Insights into additional lactone-based signaling circuits in Streptomyces: existence of acyl-homoserine lactones and LuxI/LuxR homologs in six Streptomyces species.

Acyl-homoserine lactones (AHLs), mediating pivotal physiological activities through quorum sensing (QS), have conventionally been considered limited to Gram-negative bacteria. However, few reports on the existence of AHLs in Gram-positive bacteria have questioned this conception. Streptomyces, as Gram-positive bacteria already utilizing a lactone-based QS molecule (i.e., gamma-butyrolactones), are yet to be explored for producing AHLs, considering their metabolic capacity and physiological distinction. In this regard, our study examined the potential production of AHLs within Streptomyces by deploying HPLC-MS/MS methods, which resulted in the discovery of multiple AHL productions by S. griseus, S. lavendulae FRI-5, S. clavuligerus, S. nodosus, S. lividans, and S. coelicolor A3(2). Each of these Streptomyces species possesses a combination of AHLs of different size ranges, possibly due to their distinct properties and regulatory roles. In light of additional lactone molecules, we further confirm that AHL- and GBL-synthases (i.e., LuxI and AfsA enzyme families, respectively) and their receptors (i.e., LuxR and ArpA) are evolutionarily distinct. To this end, we searched for the components of the AHL signaling circuit, i.e., AHL synthases and receptors, in the Streptomyces genus, and we have identified multiple potential LuxI and LuxR homologs in all 2,336 Streptomyces species included in this study. The 6 Streptomyces of interest in this study also had at least 4 LuxI homologs and 97 LuxR homologs. In conclusion, AHLs and associated gene regulatory systems could be more widespread within the prokaryotic realm than previously believed, potentially contributing to the control of secondary metabolites (e.g., antibiotics) and their complex life cycle, which leads to substantial industrial and clinical applications.

Isolation and screening of Thermoactinomycetaceae family members as an extremophilic poor investigated and promising natural source of antimicrobial substances.

Background and Objectives: Recent evidences have shown that methicillin-resistant Staphylococcus aureus (MRSA) can cause severe infections and is resistant to almost all commercially available antibiotics. Therefore, screening unknown sources of biological compounds such as the Thermoactinomycetaceae family as extremophilic bacteria may be helpful to find new antimicrobial agents. Materials and Methods: Various samples were collected from different ecosystems, including desert, volcano, compost, and forest. They were cultured on Soil extract agar and Water agar. The antimicrobial activity of the isolates was evaluated using agar overlay and well diffusion methods. Members of the Thermoactinomycetaceae family were selected for further study: Their ability to grow at different temperatures, NaCl concentrations, and pH values, enzyme production ability, antimicrobial secondary screening, fractionation of their supernatants and so on. Results: According to molecular identification of active isolates against MRSA, three strains, including Laceyella sacchari UTMC 2705, Thermoactinomyces sp. UTMC 2721, and Laceyella sp. UTMC 2731, belonged to Thermoactinomycetaceae were identified. The minimum inhibitory concentrations of their extracts were tested against some pathogenic bacteria, showing their antimicrobial activity with a broad spectrum. The results of TLC bioautography of the extracts showed that the most active fractions were semi-polar. Also, the results of HPLC analysis showed the existence of several UV-active compounds in their extracts. Conclusion: The present study highlighted the importance and potential of Thermoactinomycetaceae members as a less-known source of antibiotics against pathogenic bacteria.

Effect of the Nanoclay Treated Streptomyces sp. UTMC 3136 as a Bioformulation on the Growth of Helianthus annuus.

