Chapter 3. Discovering natural products from myxobacteria with emphasis on rare producer strains in combination with improved analytical methods

Myxobacteria: biology and bioactive secondary metabolites

Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.

Discovery and Characterization of a Myxobacterial Lanthipeptide with Unique Biosynthetic Features and Anti-inflammatory Activity

The genomes of myxobacteria harbor a variety of biosynthetic gene clusters encoding numerous secondary metabolites, including ribosomally synthesized and post-translationally modified peptides (RiPPs) with diverse chemical structures and biological activities. However, the biosynthetic potential of RiPPs from myxobacteria remains barely explored. Herein, we report a novel myxobacteria lanthipeptide myxococin identified from Myxococcus fulvus. Myxococins represent the first example of lanthipeptides, of which the characteristic multiple thioether rings are installed by employing a Class II lanthipeptide synthetase MfuM and a Class I lanthipeptide cyclase MfuC in a cascaded way. Unprecedentedly, we biochemically characterized the first M61 family aminopeptidase MfuP involved in RiPP biosynthesis, demonstrating that MfuP showed the activity of an endopeptidase activity. MfuP is leader-independent but strictly selective for the multibridge structure of myxococin A and responsible for unwrapping two rings via amide bond hydrolysis, yielding myxococin B. Furthermore, the X-ray crystal structure of MfuP and structural analysis, including active-site mutations, are reported. Finally, myxococins are evaluated to exhibit anti-inflammatory activity in lipopolysaccharide-induced macrophages without detectable cytotoxicity.

Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials

Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid-20^th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.

Total synthesis of Myxoprincomide, a secondary metabolite from Myxococcus xanthus

Myxoprincomide, a secondary metabolite of the myxobacterium Myxococcus xanthus DK 1622, is synthesised for the first time. The central, unusual α-ketoamide is generated at the end of the synthesis to avoid side reactions during the synthesis of this rather reactive subunit. Nevertheless, the synthetic natural product is obtained as an isomeric mixture. Detailed analytical investigations show that the identical isomeric mixture is found in the isolated natural product.

Corallococcus soli sp. Nov., a Soil Myxobacterium Isolated from Subtropical Climate, Chalus County, Iran, and Its Potential to Produce Secondary Metabolites

A novel myxobacterial strain ZKHCc1 1396^T was isolated in 2017 from a soil sample collected along Chalus Road connecting Tehran and Mazandaran, Iran. It was a Gram-negative, rod-shaped bacterial strain that displayed the general features of Corallococcus, including gliding and fruiting body formation on agar and microbial lytic activity. Strain ZKHCc1 1396^T was characterized as an aerobic, mesophilic, and chemoheterotrophic bacterium resistant to many antibiotics. The major cellular fatty acids were branched-chain iso-C_17:0 2-OH, iso-C_15:0, iso-C_17:1, and iso-C_17:0. The strain showed the highest 16S rRNA gene sequence similarity to Corallococcusterminator CA054A^T (99.67%) and C. praedator CA031B^T (99.17%), and formed a novel branch both in the 16S rRNA gene sequence and phylogenomic tree. The genome size was 9,437,609 bp, with a DNA G + C content of 69.8 mol%. The strain had an average nucleotide identity (ANI) value lower than the species cut-off (95%), and with the digital DNA–DNA hybridization (dDDH) below the 70% threshold compared to the closest type strains. Secondary metabolite and biosynthetic gene cluster analyses revealed the strain’s potential to produce novel compounds. Based on polyphasic taxonomic characterization, we propose that strain ZKHCc1 1396^T represents a novel species, Corallococcus soli sp. nov. (NCCB 100659^T = CIP 111634^T).

