Desert Environments Facilitate Unique Evolution of Biosynthetic Potential in Streptomyces

Searching for new bioactive metabolites from the bacterial genus Streptomyces is a challenging task. Combined genomic tools and metabolomic screening of Streptomyces spp. native to extreme environments could be a promising strategy to discover novel compounds. While Streptomyces of desertic origin have been proposed as a source of new metabolites, their genome mining, phylogenetic analysis, and metabolite profiles to date are scarcely documented. Here, we hypothesized that Streptomyces species of desert environments have evolved with unique biosynthetic potential. To test this, along with an extensive characterization of biosynthetic potential of a desert isolate Streptomyces sp. SAJ15, we profiled phylogenetic relationships among the closest and previously reported Streptomyces of desert origin. Results revealed that Streptomyces strains of desert origin are closer to each other and relatively distinct from Streptomyces of other environments. The draft genome of strain SAJ15 was 8.2 Mb in size, which had 6972 predicted genes including 3097 genes encoding hypothetical proteins. Successive genome mining and phylogenetic analysis revealed the presence of putative novel biosynthetic gene clusters (BGCs) with low incidence in another Streptomyces. In addition, high-resolution metabolite profiling indicated the production of arylpolyene, terpenoid, and macrolide compounds in an optimized medium by strain SAJ15. The relative abundance of different BGCs in arid Streptomyces differed from the non-arid counterparts. Collectively, the results suggested a distinct evolution of desert Streptomyces with a unique biosynthetic potential.

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A Review on Mangrove Actinobacterial Diversity: The Roles of Streptomyces and Novel Species Discovery

Progress In Microbes & Molecular Biology ◽

10.36877/pmmb.a0000024 ◽

2019 ◽

Vol 2 (1) ◽

Author(s):

Jodi Woan-Fei Law ◽

Priyia Pusparajah ◽

Nurul-Syakima Ab Mutalib ◽

Sunny Hei Wong ◽

Bey-Hing Goh ◽

...

Keyword(s):

Life Cycle ◽

Significant Contribution ◽

Novel Species ◽

Bioactive Metabolites ◽

Streptomyces Species ◽

Genus Streptomyces ◽

Species Discovery ◽

Streptomyces Spp ◽

Antibiotic Drugs ◽

The World

In the class Actinobacteria, the renowned genus Streptomyces comprised of a group of uniquely complex bacteria that capable of synthesizing a great variety of bioactive metabolites. Streptomycetes are noted to possess several special qualities such as multicellular life cycle and large linearized chromosomes. The significant contribution of Streptomyces in microbial drug discovery as witnessed through the discovery of many important antibiotic drugs has undeniably encourage the exploration of these bacteria from different environments, especially the mangrove environments. This review emphasizes on the genus Streptomyces and reports on the diversity of actinobacterial population from mangroves at different regions of the world as well as discovery of mangrove-derived novel Streptomyces species. Overall, the research on diversity of Actinobacteria in the mangrove environments remains limited. A total of 19 novel Streptomyces spp. isolated from mangroves between the year 2009 - early 2019, notably from China, India, Malaysia, and Thailand. Hence, it will be worthwhile to encourage the study of these bacteria from mangroves of different locations.

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Draft Genome Sequences of Fungus Aspergillus calidoustus

Genome Announcements ◽

10.1128/genomea.00102-16 ◽

2016 ◽

Vol 4 (2) ◽

Cited By ~ 6

Author(s):

Fabian Horn ◽

Jörg Linde ◽

Derek J. Mattern ◽

Grit Walther ◽

Reinhard Guthke ◽

...

Keyword(s):

Secondary Metabolite ◽

Genome Sequence ◽

Functional Annotation ◽

Draft Genome ◽

Genome Mining ◽

Gene Clusters ◽

Draft Genome Sequence ◽

Genome Sequences

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504) . The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

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Angucycline-like Aromatic Polyketide from a Novel Streptomyces Species Reveals Freshwater Snail Physa acuta as Underexplored Reservoir for Antibiotic-Producing Actinomycetes

Antibiotics ◽

10.3390/antibiotics10010022 ◽

2020 ◽

Vol 10 (1) ◽

pp. 22

Author(s):

Nasim Safaei ◽

Yvonne Mast ◽

Michael Steinert ◽

Katharina Huber ◽

Boyke Bunk ◽

...