Biofertilizers based on plant growth-promoting actinobacteria are used as potential alternatives to chemical fertilizers for sustainable agricultural systems. However, successful application of PGPA to agricultural land is challenging. The present study was an attempt to develop and evaluate the effect of a low-cost biofertilizer named NCTS (nanoclay-treated-Streptomyces) based on Streptomyces sp. UTMC 3136 spores amalgamated in a hybrid material of nanoclay Na-montmorillonite K10-glycerol-water substrate. In addition, the effect of NCTS on sunflower growth was investigated. In vivo tests showed a statistically significant increase in the agronomic characteristics of sunflowers treated with NCTS. Characterization of NCTS by FTIR, Raman spectroscopy, and scanning electron microscopy testified to the structural alignment and good adhesion of NCTS components. The viability of NCTS was 100% after 72 h of storage at 4 °C. Overall, the present study attempted to validate the efficacy of the formulation of Streptomyces sp. UTMC 3136 in nanoclay for growth improvement of sunflower. It was the first study to show the administration of PGPA in combination with nanomaterials as a growth enhancing biofertilization agent for sunflower.

Novel enzyme-based electrochemical and colorimetric biosensors for tetracycline monitoring in milk.

Recently, there has been a growing demand to develop portable devices for the fast detection of contaminants in food safety, healthcare, and environmental fields. Herein, two biosensing methods were designed by the use of nicotinamide adenine dinucleotide phosphate (NAD(P)H)-dependent TetX2 enzyme activity and thionine as an excellent electrochemical and colorimetric mediator/probe to monitor tetracycline (TC) in milk. The nanoporous glassy carbon electrode (NPGCE) modified with polythionine was first prepared by electrochemically and then TetX2 was immobilized onto the NPGCE using polyethyleneimine. The prepared biosensor provided a high electrocatalytic response toward NAD(P)H by significantly reducing its overpotential. The proposed biosensor exhibited a detection limit of 40 nM with a linear range of 0.1-0.8 µM for TC determination. Besides, the thionine probe was used to develop a novel colorimetric assay using a simple enzymatic color reaction within a few minutes. The limit of detection for TC was experimentally achieved as 60 nM, which was lower than the safety levels established by the World Health Organization (225 nM). The correlation between change in the color of the solution and the concentration of TC was used for quality control of milk samples, as confirmed by the standard high-performance liquid chromatography method. The results show the great potential of the proposed assays as portable instruments for on-site TC measurements.

Fruit wrapping kraft coated paper promotes the isolation of actinobacteria using ex situ and in situ methods.

Designing novel isolation methods could enhance the diversification of the available bacterial strains to biotechnology. In this study, the new ex situ and in situ cultivation methods are introduced for the isolation of actinobacteria. In the ex situ experiments, the soil suspension was spread on the isolation media located above some ordinary papers in immediate contact with the slurry of soil substrate and incubated for 16 weeks. The paper was wholly immersed in the cave soil for in situ cultivations, and the containers were buried under layers of soil in Hampoeil cave for 10 weeks. Fruit wrapping kraft coated paper, with 68.8% recovery of isolates, was a better choice in isolation of actinobacteria than other studied filter paper. Based on the molecular identification results, 19% of the isolates obtained from the in situ cultivation method had less than 98.5% similarity to known taxa of actinobacteria and potentially may represent new species. In contrast, in the standard cultivation method, 1.3% of the isolates had less than 98.5% similarity 16Sr RNA gene. This data shows that the introduced cultivation method is a promising technique for isolating less culturable or new actinobacteria.

Adaptive Evolution of Lactococcus Lactis to Thermal and Oxidative Stress Increases Biomass and Nisin Production.

High values of agitation and temperature lead to stressful conditions in the fermentations of Lactococcus lactis due to its aero-tolerant and mesophilic nature. Here, the adaptive laboratory evolution (ALE) technique was applied to increase biomass and nisin production yields by enhancing L. lactis subsp. lactis robustness at higher growth temperature and aeration rates. In two separate ALE experiments, after 162 serial transfers, optimum agitation and growth temperature of L. lactis were shifted from 40 rpm and 30 °C to 200 rpm and 37 °C, respectively. Oxidative and acid resistance were enhanced in the evolved strain. Whole-genome sequencing revealed the emergence of five single-nucleotide polymorphisms in the genome of the evolved strain in jag, DnaB, ArgR, cation transporter genes, and one putative protein. The evolved strain of L. lactis in this study has more industrial desirable features and improved nisin production capability and can act more efficiently in nisin production in stressful conditions.

