Opportunistic Sampling of Roadkill as an Entry Point to Accessing Natural Products Assembled by Bacteria Associated with Non-anthropoidal Mammalian Microbiomes

Abstract

Few secondary metabolites have been reported from mammalian microbiome bacteria despite the large numbers of diverse taxa that inhabit warm-blooded higher vertebrates. As a means to investigate natural products from these microorganisms, an opportunistic sampling protocol was developed, which focused on exploring bacteria isolated from roadkill mammals. This initiative was made possible through the establishment of a newly created discovery pipeline, which couples laser ablation electrospray ionization mass spectrometry (LAESIMS) with bioassay testing, to target biologically active metabolites from microbiome-associated bacteria. To illustrate this process, this report focuses on samples obtained from the ear of a roadkill opossum (Dideiphis virginiana) as the source of two bacterial isolates (Pseudomonas sp. and Serratia sp.) that produced several new and known cyclic lipodepsipeptides (viscosin and serrawettins, respectively). These natural products inhibited biofilm formation by the human pathogenic yeast Candida albicans at concentrations well below those required to inhibit yeast viability. Phylogenetic analysis of 16S rRNA gene sequence libraries revealed the presence of diverse microbial communities associated with different sites throughout the opossum carcass. A putative biosynthetic pathway responsible for the production of the new serrawettin analogues was identified by sequencing the genome of the Serratia sp. isolate. This study provides a functional roadmap to carrying out the systematic investigation of the genomic, microbiological, and chemical parameters related to the production of natural products made by bacteria associated with non-anthropoidal mammalian microbiomes. Discoveries emerging from these studies are anticipated to provide a working framework for efforts aimed at augmenting microbiomes to deliver beneficial natural products to a host.

Cooperative Involvement of Glycosyltransferases in the Transfer of Amino Sugars during the Biosynthesis of the Macrolactam Sipanmycin by Streptomyces sp. Strain CS149

“…However, due to the low hit rate for novel compounds obtained using classical screening approaches and the frequent rediscovery of alreadyknown compounds (2), novel strategies must be developed. Some of these approaches involve the isolation of bioactive compound microbial producers from unexplored environments, paying special attention to microorganisms associated with marine or terrestrial macroorganisms, such as sponges, plants, ants, termites, and wasps (3)(4)(5)(6), but also to mammals (7), including human beings (8). Furthermore, the development of DNA sequencing technologies and the increasing number of genomes sequenced facilitate the use of other strategies, such as transcriptome analysis by RNA sequencing (9), mining of microbial genomes or metagenomes in searching specific gene homologs (10), or new biosynthetic gene clusters (BGCs) (11), and the activation of low-expressed or silent clusters (12).…”

Petrobactin Is Exported from Bacillus anthracis by the RND-Type Exporter ApeX

“…The analytes in the plume are subjected to charge transfer by a mist of electrosprayed buffer, which ionizes and propels them to the mass spectrometer for mass-to-charge ( m / z ) analysis. The majority of LAESI applications to date have focused on mass spectrometry imaging of plant and animal tissues, although recent studies have used LAESI to sample and identify bacterial metabolites from roadkill and soybean microbiomes ( 31 – 36 ). Thus, the application of LAESI-MS for the identification of the import/export gene partners for bacterial metabolites has not been explored.…”

Bacterial pathogens: threat or treat (a review on bioactive natural products from bacterial pathogens)

“…10 and Table S1 †). 162,163 Four analogues of serrawettin W2 32b-d were recently isolated from Serratia sp. which differs based on the amino acids present (Ile or Val, Phe or Tyr) or the length of the fatty acid chain (C5 or C7).…”

“…which differs based on the amino acids present (Ile or Val, Phe or Tyr) or the length of the fatty acid chain (C5 or C7). 162 Further putative analogues (W7-W8) Fig. 10 Analogues of serratamolide (serrawettin W1) A-G (20a-g) and serrawettin W2 32a-d identified in Serratia sp.…”