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Acevedo-Barrios R, Tirado-Ballestas I, Bertel-Sevilla A, Cervantes-Ceballos L, Gallego JL, Leal MA, Tovar D, Olivero-Verbel J. Bioprospecting of extremophilic perchlorate-reducing bacteria: report of promising Bacillus spp. isolated from sediments of the bay of Cartagena, Colombia. Biodegradation 2024:10.1007/s10532-024-10079-0. [PMID: 38625437 DOI: 10.1007/s10532-024-10079-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/06/2024] [Indexed: 04/17/2024]
Abstract
Three extremophile bacterial strains (BBCOL-009, BBCOL-014 and BBCOL-015), capable of degrading high concentrations of perchlorate at a range of pH (6.5 to 10.0), were isolated from Colombian Caribbean Coast sediments. Morphological features included Gram negative strain bacilli with sizes averaged of 1.75 × 0.95, 2.32 × 0.65 and 3.08 × 0.70 μm, respectively. The reported strains tolerate a wide range of pH (6.5 to 10.0); concentrations of NaCl (3.5 to 7.5% w/v) and KClO4- (250 to 10000 mg/L), reduction of KClO4- from 10 to 25%. LB broth with NaCl (3.5-30% w/v) and KClO4- (250-10000 mg/L) were used in independent trials to evaluate susceptibility to salinity and perchlorate, respectively. Isolates increased their biomass at 7.5 % (w/v) NaCl with optimal development at 3.5 % NaCl. Subsequently, ClO4- reduction was assessed using LB medium with 3.5% NaCl and 10000 mg/L ClO4-. BBCOL-009, BBCOL-014 and BBCOL-015 achieved 10%, 17%, and 25% reduction of ClO4-, respectively. The 16 S rRNA gene sequence grouped them as Bacillus flexus T6186-2, Bacillus marisflavi TF-11 (T), and Bacillus vietnamensis 15 - 1 (T) respectively, with < 97.5% homology. In addition, antimicrobial resistance to ertapenem, vancomycine, amoxicillin clavulanate, penicillin, and erythromycin was present in all the isolates, indicating their high adaptability to stressful environments. The isolated strains from marine sediments in Cartagena Bay, Colombia are suitable candidates to reduce perchlorate contamination in different environments. Although the primary focus of the study of perchlorate-reducing and resistant bacteria is in the ecological and agricultural realms, from an astrobiological perspective, perchlorate-resistant bacteria serve as models for astrobiological investigations.
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Affiliation(s)
- Rosa Acevedo-Barrios
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia.
- Grupo de Estudios Químicos y Biológicos, Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, POB 130001, Cartagena de Indias D. T. y C, Colombia.
| | - Irina Tirado-Ballestas
- GENOMA Group, Health Sciences Department, Universidad del Sinú, Santillana Campus, Cartagena, 130015, Colombia
- Group of Functional Toxicology, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia
| | - Angela Bertel-Sevilla
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia
| | - Leonor Cervantes-Ceballos
- Group of Functional Toxicology, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia
| | - Jorge L Gallego
- Department of Engineering, University of Medellin, Medellín, 050026, Colombia
| | - María Angélica Leal
- Planetary Sciences and Astrobiology Research Group (GCPA), Universidad Nacional de Colombia and Corporación Científica Laguna, Bogotá, 111321, Colombia
- Biosphere and Cosmos Research Group (BIOC). Corporación Científica Laguna, Bogotá, 111163, Colombia
| | - David Tovar
- Planetary Sciences and Astrobiology Research Group (GCPA), Universidad Nacional de Colombia and Corporación Científica Laguna, Bogotá, 111321, Colombia
- Biosphere and Cosmos Research Group (BIOC). Corporación Científica Laguna, Bogotá, 111163, Colombia
| | - Jesús Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Zaragocilla Campus, Cartagena, 130015, Colombia
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2
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Saggu SK, Nath A, Kumar S. Myxobacteria: biology and bioactive secondary metabolites. Res Microbiol 2023; 174:104079. [PMID: 37169232 DOI: 10.1016/j.resmic.2023.104079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.
