Your browser doesn't support javascript.
loading
Montrer: 20 | 50 | 100
Résultats 1 - 20 de 1.606
Filtrer
1.
Curr Microbiol ; 81(9): 292, 2024 Aug 01.
Article de Anglais | MEDLINE | ID: mdl-39090417

RÉSUMÉ

The taxonomic relationship between Streptomyces violarus and Streptomyces violaceus was reevaluated using a polyphasic taxonomic approach in this work. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Streptomyces violarus JCM 4534 T was closely related to Streptomyces arenae ISP 5293 T. However, phylogenetic analysis based on five house-keeping gene (atpD, gyrB, recA, rpoB and trpB) showed that the evolutionary neighbor of Streptomyces violarus JCM 4534 T was Streptomyces violaceus CGMCC 4.1456 T, suggesting that there was a close genetic relationship between these two strains. The average nucleotide identity and digital DNA-DNA hybridization values between them were 97.0 and 72.9%, respectively, greater than the 96.7 and 70% cut-off points recommended for delineating a Streptomyces species. This result indicated that they belonged to the same genomic species which was also verified by a comprehensive comparison of phenotypic and chemotaxonomic characteristics between Streptomyces violarus JCM 4534 T and Streptomyces violaceus CGMCC 4.1456 T. According to all these data and the rule of priority in nomenclature, it is proposed the Streptomyces violarus (Artamonova and Krassilnikov 1960) Pridham 1970 is a later heterotypic synonym of Streptomyces violaceus (Rossi Doria 1891) Waksman 1953. In addition, based on dDDH, Streptomyces violaceus and Streptomyces violarus are simultaneously designated as two different subspecies, i.e., Streptomyces violaceus subsp. violaceus and Streptomyces violaceus subsp. violarus.


Sujet(s)
ADN bactérien , Phylogenèse , ARN ribosomique 16S , Streptomyces , Streptomyces/génétique , Streptomyces/classification , ARN ribosomique 16S/génétique , ADN bactérien/génétique , Techniques de typage bactérien , Analyse de séquence d'ADN , Hybridation d'acides nucléiques , Protéines bactériennes/génétique
2.
J Microbiol Methods ; 223: 106984, 2024 Aug.
Article de Anglais | MEDLINE | ID: mdl-38955305

RÉSUMÉ

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is the first-line method for the rapid identification of most cultured microorganisms. As for Streptomyces strains, MALDI-TOF MS identification is complicated by the characteristic incrustation of colonies in agar and the strong cell wall of Actinomycetes cells requiring the use of alternative protein extraction protocols. In this study, we developed a specific protocol to overcome these difficulties for the MALDI-TOF MS identification of Actinomycetes made on solid medium. This protocol includes incubation of colony removed from agar plate with the beta-agarase enzyme, followed by a mechanical lysis and two washes by phosphate buffer and ethanol. Twenty-four Streptomyces and two Lentzea strains isolated from Algerian desertic soils were first identified by 16S rRNA sequencing as gold standard method, rpoB gene was used as a secondary gene target when 16S rRNA did not allow species identification. In parallel the isolates were identified by using the MALDI-TOF MS protocol as reported. After the expansion of the database with the inclusion of this MSPS, the strains were analyzed again in MALDI Biotyper, and all were identified. This work demonstrates that the rapid identification of Actinomycetes can be obtained without protein extraction step frequently used in MALDI-TOF mass spectrometry with this type of microorganisms.


Sujet(s)
Actinobacteria , ARN ribosomique 16S , Microbiologie du sol , Spectrométrie de masse MALDI , Spectrométrie de masse MALDI/méthodes , ARN ribosomique 16S/génétique , Algérie , Actinobacteria/isolement et purification , Actinobacteria/génétique , Actinobacteria/classification , Actinobacteria/composition chimique , ADN bactérien/génétique , Streptomyces/isolement et purification , Streptomyces/génétique , Streptomyces/classification , Streptomyces/composition chimique , Protéines bactériennes/génétique , DNA-directed RNA polymerases/génétique , Milieux de culture/composition chimique , Analyse de séquence d'ADN , Techniques bactériologiques/méthodes , Glycosidases
3.
BMC Microbiol ; 24(1): 208, 2024 Jun 11.
Article de Anglais | MEDLINE | ID: mdl-38862894

