Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences

Ignored microbial-induced taste and odor in drinking water reservoirs: Novel insight into actinobacterial community structure, assembly, and odor-producing potential

The presence of actinobacteria in reservoirs can lead to taste and odor issues, posing potential risks to the safety of drinking water supply. However, the response of actinobacterial communities to environmental factors in drinking water reservoirs remains largely unexplored. To address this gap, this study investigated the community structure and metabolic characteristics of odor-producing actinobacteria in water reservoirs across northern and southern China. The findings revealed differences in the actinobacterial composition across the reservoirs, with Mycobacterium sp. and Candidatus Nanopelagicus being the most prevalent genera. Notably, water temperature, nutrient levels, and metal concentrations were associated with differences in actinobacterial communities, with stochastic processes playing a major role in shaping the community assembly. In addition, three strains of odor-producing actinobacteria were cultured in raw reservoir water, namely Streptomyces antibioticus LJH21, Streptomyces sp. ZEU13, and Streptomyces sp. PQK19, with peak ATP concentrations of 51 nmol/L, 66 nmol/L, and 70 nmol/L, respectively, indicating that odor-producing actinobacteria could remain metabolically active under poor nutrient pressure. Additionally, Streptomyces antibioticus LJH21 produced the highest concentration of geosmin at 24.4 ng/L. These findings enhance our understanding of regional variances and reproductive metabolic mechanisms of actinobacteria in drinking water reservoirs, providing a solid foundation for improving drinking water quality control, especially for taste and odor.

Phenotypic and Genomic Characterization of Streptomyces pakalii sp. nov., a Novel Species with Anti-Biofilm and Anti-Quorum Sensing Activity in ESKAPE Bacteria

The increasing number of infections caused by antimicrobial multi-resistant microorganisms has led to the search for new microorganisms capable of producing novel antibiotics. This work proposes Streptomyces pakalii sp. nov. as a new member of the Streptomycetaceae family. The strain ENCB-J15 was isolated from the jungle soil in Palenque National Park, Chiapas, Mexico. The strain formed pale brown, dry, tough, and buried colonies in the agar with no diffusible pigment in GAE (glucose-asparagine-yeast extract) medium. Scanning electron micrographs showed typical mycelium with long chains of smooth and oval-shaped spores (3-10 m). The strain grew in all of the International Streptomyces Project (ISP)'s media at 28-37 °C with a pH of 6-9 and 0-10% NaCl. S. pakalii ENCB-J15 assimilated diverse carbon as well as organic and inorganic nitrogen sources. The strain also exhibited significant inhibitory activity against the prodigiosin synthesis of Serratia marcescens and the inhibition of the formation and destruction of biofilms of ESKAPE strains of Acinetobacter baumannii and Klebsiella pneumoniae. The draft genome sequencing of ENCB-J15 revealed a 7.6 Mb genome with a high G + C content (71.6%), 6833 total genes, and 6746 genes encoding putative proteins. A total of 26 accessory clusters of proteins associated with carbon sources and amino acid catabolism, DNA modification, and the antibiotic biosynthetic process were annotated. The 16S rRNA gene phylogeny, core-proteome phylogenomic tree, and virtual genome fingerprints support that S. pakalii ENCB-J15 is a new species related to Streptomyces badius and Streptomyces globisporus. Similarly, its average nucleotide identity (ANI) (96.4%), average amino acid identity (AAI) (96.06%), and virtual DNA-DNA hybridization (67.3%) provide evidence to recognize it as a new species. Comparative genomics revealed that S. pakalli and its closest related species maintain a well-conserved genomic synteny. This work proposes Streptomyces pakalii sp. nov. as a novel species that expresses anti-biofilm and anti-quorum sensing activities.

Systematic bioprospection for cellulolytic actinomycetes in the Chihuahuan Desert: isolation and enzymatic profiling

The quest for microbial cellulases has intensified as a response to global challenges in biofuel production. The efficient deconstruction of lignocellulosic biomass holds promise for generating valuable products in various industries such as food, textile, and detergents. This article presents a systematic bioprospection aimed at isolating actinomycetes with exceptional cellulose deconstruction capabilities. Our methodology explored the biodiverse oligotrophic region of Cuatro Cienegas, Coahuila, within the Chihuahuan Desert. Among the evaluated actinomycetes collection, 78% exhibited cellulolytic activity. Through a meticulous screening process based on enzymatic index evaluation, we identified a highly cellulolytic Streptomyces strain for further investigation. Submerged fermentation of this strain revealed an endoglucanase enzymatic activity of 149 U/mg. Genomic analysis of strain Streptomyces sp. STCH565-A revealed unique configurations of carbohydrate-active enzyme (CAZyme) genes, underscoring its potential for lignocellulosic bioconversion applications. These findings not only highlight the significance of the Chihuahuan Desert as a rich source of cellulolytic microorganisms but also offer insights into the systematic exploration and selection of high-performing cellulolytic microorganisms for application in diverse environmental contexts. In conclusion, our bioprospecting study lays a foundation for harnessing the cellulolytic potential of actinomycetes from the Chihuahuan Desert, with implications for advancing cellulose deconstruction processes in various industries. The findings can serve as a blueprint for future bioprospecting efforts in different regions, facilitating the targeted discovery of microorganisms with exceptional cellulosic deconstruction capabilities.

Whole-genome sequencing-based characterization of Streptomyces sp. 6(4): focus on natural product

We have sequenced the whole genome of Streptomyces sp. 6(4) isolated from tomato roots that presents antifungal activity against phytopathogenic fungi, mainly Bipolaris sorokiniana. The genome has almost 7 Mb and 3368 hypothetical proteins that were analysed and characterized in Uniprot with the emphasis on biological compounds. Multilocus sequence typing (MLST) analyses were performed in an effort to characterize and identify this isolate, resulting in a new sequence type (ST), classified as ST64. Phenetic and phylogenetic trees were constructed to investigate Streptomyces sp. 6(4) evolution and sequence similarity, and the isolate is a strain closer to Streptomyces prasinus and Streptomyces viridosporus . It is known that the genus Streptomyces possess huge metabolic capacity with the presence of cryptic genes. These genes are usually present in clusters, which are responsible for the production of diverse natural products, mainly antibiotics. In addition, 6(4) showed 11 biosynthetic gene clusters through antiSMASH, including 3 polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) type clusters.

Respiratory Quinone Switches from Menaquinone to Polyketide Quinone during the Development Cycle in Streptomyces sp. Strain MNU77

Type III polyketide synthases (PKSs) found across Streptomyces species are primarily known for synthesis of a vast repertoire of clinically and industrially relevant secondary metabolites. However, our understanding of the functional relevance of these bioactive metabolites in Streptomyces physiology is still limited. Recently, a role of type III PKS harboring gene cluster in producing alternate electron carrier, polyketide quinone (PkQ) was established in a related member of the Actinobacteria, Mycobacteria, highlighting the critical role these secondary metabolites play in primary cellular metabolism of the producer organism. Here, we report the developmental stage-specific transcriptional regulation of homologous type III PKS containing gene cluster in freshwater Streptomyces sp. strain MNU77. Gene expression analysis revealed the type III PKS gene cluster to be stringently regulated, with significant upregulation observed during the dormant sporulation stage of Streptomyces sp. MNU77. In contrast, the expression levels of only known electron carrier, menaquinone biosynthetic genes were interestingly found to be downregulated. Our liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analysis of a metabolite extract from the Streptomyces sp. MNU77 spores also showed 10 times more metabolic abundance of PkQs than menaquinones. Furthermore, through heterologous complementation studies, we demonstrate that Streptomyces sp. MNU77 type III PKS rescues a respiratory defect of the Mycobacterium smegmatis type III PKS deletion mutant. Together, our studies reveal that freshwater Streptomyces sp. MNU77 robustly produces novel PkQs during the sporulation stage, suggesting utilization of PkQs as alternate electron carriers across Actinobacteria during dormant hypoxic conditions. IMPORTANCE The complex developmental life cycle of Streptomyces sp. mandates efficient cellular respiratory reconfiguration for a smooth transition from aerated nutrient-rich vegetative hyphal growth to the hypoxic-dormant sporulation stage. Polyketide quinones (PkQs) have recently been identified as a class of alternate electron carriers from a related member of the Actinobacteria, Mycobacteria, that facilitates maintenance of membrane potential in oxygen-deficient niches. Our studies with the newly identified freshwater Streptomyces sp. strain MNU77 show conditional transcriptional upregulation and metabolic abundance of PkQs in the spore state of the Streptomyces life cycle. In parallel, the levels of menaquinones, the only known Streptomyces electron carrier, were downregulated, suggesting deployment of PkQs as universal electron carriers in low-oxygen, unfavorable conditions across the Actinobacteria family.