Methods for Identifying Microbial Natural Product Compounds that Target Kinetoplastid RNA Structural Motifs by Homology and De Novo Modeled 18S rRNA

The development of novel anti-infectives against Kinetoplastids pathogens targeting proteins is a big problem occasioned by the antigenic variation in these parasites. This is also a global concern due to the zoonosis of these parasites, as they infect both humans and animals. Therefore, we need not only to create novel antibiotics, but also to speed up the development pipeline for these antibiotics. This may be achieved by using novel drug targets for Kinetoplastids drug discovery. In this study, we focused our attention on motifs of rRNA molecules that have been created using homology modeling. The RNA is the most ambiguous biopolymer in the kinetoplatid, which carries many different functions. For instance, tRNAs, rRNAs, and mRNAs are essential for gene expression both in the pro-and eukaryotes. However, all these types of RNAs have sequences with unique 3D structures that are specific for kinetoplastids only and can be used to shut down essential biochemical processes in kinetoplastids only. All these features make RNA very potent targets for antibacterial drug development. Here, we combine in silico methods combined with both computational biology and structure prediction tools to address our hypothesis. In this study, we outline a systematic approach for identifying kinetoplastid rRNA-ligand interactions and, more specifically, techniques that can be used to identify small molecules that target particular RNA. The high-resolution optimized model structures of these kineoplastids were generated using RNA 123, where all the stereochemical conflicts were solved and energies minimized to attain the best biological qualities. The high-resolution optimized model's structures of these kinetoplastids were generated using RNA 123 where all the stereochemical conflicts were solved and energies minimized to attain the best biological qualities. These models were further analyzed to give their docking assessment reliability. Docking strategies, virtual screening, and fishing approaches successfully recognized novel and myriad macromolecular targets for the myxobacterial natural products with high binding affinities to exploit the unmet therapeutic needs. We demonstrate a sensible exploitation of virtual screening strategies to 18S rRNA using natural products interfaced with classical maximization of their efficacy in phamacognosy strategies that are well established. Integration of these virtual screening strategies in natural products chemistry and biochemistry research will spur the development of potential interventions to these tropical neglected diseases.

Synthesis of New Cyclopeptide Analogues of the Miuraenamides

INTRODUCTION

Miuraenamides belong to natural marine compounds with interesting biological properties.

MATERIALS AND METHODS

Miuraenamides initiate polymerization of monomeric actin and therefore show high cytotoxicity by influencing the cytoskeleton. New derivatives of the miuraenamides have been synthesized containing an N-methylated amide bond instead of the more easily hydrolysable ester in the natural products.

RESULTS

Incorporation of an aromatic side chain onto the C-terminal amino acid of the tripeptide fragment also led to highly active new miuraenamides.

CONCLUSION

In this study, we showed that the ester bond of the natural product miuraenamide can be replaced by an N-methyl amide. The yields in the cyclization step were high and generally much better than with the corresponding esters. On the other hand, the biological activity of the new amide analogs was lower compared to the natural products, but the activity could significantly be increased by incorporation of a p-nitrophenyl group at the C-terminus of the peptide fragment.

Bioprospecting of indigenous myxobacteria from Iran and potential of Cystobacter as a source of anti-MDR compounds

Drug resistance is a critical issue in future clinical treatment. Methicillin-resistant Staphylococcus aureus (MRSA) is among the pathogens that need indispensable drug-discovery efforts. The myxobacteria are a unique group of bacteria that have recently been regarded for their potency to produce new drugs with high chemical diversity and unusual mode of actions. The present study was conducted to isolate and screen myxobacteria for the first time from Iran habitats and evaluate their antibacterial activity against the multidrug-resistant strain of S. aureus. Out of 62 soil and rotten plant samples, 51 myxobacteria were isolated. The isolates belonged to Myxococcus, Corallococcus, Pyxidicoccus, and Cystobacter genera based on morphology and 16S rRNA gene sequencing. Secondary metabolites of the selected strains were screened for activity on MDR strain with resistance to multiple antibiotic classes. The semi-purified fraction from Cystobacter sp. UTMC 4086 showed potent activity against MDR S. aureus with minimum inhibitory effect at 5 ≥ μg per mL compared with vancomycin (5 μg per mL) as well as no toxicity against Artemia salina. Hence, the strain Cystobacter sp. UTMC 4086 can be a valuable candidate for antibiotic discovery against MRSA and its metabolites can be subjected to further purification and analysis aimed at the identification of the effective chemical entity.

