scholarly journals Predatory Organisms with Untapped Biosynthetic Potential: Descriptions of Novel Corallococcus Species C. aberystwythensis sp. nov., C. carmarthensis sp. nov., C. exercitus sp. nov., C. interemptor sp. nov., C. llansteffanensis sp. nov., C. praedator sp. nov., C. sicarius sp. nov., and C. terminator sp. nov.

2019 ◽  
Vol 86 (2) ◽  
Author(s):  
Paul G. Livingstone ◽  
Oliver Ingleby ◽  
Susan Girdwood ◽  
Alan R. Cookson ◽  
Russell M. Morphew ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Novel Species ◽  
Methyl Esters ◽  
Gene Clusters ◽  
Distinct Species ◽  
Antimicrobial Activities ◽  
Biologically Active ◽  
Active Metabolites ◽  
Taxonomic Assignment ◽  
Content Type

ABSTRACT Corallococcus spp. are common soil-dwelling organisms which kill and consume prey microbes through the secretion of antimicrobial substances. Two species of Corallococcus have been described previously (Corallococcus coralloides and Corallococcus exiguus). A polyphasic approach, including biochemical analysis of fatty acid methyl esters, substrate utilization, and sugar assimilation assays, was taken to characterize eight Corallococcus species strains and the two type strains. The genomes of all strains, including that of C. exiguus DSM 14696T (newly reported here), shared an average nucleotide identity below 95% and digital DNA-DNA hybridization scores of less than 70%, indicating that they belong to distinct species. In addition, we characterized the prey range and antibiotic resistance profile of each strain, illustrating the diversity of antimicrobial activity and, thus, the potential for drug discovery within the Corallococcus genus. Each strain gave a distinct profile of properties, which together with their genomic differences supports the proposal of the eight candidate strains as novel species. The eight candidates are as follows: Corallococcus exercitus sp. nov. (AB043AT = DSM 108849T = NBRC 113887T), Corallococcus interemptor sp. nov. (AB047AT = DSM 108843T = NBRC 113888T), Corallococcus aberystwythensis sp. nov. (AB050AT = DSM 108846T = NBRC 114019T), Corallococcus praedator sp. nov. (CA031BT = DSM 108841T = NBRC 113889T), Corallococcus sicarius sp. nov. (CA040BT = DSM 108850T = NBRC 113890T), Corallococcus carmarthensis sp. nov. (CA043DT = DSM 108842T = NBRC 113891T), Corallococcus llansteffanensis sp. nov. (CA051BT = DSM 108844T = NBRC 114100T), and Corallococcus terminator sp. nov. (CA054AT = DSM 108848T = NBRC 113892T). IMPORTANCE Corallococcus is a genus of predators with broad prey ranges, whose genomes contain large numbers of gene clusters for secondary metabolite biosynthesis. The physiology and evolutionary heritage of eight Corallococcus species strains were characterized using a range of analyses and assays. Multiple metrics confirmed that each strain belonged to a novel species within the Corallococcus genus. The strains exhibited distinct patterns of drug resistance and predatory activity, which mirrored their possession of diverse sets of biosynthetic genes. The breadth of antimicrobial activities observed within the Corallococcus genus highlights their potential for drug discovery and suggests a previous underestimation of both their taxonomic diversity and biotechnological potential. Taxonomic assignment of environmental isolates to novel species allows us to begin to characterize the diversity and evolution of members of this bacterial genus with potential biotechnological importance, guiding future bioprospecting efforts for novel biologically active metabolites and antimicrobials.