Evaluation of anti-biofilm potential of biosurfactant extracted from Nocardia species.

INTRODUCTION: Bacterial natural products such as biosurfactants and surface-active agents are important compounds which exhibit many applications in the fields of medicine. AIM: The aim of the present study was to isolate and identify Nocardia strains with high biosurfactant production and antibiofilm ability. MATERIALS AND METHODS: In the present study, a biosurfactant producing Nocardia species was isolated and identified by a laboratory method. Nocardia species were initially screened and then tested for their ability to produce biosurfactant. The oil spreading test and the surface tension measurements showed that one strain was a biosurfactant producer. The strain with the best surface activity results was selected for further studies and identified by 16S rRNA gene sequencing method. Fourier transform infrared spectroscopy (FTIR) and compositional analysis proved a biosurfactant structure. RESULTS: Oil spreading test and blue agar plate test confirmed biosurfactants and extracellular anionic glycolipids. E24% assay using olive oil revealed strong emulsifying characteristic of the extracted biosurfactant with 100% emulsifying strength. FTIR spectrum indicated the presence of aliphatic hydrocarbon chain (lipid) along with the polysaccharide portion, confirming the glycolipid nature of the biosurfactant. The stability of the biosurfactant produced in different conditions was significant. Increasing concentration of BS significantly inhibited Pseudomonas aeruginosa biofilm. CONCLUSIONS: N. coubleae can be a representative of the genus Nocardia for the production of biosurfactants with beneficial physicochemical properties.

Endophytic actinobacteria of a halophytic desert plant Pteropyrum olivieri: promising growth enhancers of sunflower.

In the present study, 40 actinobacterial isolates were obtained from the roots of a desert plant, Pteropyrum olivieri and tested for extracellular hydrolytic enzyme activities, hydrogen cyanide, and siderophore production. Based on these activities, three isolates designated UTMC 2482, UTMC 2483, and UTMC 3136 were selected with an aim of developing bio-fertilizing agent to improve the growth of sunflower plants under normal conditions. The selected isolates showed 98.2, 98.4, and 100% similarities in the 16S rRNA gene sequences to Streptomyces chromofuscus, Streptomyces ambofaciens, and Streptomyces gardneri, respectively. These isolates exhibited indole acetic acid production while UTMC 2483 was found to produce 1-aminocyclopropane-1-carboxylate deaminase, as well. Sunflower seeds soaked in the bacterial spore suspensions increased the tolerance of sunflower seedlings to the stresses of salinity and water deficiency up to 270 mM of NaCl and - 2Mpa of PEG6000, respectively. Under normal conditions, inoculation with individual isolates and their consortia enhanced the yield (plant length, weight, and flower diameter) and biochemical contents (i.e. chlorophyll, protein, and oil) up to 5.3, 1.7, and 2.4 times higher than that of un-inoculated plants, significantly (p < 0.05) in greenhouse and field experiments. This is the first study demonstrating that endophytic actinobacteria from the desert plant, P. olivieri, have profound bio-fertilizing effects on the growth of sunflower.

Genome sequence and annotation of Streptomyces tendae UTMC 3329, acid and alkaline tolerant actinobacterium.

BACKGROUND AND OBJECTIVES: Streptomyces tendae is one of the most prolific actinobacteria with a wide range of biotechnological applications. Genomic data can help in better understanding and exploration of important microorganisms, however, there is a few genomic information available for this species. MATERIALS AND METHODS: Molecular identification, pH and salt tolerance of an actinobacterium, designated Streptomyces tendae UTMC 3329, isolated from a tea field soil were done. Also, genomic DNA was extracted and sequenced using Illumina platform with MPS (massively parallel sequencing) Illumina technology. Gene annotation and bioinformatic analysis were done using appropriate software and servers. RESULTS: The draft genome is ∼8.7 megabase pairs, containing 7557 predicted coding sequences. The strain was able to grow at pH 5-12 and 0-10% NaCl. The maximum growth rate of the bacterium was obtained at pH 7. The gene clusters involved in central carbon metabolism, phosphate regulation, transport system, stress responses were revealed. It was shown the presence of gene clusters of polyketides, ribosomally and non-ribosomally synthesized peptides. Various genes were found in xenobiotic degradation pathways and heavy metal resistance. CONCLUSION: The current genomic information which reveals biological features, as well as the biotechnological potential of this acid and alkaline tolerant actinobacterium, can be implemented for further research on the species.