Complete Genome Sequence of the Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035

Myxobacteria are a source of unique metabolites, including corallopyronin A (CorA), a promising antibiotic agent in preclinical development for the treatment of filariasis. To investigate the production of CorA on the genetic level, we present the complete 9.6-Mb genome sequence of the CorA producer Corallococcus coralloides B035.

Myxobacteria are a source of unique metabolites, including corallopyronin A (CorA), a promising antibiotic agent in preclinical development for the treatment of filariasis. To investigate the production of CorA on the genetic level, we present the complete 9.6-Mb genome sequence of the CorA producer Corallococcus coralloides B035.

Simulacricoccus ruber gen. nov., sp. nov., a microaerotolerant, non-fruiting, myxospore-forming soil myxobacterium and emended description of the family Myxococcaceae

A non-fruiting group of myxobacteria was previously speculated to exist in nature based on metagenomics data containing uncultured members of the order Myxococcales. Here, we describe a myxobacterial strain, designated MCy10636^T, which was isolated from a German soil sample collected in 2013. It exhibits swarming characteristics but atypically produces myxospores in the absence of fruiting bodies. The novel strain stains Gram-negative and Congo-red-negative and is characterized mesophilic, neutrophilic, chemoheterotrophic and microaerotolerant. Branched-chain fatty acids are the predominant cellular fatty acids over the straight-chain type, and contain the major fatty acids iso-C17 : 0 2-OH, C16 : 1, iso-C17 : 0 and iso-C15 : 0. Based on blastn results, the 16S rRNA gene sequence reveals similarity (97 %) to Aggregicoccus edonensis MCy1366^T, (97 %) Myxococcus macrosporus DSM 14697^T, (96 %) Corallococcus coralloides DSM2259^T and Corallococcus exiguus Cc e167^T. Phylogenetic analysis showed a novel lineage of MCy10636^T in the family Myxococcaceae, suborder Cystobacterineae. Based on polyphasic taxonomic characterization, we propose that this unusual, non-fruiting, myxospore-forming and microaerotolerant myxobacterial strain, MCy10636^T, represents a novel genus and species, Simulacricoccus ruber gen. nov., sp. nov. (DSM 106554^T=NCCB 100651^T).

Vitiosangium cumulatum gen. nov., sp. nov. and Vitiosangium subalbum sp. nov., soil myxobacteria, and emended descriptions of the genera Archangium and Angiococcus, and of the family Cystobacteraceae

Bacterial strains MCy10943T and MCy10944T were isolated in 2014 from dried Nepalese soil samples collected in 2013 from Phukot, Kalikot, Western Nepal, and Godawari, Lalitpur, Central Nepal. The novel organisms showed typical myxobacterial growth characteristics, which include swarming colony and fruiting body formation on solid surfaces, and a predatory ability to lyse micro-organisms. The strains were aerobic, mesophilic, chemoheterotrophic and showed resistance to various antibiotics. The major cellular fatty acids common to both organisms were C17 : 0 2-OH, iso-C15 : 0, C16 : 1 and iso-C17 : 0. The G+C content of the genomic DNA was 72-75 mol%. Phylogenetic analysis showed that the strains belong to the family Cystobacteraceae, suborder Cystobacterineae, order Myxococcales. The 16S rRNA gene sequences of both strains showed 97-98 % similarity to Archangium gephyra DSM 2261T andCystobacter violaceus DSM 14727T, and 96.7-97 % to Cystobacter fuscus DSM 2262T and Angiococcus disciformis DSM 52716T. Polyphasic taxonomic characterization suggested that strains MCy10943T and MCy10944T represent two distinct species of a new genus, for which the names Vitiosangium cumulatum gen. nov., sp. nov. and Vitiosangium subalbum sp. nov. are proposed. The type strain of Vitiosangium cumulatum is MCy10943T (=DSM 102952T=NCCB 100600T) while that for Vitiosangium subalbum is MCy10944T (=DSM 102953T=NCCB 100601T). In addition, emended descriptions of the genera Archangium and Angiococcus, and of the family Cystobacteraceaeare provided.

