Metabolome of human gut microbiome is predictive of host dysbiosis.

Peter E Larsen,Yang Dai

doi:10.1186/s13742-015-0084-3

Peter E Larsen, Yang Dai

Open Access

https://doi.org/10.1186/s13742-015-0084-3

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Abstract

BackgroundHumans 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.ResultsUsing 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.ConclusionsSpecific 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-015-0084-3) contains supplementary material, which is available to authorized users.

Highlights

Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health
Organisms [4, 5], aid in digesting food and provision of essential vitamins and nutrients [6,7,8,9], and maintenance of a healthy immune system [10,11,12,13]. Perturbations in these symbiotic communities can have a negative effect on the host’s health, termed dysbiosis [14], which can lead to a variety of human disease states, such as irritable bowel syndrome (IBS) [15,16,17,18,19], autoimmune disorders [20, 21], increased vulnerability to cancers [22, 23], and obesity [24,25,26,27]
Dysbiosis of the gut microbiome has been shown to coincide with increased risk of depression [28], and to affect other aspects of the human host’s mental health [29, 30]

Summary

Introduction

Humans live in constant and vital symbiosis with a closely linked bacterial ecosystem called the microbiome, which influences many aspects of human health. The human microbiome provides many crucial services to their human hosts, including defense against colonization by harmful or pathogenic organisms [4, 5], aid in digesting food and provision of essential vitamins and nutrients [6,7,8,9], and maintenance of a healthy immune system [10,11,12,13] Perturbations in these symbiotic communities can have a negative effect on the host’s health, termed dysbiosis [14], which can lead to a variety of human disease states, such as irritable bowel syndrome (IBS) [15,16,17,18,19], autoimmune disorders [20, 21], increased vulnerability to cancers [22, 23], and obesity [24,25,26,27]. Microbiome transplants have proven a powerful tool for curing otherwise intractable diseases such as IBS [31,32,33] or antibiotic resistant

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Discussion

Conclusion