Keyword(s):

High Throughput Sequencing ◽

Genome Mining ◽

Freshwater Snail ◽

Whole Genome Sequence ◽

Phylogenomic Analysis ◽

Ionization Mass ◽

Gram Positive ◽

Streptomyces Species ◽

Genus Streptomyces ◽

Physa Acuta

Antibiotic producers have mainly been isolated from soil, which often has led to the rediscovery of known compounds. In this study, we identified the freshwater snail Physa acuta as an unexplored source for new antibiotic producers. The bacterial diversity associated with the snail was characterized by a metagenomic approach using cultivation-independent high-throughput sequencing. Although Actinobacteria represented only 2% of the bacterial community, the focus was laid on the isolation of the genus Streptomyces due to its potential to produce antibiotics. Three Streptomyces strains (7NS1, 7NS2 and 7NS3) were isolated from P. acuta, and the antimicrobial activity of the crude extracts were tested against a selection of Gram-positive and Gram-negative bacteria and fungi. 7NS3 showed the strongest activity against Gram-positive bacteria and, thus, was selected for genome sequencing and a phylogenomic analysis. 7NS3 represents a novel Streptomyces species, which was deposited as Streptomyces sp. DSM 110735 at the Leibniz Institute-German Collection of Microorganisms and Cell Cultures (DSMZ). Bioassay-guided high-performance liquid chromatography (HPLC) and high-resolution electrospray ionization-mass spectrometry (HR-ESI-MS) analyses of crude extract fractions resulted in the detection of four compounds, one of which matched the compound characteristics of emycin A, an angucycline-like aromatic polyketide. Genome mining studies based on the whole-genome sequence of 7NS3 resulted in the identification of a gene cluster potentially coding for emycin A biosynthesis. Our study demonstrates that freshwater snails like P. acuta can represent promising reservoirs for the isolation of new antibiotic-producing actinobacterial species.

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Future directions for the discovery of antibiotics from actinomycete bacteria

Emerging Topics in Life Sciences ◽

10.1042/etls20160014 ◽

2017 ◽

Vol 1 (1) ◽

pp. 1-12 ◽

Cited By ~ 8

Author(s):

Rebecca Devine ◽

Matthew I. Hutchings ◽

Neil A. Holmes

Keyword(s):

New Technologies ◽

Gene Clusters ◽

Biosynthetic Gene Clusters ◽

Future Directions ◽

Streptomyces Species ◽

Genus Streptomyces ◽

New Antibiotics ◽

The Uk ◽

Almost All ◽

New Generation

Antimicrobial resistance (AMR) is a growing societal problem, and without new anti-infective drugs, the UK government-commissioned O'Neil report has predicted that infectious disease will claim the lives of an additional 10 million people a year worldwide by 2050. Almost all the antibiotics currently in clinical use are derived from the secondary metabolites of a group of filamentous soil bacteria called actinomycetes, most notably in the genus Streptomyces. Unfortunately, the discovery of these strains and their natural products (NPs) peaked in the 1950s and was then largely abandoned, partly due to the repeated rediscovery of known strains and compounds. Attention turned instead to rational target-based drug design, but this was largely unsuccessful and few new antibiotics have made it to clinic in the last 60 years. In the early 2000s, however, genome sequencing of the first Streptomyces species reinvigorated interest in NP discovery because it revealed the presence of numerous cryptic NP biosynthetic gene clusters that are not expressed in the laboratory. Here, we describe how the use of new technologies, including improved culture-dependent and -independent techniques, combined with searching underexplored environments, promises to identify a new generation of NP antibiotics from actinomycete bacteria.

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Isolation and Identification of Actinomycetes Strains from Switzerland and their Biotechnological Potential

CHIMIA International Journal for Chemistry ◽

10.2533/chimia.2020.382 ◽

2020 ◽

Vol 74 (5) ◽

pp. 382-390 ◽

Cited By ~ 1

Author(s):

Fabienne Arn ◽

David Frasson ◽

Ivana Kroslakova ◽

Fabio Rezzonico ◽

Joël F. Pothier ◽

...