Molecular and functional characterization of myxobacteria isolated from soil in India

This study reports the isolation of myxobacteria from soil collected from plains in north India. Based on the morphology and 16S rDNA sequence, the isolated myxobacteria were identified as Corallococcus sp., Pyxidicoccus sp., Myxococcus sp., Cystobacter sp. and Archangium sp. The myxobacteria were functionally characterized to assess their ability to produce antibacterial and anticancer metabolites. The isolates were found to be functionally versatile as they produced extracellular bioactive molecules that exhibited high frequency of activities against Bacillus cereus, Mycobacterium smegmatis, Enterobacter cloacae and Pseudomonas syringae. The strains also showed cytotoxic activity against the human cancer cell lines of liver, pancreas, prostrate, bone and cervix. These results indicate the importance of isolating diverse strains of myxobacteria from unexplored habitats to find novel bioactive compounds. Moreover, the bioactive molecules explored in this study are predominantly hydrophilic compounds, obviating the limitations of solubility-related aspect of drug discovery.

Racemicystis crocea gen. nov., sp. nov., a soil myxobacterium in the family Polyangiaceae

A novel bacterial strain designated MSr9521T was isolated in 2014 from a soil sample collected in 1986 from the Philippines. The novel bacterium shows myxobacterial characteristics that include pseudoplasmodial swarming, fruiting body formation and predatory ability to lyse microorganisms. The strain is chemoheterotrophic, mesophilic and aerobic. Major fatty acids are C18:1, C17:1 2-OH and iso-C15:0, and also contains trace amounts of omega-3/-6 polyunsaturated fatty acids. The G+C content of the genomic DNA is 70.4 mol%. The 16S rRNA gene sequence shows 95-96 % closest similarity to Sorangium cellulosum DSM 14627T, Polyangium fumosum Pl fu5T, Jahnella thaxteri Pl t4T and Byssovorax cruenta By c2T. The molecular phylogenetic analysis shows that the novel isolate forms a novel branch in the family Polyangiaceae, suborder Sorangiineae. Polyphasic taxonomic characterization suggests that the strain MSr9521T represents a novel species of a new genus in the family Polyangiaceae, for which the name Racemicystis crocea gen. nov., sp. nov. is proposed. The type strain of Racemicystis crocea is MSr9521T (=DSM 100773T=NCCB 100574T).

Genome Analysis of the Fruiting Body-Forming Myxobacterium Chondromyces crocatus Reveals High Potential for Natural Product Biosynthesis

Here, we report the complete genome sequence of the type strain of the myxobacterial genus Chondromyces, Chondromyces crocatus Cm c5. It presents one of the largest prokaryotic genomes featuring a single circular chromosome and no plasmids. Analysis revealed an enlarged set of tRNA genes, along with reduced pressure on preferred codon usage compared to that of other bacterial genomes. The large coding capacity and the plethora of encoded secondary metabolite biosynthetic gene clusters are in line with the capability of Cm c5 to produce an arsenal of antibacterial, antifungal, and cytotoxic compounds. Known pathways of the ajudazol, chondramide, chondrochloren, crocacin, crocapeptin, and thuggacin compound families are complemented by many more natural compound biosynthetic gene clusters in the chromosome. Whole-genome comparison of the fruiting-body-forming type strain (Cm c5, DSM 14714) to an accustomed laboratory strain which has lost this ability (nonfruiting phenotype, Cm c5 fr-) revealed genetic changes in three loci. In addition to the low synteny found with the closest sequenced representative of the same family, Sorangium cellulosum, extensive genetic information duplication and broad application of eukaryotic-type signal transduction systems are hallmarks of this 11.3-Mbp prokaryotic genome.

