Mapping Microbial Response Metabolomes for Induced Natural Product Discovery

Intergeneric
microbial interactions may originate a significant
fraction of secondary metabolic gene regulation in nature. Herein,
we expose a genomically characterized Nocardiopsis strain, with untapped polyketide biosynthetic potential, to intergeneric
interactions via coculture with low inoculum exposure to Escherichia, Bacillus, Tsukamurella, and Rhodococcus. The challenge-induced responses of extracted
metabolites were characterized via multivariate statistical and self-organizing
map (SOM) analyses, revealing the magnitude and selectivity engendered
by the limiting case of low inoculum exposure. The collected inventory
of cocultures revealed substantial metabolomic expansion in comparison
to monocultures with nearly 14% of metabolomic features in cocultures
undetectable in monoculture conditions and many features unique to
coculture genera. One set of SOM-identified responding features was
isolated, structurally characterized by multidimensional NMR, and
revealed to comprise previously unreported polyketides containing
an unusual pyrrolidinol substructure and moderate and selective cytotoxicity.
Designated ciromicin A and B, they are detected across mixed cultures
with intergeneric preferences under coculture conditions. The structural
novelty of ciromicin A is highlighted by its ability to undergo a
diastereoselective photochemical 12-π electron rearrangement
to ciromicin B at visible wavelengths. This study shows how organizing
trends in metabolomic responses under coculture conditions can be
harnessed to characterize multipartite cultures and identify previously
silent secondary metabolism.