiotic Lactobacillus and Bifidobacteria could be found in the classes Bacilli and Actinobacteria, respectively (Fig. 1 and Table 1)
For the Bifidobacteria, we propose two distinct subclusters (Bi1 and Bi2), which differed in the reactions involved in energy metabolism and membrane biosynthesis (Fig. 5c)
Summary
The human gastrointestinal tract harbors a diverse microbial community, in which metabolic phenotypes play important roles for the human host. Recent developments in meta-omics attempt to unravel metabolic roles of microbes by linking genotypic and phenotypic characteristics. This connection, still remains poorly understood with respect to its evolutionary and ecological context. Sequencing the (ideally) entire genomic content (i.e., metagenomic sequencing) of the intestinal microbiota has allowed the establishment of a catalog of main groups of microorganisms present in the gastrointestinal tract and potential metabolic pathways [3] by avoiding culturing and isolation of individual microbial organisms.
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