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

Biomolecules ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 673
Author(s):  
Kattia Núñez-Montero ◽  
Damián Quezada-Solís ◽  
Zeinab G. Khalil ◽  
Robert J. Capon ◽  
Fernando D. Andreote ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Secondary Metabolites ◽  
Culture Media ◽  
Genome Mining ◽  
Gene Clusters ◽  
Culture Conditions ◽  
Bioactive Metabolites ◽  
Bacterial Strains ◽  
Antarctic Bacteria ◽  
New Antibiotics

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

scholarly journals Potential secondary metabolite biosynthetic gene clusters and antibacterial activity of novel taxa Gandjariella

2020 ◽  
Vol 21 (12) ◽  
Author(s):  
Fitria Ningsih ◽  
Dhian Chitra Ayu Fitria Sari ◽  
Shuhei Yabe ◽  
Akira Yokota ◽  
Wellyzar Sjamsuridzal
Keyword(s):  
Antibacterial Activity ◽  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Polyketide Synthase ◽  
Gene Clusters ◽  
Gellan Gum ◽  
Biosynthetic Gene ◽  
Bacterial Strains ◽  
Biosynthetic Gene Clusters ◽  
Novel Taxa

Abstract. Ningsih F, Sari DCAF, Yabe S, Yokota A, Sjamsuridzal W. 2020. Potential secondary metabolite biosynthetic gene clusters and antibacterial activity of novel taxa Gandjariella. Biodiversitas 21: 5674-5684. Microbial resistance to available antibiotics has gained increasing attention in recent years and led to the urgent search for active secondary metabolites from novel microbial taxa. This study aimed to assess putative secondary metabolite biosynthetic gene clusters (BGCs) in the genome of a novel thermophilic Actinobacteria type strain Gandjariella thermophila SL3-2-4T and screen for its antibacterial activity. Four other related novel candidate Actinobacteria strains, isolated from forest soil in the Cisolok geothermal area (West Java, Indonesia), were also screened for antibacterial activity in various media solidified with gellan gum. The genome of the SL3-2-4T strain contained 21 antiSMASH-identified secondary metabolite regions harboring BGCs. These BGCs were for polyketide synthase, non-ribosomal peptide synthase, and ribosomally synthesized and post-translationally modified peptide family clusters. Three BGC regions displayed 50-100% similarity with known secondary metabolites. Thirteen and five regions displayed low (4-35%) and no similarity with known BGCs for secondary metabolites, respectively. Strains SL3-2-4T and SL3-2-7 on MM 2 medium solidified with gellan gum at 45 °C for 14 days demonstrated inhibitory activity against all Gram-positive, but not Gram-negative bacteria. Strain SL3-2-10 on ISP 3 gellan gum medium incubated for seven days only active against K. rhizophila NBRC 12078. Strains SL3-2-6 and SL3-2-9 did not exhibit any antibacterial activity against the tested bacterial strains on the three tested media. The results indicated that novel taxa have the potential for the discovery of active secondary metabolites.

scholarly journals Isolation of endophytic bacteria from the leaves of Anredera cordifolia CIX1 for metabolites and their biological activities

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Celiwe Innocentia Nxumalo ◽  
Londeka Sibusisiwe Ngidi ◽  
Jabulani Siyabonga Emmanuel Shandu ◽  
Tsolanku Sidney Maliehe
Keyword(s):  
Antibacterial Activity ◽  
Secondary Metabolites ◽  
Inhibitory Concentration ◽  
Antioxidant Activities ◽  
Biological Activities ◽  
Penicillin G ◽  
Gas Chromatography Mass Spectrometry ◽  
Bioactive Metabolites ◽  
Chemical Components ◽  
Bacterial Strains