Keyword(s):

Draft Genome ◽

Genome Mining ◽

Bioactive Compound ◽

Gene Clusters ◽

Natural Compounds ◽

Rrna Gene ◽

Cultivation Conditions ◽

Screening Assay ◽

Isolation And Identification ◽

Bioinformatics Analyses

Actinomycetes strains isolated from different habitats in Switzerland were investigated for production of antibacterial and antitumoral compounds. Based on partial 16S rRNA gene sequences, the isolated strains were identified to genus level. Streptomyces as the largest genus of Actinobacteriawas isolated the most frequently. A screening assay using the OmniLog instrument was established to facilitate the detection of active compounds from actinomycetes. Extracts prepared from the cultivated strains able to inhibit Staphylococcus aureusand Escherichia coliwere further analysed by HPLC and MALDI-TOF MS to identify the produced antibiotics. In this study, the bioactive compound echinomycin was identified from two isolated Streptomycesstrains. Natural compounds similar to TPU-0037-C, azalomycin F4a 2-ethylpentyl ester, a derivative of bafilomycin A1, milbemycin-α8 and dihydropicromycin were detected from different isolated Streptomyces strains. Milbemycin-α8 showed cytotoxic activity against HT-29 colon cancer cells. The rare actinomycete,Micromonospora sp. Stup16_C148 produced a compound that matches with the antibiotic bottromycin A2. The draft genome sequence from Actinokineospora strain B136.1 was determined using Illumina and nanopore-based technologies. The isolated strain was not able to produce antibacterial compounds under standard cultivation conditions. The antiSMASH bioinformatics analyses of the genome from strain B136.1 identified biosynthetic gene clusters with identity values between 4% to 90% to known gene clusters encoding antibiotics. The combinations of cultivation conditions, screening assays, analytical methods and genome mining are important tools to characterize strains of actinomycetes for the identification of their potential to produce natural compounds with antimicrobial activity.

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Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds

Biomolecules ◽

10.3390/biom10050673 ◽

2020 ◽

Vol 10 (5) ◽

pp. 673

Author(s):

Kattia Núñez-Montero ◽

Damián Quezada-Solís ◽

Zeinab G. Khalil ◽

Robert J. Capon ◽

Fernando D. Andreote ◽

...

Keyword(s):

Antibacterial Activity ◽

Secondary Metabolites ◽

Culture Media ◽

Genome Mining ◽

Gene Clusters ◽

Culture Conditions ◽

Bioactive Metabolites ◽

Bacterial Strains ◽

Antarctic Bacteria ◽

New Antibiotics

Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new “-omics” comparative approaches for drug discovery.

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Isolation and Characterization of Plant-Pathogenic Streptomyces Species Associated with Common Scab-Infected Potato Tubers in Newfoundland

Phytopathology ◽

10.1094/phyto-05-15-0125-r ◽

2016 ◽

Vol 106 (2) ◽

pp. 123-131 ◽

Cited By ~ 15

Author(s):

Joanna K. Fyans ◽

Luke Bown ◽

Dawn R. D. Bignell

Keyword(s):

Common Scab ◽

Virulence Gene ◽

Potato Scab ◽

Potato Tubers ◽

Streptomyces Species ◽

Genus Streptomyces ◽

Thaxtomin A ◽

Streptomyces Spp ◽

Putative Virulence Gene ◽

Isolation And Characterization

Potato common scab (CS) is an economically important crop disease that is caused by several members of the genus Streptomyces. In this study, we characterized the plant-pathogenic Streptomyces spp. associated with CS-infected potato tubers harvested in Newfoundland, Canada. A total of 17 pathogenic Streptomyces isolates were recovered from potato scab lesions, of which eight were determined to be most similar to the known CS pathogen S. europaeiscabiei. All eight S. europaeiscabiei isolates were found to produce the thaxtomin A phytotoxin and to harbor the nec1 virulence gene, and most also carry the putative virulence gene tomA. The remaining isolates appear to be novel pathogenic species that do not produce thaxtomin A, and only two of these isolates were determined to harbor the nec1 or tomA genes. Of the non-thaxtomin-producing isolates, strain 11-1-2 was shown to exhibit a severe pathogenic phenotype against different plant hosts and to produce a novel, secreted phytotoxic substance. This is the first report documenting the plant-pathogenic Streptomyces spp. associated with CS disease in Newfoundland. Furthermore, our findings provide further evidence that phytotoxins other than thaxtomin A may also contribute to the development of CS by Streptomyces spp.