Curtobacterium allii sp. nov., the actinobacterial pathogen causing onion bulb rot

A Gram-stain-positive, aerobic, and non-spore-forming bacterial strain, 20TX0166^T, was isolated from a diseased onion bulb in Texas, USA. Upon testing its pathogenicity on onion bulb, it produced pathogenic response which makes it first species of pathogen belonging to the phylum actinobacteria detected in onion. Phylogenetic analysis of the 16S rRNA gene sequence revealed that the strain belonged to the genus Curtobacterium and was most similar to Curtobacterium flaccumfaciens LMG 3645^T (100%), C. pusillum DSM 20527^T (99.5%), and C. oceanosedimentum ATCC 31317^T (99.5%). The estimated genome size of the novel species was 4.0 Mbp with a G + C content of 70.8%. The orthologous ANI (orthoANIu), ANI based on blast (ANIb), and dDDH values between the novel strain and the closest relative, C. flaccumfaciens LMG 3645^T, were 95.7%, 95.4%, and 63.3%, respectively. These values were below the recommended species cut-off threshold of 96% (ANI) and 70% (dDDH), suggesting the strain may be a novel species. Physiologic and phenotypic characters of this novel strain were also unique when compared with the closely related species. The major cellular fatty acids of this strain were anteiso-C_15:0 and anteiso-C_17:0. Using a polyphasic approach based on phenotypic and genotypic analyses, strain 20TX0166^T represents a novel species of the genus Curtobacterium, and the name Curtobacterium allii sp. nov. is proposed. The type strain is 20TX0166^T (= LMG 32517^T = CIP112023^T = NCIMB 15427^T).

Screening for Anti Mycobacterium tuberculosis Activity of Streptomyces sp. from Lapindo Mud in Sidoarjo, Indonesia

BACKGROUND: Streptomyces sp. from Indonesian soil have not been explored and isolated to find new strains as a source of antibiotics for the treatment of tuberculosis (TB) disease. AIM: In this study, the effect of Streptomyces spp. from Lapindo mud in Sidoarjo, Indonesia be observed, to find out whether Streptomyces spp. has anti-TB activity. METHODS: The primers Strep F; 5-AGAGTTTGAT CCTGKGTCAG-3 and Strep R; 5-AAGGGAG GTGATCCAKKGKGA-3 were used in polymerase chain reaction amplification of the 16S rRNA gene against Streptomyces strains. The anti-TB activity of Streptomyces sp. was determined by broth dilution method using Middlebrook 7H9 media. RESULTS: The results showed that new types of Streptomyces spp., namely, Streptomyces A, Streptomyces D, Streptomyces Ea, Streptomyces Ep, Streptomyces I, Streptomyces F, and Streptomyces G from garbage dump soils. This result also showed that the activity of Streptomyces I, Streptomyces F, and Streptomyces G could inhibit the Mycobacterium TB growth by with inhibitory zones, respectively, 2 ± 0.3; 8 ± 0.7 and 15 ± 0.9mm, while Streptomyces A, Streptomyces D, Streptomyces Ea, and Streptomyces Ep did not inhibit M. TB. CONCLUSION: Thus, from the results obtained, it can be concluded that Streptomyces extract mainly Streptomyces G has promising anti-TB activity by preliminary in vitro techniques. Therefore, it has the definite potential as a source of compounds that may be developed further into antimycobacterial drugs.

Isolation and Identification of Bioactive Compounds from Streptomyces actinomycinicus PJ85 and Their In Vitro Antimicrobial Activities against Methicillin-Resistant Staphylococcus aureus

Antibiotic-resistant strains are a global health-threatening problem. Drug-resistant microbes have compromised the control of infectious diseases. Therefore, the search for a novel class of antibiotic drugs is necessary. Streptomycetes have been described as the richest source of bioactive compounds, including antibiotics. This study was aimed to characterize the antibacterial compounds of Streptomyces sp. PJ85 isolated from dry dipterocarp forest soil in Northeast Thailand. The 16S rRNA gene sequence and phylogenetic analysis showed that PJ85 possessed a high similarity to Streptomyces actinomycinicus RCU-197^T of 98.90%. The PJ85 strain was shown to produce antibacterial compounds that were active against Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA). The active compounds of PJ85 were extracted and purified using silica gel column chromatography. Two active antibacterial compounds, compound 1 and compound PJ85_F39, were purified and characterized with spectroscopy, including liquid chromatography and mass spectrometry (LC-MS). Compound 1 was identified as actinomycin D, and compound PJ85_F39 was identified as dihomo-γ-linolenic acid (DGLA). To the best of our knowledge, this is the first report of the purification and characterization of the antibacterial compounds of S. actinomycinicus.

Analysis of Streptomyces Volatilomes Using Global Molecular Networking Reveals the Presence of Metabolites with Diverse Biological Activities

Streptomyces species produce a wide variety of specialized metabolites, some of which are used for communication or competition for resources in their natural environments. In addition, many natural products used in medicine and industry are derived from Streptomyces, and there has been interest in their capacity to produce volatile organic compounds (VOCs) for different industrial and agricultural applications. Recently, a machine-learning workflow called MSHub/GNPS was developed, which enables auto-deconvolution of gas chromatography-mass spectrometry (GC-MS) data, molecular networking, and library search capabilities, but it has not been applied to Streptomyces volatilomes. In this study, 131 Streptomyces isolates from the island of Newfoundland were phylogenetically typed, and 37 were selected based on their phylogeny and growth characteristics for VOC analysis using both a user-guided (conventional) and an MSHub/GNPS-based approach. More VOCs were annotated by MSHub/GNPS than by the conventional method. The number of unknown VOCs detected by the two methods was higher than those annotated, suggesting that many novel compounds remain to be identified. The molecular network generated by GNPS can be used to guide the annotation of such unknown VOCs in future studies. However, the number of overlapping VOCs annotated by the two methods is relatively small, suggesting that a combination of analysis methods might be required for robust volatilome analysis. More than half of the VOCs annotated with high confidence by the two approaches are plant-associated, many with reported bioactivities such as insect behavior modulation. Details regarding the properties and reported functions of such VOCs are described. IMPORTANCE This study represents the first detailed analysis of Streptomyces volatilomes using MSHub/GNPS, which in combination with a routinely used conventional method led to many annotations. More VOCs could be annotated using MSHub/GNPS as compared to the conventional method, many of which have known antimicrobial, anticancer, and insect behavior-modulating activities. The identification of numerous plant-associated VOCs by both approaches in the current study suggests that their production could be a more widespread phenomenon by members of the genus, highlighting opportunities for their large-scale production using Streptomyces. Plant-associated VOCs with antimicrobial activities, such as 1-octen-3-ol, octanol, and phenylethyl alcohol, have potential applications as fumigants. Furthermore, many of the annotated VOCs are reported to influence insect behavior, alluding to a possible explanation for their production based on the functions of other recently described Streptomyces VOCs in dispersal and nutrient acquisition.

