Enhancing chemical and biological diversity by co-cultivation

Changing the Inoculum Type From Preculture to Spore Suspension Markedly Alters the Production of Secondary Metabolites in Filamentous Microbial Coculture

The shake flask cocultures of Aspergillus terreus and Streptomyces rimosus were investigated with regard to the production of mevinolinic acid (lovastatin), oxytetracycline, and other secondary metabolites (SMs). The aim of the study was to determine the effect of inoculum type (spore suspension or preculture) on the levels of SMs in the fermentation broth. Altogether, 17 SMs were detected, including 4 products with confirmed identities, 10 putatively annotated metabolites, and 3 unknown molecules. As observed over the course of qualitative and quantitative analyses, the selection of inoculum type markedly influenced the SM-related outcomes of cocultures. Depending on the coculture initiation procedure, replacing the preculture with spore inoculum positively affected the biosynthesis of oxytetracycline, butyrolactone I, (+)-geodin, as well as the molecules putatively identified as rimocidin, CE-108, and (+)-erdin. It was concluded that the comparative analyses of SM production in filamentous microbial cocultures and monocultures are dependent on the type of inoculum and thus the diversification of inocula is highly recommended in such studies. Furthermore, it was demonstrated that designing a coculture experiment that involves only a single type of inoculum may lead to the underestimation of biosynthetic repertoires of filamentous microorganisms.

Enhancing Antifungal Drug Discovery Through Co-Culture with Antarctic Streptomyces albidoflavus Strain CBMAI 1855

Fungal infections pose a growing public health threat, creating an urgent clinical need for new antifungals. Natural products (NPs) from organisms in extreme environments are a promising source for novel drugs. Streptomyces albidoflavus CBMAI 1855 exhibited significant potential in this regard. This study aimed to (1) assess the antifungal spectrum of the CBMAI 1855 extract against key human pathogens, (2) elicit NP production through co-cultivation with fungi, correlating the metabolites with the biosynthetic gene clusters (BGCs), and (3) perform in silico toxicity predictions of the identified compounds to analyze their suitability for drug development. The crude extract of CBMAI 1855 exhibited broad-spectrum antifungal activity. The metabolomic analysis identified antifungal NPs such as antimycin A, fungimycin, surugamides, 9-(4-aminophenyl)-3,7-dihydroxy-2,4,6-trimethyl-9-oxo-nonoic acid, and ikarugamycin, with the latter two predicted to be the most suitable for drug development. Genome mining revealed three cryptic BGCs potentially encoding novel antifungals. These BGCs warrant a detailed investigation to elucidate their metabolic products and harness their potential. CBMAI 1855 is a prolific producer of multiple antifungal agents, offering a valuable source for drug discovery. This study highlights the importance of exploring microbial interactions to uncover therapeutics against fungal infections, with a detailed exploration of cryptic BGCs offering a pathway to novel antifungal compounds.

Profiling of bioactive secondary metabolites from Aspergillus niger against a guava wilt pathogen, Fusarium oxysporum f. sp. psidii

Guava wilt is a devastating soil-borne disease that causes significant losses in guava orchards. Management of the disease is very challenging once established in the field. Therefore, there is a need to explore for an effective, economical, and sustainable management strategies. Aspergillus niger, a bio-control fungus, has been demonstrated effectiveness against various soil-borne pathogens including guava wilt pathogens. It produces a diverse hydrolysing enzymes and secondary metabolites. However, no extensive study has been undertaken to profile the secondary metabolites of A. niger. In this investigation, we assessed eleven A. niger strains (AN-1 to AN-11) against four guava wilt pathogens (Fusarium oxysporum f. sp. psidii, F. falciforme, F. chlamydosporum, and F. verticillioides) using a dual culture assay. All strains demonstrated effective by restricting the mycelial growth of pathogens, among them AN-11 displayed maximum inhibition of 86.33%, followed by the AN-3 (84.27%). The UPLC-QToF-ESIMS analysis was undertaken to explore the secondary metabolites of AN-11 responsible for inhibiting F. oxysporum f. sp. psidii. The crude extracts were obtained from F. oxysporum f. sp. psidii, AN-11 and their interaction using ethyl acetate as a solvent. After evaporating, the crude fractions were analysed using UPLC-QToF-ESIMS with an Acquity UPLC and a SCIEX SelexION Triple QuadTM 5500 System. From the ethyl acetate extract of F. oxysporum f. sp. psidii, approximately 14 metabolites involved in pathogenicity were identified. Similarly, analysis of AN-11 crude extract revealed 25 metabolites, and notably, 41 metabolites were identified during the interaction between AN-11 and F. oxysporum f. sp. psidii, including kotanin, isokotanin A, aurofusarin, kojic acid, pyranonigrin, aurasperone F, hexylitaconic acid, asperazine, bicoumanigrin, chloramphenicol, cephalosporin C, fusarin C, zearalonone, fonsecin B, malformin A, and others. Among these, 21 metabolites were produced only during the interaction and have antimicrobial properties. This study highlights the significant potential of the AN-11 strain in generating a diverse array of non-volatile secondary metabolites with antimicrobial properties. These metabolites could be further extracted and investigated for their efficacy against other soil borne pathogens and potentially developed into formulations for controlling plant diseases.