Abstract Background Endophytes, especially those that are found from ethnopharmacologically noteworthy medicinal plants have attracted attention due to their diverse bioactive metabolites of pharmacological importance. Methods This study aimed at isolating endophytic bacterium from the leaves of Anredera cordifolia CIX1 for its bioactive metabolites. The endophytic isolates were identified by 16S rRNA sequence and investigated for antibiotic sensitivity using different antibiotics. The secondary metabolites were evaluated for antibacterial activity against four bacterial strains. The 2-diphenyl-1-picrylhydrazyl (DPPH) and 2, 2′-azinobis (3- ethylbenzothiazoline-6-sulfonic acid) (ABTS) methods were used to assess their scavenging activities. The chemical components were analysed by gas chromatography-mass spectrometry (GC-MS). Results Out of 13 isolates, Isolate 1 was identified as Pseudomonas aeruginosa CP043328.1. It was resistant to clindamycin, ertapenem, penicillin G, amoxicillin, cephalothin and kanamycin but sensitive to imipenem, meropenem, and gentamycin. Its extract demonstrated antibacterial activity with minimum inhibitory concentration value of 0.098 against Bacillus cereus (ATCC 10102) and Staphylococcus aureus (ATCC 25925) and 0.391 mg/ml against Escherichia coli (ATCC 25922) and Proteus mirabilis (ATCC 25933). The extract revealed DPPH and ABTS scavenging activities with half maximal inhibitory concentration value of 0.650 mg/ml and 0.15 mg/ml, respectively. The GC-MS revealed a total of 15 compounds with diisooctyl phthalate (50.51%) and [1, 2, 4] oxadiazole, 5-benzyl-3 (10.44%) as major components. Conclusions P. aeruginosa CP043328.1 produced secondary metabolites with antibacterial and antioxidant activities.

scholarly journals Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria

2020 ◽  
Author(s):  
Jenny Schwarz ◽  
Stephan Lütz
Keyword(s):  
Secondary Metabolite ◽  
Genome Mining ◽  
Gene Clusters ◽  
Culture Conditions ◽  
Bacterial Strains ◽  
The Past ◽  
Desferrioxamine B ◽  
Prior Literature ◽  
The One ◽  
Literature Coverage

Over the past decade, the One Strain Many Compounds (OSMAC) approach has been established for silent gene cluster activation and elicitation of secondary metabolite production, but so far the full secondary metabolome of a biosynthetically promising bacterium has not been elucidated yet. Here, we investigate the ability of seven categories of OSMAC conditions to enhance the diversity of new mass features from bacterial strains with little literature coverage but high biosynthetic potential. The strains Bacillus. amyloliquefaciens DSM7, Corallococcus. coralloides DSM2259, Pyxidicoccus. fallax HKI727, Rhodococcus. jostii DSM44719, and Streptomyces. griseochromogenes DSM40499 were selected after genome mining with antiSMASH. After cultivation under OSMAC conditions, the generated extracts were subjected to LC-MS and MZmine analysis to determine new mass features and evaluate the tested culture conditions. 4 predicted compounds, bacillibactin, desferrioxamine B, myxochelin A, and surfactin, were identified and up to 147 new mass features were detected in the generated extracts, which greatly surpasses the number of predicted gene clusters. Among the new mass features are bioactive compounds that were so far unreported for the strains such as cyclo-(Tyr-Pro) from DSM7 and nocardamin from DSM2259. Furthermore, the tested culture conditions were evaluated regarding their suitability for the generation of new mass features from the selected strains and promising new starting points for further screenings are postulated. Especially culture conditions with little prior literature coverage are responsible for the activation of predicted gene clusters

scholarly journals Triaging of Culture Conditions for the Enhanced Discovery of Secondary Metabolites from Different Bacteria

2020 ◽  
Author(s):  
Jenny Schwarz ◽  
Stephan Lütz
Keyword(s):  
Secondary Metabolite ◽  
Genome Mining ◽  
Gene Clusters ◽  
Culture Conditions ◽  
Secondary Metabolite Production ◽  
Bacterial Strains ◽  
Metabolite Production ◽  
Desferrioxamine B ◽  
Prior Literature ◽  
Literature Coverage

Over the past decade, the One Strain Many Compounds (OSMAC) approach has been established for silent gene cluster activation and elicitation of secondary metabolite production, but so far the full secondary metabolome of a biosynthetically promising bacterium has not been elucidated yet. Here, we investigate the ability of seven categories of OSMAC conditions to elicit new mass features from bacterial strains with little literature coverage but high biosynthetic potential. The strains B. amyloliquefaciens DSM7, C. coralloides DSM2259, P. fallax HKI727, R. jostii DSM44719 and S. griseochromogenes DSM40499 were selected after genome mining with antiSMASH. After cultivation under OSMAC conditions, the generated extracts were subjected to LC/MS and MZmine analysis to determine new mass features, expressed gene clusters and evaluate the tested culture conditions. 4 predicted compounds, bacillibactin, desferrioxamine B, myxochelin A and surfactin, were identified and up to 147 new mass features were detected in the generated extracts, which greatly surpasses the number of predicted gene clusters. Among the new mass features are bioactive compounds which were so far unreported for the strains such as cyclo-(Tyr-Pro) from DSM7 and nocardamin from DSM2259. Furthermore, the tested culture conditions were evaluated regarding their suitability for the generation of new mass features from the selected strains and promising new starting points for further screenings are postulated. Especially culture conditions with little prior literature coverage are responsible for the activation of secondary metabolite production.