Lachnellins A, B, C, D, and Naphthalene-l,3,8-triol, Biologically Active Compounds from a Lachnellula Species (Ascomycetes)

1996 ◽  
Vol 51 (7-8) ◽  
pp. 500-512 ◽  
Author(s):  
Martin Semar ◽  
Heidrun Anke ◽  
Wolf-Rüdiger Arendholz ◽  
Robert Veiten ◽  
Wolfgang Steglich
Keyword(s):  
Serum Albumin ◽  
Reactive Intermediates ◽  
Antimicrobial Activities ◽  
Malate Synthase ◽  
Biologically Active ◽  
Inhibiting Activity ◽  
Active Metabolites ◽  
Submerged Cultures ◽  
Active Compounds ◽  
Biologically Active Metabolites

Abstract In the course of our search for new biologically active metabolites, lachnellin A (1), a metabolite with high cytotoxic and antimicrobial activities, the structurally related lachnellins B, C and D (3, 4, 7), and naphthalene-1,3,8-triol (8), an inhibitor of malate synthase (EC 4.1.3.2), were isolated from submerged cultures of the ascomycete Lachnellula sp. A 32 -8 9 . The antimicrobial, cytotoxic and phytotoxic activities of lachnellin A depended on its reactivity and could be abolished by the addition of cysteine. The enzyme inhibiting activity of (8) was due to reactive intermediates during melanization and was no longer observed in the presence of serum albumin. In addition, rac-scytalone (9), (+)-trans-3,4-dihydro-3,4,8-trihy-droxy-1(2H)-naphthalenone (10). 2,5-dihydroxytoluene (11), and (R)-(-)-5-methylmellein (12) were obtained from the same source and biologically characterized.

scholarly journals Diversity and antimicrobial potential of Actinobacteria isolated from diverse marine sponges along the Beibu Gulf of the South China Sea

2019 ◽  
Vol 95 (7) ◽  
Author(s):  
Tan Liu ◽  
Shufei Wu ◽  
Ruizhen Zhang ◽  
Dexiang Wang ◽  
Jun Chen ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Gene Clusters ◽  
Antimicrobial Activities ◽  
Marine Sponges ◽  
Biologically Active ◽  
Beibu Gulf ◽  
China Sea ◽  
Promising Source ◽  
Strong Antimicrobial Activity

ABSTRACT Marine sponge-associated microorganisms have proven to be a very promising source of biologically active and pharmaceutically important natural products. In this study, we investigated the diversity and antibacterial potential of bacteria from 49 sponge species isolated from the Beibu Gulf, South China Sea, belonging to 16 genera and several unidentified taxa. Using a variety of selective media, 363 strains with different morphologies were identified to six bacterial taxa, including Proteobacteria (α-subgroup 85 and γ-subgroup 59), Actinobacteria (123), Firmicutes (90), Bacteroidetes (5) and Brevundimonas (1). Media ISP2 and R2A were the most effective for isolating Actinobacteria. One hundred and twenty-three actinobacterial strains clustered into 21 genera identified by 16S rDNA gene sequencing, most of which were from the genus Microbacterium, followed by Pseudonocardia, Streptomyces, Kocuria, Aeromicrobium, Brachybacterium and Nocardiopsis, constituted 82% of total actinobacterial isolates. By using the minimal medium, 92 actinobacterial isolates showed antimicrobial activities, and 51 strains displayed moderate to strong antimicrobial activity that inhibited the growth of more than half of the bacteria tested in this study. Functional genes related to secondary metabolites were screened, revealing that 10% (12/123) of actinobacterial isolates contained PKS-KS genes, 18% (22/123) harbored NRPS-A genes and 6% (7/123) had hybrid PKS-NRPS gene clusters. The sponges Haliclona sp., Callyspongia sp. and Desmacella sp., belonging to class Demonspongiae, and Leucaltis sp. from the class Calcarea, were dominant hosts, harboring the most diverse actinobacterial genera with stronger antimicrobial activities and more diverse PKS/NRPS genes.

scholarly journals Cryptic, solo acylhomoserine lactone synthase from predatory myxobacterium suggests beneficial contribution to prey quorum signaling

2019 ◽  
Author(s):  
Hanan Albataineh ◽  
Maya Duke ◽  
Sandeep K. Misra ◽  
Joshua S. Sharp ◽  
D. Cole Stevens
Keyword(s):  
Microbial Communities ◽  
Gene Clusters ◽  
Biologically Active ◽  
Interspecies Interactions ◽  
Active Metabolites ◽  
Lytic Enzymes ◽  
Cultivation Conditions ◽  
Acylhomoserine Lactone ◽  
Polymicrobial Communities ◽  
Axenic Cultivation