A systematic approach to determine the outcome of the competition between two microbial species in bioreactor cocultures

The two-species microbial cocultures are effective in terms of awakening the cryptic biosynthetic pathways. They may also lead to the improved production of previously discovered molecules. Importantly, only a few outcomes of the cocultures may prove desirable, namely those leading to the formation of useful secondary metabolites. To address this issue, a method allowing for the evaluation of the final outcome of the co-culture process and fine-tune the cocultivation strategy was proposed. The systematic approach was supported by the experimental data from the bioreactor runs with the participation of Aspergillus terreus and Penicillium rubens confronted with Streptomyces rimosus and Streptomyces noursei. Kinetic, morphological and metabolic aspects of dominance were analysed via the newly proposed formula describing the dominance pattern. The suggested method involved the determination of the numerical value representing the dominance level. When it was high (value 1) no useful metabolites were formed apart from those originating from the winning counterpart. But either for the partial dominances or when the winning organism changed within the run or when the competition ended in draw, the number of the secondary metabolites of interest in the broth was the highest. Next, the systematic approach illustrated how the delayed inoculation strategy influenced the level of dominance leading to the change of winning counterpart and the set of metabolites produced. The proposed systematic approach allows for the reliable determination of the level of dominance in the two-species cocultures to seek for the potentially useful substances for future applications.

Initial pH determines the morphological characteristics and secondary metabolite production in Aspergillus terreus and Streptomyces rimosus cocultures

The influence of the initial pH on the morphology and secondary metabolite production in cocultures and axenic cultures of Aspergillus terreus and Streptomyces rimosus was investigated. The detected secondary metabolites (6 of bacterial and 4 of fungal origin) were not found in the cultures initiated at pH values less than or equal to 4.0. The highest mean levels of oxytetracycline were recorded in S. rimosus axenic culture at pH 5.0. Initiating the axenic culture at pH 5.9 led to visibly lower product levels, yet the presence of A. terreus reduced the negative effect of non-optimal pH and led to higher oxytetracycline titer than in the corresponding S. rimosus axenic culture. The cocultivation initiated at pH 5.0 or 5.9 triggered the formation of oxidized rimocidin. The products of A. terreus were absent in the cocultures. At pH 4.0, the striking morphological differences between the coculture and the axenic cultures were recorded.

Synthetic Biology of Natural Products Engineering: Recent Advances Across the Discover-Design-Build-Test-Learn Cycle

Advances in genome engineering and associated technologies have reinvigorated natural products research. Here we highlight the latest developments in the field across the discover-design-build-test-learn cycle of bioengineering, from recent progress in computational tools for AI-supported genome mining, enzyme and pathway engineering, and compound identification to novel host systems and new techniques for improving production levels, and place these trends in the context of responsible research and innovation, emphasizing the importance of anticipatory analysis at the early stages of process development.