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Affiliation(s)
- Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India - 144004.
| | - Amar Nath
- University Centre of Excellence in Research, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
| | - Shiv Kumar
- Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
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3
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Wang Z, Xu M, Li F, Bai Y, Hou J, Li X, Cao R, Deng Y, Jiang Y, Wang H, Yang W. Changes in soil bacterial communities and functional groups beneath coarse woody debris across a subalpine forest successional series. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
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4
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Soil substrate culturing approaches recover diverse members of Actinomycetota from desert soils of Herring Island, East Antarctica. Extremophiles 2022; 26:24. [PMID: 35829965 PMCID: PMC9279279 DOI: 10.1007/s00792-022-01271-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 06/06/2022] [Indexed: 11/12/2022]
Abstract
Antimicrobial resistance is an escalating health crisis requiring urgent action. Most antimicrobials are natural products (NPs) sourced from Actinomycetota, particularly the Streptomyces. Underexplored and extreme environments are predicted to harbour novel microorganisms with the capacity to synthesise unique metabolites. Herring Island is a barren and rocky cold desert in East Antarctica, remote from anthropogenic impact. We aimed to recover rare and cold-adapted NP-producing bacteria, by employing two culturing methods which mimic the natural environment: direct soil culturing and the soil substrate membrane system. First, we analysed 16S rRNA gene amplicon sequencing data from 18 Herring Island soils and selected the soil sample with the highest Actinomycetota relative abundance (78%) for culturing experiments. We isolated 166 strains across three phyla, including novel and rare strains, with 94% of strains belonging to the Actinomycetota. These strains encompassed thirty-five ‘species’ groups, 18 of which were composed of Streptomyces strains. We screened representative strains for genes which encode polyketide synthases and non-ribosomal peptide synthetases, indicating that 69% have the capacity to synthesise polyketide and non-ribosomal peptide NPs. Fourteen Streptomyces strains displayed antimicrobial activity against selected bacterial and yeast pathogens using an in situ assay. Our results confirm that the cold-adapted bacteria of the harsh East Antarctic deserts are worthy targets in the search for bioactive compounds.
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5
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Sharma A, Kumar A, Babu V, Ali A, Katoch M. Myxobacteria from animal dung pellets collected from northwestern Himalayas: A new source of di-isobutyl phthalate. J Basic Microbiol 2021; 62:162-173. [PMID: 34923648 DOI: 10.1002/jobm.202100518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/03/2021] [Accepted: 12/03/2021] [Indexed: 11/10/2022]
Abstract
Myxobacteria have emerged as a rich manufacturer of a wide array of natural products captivating both the academic and drug discovery communities. Attempts to unearth novel bioactive, myxobacteria from unexploited habitats are far from exhaustion. This study reports the isolation of myxobacteria from dung pellets collected from various regions of northwestern Himalayas. The isolated myxobacteria were functionally characterized to evaluate their bioactive capability. Of all the isolates, ST/P/71 exhibited broad range activities such as anticancer against all the four human cancer cell lines with IC50 in range of 2.03-9.65 µg/ml, antimicrobial against all the tested human pathogens, also exhibiting biofilm inhibition with MBIC50 at 10.4 µg/ml against Salmonella typhimurium. Consequently, ST/P/71 was chosen for fermentation and isolation of bioactive secondary metabolite through semi-preparative HPLC. It yielded compound 1, characterized as di-isobutyl phthalate (DiBP) based on nuclear magnetic resonance (NMR) and mass data. DiBP exhibited promising cytotoxic activity against the lung cancer cell line (A549) at an IC50 values 3.09 µg/ml and biofilm inhibition activity against Bacillus subtilis and Salmonella typhimurium with MBIC50 2.703 and 9.263 µg/ml, respectively. ST/P/71 was identified as Myxococcus fulvus. Thus, M. fulvus ST/P/71 isolated from northwestern Himalayas is a new source of DiBP.
