Whole‐Cell MALDI‐ToF MS Coupled with Untargeted Metabolomics Facilitates Investigations of Microbial Chemical Interactions

Abstract

The emergence of drug-resistant pathogens necessitates the development of new countermeasures. In this regard, the introduction of probiotics to directly attack or competitively exclude pathogens presents a useful strategy. Application of this approach requires an understanding of how a probiotic and its target pathogen interact. A key means of probioticpathogen interaction involves the production of small molecules called natural products (NPs). Here, we report the use of whole-cell matrix-assisted laser desorption/ionization time-offlight (MALDI-ToF) mass spectrometry to characterize NP production by candidate probiotics (mouse airway microbiome isolates) when co-cultured with the respiratory pathogen Burkholderia. We found that a Bacillus velezensis strain inhibits growth of and elicits NP production by Burkholderia thailandensis. Dereplication of known NPs detected in the metabolome of this B. velezensis strain suggests that a previously unannotated bioactive compound is involved. Thus, we present the use of whole-cell MALDI as a broadly applicable method for screening the NP composition of microbial co-cultures; this can be combined with other -omics methods to characterize probioticpathogen and other microbe-microbe interactions.

Niche exclusion of a lung pathogen in mice with designed probiotic communities

“…To understand the degree to which CP8’s secondary metabolite is responsible for mediating the competitive phenotype observed in Figure 1C, we aimed to create a knockout of this molecule in CP8. From prior analyses, CP8 is predicted to encode production of 22 specialized metabolites 20 . The synthesis of all of the top hits are dependent on sfp , a phosphopantetheinyl transferase which catalyzes conversion of these metabolites into their active holo-form.…”