Co-Culture of Gut Bacteria and Metabolite Extraction Using Fast Vacuum Filtration and Centrifugation

This protocol describes a robust method for the extraction of intra and extracellular metabolites of gut bacterial mono and co-cultures. In recent years, the co-culture techniques employed in the field of microbiology have demonstrated significant importance in regard to understanding cell-cell interactions, cross-feeding, and the metabolic interactions between different bacteria, fungi, and microbial consortia which enable the mimicking of complex co-habitant conditions. This protocol highlights a robust reproducible physiologically relevant culture and extraction protocol for the co-culture of gut bacterium. The novel extraction steps are conducted without using quenching and cell disruption through bead-cell methods, freeze-thaw cycles, and sonication, which tend to affect the physical and biochemical properties of intracellular metabolites and secretome. The extraction procedure of inoculated bacterial co-cultures and monocultures use fast vacuum filtration and centrifugation. The extraction methodology is fast, effective, and robust, requiring 4 h to complete.

Co-existence of two antibiotic-producing marine bacteria: Pseudoalteromonas piscicida reduce gene expression and production of the antibacterial compound, tropodithietic acid, in Phaeobacter sp

Many bacteria co-exist and produce antibiotics, yet we know little about how they cope and occupy the same niche. The purpose of the present study was to determine if and how two potent antibiotic-producing marine bacteria influence the secondary metabolome of each other. We established an agar- and broth-based system allowing co-existence of a Phaeobacter species and Pseudoalteromonas piscicida that, respectively, produce tropodithietic acid (TDA) and bromoalterochromides (BACs). Co-culturing of Phaeobacter sp. strain A36a-5a on Marine Agar with P. piscicida strain B39bio caused a reduction of TDA production in the Phaeobacter colony. We constructed a transcriptional gene reporter fusion in the tdaC gene in the TDA biosynthetic pathway in Phaeobacter and demonstrated that the reduction of TDA by P. piscicida was due to the suppression of the TDA biosynthesis. A stable liquid co-cultivation system was developed, and the expression of tdaC in Phaeobacter was reduced eightfold lower (per cell) in the co-culture compared to the monoculture. Mass spectrometry imaging of co-cultured colonies revealed a reduction of TDA and indicated that BACs diffused into the Phaeobacter colony. BACs were purified from Pseudoalteromonas; however, when added as pure compounds or a mixture they did not influence TDA production. In co-culture, the metabolome was dominated by Pseudoalteromonas features indicating that production of other Phaeobacter compounds besides TDA was reduced. In conclusion, co-existence of two antibiotic-producing bacteria may be allowed by one causing reduction in the antagonistic potential of the other. The reduction (here of TDA) was not caused by degradation but by a yet uncharacterized mechanism allowing Pseudoalteromonas to reduce expression of the TDA biosynthetic pathway.IMPORTANCEThe drug potential of antimicrobial secondary metabolites has been the main driver of research into these compounds. However, in recent years, their natural role in microbial systems and microbiomes has become important to determine the assembly and development of microbiomes. Herein, we demonstrate that two potent antibiotic-producing bacteria can co-exist, and one mechanism allowing the co-existence is the specific reduction of antibiotic production in one bacterium by the other. Understanding the molecular mechanisms in complex interactions provides insights for applied uses, such as when developing TDA-producing bacteria for use as biocontrol in aquaculture.

Preliminary Bioactivity Assessment of Myrothecium Species (Stachybotryaceae) Crude Extracts against Aedes aegypti (Diptera: Culicidae): A First Approach from This Phytopathogenic Fungi

Mosquitoes, as insect vectors, play a crucial role in transmitting viruses and parasites, leading to millions of human deaths in tropical and subtropical regions worldwide. This study aimed to evaluate the effects of ethanolic extracts of three species within the genus Myrothecium (M. roridum, M. dimerum, and M. nivale) on Aedes aegypti mosquito larvae to assess the inhibitory effect on growth and development, as well as to determine mortality. We quantify the average lethal concentrations and provide a qualitative characterization of the chemical groups responsible for their potential. Phytochemical screening revealed the presence of alkaloids, flavonoids, and terpenoids in the ethanolic extracts of the three fungal species. Tannins were found only in the extracts of M. dimerum and M. roridum. We observed a clear dependence of the effects of the crude extracts on mosquito larvae on the concentrations used and the duration of exposure. The toxic effect was observed after 48 h at a concentration of 800 ppm for both M. dimerum and M. nivale, while M. roridum showed effectiveness after 72 h. All three species within the genus Myrothecium exhibited 100% biological activity after 72 h of exposure at 600 ppm. At lower concentrations, there was moderate growth and development inhibitory activity in the insect life cycle. The study highlights the effectiveness of crude Myrothecium extracts in combating mosquito larvae, with effects becoming apparent between 48 and 72 h of exposure. This initial approach underscores the potential of the fungus's secondary metabolites for further in-depth analysis of their individual effects or synergies between them.

