Metabolic profiling of bacterial co-cultures reveals intermicrobiome interactions and dominant species

In animal production, the use of probiotic microorganisms has increased since the ban on antibiotic growth promoters in 2006. The added microorganisms interact with the microbiome of the animals, whereby the probiotic activity is not fully understood. Several microorganisms of the genus Bacillus are already known for their probiotic activity and are applied as feed supplements to increase the health status of the animals. They are thought to interact with Escherichia coli, one of the most abundant bacteria in the animal gut. In biotechnological applications, co-culturing enables the regulation of bacterial interaction or the production of target metabolites. The basic principles of multi-imaging high-performance thin-layer chromatography (HPTLC) with upstream cultivation were further developed to analyze the metabolic profiles of three axenic bacilli cultures compared to their co-cultures with E. coli DSM 18039 (K12). The comparative profiling visualized bacteria's metabolic interactions and showed how the presence of E. coli affects the metabolite formation of bacilli. The characteristic metabolic profile images showed not only the influence of microbiomes but also of inoculation, cultivation and nutrients on the commercial probiotic. The formation of antimicrobially active metabolites, detected via three different planar bioassays, was influenced by the presence of other microorganisms, especially in the probiotic. This first application of multi-imaging HPTLC in the field of co-culturing enabled visualization of metabolic interactions of bacteria via their produced chemical as well as bioactive metabolite profiles. The metabolic profiling provided evidence of bacterial interactions, intermicrobiome influences and dominant species in the co-culture.