The intricate molecular identification of Streptomyces: a case study on Antarctic soil isolates

Despite the worldwide use of 16S rRNA to identify bacterial species, the use of this gene does not discriminate the 750 species in the genus Streptomyces. A MLST scheme was constructed with rpoB, gyrB, recA, trpB and atpD genes to access the genomic variances in Streptomyces species evolution. We analyze the housekeeping genes in 49 Streptomyces isolates from Antarctic soil. It was used two different databases, GenBank and EzBioCloud to compare the 16S sequences. The species founded in both databases are not the same, but in both cases, a few isolates achieve the necessary high percentage to consider the identification. There is a lack of deposited sequences in the other genes, as the data in GenBank proved to be insufficient. Isolate LMA323St_9 has the potential to be studied as a novel species. Besides that, the use of housekeeping genes gives robust phylogenetic information to understand in group relationships.

Integrated Metabolomic, Molecular Networking, and Genome Mining Analyses Uncover Novel Angucyclines From Streptomyces sp. RO-S4 Strain Isolated From Bejaia Bay, Algeria

Multi-omic approaches have recently made big strides toward the effective exploration of microorganisms, accelerating the discovery of new bioactive compounds. We combined metabolomic, molecular networking, and genomic-based approaches to investigate the metabolic potential of the Streptomyces sp. RO-S4 strain isolated from the polluted waters of Bejaia Bay in Algeria. Antagonistic assays against methicillin-resistant Staphylococcus aureus with RO-S4 organic extracts showed an inhibition zone of 20 mm by using the agar diffusion method, and its minimum inhibitory concentration was 16 μg/ml. A molecular network was created using GNPS and annotated through the comparison of MS/MS spectra against several databases. The predominant compounds in the RO-S4 extract belonged to the angucycline family. Three compounds were annotated as known metabolites, while all the others were putatively new to Science. Notably, all compounds had fridamycin-like aglycones, and several of them had a lactonized D ring analogous to that of urdamycin L. The whole genome of Streptomyces RO-S4 was sequenced to identify the biosynthetic gene cluster (BGC) linked to these angucyclines, which yielded a draft genome of 7,497,846 bp with 72.4% G+C content. Subsequently, a genome mining analysis revealed 19 putative biosynthetic gene clusters, including a grincamycin-like BGC with high similarity to that of Streptomyces sp. CZN-748, that was previously reported to also produce mostly open fridamycin-like aglycones. As the ring-opening process leading to these compounds is still not defined, we performed a comparative analysis with other angucycline BGCs and advanced some hypotheses to explain the ring-opening and lactonization, possibly linked to the uncoupling between the activity of GcnE and GcnM homologs in the RO-S4 strain. The combination of metabolomic and genomic approaches greatly improved the interpretation of the metabolic potential of the RO-S4 strain.

Streptomyces benahoarensis sp. nov. Isolated From a Lava Tube of La Palma, Canary Islands, Spain

Two Streptomyces strains, labeled as MZ03-37^T and MZ03-48, were isolated from two different samples, a mucolite-type speleothem and a microbial mat on the walls of a lava tube from La Palma Island (Canary Islands). Phylogenetic analysis based on concatenated sequences of six housekeeping genes indicated that both strains belonged to the same species. The closest relatives for both strains were Streptomyces palmae CMU-AB204^T (98.71%), Streptomyces catenulae NRRL B-2342^T (98.35%), and Streptomyces ramulosus NRRL B-2714^T (98.35%). Multi-locus sequence analysis (MLSA), based on five house-keeping gene alleles (i.e., atpD, gyrB, recA, rpoB, and trpB), indicated that both isolated strains were closely related to S. catenulae NRRL B-2342^T. Whole-genome average nucleotide identity (ANI) scores of both strains were in the threshold value for species delineation with the closest species. Both strains presented a G+C content of 72.1 mol%. MZ03-37^T was light brown in substrate and white in aerial mycelium, whereas MZ03-48 developed a black aerial and substrate mycelium. No pigment diffusion was observed in both strains. They grew at 10°C-37°C (optimum 28°C-32°C) and in the presence of up to 15% (w/v) NaCl. MZ03-37^T grew at pH 5-10 (optimal 6-9), whereas MZ03-48 grew at pH 4-11 (optimal 5-10). LL-Diaminopimelic acid was the main diamino acid identified. The predominant fatty acids in both strains were iso-C_16:0, anteiso-C_15:0, C_16:0, and iso-C_14:0. The major isoprenoid quinones were MK-9(H6) and MK-9(H8), and the main polar lipids were aminolipid, phospholipid, and phosphoglycolipid. In silico analyses for functional annotation predicted the presence of gene clusters involved in resistome mechanisms and in the synthesis of described antimicrobials such as linocin-M18 and curamycin, as well as different genes likely involved in mechanisms for active compound synthesis, both already described and not discovered so far. On the basis of their phylogenetic relatedness and their phenotypic and genotypic features, the strains MZ03-37^T and MZ03-48 represented a novel species within the genus Streptomyces, for which the name Streptomyces benahoarensis sp. nov. is proposed. The type strain is MZ03-37^T (= CECT 9805 = DSMZ 8002); and MZ03-48 (= CECT 9806 = DSMZ 8011) is a reference strain.

Disentangling host-microbiota complexity through hologenomics

Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.

Great diversity of KSα sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products

Polyketide synthases (PKSs) are multidomain enzymes in microorganisms that synthesize complex, bioactive molecules. PKS II systems are iterative, containing only a single representative of each domain: ketosynthase alpha (KS[Formula: see text]), ketosynthase beta and the acyl carrier protein. Any gene encoding for one of these domains is representative of an entire PKS II biosynthetic gene cluster (BGC). Bat skin surfaces represent an extreme environment prolific in Actinobacteria that may constitute a source for bioactive molecule discovery. KS[Formula: see text] sequences were obtained from culturable bacteria from bats in the southwestern United States. From 467 bat bacterial isolates, we detected 215 (46%) had KS[Formula: see text] sequences. Sequencing yielded 210 operational taxonomic units, and phylogenetic placement found 45 (21%) shared <85% homology to characterized metabolites. Additionally, 16 Actinobacteria genomes from the bat microbiome were analyzed for biosynthetic capacity. A range of 69-93% of the BGCs were novel suggesting the bat microbiome may contain valuable uncharacterized natural products. Documenting and characterizing these are important in understanding the susceptibility of bats to emerging infectious diseases, such as white-nose syndrome. Also noteworthy was the relationship between KS [Formula: see text] homology and total BGC novelty within each fully sequenced strain. We propose amplification and detection of KS[Formula: see text] could predict a strain's global biosynthetic capacity.

Streptomyces spp. Isolated from Marine and Caatinga Biomes in Brazil for the Biological Control of Duponchelia fovealis

Actinobacteria have been drawing attention due to their potential for the development of new pest control products. We hereby assess the effects of Streptomyces isolated from marine and caatinga biomes against Duponchelia fovealis Zeller (Lepidoptera: Crambidae), a pest associated with the strawberry culture at a global scale. To this end, eggs deposited by adults were immersed for 5 s in a bacterial suspension, and the larvae were fed on leaflets placed in glass tubes containing bacterial suspensions. In both treatments, the control was a saline solution. The bioassays demonstrated that the Streptomyces strains were able to cause the death of D. fovealis eggs (≈ 40%) and larvae (≈ 65%) compared to untreated eggs (1.4%) and larvae (2.0%). The crude extract of strain T49 and the chitinase extract of strain T26 affected larval growth when applied directly to the thorax of first-instar larvae (larval-adult lifespan of 65.3 ± 0.5 days and 67.5 ± 0.7 days, respectively; survival of 61.2 ± 1.2%) in relation to the control treatment (larval-adult lifespan of 41.75 ± 0.2 days and survival of 83.7 ± 2.6%). The Streptomyces spp. strains T41, T49, and T50 caused antifeeding activity. Apart from larval mortality, the adults that emerged from the larvae exposed to the extracts presented morphological abnormalities, and the moths' chitin spectra showed clear alterations to the pupa and wings. Our studies show, for the very first time, that Streptomyces isolated from the marine environment and the Caatinga biome are effective at provoking the mortality of D. fovealis and are promising agents for developing new products with biological control properties.

