Trends in the search for bioactive microbial metabolites

Regulation of Intestinal Barrier Function by Microbial Metabolites

The human gastrointestinal tract (GI) harbors a diverse population of microbial life that continually shapes host pathophysiological responses. Despite readily available abundant metagenomic data, the functional dynamics of gut microbiota remain to be explored in various health and disease conditions. Microbiota generate a variety of metabolites from dietary products that influence host health and pathophysiological functions. Since gut microbial metabolites are produced in close proximity to gut epithelium, presumably they have significant impact on gut barrier function and immune responses. The goal of this review is to discuss recent advances on gut microbial metabolites in the regulation of intestinal barrier function. While the mechanisms of action of these metabolites are only beginning to emerge, they mainly point to a small group of shared pathways that control gut barrier functions. Amidst expanding technology and broadening knowledge, exploitation of beneficial microbiota and their metabolites to restore pathophysiological balance will likely prove to be an extremely useful remedial tool.

Identifying the Biosynthetic Gene Cluster for Triacsins with an N-Hydroxytriazene Moiety

Triacsins are a family of natural products having in common an N-hydroxytriazene moiety not found in any other known secondary metabolites. Though many studies have examined the biological activity of triacsins in lipid metabolism, their biosynthesis has remained unknown. Here we report the identification of the triacsin biosynthetic gene cluster in Streptomyces aureofaciens ATCC 31442. Bioinformatic analysis of the gene cluster led to the discovery of the tacrolimus producer Streptomyces tsukubaensis NRRL 18488 as a new triacsin producer. In addition to targeted gene disruption to identify necessary genes for triacsin production, stable isotope feeding was performed in vivo to advance the understanding of N-hydroxytriazene biosynthesis.

Characterization of ankaflavin from Penicillium aculeatum and its cytotoxic properties

The pigment was extracted from Penicillium aculeatum, purified and characterized as Ankaflavin by spectroscopic analysis. The stability of the pigment was determined under various conditions and was found to possess high stability. The cytotoxicity property of the purified pigment was determined by MTT assay in MCF-7, HCT116 and PC-3 and the studies were compared with its activity in CHOK1 cells. In MCF-7 and in CHOK 1 cells, the pigment exhibited very less toxicity. However, significant cytotoxicity was observed in HCT116 and PC-3 cells with IC₅₀ of 162 μg mL^-1 and 85 μg mL^-1 for HCT116 and PC-3 cells respectively. In vitro toxicity was tested by haemolysis assay and MTT assay in HEK 293 cells. The pigment showed least cytotoxicity (<5%) at 160 and 320 μg mL^-1 concentrations HEK 293 cells and negligible (<5%) toxicity on human erythrocytes at 160 and 320 μg mL^-1, the highest concentrations tested.

SParticle, an algorithm for the analysis of filamentous microorganisms in submerged cultures

Streptomycetes are filamentous bacteria that produce a plethora of bioactive natural products and industrial enzymes. Their mycelial lifestyle typically results in high heterogeneity in bioreactors, with morphologies ranging from fragments and open mycelial mats to dense pellets. There is a strong correlation between morphology and production in submerged cultures, with small and open mycelia favouring enzyme production, while most antibiotics are produced mainly in pellets. Here we describe SParticle, a Streptomyces Particle analysis method that combines whole slide imaging with automated image analysis to characterize the morphology of submerged grown Streptomyces cultures. SParticle allows the analysis of over a thousand particles per hour, offering a high throughput method for the imaging and statistical analysis of mycelial morphologies. The software is available as a plugin for the open source software ImageJ and allows users to create custom filters for other microbes. Therefore, SParticle is a widely applicable tool for the analysis of filamentous microorganisms in submerged cultures.

Microbial metabolites in nutrition, healthcare and agriculture

Microorganisms are a promising source of an enormous number of natural products, which have made significant contribution to almost each sphere of human, plant and veterinary life. Natural compounds obtained from microorganisms have proved their value in nutrition, agriculture and healthcare. Primary metabolites, such as amino acids, enzymes, vitamins, organic acids and alcohol are used as nutritional supplements as well as in the production of industrial commodities through biotransformation. Whereas, secondary metabolites are organic compounds that are largely obtained by extraction from plants or tissues. They are primarily used in the biopharmaceutical industry due to their capability to reduce infectious diseases in human beings and animals and thus increase the life expectancy. Additionally, microorganisms and their products inevitably play a significant role in sustainable agriculture development.

