Dataset Information

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.

ABSTRACT: DNA derived from environmental samples is a rich source of novel bioactive molecules. The choice of the habitat to be sampled predefines the properties of the biomolecules to be discovered due to the physiological adaptation of the microbial community to the prevailing environmental conditions. We have constructed a metagenomic library in Escherichia coli DH10b with environmental DNA (eDNA) isolated from the microbial community of a slaughterhouse drain biofilm consisting mainly of species from the family Flavobacteriaceae. By functional screening of this library we have identified several lipases, proteases and two clones (SA343 and SA354) with biosurfactant and hemolytic activities. Sequence analysis of the respective eDNA fragments and subsequent structure homology modelling identified genes encoding putative N-acyl amino acid synthases with a unique two-domain organisation. The produced biosurfactants were identified by NMR spectroscopy as N-acyltyrosines with N-myristoyltyrosine as the predominant species. Critical micelle concentration and reduction of surface tension were similar to those of chemically synthesised N-myristoyltyrosine. Furthermore, we showed that the newly isolated N-acyltyrosines exhibit antibiotic activity against various bacteria. This is the first report describing the successful application of functional high-throughput screening assays for the identification of biosurfactant producing clones within a metagenomic library.

SUBMITTER: Thies S

PROVIDER: S-EPMC4897644 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.

Thies Stephan S Rausch Sonja Christina SC Kovacic Filip F Schmidt-Thaler Alexandra A Wilhelm Susanne S Rosenau Frank F Daniel Rolf R Streit Wolfgang W Pietruszka Jörg J Jaeger Karl-Erich KE

Scientific reports 20160608

DNA derived from environmental samples is a rich source of novel bioactive molecules. The choice of the habitat to be sampled predefines the properties of the biomolecules to be discovered due to the physiological adaptation of the microbial community to the prevailing environmental conditions. We have constructed a metagenomic library in Escherichia coli DH10b with environmental DNA (eDNA) isolated from the microbial community of a slaughterhouse drain biofilm consisting mainly of species from ...[more]

PMID: 27271534

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Project description:Glycolipid biosurfactants are the most prominent group of microbial biosurfactants, comprising rhamnolipids, sophorolipids and mannosylerythritol lipids (MELs). Usually, large amounts of hydrophobic substrates (e.g., vegetable oils) are used to achieve high titers (~200 g/L) of a crude product of low purity at values limited to 50-60%, contaminated with unconsumed triacylglycerol and residual free fatty acids and monoacylglycerides. The methods reported for the removal of these contaminants use a mixture of organic solvents, compromising solvent recyclability and increasing final process costs. This study reports, for the first time, an innovative downstream method for MELs, in which 90% of the triacylglycerols are separated from the crude MEL mixture in a first stage and the other lipid derivatives (free fatty acids, mono- and diacylglycerols) are removed by organic solvent nanofiltration (OSN). Three commercially available membranes (GMT-oNF-2, PuraMEm-600 and DuramMem-500) and several homemade membranes, casted from 22, 24 or 26% (w/v) polybenzimidazole (PBI) solutions, were assessed for crude MELs purification by diafiltration. A final purity of 87-90% in the MELs was obtained by filtering two diavolumes of methanol or ethyl acetate solutions through a PBI 26% membrane, resulting in MELs losses of 14.7 ± 6.1% and 15.3 ± 2.2%, respectively. Higher biosurfactant purities can be archived using the PBI 26% membrane at higher DV, but at the cost of higher product losses. Namely, in MeOH, the use of 6 DV leads to losses of 32% for MELs and 18% for sophorolipids. To obtain MELs at reagent grade with purities equal or higher than 97%, a two-sequential cascade filtration approach was implemented using the commercial membrane, GMT-oNF. In such a process, MELs with 98% purity was obtained at the cost of 11.6% MELs losses. Finally, decoloration, important in some applications, was successfully assessed using activated carbon. Overall, this study reports a unique solution for microbial biosurfactants production with minimal product losses, enabling solvent recycling and potentially reducing costs.

Project description:BACKGROUND: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. METHODOLOGY/PRINCIPAL FINDINGS: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. CONCLUSIONS/SIGNIFICANCE: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with different protocols are not suitable for comparative metagenomics.

Dataset Information

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.

Publications

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.

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