Mining Indonesian Microbial Biodiversity for Novel Natural Compounds by a Combined Genome Mining and Molecular Networking Approach.

Indonesia is one of the most biodiverse countries in the world and a promising resource for novel natural compound producers. Actinomycetes produce about two thirds of all clinically used antibiotics. Thus, exploiting Indonesia's microbial diversity for actinomycetes may lead to the discovery of novel antibiotics. A total of 422 actinomycete strains were isolated from three different unique areas in Indonesia and tested for their antimicrobial activity. Nine potent bioactive strains were prioritized for further drug screening approaches. The nine strains were cultivated in different solid and liquid media, and a combination of genome mining analysis and mass spectrometry (MS)-based molecular networking was employed to identify potential novel compounds. By correlating secondary metabolite gene cluster data with MS-based molecular networking results, we identified several gene cluster-encoded biosynthetic products from the nine strains, including naphthyridinomycin, amicetin, echinomycin, tirandamycin, antimycin, and desferrioxamine B. Moreover, 16 putative ion clusters and numerous gene clusters were detected that could not be associated with any known compound, indicating that the strains can produce novel secondary metabolites. Our results demonstrate that sampling of actinomycetes from unique and biodiversity-rich habitats, such as Indonesia, along with a combination of gene cluster networking and molecular networking approaches, accelerates natural product identification.

Applications and Restrictions of Integrated Genomic and Metabolomic Screening: An Accelerator for Drug Discovery from Actinomycetes?

Since the golden age of antibiotics in the 1950s and 1960s actinomycetes have been the most prolific source for bioactive natural products. However, the number of discoveries of new bioactive compounds decreases since decades. New procedures (e.g., activating strategies or innovative fermentation techniques) were developed to enhance the productivity of actinomycetes. Nevertheless, compound identification remains challenging among others due to high rediscovery rates. Rapid and cheap genome sequencing as well as the advent of bioinformatical analysis tools for biosynthetic gene cluster identification in combination with mass spectrometry-based molecular networking facilitated the tedious process of dereplication. In recent years several studies have been dedicated to accessing the biosynthetic potential of Actinomyces species, especially streptomycetes, by using integrated genomic and metabolomic screening in order to boost the discovery rate of new antibiotics. This review aims to present the various possible applications of this approach as well as the newly discovered molecules, covering studies between 2014 and 2021. Finally, the effectiveness of this approach with regard to find new bioactive agents from actinomycetes will be evaluated.

Indolizidines from Actinomycetes: An Overview of Producers, Biosynthesis and Bioactivities.

Indolizidines have long been recognized for their valuable bioactivities, their common feature being a bicyclic structure connected via a nitrogen atom. Traditionally, plants have been identified as the primary producers. However, recent discoveries have revealed that certain bacterial strains belonging to the genus of actinomycetes also possess the ability to synthesize various indolizidine-based compounds. Among these strains, Streptomyces sp. HNA39, Saccharopolyspora sp. RL78, and Streptomyces NCIB 11649 have been identified as producers of cyclizidines, characterized by their distinctive cyclopropyl moiety. Additionally, Streptomyces griseus OS-3601 synthesizes a unique class of indolizidine derivatives known as iminimycins, distinguished by their rare imine-cation structure. Protoplast fusion of a Streptomyces griseus strain with Streptomyces tenjimariensis resulted in a new indolizidine named indolizomycin. This review aims to provide an overview of known bacterial indolizidine producers, summarize current knowledge regarding the biosynthesis of cyclizidines and iminimycins, and assess their respective bioactivities.

Postural motion perception during vestibular stimulation depends on the motion perception threshold in persistent postural-perceptual dizziness.