Minicystis rosea gen. nov., sp. nov., a polyunsaturated fatty acid-rich and steroid-producing soil myxobacterium

A bacterial strain designated SBNa008(T) was isolated from a Philippine soil sample. It exhibited the general characteristics associated with myxobacteria, such as swarming of Gram-negative vegetative rod cells, fruiting body and myxospore formation and predatory behaviour in lysing micro-organisms. The novel strain was characterized as mesophilic, chemoheterotrophic and aerobic. The major fatty acids were C(20:4)ω6,9,12,15 all cis (arachidonic acid), iso-C(15 : 0), C(17 : 1) 2-OH and iso-C(15 : 0) dimethylacetal. Interestingly, SBNa008(T) contained diverse fatty acids belonging to the commercially valuable polyunsaturated omega-6 and omega-3 families, and a highly conjugated dihydroxylated C28 steroid. The G+C content of the genomic DNA was 67.3 mol%. The 16S rRNA gene sequence revealed 95-96% similarity to sequences derived from clones of uncultured bacteria and 94-95% similarity to cultured members of the suborder Sorangiineae. Phylogenetic analysis revealed that strain SBNa008(T) formed a novel lineage in the suborder Sorangiineae. Based on a polyphasic taxonomic characterization, we propose that strain SBNa008(T) represents a novel genus and species, Minicystis rosea gen. nov., sp. nov. The type strain of Minicystis rosea is SBNa008(T) ( =DSM 24000(T) =NCCB 100349(T)).

Vulgatibacter incomptus gen. nov., sp. nov. and Labilithrix luteola gen. nov., sp. nov., two myxobacteria isolated from soil in Yakushima Island, and the description of Vulgatibacteraceae fam. nov., Labilitrichaceae fam. nov. and Anaeromyxobacteraceae fam. nov

Two myxobacterial strains (designated B00001(T) and B00002(T)) were isolated from forest soil samples collected from Yakushima Island, Kagoshima, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains B00001(T) and B00002(T) respectively formed independent branches within the suborders Cystobacterineae and Sorangiineae and were most closely related to Cystobacter armeniaca DSM 14710(T) (90.4% similarity) and Byssovorax cruenta DSM 14553(T) (91.3%). Neither strain showed typical features of myxobacteria such as bacteriolytic action or fruiting body formation, but both had high DNA G+C contents (66.3-68.3 mol%). Swarming motility was observed in strain B00002(T) only. Cells of both strains were vegetative, chemoheterotrophic, mesophilic, strictly aerobic, Gram-negative, motile rods, and both strains exhibited esterase lipase (C8), leucine arylamidase, naphthol-AS-BI-phosphohydrolase and β-galactosidase activities. Strain B00001(T) contained MK-7 as the predominant respiratory quinone and the major fatty acid was iso-C15:0. In contrast, strain B00002(T) contained MK-8 as the major cellular quinone and the major fatty acids were C16 : 1ω5c and iso-C17 : 0. Based on the phenotypic and genotypic data presented, strains B00001(T) and B00002(T) represent novel genera and species, for which we propose the names Vulgatibacter incomptus gen. nov., sp. nov. and Labilithrix luteola gen. nov., sp. nov., respectively. The type strains of Vulgatibacter incomptus and Labilithrix luteola are B00001(T) ( = NBRC 109945(T) = DSM 27710(T)) and B00002(T) ( = NBRC 109946(T) = DSM 27648(T)), respectively. The new genera are assigned to the new families Vulgatibacteraceae fam. nov. and Labilitrichaceae fam. nov., respectively. In addition, Anaeromyxobacteraceae fam. nov., is proposed to accommodate the genus Anaeromyxobacter, which is related to the genus Vulgatibacter.