RÉSUMÉ

BACKGROUND: Antimicrobial resistance (AMR) is a serious worldwide public health concern that needs immediate action. Probiotics could be a promising alternative for fighting antibiotic resistance, displaying beneficial effects to the host by combating diseases, improving growth, and stimulating the host immune responses against infection. This study was conducted to evaluate the probiotic, antibacterial, and antibiofilm potential of Streptomyces levis strain HFM-2 isolated from the healthy human gut. RESULTS: In vitro antibacterial activity in the cell-free supernatant of S. levis strain HFM-2 was evaluated against different pathogens viz. K. pneumoniae sub sp. pneumoniae, S. aureus, B. subtilis, VRE, S. typhi, S. epidermidis, MRSA, V. cholerae, M. smegmatis, E. coli, P. aeruginosa and E. aerogenes. Further, the ethyl acetate extract from S. levis strain HFM-2 showed strong biofilm inhibition against S. typhi, K. pneumoniae sub sp. pneumoniae, P. aeruginosa and E. coli. Fluorescence microscopy was used to detect biofilm inhibition properties. MIC and MBC values of EtOAc extract were determined at 500 and 1000 µg/mL, respectively. Further, strain HFM-2 showed high tolerance in gastric juice, pancreatin, bile, and at low pH. It exhibited efficient adhesion properties, displaying auto-aggregation (97.0%), hydrophobicity (95.71%, 88.96%, and 81.15% for ethyl acetate, chloroform and xylene, respectively), and showed 89.75%, 86.53%, 83.06% and 76.13% co-aggregation with S. typhi, MRSA, S. pyogenes and E. coli, respectively after 60 min of incubation. The S. levis strain HFM-2 was susceptible to different antibiotics such as tetracycline, streptomycin, kanamycin, ciprofloxacin, erythromycin, linezolid, meropenem, amikacin, gentamycin, clindamycin, moxifloxacin and vancomycin, but resistant to ampicillin and penicillin G. CONCLUSION: The study shows that S. levis strain HFM-2 has significant probiotic properties such as good viability in bile, gastric juice, pancreatin environment, and at low pH; proficient adhesion properties, and antibiotic susceptibility. Further, the EtOAc extract of Streptomyces levis strain HFM-2 has a potent antibiofilm and antibacterial activity against antibacterial-resistant clinical pathogens.


Sujet(s)
Antibactériens , Biofilms , Tests de sensibilité microbienne , Probiotiques , Streptomyces , Biofilms/effets des médicaments et des substances chimiques , Biofilms/croissance et développement , Humains , Probiotiques/pharmacologie , Streptomyces/physiologie , Streptomyces/classification , Streptomyces/isolement et purification , Streptomyces/composition chimique , Antibactériens/pharmacologie , Bactéries/effets des médicaments et des substances chimiques , Bactéries/classification , Tube digestif/microbiologie
4.
Nucleic Acids Res ; 52(13): 7487-7503, 2024 Jul 22.
Article de Anglais | MEDLINE | ID: mdl-38908028

RÉSUMÉ

Filamentous Actinobacteria, recently renamed Actinomycetia, are the most prolific source of microbial bioactive natural products. Studies on biosynthetic gene clusters benefit from or require chromosome-level assemblies. Here, we provide DNA sequences from >1000 isolates: 881 complete genomes and 153 near-complete genomes, representing 28 genera and 389 species, including 244 likely novel species. All genomes are from filamentous isolates of the class Actinomycetia from the NBC culture collection. The largest genus is Streptomyces with 886 genomes including 742 complete assemblies. We use this data to show that analysis of complete genomes can bring biological understanding not previously derived from more fragmented sequences or less systematic datasets. We document the central and structured location of core genes and distal location of specialized metabolite biosynthetic gene clusters and duplicate core genes on the linear Streptomyces chromosome, and analyze the content and length of the terminal inverted repeats which are characteristic for Streptomyces. We then analyze the diversity of trans-AT polyketide synthase biosynthetic gene clusters, which encodes the machinery of a biotechnologically highly interesting compound class. These insights have both ecological and biotechnological implications in understanding the importance of high quality genomic resources and the complex role synteny plays in Actinomycetia biology.


Sujet(s)
Actinobacteria , Génome bactérien , Famille multigénique , Polyketide synthases , Génome bactérien/génétique , Actinobacteria/génétique , Actinobacteria/classification , Actinobacteria/métabolisme , Polyketide synthases/génétique , Polyketide synthases/métabolisme , Streptomyces/génétique , Streptomyces/classification , Streptomyces/métabolisme , Phylogenèse , Génomique/méthodes
5.
Curr Microbiol ; 81(8): 223, 2024 Jun 14.
Article de Anglais | MEDLINE | ID: mdl-38874598

RÉSUMÉ

Two endophytic actinobacteria, strains MK5T and MK7, were isolated from the surface-sterilized root of Jasmine rice (Oryza sativa KDML 105). These strains were aerobic actinobacteria with a well-developed substrate and aerial mycelia that formed spiral spore chains. The type strains that shared the high 16S rRNA gene sequence similarity with both strains were Streptomyces naganishii NBRC 12892T (99.4%), "Streptomyces griseicoloratus" TRM S81-3T (99.2%), and Streptomyces spiralis NBRC 14215T (98.9%). Strains MK5T and MK7 are the same species sharing a digital DNA-DNA hybridization (dDDH) value of 95.3% and a 16S rRNA gene sequence similarity of 100%. Chemotaxonomic data confirmed the affiliation of strains MK5T and MK7 to the genus Streptomyces. Strains MK5T and MK7 contained MK-9(H4) as a major menaquinone; the whole-cell sugar of both strains was galactose and glucose. The strain MK5T shared 93.4% average nucleotide identity (ANI)-Blast, 95.5% ANI-MUMmer, 93% average amino acid identity, and 61.3% dDDH with S. spiralis NBRC 14215T. The polyphasic approach confirmed that strain MK5T represents a novel species, and the name Streptomyces mahasarakhamensis sp. nov. is proposed. The type strain is MK5T (= TBRC 17754 = NRRL B-65683). Genome mining, using an in silico approach and searching biosynthesis gene clusters of strains MK5T and MK7, revealed that the genomes contained genes encoding proteins relating to plant growth promotion, bioactive compounds, and beneficial enzymes. Strains MK5T and MK7 could produce indole acetic acid and solubilize phosphate in vitro.