AbstractConsidered a key taxon in microbial communities, myxobacteria exist as coordinated swarms that utilize an excreted combination of lytic enzymes and specialized metabolites to facilitate predation of numerous microbial phyla. This capacity to produce biologically active metabolites and the associated abundance of natural product biosynthetic pathways contained within their genomes have motivated continued drug discovery efforts from myxobacteria. Of all the biosynthetic gene clusters associated with myxobacteria deposited in the antiSMASH database (∼1,000 total), only one putative acylhomoserine lactone synthase, agpI, was observed in genome data from the myxobacterium Archangium gephyra. Without an acylhomoserine lactone (AHL) receptor also apparent in the genome of A. gephyra, we sought to determine if AgpI was the first example of an orphaned AHL synthase. Herein we report the bioinformatic assessment of AgpI and discovery of a second myxobacterial AHL synthase from Vitiosangium sp. strain GDMCC 1.1324. During axenic cultivation conditions, no detectible AHL metabolites were observed in A. gephyra extracts. However, heterologous expression of each synthase in Escherichia coli provided detectible quantities of 3 AHL signals including 2 known AHLs, C8-AHL and C9-AHL. These results suggest that A. gephyra AHL production is dormant during axenic cultivation conditions and requires an unknown external cue for activation. The orphaned AHL synthase, AgpI, is the first to be reported from a predatory myxobacterium, and predator production of prey quorum signals provides unique insight into interspecies crosstalk within polymicrobial communities.ImportanceThe presence of orphaned quorum signal receptors and associated recognition and response to exogenous acylhomoserine lactone quorum signals observed in microbial communities provides evidence for small molecule-mediated interspecies interactions. While the high occurrence of orphaned AHL receptors from bacteria that do not produce cognate AHL signals suggests the involvement of AHL signals as a shared chemical resource in polymicrobial communities, no orphaned AHL synthases have been determined to be functional in a species without an associated AHL receptor. An orphan signal synthase from a predatory myxobacterium provides an alternative perspective on the evolution and benefits of quorum signaling systems within these communities.

scholarly journals The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Gordon Webster ◽  
Alex J. Mullins ◽  
Aimee S. Bettridge ◽  
Cerith Jones ◽  
Edward Cunningham-Oakes ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Novel Species ◽  
Wood Decay ◽  
Gene Clusters ◽  
Antagonistic Activity ◽  
Biosynthetic Gene Clusters ◽  
Decay Fungi ◽  
Content Type ◽  
Wood Decay Fungi ◽  
Novel Taxa

Three strains of fungus-associated Burkholderiales bacteria with antagonistic activity against Gram-negative plant pathogens were genome sequenced to investigate their taxonomic placement and potential for antimicrobial specialized metabolite production. The selected strains were identified as novel taxa belonging to the genus Paraburkholderia and carry multiple biosynthetic gene clusters.

scholarly journals Bacillus polymachus sp. nov., with a broad range of antibacterial activity, isolated from forest topsoil samples by using a modified culture method