Identification of Streptomyces spp. from garbage dump soils in Surabaya, Indonesia

Background and Aim:

Streptomyces is a well-known agent of secondary metabolite production. This study aimed to identify Streptomyces spp. from garbage dump soils in Surabaya based on the 16S rRNA gene sequence. Moreover, the structure of new chemical compounds used for treating infectious diseases in humans, animals, and plants was elucidated.

Materials and Methods:

We isolated Streptomyces spp. from garbage dump soils in Surabaya. In this study, all isolates were characterized according to phenotype, and they were also confirmed by 16S rRNA gene sequence analysis using real-time polymerase chain reaction. Multiple sequence alignment and molecular phylogeny analyses were conducted using the MEGA 5.0 software, and then the TREE VIEW program was used to display the phylogenetic tree. The level of DNA similarity was also evaluated using the basic local alignment search tool (BLAST) program and then compared with nucleotide sequences stored in the GenBank database using National Center for Biotechnology Information BLAST.

Results:

The eight Streptomyces spp. showed different nucleotide sequence lengths in gel electrophoresis and photography, which is in accordance with the results observed in the phylogenetic tree. New types of Streptomyces spp., Sp-C, Sp-D, Sp-Ep, Sp-G, and Sp-I, were found from the waste heap in Surabaya. Of these, Sp-Ep was very closely related to Streptomyces indonesiasis and Streptomycesnashvillensis. Sp-F was identified as Streptomyces levis strain NRRL B-24299, and Sp-C was identified as Synodontis filamentosus. Sp-D was related to Sida javensis and Staphylococcus roseus. Sp-G was related to Streptomyces roseoviridis strain NBRC 12911 and Streptomyces thermocarboxydovorans strain AT52. Sp-I was related to Streptomyces cangkringensis and Streptomyces asiaticus. Finally, Sp-A was related to Sansevieria laurentii strain LMG 19959.

Conclusion:

Based on the phylogenetic tree, new strains of Streptomyces isolate, namely, Sp-D, Sp-Ep, Sp-G, and Sp-I, were found in the garbage dump soils of Surabaya. This new strain can produce antibiotics to be used as an alternative to antibiotics; however, further research is needed to confirm the activity.

Strategies to access biosynthetic novelty in bacterial genomes for drug discovery

Bacteria provide a rich source of natural products with potential therapeutic applications, such as novel antibiotic classes or anticancer drugs. Bioactivity-guided screening of bacterial extracts and characterization of biosynthetic pathways for drug discovery is now complemented by the availability of large (meta)genomic collections, placing researchers into the postgenomic, big-data era. The progress in next-generation sequencing and the rise of powerful computational tools provide unprecedented insights into unexplored taxa, ecological niches and 'biosynthetic dark matter', revealing diverse and chemically distinct natural products in previously unstudied bacteria. In this Review, we discuss such sources of new chemical entities and the implications for drug discovery with a particular focus on the strategies that have emerged in recent years to identify and access novelty.

Polymethine dyes for PDT: recent advances and perspectives to drive future applications

It has been proved that the effectiveness of photodynamic therapy (PDT) is closely related to the intrinsic features of the photosensitizer (PS). Over the recent years, several efforts have been devoted to the discovery of novel and more efficient photosensitizers showing higher efficacy and lower side effects. In this context, squaraine and cyanine dyes have been reported to potentially overcome the drawbacks related to the traditional PSs. In fact, squaraines and cyanines are characterized by sharp and intense absorption bands and narrow emission bands with high extinction coefficients typically in the red and near-infrared region, good photo and thermal stability and a strong fluorescent emission in organic solvents. In addition, biocompatibility and low toxicity make them suitable for biological applications. Despite these interesting intrinsic features, their chemical instability and self-aggregation properties in biological media still limit their use in PDT. To overcome these drawbacks, the self-assembly and incorporation into smart nanoparticle systems are forwarded promising approaches that can control their physicochemical properties, providing rational solutions for the limitation of free dye administration in the PDT application. The present review summarizes the latest advances in squaraine and cyanine dyes for PDT application, analyzing the different strategies, i.e.the self-assembly and the incorporation into nanoparticles, to further enhance their photochemical properties and therapeutic potential. The in vivo assessments are still limited, thus further delaying their effective application in PDT.

Re-classification of Streptomyces venezuelae strains and mining secondary metabolite biosynthetic gene clusters

Streptomyces species have attracted considerable interest as a reservoir of medically important secondary metabolites, which are even diverse and different between strains. Here, we reassess ten Streptomyces venezuelae strains by presenting the highly resolved classification, using 16S rRNA sequencing, MALDI-TOF MS protein profiling, and whole-genome sequencing. The results revealed that seven of the ten strains were misclassified as S. venezuelae species. Secondary metabolite biosynthetic gene cluster (smBGC) mining and targeted LC-MS/MS based metabolite screening of S. venezuelae and misclassified strains identified in total 59 secondary metabolites production. In addition, a comparison of pyrrolamide-type antibiotic BGCs of four misclassified strains, followed by functional genomics, revealed that athv28 is critical in the synthesis of the anthelvencin precursor, 5-amino-3,4-dihydro-2H-pyrrole-2-carboxylate (ADPC). Our findings illustrate the importance of the accurate classification and better utilization of misclassified Streptomyces strains to discover smBGCs and their secondary metabolite products.

Knowledge, Attitudes, and Practices Regarding Brucellosis among Parents in Aseer Region, Southwestern Saudi Arabia

This study aimed to investigate the knowledge, attitudes, and practices regarding brucellosis among parents in the Aseer region of southwestern Saudi Arabia in order to estimate the population sectors that are at high risk for accidental exposure to brucellosis. This was a cross-sectional survey conducted in 2018, including 311 participants representing various genders, ages, and levels of education. Bivariate analysis showed a significant association of good awareness of the disease with the male gender and higher education levels. Of the 311 participants, 90.0% had good knowledge, whereas 10.0% showed inadequate knowledge about brucellosis. Practices and attitudes regarding brucellosis were satisfactory as participants did not eat meat from their own animals (52.7%), did not practice slaughtering (71.4%), did not participate in the birth of animals (91.3%), were not exposed to abortion in animals (93.2%), and practiced burial of aborted animal fetuses (59.2%). The practice regarding brucellosis was unsatisfactory as 66.6% never wore gloves when dealing with animals. The study concluded that the majority of parents showed fair and positive knowledge, attitudes, and practices regarding brucellosis and found that gender and education were determinants of satisfactory awareness.

Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities

The marine ecosystem has become the hotspot for finding antibiotic-producing actinomycetes across the globe. Although marine-derived actinomycetes display strain-level genomic and chemodiversity, it is unclear whether functional traits, i.e., antibiotic activity, vary in near-identical Streptomyces species. Here, we report culture-dependent isolation, antibiotic activity, phylogeny, biodiversity, abundance, and distribution of Streptomyces isolated from marine sediments across the west-central Philippines. Out of 2212 marine sediment-derived actinomycete strains isolated from 11 geographical sites, 92 strains exhibited antibacterial activities against multidrug-resistant Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. The 16S rRNA and rpoB gene sequence analyses confirmed that antibiotic-producing strains belong to the genus Streptomyces, highlighting Streptomyces parvulus as the most dominant species and three possible new species. Antibiotic-producing Streptomyces strains were highly diverse in Southern Antique, and species diversity increase with marine sediment depth. Multiple strains with near-identical 16S rRNA and rpoB gene sequences displayed varying strength of antibiotic activities. The genotyping of PKS and NRPS genes revealed that closely related antibiotic-producing strains have similar BGC domains supported by their close phylogenetic proximity. These findings collectively suggest Streptomyces' intraspecies adaptive characteristics in distinct ecological niches that resulted in outcompeting other bacteria through differential antibiotic production.

MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data

The 16S rRNA gene amplicon sequencing is a popular technique that provides accurate characterization of microbial taxonomic abundances but does not provide any functional information. Several tools are available to predict functional profiles based on 16S rRNA gene sequence data that use different genome databases and approaches. As variable regions of partially-sequenced 16S rRNA gene cannot resolve taxonomy accurately beyond the genus level, these tools may give inflated results. Here, we developed 'MicFunPred', which uses a novel approach to derive imputed metagenomes based on a set of core genes only, thereby minimizing false-positive predictions. On simulated datasets, MicFunPred showed the lowest False Positive Rate (FPR) with mean Spearman's correlation of 0.89 (SD = 0.03), while on seven real datasets the mean correlation was 0.75 (SD = 0.08). MicFunPred was found to be faster with low computational requirements and performed better or comparable when compared with other tools.

Biodiversity of Actinomycetes from Heavy Metal Contaminated Technosols

Technosols are artificial soils generated by diverse human activities and frequently contain toxic substances resulting from industrial processes. Due to lack of nutrients and extreme physico-chemical properties, they represent environments with limited bacterial colonization. Bacterial populations of technosols are dominated usually by Actinobacteria, including streptomycetes, known as a tremendous source of biotechnologically important molecules. In this study, the biodiversity of streptomycete-like isolates from several technosols, mainly mine soils and wastes (landfills and sludge) in Slovakia, was investigated. The combination of basic morphological and biochemical characterisations, including heavy metal resistance determination, and molecular approaches based on 16S rRNA gene analysis were used for the identification of the bacterial strains. From nine isolates of Actinobacteria collected from different habitats, one was found to represent a new species within the Crossiella genus. Eight other isolates were assigned to the genus Streptomyces, of which at least one could represent a new bacterial species. Some isolates showed high resistance to Pb, Zn, Cu or Ni. The most tolerated metal was Pb. The results obtained in this study indicate that technosols are a prospective source of new actinomycete species resistant to heavy metals what underlines their bioremediation potential.

Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

Background

Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates.

Results

We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species.

Conclusions

Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07546-w.

Whole genome sequencing of Streptomyces actuosus ISP-5337, Streptomyces sioyaensis B-5408, and Actinospica acidiphila B-2296 reveals secondary metabolomes with antibiotic potential

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Whole genome sequencing of Actinomycetes reveals metabolic potential.

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High quality genomes are necessary for mining of biosynthetic gene clusters.

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Characterization of thiopeptides by high resolution mass spectrometry.

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Thiopeptides are potent antibacterials against Staphylococcus aureus.

Streptomycetes are bacteria of biotechnological importance since they are avid producers of secondary metabolites, including antibiotics. Progress in genome mining has recently shown that Streptomyces species encode for many biosynthetic gene clusters which are mostly unexplored. Here, we selected three Actinomycetes species for whole genome sequencing that are known to produce potent thiopeptide antibiotics. Streptomyces actuosus biosynthesizes nosiheptide, Streptomyces sioyaensis produces siomycin, and Actinospica acidiphila is a member of the Actinomycete subfamily. Bioinformatic analyses demonstrated diverse secondary metabolomes with multiple antibiotic-encoding gene clusters. Detailed mass spectrometry analysis of metabolite extracts verified the active expression of nosiheptide and siomycin from S. actuosus and S. sioyaensis while fractionation of the bacterial extracts and subsequent challenge against Staphylococcus aureus demonstrated potent antibiotic activity of fractions containing these compounds. Whole genome sequencing of these species facilitates future bioengineering efforts for thiopeptides and characterization of relevant secondary metabolites.

Continental-Scale Gene Flow Prevents Allopatric Divergence of Pelagic Freshwater Bacteria

Allopatric divergence is one of the principal mechanisms for speciation of macro-organisms. Microbes by comparison are assumed to disperse more freely and to be less limited by dispersal barriers. However, thermophilic prokaryotes restricted to geothermal springs have shown clear signals of geographic isolation, but robust studies on this topic for microbes with less strict habitat requirements are scarce. Furthermore, it has only recently been recognized that homologous recombination among conspecific individuals provides species coherence in a wide range of prokaryotes. Recombination barriers thus may define prokaryotic species boundaries, yet, the extent to which geographic distance between populations gives rise to such barriers is an open question. Here, we investigated gene flow and population structure in a widespread species of pelagic freshwater bacteria, Polynucleobacter paneuropaeus. Through comparative genomics of 113 conspecific strains isolated from freshwater lakes and ponds located across a North–South range of more than 3,000 km, we were able to reconstruct past gene flow events. The species turned out to be highly recombinogenic as indicated by significant signs of gene transfer and extensive genome mosaicism. Although genomic differences increased with spatial distance on a regional scale (<170 km), such correlations were mostly absent on larger scales up to 3,400 km. We conclude that allopatric divergence in European P. paneuropaeus is minor, and that effective gene flow across the sampled geographic range in combination with a high recombination efficacy maintains species coherence.

The biogeography of Streptomyces in New Zealand enabled by high-throughput sequencing of genus-specific rpoB amplicons

We evaluated Streptomyces biogeography in soils along a 1200 km latitudinal transect across New Zealand (NZ). Streptomyces diversity was examined using high-throughput sequencing of rpoB amplicons generated with a Streptomyces specific primer set. We detected 1287 Streptomyces rpoB operational taxonomic units (OTUs) with 159 ± 92 (average ± SD) rpoB OTUs per site. Only 12% (n = 149) of these OTUs matched rpoB sequences from cultured specimens (99% nucleotide identity cutoff). Streptomyces phylogenetic diversity (Faith's PD) was correlated with soil pH, mean annual temperature and plant community richness (Spearman's r: 0.77, 0.64 and -0.79, respectively; P < 0.05), but not with latitude. In addition, soil pH and plant community richness both explained significant variation in Streptomyces beta diversity. Streptomyces communities exhibited both high dissimilarity and strong dominance of one or a few species at each site. Taken together, these results suggest that dispersal limitation due to competitive interactions limits the colonization success of spores that relocate to new sites. Cultivated Streptomyces isolates represent a major source of clinically useful antibiotics, but only a small fraction of extant diversity within the genus have been identified and most species of Streptomyces have yet to be described.

Production of Plant-Associated Volatiles by Select Model and Industrially Important Streptomyces spp

The Streptomyces produce a great diversity of specialized metabolites, including highly volatile compounds with potential biological activities. Volatile organic compounds (VOCs) produced by nine Streptomyces spp., some of which are of industrial importance, were collected and identified using gas chromatography–mass spectrometry (GC-MS). Biosynthetic gene clusters (BGCs) present in the genomes of the respective Streptomyces spp. were also predicted to match them with the VOCs detected. Overall, 33 specific VOCs were identified, of which the production of 16 has not been previously reported in the Streptomyces. Among chemical classes, the most abundant VOCs were terpenes, which is consistent with predicted biosynthetic capabilities. In addition, 27 of the identified VOCs were plant-associated, demonstrating that some Streptomyces spp. can also produce such molecules. It is possible that some of the VOCs detected in the current study have roles in the interaction of Streptomyces with plants and other higher organisms, which might provide opportunities for their application in agriculture or industry.

Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline

One of the major methods to identify microbial community composition, to unravel microbial population dynamics, and to explore microbial diversity in environmental samples is high-throughput DNA- or RNA-based 16S rRNA (gene) amplicon sequencing in combination with bioinformatics analyses. However, focusing on environmental samples from contrasting habitats, it was not systematically evaluated (i) which analysis methods provide results that reflect reality most accurately, (ii) how the interpretations of microbial community studies are biased by different analysis methods and (iii) if the most optimal analysis workflow can be implemented in an easy-to-use pipeline. Here, we compared the performance of 16S rRNA (gene) amplicon sequencing analysis tools (i.e., Mothur, QIIME1, QIIME2, and MEGAN) using three mock datasets with known microbial community composition that differed in sequencing quality, species number and abundance distribution (i.e., even or uneven), and phylogenetic diversity (i.e., closely related or well-separated amplicon sequences). Our results showed that QIIME2 outcompeted all other investigated tools in sequence recovery (>10 times fewer false positives), taxonomic assignments (>22% better F-score) and diversity estimates (>5% better assessment), suggesting that this approach is able to reflect the in situ microbial community most accurately. Further analysis of 24 environmental datasets obtained from four contrasting terrestrial and freshwater sites revealed dramatic differences in the resulting microbial community composition for all pipelines at genus level. For instance, at the investigated river water sites Sphaerotilus was only reported when using QIIME1 (8% abundance) and Agitococcus with QIIME1 or QIIME2 (2 or 3% abundance, respectively), but both genera remained undetected when analyzed with Mothur or MEGAN. Since these abundant taxa probably have implications for important biogeochemical cycles (e.g., nitrate and sulfate reduction) at these sites, their detection and semi-quantitative enumeration is crucial for valid interpretations. A high-performance computing conformant workflow was constructed to allow FAIR (Findable, Accessible, Interoperable, and Re-usable) 16S rRNA (gene) amplicon sequence analysis starting from raw sequence files, using the most optimal methods identified in our study. Our presented workflow should be considered for future studies, thereby facilitating the analysis of high-throughput 16S rRNA (gene) sequencing data substantially, while maximizing reliability and confidence in microbial community data analysis.