Streptomyces-Fungus Co-Culture Enhances the Production of Borrelidin and Analogs: A Genomic and Metabolomic Approach

The marine Streptomyces harbor numerous biosynthetic gene clusters (BGCs) with exploitable potential. However, many secondary metabolites cannot be produced under laboratory conditions. Co-culture strategies of marine microorganisms have yielded novel natural products with diverse biological activities. In this study, we explored the metabolic profiles of co-cultures involving Streptomyces sp. 2-85 and Cladosporium sp. 3-22-derived from marine sponges. Combining Global Natural Products Social (GNPS) Molecular Networking analysis with natural product database mining, 35 potential antimicrobial metabolites annotated were detected, 19 of which were exclusive to the co-culture, with a significant increase in production. Notably, the Streptomyces-Fungus interaction led to the increased production of borrelidin and the discovery of several analogs via molecular networking. In this study, borrelidin was first applied to combat Saprolegnia parasitica, which caused saprolegniosis in aquaculture. We noted its superior inhibitory effects on mycelial growth with an EC50 of 0.004 mg/mL and on spore germination with an EC50 of 0.005 mg/mL compared to the commercial fungicide, preliminarily identifying threonyl-tRNA synthetase as its target. Further analysis of the associated gene clusters revealed an incomplete synthesis pathway with missing malonyl-CoA units for condensation within this strain, hinting at the presence of potential compensatory pathways. In conclusion, our findings shed light on the metabolic changes of marine Streptomyces and fungi in co-culture, propose the potential of borrelidin in the control of aquatic diseases, and present new prospects for antifungal applications.

Volatile communication in Actinobacteria: a language for secondary metabolism regulation

BACKGROUND

Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group.

RESULTS

We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities.

CONCLUSIONS

This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.

Transport and risk of airborne pathogenic microorganisms in the process of decentralized sewage discharge and treatment

Sewage treatment processes are a critical anthropogenic source of bioaerosols and may present significant health risks to plant workers. Compared with the specialization and scale of urban sewage treatment, many decentralized treatment models are flexible and extensive. These treatment facilities are usually close to residential areas owing to the pipe network layout and other restrictions. Bioaerosols generated by these facilities may present a serious and widespread occupational and non-occupational exposure risk to nearby residents, particularly the elderly and children. An understanding of the characteristics and exposure risks of bioaerosols produced during decentralized sewage treatment is lacking. We compared bioaerosol emission characteristics and potential exposure risks under four decentralized sewage discharge methods and treatment models: small container collection (SCC), open-channel discharge (OCD), single household/combined treatment (SHCT), and centralized treatment (CT) in northwest China. The OCD mode had the highest bioaerosol production, whereas the CT mode had the lowest. The OCD model contained the most pathogenic bacterial species, up to 43 species, including Sphingomonas, Pseudomonas, Cladosporium, and Alternaria. Risk assessments indicated bioaerosol exposure was lower in the models with sewage treatment (SHCT and CT) than in those without (SCC and OCD). Different populations exhibited large variations in potential risks owing to differences in time spent indoors and outdoors. The highest risk was observed in males exposed to the SCC model. This study provides a theoretical basis and theories for the future joint prevention and control of the bioaerosol exposure risk from decentralized sewage treatment.