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 704-709 ◽  
Author(s):  
Tuan Manh Nguyen ◽  
Jaisoo Kim
Keyword(s):  
Staphylococcus Epidermidis ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Culture Method ◽  
Antimicrobial Activities ◽  
Microporous Membrane ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A new, modified culture method that utilizes a transwell plate with a 0.4 µm pore-size microporous membrane was developed. This system allows only trace nutrients from the soil into the liquid culture through the microporous membrane. The method is a more powerful tool for the discovery of novel species from soils than are traditional methods. Such newly identified species could potentially produce useful metabolites. A bacterial strain, T515T, was isolated using this modified culture method. Growth of strain T515T occurred at pH 4–9 in a temperature range between 20 °C and 40 °C and in the presence of 0–2 % (w/v) NaCl on R2A agar. Colonies on the agar plates were tiny, white, and convex after 5 days incubation at 28 °C. Comparative analysis of the nearly full-length 16S rRNA gene sequence of strain T515T revealed close pairwise similarity with species of the genus Bacillus , and strain T515T was most closely related to Bacillus panaciterrae Gsoil 1517T (96.7 %) and Bacillus funiculus NAF001T (96.0 %). The major quinone of strain T515T was menaquinone-7 (MK-7) and the major fatty acids were iso-C15 : 0 (45.5 %), anteiso-C15 : 0 (23.2 %) and C16 : 0 (10.9 %). The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Strain T515T was sensitive to streptomycin and tetracycline, but resistant to rifampicin (0.125 µg ml−1), ampicillin (0.5 µg ml−1) and chloramphenicol (1 µg ml−1). The strain showed antimicrobial activities against the six strains tested: Bacillus subtilis KEMB 51201-001, Staphylococcus aureus KEMB 4659, Pseudomonas aeruginosa KACC 10185, Staphylococcus epidermidis KACC 13234, Paenibacillus larvae KACC 14031 and Escherichia coli KEMB 212-234. Based on these results, strain T515T represents a novel species of the genus Bacillus with the proposed name, Bacillus polymachus sp. nov. The type strain is T515T ( = KEMB 9005-168T = KACC 18242T = NBRC 110614T).

scholarly journals Genome-based classification of three novel actinobacteria from the Karakum Desert: Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov

2020 ◽  
Vol 70 (3) ◽  
pp. 1993-2002 ◽  
Author(s):  
Hayrettin Saygin ◽  
Hilal Ay ◽  
Kiymet Guven ◽  
Nevzat Sahin
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Morphological Characteristics ◽  
Distinct Species ◽  
Diaminopimelic Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

Three isolates, 5K138T, 8K307T and KC603T, with typical morphological characteristics of members of the genus Jiangella were obtained during a study searching for novel actinobacteria with biosynthetic potential from the Karakum Desert. A polyphasic approach was adopted to determine taxonomic affiliations of the strains. The strains showed chemotaxonomic properties consistent with their classification as representing members of the genus Jiangella such as ll-diaminopimelic acid in the cell wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol as major polar lipids as well as MK-9(H4) as a major menaquinone. Pairwise sequence comparisons of the 16S rRNA genes showed that the strains were closely related to Jiangella alba DSM 45237T, Jiangella rhizosphaerae NEAU-YY265T and Jiangella mangrovi 3SM4-07T with higher than 99 % sequence identities. However, a combination of phenotypic and phylogenetic approaches as well as genome-based comparative analyses confirmed the taxonomic positions of these strains as representing distinct species within the genus Jiangella . Therefore, strains 5K138T, 8K307T and KC603T should each be classified as representing a novel species within the genus Jiangella , for which the names Jiangella asiatica sp. nov., Jiangella aurantiaca sp. nov. and Jiangella ureilytica sp. nov. are proposed, respectively. The type strains of the proposed novel species are as follows: Jiangella asiatica 5K138T (=JCM 33518T=CGMCC 4.7672T), Jiangella aurantiaca 8K307T (=JCM 33519T=CGMCC 4.7621T) and Jiangella ureilytica KC603T (=JCM 33520T=CGMCC 4.7618T).

Whether viable and dead probiotic are equally efficacious?

2018 ◽  
Vol 48 (2) ◽  
pp. 285-300 ◽  
Author(s):  
S. Sarkar
Keyword(s):  
Functional Properties ◽  
Health Benefits ◽  
World Market ◽  
Biologically Active ◽  
Live Cells ◽  
Active Metabolites ◽  
Content Type ◽  
Factors Affecting ◽  
The Status ◽  
Metabolic Activities