Antibacterial metabolites from the Actinomycete Streptomyces sp. P294

The Actinomycete strain P294 was isolated from soil and identified as Streptomyces sp. based upon the results of 16S rRNA sequence analysis. Three compounds obtained from the solid fermentation products of this strain have been determined by 1D, 2D NMR and HRMS experiments. These compounds include two new compounds angumycinones C (1) and D (2), and the known compound X-14881 E (3). All compounds were assayed for antibacterial and nematicidal activity. The results showed the three compounds had different degrees of inhibitory activity against several target bacteria but no significant toxicity against the nematode Caenorhabditis elegans.

Antagonistic potential of native strain Streptomyces aurantiogriseus VSMGT1014 against sheath blight of rice disease

A total of 132 actinomycetes was isolated from different rice rhizosphere soils of Tamil Nadu, India, among which 57 showed antagonistic activity towards Rhizoctonia solani, which is sheath blight (ShB) pathogen of rice and other fungal pathogens such as Macrophomina phaseolina, Fusarium oxysporum, Fusarium udum and Alternaria alternata with a variable zone of inhibition. Potential actinomycete strain VSMGT1014 was identified as Streptomyces aurantiogriseus VSMGT1014 based on the morphological, physiological, biochemical and 16S rRNA sequence analysis. The strain VSMGT1014 produced lytic enzymes, secondary metabolites, siderophore, volatile substance and indole acetic acid. Crude metabolites of VSMGT1014 showed activity against R. solani at 5 µg ml(-1); however, the prominent inhibition zone was observed from 40 to 100 µg ml(-1). Reduced lesion heights observed in culture, cells-free filtrate, crude metabolites and carbendazim on challenge with pathogen in the detached leaf assay. The high content screening test clearly indicated denucleation of R. solani at 5 µg ml(-1) treatment of crude metabolite and carbendazim respectively. The results conclude that strain VSMGT1014 was found to be a potential candidate for the control of ShB of rice as a bio fungicide.

Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry

Background

Structure elucidation of unknown small molecules by mass spectrometry is a challenge despite advances in instrumentation. The first crucial step is to obtain correct elemental compositions. In order to automatically constrain the thousands of possible candidate structures, rules need to be developed to select the most likely and chemically correct molecular formulas.

Results

An algorithm for filtering molecular formulas is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds. Formulas are ranked according to their isotopic patterns and subsequently constrained by presence in public chemical databases. The seven rules were developed on 68,237 existing molecular formulas and were validated in four experiments. First, 432,968 formulas covering five million PubChem database entries were checked for consistency. Only 0.6% of these compounds did not pass all rules. Next, the rules were shown to effectively reducing the complement all eight billion theoretically possible C, H, N, S, O, P-formulas up to 2000 Da to only 623 million most probable elemental compositions. Thirdly 6,000 pharmaceutical, toxic and natural compounds were selected from DrugBank, TSCA and DNP databases. The correct formulas were retrieved as top hit at 80–99% probability when assuming data acquisition with complete resolution of unique compounds and 5% absolute isotope ratio deviation and 3 ppm mass accuracy. Last, some exemplary compounds were analyzed by Fourier transform ion cyclotron resonance mass spectrometry and by gas chromatography-time of flight mass spectrometry. In each case, the correct formula was ranked as top hit when combining the seven rules with database queries.

Conclusion

The seven rules enable an automatic exclusion of molecular formulas which are either wrong or which contain unlikely high or low number of elements. The correct molecular formula is assigned with a probability of 98% if the formula exists in a compound database. For truly novel compounds that are not present in databases, the correct formula is found in the first three hits with a probability of 65–81%. Corresponding software and supplemental data are available for downloads from the authors' website.