Genome-scale exploration of transcriptional regulation in the nisin Z producer Lactococcus lactis subsp. lactis IO-1.

Transcription is of the most crucial steps of gene expression in bacteria, whose regulation guarantees the bacteria's ability to adapt to varying environmental conditions. Discovering the molecular basis and genomic principles of the transcriptional regulation is thus one of the most important tasks in cellular and molecular biology. Here, a comprehensive phylogenetic footprinting framework was implemented to predict maximal regulons of Lactococcus lactis subsp. lactis IO-1, a lactic acid bacterium known for its high potentials in nisin Z production as well as efficient xylose consumption which have made it a promising biotechnological strain. A total set of 321 regulons covering more than 90% of all the bacterium's operons have been elucidated and validated according to available data. Multiple novel biologically-relevant members were introduced amongst which arsC, mtlA and mtl operon for BusR, MtlR and XylR regulons can be named, respectively. Moreover, the effect of riboflavin on nisin biosynthesis was assessed in vitro and a negative correlation was observed. It is believed that understandings from such networks not only can be useful for studying transcriptional regulatory potentials of the target organism but also can be implemented in biotechnology to rationally design favorable production conditions.

Antibacterial properties of a bacterial cellulose CQD-TiO2 nanocomposite.

Antibacterial dressing can prevent the occurrence of many infections of wounds. Bacterial cellulose (BC) has the ability to carry and transfer the medicine to achieve a wound healing bandage. In this study, Carbon Quantum Dots-Titanium dioxide (CQD-TiO2) nanoparticles (NP) were added to BC as antibacterial agents. FTIR Spectroscopy illuminated that NPs were well-bonded to BC. Interestingly, MIC test proved that BC/CQD-TiO2 nanostructure (NS) has anti-bacterial properties against Staphylococcus aureus. The findings indicated that, CQD-TiO2 NPs have stronger antibacterial properties with better tensile strength compared to CQD NPs, in a concentration-dependent manner. Toxicity of CQD-TiO2 NPs on human L929 fibroblast cells was also evaluated. Most importantly, the results of the scratch test indicated that the NS was effective in wound healing in L929 cells. The approach in this study may provide an alternative to make an antibacterial wound dressing to achieve an effective drug-based bandage.

Optimized bioleaching of copper by indigenous cyanogenic bacteria isolated from the landfill of e-waste.

In this study, indigenous cyanogenic bacterial strains were isolated on nutrient, minimal salt, and soil extract media at various culture conditions from two distinct landfills of e-waste, Iran. Based on their cyanide formation profiles, five most potent isolates were selected for optimization and to this end, the influence of the most effective factors on cyanide production including pH, glycine concentration and temperature were assessed using one-factor at a time method (OFAT). Initial pH of 7, glycine concentration of 2 g/L and temperature of 30°C were obtained as optimal conditions for most of the isolates. Additionally, two bioleaching processes were applied for each bacteria to detect the effect of optimal conditions on bioleaching and to assay their potential in the mobilization of copper. Under optimal conditions and pulp density of 1 g/L, copper recoveries were recorded as 96.73%, 82.49%, 81.17%, 41.72%, and 31.52% by S22, N13, N37, N23, and N41 respectively during 10 days which is approximately 1.5-5 times higher than the recovery obtained without optimization. During the optimization and the bioleaching process, the pH fluctuation of the flasks was monitored which validated the activity of the microorganisms.

In-Situ Recovery of Persipeptides from Streptomyces zagrosensis Fermentation Broth by Enhanced Adsorption.

