【第二季】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 exact media matches as just described, we tested whether these associations would also hold for partial matches between lab media. We considered two organisms to have a partial medium match if a comparison of the best matching media of the two organisms (or of the sets formed from the unions of components from all of their listed media) exceeded a specified similarity threshold (see Methods for details). Indeed, over a range of thresholds and with all combinations of these metrics, the correlations between media similarity and ecological or phylogenetic relatedness are maintained (see Supplementary Fig. 13). These associations not only indicate that ecological or phylogenetic data may be helpful in guiding culturing of organisms on known lab media, but, importantly, that these data may be usable for determining likely subsets of media to include for a given organism when developing novel media formulations.

Predicting new organism–media pairings via transitivity

A fundamental property in logic and math is the potential transitivity of a given relation R; that is, if R is transitive, then (ARB and BRC) implies that (ARC). To better understand the known patterns of microbial growth in KOMODO, we asked whether the property ‘organism sharing of media’ is transitive. To test this, we searched the KOMODO data for growth media patterns involving three organisms A, B and C, in which it is given that A and B grow together on a certain medium (m1), B and C grow together on another medium (m2) and C grows on a third medium (m3; see Fig. 4a). Given this pattern and assuming transitivity, we predicted that organism A would be more likely than a randomly chosen organism to grow on m3 (see Methods for details). Out of 1,000 such tests, we identified 694 positive (that is, documented growth) instances of transitivity versus only 1 positive case among the 1,000 randomly selected organisms. This result strongly indicates that media preferences are indeed transitive (binomial P<1e?186).

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