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Fig. 3 | GigaScience

Fig. 3

From: Metabolome of human gut microbiome is predictive of host dysbiosis

Fig. 3

Outline of enzyme function profile prediction and metabolome modeling from microbiome community data. In a, data from multiple observations from the microbiome are collected in the form of 16S rRNA abundances. For each observation in each dataset, where a single observation is denoted in the cartoon by red box, the microbiome population is described as a vector of normalized bacterial abundances, p. In this cartoon example, the microbiome is composed of four taxa, T 1–4. In b, the microbiome population is used to predict the enzyme function profile using a matrix of average enzyme function counts for all bacterial taxa, E. Matrix E is generated from analysis of published and annotated bacterial genomes. In this cartoon, there are six possible enzyme functions, EC 1–6. In the matrix presented, for example, the average genome of taxa 1 contains two genes annotated with enzyme function EC-4. The result of this step is a matrix for the microbiome’s enzyme function profile, g. In c, the normalized enzyme function profile g’ is used to calculate a model of the community metabolome as a vector of PRMT scores. This uses an interaction matrix M of enzyme functions and metabolites. In the cartoon example, M is comprised of the six enzyme activities in g and seven possible metabolites, m 1–7. Matrix M is generated from available databases of all possible bacterial metabolic reactions for all enzyme activities found in enzyme function profile

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