利用微生物培養(yǎng)基的景觀來預測新的有機體媒體配對

In contrast, the distribution of the number of media an organism is listed to grow on does not follow a power law, but rather follows an exponentially decaying distribution with the largest number of established media per organism in DSMZ being 4 (Fig. 2c). This pairing of organisms with media is from the internal databank of DSMZ, and clearly reflects heavy under-sampling because of an investigator bias, as researchers would typically seek only one or a few media per organism, rather than exhaustively seeking all media that an organism might grow on. Indeed, only 0.04% of potential organism–media pairings are listed in the database (and only positive growth phenotypes are listed); it is highly likely that many more pairings could enable growth, as supported by the in vitro success of our novel growth predictions (see section below). We also examined how many components both defined and non-defined media contain (with each complex category present in a medium considered to be one ‘component’—see Fig. 2d). There is a large range of media sizes (that is, the number of distinct components making up a medium) even among fully defined media, reflecting the variable inclusion of trace element and vitamin mixtures aside from likely differences in biological needs of bacteria. Few truly minimal media, that is, those containing the smallest number of distinct nutrients possible while still enabling a microorganism to grow, exist in the DSMZ database (or are listed as such), reflecting the typical goal of culturing efforts to get microorganisms into culture quickly and easily, rather than to determine their minimal nutritional requirements.

The pH values of media range from 0.8 to 10.1, with 76% of media having a pH between 6 and 8, 15% below 6 and only 9% above 8 (Fig. 2e). It is notable that alkaline media are fewer and closer to neutral pH than the acidic media. This is despite the large diversity of high pH-tolerating organisms in, for example, soda lakes, which have pHs of up to around 12 and are among the photosynthetically most productive environments on the Earth18. High pH-tolerant organisms might represent a gap in the ranges of investigated organisms. However, the distribution of media also may reflect neutralizing/acidifying effects of CO2 on natural macro-environments, whereby environments without a replenishing source of alkalinity tend to drift down the pH scale, and thus are indeed less common than more neutral or acidic environments18.