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.

Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing

“…Another limitation is that our E.coli recipient cells receive foreign DNA only from other E.coli strains, whereas many gene transfer events in nature involve more distantly related organisms [ 8 ]. Metagenomic experiments suggest that such distant transfer events can often create novel beneficial phenotypes [ 85 , 86 ]. Thus, an exciting next step would consist of transferring genes between progressively more distantly related species, to study whether the reduced transfer efficiency [ 72 ] is compensated by increased transfer benefits in one or multiple novel environments, and to observe how bacteria rewire these genes to evolve new adaptive traits.…”

Going Green and Cold: Biosurfactants from Low-Temperature Environments to Biotechnology Applications

“…Functional metagenomics can lead to the discovery of unknown biosurfactants and is especially suited for extreme habitats where many native microorganisms may not be cultivable [68]. Although there are several technical pitfalls related to the expression in heterologous systems, the lack of reliable high-throughput screening assays, and finally the extensive analytical work required to characterize the chemical structure of new biomolecules, this approach has succeeded in identifying entirely new types of biosurfactants [69,70]. organic material is very low.…”

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

“…As of today, metagenomic data originating from a wide range of ecosystems make up a large fraction of the sequences stored in public databases ( Qin et al, 2010 ; Bork et al, 2015 ). Researchers have used metagenomics to discover new bioactive molecules ( Lorenz & Eck, 2005 ; Thies et al, 2016 ), investigate the functional potential of ecosystems ( Tringe et al, 2005 ; Al-Amoudi et al, 2016 ), and access the genomic context of uncultivated microorganisms ( Tyson et al, 2004 ; Haroon et al, 2016 ; Delmont et al, 2017 ). Metagenomic data also provide a means to quantify the abundance and relative distribution of genomes in environmental samples through read recruitment ( Tyson et al, 2004 ; Dutilh et al, 2014 ; Eren et al, 2015 ).…”