Whole genome-based reclassification of several species of the genus Microbispora

The classification of Microbispora, a bacterial genus of significant ecological, agricultural, biotechnological, and clinical importance, has traditionally been carried out based on 16S rRNA gene sequences or phenotypic characteristics, which may lead to equivocal conclusions and it is not in line with the current standards. Moreover, some of the recent species descriptions have not been made using whole genome sequences (WGS), or when used, not all the species were included in the analyses. Consequently, some of the taxonomic conclusions drawn are equivocal, and therefore some currently accepted species should be synonymized. In this study, we revised the taxonomy of the genus Microbispora using digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values, and by reconstructing phylogenetic relationships using whole genome sequences. Based on the clear phylogenomic separations and on the sequence divergence values, we propose to elevate Microbispora rosea subsp. rosea and Microbispora rosea subsp. aerata to the species level, and therefore to create Microbispora aerata sp. nov. with JCM 3076T (= DSM 43176T = ATCC 15448T = IFO 14624T = NBRC 14624T = VKM Ac-1507T) as the type strain. Hence, with this proposition, the correct name for Microbispora rosea subsp. rosea is M. rosea. Furthermore, we propose to reclassify M. camponoti as a subspecies within M. bryophytorum. Consequently, we propose the creation of the following two subspecies: Microbispora bryophytorum subsp. bryophytorum subsp. nov. with DSM 46710T (= CGMCC 4.7138T = NEAU TX2-2T) as the type strain, and Microbispora bryophytorum subsp. camponoti subsp. nov., comb. nov. with DSM 2C-HV3T (= DSM 100527T = CGMCC 4.7281T) as the type strain. In addition, we propose to reinstate M. amethystogenes as an independent species and not as a M. rosea synonym, and reclassify "M. cellulosiformans" as a subspecies within M. amethystogenes. Hence, we propose the creation of the following two subspecies: Microbispora amethystogenes subsp. amethystogenes subsp. nov. with NBRC 101907T (= DSM 43164T = JCM 3021T = NRRL B-2637T) as the type strain, and Microbispora amethystogenes subsp. cellulosiformans subsp. nov., comb. nov. with Gxj-6T (= DSM 109712T = CGMCC 4.7605T) as the type strain. Lastly, we propose M. fusca NEAU-HEGS1-5T and "M. tritici" MT50T as later homotypic synonyms of M. triticiradicis NEAU-HRDPA2-9T.

Endophytic actinobacteria of Hymenachne amplexicaulis from the Brazilian Pantanal wetland produce compounds with antibacterial and antitumor activities

The increase in the number of deaths from infections caused by multidrug-resistant bacteria and cancer diseases highlights the need for new molecules with biological activity. Actinobacteria represent a potential source of new compounds, as these microorganisms have already produced a great diversity of clinically employed antibiotics. Endophytes from unexplored biomes, such as the Pantanal (the largest wetland in the world), can be a source of new molecules. Hymenachne amplexicaulis is among the unexplored native plants of the Pantanal in terms of its endophytic community. This plant is considered a weed in other countries due to its ability to adapt and compete with native plants, and there is evidence to suggest that the endophytic community of H. amplexicaulis plays an important role in this competitiveness. To explore its therapeutic potential, the present study isolated, identified (using partial sequence of the 16S rDNA) and bioprospected H. amplexicaulis endophytic actinobacteria. Ten isolates belonging to the genera Streptomyces, Microbispora, Leifsonia, and Verrucosispora were obtained from root fragments. The susceptibility profile of the isolates to the different classes of antibiotics was evaluated, with 80 % of the isolates showing resistance to the antibiotics Nalidixic Acid, Ampicillin, Chloramphenicol, Oxacillin, and Rifampicin. To assess antibacterial and antitumor activities, methanolic extracts were obtained by fermentation in SG culture medium at 36 °C at 180 rpm for 10 days. The extract produced from the S. albidoflavus CMRP4854 isolate was the only one to show activity against the Gram-negative bacterium Acinetobacter baumanii. Due to the great clinical importance of this pathogen and the difficulty in obtaining active compounds against it, the CMRP4854 isolate should be further investigated for the identification of active compounds and mode of action. We also emphasize the results obtained by the extract of the isolates Streptomyces albidoflavus CMRP4852 and Verrucosispora sp. CMRP4860 that presented antibacterial effect against Methicilin-resistant Staphylococcus aureus (MRSA) (MIC: 1.5 μg/mL and 13 μg/mL, respectively) and Vancomycin-resistant Enterococcus (VRE) (MIC: 40 μg/mL for both extracts). Extracts (200 μg/mL) of these two endophytes also showed selective cytotoxicity action against murine B16-F10 melanoma cells. However, the CMRP4852 extract also affected the density of normal cells. Due to these results, the crude extract of isolate CMRP4860 Verrucosispora sp., which was the only one that presented cytotoxicity and reduced cell density only in tumor cells, was selected for subsequent analysis involving scale-up fermentation of the CMRP4860 resulting in 9 fractions that were tested against both bacteria and tumor cells, with particular fractions showing promise and meriting further investigation. Taken together, the results of this study not only show for the first time that the endophytic community of H. amplexicaulis actinobacteria can produce secondary metabolites that potentially possess important antibacterial and cytotoxic properties, but also reinforce the pressing need to conserve biomes such as the Brazilian Pantanal.