Patients with persistent postural-perceptual dizziness (PPPD) perceive postural instability larger than the observed sway. It is unknown whether the concept of postural misperception prevails during vestibular stimulation and whether it may account for the unsteadiness patients complain during body movements. We tested the hypothesis of an abnormal sensory-perceptual scaling mechanism in PPPD by recording objective, perceived, and the reproduced postural sway under various standing conditions, modulating visual and proprioceptive input, by binaural galvanic vestibular stimulation (GVS). We related postural sway speed to individual vestibular motion perceptional thresholds and disease-related PPPD questionnaires in 32 patients and 28 age-matched healthy control subjects (HC). All participants showed normal vestibular function tests on quantitative testing at the time of enrollment. The perception threshold of GVS was lower in patients. Compared to HC, patients showed and perceived larger sway on the firm platform. With GVS, posturo-perceptual ratios did not show group differences. The ratio of reproduced to real postural sway showed no group differences indicating normal postural sway perception during vestibular stimulation. Noticeably, only in patients, reproduced postural instability became larger with lower individual thresholds of vestibular motion detection. We conclude that posturo-perceptual (metacognitive) scaling of postural control seems to be largely preserved in PPPD during GVS. Vestibular stimulation does not destabilize patients more than HC, even in challenging postural conditions. Low individual thresholds of vestibular motion perception seem to facilitate instability and postural misperception on solid grounds. This conclusion is important for an effective physical therapy with vestibular exercises in PPPD.

Visual and vestibular motion perception in persistent postural-perceptual dizziness (PPPD).

Persistent postural-perceptual dizziness (PPPD) is a chronic disorder of perceived unsteadiness. Symptoms can be exacerbated in visually complex stationary or moving environment. Visual dependence and increased motion sensitivity are predictors for PPPD but its pathophysiology remains unknown. We hypothesized an abnormal sensory-perceptual scaling mechanism in PPPD and tested visual- and vestibular perceptional thresholds in 32 patients and 28 age-matched healthy control subjects (HC). All participants showed normal vestibular function tests on quantitative testing. Visual motion coherence thresholds were assessed by random dot kinetomatograms. Vestibular perceptional thresholds of egomotion were assessed by binaural galvanic vestibular stimulation (GVS) and passive chair rotation around an earth-vertical axis. Chair rotation trials were contrasted with no-motion (sham) stimulus trials. Mean thresholds of visual motion perception were higher in patients compared to HC. The perception threshold of GVS was lower in patients but the threshold of correctly perceived egomotion during chair rotation did not differ. Interestingly, the number of trials with correct perception in the no-motion condition increased with the threshold of correct responses for rotatory egomotion in patients. Unlike expected, PPPD patients required more coherently moving random dots than HC to perceive visual motion. A poorer complex visual motion recognition, e.g., traffic visual stimuli, may increase anxiety and levels of uncertainty as visuomotor reactions might occur delayed. The vestibular rotatory perception threshold predicted the probability of making false assignments in the sham condition in PPPD, i.e., patients who readily recognize the correct egomotion direction are prone to perceive egomotion in the no-motion condition. As this relation was not found in healthy subjects, it may reflect an abnormal sensory-perceptual scaling feature of PPPD.

Disclosing the Potential of the SARP-Type Regulator PapR2 for the Activation of Antibiotic Gene Clusters in Streptomycetes.

Streptomyces antibiotic regulatory protein (SARP) family regulators are well-known activators of antibiotic biosynthesis in streptomycetes. The respective genes occur in various types of antibiotic gene clusters encoding, e.g., for polyketides, ribosomally and non-ribosomally synthesized peptides, or ß-lactam antibiotics. We found that overexpression of the SARP-type regulator gene papR2 from Streptomyces pristinaespiralis in Streptomyces lividans leads to the activation of the silent undecylprodigiosin (Red) gene cluster. The activation happens upon the inducing function of PapR2, which takes over the regulatory role of RedD, the latter of which is the intrinsic SARP regulator of Red biosynthesis in S. lividans. Due to the broad abundance of SARP genes in different antibiotic gene clusters of various actinomycetes and the uniform activating principle of the encoded regulators, we suggest that this type of regulator is especially well suited to be used as an initiator of antibiotic biosynthesis in actinomycetes. Here, we report on a SARP-guided strategy to activate antibiotic gene clusters. As a proof of principle, we present the PapR2-driven activation of the amicetin/plicacetin gene cluster in the novel Indonesian strain isolate Streptomyces sp. SHP22-7.

Complete Genome Sequence of the Putative Phosphonate Producer Streptomyces sp. Strain I6, Isolated from Indonesian Mangrove Sediment.

Streptomyces sp. strain I6 is a novel strain isolated from an Indonesian mangrove sediment sample. Bioinformatic analysis of the genome sequence of Streptomyces sp. I6 revealed 23 biosynthetic gene clusters. One of them encodes the synthesis of a putative phosphonate secondary metabolite, a class of underexplored natural compounds with great pharmaceutical potential.