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Affiliation(s)
- Arushi Sharma
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Amit Kumar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Quality Management and Instrumentation Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Vikash Babu
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Asif Ali
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Meenu Katoch
- Fermentation and Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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6
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Schneider YK. Bacterial Natural Product Drug Discovery for New Antibiotics: Strategies for Tackling the Problem of Antibiotic Resistance by Efficient Bioprospecting. Antibiotics (Basel) 2021; 10:antibiotics10070842. [PMID: 34356763 PMCID: PMC8300778 DOI: 10.3390/antibiotics10070842] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/25/2022] Open
Abstract
The problem of antibiotic resistance has become a challenge for our public health and society; it has allowed infectious diseases to re-emerge as a risk to human health. New antibiotics that are introduced to the market face the rise of resistant pathogens after a certain period of use. The relatively fast development of resistance against some antibiotics seems to be closely linked to their microbial origin and function in nature. Antibiotics in clinical use are merely products of microorganisms or derivatives of microbial products. The evolution of these antimicrobial compounds has progressed with the evolution of the respective resistance mechanisms in microbes for billions of years. Thus, antimicrobial resistance genes are present within the environment and can be taken up by pathogens through horizontal gene transfer. Natural products from bacteria are an important source of leads for drug development, and microbial natural products have contributed the most antibiotics in current clinical use. Bioprospecting for new antibiotics is a labor-intensive task as obstacles such as redetection of known compounds and low compound yields consume significant resources. The number of bacterial isolates one can theoretically investigate for new secondary metabolites is, on the other hand, immense. Therefore, the available capacity for biodiscovery should be focused on the most promising sources for chemical novelty and bioactivity, employing the appropriate scientific tools. This can be done by first looking into under- or unexplored environments for bacterial isolates and by focusing on the promising candidates to reduce the number of subjects.
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Affiliation(s)
- Yannik K Schneider
- Marbio, Faculty for Fisheries, Biosciences and Economy, UiT-The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway
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7
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Bertel-Sevilla A, Cervantes-Ceballos L, Tirado-Ballestas I, Maldonado-Rojas W, Alzate-Restrepo J, Olivero-Verbel J. Biodegradation of biodiesel-oil by Cellulosimicrobium sp. Isolated from Colombian Caribbean soils. ENVIRONMENTAL TECHNOLOGY 2020; 41:2337-2349. [PMID: 30596345 DOI: 10.1080/09593330.2018.1564798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
Biodiesel is considered to be a natural substitute for fossil fuel. The comparatively low toxicity of biodiesel and its susceptibility to microbial biodegradation could reduce its environmental impact. Currently, biodiesel is sold previously mixed with petroleum-based hydrocarbons. The aim of this work was to measure the biodegradation potential of commercially available biodiesel, using bacterial strains (BBCOL-001, BBCOL-002, and BBCOL-003) isolated from a tropical forest soils in the Colombian Caribbean. According to nucleotide sequencing of the gene encoding for 16S rRNA, the strains belong to members of the genus Cellulosimicrobium. GC-MS analysis showed that biodiesel-oil alkanes were degraded by an average of 81.5% with optical density reaching 0.2-0.3 in minimal salt media at 37°C for 5 days. Individual diesel-oil alkanes were degraded by the strains at rates between 64.9% to 100%. The increase in bacterial biomass confirmed the use of the substrates by the microorganisms, suggesting these hydrocarbons are a carbon source. Changes in the biochemical behaviour of the strains suggested their capacity to adapt to environmental conditions might be an important resource for bioremediation.
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Affiliation(s)
- Angela Bertel-Sevilla
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Leonor Cervantes-Ceballos
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Irina Tirado-Ballestas
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Wilson Maldonado-Rojas
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
| | - Juan Alzate-Restrepo
- Centro Nacional de Secuenciación Genómica-CNSG, Sede de Investigación Universitaria-SIU, Universidad de Antioquia, Medellin, Colombia
| | - Jesus Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, University of Cartagena, Cartagena, Colombia
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8
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Bioprospecting of indigenous myxobacteria from Iran and potential of Cystobacter as a source of anti-MDR compounds. Folia Microbiol (Praha) 2020; 65:639-648. [PMID: 31907732 DOI: 10.1007/s12223-019-00768-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/23/2019] [Indexed: 12/21/2022]
Abstract
Drug resistance is a critical issue in future clinical treatment. Methicillin-resistant Staphylococcus aureus (MRSA) is among the pathogens that need indispensable drug-discovery efforts. The myxobacteria are a unique group of bacteria that have recently been regarded for their potency to produce new drugs with high chemical diversity and unusual mode of actions. The present study was conducted to isolate and screen myxobacteria for the first time from Iran habitats and evaluate their antibacterial activity against the multidrug-resistant strain of S. aureus. Out of 62 soil and rotten plant samples, 51 myxobacteria were isolated. The isolates belonged to Myxococcus, Corallococcus, Pyxidicoccus, and Cystobacter genera based on morphology and 16S rRNA gene sequencing. Secondary metabolites of the selected strains were screened for activity on MDR strain with resistance to multiple antibiotic classes. The semi-purified fraction from Cystobacter sp. UTMC 4086 showed potent activity against MDR S. aureus with minimum inhibitory effect at 5 ≥ μg per mL compared with vancomycin (5 μg per mL) as well as no toxicity against Artemia salina. Hence, the strain Cystobacter sp. UTMC 4086 can be a valuable candidate for antibiotic discovery against MRSA and its metabolites can be subjected to further purification and analysis aimed at the identification of the effective chemical entity.