Sujet(s)
ADN bactérien , Endophytes , Oryza , Phylogenèse , ARN ribosomique 16S , Streptomyces , Oryza/microbiologie , Streptomyces/génétique , Streptomyces/isolement et purification , Streptomyces/classification , Streptomyces/métabolisme , ARN ribosomique 16S/génétique , Endophytes/génétique , Endophytes/classification , Endophytes/isolement et purification , Endophytes/métabolisme , ADN bactérien/génétique , Racines de plante/microbiologie , Facteur de croissance végétal/métabolisme , Vitamine K2/analogues et dérivés , Techniques de typage bactérien , Analyse de séquence d'ADN , Hybridation d'acides nucléiques , Acides gras/métabolisme , Composition en bases nucléiques
6.
mSphere ; 9(7): e0066723, 2024 Jul 30.
Article de Anglais | MEDLINE | ID: mdl-38864637

RÉSUMÉ

Botrytis cinerea is a necrotrophic phytopathogen able to attack more than 200 different plant species causing strong yield losses worldwide. Many synthetic fungicides have been developed to control this disease, resulting in the rise of fungicide-resistance B. cinerea strains. The aim of this study was to identify Streptomyces strains showing antagonistic activity against B. cinerea to contribute to plant protection in an environmentally friendly way. We isolated 15 Actinomycete strains from 9 different Swiss soils. The culture filtrates of three isolates showing antifungal activity inhibited spore germination and delayed mycelial growth of B. cinerea. Infection experiments showed that Arabidopsis thaliana plants were more resistant to this pathogen after leaf treatment with the Streptomyces filtrates. Bioassay-guided isolation of the active compounds revealed the presence of germicidins A and B as well as of oligomycins A, B, and E. While germicidins were mostly inactive, oligomycin B reduced the mycelial growth of B. cinerea significantly. Moreover, all three oligomycins inhibited this fungus' spore germination, suggesting that these molecules might contribute to the Streptomyces's ability to protect plants against infection by the broad host-pathogen Botrytis cinerea. IMPORTANCE: This study reports the isolation of new Streptomyces strains with strong plant-protective potential mediated by their production of specialized metabolites. Using the broad host range pathogenic fungus Botrytis cinerea, we demonstrate that the cell-free filtrate of selected Streptomyces isolates efficiently inhibits different developmental stages of the fungus, including mycelial growth and the epidemiologically relevant spore germination. Beyond in vitro experiments, the strains and their metabolites also efficiently protected plants against the disease caused by this pathogen. This work further identifies oligomycins as active compounds involved in the observed antifungal activity of the strains. This work shows that we can harness the natural ability of soil-borne microbes and of their metabolites to efficiently fight other microbes responsible for significant crop losses. This opens the way to the development of environmentally friendly health protection measures for crops of agronomical relevance, based on these newly isolated strains or their metabolic extracts containing oligomycins.


Sujet(s)
Arabidopsis , Botrytis , Oligomycines , Maladies des plantes , Microbiologie du sol , Streptomyces , Botrytis/effets des médicaments et des substances chimiques , Botrytis/croissance et développement , Streptomyces/classification , Streptomyces/génétique , Streptomyces/isolement et purification , Arabidopsis/microbiologie , Maladies des plantes/microbiologie , Maladies des plantes/prévention et contrôle , Oligomycines/pharmacologie , Suisse , Spores fongiques/effets des médicaments et des substances chimiques , Spores fongiques/croissance et développement , Antifongiques/pharmacologie , Mycelium/effets des médicaments et des substances chimiques , Mycelium/croissance et développement
7.
Arch Microbiol ; 206(6): 256, 2024 May 11.
Article de Anglais | MEDLINE | ID: mdl-38734826

RÉSUMÉ

A novel actinobacterium strain, designated HUAS 2-6 T, was isolated from the rhizosphere soil of Camellia oleifera Abel collected from Taoyuan County, Northwestern Hunan Province, South China. This strain was subjected to a polyphasic taxonomic study. Strain HUAS 2-6 T is characterized by morphology typical of members of the genus Streptomyces, with deep purplish vinaceous aerial mycelia and deep dull lavender substrate mycelia. Strain HUAS 2-6 T, based on the full-length 16S rRNA gene sequence analysis, exhibited the highest similarities to S. puniciscabiei S77T (99.31%), S. filipinensis NBRC 12860 T (99.10%), S. yaanensis CGMCC 4.7035 T (99.09%), S. fodineus TW1S1T (99.08%), S. broussonetiae CICC 24819 T (98.76%), S. achromogenes JCM 4121 T (98.69%), S. barringtoniae JA03T (98.69%), and less than 98.70% with other validly species. In phylogenomic tree, strain HUAS 2-6 T was clustered together with S. broussonetiae CICC 24819 T, suggesting that they were closely related to each other. However, average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) between them were much less than the species cutoff values (ANI 96.7% and dDDH 70%). Moreover, in phenotypic and chemotaxonomic characteristics, strain HUAS 2-6 T is distinct from S. broussonetiae CICC 24819 T. On the basis of the polyphasic data, strain HUAS 2-6 T is proposed to represent a novel species, Streptomyces camelliae sp. nov. (= MCCC 1K04729T = JCM 35918 T).


