Metabolome of human gut microbiome is predictive of host dysbiosis

GigaScience

Yang Dai¹  Peter E. Larsen² 

[1] Bioengineering Department, University of Illinois at Chicago, 851 South Morgan, SEO218, Chicago 60607, IL, USA;Argonne National Laboratory, Biosciences Division, 9700 South Cass Ave, Argonne 60439, IL, USA

关键词: Microbial communities;    Metagenomics;    Metabolome modeling;    Machine learning;    Human microbiome;    Gut microbiome;    Dysbiosis;   

Others  :  1224896
DOI  :  10.1186/s13742-015-0084-3

 received in 2015-04-30, accepted in 2015-08-28,  发布年份 2015

【 摘 要 】

Background

Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. When this microbial ecosystem becomes disrupted, the health of the human host can suffer; a condition called dysbiosis. However, the community compositions of human microbiomes also vary dramatically from individual to individual, and over time, making it difficult to uncover the underlying mechanisms linking the microbiome to human health. We propose that a microbiome’s interaction with its human host is not necessarily dependent upon the presence or absence of particular bacterial species, but instead is dependent on its community metabolome; an emergent property of the microbiome.

Results

Using data from a previously published, longitudinal study of microbiome populations of the human gut, we extrapolated information about microbiome community enzyme profiles and metabolome models. Using machine learning techniques, we demonstrated that the aggregate predicted community enzyme function profiles and modeled metabolomes of a microbiome are more predictive of dysbiosis than either observed microbiome community composition or predicted enzyme function profiles.

Conclusions

Specific enzyme functions and metabolites predictive of dysbiosis provide insights into the molecular mechanisms of microbiome–host interactions. The ability to use machine learning to predict dysbiosis from microbiome community interaction data provides a potentially powerful tool for understanding the links between the human microbiome and human health, pointing to potential microbiome-based diagnostics and therapeutic interventions.

【 授权许可】

   
2015 Larsen and Dai.

【 图 表 】

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