Purpose Consumer inclination towards probiotic foods has been stimulated due to well-documented evidence of health benefits of probiotic-containing products and consumer demand for natural products. It is assumed that the viability and metabolic activities of probiotics are essential for extending health benefits and for successful marketing of probiotics as a functional food. The purpose of this paper is to demonstrate that even dead or inactivated probiotic cells could extend health benefits, indicating that probiotic viability is not always necessary for exhibiting health benefits. Design/methodology/approach Attempt has been made to review the literature on the status of probiotic foods available in the world market, their impact on the gut flora and the various factors affecting their viability. Both review and research papers related to efficacy of inactivated, killed or dead probiotic cells towards health benefits have been considered. Keywords used for data search included efficacy of viable or killed, inactivated probiotic cells. Findings The reviewed literature indicated that inactivated, killed or dead probiotic cells also possess functional properties but live cells are more efficacious. All live probiotic cultures are not equally efficacious, and accordingly, dead or inactivated cells did not demonstrate functional properties to extend health benefits to all diseases. Originality/value Capability of non-viable microorganisms to confer health benefits may attract food manufacturers owing to certain advantages over live probiotics such as longer shelf-life, handling and transportation and reduced requirements for refrigerated storage and inclusion of non-bacterial, biologically active metabolites present in fermented milks’ fraction as dried powders to food matrixes may result in the development of new functional foods.

Pontibacter aquaedesilientis sp. nov., isolated from Jeongbang Waterfall, Jeju Island

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Geeta Chhetri ◽  
Taegun Seo
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Stream Water ◽  
Draft Genome ◽  
Gene Clusters ◽  
Jeju Island ◽  
Rrna Gene ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type

A red-pigmented, aerobic, motile by gliding, pleomorphic to long-rods and divided by budding bacterium, Gram-stain negative bacterium, designated JH31T, was isolated from stream water of Jeongbang Waterfall, famous feature of Jeju Island, Republic of Korea. The cells grew at 9–40 °C (optimum, 28–30 °C), at pH 5.0–10.0 (pH 6.5–7.5) and with 0–6% NaCl (0% NaCl). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JH31T forms a lineage within the family Hymenobacteriaceae and clusters with its closest related species Pontibacter virorsus KCTC 42941T (98.1%), Pontibacter salisaro KACC 16885T (98.0%), Pontibacter amylolyticus JCM 19653T (97.2%), Pontibacter ramchanderi KACC 17384T (97.2%) and Pontibacter lucknowensis DM9T (96.4%). Strain JH31T produced carotenoid-type pigments but no flexirubin-type pigments. The genome was 4117105 bp long with 18 contigs and 3509 protein-coding genes. The DNA G+C content was 49.7 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between the genome sequence of strain JH31T and its closely related reference strains were less than 19 and 72%, respectively. The draft genome of strain JH31T contained vital gene clusters involved in resistance against various metals, antibiotics, toxic compounds and radiation. The respiratory quinone of strain JH31T was menaquinone 7 and the predominant cellular fatty acids were iso-C15:0, and summed feature 4 (comprising iso-C17:1 I and/or anteiso B). The major polar lipids were phosphatidylethanolamine, three unidentified glycolipids, one unidentified phospholipid, one unidentified phosphoglycolipid and one unidentified aminoglycolipid. The phylogenetic, physiochemical and biochemical data showed that strain JH31T should represent a novel species in the genus Pontibacter , for which the name Pontibacter aquaedesilientis sp. nov. is proposed. The type strain for this novel species is JH31T (KACC 21705T=NBRC 114480T).

scholarly journals Genome Sequence of Streptomyces cavourensis 1AS2a, a Rhizobacterium Isolated from the Brazilian Cerrado Biome

2019 ◽  
Vol 8 (18) ◽  
Author(s):  
Harold Alexander Vargas Hoyos ◽  
Suikinai Nobre Santos ◽  
Gabriel Padilla ◽  
Itamar Soares Melo
Keyword(s):  
Gene Clusters ◽  
Antimicrobial Activities ◽  
Open Reading Frames ◽  
Biosynthetic Gene ◽  
Brazilian Cerrado ◽  
Neotropical Savanna ◽  
Biosynthetic Gene Clusters ◽  
Content Type ◽  
Wheat Rhizosphere ◽  
Reading Frames

Streptomyces cavourensis strain 1AS2a, isolated from wheat rhizosphere in the Brazilian Neotropical savanna, exhibits strong antimicrobial activities. Its genome comprises 7,600,475 bp with 6,590 open reading frames (ORFs) that reveal 30 biosynthetic gene clusters (BGCs).

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