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9
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Suleiman AKA, Harkes P, van den Elsen S, Holterman M, Korthals GW, Helder J, Kuramae EE. Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 695:133885. [PMID: 31756853 DOI: 10.1016/j.scitotenv.2019.133885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/10/2019] [Indexed: 06/10/2023]
Abstract
Anthropogenic modification of soil systems has diverse impacts on food web interactions and ecosystem functioning. To understand the positive, neutral or adverse effects of agricultural practices on the associations of community members of soil microbes and microfaunal biomes, we characterized the effects of different fertilization types (organic, inorganic and a combination of organic and inorganic) on the food web active communities in the bulk soil and rhizosphere compartments in field conditions. We examined the influence of fertilization on (i) individual groups (bacteria, protozoa and fungi as microbe representatives and metazoans as microfauna representatives) and (ii) inter-kingdom interactions (focusing on the interactions between bacteria and eukaryotic groups) both neglecting and considering environmental factors in our analysis in combination with the microbial compositional data. Our results revealed different patterns of biota communities under organic versus inorganic fertilization, which shaped food web associations in both the bulk and rhizosphere compartments. Overall, organic fertilization increased the complexity of microbial-microfaunal ecological associations with inter- and intra- connections among categories of primary decomposers (bacteria and fungi) and predators (protozoa and microfauna) and differences in potential function in the soil food web in both the bulk and rhizosphere compartments. Furthermore, the inter-connections between primary decomposers and predators in bulk soil were more pronounced when environmental factors were considered. We suggest that organic fertilization selects bacterial orders with different potential ecological functions and interactions as survival, predation and cooperation due to more complex environment than those of inorganic or combined fertilization. Our findings support the importance of a comprehensive understanding of trophic food web patterns for soil management systems.
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Affiliation(s)
- Afnan K A Suleiman
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
| | - Paula Harkes
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Sven van den Elsen
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Martijn Holterman
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Gerard W Korthals
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands; Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands.
| | - Johannes Helder
- Wageningen University and Research Centre (WUR), Laboratory of Nematology, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Microbial Ecology, Wageningen, the Netherlands.
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Sierra-García IN, Romero-Tabarez M, Orduz-Peralta S. Determinación de la actividad antimicrobiana e insecticida de extractos producidos por bacterias aisladas de suelo. ACTUALIDADES BIOLÓGICAS 2017. [DOI: 10.17533/96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Colombia es considerado uno de los países con mayor diversidad biológica, sin embargo, muy poca de esa diversidad ha sido explorada para identificar sustancias biológicamente activas. Los metabolitos secundarios bacterianos pueden presentar actividad frente a patógenos de plantas y animales y representan alternativas biotecnológicas para la industria. El objetivo de este estudio fue evaluar el potencial de diferentes cepas bacterianas aisladas de suelo, para producir sustancias biológicamente activas como antibacterianos, antifúngicos e insecticidas. Un total de 92 extractos metanólicos de metabolitos secundarios bacterianos fueron evaluados. La actividad antibacterial y antifúngica se evaluó mediante el ensayo de difusión en agar frente a diversas bacterias como Bacillus subtilis, Enterococcus faecalis, Escherichia coli y Staphylococcus aureus frente a diferentes hongos Alternaria sp., Colletotrichum sp., Fusarium sp., Pestalotia sp. y Verticillium sp. La actividad insecticida se evaluó determinando el efecto de los extractos sobre la mortalidad de larvas de Aedes aegypti (Diptera) y Spodoptera frugiperda (Lepidoptera). Se determinó que el 50% de los aislamientos bacterianos tuvieron algún tipo de actividad, aunque la mayor actividad biológica se detectó en los extractos producidos por bacterias del género Bacillus, identificados por medio de análisis del ADN ribosomal 16S y por caracterización bioquímica con API® 50 CHB, MicroLogTM y Biolog. Las especies del género Bacillus identificadas han sido caracterizadas como productoras de compuestos antimicrobianos de amplio espectro o de varios compuestos con diferentes actividades. La actividad biológica presentada por los extractos evidencian que los microorganismos terrestres y especialmente, las especies de Bacillus son productores prolíficos de diversas sustancias bioactivas.