Sujet(s)
Camellia , ADN bactérien , Phylogenèse , ARN ribosomique 16S , Rhizosphère , Microbiologie du sol , Streptomyces , Streptomyces/isolement et purification , Streptomyces/génétique , Streptomyces/classification , Camellia/microbiologie , ARN ribosomique 16S/génétique , ADN bactérien/génétique , Chine , Acides gras/analyse , Techniques de typage bactérien , Analyse de séquence d'ADN , Composition en bases nucléiques
8.
Appl Environ Microbiol ; 90(6): e0060024, 2024 Jun 18.
Article de Anglais | MEDLINE | ID: mdl-38771054

RÉSUMÉ

Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.


Sujet(s)
Famille multigénique , Phylogenèse , Voies de biosynthèse/génétique , Streptomyces/génétique , Streptomyces/métabolisme , Streptomyces/classification , Lysobacter/génétique , Lysobacter/métabolisme , Lysobacter/classification , Biologie informatique , Lactames/métabolisme
9.
Article de Anglais | MEDLINE | ID: mdl-38767616

RÉSUMÉ

A Gram-stain-positive actinomycete, designated REN17T, was isolated from fermented grains of Baijiu collected from Sichuan, PR China. It exhibited branched substrate mycelia and a sparse aerial mycelium. The optimal growth conditions for REN17T were determined to be 28 °C and pH 7, with a NaCl concentration of 0 % (w/v). ll-Diaminopimelic acid was the diagnostic amino acid of the cell-wall peptidoglycan and the polar lipids were composed of phosphatidylethanolamine, phosphatidylinositol, an unidentified phospholipid, two unidentified lipids and four unidentified glycolipids. The predominant menaquinone was MK-9 (H2), MK-9 (H4), MK-9 (H6) and MK-9 (H8). The major fatty acids were iso-C16 : 0. The 16S rRNA sequence of REN17T was most closely related to those of Streptomyces apricus SUN 51T (99.8 %), Streptomyces liliiviolaceus BH-SS-21T (99.6 %) and Streptomyces umbirnus JCM 4521T (98.9 %). The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identify values between REN17T and its closest replated strain, of S. apricus SUN 51T, were 35.9, 88.9 and 87.3 %, respectively. Therefore, REN17T represents a novel species within the genus Streptomyces, for which the name Streptomyces beigongshangae sp. nov. is proposed. The type strain is REN17T (=GDMCC 4.193T=JCM 34712T). While exploring the function of the strain, REN17T was found to possess the ability to transform major ginsenosides of Panax notoginseng (Burk.) F.H. Chen (Araliaceae) into minor ginsenoside through HPLC separation, which was due to the presence of ß-glucosidase. The recombinant ß-glucosidase was constructed and purified, which could produce minor ginsenosides of Rg3 and C-K. Finally, the enzymatic properties were characterized.


Sujet(s)
Techniques de typage bactérien , ADN bactérien , Acides gras , Fermentation , Ginsénosides , Hybridation d'acides nucléiques , Panax notoginseng , Phylogenèse , ARN ribosomique 16S , Analyse de séquence d'ADN , Streptomyces , Vitamine K2 , ARN ribosomique 16S/génétique , Acides gras/composition chimique , Streptomyces/isolement et purification , Streptomyces/génétique , Streptomyces/classification , Vitamine K2/analogues et dérivés , ADN bactérien/génétique , Chine , Panax notoginseng/microbiologie , Ginsénosides/métabolisme , Peptidoglycane , Grains comestibles/microbiologie , Acide diamino-pimélique , Phospholipides/composition chimique , Composition en bases nucléiques
10.
Article de Anglais | MEDLINE | ID: mdl-38695864

RÉSUMÉ

A novel actinobacterium, designated strain CWNU-1T, was isolated from the rhizospheric soil of Fritillaria cirrhosa D. Don and examined using a polyphasic taxonomic approach. The organism developed pale blue aerial mycelia that was simply branched and terminated in open or closed coils of three or more volutions on International Streptomyces Project 3 agar. Spores were ellipsoidal to cylindrical with wrinkled surfaces. The strain showed high 16S rRNA gene sequence similarity to Streptomyces kurssanovii NBRC 13192T (98.8 %), Streptomyces xantholiticus NBRC 13354T (98.7 %) and Streptomyces peucetius JCM 9920T (98.6 %). The phylogenetic result based on 16S rRNA gene and genome sequences clearly demonstrated that strain CWNU-1T formed an independent phylogenetic lineage. On the basis of orthologous average nucleotide identity, CWNU-1T was most closely related to Streptomyces inusitatus NBRC 13601T with 79.3 % identity. The results of the digital DNA-DNA hybridization analysis also indicated low levels of relatedness with other species, as the highest value was observed with S. inusitatus NBRC 13601T (25.3 %). With reference to phenotypic characteristics, phylogenetic data, orthologous average nucleotide identity and digital DNA-DNA hybridization results, strain CWNU-1T was readily distinguished from its most closely related strains and classified as representing a novel species, for which the name Streptomyces albipurpureus sp. nov. is proposed. The type strain is CWNU-1T (=CGMCC 4.7758T=MCCC 1K07402T=JCM 35391T).