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A New Strain of Streptomyces Causing Common Scab in Potato

Plant Disease ◽

10.1094/pdis-91-4-0352 ◽

2007 ◽

Vol 91 (4) ◽

pp. 352-359 ◽

Cited By ~ 23

Author(s):

Leslie A. Wanner

Keyword(s):

16S Rdna ◽

Horizontal Transfer ◽

Common Scab ◽

The United States ◽

Streptomyces Species ◽

Genus Streptomyces ◽

16S Rdna Sequence ◽

Genes Encoding ◽

Pathogenicity Determinant ◽

Serious Disease

Common scab is a serious disease of potatoes (Solanum tuberosum) and other root and tuber crops, affecting the quality and market value of these crops. The disease is caused by gram-positive soil bacteria in the genus Streptomyces. A new common scab-causing streptomycete was isolated from scabby potatoes originating in southeastern Idaho. Research has supported a model of horizontal transfer of pathogenicity determinants among streptomycetes, and the new strain has hallmarks of the recently characterized Streptomyces pathogenicity island (PAI); it has genes encoding the synthetase for the pathogenicity determinant thaxtomin and for a second pathogenicity factor, tomatinase, although it lacks a third gene characteristic of the Streptomyces PAI, the nec1 gene. The new strain has a unique 16s rDNA gene sequence closely related to those of other pathogenic Streptomyces species. This 16s rDNA sequence was also found in isolates lacking a PAI, suggesting that the new pathogenic strain arose by horizontal transfer of a PAI into a saprophytic streptomycete. Isolates of the new strain are pathogenic on radish and potato, and are more virulent than the S. scabies type strain. In addition to scab lesions on potato tubers, lesions were also seen on underground stems and stolons. This new strain represents additional complexity in the pathogenic strains causing plant disease in the United States.

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Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of Pseudomonas syringae pv. tomato isolated between 1992 and 2008 Reveals achromobactin virulence cluster that is absent in the reference strain DC3000

Phytopathology ◽

10.1094/phyto-08-21-0353-a ◽

2021 ◽

Author(s):

James Tambong ◽

Renlin Xu ◽

Diane Cuppels ◽

Julie T Chapados ◽

suzanne Gerdis ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Draft Genome ◽

Genome Mining ◽

Gene Clusters ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Protein Coding ◽

Genome Data ◽

Bacterial Speck Disease

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck disease of field and greenhouse tomato plants. Only one Canadian whole genome sequence of this economically important pathogen is publicly available in NCBI GenBank. Here, we report 33 whole genome sequences of Canadian strains of P. syringae pv. tomato isolated in Ontario, Canada, between 1992 and 2008. The genome sequences exhibited average nucleotide identity values of 98.64-98.72 % with P. syringae pv. tomato ICMP 2844PT and DC3000, validating the taxonomic standing of these Canadian strains. The genome sizes ranged from 6.20-6.39 Mbp with G+C content of 58.6% and comprised 5,889-6,166 protein-coding sequences (CDSs). The strains had pan- and core-genomes of 6808 and 4,993 gene clusters, respectively. Genome mining of the strains for virulence factors identified typical adherence genes, proteins related to antiphagocytosis, secretion system apparatuses and effectors. Also, partial or complete achromobactin biosynthetic cluster and iron transport genes were identified in all the Canadian strains but absent in P. syringae pv. tomato DC3000 or ICMP 2844 (pathotype). These new whole genome data of Canadian strains of P. syringae pv. tomato could be useful resources in understanding the evolution of this pathogen.

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Whole genome sequence of Streptomyces humi strain MUSC 119T isolated from intertidal soil

Progress in Drug Discovery & Biomedical Science ◽

10.36877/pddbs.0000020 ◽

2019 ◽

Vol 2 (1) ◽

Author(s):

Hooi-Leng Ser ◽

Wen-Si Tan ◽

Wai-Fong Yin ◽

Kok-Gan Chan ◽

Nurul Syakima Ab Mutalib ◽

...

Keyword(s):

Gene Clusters ◽

Whole Genome Sequence ◽

Whole Genome ◽

Biosynthetic Gene Clusters ◽

Streptomyces Species ◽

Genus Streptomyces ◽

The Past ◽

Mangrove Soil ◽

Natural Product Research ◽

Biochemical Assays

Over the past few decades, microorganisms have made major contribution in natural product research, particularly those from the genus Streptomyces. Streptomyces humi MUSC 119T was previously isolated as novel streptomycete from mangrove soil in Malaysia. During the screening programme for bioactive strains, this strain was discovered to possess antioxidant activity – scavenging and reducing accumulation of free radicals in biochemical assays. Consequently, whole genome sequencing was performed to evaluate genomic potential of the strain. Based on our analysis, the genome size of MUSC 119T is described to be 10.01 Mbps with G + C content of 71.80%. Based on antiSMASH analysis, the strain possess great genomic potential, having nine biosynthetic gene clusters displaying high similarities to known gene clusters. These findings indicates that mangrove Streptomyces species like MUSC 119T may potentially play an important role in drug development process, while the availability of its whole genome sequences allows further manipulation to isolate and identify compound of interest.

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