Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Bauer, Eugen; Laczny, Cedric; Magnusdottir, Stefania; Wilmes, Paul; Thiele, Ines
• Is Part Of: Microbiome. Volume 3:Issue 1(2015)
• Page Start: 1
• Page End: 13
• Publication Date: 2015-12
• Subjects: Genome-scale metabolic reconstructions -- Metabolic modeling -- Metagenomics -- Intestinal microbiota -- Evolution -- Ecology; Microbiology -- Periodicals; Microorganisms -- Periodicals; Medical microbiology -- Periodicals; Soil microbiology -- Periodicals; Microbiological Phenomena -- Periodicals; Environmental Microbiology -- Periodicals; Medical microbiology; Microbiology; Microorganisms; Soil microbiology; Periodicals; Electronic journals; 579.17
• DOI: 10.1186/s40168-015-0121-6
• Languages: English
• ISSNs: 2049-2618

Abstract

Abstract Background 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, however, still remains poorly understood with respect to its evolutionary and ecological context. Results We 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 theLactobacilli as well as two clusters within theBifidobacteria andBacteroides . Conclusions We 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.