Sujet(s)
Techniques de typage bactérien , Composition en bases nucléiques , ADN bactérien , Acides gras , Fritillaria , Hybridation d'acides nucléiques , Phylogenèse , ARN ribosomique 16S , Rhizosphère , Analyse de séquence d'ADN , Microbiologie du sol , Streptomyces , Streptomyces/génétique , Streptomyces/classification , Streptomyces/isolement et purification , ARN ribosomique 16S/génétique , ADN bactérien/génétique , Acides gras/analyse , Fritillaria/microbiologie , Vitamine K2/analogues et dérivés
11.
Microbiome ; 12(1): 83, 2024 May 09.
Article de Anglais | MEDLINE | ID: mdl-38725008

RÉSUMÉ

BACKGROUND: Fungi and bacteria coexist in a wide variety of environments, and their interactions are now recognized as the norm in most agroecosystems. These microbial communities harbor keystone taxa, which facilitate connectivity between fungal and bacterial communities, influencing their composition and functions. The roots of most plants are associated with arbuscular mycorrhizal (AM) fungi, which develop dense networks of hyphae in the soil. The surface of these hyphae (called the hyphosphere) is the region where multiple interactions with microbial communities can occur, e.g., exchanging or responding to each other's metabolites. However, the presence and importance of keystone taxa in the AM fungal hyphosphere remain largely unknown. RESULTS: Here, we used in vitro and pot cultivation systems of AM fungi to investigate whether certain keystone bacteria were able to shape the microbial communities growing in the hyphosphere and potentially improved the fitness of the AM fungal host. Based on various AM fungi, soil leachates, and synthetic microbial communities, we found that under organic phosphorus (P) conditions, AM fungi could selectively recruit bacteria that enhanced their P nutrition and competed with less P-mobilizing bacteria. Specifically, we observed a privileged interaction between the isolate Streptomyces sp. D1 and AM fungi of the genus Rhizophagus, where (1) the carbon compounds exuded by the fungus were acquired by the bacterium which could mineralize organic P and (2) the in vitro culturable bacterial community residing on the surface of hyphae was in part regulated by Streptomyces sp. D1, primarily by inhibiting the bacteria with weak P-mineralizing ability, thereby enhancing AM fungi to acquire P. CONCLUSIONS: This work highlights the multi-functionality of the keystone bacteria Streptomyces sp. D1 in fungal-bacteria and bacterial-bacterial interactions at the hyphal surface of AM fungi. Video Abstract.


Sujet(s)
Hyphae , Microbiote , Mycorhizes , Racines de plante , Microbiologie du sol , Streptomyces , Mycorhizes/physiologie , Mycorhizes/classification , Streptomyces/classification , Streptomyces/isolement et purification , Streptomyces/génétique , Streptomyces/physiologie , Hyphae/croissance et développement , Racines de plante/microbiologie , Phosphore/métabolisme , Interactions microbiennes/physiologie , Sol/composition chimique , Bactéries/classification , Bactéries/génétique , Bactéries/isolement et purification , Bactéries/métabolisme
12.
Article de Anglais | MEDLINE | ID: mdl-38713186

RÉSUMÉ

Two novel actinobacteria, designated as LP05-1T and LP11T, were isolated from the lichen Pyxine cocoes (Sw.) Nyl. collected in Bangkok, Thailand. Genotypic and phenotypic analyses revealed that both strains represented members of the genus Streptomyces. The 16S rRNA gene of LP05-1T showed the highest similarity to the genome of Streptomyces gelaticus (98.41 %), while the 16S rRNA gene of LP11T was most similar to that of Streptomyces cinerochromogenes (98.93 %). The major menaquinones in LP05-1T were MK-9(H8), MK-9(H6), MK-9(H4) and MK-9(H2), and in LP11T, they were MK-9(H8) and MK-9(H6). Both strains exhibited the major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, with LP05-1T also possessing iso-C17 : 0. The polar lipids of LP05-1T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified lipid, while those of LP11T consisted of phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid and an unidentified glycolipid. The digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) values indicated that both strains are distinct from each other with values below 70 and 95 %, respectively. dDDH, ANI by blast (ANIb) and ANI by MUMmer (ANIm) values between LP05-1T and its closely related type strains were 26.07-26.80 %, 81.24-82.01 % and 86.82-86.96 %, respectively, while those for LP11T and its closely related type strains were 30.70-31.70 %, 84.09-85.31 % and 88.02-88.39 %, respectively. The results of the taxonomic investigation, including dDDH and ANI values, indicate that LP05-1T and LP11T are novel type strains of two novel species within the genus Streptomyces. The names proposed are Streptomyces pyxinae sp. nov. for strain LP05-1T (=TBRC 15494T, =NBRC 115434T) and Streptomyces pyxinicus sp. nov. for strain LP11T (=TBRC 15493T, =NBRC 115421T).