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11
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Molecular and functional characterization of myxobacteria isolated from soil in India. 3 Biotech 2017; 7:112. [PMID: 28567623 DOI: 10.1007/s13205-017-0722-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/06/2017] [Indexed: 10/19/2022] Open
Abstract
This study reports the isolation of myxobacteria from soil collected from plains in north India. Based on the morphology and 16S rDNA sequence, the isolated myxobacteria were identified as Corallococcus sp., Pyxidicoccus sp., Myxococcus sp., Cystobacter sp. and Archangium sp. The myxobacteria were functionally characterized to assess their ability to produce antibacterial and anticancer metabolites. The isolates were found to be functionally versatile as they produced extracellular bioactive molecules that exhibited high frequency of activities against Bacillus cereus, Mycobacterium smegmatis, Enterobacter cloacae and Pseudomonas syringae. The strains also showed cytotoxic activity against the human cancer cell lines of liver, pancreas, prostrate, bone and cervix. These results indicate the importance of isolating diverse strains of myxobacteria from unexplored habitats to find novel bioactive compounds. Moreover, the bioactive molecules explored in this study are predominantly hydrophilic compounds, obviating the limitations of solubility-related aspect of drug discovery.
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Charousová I, Steinmetz H, Medo J, Javoreková S, Wink J. Soil myxobacteria as a potential source of polyketide-peptide substances. Folia Microbiol (Praha) 2017; 62:305-315. [DOI: 10.1007/s12223-017-0502-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/26/2017] [Indexed: 02/06/2023]
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13
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Wang W, Wang H, Feng Y, Wang L, Xiao X, Xi Y, Luo X, Sun R, Ye X, Huang Y, Zhang Z, Cui Z. Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River. Sci Rep 2016; 6:35046. [PMID: 27725750 PMCID: PMC5057158 DOI: 10.1038/srep35046] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/15/2016] [Indexed: 12/17/2022] Open
Abstract
Soil microorganisms play a crucial role in the biogeochemical cycling of nutrient elements and maintaining soil health. We aimed to investigate the response of bacteria communities to organic farming over different crops (rice, tea and vegetable) along the middle and lower reaches of the Yangtze River of China. Compared with conventional farming, organic farming significantly increased soil nutrients, soil enzyme activities, and bacterial richness and diversity. A Venn diagram and principal component analysis revealed that the soils with 3 different crops under organic farming have more number and percent of shared OTUs (operational taxonomic units), and shared a highly similar microbial community structure. Under organic farming, several predominant guilds and major bacterial lineages (Rhizobiales, Thiotrichaceae, Micromonosporaceae, Desulfurellaceae and Myxococcales) contributing to nutrient (C, N, S and P) cycling were enriched, whereas the relative abundances of acid and alkali resistant microorganisms (Acidobacteriaceae and Sporolactobacillaceae) were increased under conventional farming practices. Our results indicated that, for all three crops, organic farming have a more stable microflora and the uniformity of the bacterial community structure. Organic agriculture significantly increased the abundance of some nutrition-related bacteria, while reducing some of the abundance of acid and alkali resistant bacteria.