scholarly journals Discovery of a polybrominated aromatic secondary metabolite from a planctomycete points at an ambivalent interaction with its macroalgae host

2019 ◽  
Author(s):  
Fabian Panter ◽  
Ronald Garcia ◽  
Angela Thewes ◽  
Nestor Zaburannyi ◽  
Boyke Bunk ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Biological Activities ◽  
Genome Mining ◽  
Gene Clusters ◽  
Laboratory Culture ◽  
Culture Conditions ◽  
Herbicidal Activity ◽  
Spectrometric Analysis ◽  
Plant Toxin

AbstractThe roles of the majority of bacterial secondary metabolites, especially those from uncommon sources are yet elusive even though many of these compounds show striking biological activities. To further investigate the secondary metabolite repertoire of underexploited bacterial families, we chose to analyze a novel representative of the yet untapped bacterial phylum Planctomycetes for the production of secondary metabolites under laboratory culture conditions. Development of a planctomycetal high density cultivation technique in combination with high resolution mass spectrometric analysis revealed Planctomycetales strain 10988 to produce the plant toxin 3,5 dibromo p-anisic acid. This molecule represents the first secondary metabolite reported from any planctomycete. Genome mining revealed the biosynthetic origin of this doubly brominated secondary metabolite and a biosynthesis model for the com-pound was devised. Comparison of the biosynthetic route to biosynthetic gene clusters responsible for formation of polybrominated small aromatic compounds reveals evidence for an evolutionary link, while the compound’s herbicidal activity points towards an ambivalent role of the metabolite in the planctomycetal ecosystem.

scholarly journals Metabolic profiling and antibacterial activity of Eryngium pristis Cham. & Schltdl. - prospecting for its use in the treatment of bacterial infections

2021 ◽  
Vol 5 (1) ◽  
pp. 020-028
Author(s):  
Fernandes Laura Silva ◽  
da Costa Ygor Ferreira Garcia ◽  
de Bessa Martha Eunice ◽  
Ferreira Adriana Lucia Pires ◽  
do Amaral Corrêa José Otávio ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Bioactive Compounds ◽  
Metabolic Profile ◽  
Bacterial Infections ◽  
Ethanolic Extract ◽  
Multidrug Resistant ◽  
Gas Chromatography Mass Spectrometry ◽  
Resistant Bacteria ◽  
Bacterial Strains ◽  
New Antibiotics

Morbidity and mortality of the infected patients by multidrug-resistant bacteria have increased, emphasizing the urgency of fight for the discovery of new innovative antibiotics. In this sense, natural products emerge as valuable sources of bioactive compounds. Among the biodiversity, Eryngium pristis Cham. & Schltdl. (Apiaceae Lindl.) is traditionally used to treat thrush and ulcers of throat and mouth, as diuretic and emmenagogue, but scarcely known as an antimicrobial agent. With this context in mind, the goals of this study were to investigate the metabolic profile and the antibacterial activity of ethanolic extract (EE-Ep) and hexane (HF-Ep), dichloromethane (DF-Ep), ethyl acetate (EAF-Ep) and butanol (BF-Ep) fractions from E. pristis leaves. Gas Chromatography-Mass Spectrometry (GC-MS) was performed to stablish the metabolic profile and revealed the presence of 12 and 14 compounds in EAF-Ep and HF-Ep, respectively. β-selinene, spathulenol, globulol, 2-methoxy-4-vinylphenol, α-amyrin, β-amyrin, and lupeol derivative were some of phytochemicals identified. The antibacterial activity was determined by Minimal Inhibitory Concentration (MIC) using the broth micro-dilution against eight ATCC® and five methicillin-resistant Staphylococcus aureus (MRSA) clinical strains. HF-Ep was the most effective (MIC ≤ 5,000 µg/µL), being active against the largest part of tested Gram-positive and Gram-negative bacterial strains, including MRSA, with exception of Escherichia coli (ATCC 25922) and Pseudomonas aeruginosa (ATCC 9027) and (ATCC 27853). These results suggest that E. pristis is a natural source of bioactive compounds for the search of new antibiotics which can be an interesting therapeutic approach to recover patients mainly infected by MRSA strains.

