Enhancing chemical and biological diversity by co-cultivation

Abstract

In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.

A significant antibiofilm and antimicrobial activity of chitosan-polyacrylic acid nanoparticles against pathogenic bacteria

“…In this context, co-culturing with several types of microorganisms, as often occurs in natural settings, could enhance the environmental conditions by reducing the concentrations of oxygen and altering the secondary metabolite levels ( Wu et al, 2016 ). Definitely, microbial co-culture, which includes growing two or more microorganisms in the same small space, has been addressed as a potential method for triggering cryptic pathways ( Selegato and Castro-Gamboa, 2023 ). A previous studies proved different types of microorganisms, such as Saccharomyces cerevisiae, a species of yeast, and Lactobacillus plantarum, a strain of probiotics, could form a mixed-species biofilm on a glass surface in liquid media to improve their capacity and endure challenging conditions ( Furukawa et al, 2015 , Nozaka et al, 2014 , Yin et al, 2019 ).…”

Exploring Culture Media Diversity to Produce Fungal Secondary Metabolites and Cyborg Cells

“…Conversely, adding a mixture of MgSO 4 , NaNO 3 , and NaCl in the medium induced a significant variation in the metabolite profile, discovering nine additional secondary metabolites. These include the butyrolactone derivative bulgariline D (19), two 1,3-oxazines bulgarixine A (20), and bulgarixine B (21), five α-pyrones -bulgariapyrone A (22), bulgariapyrone B (23), bulgariapyrone C (24), bulgariapyrone D ( 25), bulgariapyrone A (26), and (À )-(S)-flavipesin B (27), along with the known compound bulgarialactone D (28). [18] Notably, compounds 21, 23-25 were not detected in fungal cultures lacking salts.…”

“…In this context, various culture media, diverse flask types, and cultivation conditions should be systematically tested to ascertain the ideal requirements for producing a particular metabolite (target mycobolome) or for obtaining the metabolome of the microorganism (untargeted mycobolome) under analysis. While this manuscript primarily addresses culture medium formulations, it is essential to acknowledge that complementary strategies, such as co-culturing, [19,41] addition of elicitors and epigenetic manipulation, [38,42] enzymatic inhibitors, activation of silent genes, [15,43] and gene regulation, [44] are valuable tools for enhancing and diversifying the production of these compounds.…”

“…Numerous reviews highlight notable and successful examples using OSMAC strategies, which involve modifying the medium composition, cultivation conditions, co-cultivation with other strain(s), and incorporating enzyme inhibitor(s) or biosynthetic precursor(s). [16][17][18][19] A peculiar aspect of filamentous fungi is their ability to develop in aqueous solutions containing nanomaterials. When filamentous fungi are cultivated in such media, the dispersed nanomaterials in the solution become integrated into the cell structure, shaping a cyborg cell.…”

“…This methodology explores the potential of cultivating a single species under various conditions to unveil metabolic diversity, consequently revealing novel compounds with new biological prospects. Numerous reviews highlight notable and successful examples using OSMAC strategies, which involve modifying the medium composition, cultivation conditions, co‐cultivation with other strain(s), and incorporating enzyme inhibitor(s) or biosynthetic precursor(s) [16–19] …”