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Affiliation(s)
- Wenhui Wang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Hui Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Youzhi Feng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lei Wang
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Xingji Xiao
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Yunguan Xi
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Xue Luo
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruibo Sun
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology of Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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Hemala L, Zhang D, Margesin R. Cold-active antibacterial and antifungal activities and antibiotic resistance of bacteria isolated from an alpine hydrocarbon-contaminated industrial site. Res Microbiol 2014; 165:447-56. [DOI: 10.1016/j.resmic.2014.05.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 05/12/2014] [Indexed: 01/06/2023]
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15
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Wang Y, Li X, Zhang W, Zhou X, Li YZ. The groEL2 gene, but not groEL1, is required for biosynthesis of the secondary metabolite myxovirescin in Myxococcus xanthus DK1622. MICROBIOLOGY-SGM 2014; 160:488-495. [PMID: 24425771 DOI: 10.1099/mic.0.065862-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Myxococcus xanthus DK1622 possesses two copies of the groEL gene: groEL1, which participates in development, and groEL2, which is involved in the predatory ability of cells. In this study, we determined that the groEL2 gene is required for the biosynthesis of the secondary metabolite myxovirescin (TA), which plays essential roles in predation. The groEL2-knockout mutant strain was defective in producing a zone of inhibition and displayed decreased killing ability against Escherichia coli, while the groEL1-knockout mutant strain exhibited little difference from the wild-type strain DK1622. HPLC revealed that deletion of the groEL2 gene blocked the production of TA, which was present in the groEL1-knockout mutant. The addition of exogenous TA rescued the inhibition and killing abilities of the groEL2-knockout mutant against E. coli. Analysis of GroEL domain-swapping mutants indicated that the C-terminal equatorial domain of GroEL2 was essential for TA production, while the N-terminal equatorial or apical domains of GroEL2 were not sufficient to rescue TA production of the groEL2 knockout.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - Xi Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - Wenyan Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - Xiuwen Zhou
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, PR China
| | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, PR China
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16
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Kumbhar C, Watve M. Why antibiotics: A comparative evaluation of different hypotheses for the natural role of antibiotics and an evolutionary synthesis. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ns.2013.54a005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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The UHPLC-DAD fingerprinting method for analysis of extracellular metabolites of fungi of the genus Geosmithia (Acomycota: Hypocreales). Anal Bioanal Chem 2011; 400:2943-52. [DOI: 10.1007/s00216-011-4982-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 03/31/2011] [Accepted: 04/02/2011] [Indexed: 10/18/2022]
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18
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Brunati M, Rojas JL, Sponga F, Ciciliato I, Losi D, Göttlich E, de Hoog S, Genilloud O, Marinelli F. Diversity and pharmaceutical screening of fungi from benthic mats of Antarctic lakes. Mar Genomics 2009; 2:43-50. [PMID: 21798171 DOI: 10.1016/j.margen.2009.04.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Revised: 04/01/2009] [Accepted: 04/08/2009] [Indexed: 10/20/2022]
Abstract
During the MICROMAT project, the fungal diversity of microbial mats growing in the benthic environment of Antarctic lakes was accessed for the discovery of novel antibiotics and anticancers. In all, 160 filamentous fungi belonging to fifteen different genera and 171 yeasts were isolated from 11 lakes, classified and cultivated in different media and at different temperatures. Filamentous fungi were then screened to discover novel antimicrobial and cytotoxic compounds. A total of 1422 extracts were prepared by solid phase extraction of the culture broths or by biomass solvent extraction. 47 (29%) filamentous fungi showed antimicrobial activity; most of them inhibited the growth of gram-positive Staphyloccus aureus (14%), gram-negative E. coli (10%), and of yeasts Candida albicans (11%) and Cryptococcus neoformans (8%). Less activity was detected against representatives of enterobacteria and filamentous fungi. The most productive in terms of bioactivities were cold-tolerant cosmopolitan hyphomycetes such as Penicillium, Aspergillus, Beauveria and Cladosporium. Two bioactive bis-anthraquinones (rugulosin and skyrin) were identified by LC-MS as the main products in a strain of Penicillium chrysogenum isolated from a saline lake in the Vestfold Hills. LC-MS fractionation of extracts from two diverse species of Aspergillus, that exhibited relatively potent antimicrobial activities, evidenced a chemical novelty that was further investigated. To our knowledge, this is the first report of new antibiotics produced by fungi from benthic microbial mats from Antarctic lakes. It can be concluded that these microbial assemblages represent an extremely rich source for the isolation of new strains producing novel bioactive metabolites with the potential to be developed as drugs.