Sujet(s)
Techniques de typage bactérien , Composition en bases nucléiques , ADN bactérien , Acides gras , Lichens , Phylogenèse , ARN ribosomique 16S , Analyse de séquence d'ADN , Streptomyces , Vitamine K2 , Vitamine K2/analogues et dérivés , ARN ribosomique 16S/génétique , Lichens/microbiologie , Vitamine K2/analyse , ADN bactérien/génétique , Streptomyces/génétique , Streptomyces/isolement et purification , Streptomyces/classification , Acides gras/composition chimique , Thaïlande , Hybridation d'acides nucléiques , Phospholipides
13.
Environ Microbiol Rep ; 16(2): e13266, 2024 Apr.
Article de Anglais | MEDLINE | ID: mdl-38653477

RÉSUMÉ

The Gram-positive bacteria Streptomyces davaonensis and Streptomyces cinnabarinus have been the only organisms known to produce roseoflavin, a riboflavin (vitamin B2) derived red antibiotic. Using a selective growth medium and a phenotypic screening, we were able to isolate a novel roseoflavin producer from a German soil sample. The isolation procedure was repeated twice, that is, the same strain could be isolated from the same location in Berlin 6 months and 12 months after its first isolation. Whole genome sequencing of the novel roseoflavin producer revealed an unusual chromosomal arrangement and the deposited genome sequence of the new isolate (G + C content of 71.47%) contains 897 genes per inverted terminal repeat, 6190 genes in the core and 107 genes located on an illegitimate terminal end. We identified the roseoflavin biosynthetic genes rosA, rosB and rosC and an unusually high number of riboflavin biosynthetic genes. Overexpression of rosA, rosB and rosC in Escherichia coli and enzyme assays confirmed their predicted functions in roseoflavin biosynthesis. A full taxonomic analysis revealed that the isolate represents a previously unknown Streptomyces species and we propose the name Streptomyces berlinensis sp. nov. for this roseoflavin producer.


Sujet(s)
Phylogenèse , Riboflavine , Riboflavine/analogues et dérivés , Microbiologie du sol , Streptomyces , Streptomyces/génétique , Streptomyces/classification , Streptomyces/métabolisme , Streptomyces/isolement et purification , Riboflavine/métabolisme , Riboflavine/biosynthèse , Composition en bases nucléiques , Génome bactérien , Séquençage du génome entier , Allemagne , Antibactériens/biosynthèse , Antibactériens/métabolisme
14.
Biosci Biotechnol Biochem ; 88(6): 689-695, 2024 May 22.
Article de Anglais | MEDLINE | ID: mdl-38549421

RÉSUMÉ

Streptomyces sp. SN-593, a reveromycin producer, was previously thought to belong to the genus Streptomyces based on its morphological and chemotaxonomic characteristics. In this paper, we re-considered its taxonomic position according to the current criteria. Phylogenetic analysis using 16S rRNA gene sequences showed that the strain belongs to the genus Actinacidiphila. In multilocus sequence and phylogenomic analyses, the strain SN-593 represented a distinct evolutionary lineage within this genus, and its closest neighbor was A. yanglinensis. Digital DNA-DNA hybridization indicated that the strain shares less than 32% DNA-DNA relatedness with the type strains of closely related species, confirming this strain is a novel genomospecies. According to its phenotypic distinctiveness from the closest neighbor, we propose Actinacidiphila reveromycinica sp. nov. for the strain SN-593T. Additionally, as Streptomyces acidipaludis belonged to the genus Actinacidiphila in these analyses, it should be transferred to the genus, for which Actinacidiphila acidipaludis comb. nov. is proposed.


Sujet(s)
Phylogenèse , ARN ribosomique 16S , Streptomyces , ARN ribosomique 16S/génétique , Streptomyces/classification , Streptomyces/métabolisme , Streptomyces/génétique , Hybridation d'acides nucléiques
15.
Microb Genom ; 9(5)2023 05.
Article de Anglais | MEDLINE | ID: mdl-37166955

RÉSUMÉ

The deep sea is known to host novel bacteria with the potential to produce a diverse array of undiscovered natural products. Thus, understanding these bacteria is of broad interest in ecology and could also underpin applied drug discovery, specifically in the area of antimicrobials. Here, we isolate a new strain of Streptomyces from the tissue of the deep-sea sponge Polymastia corticata collected at a depth of 1869 m from the Gramberg Seamount in the Atlantic Ocean. This strain, which was given the initial designation A15ISP2-DRY2T, has a genome size of 9.29 Mb with a G+C content of 70.83 mol%. Phylogenomics determined that A15ISP2-DRY2T represents a novel species within the genus Streptomyces as part of the Streptomyces aurantiacus clade. The biosynthetic potential of A15ISP2-DRY2T was assessed relative to other members of the S. aurantiacus clade via comparative gene cluster family (GCF) analysis. This revealed a clear congruent relationship between phylogeny and GCF content. A15ISP2-DRY2T contains six unique GCFs absent elsewhere in the clade. Culture-based assays were used to demonstrate the antibacterial activity of A15ISP2-DRY2T against two drug-resistant human pathogens. Thus, we determine A15ISP2-DRY2T to be a novel bacterial species with considerable biosynthetic potential and propose the systematic name 'Streptomyces ortus' sp. nov.