Evaluation of BOX-PCR and REP-PCR as Molecular Typing Tools for Antarctic Streptomyces

Molecular studies led to the resurgence of natural products research from genus Streptomyces, already known for their long history and importance for the pharmaceutical industry. However, species belonging to this genus are difficult to identify and the most commonly used techniques, which are based on 16S rRNA sequencing, do not discriminate between related species. In this work, amplification profiles generated from BOX-PCR and REP-PCR of 49 Antarctic soil streptomycetes were compared to evaluate the diversity present in the group and to characterize the bacterial isolates, along with some 16S rRNA amplifications. The BOX-A1R primer exhibit clearer amplification fragments, different from the amplification patterns obtained using the REP 1R and 2R primers. A higher diversity was observed with REP-PCR amplifications, even though a larger number of fragments was obtained with BOX-A1R primer amplifications. There are at least four isolates that showed great similarity (about 90%) in both techniques. In other hand, there are two others that are 90% similar in BOX-PCR, but distant in REP-PCR, showing only 40% of similarity. Results of the combination of BOX-PCR and REP-PCR represent a simple and low-cost method to discriminate between Streptomyces strains. There is no species identification with only the 16S rRNA, most isolates seem to be related to S. globisporus. Further studies added to the obtained results may provide better data to help the characterization of these microorganisms.

Molecular Identification and Antimicrobial Potential of Streptomyces Species from Nepalese Soil

Streptomyces are widely used for the production of secondary metabolites with diverse biological activities, including antibiotics. The necessity of alternative antimicrobial agents against multidrug-resistant pathogens is indispensable. However, the production of new therapeutics is delayed in recent days. Thus, the isolation of new Streptomyces species has drawn attention. Nepal-a country rich in biodiversity-has got high possibilities for the discovery of members of actinomycetes, especially in the higher altitudes. However, in vain, only a few screening research works have been reported from Nepal to date. Streptomyces species were isolated on ISP4 media, and characterization was performed according to morphological similarity and 16S rRNA sequence similarity using bioinformatic tools. Ethyl acetate extracts of Streptomyces species were prepared, and the antimicrobial activity was carried out using agar well diffusion technique. In this report, 18 Streptomyces species isolated from the soil were reported based on sequence analysis of 16S rRNA. Among them, 12 isolates have shown antibacterial activity against extended-spectrum beta-lactamase- (ESBL-) producing Escherichia coli. Here, we have also analyzed 16S rRNA in 27 Streptomyces species whose whole-genome sequence is available, which has revealed that some species have multiple copies of the 16S gene (∼1.5 kb) with significant variation in nucleotides. In contrast, some Streptomyces species shared identical DNA sequences in multiple copies of 16S rRNA. The sequencing of numerous copies of 16S rRNA is not necessary, and the molecular sequencing of this region is not sufficient for the identification of bacterial species. The Streptomyces species-derived ethyl acetate extracts from Nepalese soil demonstrate potential activity against ESBL-producing E. coli. Thus, they are potential candidates for antibiotics manufacturing in the future.

Bacterial dispersal and biogeography as underappreciated influences on phytobiomes

Bacterial strains are not distributed evenly throughout the environment. Here I explore how differential distribution and dispersal patterns of bacteria could affect interactions and coevolutionary dynamics with plants, and highlight ways that variation could be taken advantage of to develop robust and effective microbial consortia to inoculate crops. Questions about biogeographical patterns in viruses, fungi, and other eukaryotes are equally as prevalent and important for agriculture, and are in some cases more thoroughly explored. For simplicity as well as to bring attention to bacterial biogeography and dispersal in the context of plant interactions, I focus solely on bacterial patterns and questions for this article. The next few years will no doubt bring great advances in our understanding of dispersal capabilities and population dynamics for many plant-associated bacteria, and one of the next looming challenges will be learning to harvest this diversity in ways that can benefit agriculture.

Antifungal Potential of the Skin Microbiota of Hibernating Big Brown Bats (Eptesicus fuscus) Infected With the Causal Agent of White-Nose Syndrome

Little is known about skin microbiota in the context of the disease white-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans (Pd), that has caused enormous declines of hibernating North American bats over the past decade. Interestingly, some hibernating species, such as the big brown bat (Eptesicus fuscus), appear resistant to the disease and their skin microbiota could play a role. However, a comprehensive analysis of the skin microbiota of E. fuscus in the context of Pd has not been done. In January 2017, we captured hibernating E. fuscus, sampled their skin microbiota, and inoculated them with Pd or sham inoculum. We allowed the bats to hibernate in the lab under controlled conditions for 11 weeks and then sampled their skin microbiota to test the following hypotheses: (1) Pd infection would not disrupt the skin microbiota of Pd-resistant E. fuscus; and (2) microbial taxa with antifungal properties would be abundant both before and after inoculation with Pd. Using high-throughput 16S rRNA gene sequencing, we discovered that beta diversity of Pd-inoculated bats changed more over time than that of sham-inoculated bats. Still, the most abundant taxa in the community were stable throughout the experiment. Among the most abundant taxa, Pseudomonas and Rhodococcus are known for antifungal potential against Pd and other fungi. Thus, in contrast to hypothesis 1, Pd infection destabilized the skin microbiota but consistent with hypothesis 2, bacteria with known antifungal properties remained abundant and stable on the skin. This study is the first to provide a comprehensive survey of skin microbiota of E. fuscus, suggesting potential associations between the bat skin microbiota and resistance to the Pd infection and WNS. These results set the stage for future studies to characterize microbiota gene expression, better understand mechanisms of resistance to WNS, and help develop conservation strategies.

Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community

The diversity and distribution of specialized metabolite gene clusters within a community of bacteria living in the same soil habitat are poorly documented. Here we analyzed the genomes of 8 Streptomyces isolated at micro-scale from a forest soil that belong to the same species or to different species. The results reveal high levels of diversity, with a total of 261 biosynthesis gene clusters (BGCs) encoding metabolites such as terpenes, polyketides (PKs), non-ribosomal peptides (NRPs) and ribosomally synthesized and post-translationally modified peptides (RiPPs) with potential bioactivities. A significant part of these BGCs (n = 53) were unique to only one strain when only 5 were common to all strains. The metabolites belong to very diverse chemical families and revealed that a large diversity of metabolites can potentially be produced in the community. Although that analysis of the global metabolome using GC-MS revealed that most of the metabolites were shared between the strains, they exhibited a specific metabolic pattern. We also observed that the presence of these accessory pathways might result from frequent loss and gain of genes (horizontal transfer), showing that the potential of metabolite production is a dynamic phenomenon in the community. Sampling Streptomyces at the community level constitutes a good frame to discover new biosynthetic pathways and it appears as a promising reservoir for the discovery of new bioactive compounds.