Discovery, chemistry, and chemical biology of microbial products

Our long-standing and continual screening of microorganisms, especially for antiparasitic agents, has produced a wide variety of compounds of global importance, such as the avermectins. Recent discoveries include nafuredin, atpenins, argifin, and argadin. Nafuredin is a helminth-specific inhibitor of electron-transport enzyme, complex I, which exhibits anthelmintic activity againstHaemonchus contortusin sheep. The atpenins are the most potent complex II inhibitors ever reported. Co-crystallization study of atpenin A5 andE. colicomplex II indicated the binding mechanism of ubiquinone to complex II. Argifin and argadin are the first cyclic peptides to inhibit chitinase at low concentration. Though structurally similar, their chitinase inhibition mechanisms are quite different.

Wortmannilactones A-D, 22-membered triene macrolides from Talaromyces wortmannii

The fungus Talaromyces wortmannii, isolated from a soil sample collected in China's Yunnan province, produced four novel 22-membered macrolides, namely, wortmannilactones A-D (1-4). Structures 1-4 were elucidated by extensive 1D and 2D NMR and MS spectral analyses. Compounds 1-4 exhibited in vitro cytotoxic activity against several human cancer cell lines with IC50 values ranging from 28.7 to 130.5 microM.

Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor

The goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. We built metagenomic libraries with DNA from soil on the floodplain of the Tanana River in Alaska. We extracted DNA directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. To identify clones of interest, we designed a high throughput "intracellular" screen, designated METREX, in which metagenomic DNA is in a host cell containing a biosensor for compounds that induce bacterial quorum sensing. If the metagenomic clone produces a quorum-sensing inducer, the cell produces green fluorescent protein (GFP) and can be identified by fluorescence microscopy or captured by fluorescence-activated cell sorting. Our initial screen identified 11 clones that induce and two that inhibit expression of GFP. The intracellular screen detected quorum-sensing inducers among metagenomic clones that a traditional overlay screen would not. One inducing clone carries a LuxI homologue that directs the synthesis of an N-acyl homoserine lactone quorum-sensing signal molecule. The LuxI homologue has 62% amino acid sequence identity to its closest match in GenBank, AmfI from Pseudomonas fluorescens, and is on a 78-kb insert that contains 67 open reading frames. Another inducing clone carries a gene with homology to homocitrate synthase. Our results demonstrate the power of an intracellular screen to identify functionally active clones and biologically active small molecules in metagenomic libraries.

Bioactive Microbial Metabolites

The short history, specific features and future prospects of research of microbial metabolites, including antibiotics and other bioactive metabolites, are summarized. The microbial origin, diversity of producing species, functions and various bioactivities of metabolites, unique features of their chemical structures are discussed, mainly on the basis of statistical data. The possible numbers of metabolites may be discovered in the future, the problems of dereplication of newly isolated compounds as well as the new trends and prospects of the research are also discussed.

Insecticidal activity of penitrems, including penitrem G, a new member of the family isolated from Penicillium crustosum

Penitrem G (7), a new indole-diterpenoid compound, has been isolated together with the already known mycotoxins penitrems A-D (1-4) and F (6) from the mycelium of Penicillium crustosum Thom. The structure of penitrem G was established on the basis of spectroscopic data. In addition, paspaline (8), another indole-diterpenoid mycotoxin that has not been previously described in this fungus, was also isolated. These compounds were tested for insecticidal activity against the hemipteran Oncopeltus fasciatus Dallas and the dipteran Ceratitis capitata Wiedemann. Penitrems A-D and F showed convulsive and insecticidal activities against both insect species. In addition, important reductions in the fecundity and fertility of the surviving C. capitata females were observed. In contrast, penitrem G and paspaline did not show any kind of activity. Mortality data and sublethal effects of the treatments have allowed preliminary structure-activity relationships to be proposed.

The natural functions of secondary metabolites

Secondary metabolites, including antibiotics, are produced in nature and serve survival functions for the organisms producing them. The antibiotics are a heterogeneous group, the functions of some being related to and others being unrelated to their antimicrobial activities. Secondary metabolites serve: (i) as competitive weapons used against other bacteria, fungi, amoebae, plants, insects, and large animals; (ii) as metal transporting agents; (iii) as agents of symbiosis between microbes and plants, nematodes, insects, and higher animals; (iv) as sexual hormones; and (v) as differentiation effectors. Although antibiotics are not obligatory for sporulation, some secondary metabolites (including antibiotics) stimulate spore formation and inhibit or stimulate germination. Formation of secondary metabolites and spores are regulated by similar factors. This similarity could insure secondary metabolite production during sporulation. Thus the secondary metabolite can: (i) slow down germination of spores until a less competitive environment and more favorable conditions for growth exist; (ii) protect the dormant or initiated spore from consumption by amoebae; or (iii) cleanse the immediate environment of competing microorganisms during germination.