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Affiliation(s)
- Mara Brunati
- Vicuron Pharmaceuticals (formerly Biosearch Italia S.p.A), Via R. Lepetit 34, 21040 Gerenzano Varese, Italy
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19
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Rojas JL, Martín J, Tormo JR, Vicente F, Brunati M, Ciciliato I, Losi D, Van Trappen S, Mergaert J, Swings J, Marinelli F, Genilloud O. Bacterial diversity from benthic mats of Antarctic lakes as a source of new bioactive metabolites. Mar Genomics 2009; 2:33-41. [PMID: 21798170 DOI: 10.1016/j.margen.2009.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Revised: 01/22/2009] [Accepted: 03/02/2009] [Indexed: 11/19/2022]
Abstract
During the MICROMAT project, the bacterial diversity of microbial mats growing in the benthic environment of Antarctic lakes was accessed for the discovery of novel antibiotics. In all, 723 Antarctic heterotrophic bacteria belonging to novel and/or endemic taxa in the α-, β- and γ-subclasses of the Proteobacteria, the Bacteroidetes branch, and of the high and low percentage G+C Gram-positives, were isolated, cultivated in different media and at different temperatures, and then screened for the production of antimicrobial activities. A total of 6348 extracts were prepared by solid phase extraction of the culture broths or by biomass solvent extraction. 122 bacteria showed antibacterial activity against the Gram-positives Staphylococcus aureus and to a lower extent Enterococcus faecium, and versus the Gram-negative Escherichia coli. Few of these strains showed also some antifungal activity against Cryptococcus neoformans, Aspergillus fumigatus and to a lower extent Candida albicans. LC-MS fractionation of extracts from a subset of strains (hits) that exhibited relatively potent antibacterial activities evidenced a chemical novelty that was further investigated. Two strains of Arthrobacter agilis produced potent antibacterial compounds with activity against Gram-positives and possibly related to novel cyclic thiazolyl peptides. To our knowledge, this is the first report of new antibiotics produced by bacteria from benthic microbial mats from Antarctic lakes. With no doubts these microbial assemblages represent an extremely rich source for the isolation of new strains producing novel bioactive metabolites with the potential to be developed as antibiotic compounds.
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Affiliation(s)
- Jose Luis Rojas
- CIBE, Merck Research Laboratories, Merck Sharp and Dohme de España S.A., Josefa Valcárcel 38, E-28027 Madrid, Spain
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20
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Marinelli F. Chapter 2 From Microbial Products to Novel Drugs that Target a Multitude of Disease Indications. Methods Enzymol 2009; 458:29-58. [DOI: 10.1016/s0076-6879(09)04802-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Discovering the hidden secondary metabolome of Myxococcus xanthus: a study of intraspecific diversity. Appl Environ Microbiol 2008; 74:3058-68. [PMID: 18378661 DOI: 10.1128/aem.02863-07] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
As a monophyletic group, the myxobacteria are known to produce a broad spectrum of secondary metabolites. However, the degree of metabolic diversity that can be found within a single species remains unexplored. The model species Myxococcus xanthus produces several metabolites also present in other myxobacterial species, but only one compound unique to M. xanthus has been found to date. Here, we compare the metabolite profiles of 98 M. xanthus strains that originate from 78 locations worldwide and include 20 centimeter-scale isolates from one location. This screen reveals a strikingly high level of intraspecific diversity in the M. xanthus secondary metabolome. The identification of 37 nonubiquitous candidate compounds greatly exceeds the small number of secondary metabolites previously known to derive from this species. These results suggest that M. xanthus may be a promising source of future natural products and that thorough intraspecific screens of other species could reveal many new compounds of interest.