Scrutinizing the scaffolds of marine biosynthetics from different source organisms: Gram-negative cultured bacterial products enter center stage

Compounds from macro marine organisms are presumed to owe their biosynthetic origins to associated microbial symbionts, although few definitive examples exist. An upsurge in the recent literature from 2012 to 2013 has shown that four compounds previously reported from macro marine organisms are in fact biosynthesized by non-photosynthetic Gram-negative bacteria (NPGNB). Structural parallels between compounds isolated from macro marine organisms and NPGNB producers form the basis of this review. Although less attention has been given to investigating the chemistry of NPGNB sources, there exists a significant list of structural parallels between NPGNB and macro marine organism-derived compounds. Alternatively, of the thousands of compounds isolated from Gram-positive actinomycetes, few structural parallels with macro marine organisms are known. A summary of small molecules isolated from marine NPGNB sources is presented, including compounds isolated from marine myxobacteria. From this assemblage of structural parallels and diverse chemical structures, it is hypothesized that the potential for the discovery of inspirational molecules from NPGNB sources is vast and that the recent spike in the literature of macro marine compounds owing their biosynthetic origin to NPGNB producers represents a turning point in the field.

Antimicrobial peptides from marine proteobacteria

After years of inadequate use and the emergence of multidrug resistant (MDR) strains, the efficiency of "classical" antibiotics has decreased significantly. New drugs to fight MDR strains are urgently needed. Bacteria hold much promise as a source of unusual bioactive metabolites. However, the potential of marine bacteria, except for Actinomycetes and Cyanobacteria, has been largely underexplored. In the past two decades, the structures of several antimicrobial compounds have been elucidated in marine Proteobacteria. Of these compounds, polyketides (PKs), synthesised by condensation of malonyl-coenzyme A and/or acetyl-coenzyme A, and non-ribosomal peptides (NRPs), obtained through the linkage of (unusual) amino acids, have recently generated particular interest. NRPs are good examples of naturally modified peptides. Here, we review and compile the data on the antimicrobial peptides isolated from marine Proteobacteria, especially NRPs.

Future potential for anti-infectives from bacteria - how to exploit biodiversity and genomic potential

The early stages of antibiotic development include the identification of novel hit compounds. Since actinomycetes and myxobacteria are still the most important natural sources of active metabolites, we provide an overview on these producers and discuss three of the most promising approaches toward finding novel anti-infectives from microorganisms. These are defined as the use of biodiversity to find novel producers, the variation of culture conditions and induction of silent genes, and the exploitation of the genomic potential of producers via "genome mining". Challenges that exist beyond compound discovery are outlined in the last section.

Discovery and biological activity of new chondramides from Chondromyces sp

Myxobacteria have proven to be highly valuable sources of natural products, as they produce a variety of secondary metabolites with unique structures and often new modes of action. In this study, high-content screening is demonstrated to be a convenient tool for bioactivity-guided isolation of natural products from crude bacterial extracts. By the application of focused, image-based screens we were able to identify over 30 novel chondramide derivatives from Chondromyces sp. MSr9030, some of which were present in only minute amounts. These cyclic depsipeptides were shown to target actin filaments with a similar binding mode to that of the mushroom toxin phalloidin. Fermentations of the myxobacterial strain were carried out under improved cultivation conditions, and supplementation of the culture broth with potassium bromide afforded the production of brominated analogues that are superior (in terms of biological activity) to all chondramides described to date. Initial biological profiling of 11 new derivatives in comparison to the reference compounds (chondramides A-C) showed that bromo-chondramide C3 and propionyl-bromo-chondramide C3 are the most active in cell-based studies, with GI₅₀ values on human cancer cell lines in the low nanomolar range. Given that these brominated C3 analogues were also less potent on noncancerous human cells (by a factor of 2 to 4 in comparison to cancer cell lines), our results can aid further structure-activity relationship-guided development of chondramides, either as molecular probes or pharmaceutical agents.

