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We developed a co-culturing device that allows culturing of multispecies microbial strains that are physically separated but can exchange dissolved or colloidal chemical signals and then performed a metabolomics survey of the secondary metabolisms of both a fungal-bacterial community and an actinomycetic-actinomycetic community using a metabolomic approach integrating LC-MS analysis, conventional statistical tools and molecular networking. LC-MS measurements revealed a pronounced influence of the chemical communication on the metabolic profiles of synthetic communities with a group of molecules being newly-induced or upregulated in co-cultures. More specifically, a class of unusual diphenyl ethers with polyhydroxy sidechains including a novel antibiotic was discovered to be induced by chemical communication in the community composed of Cladosporium sp. WUH1 and Bacillus subtilis CMCC（B） 63501. Further investigation on the fungal-bacterial cross-talk inferred that the production of these diphenyl ethers might be a defensive response against the growth inhibition resulting from surfactins, a class of antifungal cyclopeptides, secreted by B. subtilis.We conducted a MS-based metabolomics survey to investigate the effect of chemical communication on the secondary metabolism of a fungal-bacterial community comprising Penicillium citrinum Y34 and Pseudomonas aeruginosa CMCC（B）10104. Analysis of the molecular map generated by MS molecular networking techniques revealed new citrinin-related metabolites secreted by Penicillium citrinum while the production of these molecules was limited for further structural elucidation in the stationary co-cultures. Hence, a new co-culture device with external mechanical forces was then developed to accelerate the exchange of chemical information andmultivariate data analysis combined with molecular mapping prioritized two cross-talk-induced citrinin analogues which were positively-correlated with the exchange rate in the new co-cultures. MS-guided isolation resulted in the characterization of the previously undescribed antibiotic citrinolide. This highly-oxidized citrinin adduct representing a novel skeleton showed significantly enhanced antibiotic property against the partner strain P.aeruginosa than its precursor citrinin, suggesting a role in the microbial competition during the cross-talk.