Microbispora clausenae sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f

An endophytic actinobacterium, strain CLES2T, was discovered from the surface-sterilized stem of a Thai medicinal plant, Clausena excavala Burm. f., collected from the Phujong-Nayoa National Park, Ubon Ratchathani Province, Thailand. The results of a polyphasic taxonomic study identified this strain as a member of the genus Microbispora and a Gram-stain-positive, aerobic actinobacterium. It had well-developed substrate mycelia, which were non-motile and possessed paired spores. A phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this strain in the family Streptosporangiaceae, being most closely related to Microbispora bryophytorum NEAU-TX2-2T (99.4 %), Microbispora camponoti 2C-HV3T (99.2 %), Microbispora catharanthi CR1-09T (99.2 %) and Microbispora amethystogenes JCM 3021T and Microbispora fusca NEAU-HEGS1-5T (both at 99.1 %). The major cellular fatty acid of this strain was iso-C16 : 0 and major menaquinone was MK-9(H4). The polar lipid profile of strain CLES2T contained diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol and phosphatidylinositol dimannosides. These chemotaxonomic data confirmed the affiliation of strain CLES2T to the genus Microbispora. The DNA G+C content of this strain was 70 mol%. Digital DNA-DNA hybridization and average nucleotide identity blast values between strain CLES2T and M. catharanthi CR1-09T were 62.4 and 94.0 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain CLES2T from its closest species with valid names. The name proposed for the new species is Microbispora clausenae sp. nov. The type strain is CLES2T (=DSM 101759T=NRRL B-65340T).

A novel diterpene agent isolated from Microbispora hainanensis strain CSR-4 and its in vitro and in silico inhibition effects on acetylcholine esterase enzyme

An actinomycete strain CSR-4 was isolated from the rhizosphere soil of Zingiber montanum. Taxonomic characterization revealed strain CSR-4 was a member of the genus Microbispora. Whole-genome sequence analysis exhibited the highest average nucleotide identity (ANI) value (95.34%) and digital DNA–DNA hybridization (DDH) value (74.7%) between strain CSR-4 and the closest relative M. hainanensis DSM 45428^T, which was in line with the assignment to same species. In addition, a new diterpene compound, 2α-hydroxy-8(14), 15-pimaradien-17, 18-dioic acid, and nine known compounds were isolated from the ethyl acetate crude extract of fermentation broth. Interestingly, a new diterpene displayed the suppressive effect on the recombinant human acetylcholinesterase (rhAChE) enzymes (IC₅₀ 96.87 ± 2.31 μg/ml). In silico studies based on molecular docking and molecular dynamics (MD) simulations were performed to predict a binding mode of the new compound into the binding pocket of the rhAChE enzyme and revealed that some amino acids in the peripheral anions site (PAS), anionic subsite, oxyanion site and catalytic active site (CAS) of the rhAChE have interacted with the compound. Therefore, our new compound could be proposed as a potential active human AChE inhibitor. Moreover, the new compound can protect significantly the neuron cells (% neuron viability = 88.56 ± 5.19%) from oxidative stress induced by serum deprivation method at 1 ng/ml without both neurotoxicities on murine P19-derived neuron cells and cytotoxicity against Vero cells.

Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity

Actinobacteria are one of the most important and efficient groups of natural metabolite producers. The genus Streptomyces have been recognized as prolific producers of useful natural compounds as they produced more than half of the naturally-occurring antibiotics isolated to-date and continue as the primary source of new bioactive compounds. Lately, Streptomyces groups isolated from different environments produced the same types of compound, possibly due to frequent genetic exchanges between species. As a result, there is a dramatic increase in demand to look for new compounds which have pharmacological properties from another group of Actinobacteria, known as rare actinobacteria; which is isolated from special environments such as mangrove. Recently, mangrove ecosystem is becoming a hot spot for studies of bioactivities and the discovery of natural products. Many novel compounds discovered from the novel rare actinobacteria have been proven as potential new drugs in medical and pharmaceutical industries such as antibiotics, antimicrobials, antibacterials, anticancer, and antifungals. This review article highlights the latest studies on the discovery of natural compounds from the novel mangrove rare actinobacteria and provides insight on the impact of these findings.

Microbispora bryophytorum sp. nov., an actinomycete isolated from moss (Bryophyta)

A novel endophytic actinomycete, designated strain NEAU-TX2-2T, was isolated from moss and characterized using a polyphasic approach. The isolate was found to have morphological characteristics typical of the genus Microbispora . The isolate formed longitudinally paired spores on the tips of short sporophores that branched from aerial hyphae. Analysis of the 16S rRNA gene sequence supported the assignment of the novel strain to the genus Microbispora , and strain NEAU-TX2-2T exhibited 99.08 and 98.62 % gene sequence similarities to Microbispora amethystogenes JCM 3021T and Microbispora rosea subsp. rosea JCM 3006T, respectively. However two tree-making algorithms supported the position that strain NEAU-TX2-2T formed a distinct clade with M. rosea subsp. rosea JCM 3006T. A low level of DNA–DNA relatedness allowed the isolate to be differentiated from M. amethystogenes JCM 3021T and M. rosea subsp. rosea JCM 3006T. Moreover, strain NEAU-TX2-2T could also be distinguished from its closest phylogenetic relatives by morphological and physiological characteristics. Therefore, it is proposed that strain NEAU-TX2-2T represents a novel species of the genus Microbispora for which the name Microbispora bryophytorum sp. nov. is proposed. The type strain is NEAU-TX2-2T ( = CGMCC 4.7138T = DSM 46710T).