Sujet(s)
Porifera , Streptomyces , Streptomyces/composition chimique , Streptomyces/classification , Streptomyces/isolement et purification , Eau de mer/microbiologie , Microbiologie de l'eau , Porifera/microbiologie , Animaux , Composition en bases nucléiques , Génome bactérien
16.
Article de Anglais | MEDLINE | ID: mdl-35559756

RÉSUMÉ

Although 16S rRNA gene sequences are conventionally analysed in bacterial systematics, their resolution is not sufficient for species identification. Multilocus sequence analysis (MLSA) is a powerful method for species identification as well as the elucidation of phylogenetic relationships in the genus Streptomyces. Gene sequences of atpD, gyrB, recA, rpoB and trpB are generally used in MLSA for Streptomyces species. This study aims to evaluate the sequence analysis of one gene instead of all five genes to be employed for species identification. The resolution of atpD gene sequences was not necessarily able to distinguish closely related species. In contrast, trpB gene sequence similarities correlated to the MLSA-based evolutionary distances, especially among closely related strains. A pairwise similarity of 97.9 % in trpB gene sequences was proposed as the threshold for species delineation based on the feasibility examined using strain pairs that shared >99.93 % pairwise 16S rRNA gene sequence similarities. Resequencing the five housekeeping genes followed by MLSA suggested that Streptomyces anthocyanicus and Streptomyces tricolor are synonyms of Streptomyces violaceoruber.


Sujet(s)
Gènes essentiels , Phylogenèse , Streptomyces , Techniques de typage bactérien , Composition en bases nucléiques , ADN bactérien/génétique , Gènes bactériens , Typage par séquençage multilocus , ARN ribosomique 16S/génétique , Analyse de séquence d'ADN , Streptomyces/classification , Streptomyces/génétique
17.
Article de Anglais | MEDLINE | ID: mdl-35188884

RÉSUMÉ

Two new marine actinobacteria, designated as J2-1T and J2-2T, were isolated from a coral, Favites pentagona, collected from Rayong Province, Thailand. The taxonomic positions of the two strains were identified based on polyphasic taxonomy. Based on morphological characteristics and chemotaxonomy, strains J2-1T and J2-2T were identified as members of the genus Streptomyces and Kineosporia, respectively. Strains J2-1T and J2-2T showed the highest 16S rRNA gene sequence similarity to Streptomyces broussonetiae T44T (98.62 %) and Kineosporia babensis VN05A0415T (98.08 %), respectively. Strain J2-1T had chemotaxonomic properties resembling members of the genus Streptomyces. ll-Diaminopimelic acid, glucose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositolmannoside, unidentified aminolipid and five unidentified phospholipids were detected as the polar lipids. The major cellular fatty acids were C16 : 0 iso, C15 : 0 anteiso, C15 : 0 iso, C16 : 0, C17 : 0 anteiso, C14 : 0 iso and C17 : 0 iso. Strain J2-2T a showed similar cell composition to members of the genus Kineosporia. Both isomers of ll- and meso-diaminopimelic acid were detected in the peptidoglycan. Arabinose, galactose, madurose and xylose were observed in the whole-cell hydrolysate. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylcholine, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were C16 : 0, C18 : 1 ω9c, C18 : 0 10-methyl, tuberculostearic acid, C18 : 0 and C17 : 0. Both strains could be distinguished from their closely related type strains according to their phenotypic characteristics. Comparative genome analysis indicated the delineation of two novel species based on digital DNA-DNA hybridization and average nucleotide identity values, which were below 70 and 95 %, respectively. The names proposed are Streptomyces corallincola sp. nov. (J2-1T=TBRC 13503T=NBRC 115066T) and Kineosporia corallincola sp. nov. (J2-2T=TBRC 13504T=NBRC 114885T).