Aetheramides A and B, potent HIV-inhibitory depsipeptides from a myxobacterium of the new genus "Aetherobacter"

Aetheramides are structurally distinctive cyclic peptides isolated from a novel myxobacterial genus proposed to be termed "Aetherobacter". The structures were solved by a combination of NMR analyses, quantum mechanical calculations, and chemical derivatizations. Aetheramides which contain a unique polyketide moiety and two amino acid residues potently inhibited HIV-1 infection with IC(50) values of ~0.015 μM. Furthermore aetheramides showed cytostatic activity against human colon carcinoma (HCT-116) cells with IC(50) values of 0.11 μM.

Methods to optimize myxobacterial fermentations using off-gas analysis

Background

The influence of carbon dioxide and oxygen on microbial secondary metabolite producers and the maintenance of these two parameters at optimal levels have been studied extensively. Nevertheless, most studies have focussed on their influence on specific product formation and condition optimization of established processes. Considerably less attention has been paid to the influence of reduced or elevated carbon dioxide and oxygen levels on the overall metabolite profiles of the investigated organisms. The synergistic action of both gases has garnered even less attention.

Results

We show that the composition of the gas phase is highly important for the production of different metabolites and present a simple approach that enables the maintenance of defined concentrations of both O₂ and CO₂ during bioprocesses over broad concentration ranges with a minimal instrumental setup by using endogenously produced CO₂. The metabolite profiles of a myxobacterium belonging to the genus Chondromyces grown under various concentrations of CO₂ and O₂ showed considerable differences. Production of two unknown, highly cytotoxic compounds and one antimicrobial substance was found to increase depending on the gas composition. In addition, the observation of CO₂ and O₂ in the exhaust gas allowed optimization and control of production processes.

Conclusions

Myxobacteria are becoming increasingly important due to their potential for bioactive secondary metabolite production. Our studies show that the influence of different gas partial pressures should not be underestimated during screening processes for novel compounds and that our described method provides a simple tool to investigate this question.

Sandaracinus amylolyticus gen. nov., sp. nov., a starch-degrading soil myxobacterium, and description of Sandaracinaceae fam. nov

A novel starch-degrading myxobacterium designated NOSO-4T (new organism of the Sorangiineae strain 4) was isolated in 1995 from a soil sample containing plant residues, collected in Lucknow, Uttar Pradesh, India. The novel bacterium shows typical myxobacterial characteristics such as Gram-negative, rod-shaped vegetative cells, swarming colonies, fruiting body-like aggregates and bacteriolytic activity. The strain is mesophilic, strictly aerobic and chemoheterotrophic. Based on 16S rRNA gene sequences, NOSO-4T shows highest similarity (96.2 %) with the unidentified bacterial strain O29 (accession no. FN554397), isolated from leek (Allium porrum) rhizosphere, and to the myxobacteria Jahnella thaxteri (88.9 %) and Chondromyces pediculatus (88.5 %). Major fatty acids are C17 : 1 2-OH, C20 : 4ω6 (arachidonic acid), and the straight-chain fatty acids C17 : 0, C15 : 0 and C16 : 0. The genomic DNA G+C content of the novel isolate is 66.8 mol%. It is proposed that strain NOSO-4T represents a novel species in a new genus, i.e. Sandaracinus amylolyticus gen. nov., sp. nov., but also belongs to a new family, Sandaracinaceae fam. nov. The type strain of the type species, S. amylolyticus sp. nov., is NOSO-4T ( = DSM 53668T = NCCB 100362T).

p-hydroxyacetophenone amides from Cystobacter ferrugineus, strain Cb G35

A family of six novel p-hydroxyacetophenone amides, 1-6, was isolated from Cystobacter ferrugineus, strain Cb G35. Their structures were elucidated by ESI-TOF mass spectrometry and NMR spectroscopy. Feeding experiments with labeled [¹³C₉,¹⁵N]-tyrosine and [d₁₀]-leucine identified the biosynthetic precursors of 1.