The Earth's bounty: assessing and accessing soil microbial diversity

The study of microbial diversity represents a major opportunity for advances in biology and biotechnology. Recent progress in molecular microbial ecology shows that the extent of microbial diversity in nature is far greater than previously thought. Here, we discuss methods to analyse microorganisms from natural environments without culturing them and new approaches for gaining access to the genetic and chemical resources of these microorganisms.

Insecticidal, anti-juvenile hormone, and fungicidal activities of organic extracts from different Penicillium species and their isolated active components

Organic extracts from mycelium and culture broth of 21 Penicillium isolates have been tested for insecticidal, insect anti-juvenile hormone (anti-JH), and antifungal activities. Culture broth extracts were the most active, mainly against insects; nearly 25% of them have shown high entomotoxicity (100% mortality at 100 microg/cm(2)). A strong in vivo anti-JH activity against Oncopeltus fasciatus Dallas was detected in the culture broth extracts from P. brevicompactum P79 and P88 isolates. The two new natural products isolated from P79, N-(2-methyl-3-oxodec-8-enoyl)-2-pyrroline (1) and 2-hept-5-enyl-3-methyl-4-oxo-6,7,8,8a-tetrahydro-4H-pyrrolo[2,1-b]-1, 3-oxazine (2), possessed anti-JH and insecticidal activity, respectively, against O. fasciatus. Synthesized natural compound 1 has shown an ED(50) of 0.7 microg/nymph when assayed on newly molted fourth-instar nymphs of O. fasciatus. Promising biological activities have also been detected in the synthetic precursors.

Novel screen methodologies for identification of new microbial metabolites with pharmacological activity

Micro-organisms continue to provide an important source of chemical diversity for the discovery of compounds with new biological activities. Microbial metabolites discovered recently using assays to detect compounds with potential pharmacological utility are surveyed and found to represent an extensive range of structural types produced by a wide variety of organisms. Assays used for screening samples produced by microbial processes must be robust, sensitive and specific and able to operate above a background of potential interferences from a number of sources. Discovery assays currently in use fall into three main categories cell-based, receptor-ligand interaction and enzyme inhibition assays. Trends in the use of these assays and new developments in assay technology applicable to the screening of microbial samples are examined with particular reference to the high throughput screening environment. For microbial screening to be a competitive route to new drug leads, the disciplines involved must be engineered into a seamlessly integrated process to deliver novel compounds with the required biological properties rapidly.

Rapid analysis of antibiotic-containing mixtures from fermentation broths by using liquid chromatography-electrospray ionization-mass spectrometry and matrix-assisted laser desorption ionization-time-of-flight-mass spectrometry

A crucial step in the isolation of antibiotic substances is establishing whether or not the isolated material represents a new chemical entity. Because of the importance of molecular weight to this process-known as dereplication-mass spectrometry has traditionally played an active role. In this communication a strategy for utilizing liquid chromatography-mass spectrometry (LC/MS) for novelty assessment is described. Crude extracts (20-50 µg) are chromatographed by conventional bore high-performance liquid chromatography (1 mL/min) after which a postcolumn split to divert roughly one-tenth of the sample to the mass spectrometer for molecular weight determination by electrospray ionization (ESI) mass spectrometry. The majority of the effluent is sent to a UV detector and ultimately collected as 1-min fractions for biological testing. As a secondary confirmation of molecular weight, an aliquot of each fraction (< 5%) is taken for analysis by matrix-assisted laser desorption ionization (MALDI). The improved efficiency of this approach over more traditional schemes utilizing off-line fraction collection and conventional ionization methods can be explained by several factors. First, the superior sensitivity of ESI and MALDI means that less material is required for successful analysis. Second, on-line LC/MS optimizes the efficiency of sample transfer and saves both time and labor. Furthermore, the concentration dependence of ESI allows a majority of the material injected for LC/MS to be recovered for biological testing without compromising the signal available for molecular weight determination. As a validation of the above method, crude extracts containing two well-characterized antibiotics-teicoplanin and phenelfamycin-were examined. Results from these analyses are presented along with data from the analysis of a potent unknown antifungal sample.

