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Functional Metagenomics
The use of metagenomic libraries to discover novel genes for functions of interest from microbial communities
Curated by Trevor Charles
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Functional Metagenomics Reveals Novel Pathways of Prebiotic Breakdown by Human Gut Bacteria

Functional Metagenomics Reveals Novel Pathways of Prebiotic Breakdown by Human Gut Bacteria | Functional Metagenomics | Scoop.it

The human intestine hosts a complex bacterial community that plays a major role in nutrition and in maintaining human health. A functional metagenomic approach was used to explore the prebiotic breakdown potential of human gut bacteria, including non-cultivated ones. Two metagenomic libraries, constructed from ileum mucosa and fecal microbiota, were screened for hydrolytic activities on the prebiotic carbohydrates inulin, fructo-oligosaccharides, xylo-oligosaccharides, galacto-oligosaccharides and lactulose. The DNA inserts of 17 clones, selected from the 167 hits that were identified, were pyrosequenced in-depth, yielding in total 407, 420 bp of metagenomic DNA. From these sequences, we discovered novel prebiotic degradation pathways containing carbohydrate transporters and hydrolysing enzymes, for which we provided the first experimental proof of function. Twenty of these proteins are encoded by genes that are also present in the gut metagenome of at least 100 subjects, whatever are their ages or their geographical origin. The sequence taxonomic assignment indicated that still unknown bacteria, for which neither culture conditions nor genome sequence are available, possess the enzymatic machinery to hydrolyse the prebiotic carbohydrates tested. The results expand the vision on how prebiotics are metabolized along the intestine, and open new perspectives for the design of functional foods.

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Antibacterial enzymes from the functional screening of metagenomic libraries hosted in Ralstonia metallidurans - Iqbal - 2014 - FEMS Microbiology Letters - Wiley Online Library

Antibacterial enzymes from the functional screening of metagenomic libraries hosted in Ralstonia metallidurans - Iqbal - 2014 - FEMS Microbiology Letters - Wiley Online Library | Functional Metagenomics | Scoop.it

Phenotype-based screening of bacterial metagenomic libraries provides an avenue for the discovery of novel genes, enzymes, and metabolites that have a variety of potential clinical and industrial uses. Here, we report the identification of a functionally diverse collection of antibacterially active enzymes from the phenotypic screening of 700 000 cosmid clones prepared from Arizona soil DNA and hosted inRalstonia metallidurans. Environmental DNA clones surrounded by zones of growth inhibition in a bacterial overlay assay were found, through bioinformatics and functional analyses, to encode enzymes with predicted peptidase, lipase, and glycolytic activities conferring antibiosis. The antibacterial activities observed in our R. metallidurans-based assay could not be replicated with the same clones in screens usingEscherichia coli as a heterologous host, suggesting that the large-scale screening of metagenomic libraries for antibiosis using phylogenetically diverse hosts should be a productive strategy for identifying enzymes with functionally diverse antibacterial activities.

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PNAS: Discovery of indolotryptoline antiproliferative agents by homology-guided metagenomic screening -- Chang and Brady

Natural product discovery by random screening of broth extracts derived from cultured bacteria often suffers from high rates of redundant isolation, making it ever more challenging to identify novel biologically interesting natural products. Here we show that homology-based screening of soil metagenomes can be used to specifically target the discovery of new members of traditionally rare, biomedically relevant natural product families. Phylogenetic analysis of oxy-tryptophan dimerization gene homologs found within a large soil DNA library enabled the identification and recovery of a unique tryptophan dimerization biosynthetic gene cluster, which we have termed the bor cluster. When heterologously expressed in Streptomyces albus, this cluster produced an indolotryptoline antiproliferative agent with CaMKIIδ kinase inhibitory activity (borregomycin A), along with several dihydroxyindolocarbazole anticancer/antibiotics (borregomycins B–D). Similar homology-based screening of large environmental DNA libraries is likely to permit the directed discovery of new members within other previously rare families of bioactive natural products.

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Phylogenetically novel LuxI/LuxR-type Quorum Sensing Systems Isolated Using a Metagenomic Approach

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The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

This is cool, but it isn't really metagenomics, is it?

