利用微生物培養基的景觀來預測新的有機體媒體配對

In addition to pH, we examined salt usage across media. Principle component analysis of the media-by-component concentration matrix revealed that Na+ and Cl? ions are the most dominant components separating all media, as they are frequently used and are often present at high concentration values (see Supplementary Figs 2 and 3 and Supplementary Note 2 for details).

To gain a more complete picture of component usage across the tree of life, we examined which components are used in the media of the most genera (Fig. 2f, left bar graph). We observed that the most frequent components are biologically common ions/salts that are usually present as macronutrients (1–100?mM), followed by trace metal elements and vitamins (which are present in 0.1–10?μM and 1–1,000?nM ranges, respectively; see concentrations bar on the left of Fig. 2f). Also frequent across genera are some complex media components (peptone and meat extract) and the carbon sources (glucose and starch). Some of these components might be added to many media but are not selective between related organisms. To better understand which components are actually differentiating between similar species, we checked the number of genera in which a component is present in media for some species/strains but not for others. We did this first taking into account all media, and then only considering fully defined media (Fig. 2f, middle two bar graphs). Strikingly, when considering only fully defined media, the components that are differential across the most genera are trace metals and vitamins/coenzymes, despite their being less commonly used across genera than the common ions/salts. This signal was likely hidden when also including non-defined media as complex components such as meat extract provide many of these trace components at once. Supporting this observation, the ‘complex-meat’ category is a highly differentiating component across genera when considering all media—see second bar graph in Fig. 2f.

This analysis points to trace compounds such as metal ions and cofactors as key ingredients to consider when trying to grow new species from within cultured genera, a principle that has been noted recently in trying to culture as-yet-uncultured genera as well1, 19. For comparison, we also extracted from KOMODO all instances where a nutritional ingredient is specifically added, removed or has its concentration changed from a base medium in order to grow a given strain, and assessed the number of genera in which each component is altered this way (Fig. 2f, right bar graph).