BACKGROUND: Drug discovery process is growing considerably due to the noteworthy resource of natural products. Persipeptides A and B are cyclopeptide antibiotics, which are produced by Streptomyces zagrosensis UTMC 1154. Although extraction of culture broth with the help of solvent has been optimized previously, no effort for In-Situ extraction of persipeptides has been done yet. OBJECTIVE: To produce a high quantity of persipeptides for further drug evaluation, it is crucial to design approaches aimed at improvement of the extraction yield. MATERIALS AND METHODS: Amberlite XAD-16N was employed into the fermentation culture medium of S. zagrosensis in order to enhance the In-Situ extraction of persipeptides. Effects of resin content (%), resin addition time (h), and fermentation time (day) were investigated by a two-level full factorial experimental design. RESULTS: The main factors of resin content (%) and the interaction of resin content (%) with resin addition time (day) were found to be important using ANOVA. The results showed the amount of 0.33 % (w.v-1) amberlite XAD-16N added at 27.2 h post-inoculation was the most effective combination to increase the efficiency of In-Situ adsorption capacity of persipeptides. CONCLUSIONS: The provided method requires 3.3 g resin and 200 mL methanol for the extraction of persipeptides from each liter of fermentation culture of S. zagrosensis in less than 15 min. Apart from cost-efficiently and simplicity, this procedure enhanced the recovery of persipeptides by 7 % and 3 times, compared to ISP2 medium without any resin after 4 and 7 days of fermentation, respectively. Therefore, this method can be regarded as a cost-efficient enhancement approach for the production of these newly-discovered metabolites before implementing the genetic manipulation or intensive media optimization, demanding considerable time and effort.

A Study on actinobacterial diversity of Hampoeil cave and screening of their biological activities.

Caves are oligotrophic, dark and less-explored environments and are considered as sources of promising microbial strains in biotechnology. Hampoeil Cave is located in massive dolomite with thin bedded limestone in northwestern of Iran. In an isolation and screening program, various samples from soil, water, floor, wall and ceiling of Hampoeil cave and its invertebrates were collected. Four various treatments and 10 different isolation media were used for the isolation of the actinobacteria. Screening of the isolates for antimicrobial activity against 10 bacteria and fungi, 5 hydrolytic enzymes production and resistance to 5 heavy metals have been performed. Among 33 various samples, 76 actinobacteria from various genera, including Streptomyces, Micromonospora, Micrococcus, Kocuria and Corynebacterium were isolated. Eighty percent of the strains had one of the studied hydrolytic enzyme activity. At least one type of antimicrobial activity was seen in 25.3% of the isolates. Resistance to one metal or more was seen in 26.32% of the isolates. The ratio of rare-actinobacteria in the oligotrophic samples to enriched samples is 20% more than Streptomyces. Percentage of strains with the highest activity in esterase, amylase, DNase, protease or lipase activity that were isolated from organic-rich environmental samples were 100, 100, 100, 82 and 82%, respectively. Also, 26.32% of the actinobacterial isolates resisted to heavy metals. It was concluded that Hampoeil cave is a good source in finding cave-living actinobacteria potent in producing hydrolytic enzymes and bioremediation.

Structural and functional evaluation of recombinant histidine phosphokinase NisK and response regulator NisR: in silico and experimental approach.

In the two-component system of NisRK from Lactococcus lactis, the production of nisin is affected by transmembrane NisK and activation of intracellular NisR. The transcription of nisin structural genes can be induced by derivatives of nisin. NisR activation leads to the activation of nisA/Z transcription, which encodes the nisin maturation machinery, nisin regulation and activation of the nisFEG operon to confer immunity. The aim of this study was to express the Lactococcus lactis histidine phosphokinase NisK and response regulator NisR in E. coli, and to perform activity assays and in silico analysis. In silico methods were applied to study the properties and structures of the NisK and NisR proteins, including prediction of physicochemical characteristics, secondary and tertiary structure, stability and ligand-receptor interactions.pET32a and pET28a vectors containing synthetic nisK and nisR genes were transformed into E. coli followed by IPTG induction. SDS-PAGE and western blotting methods were applied to confirm the presence and identity of the amplified proteins. Following purification, the proteins were dialyzed and then prepared for activity assay. The CAI index showed that the genes was compatible with the E. coli host and that the proteins have effective expression. Also, the mRNA prediction results suggest that there is enough mRNA stability for efficient translation in the new host. NisK and NisR recombinant proteins were expressed in E. coli with half - lives of around 10 h and were confirmed with molecular weights of 27 kDa and 69 kDa, respectively, by SDS-PAGE and western blotting. The secondary structure of the recombinant proteins as predicted by circular dichroism spectroscopy was similar to the in silico protein structures. Activity assay of recombinant NisK was performed by measuring the amount of consumed ATP according to the light produced by luciferase. Because NisK and NisR have a direct impact on each other, they have an essential role in increasing the production of nisin and they can be used in different research fields. Our results demonstrated that recombinant proteins NisK and NisR preserved their structure and function after expression.

