Actinomadura algeriensis sp. nov., an actinobacterium isolated from Saharan soil

A New Saharan Strain of Streptomyces sp. GSB-11 Produces Maculosin and N-acetyltyramine Active Against Multidrug-Resistant Pathogenic Bacteria

Multi-resistant bacterial pathogens are a major public health problem for treating nosocomial infections owing to their high resistance to antibiotics. The objective of this research was to characterize the bioactive molecules secreted by a novel moderately halophilic actinobacterium strain, designated GSB-11, exhibiting a strong antagonistic activity against several multidrug-resistant pathogenic bacteria. This potential strain was identified by phenotypic, genotypic (16S rRNA), and phylogenetic analyses. GSB-11 was related to "Streptomyces acrimycini" NBRC 12736 ^T with 99.59% similarity. Molecular screening by PCR assay demonstrated that the strain possesses two biosynthetic genes coding for NRPS and PKS-II. Two active compounds GSB11-6 and GSB11-7 were extracted from the cell-free culture supernatant of Bennett medium and purified using reversed-phase HPLC. According to spectrometric (mass spectrum) and spectroscopic (¹H NMR, ¹³C NMR, ¹H-¹H COSY, and ¹H-¹³C HMBC) spectra analyses, the compounds GSB11-6 and GSB11-7 were identified to be maculosin and N-acetyltyramine, respectively. Their minimum inhibitory concentrations (MIC) revealed interesting values against certain multidrug-resistant pathogenic bacteria. They were between 5 and 15 mg/mL for GSB11-6, 10 and 30 mg/mL for GSB11-7. To our best knowledge, this is the first study of these active substances isolated from "Streptomyces acrimycini" showing an interesting antibacterial activity. Therefore, these essential compounds could be candidates for future research against multidrug-resistant bacteria.

specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data

BACKGROUND

Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3 ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.

RESULTS

We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.

CONCLUSIONS

specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.

Free Radicals and Actinobacteria as a Misexplored Goldmine of Antioxidant Compounds

Free radicals are highly reactive unstable molecules, which can be synthesized in different ways, considered harmful and threatening to humans; these chemical species have free traffic throughout the human body, interacting with biological molecules and human body organ tissues. The interaction between free radicals and biological molecules is the main factor for disease development or pre-existing disease symptoms aggravation. Antioxidants are chemical compounds able to donate electric charge to stabilize molecules such as free radicals. Recent studies have proved the benefits of antioxidants intake in health improvement. In this way, the search for natural sources of antioxidants has become an ascending trend. In this field, the microbial sources are considered poorly explored compared to the numerous amount of other compounds obtained from them, especially from Actinobacteria. The searched literature about Actinobacteria highlights an important capacity of producing natural antioxidants; however, there is a lack of in vivo studies of these isolated compounds. In this review, we gathered information that supports our point of view that Actinobacteria is a truly renewable and superficially explored source of natural antioxidants. Furthermore, our purpose is also to point this limitation and stimulate more researches in this area.

Actinobacteria Derived from Algerian Ecosystems as a Prominent Source of Antimicrobial Molecules

Actinobacteria, in particular "rare actinobacteria" isolated from extreme ecosystems, remain the most inexhaustible source of novel antimicrobials, offering a chance to discover new bioactive metabolites. This is the first overview on actinobacteria isolated in Algeria since 2002 to date with the aim to present their potential in producing bioactive secondary metabolites. Twenty-nine new species and one novel genus have been isolated, mainly from the Saharan soil and palm groves, where 37.93% of the most abundant genera belong to Saccharothrix and Actinopolyspora. Several of these strains were found to produce antibiotics and antifungal metabolites, including 17 new molecules among the 50 structures reported, and some of these antibacterial metabolites have shown interesting antitumor activities. A series of approaches used to enhance the production of bioactive compounds is also presented as the manipulation of culture media by both classical methods and modeling designs through statistical strategies and the associations with diverse organisms and strains. Focusing on the Algerian natural sources of antimicrobial metabolites, this work is a representative example of the potential of a closely combined study on biology and chemistry of natural products.

Actinomadura barringtoniae sp. nov., an endophytic actinomycete isolated from the roots of Barringtonia acutangula (L.) Gaertn

A novel actinomycete strain, designated GKU 128^T, isolated from the roots of an Indian oak tree [Barringtonia acutangula (L.) Gaertn.] at Khao Khitchakut district, Chantaburi province, Thailand, was characterized by using a polyphasic approach. The strain formed a branched substrate and aerial mycelia which differentiated into straight to flexuous chains of smooth-ornamented spores. Analysis of the cell wall revealed the presence of meso-diaminopimelic acid and N-acetylmuramic acid in the peptidoglycan. The whole-cell sugars were glucose, madurose, mannose, rhamnose and ribose. Mycolic acids were absent. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside. The predominant menaquinones were MK-9(H6), MK-9(H8), MK-9(H0) and MK-9(H4). The major fatty acids were C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). The genomic DNA G+C content was 70.5 mol%. Based on 16S rRNA gene sequence analysis, strain GKU 128^T was closely related to the type strains of Actinomadura nitritigenes NBRC 15918^T (99.2 % sequence similarity) and Actinomadura fibrosa JCM 9371^T (98.7 %). The levels of DNA-DNA relatedness between strain GKU 128^T and the closely related type species were less than 19 %. On the basis of phenotypic and genotypic characteristics, strain GKU 128^T could be distinguished from its closely related type strains and represents a novel species of the genus Actinomadura, for which the name Actinomadura barringtoniae sp. nov. (=TBRC 7225^T=NBRC 113074^T) is proposed.

Actinomadura alkaliterrae sp. nov., isolated from an alkaline soil

A polyphasic study was undertaken to establish the taxonomic status of an Actinomadura strain isolated from the margin of a saline, alkaline lake in Central Anatolia, Turkey. Strain D310AT^T was shown to have chemotaxonomic, cultural and morphological properties consistent with its classification in the genus Actinomadura such as hooked or irregular spiral spore chains, meso-diaminopimelic acid as the major cell wall diaminopimelic acid, and diphosphatidylglycerol and phosphatidylinositol as major polar lipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain D310AT^T is closely, albeit loosely, associated with Actinomadura darangshiensis DLS-70^T with 97.2% sequence similarity, but was readily separated from the latter using diverse phenotypic properties. Consequently, the isolate is considered to represent a new species of Actinomadura for which the name Actinomadura alkaliterrae sp. nov. is proposed, with the type strain D310AT^T (=DSM 101185^T = KCTC 39657^T).