A highly conjugated dihydroxylated C28 steroid from a myxobacterium

In the course of our search for novel secondary metabolites, the CHCl3-MeOH extract of the novel myxobacterial strain Sorangiineae SBNa008 was shown to be active against human SW480 colon adinocarcinoma cells. Bioassay-guided fractionation of the extract yielded a highly conjugated novel, sterol 9α,11α-dihydroxyergosta-4,6,8(14),22-tetraen-3-one, 1. The structure and the relative stereochemistry of 1 were established from interpretation of spectroscopic data and X-ray crystallography.

Fatty acid-related phylogeny of myxobacteria as an approach to discover polyunsaturated omega-3/6 Fatty acids

In an analysis of 47 aerobic myxobacterial strains, representing 19 genera in suborders Cystobacterineae, Nannocystineae, Sorangiineae, and a novel isolate, "Aetherobacter" SBSr008, an enormously diverse array of fatty acids (FAs) was found. The distribution of straight-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs) supports the reported clustering of strains in the phylogenetic tree based on 16S rRNA genes. This finding additionally allows the prediction and assignment of the novel isolate SBSr008 into its corresponding taxon. Sorangiineae predominantly contains larger amounts of SCFA (57 to 84%) than BCFA. On the other hand, Cystobacterineae exhibit significant BCFA content (53 to 90%), with the exception of the genus Stigmatella. In Nannocystineae, the ratio of BCFA and SCFA seems dependent on the taxonomic clade. Myxobacteria could also be identified and classified by using their specific and predominant FAs as biomarkers. Nannocystineae is remarkably unique among the suborders for its absence of hydroxy FAs. After the identification of arachidonic (AA) FA in Phaselicystidaceae, eight additional polyunsaturated fatty acids (PUFAs) belonging to the omega-6 and omega-3 families were discovered. Here we present a comprehensive report of FAs found in aerobic myxobacteria. Gliding bacteria belonging to Flexibacter and Herpetosiphon were chosen for comparative analysis to determine their FA profiles in relation to the myxobacteria.

Expanded phylogeny of myxobacteria and evidence for cultivation of the 'unculturables'

An expanded neighbour-joining tree of myxobacteria is presented based on the analysis of 16S rRNA gene sequences of 101 strains (including types) representing 3 suborders, 6 families, 20 genera, 46 species, and 12 other novel taxa. The distinctions amongst members of the three suborders (Sorangiineae, Cytobacterineae and Nannocystineae) are reaffirmed. The positions of anaerobic myxobacteria, novel groups (Pyxidicoccus and several Cystobacter species) in Cystobacterineae, the marine genera (Plesiocystis, Haliangium, Enhygromyxa), and two additional novel taxa ('Paraliomyxa miuraensis', brackish-water isolate) were together revealed for the first time. Changes in the nomenclature of several isolates (Polyangium vitellinum Pl vt1(T), Polyangium thaxteri Pl t3, Polyangium cellulosum, NOSO-1, NOCB-2, NOCB-4) are also highlighted. Suborders Sorangiineae and Nannocystineae hold great promise for novel strain discovery. In Sorangiineae, the new family Phaselicystidaceae, with a monotypic genus, was added. Nine additional novel taxa were discovered in this suborder for which new genera or even families may be erected in the near future. These taxa appear to represent the so-called viable but not culturable (VBNC) group of myxobacteria. Based on at least 4% phylogenetic distance, new clades were formed comprising of novel Nannocystineae and Sorangiineae isolates. Overall, the myxobacteria, on the basis of bracket distance, could be divided into 16 clusters, as supported by tree topology and a morphology-based approach.