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22
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Biondi N, Tredici MR, Taton A, Wilmotte A, Hodgson DA, Losi D, Marinelli F. Cyanobacteria from benthic mats of Antarctic lakes as a source of new bioactivities. J Appl Microbiol 2008; 105:105-15. [PMID: 18217933 DOI: 10.1111/j.1365-2672.2007.03716.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To exploit the cyanobacterial diversity of microbial mats growing in the benthic environment of Antarctic lakes for the discovery of novel antibiotic and antitumour activities. METHODS AND RESULTS In all, 51 Antarctic cyanobacteria isolated from benthic mats were cultivated in the laboratory by optimizing temperature, irradiance and mixing. Productivity was generally very low (</=60 mg l(-1) d(-1)) with growth rates (mu) in the range of 0.02-0.44 d(-1). Growth rates were limited by photosensitivity, sensitivity to air bubbling, polysaccharide production or cell aggregation. Despite this, 126 extracts were prepared from 48 strains and screened for antimicrobial and cytotoxic activities. Seventeen cyanobacteria showed antimicrobial activity (against the Gram-positive Staphylococcus aureus, the filamentous fungus Aspergillus fumigatus or the yeast Cryptococcus neoformans), and 25 were cytotoxic. The bioactivities were not in accordance with the phylogenetic grouping, but rather strain-specific. One active strain was cultivated in a 10-l photobioreactor. CONCLUSIONS Isolation and mass cultivation of Antarctic cyanobacteria and LC-MS (liquid chromatography/mass spectrometry) fractionation of extracts from a subset of those strains (hits) that exhibited relatively potent antibacterial and/or antifungal activities, evidenced a chemical novelty worthy of further investigation. SIGNIFICANCE AND IMPACT OF THE STUDY Development of isolation, cultivation and screening methods for Antarctic cyanobacteria has led to the discovery of strains endowed with interesting antimicrobial and antitumour activities.
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Affiliation(s)
- N Biondi
- Dipartimento di Biotecnologie Agrarie, Universita' degli Studi di Firenze, Firenze, Italy
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23
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Singh SB, Pelaez F. Biodiversity, chemical diversity and drug discovery. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2007; 65:141, 143-74. [PMID: 18084915 DOI: 10.1007/978-3-7643-8117-2_4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Drugs developed from microbial natural products are in the fundaments of modern pharmaceutical companies. Despite decades of research, all evidences suggest that there must remain many interesting natural molecules with potential therapeutic application yet to be discovered. Any efforts to successfully exploit the chemical diversity of microbial secondary metabolites need to rely heavily on a good understanding of microbial diversity, being the working hypothesis that maximizing biological diversity is the key strategy to maximizing chemical diversity. This chapter presents an overview of diverse topics related with this basic principle, always in relation with the discovery of novel secondary metabolites. The types of microorganisms more frequently used for natural products discovery are briefly reviewed, as well as the differences between terrestrial and marine habitats as sources of bioactive secondary metabolite producers. The concepts about microbial diversity as applied to prokaryotes have evolved in the last years, but recent data suggest the existence of true biogeographic patterns of bacterial diversity, which are also discussed. Special attention is dedicated to the existing strategies to exploit the microbial diversity that is not easy to tackle by conventional approaches. This refers explicitly to the current attempts to isolate and cultivate the previously uncultured bacteria, including the application of high throughput techniques. Likewise, the advances of microbial molecular biology has allowed the development of metagenomic approaches, i.e., the expression of biosynthetic pathways directly obtained from environmental DNA and cloned in a suitable host, as another way of accessing microbial genetic resources. Also, approaches relying on the genomics of metabolite producers are reviewed.
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Affiliation(s)
- Sheo B Singh
- Merck Research Laboratories, Rahway, New Jersey 07065, USA.
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24
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Peláez F. The historical delivery of antibiotics from microbial natural products—Can history repeat? Biochem Pharmacol 2006; 71:981-90. [PMID: 16290171 DOI: 10.1016/j.bcp.2005.10.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2005] [Revised: 09/23/2005] [Accepted: 10/05/2005] [Indexed: 11/22/2022]
Abstract
Microbial natural products are the origin of most of the antibiotics on the market today. However, research in antibiotics and natural products has declined significantly during the last decade as a consequence of diverse factors, among which the lack of interest of industry in the field and the strong competition from collections of synthetic compounds as source of drug leads. As a consequence, there is an alarming scarcity of new antibiotic classes in the pipelines of the pharmaceutical industry. Still, microbial natural products remain the most promising source of novel antibiotics, although new approaches are required to improve the efficiency of the discovery process. The impact of microbial biodiversity, the influence of growth conditions on the production of secondary metabolites, the choice of the best approach at the screening step and the challenges faced during the isolation and identification of the active compounds are examined in this review as the critical factors contributing to success in the effort of antibiotic discovery from microbial natural products.
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Affiliation(s)
- Fernando Peláez
- Centro de Investigación Básica, Merck, Sharp & Dohme de España, S.A. Josefa Valcárcel 38, E-28027 Madrid, Spain.
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