Natural product discovery in soil actinomycetes: unlocking their potential within an ecological context

Natural products (NPs) produced by bacteria, particularly soil actinomycetes, often possess diverse bioactivities and play a crucial role in human health, agriculture, and biotechnology. Soil actinomycete genomes contain a vast number of predicted biosynthetic gene clusters (BGCs) yet to be exploited. Understanding the factors governing NP production in an ecological context and activating cryptic and silent BGCs in soil actinomycetes will provide researchers with a wealth of molecules with potential novel applications. Here, we highlight recent advances in NP discovery strategies employing ecology-inspired approaches and discuss the importance of understanding the environmental signals responsible for activation of NP production, particularly in a soil microbial community context, as well as the challenges that remain.

Vibrational imaging of metabolites for improved microbial cell strains

Significance

Biomanufacturing utilizes modified microbial systems to sustainably produce commercially important biomolecules for use in agricultural, energy, food, material, and pharmaceutical industries. However, technological challenges related to non-destructive and high-throughput metabolite screening need to be addressed to fully unlock the potential of synthetic biology and sustainable biomanufacturing.

Aim

This perspective outlines current analytical screening tools used in industrial cell strain development programs and introduces label-free vibrational spectro-microscopy as an alternative contrast mechanism.

Approach

We provide an overview of the analytical instrumentation currently used in the "test" portion of the design, build, test, and learn cycle of synthetic biology. We then highlight recent progress in Raman scattering and infrared absorption imaging techniques, which have enabled improved molecular specificity and sensitivity.

Results

Recent developments in high-resolution chemical imaging methods allow for greater throughput without compromising the image contrast. We provide a roadmap of future work needed to support integration with microfluidics for rapid screening at the single-cell level.

Conclusions

Quantifying the net expression of metabolites allows for the identification of cells with metabolic pathways that result in increased biomolecule production, which is essential for improving the yield and reducing the cost of industrial biomanufacturing. Technological advancements in vibrational microscopy instrumentation will greatly benefit biofoundries as a complementary approach for non-destructive cell screening.

Heterologous expression facilitates the discovery and characterization of marine microbial natural products

Microbial natural products and their derivatives have been developed as a considerable part of clinical drugs and agricultural chemicals. Marine microbial natural products exhibit diverse chemical structures and bioactivities with substantial potential for the development of novel pharmaceuticals. However, discovering compounds with new skeletons from marine microbes remains challenging. In recent decades, multiple approaches have been developed to discover novel marine microbial natural products, among which heterologous expression has proven to be an effective method. Facilitated by large DNA cloning and comparative metabolomic technologies, a few novel bioactive natural products from marine microorganisms have been identified by the expression of their biosynthetic gene clusters (BGCs) in heterologous hosts. Heterologous expression is advantageous for characterizing gene functions and elucidating the biosynthetic mechanisms of natural products. This review provides an overview of recent progress in heterologous expression-guided discovery, biosynthetic mechanism elucidation, and yield optimization of natural products from marine microorganisms and discusses the future directions of the heterologous expression strategy in facilitating novel natural product exploitation.

Phenotypic heterogeneity in Streptomyces colonies

Streptomyces are a large genus of multicellular bacteria best known for their prolific production of bioactive natural products. In addition, they play key roles in the mineralisation of insoluble resources, such as chitin and cellulose. Because of their multicellular mode of growth, colonies of interconnected hyphae extend over a large area that may experience different conditions in different parts of the colony. Here, we argue that within-colony phenotypic heterogeneity can allow colonies to simultaneously respond to divergent inputs from resources or competitors that are spatially and temporally dynamic. We discuss causal drivers of heterogeneity, including competitors, precursor availability, metabolic diversity and division of labour, that facilitate divergent phenotypes within Streptomyces colonies. We discuss the adaptive causes and consequences of within-colony heterogeneity, highlight current knowledge (gaps) and outline key questions for future studies.

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

Fungi are microorganisms of significant biotechnological importance due to their ability to provide food and produce several value-added secondary metabolites and enzymes. Its products move billions of dollars in the pharmaceutical, cosmetics, and additives sectors. These microorganisms also play a notable role in bionanotechnology, leading to the production of hybrid biological-inorganic materials (such as cyborg cells) and the use of their enzyme complex in the biosynthesis of nanoparticles. In this sense, optimizing the fungal growth process is necessary, with selecting the cultivation medium as one of the essential factors for the microorganism to reach its maximum metabolic expression. The culture medium's composition can also impact the nanomaterial's stability and prevent the incorporation of nanoparticles into fungal cells. Therefore, our main objectives are the following: (1) compile and discuss the most commonly employed culture media for the production of fungal secondary metabolites and the formation of cyborg cells, accompanied by preparation methods; (2) provide a six-step guide to investigating the fungal metabolomic profile and (3) discuss the main procedures of microbial cultivation to produce fungal cyborg cells.