Growth and cyclosporin A production by an indigenously isolated strain of Tolypocladium inflatum

A fungal culture isolated from a local soil sample which showed antifungal activity and produced cyclosporin A, was identified as Tolypocladium inflatum. The culture grew best in a medium containing 1% maltose (pH 5-6) when inoculated with a one-day-old inoculum at 2% (V/V) concentration. Under batch fermentation conditions, growth and cyclosporin A production were better in complex media (24.6 g biomass and 205 mg cyclosporin A per liter) in comparison with synthetic media (6.84 g biomass and 35 mg cyclosporin A per liter). While addition of peptone increased culture growth (high biomass yield), supplementation with casein acid hydrolyzate favored cyclosporin A production.

High-performance liquid chromatography comparison of supercritical-fluid extraction and solvent extraction of microbial fermentation products

The use of supercritical fluids for the extraction of biologically active compounds from the biomass of microbial fermentations has been compared with extraction using the organic solvents methanol and dichloromethane. Compounds representing a range of structural types were selected for investigation. All the extracts obtained were examined using reversed-phase high-performance liquid chromatography. The extractability of metabolites using unmodified and methanol-modified supercritical-fluid carbon dioxide was examined in particular detail for six microbial metabolites: chaetoglobosin A, mycolutein, luteoreticulin, 7,8-dihydro-7,8-epoxy-1-hydroxy-3-hydroxymethyl-xanthone-8-carboxyl ic acid methyl ester, sydowinin B and elaiophylin. The extraction strength of supercritical-fluid carbon dioxide alone appeared to be lower than that of dichloromethane. All the components of interest that were extractable with dichloromethane and methanol were also extractable with methanol-modified carbon dioxide.

The search for novel microbial fine chemicals, agrochemicals and biopharmaceuticals

An ever-increasing number of fine chemicals and enzymes is now produced based on microbial biotechnology. Microbial products generally display desired chirality, are biodegradable and are produced from renewable (agro)-substrates. Bioconversion reactions, based on the use of (immobilised) biocatalysts (cell or enzymes), yield interesting regio- and enantioselective molecules under mild reaction conditions, starting from racemic precursors. Furthermore these bioprocesses have a positive environmental impact. Ingenious screening procedures for novel microbial primary and secondary metabolites, bioactive peptides, proteins and enzymes reveal that only the tip of the iceberg has been explored. Examples of such novel microbial products pertain to enzymes, enzyme-inhibitors, biopolysaccharides, bio-plastics, bioactive peptides, bacteriocins, targeted toxins, alkaloids, steroids, immunomodulators, vaccines, antibiotics and lantibiotics, biopesticides, vitamins and related growth factors, amino acids and specialty sugars, polyols and organic acids, biomagnets, bioflavours and biopigments. Several trends are discussed which are now in vogue to detect novel useful compounds from microbes. Examples are given of those microbial metabolites and enzymes, which have attracted industrial interest.

Mechanistic studies and biological activity of bioxalomycin alpha 2, a novel antibiotic produced by Streptomyces viridodiastaticus subsp. "litoralis" LL-31F508

The bioxalomycins, a novel complex of broad-spectrum antibiotics, were isolated from fermentations of Streptomyces viridodiastaticus subsp. "litoralis" LL-31F508. Bioxalomycin alpha 2, the major component of this complex, exhibited antibacterial activity. The MICs ranged from < or = 0.002 to 0.008 micrograms/ml for gram-positive organisms and from 0.50 to 4 micrograms/ml for gram-negative organisms. Bioxalomycin alpha 2 was found to be bactericidal and to inhibit bacterial DNA synthesis preferentially. Bioxalomycin alpha 2 protected mice from a lethal challenge with Staphylococcus aureus Smith. The 50% effective dose of bioxalomycin alpha 2 administered orally was 10 times greater than that when the drug was given subcutaneously or intravenously. These data suggest a stability or bioavailability problem when the compound is administered orally.