Optimization of Streptomyces peucetius var. caesius N47 cultivation and ?-rhodomycinone production using experimental designs and response surface methods

Kiviharju, Kristiina; Leisola, Matti; Eerikäinen, Tero

doi:10.1007/s10295-004-0172-3

Cited by 15 publications

(8 citation statements)

References 23 publications

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“…While mixture experiments occur most frequently in areas such as chemistry and agriculture, they have also been applied in the biological sciences. Mixture designs can be used for screening complex medium components in the cultivation of bacteria and evaluating the influence of nutrients on bacterial byproducts and growth [ 26 - 30 ]. For instance, Kiviharju et al [ 26 ] apply a mixture design for the screening of suitable complex medium components in the cultivation of S. peucetius var.…”

Section: Introductionmentioning

confidence: 99%

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

et al. 2015

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BackgroundCharacterizing microbial communities via next-generation sequencing is subject to a number of pitfalls involving sample processing. The observed community composition can be a severe distortion of the quantities of bacteria actually present in the microbiome, hampering analysis and threatening the validity of conclusions from metagenomic studies. We introduce an experimental protocol using mock communities for quantifying and characterizing bias introduced in the sample processing pipeline. We used 80 bacterial mock communities comprised of prescribed proportions of cells from seven vaginally-relevant bacterial strains to assess the bias introduced in the sample processing pipeline. We created two additional sets of 80 mock communities by mixing prescribed quantities of DNA and PCR product to quantify the relative contribution to bias of (1) DNA extraction, (2) PCR amplification, and (3) sequencing and taxonomic classification for particular choices of protocols for each step. We developed models to predict the “true” composition of environmental samples based on the observed proportions, and applied them to a set of clinical vaginal samples from a single subject during four visits.ResultsWe observed that using different DNA extraction kits can produce dramatically different results but bias is introduced regardless of the choice of kit. We observed error rates from bias of over 85% in some samples, while technical variation was very low at less than 5% for most bacteria. The effects of DNA extraction and PCR amplification for our protocols were much larger than those due to sequencing and classification. The processing steps affected different bacteria in different ways, resulting in amplified and suppressed observed proportions of a community. When predictive models were applied to clinical samples from a subject, the predicted microbiome profiles were better reflections of the physiology and diagnosis of the subject at the visits than the observed community compositions.ConclusionsBias in 16S studies due to DNA extraction and PCR amplification will continue to require attention despite further advances in sequencing technology. Analysis of mock communities can help assess bias and facilitate the interpretation of results from environmental samples.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-015-0351-6) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

et al. 2015

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“…Optimization of culture medium by response surface methodology is an effective method widely utilized in microbial enzyme production [25][26][27]. Almost all keratinases are inducible, and different keratin-containing materials such as feathers, hair and wool can be used as substrates for keratinase production [19].…”

Section: Introductionmentioning

confidence: 99%

Medium optimization for keratinase production in hair substrate by a new Bacillus subtilis KD-N2 using response surface methodology

Cai

Zheng

2009

J Ind Microbiol Biotechnol

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Culture medium for keratinase production from hair substrate by a new Bacillus subtilis strain, KD-N2, was optimized. Effects of culture conditions on keratinase production were tested, and optimal results were obtained with 10% inocula (v/v), 16 g/L hair substrate, an initial pH value of 6.5 and a culture volume of 20 mL. Several carbon sources (sucrose, cornflour) and nitrogen sources (yeast extract, tryptone and peptone) had positive effects on keratinase production, with sucrose giving optimal results. To improve keratinase yield, statistically based experimental designs were applied to optimize the culture medium. Fractional factorial design (FFD) experiments showed that MgSO4 and K2HPO4 were the most significant factors affecting keratinase production. Further central composite design (CCD) experiments indicated that the optimal MgSO4 and K2HPO4 concentrations were 0.91 and 2.38 g/L, respectively. Using an optimized fermentation medium (g/L: NaCl 1.0, CaCl2 0.05, KH2PO4 0.7, sucrose 3, MgSO4 0.91, K2HPO4 2.38), keratinase activity increased to 125 U/mL, an approximate 1.7-fold increase over the previous activity (75 U/mL). Human hair was degraded during the submerged cultivation.

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“…The cultural factor optimization plays a remarkable role in the productivity and economics of the essential process [13][14][15][16][17][18][19]. Hence, our study was aimed to the isolation of Streptomyces sp.…”

Section: Introductionmentioning

confidence: 99%

Optimization Production Conditions of Antibacterial Metabolite From Streptomyces Sp.

Al-Ghazali

Omran

2017

Asian J Pharm Clin Res

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Objectives: The paper aimed to isolate Streptomyces strain having the ability to produce antibacterial metabolites and optimize some environmental parameters for excellent antibiotic production.Methods: Different soil samples were collected from extreme environments of desert regions at Karbala Province, Iraq. Actinomycetes were isolated using different media. The primary screening for antibacterial production was accomplished, and the antibacterial activities were tested against pathogenic bacteria, including Escherichia coli, Staphylococcus aureus, Streptococcus agalactiae, and Pseudomonas aeruginosa. The most potent strain was chosen for optimizing some of environmental parameters to increase the bioactive metabolite production. Different parameters were studied such as culture media, temperature, pH, and agitation rate.Results: About eight Streptomyces strains were isolated from soil samples. All isolates appeared variable levels of antibiotic productions against Grampositive and negative pathogenic bacteria, and the best one was Streptomyces sp. LHR 9. The antibacterial metabolite production from Streptomyces sp. LHR 9 was affected by various cultural parameters. Glucose soybean meal broth as a fermentation medium at pH 7 yielded the highest antibiotic production under the optimal fermentation conditions, including the temperature at 35°C with 200 rpm (revolution/min) agitation rate and 7 days incubation period. Conclusion:The Streptomyces sp. LHR 9 showed antibacterial activity against both Gram-positive and negative pathogenic bacteria. It may consider as a potential source of drug production. Further study needs to purification and characterization of antibiotic and analyzes the mechanism for the antimicrobial activity of this bioactive compound.

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Optimization of Streptomyces peucetius var. caesius N47 cultivation and ?-rhodomycinone production using experimental designs and response surface methods

Cited by 15 publications

References 23 publications

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

Medium optimization for keratinase production in hair substrate by a new Bacillus subtilis KD-N2 using response surface methodology

Optimization Production Conditions of Antibacterial Metabolite From Streptomyces Sp.

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