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

Chitosan is known to exert antimicrobial activity without the need for any chemical modification; however, new derivatives of chitosan can be created to target multi-drug resistant bacteria. In this study, chitosan (CS) was cross-linked with sodium tripolyphosphate to form nanoparticles, which were then coated with polyacrylic acid (PAA). The SEM images revealed that the CS-PAA nanoparticles had spherical shapes with smooth surfaces and the size of the dried nanoparticles was approximately 222 nm. Biofilm formation was significantly inhibited by 0.5 mg/mL of CS-PAA. In-situ optical microscopy showed that CS-PAA nanoparticles inhibited the bacterial biofilm formation in Campylobacter jejuni, Pseudomonas aeruginosa, and Escherichia coli after a single treatment with 40 μg. Additionally, 20 µg of CS-PAA nanoparticles demonstrated antibacterial activity against the growth of C. jejuni, P. aeruginosa, and E. coli with notable inhibitory zones of 9, 12, and 13 mm, respectively (P < 0.01). The development of a novel and ecofriendly method for the preparation of chitosan nanoparticles through an interaction of chitosan with PAA shows promise tool to combat bacterial infections and validates effective antibacterial and antibiofilm properties against antibiotic resistant pathogens.

Investigating the Stirred Tank Bioreactor Co-Cultures of the Secondary Metabolite Producers Streptomyces noursei and Penicillium rubens

The stirred tank bioreactor co-cultures of the filamentous fungus Penicillium rubens and actinomycete Streptomyces noursei were studied with regard to secondary metabolite (SM) production, sugar consumption, and dissolved oxygen levels. In addition to the quantitative analysis of penicillin G and nystatin A1, the broad repertoire of 22 putatively identified products was semi-quantitatively evaluated with the use of UPLC-MS. Three co-cultivation variants differing with respect to the co-culture initiation method (i.e., the simultaneous inoculation of P. rubens and S. noursei and the 24 or 48 h inoculation delay of S. noursei relative to P. rubens) were investigated. All the co-cultures were carried out in parallel with the corresponding monoculture controls. Even though S. noursei showed the tendency to outperform P. rubens and inhibit the production of fungal secondary metabolites, the approach of simultaneous inoculation was effective in terms of enhancing the production of some S. noursei SMs, namely desferrioxamine E, deshydroxynocardamine, and argvalin. S. noursei displayed the capability of adaptation and SM production even after being inoculated into the 24 or 48 h culture of P. rubens. Interestingly, S. noursei turned out to be more efficient in terms of secondary metabolite production when its inoculation time relative to P. rubens was delayed by 48 h rather than by 24 h. The study demonstrated that the prolongation of inoculation delays can be beneficial for production-related performance in some co-culture systems.

Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview

Co-cultivation is an effective method of inducing the production of specialized metabolites (SMs) in microbial strains. By mimicking the ecological interactions that take place in natural environment, this approach enables to trigger the biosynthesis of molecules which are not formed under monoculture conditions. Importantly, microbial co-cultivation may lead to the discovery of novel chemical entities of pharmaceutical interest. The experimental efforts aimed at the induction of SMs are greatly facilitated by computational techniques. The aim of this overview is to highlight the relevance of computational methods for the investigation of SM induction via microbial co-cultivation. The concepts related to the induction of SMs in microbial co-cultures are briefly introduced by addressing four areas associated with the SM induction workflows, namely the detection of SMs formed exclusively under co-culture conditions, the annotation of induced SMs, the identification of SM producer strains, and the optimization of fermentation conditions. The computational infrastructure associated with these areas, including the tools of multivariate data analysis, molecular networking, genome mining and mathematical optimization, is discussed in relation to the experimental results described in recent literature. The perspective on the future developments in the field, mainly in relation to the microbiome-related research, is also provided.