Streptomyces lydicamycinicus sp. nov. and Its Secondary Metabolite Biosynthetic Gene Clusters for Polyketide and Nonribosomal Peptide Compounds

(1) Background: Streptomyces sp. TP-A0598 derived from seawater produces lydicamycin and its congeners. We aimed to investigate its taxonomic status; (2) Methods: A polyphasic approach and whole genome analysis are employed; (3) Results: Strain TP-A0598 contained ll-diaminopimelic acid, glutamic acid, glycine, and alanine in its peptidoglycan. The predominant menaquinones were MK-9(H₆) and MK-9(H₈), and the major fatty acids were C_16:0, iso-C_15:0, iso-C_16:0, and anteiso-C_15:0. Streptomyces sp. TP-A0598 showed a 16S rDNA sequence similarity value of 99.93% (1 nucleottide difference) to Streptomyces angustmyceticus NRRL B-2347^T. The digital DNA–DNA hybridisation value between Streptomyces sp. TP-A0598 and its closely related type strains was 25%–46%. Differences in phenotypic characteristics between Streptomyces sp. TP-A0598 and its phylogenetically closest relative, S. angustmyceticus NBRC 3934^T, suggested strain TP-A0598 to be a novel species. Streptomyces sp. TP-A0598 and S. angustmyceticus NBRC 3934^T harboured nine and 13 biosynthetic gene clusters for polyketides and nonribosomal peptides, respectively, among which only five clusters were shared between them, whereas the others are specific for each strain; and (4) Conclusions: For strain TP-A0598, the name Streptomyces lydicamycinicus sp. nov. is proposed; the type strain is TP-A0598^T (=NBRC 110027^T).

Isolation, Characterization, and Complete Genome Sequence of a Bradyrhizobium Strain Lb8 From Nodules of Peanut Utilizing Crack Entry Infection

In many legumes, the colonization of roots by rhizobia is via "root hair entry" and its molecular mechanisms have been extensively studied. However, the nodulation of peanuts (Arachis hypogaea L.) by Bradyrhizobium strains requires an intercellular colonization process called "crack entry," which is understudied. To understand the intercellular crack entry process, it is critical to develop the tools and resources related to the rhizobium in addition to focus on investigating the mechanisms of the plant host. In this study, we isolated a Bradyrhizobium sp. strain, Lb8 from peanut root nodules and sequenced it using PacBio long reads. The complete genome sequence was a circular chromosome of 8,718,147 base-pair (bp) with an average GC content of 63.14%. No plasmid sequence was detected in the sequenced DNA sample. A total of 8,433 potential protein-encoding genes, one rRNA cluster, and 51 tRNA genes were annotated. Fifty-eight percent of the predicted genes showed similarity to genes of known functions and were classified into 27 subsystems representing various biological processes. The genome shared 92% of the gene families with B. diazoefficens USDA 110^T. A presumptive symbiosis island of 778 Kb was detected, which included two clusters of nif and nod genes. A total of 711 putative protein-encoding genes were in this region, among which 455 genes have potential functions related to symbiotic nitrogen fixation and DNA transmission. Of 21 genes annotated as transposase, 16 were located in the symbiosis island. Lb8 possessed both Type III and Type IV protein secretion systems, and our work elucidated the association of flagellar Type III secretion systems in bradyrhizobia. These observations suggested that complex rearrangement, such as horizontal transfer and insertion of different DNA elements, might be responsible for the plasticity of the Bradyrhizobium genome.

Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria

Streptomyces bacteria are known for their prolific production of secondary metabolites, many of which have been widely used in human medicine, agriculture and animal health. To guide the effective prioritization of specific biosynthetic gene clusters (BGCs) for drug development and targeting the most prolific producer strains, knowledge about phylogenetic relationships of Streptomyces species, genome-wide diversity and distribution patterns of BGCs is critical. We used genomic and phylogenetic methods to elucidate the diversity of major classes of BGCs in 1,110 publicly available Streptomyces genomes. Genome mining of Streptomyces reveals high diversity of BGCs and variable distribution patterns in the Streptomyces phylogeny, even among very closely related strains. The most common BGCs are non-ribosomal peptide synthetases, type 1 polyketide synthases, terpenes, and lantipeptides. We also found that numerous Streptomyces species harbor BGCs known to encode antitumor compounds. We observed that strains that are considered the same species can vary tremendously in the BGCs they carry, suggesting that strain-level genome sequencing can uncover high levels of BGC diversity and potentially useful derivatives of any one compound. These findings suggest that a strain-level strategy for exploring secondary metabolites for clinical use provides an alternative or complementary approach to discovering novel pharmaceutical compounds from microbes.

Taxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces

The advent of culture independent approaches has greatly facilitated insights into the vast diversity of bacteria and the ecological importance they hold in nature and human health. Recently, metagenomic surveys and other culture-independent methods have begun to describe the distribution and diversity of microbial metabolism across environmental conditions, often using 16S rRNA gene as a marker to group bacteria into taxonomic units. However, the extent to which similarity at the conserved ribosomal 16S gene correlates with different measures of phylogeny, metabolic diversity, and ecologically relevant gene content remains contentious. Here, we examine the relationship between 16S identity, core genome divergence, and metabolic gene content across the ancient and ecologically important genus Streptomyces. We assessed and quantified the high variability of average nucleotide identity (ANI) and ortholog presence/absence within Streptomyces, even in strains identical by 16S. Furthermore, we identified key differences in shared ecologically important characters, such as antibiotic resistance, carbohydrate metabolism, biosynthetic gene clusters (BGCs), and other metabolic hallmarks, within 16S identities commonly treated as the same operational taxonomic units (OTUs). Differences between common phylogenetic measures and metabolite-gene annotations confirmed this incongruence. Our results highlight the metabolic diversity and variability within OTUs and add to the growing body of work suggesting 16S-based studies of Streptomyces fail to resolve important ecological and metabolic characteristics.

Massive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics

Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.

In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.

Comparative Genomics of Marine Sponge-Derived Streptomyces spp. Isolates SM17 and SM18 With Their Closest Terrestrial Relatives Provides Novel Insights Into Environmental Niche Adaptations and Secondary Metabolite Biosynthesis Potential

The emergence of antibiotic resistant microorganisms has led to an increased need for the discovery and development of novel antimicrobial compounds. Frequent rediscovery of the same natural products (NPs) continues to decrease the likelihood of the discovery of new compounds from soil bacteria. Thus, efforts have shifted toward investigating microorganisms and their secondary metabolite biosynthesis potential, from diverse niche environments, such as those isolated from marine sponges. Here we investigated at the genomic level two Streptomyces spp. strains, namely SM17 and SM18, isolated from the marine sponge Haliclona simulans, with previously reported antimicrobial activity against clinically relevant pathogens; using single molecule real-time (SMRT) sequencing. We performed a series of comparative genomic analyses on SM17 and SM18 with their closest terrestrial relatives, namely S. albus J1074 and S. pratensis ATCC 33331 respectively; in an effort to provide further insights into potential environmental niche adaptations (ENAs) of marine sponge-associated Streptomyces, and on how these adaptations might be linked to their secondary metabolite biosynthesis potential. Prediction of secondary metabolite biosynthetic gene clusters (smBGCs) indicated that, even though the marine isolates are closely related to their terrestrial counterparts at a genomic level; they potentially produce different compounds. SM17 and SM18 displayed a better ability to grow in high salinity medium when compared to their terrestrial counterparts, and further analysis of their genomes indicated that they possess a pool of 29 potential ENA genes that are absent in S. albus J1074 and S. pratensis ATCC 33331. This ENA gene pool included functional categories of genes that are likely to be related to niche adaptations and which could be grouped based on potential biological functions such as osmotic stress, defense; transcriptional regulation; symbiotic interactions; antimicrobial compound production and resistance; ABC transporters; together with horizontal gene transfer and defense-related features.

