利用微生物培養基的景觀來預測新的有機體媒體配對

KOMODO reveals global patterns of media and compound usage

Typical patterns of media usage and composition in KOMODO can reveal fundamental trends in microbial nutrition, as well as gaps and investigator biases. To gain an overview of these relationships, we built histograms of component, media and organism distributions across the database (Fig. 2a–d). We observed that component usage across media, and media usage across organisms both follow power-laws, which suggests a ‘rich gets richer’ structure to the assignment of phenotypes and component usages (Fig. 2a,b). This structure might reflect converging nutrient requirements among organisms, the preferential way in which ‘successful’ media are selected for organisms by human investigators, or both.

Figure 2: Large-scale properties of known media.

(a) Distributions of components in media. This includes both defined and complex/undefined components, where undefined components are grouped into their complex categories and each category present in a medium is counted as one component.

(b) Distributions of media by the number of organisms that grow on them.

(c) Distributions of the number of media that organisms grow on.

(d) Distribution of media by the number of components within them.

(e) Distribution of pH values of known media. Red squares in a and b denote the bins used for the power law fit.

(f) The 40 most frequently used media components across genera. Ions listed here were typically added to media as salts, which we assume completely dissociate in solution (for example, MgCl2 becomes Mg2+ and Cl?). Components are broken into four groups: biologically common ions/compounds, trace metals/metalloids, vitamins/coenzymes and other. Within each group, components are listed in order of their frequency of usage across genera, from most to least. Left of the bar graphs is a list of average concentrations of each component in media across KOMODO, listed in units of log10(molar concentration). A component is ‘differential’ in a genus if it appears in media for some strains in that genus but not others.