Coexistence of Anticoagulant and Anti-vascular Calcification Activities in Kribbella sp. UTMC 267 Metabolites.

Thrombotic disorders increase the risk of cardiovascular/cerebrovascular complications and represent a major health problem worldwide. Anticoagulants are extensively used in treatment of these disorders. Vitamin K antagonists, like Warfarin, are frequently used in medication. Vascular calcification (VC) is a significant side-effect of vitamin K antagonists especially Warfarin. There is an urgent need to find natural, efficient, non-toxic, and cost effective anticoagulants without dangerous side-effect like VC. In the present study, we evaluated the potential of thirteen fermentation broth extracts of actinobacteria (FBEA) (200 µg mL-1) to prolong whole blood prothrombin time (PT)/international normalized ratio (INR) and activated partial thromboplastin time (APTT). The fractions of the most effective FBEA were further investigated for their inhibitory effect on VC. The results showed PT/INR of the healthy blood samples was sensitive to the presence of five FBEA. Their INR index fell in the 1.2 to 8.6 range and six FBEA prolonged both PT/INR and APTT parameters (1.7-5 INR, and 46-59 s for APTT). The fractions of Kribbella sp. UTMC 267 FBE (200 µg mL-1), as the most efficient FBE, only inhibited intrinsic and common pathways of coagulation (APTT). Under calcification condition, Kribbella sp. UTMC 267 fractions (20 µg mL-1) showed significant inhibitory effect on VC in alizarin red staining (13.3-76 %) and alkaline phosphatase activity of VSMCs (33-62%). They also inhibited osteopontin mRNA expression in treated vascular smooth muscle cells (VSMCs) under that situation. So, we can introduce Kribbella sp. UTMC 267 FBE as a good candidate for more investigation on thrombotic medication.

Genome mining for ribosomally synthesised and post-translationally modified peptides (RiPPs) reveals undiscovered bioactive potentials of actinobacteria.

One of the most diverse groups of bioactive bacterial metabolites is the ribosomally synthesised and post-translationally modified peptides (RiPPs) with different bioactivities. The process of genome mining has made it possible to predict the presence of such clusters among the huge genomic data available today. Despite the great potential of actinobacteria in producing natural products and the myriad of completely sequenced genomes available, a comprehensive genome mining of these bacteria for RiPPs is lacking. Here, a collection of 629 complete actinobacterial genomes were analysed to explore their RiPP biosynthesis potential. Using BAGEL3 genome mining tool, the presence of 477 RiPP biosynthesis gene clusters (BGCs) was shown, including all known classes of bacterial RiPPs. RiPP-encoding potential was shown to be widespread among different members of actinobacteria especially within the plant and soil-inhabiting strains. The notable presence of LAP BGCs in plant-associating actinobacteria was also illustrated. Streptomyces, Amycolatopsis, Kitasatospora and Frankia showed greater potential in RiPP biosynthesis while lanthipeptides and lasso peptides were the most distributed RiPPs. Three cyanobactin BGCs were also detected. Generally evidence of promising ability of actinobacteria to synthesise diverse classes of RiPPs as well as information needed to rationally select appropriate taxa for rational screening of specific RiPPs are presented.

A novel electrochemical biosensor based on TetX2 monooxygenase immobilized on a nano-porous glassy carbon electrode for tetracycline residue detection.