scholarly journals Genome mining of a marine-derived Streptomyces sp. PDH23 isolated from sponge in Da Nang sea for secondary metabolite gene clusters

2021 ◽  
Vol 18 (4) ◽  
pp. 709-721
Author(s):  
Le Ngoc Giang ◽  
Le Thi Hong Minh ◽  
Vu Thi Quyen ◽  
Nguyen Mai Anh ◽  
Nguyen Thi Kim Cuc ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Antimicrobial Agents ◽  
Biological Activities ◽  
Wide Spectrum ◽  
Genome Mining ◽  
Gc Content ◽  
Gene Clusters ◽  
Gram Positive ◽  
16S Rrna Analysis ◽  
Streptomyces Sp

The streptomyces is one of the best characterized ubiquitous filamentous bacteria from the actinobacteriaclass. They are known to produce thousands of specialized metabolite biosynthesis gene clusters (SMBG). Their SMBG clusters have multiple activities ranging from antimicrobial, antitumor, antiviral and probiotic. Streptomyces strain and their isolates with interesting biological activities against gram-positive and gram-negative indicator strains was recently characterised. Currently, they are employed in more than half of all antibiotics used in human and veterinary medicine. With the increase in drug resistance bacteria, it is important to mine for new natural chemicals.In this study, screening via disk-diffusion agar method revealed that Streptomyces sp. PDH23 isolated from the Rhabdastrellaglobostellata marine sponge sample from Da Nang, Vietnam produce antimicrobial agents with a wide spectrum of activities. This species can produce highly active enzymes, which breakdown celluloses, amyloses and proteins. On top of that they are shown to restrict the grow of the gram positive Bacillus cereus ATCC14579 (BC), Staphylococcus aureus ATCC25923 (SA), the gram-negativeVibrio parahaemolyticus ATCC17802 (VP) and the Candida albicans ATCC10231 fungus (CA). They are antimethicillin-resistant S. aureus(MRSA) ATCC33591 andmethicillin-resistantS. epidermidis (MRSE) ATCC35984. The taxonomy of PDH23 was characterized using 16S rRNA analysis. Whole genome sequencing of PDH23 showed 8594820 base pairs with GC content of 72.03%. Mining of secondary metabolites reveals gene clusters responsible for the biosynthesis of known and/or novel secondary metabolites, including different types of terpene, NRPS-like , PKS, PKS-like, hglE-KS, betalactone, melanin, t1pks, t2pks, t3pks, nrps, indole, siderophore, bacteriocin, ectoine, butyrolactone, phenazine.

scholarly journals Genome mining and UHPLC-MS/MS illuminate the specificity of secondary metabolite synthetic gene clusters in Bacillus subtilis NCD-2

2020 ◽  
Author(s):  
Zhenhe Su ◽  
Xiuye Chen ◽  
Xiaomeng Liu ◽  
Qinggang Guo ◽  
Shezeng Li ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Biological Activities ◽  
Genome Mining ◽  
Gene Clusters ◽  
Synthetic Gene ◽  
Integrative Approach ◽  
Amino Acid Sequence Similarity ◽  
Genetic Characteristics

Abstract Background Bacillus subtilisstrain NCD-2 is anexcellent biocontrol agent against plant soil-borne diseases and shows broad-spectrum antifungal activities. This study aimed to explore all the secondary metabolite synthetic gene clusters and related bioactive compounds in NCD-2. An integrative approach, which coupled genome mining with structural identification technologies using ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry (UHPLC-MS/MS), was conducted to interpret the chemical origins of the significant biological activities in NCD-2. Results Genome mining revealed that NCD-2 contained nine gene clustershaving predicted functionsinvolving secondary metabolites with bioactive abilities. They encoded six known products-fengycin, surfactin, bacillaene, subtilosin, bacillibactin, and bacilysin-as well as three unknown products.Interestingly, the synthetic gene clusters for surfactin and fengycin showed 83% and 92% amino acid sequence similarity levels with the corresponding productsin Bacillus velezensisstrain FZB42. A further comparison of gene clusters encoding fengycin and surfactinrevealed that strain NCD-2 had lost thefenC and fenDgenes in the fengycinbiosynthetic operon, and that the surfactin synthetic enzyme-related gene srfAB was divided into two parts.Abioinformatics analysis showed that fenEAmay function as fenCD in synthesizing fengycinand that the structure of thisfengycin synthetic gene clusteris likely unique to NCD-2.Five kinds of fengycin,with 26 homologs, and surfactin,with 4 homologs,were detectedfrom strain NCD-2, which indicated the non-typical and unique nature of this fengycin biosynthetic gene cluster.To the best of our knowledge, this is the first report of a non-typical gene cluster related to fengycin synthesis. Conclusions The data provide the genetic characteristics of secondary metabolite synthetic gene clusters for fengycinand surfactin in B. subtilis NCD-2, including the unique synthetic mechanism for fengycin, and suggest that bioactive secondary metabolites explain the biological activities of NCD-2.