Different Secondary Metabolite Profiles of Phylogenetically almost Identical Streptomyces griseus Strains Originating from Geographically Remote Locations

As Streptomyces have shown an outstanding capacity for drug production, different campaigns in geographically distant locations currently aim to isolate new antibiotic producers. However, many of these newly isolated Streptomyces strains are classified as identical to already described species. Nevertheless, as discrepancies in terms of secondary metabolites and morphology are possible, we compared two Streptomyces strains with identical 16S rRNA gene sequences but geographically distant origins. Chosen were an Easter Island Streptomyces isolate (Streptomyces sp. SN25_8.1) and the next related type strain, which is Streptomyces griseus subsp. griseus DSM 40236^T isolated from Russian garden soil. Compared traits included phylogenetic relatedness based on 16S rRNA gene sequences, macro and microscopic morphology, antibiotic activity and secondary metabolite profiles. Both Streptomyces strains shared several common features, such as morphology and core secondary metabolite production. They revealed differences in pigmentation and in the production of accessory secondary metabolites which appear to be strain-specific. In conclusion, despite identical 16S rRNA classification Streptomyces strains can present different secondary metabolite profiles and may well be valuable for consideration in processes for drug discovery.

Habitat fragmentation is associated with dietary shifts and microbiota variability in common vampire bats

Host ecological factors and external environmental factors are known to influence the structure of gut microbial communities, but few studies have examined the impacts of environmental changes on microbiotas in free-ranging animals. Rapid land-use change has the potential to shift gut microbial communities in wildlife through exposure to novel bacteria and/or by changing the availability or quality of local food resources. The consequences of such changes to host health and fitness remain unknown and may have important implications for pathogen spillover between humans and wildlife. To better understand the consequences of land-use change on wildlife microbiotas, we analyzed long-term dietary trends, gut microbiota composition, and innate immune function in common vampire bats (Desmodus rotundus) in two nearby sites in Belize that vary in landscape structure. We found that vampire bats living in a small forest fragment had more homogenous diets indicative of feeding on livestock and shifts in microbiota heterogeneity, but not overall composition, compared to those living in an intact forest reserve. We also found that irrespective of sampling site, vampire bats which consumed relatively more livestock showed shifts in some core bacteria compared with vampire bats which consumed relatively less livestock. The relative abundance of some core microbiota members was associated with innate immune function, suggesting that future research should consider the role of the host microbiota in immune defense and its relationship to zoonotic infection dynamics. We suggest that subsequent homogenization of diet and habitat loss through livestock rearing in the Neotropics may lead to disruption to the microbiota that could have downstream impacts on host immunity and cross-species pathogen transmission.

Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus

Streptomyces rimosus is best known as the primary source of the tetracycline class of antibiotics, most notably oxytetracycline, which have been widely used against many gram-positive and gram-negative pathogens and protozoan parasites. However, despite the medical and agricultural importance of S. rimosus, little is known of its evolutionary history and genome dynamics. In this study, we aim to elucidate the pan-genome characteristics and phylogenetic relationships of 32 S. rimosus genomes. The S. rimosus pan-genome contains more than 22,000 orthologous gene clusters, and approximately 8.8% of these genes constitutes the core genome. A large part of the accessory genome is composed of 9,646 strain-specific genes. S. rimosus exhibits an open pan-genome (decay parameter α = 0.83) and high gene diversity between strains (genomic fluidity φ = 0.12). We also observed strain-level variation in the distribution and abundance of biosynthetic gene clusters (BGCs) and that each individual S. rimosus genome has a unique repertoire of BGCs. Lastly, we observed variation in recombination, with some strains donating or receiving DNA more often than others, strains that tend to frequently recombine with specific partners, genes that often experience recombination more than others, and variable sizes of recombined DNA sequences. We conclude that the high levels of inter-strain genomic variation in S. rimosus is partly explained by differences in recombination among strains. These results have important implications on current efforts for natural drug discovery, the ecological role of strain-level variation in microbial populations, and addressing the fundamental question of why microbes have pan-genomes.

Exclusivity offers a sound yet practical species criterion for bacteria despite abundant gene flow

BACKGROUND

The question of whether bacterial species objectively exist has long divided microbiologists. A major source of contention stems from the fact that bacteria regularly engage in horizontal gene transfer (HGT), making it difficult to ascertain relatedness and draw boundaries between taxa. A natural way to define taxa is based on exclusivity of relatedness, which applies when members of a taxon are more closely related to each other than they are to any outsider. It is largely unknown whether exclusive bacterial taxa exist when averaging over the genome or are rare due to rampant hybridization.

RESULTS

Here, we analyze a collection of 701 genomes representing a wide variety of environmental isolates from the family Streptomycetaceae, whose members are competent at HGT. We find that the presence/absence of auxiliary genes in the pan-genome displays a hierarchical (tree-like) structure that correlates significantly with the genealogy of the core-genome. Moreover, we identified the existence of many exclusive taxa, although individual genes often contradict these taxa. These conclusions were supported by repeating the analysis on 1,586 genomes belonging to the genus Bacillus. However, despite confirming the existence of exclusive groups (taxa), we were unable to identify an objective threshold at which to assign the rank of species.

CONCLUSIONS

The existence of bacterial taxa is justified by considering average relatedness across the entire genome, as captured by exclusivity, but is rejected if one requires unanimous agreement of all parts of the genome. We propose using exclusivity to delimit taxa and conventional genome similarity thresholds to assign bacterial taxa to the species rank. This approach recognizes species that are phylogenetically meaningful, while also establishing some degree of comparability across species-ranked taxa in different bacterial clades.

Comparative Genomics among Closely Related Streptomyces Strains Revealed Specialized Metabolite Biosynthetic Gene Cluster Diversity

Specialized metabolites are of great interest due to their possible industrial and clinical applications. The increasing number of antimicrobial resistant infectious agents is a major health threat and therefore, the discovery of chemical diversity and new antimicrobials is crucial. Extensive genomic data from Streptomyces spp. confirm their production potential and great importance. Genome sequencing of the same species strains indicates that specialized metabolite biosynthetic gene cluster (SMBGC) diversity is not exhausted, and instead, a pool of novel specialized metabolites still exists. Here, we analyze the genome sequence data from six phylogenetically close Streptomyces strains. The results reveal that the closer strains are phylogenetically, the number of shared gene clusters is higher. Eight specialized metabolites comprise the core metabolome, although some strains have only six core gene clusters. The number of conserved gene clusters common between the isolated strains and their closest phylogenetic counterparts varies from nine to 23 SMBGCs. However, the analysis of these phylogenetic relationships is not affected by the acquisition of gene clusters, probably by horizontal gene transfer events, as each strain also harbors strain-specific SMBGCs. Between one and 15 strain-specific gene clusters were identified, of which up to six gene clusters in a single strain are unknown and have no identifiable orthologs in other species, attesting to the existing SMBGC novelty at the strain level.

IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences

BACKGROUND

Microbiome studies often involve sequencing a marker gene to identify the microorganisms in samples of interest. Sequence classification is a critical component of this process, whereby sequences are assigned to a reference taxonomy containing known sequence representatives of many microbial groups. Previous studies have shown that existing classification programs often assign sequences to reference groups even if they belong to novel taxonomic groups that are absent from the reference taxonomy. This high rate of "over classification" is particularly detrimental in microbiome studies because reference taxonomies are far from comprehensive.

RESULTS

Here, we introduce IDTAXA, a novel approach to taxonomic classification that employs principles from machine learning to reduce over classification errors. Using multiple reference taxonomies, we demonstrate that IDTAXA has higher accuracy than popular classifiers such as BLAST, MAPSeq, QIIME, SINTAX, SPINGO, and the RDP Classifier. Similarly, IDTAXA yields far fewer over classifications on Illumina mock microbial community data when the expected taxa are absent from the training set. Furthermore, IDTAXA offers many practical advantages over other classifiers, such as maintaining low error rates across varying input sequence lengths and withholding classifications from input sequences composed of random nucleotides or repeats.

CONCLUSIONS

IDTAXA's classifications may lead to different conclusions in microbiome studies because of the substantially reduced number of taxa that are incorrectly identified through over classification. Although misclassification error is relatively minor, we believe that many remaining misclassifications are likely caused by errors in the reference taxonomy. We describe how IDTAXA is able to identify many putative mislabeling errors in reference taxonomies, enabling training sets to be automatically corrected by eliminating spurious sequences. IDTAXA is part of the DECIPHER package for the R programming language, available through the Bioconductor repository or accessible online ( http://DECIPHER.codes ).