Different carbon-based nanostructures were used to investigate direct electron transfer (DET) of TetX2 monooxygenase (TetX2), and an enzyme-based biosensor for sensitive determination of tetracycline (TC) also fabricated. A polyethyleneimine (PEI) with positive charge groups was used for immobilization of TetX2 on modified glassy carbon electrodes. Cyclic voltammetry (CV) was employed to study the electrochemical characteristics of the immobilized enzyme and the performance of the proposed biosensor. Amongst multiple carbon-modified electrodes, nano-porous glassy carbon electrode (NPGCE) was selected because of its amplified signal response for flavin adenine dinucleotide (FAD) and superior electrocatalytic behavior toward oxygen reduction. The cyclic voltammogram of PEI/TetX2/NPGCE showed two couple of well-defined and quasi-reversible redox peaks of FAD, consistent with the realization of DET. The prepared electrode was then successfully introduced as a biosensing interface based on the oxygen reduction peak current, resulting in a linear range response from 0.5 to 5 µM with a good detection limit of 18 nM. The as-fabricated electrode demonstrates a fast response and excellent stability for the detection of TC. The results indicate that this simple, rapid, eco-friendly and economic strategy of PEI/TetX2/NPGCE preparation has potential for the fabrication of an enzyme-based biosensor for the practical detection of TC in food products.

Effects of microbial volatile organic compounds on Ganoderma lucidum growth and ganoderic acids production in Co-v-cultures (volatile co-cultures).

Co-v-culture (co-cultivations of physically separated microbes that only interact through the air) systems were designed to investigate the effects of microbial volatile organic compounds (mVOCs) from about 20 different microbes, on a medicinal fungus, Ganoderma lucidum. For more accuracy in co-cultivations, a novel synchronized cultivation approach was tested for culturing G. lucidum. The hyphal growth of G. lucidum and the content of its ganoderic acids (GAs) were measured. In almost all of the co-v-cultures, there was an inhibiting effect on hyphal growth and a promoting effect on GAs contents. In inducing GAs production, Bacillus cereus PTCC 1247 and Pseudomonas aeruginosa UTMC 1404 were the most effective ones, as, compared to control cultures, GAs content increased 2.8 fold. Comparing different co-v-cultivations demonstrated that the concentrations of mVOCs, oxygen, and carbon dioxide were the main players in co-v-cultures. No correlation was found between hyphal growth and GAs production. Strains of the same species imposed totally different effects on hyphal growth or GAs production. This study has investigated the effects of mVOCs on G. lucidum for the first time. Moreover, it suggests that co-v-cultivation may be a promising biotechnological approach to improve the production in G. lucidum.

Sequence-based analysis and prediction of lantibiotics: A machine learning approach.

Lantibiotics, an important group of ribosomally synthesized peptides, represent an important arsenal of novel promising antimicrobials showing high potency in fighting against the prevalence of antibiotic resistance among microbial pathogens. However, due to the lack of high throughput strategies for the isolation and identification of these compounds, our information regarding their structure and especially sequence-based properties is far from complete. Therefore, in the present study, a comprehensive sequence-based analysis of these peptides was performed with the help of machine learning approach together with a feature selection technique. Meanwhile, an attempt to develop an accurate computational model for prediction of lantibiotics was made via constructing two datasets of 280 and 190 lantibiotic and non-lantibiotic antimicrobial peptide sequences, respectively. Based on the conducted approach and as a result of our search for a subset of relevant features of lantibiotics, particular types of sequenced-based features were observed to be preferred in lantibiotics, the knowledge-based implementation of which can be used as strategies for lantibiotic bioengineering purposes. Moreover, a SMO-based classifier was developed for the prediction of lantibiotics with the accuracy and specificity values of 88.5% and 94%, respectively which shows the great potential of the developed algorithm for the prediction of lantibiotcs. Conclusively, the accurate predictor algorithm as well as the identified sequence-based distinctiveness properties of lantibiotics can give valuable information in both the fields of lantibiotic discovery and bioengineering.