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Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion - Cheng - 2012 - FEMS Microbiology Letters - Wiley Online Library

Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion - Cheng - 2012 - FEMS Microbiology Letters - Wiley Online Library | Functional Metagenomics | Scoop.it
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Identification and characterization of new LuxR/LuxI-type quorum sensing systems from metagenomic libraries - Hao - 2009 - Environmental Microbiology - Wiley Online Library

Identification and characterization of new LuxR/LuxI-type quorum sensing systems from metagenomic libraries - Hao - 2009 - Environmental Microbiology - Wiley Online Library | Functional Metagenomics | Scoop.it
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Metagenomics and novel gene discovery: Promise and potential for novel therapeutics

Metagenomics and novel gene discovery: Promise and potential for novel therapeutics | Functional Metagenomics | Scoop.it
Metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. Herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of each type of approach, as well as potential solutions. Furthermore, we discuss the potential for metagenomic biotherapeutic discovery, with a particular focus on the human gut microbiome and finally, we outline how the discovery of novel genes may be used to create bioengineered probiotics.
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Frontiers | Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries | Terrestrial Microbiology

Recent advances in sequencing technologies generate new predictions and hypotheses about the functional roles of environmental microorganisms. Yet, until we can test these predictions at a scale th...
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PLOS ONE: The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases

PLOS ONE: The Metagenome-Derived Enzymes LipS and LipT Increase the Diversity of Known Lipases | Functional Metagenomics | Scoop.it

Triacylglycerol lipases (EC 3.1.1.3) catalyze both hydrolysis and synthesis reactions with a broad spectrum of substrates rendering them especially suitable for many biotechnological applications. Most lipases used today originate from mesophilic organisms and are susceptible to thermal denaturation whereas only few possess high thermotolerance. Here, we report on the identification and characterization of two novel thermostable bacterial lipases identified by functional metagenomic screenings. Metagenomic libraries were constructed from enrichment cultures maintained at 65 to 75°C and screened resulting in the identification of initially 10 clones with lipolytic activities. Subsequently, two ORFs were identified encoding lipases, LipS and LipT. Comparative sequence analyses suggested that both enzymes are members of novel lipase families. LipS is a 30.2 kDa protein and revealed a half-life of 48 h at 70°C. The lipT gene encoded for a multimeric enzyme with a half-life of 3 h at 70°C. LipS had an optimum temperature at 70°C and LipT at 75°C. Both enzymes catalyzed hydrolysis of long-chain (C12 and C14) fatty acid esters and additionally hydrolyzed a number of industry-relevant substrates. LipS was highly specific for (R)-ibuprofen-phenyl ester with an enantiomeric excess (ee) of 99%. Furthermore, LipS was able to synthesize 1-propyl laurate and 1-tetradecyl myristate at 70°C with rates similar to those of the lipase CalB from Candida antarctica. LipS represents the first example of a thermostable metagenome-derived lipase with significant synthesis activities. Its X-ray structure was solved with a resolution of 1.99 Å revealing an unusually compact lid structure.

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PLOS ONE: Functional Metagenomics Unveils a Multifunctional Glycosyl Hydrolase from the Family 43 Catalysing the Breakdown of Plant Polymers in the Calf Rumen

PLOS ONE: Functional Metagenomics Unveils a Multifunctional Glycosyl Hydrolase from the Family 43 Catalysing the Breakdown of Plant Polymers in the Calf Rumen | Functional Metagenomics | Scoop.it
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Metagenomic Analysis of Streptomyces lividans Reveals Host-Dependent Functional Expression

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Harvesting of novel polyhydroxyalkanaote (PHA) synthase encoding genes from a soil metagenome library using phenotypic screening - Schallmey - 2011 - FEMS Microbiology Letters - Wiley Online Library

Harvesting of novel polyhydroxyalkanaote (PHA) synthase encoding genes from a soil metagenome library using phenotypic screening - Schallmey - 2011 - FEMS Microbiology Letters - Wiley Online Library | Functional Metagenomics | Scoop.it
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Open resource metagenomics: a model for sharing metagenomic libraries | Neufeld | Standards in Genomic Sciences

Open resource metagenomics: a model for sharing metagenomic libraries...
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