Sujet(s)
Actinobacteria , Anthozoa , Phylogenèse , Streptomyces , Actinobacteria/classification , Actinobacteria/isolement et purification , Animaux , Anthozoa/microbiologie , Techniques de typage bactérien , Composition en bases nucléiques , ADN bactérien/génétique , Acides gras/composition chimique , Hybridation d'acides nucléiques , Phospholipides/composition chimique , ARN ribosomique 16S/génétique , Analyse de séquence d'ADN , Streptomyces/classification , Streptomyces/isolement et purification , Thaïlande
18.
Article de Anglais | MEDLINE | ID: mdl-35037846

RÉSUMÉ

A novel Streptomyces strain, SUN51T, was isolated from soils sampled in Wisconsin, USA, as part of a Streptomyces biogeography survey. Genome sequencing revealed that this strain had less than 90 % average nucleotide identity (ANI) to type species of Streptomyces: SUN51T was most closely related to Streptomyces dioscori A217T (99.5 % 16S rRNA gene identity, 89.4 % ANI). Genome size was estimated at 8.81 Mb, and the genome DNA G+C content was 72 mol%. The strain possessed the cellular fatty acids anteiso-C15 : 0, iso-C16 : 0, 16 : 1 ω7c, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0. The predominant menaquinones were MK-9 H4, MK-9 H6 and MK-9 H8. Strain SUN51T contained the polar lipids phosphatidic acid, phosphatidyl ethanolamine, phosphatidyl glycerol and diphosphatidyl glycerol. The cell wall contained ll-diaminopimelic acid. The strain could grow on a broad range of carbon sources and tolerate temperatures of up to 40 °C. The results of the polyphasic study confirmed that this isolate represents a novel species of the genus Streptomyces, for which the name Streptomyces apricus sp. nov. is proposed. The type strain of this species is SUN51T (=NRRL B-65543T=JCM 33736T).


Sujet(s)
Phylogenèse , Microbiologie du sol , Streptomyces , Techniques de typage bactérien , Composition en bases nucléiques , ADN bactérien/génétique , Acides gras/composition chimique , Phospholipides/composition chimique , ARN ribosomique 16S/génétique , Analyse de séquence d'ADN , Streptomyces/classification , Streptomyces/isolement et purification , Wisconsin
19.
Article de Anglais | MEDLINE | ID: mdl-35038290

RÉSUMÉ

An endophytic Streptomyces-like micro-organism, designated strain PRB2-1T was isolated from root tissue of Epipremnum aureum (Linden and André) G.S. Bunting. The typical morphological and chemotaxonomic characteristics, i.e. the ability to produce straight spore chains directly on aerial mycelium and the presence of ll-diaminopimelic acid in cell-wall peptidoglycan, were consistent with its assignment to the genus Streptomyces. 16S rRNA gene analysis showed that strain PRB2-1T is a member of the genus Streptomyces with the highest similarity to Streptomyces bryophytorum DSM 42183T (98.4 %). Moreover, the draft genome sequence of strain PRB2-1T exhibited low average nucleotide identity by blast (79.9-83.8 %) and digital DNA-DNA hybridization (24.9-28.3 %) values to the reference strains, which were well below the species circumscription threshold. The DNA G+C content of genomic DNA was 73.6 mol%. Comparison of phenotypic characteristics and whole-genome sequence between strain PRB2-1T and its close relatives indicated that strain PRB2-1T could be classified as a novel species of the genus Streptomyces. Thus the name, Streptomyces epipremni sp. nov. is proposed for the strain. The type strain is PRB2-1T (=TBRC 7642T=NBRC 113169T).


Sujet(s)
Araceae/microbiologie , Phylogenèse , Streptomyces , Techniques de typage bactérien , Composition en bases nucléiques , ADN bactérien/génétique , Acide diamino-pimélique/composition chimique , Acides gras/composition chimique , Racines de plante/microbiologie , ARN ribosomique 16S/génétique , Analyse de séquence d'ADN , Streptomyces/classification , Streptomyces/isolement et purification
20.
Article de Anglais | MEDLINE | ID: mdl-35085064

RÉSUMÉ

Fourteen strains of Streptomyces isolated from scab lesions on potato are described as members of a novel species based on genetic distance, morphological observation and biochemical analyses. Morphological and biochemical characteristics of these strains are distinct from other described phytopathogenic species. Strain NE06-02DT has white aerial mycelium and grey, cylindrical, smooth spores on rectus-flexibilis spore chains. Members of this species group can utilize most of the International Streptomyces Project sugars, utilize melibiose and trehalose, produce melanin, grow on 6-7 % NaCl and pH 5-5.5 media, and are susceptible to oleandomycin (100 µg ml-1), streptomycin (20 µg ml-1) and penicillin G (30 µg ml-1). Though the 16S rRNA gene sequences from several members of this novel species are identical to the Streptomyces bottropensis 16S rRNA gene sequence, whole-genome average nucleotide identity and multi-locus sequence analysis confirm that the strains are members of a novel species. Strains belonging to this novel species have been isolated from the United States, Egypt and China with the earliest known members being isolated in 1961 from common scab lesions of potato in both California, USA, and Maine, USA. The name Streptomyces caniscabiei sp. nov. is proposed for strain NE06-02DT (=DSM111602T=ATCC TSD-236T) and the other members of this novel species group.


Sujet(s)
Phylogenèse , Maladies des plantes/microbiologie , Solanum tuberosum , Streptomyces , Techniques de typage bactérien , Composition en bases nucléiques , ADN bactérien/génétique , Acides gras/composition chimique , ARN ribosomique 16S/génétique , Analyse de séquence d'ADN , Solanum tuberosum/microbiologie , Streptomyces/classification , Streptomyces/isolement et purification
SÉLECTION CITATIONS
DÉTAIL DE RECHERCHE