scholarly journals A global survey of specialized metabolic diversity encoded in bacterial genomes

2021 ◽  
Author(s):  
Athina Gavriilidou ◽  
Satria A Kautsar ◽  
Nestor Zaburannyi ◽  
Daniel Krug ◽  
Rolf Mueller ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Evolutionary History ◽  
Gene Clusters ◽  
Chemical Diversity ◽  
Metabolic Diversity ◽  
Bacterial Genomes ◽  
Biosynthetic Gene Clusters ◽  
Taxonomic Rank ◽  
New Antibiotics ◽  
Biosynthetic Machinery

Bacterial secondary metabolites have been studied for decades for their usefulness as drugs, such as antibiotics. However, the identification of new structures has been decelerating, in part due to rediscovery of known compounds. Meanwhile, multi-resistant pathogens continue to emerge, urging the need for new antibiotics. It is unclear how much chemical diversity exists in Nature and whether discovery efforts should be focused on established antibiotic producers or rather on understudied taxa. Here, we surveyed around 170,000 bacterial genomes as well as several thousands of Metagenome Assembled Genomes (MAGs) for their diversity in Biosynthetic Gene Clusters (BGCs) known to encode the biosynthetic machinery for producing secondary metabolites. We used two distinct algorithms to provide a global overview of the biosynthetic diversity present in the sequenced part of the bacterial kingdom. Our results indicate that only 3% of genomic potential for natural products has been experimentally discovered. We connect the emergence of most biosynthetic diversity in evolutionary history close to the taxonomic rank of genus. Despite enormous differences in potential among taxa, we identify Streptomyces as by far the most biosynthetically diverse based on currently available data. Simultaneously, our analysis highlights multiple promising high-producing taxas that have thus far escaped investigation.

scholarly journals Antibacterial and antioxidant activities of Licania tomentosa (Benth.) fritsch (crhysobalanaceae)

2012 ◽  
Vol 64 (2) ◽  
pp. 459-464 ◽  
Author(s):  
J.B.N.F. Silva ◽  
I.R.A. Menezes ◽  
H.D.M. Coutinho ◽  
F.F.G. Rodrigues ◽  
J.G.M. Costa ◽  
...  
Keyword(s):  
Antibacterial Activity ◽  
Secondary Metabolites ◽  
Inhibitory Concentration ◽  
Antioxidant Activities ◽  
Positive Control ◽  
Antioxidative Capacity ◽  
Bacterial Strains ◽  
Hydroalcoholic Extract ◽  
Phytochemical Composition ◽  
Antibacterial Assay

This work describes the chemical composition, and evaluates the antimicrobial and antioxidant activities of a hydroalcoholic extract from the leaves of the Licania tomentosa. Gram positive and negative bacterial strains were used in this work. Examination of the phytochemical composition of L. tomentosa revealed the presence of secondary metabolites such as tannins, flavonoids, saponins, alkaloids, steroids and triterpenoids. An antibacterial assay pointed out that the extract had a lower minimal inhibitory concentration (MIC - 32 ?g/mL) towards Staphylococcus aureus (ATCC12692). The extract also presented antibacterial activity against other assayed bacteria, with the MIC varying between 64 and 512 ?g/ mL. Our findings reveal that the extract presented an antioxidative capacity lower than that of BHT at the same concentration, used as positive control. Our results suggest that the levels and combinations between the secondary metabolites of this plant should be investigated to explain the demonstrated antibacterial activity.

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