Current and future resources for functional metagenomics

Functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted DNA of mixed microbial populations. A functional approach relies on the construction and screening of metagenomic libraries—physical libraries that contain DNA cloned from environmental metagenomes. The information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. In this Perspective, we begin by summarizing the technical challenges of constructing metagenomic libraries and emphasize their value as resources. We then discuss libraries constructed using the popular cloning vector, pCC1FOS, and highlight the strengths and shortcomings of this system, alongside possible strategies to maximize existing pCC1FOS-based libraries by screening in diverse hosts. Finally, we discuss the known bias of libraries constructed from human gut and marine water samples, present results that suggest bias may also occur for soil libraries, and consider factors that bias metagenomic libraries in general. We anticipate that discussion of current resources and limitations will advance tools and technologies for functional metagenomics research.

[1]  A. Casanueva,et al.  An unusual feruloyl esterase belonging to family VIII esterases and displaying a broad substrate range , 2015 .

[2]  Trevor C. Charles,et al.  Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries , 2015, Microbiome.

[3]  E. Papoutsakis,et al.  Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries , 2015, Nature Communications.

[4]  H. Santos,et al.  Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus , 2015, Front. Microbiol..

[5]  S. Böhnke,et al.  A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity , 2014, The ISME Journal.

[6]  S. Tangphatsornruang,et al.  Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities , 2015, Biotechnology for Biofuels.

[7]  Dae-Hee Lee,et al.  A novel psychrophilic alkaline phosphatase from the metagenome of tidal flat sediments , 2015, BMC Biotechnology.

[8]  V. Amarelle,et al.  Construction and screening of a functional metagenomic library to identify novel enzymes produced by Antarctic bacteria , 2015 .

[9]  W. Liebl,et al.  Alternative hosts for functional (meta)genome analysis , 2014, Applied Microbiology and Biotechnology.

[10]  Trevor C. Charles,et al.  Versatile broad-host-range cosmids for construction of high quality metagenomic libraries. , 2014, Journal of microbiological methods.

[11]  Ümit V. Çatalyürek,et al.  Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows , 2013, PloS one.

[12]  Eoin L. Brodie,et al.  Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries , 2013, Front. Microbiol..

[13]  J. Doré,et al.  Functional Metagenomics Reveals Novel Pathways of Prebiotic Breakdown by Human Gut Bacteria , 2013, PloS one.

[14]  P. Cornelis,et al.  Identification of a metagenomic gene cluster containing a new class A beta-lactamase and toxin-antitoxin systems , 2013, MicrobiologyOpen.

[15]  W. Streit,et al.  Functional Screening of Metagenome and Genome Libraries for Detection of Novel Flavonoid-Modifying Enzymes , 2013, Applied and Environmental Microbiology.

[16]  David A. Mead,et al.  Meeting Report: 1st International Functional Metagenomics Workshop May 7–8, 2012, St. Jacobs, Ontario, Canada. , 2013, Standards in genomic sciences.

[17]  E. Santero,et al.  Heterologous viral expression systems in fosmid vectors increase the functional analysis potential of metagenomic libraries , 2013, Scientific Reports.

[18]  E. Delong,et al.  Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis , 2012, The ISME Journal.

[19]  K. Miyazaki,et al.  Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli , 2012, Proceedings of the National Academy of Sciences.

[20]  Melina Fan,et al.  Addgene provides an open forum for plasmid sharing , 2012, Nature Biotechnology.

[21]  Trevor C. Charles,et al.  Site-specific bacterial chromosome engineering: ΦC31 integrase mediated cassette exchange (IMCE). , 2012, Journal of visualized experiments : JoVE.

[22]  Katja Engel,et al.  Nonlinear electrophoresis for purification of soil DNA for metagenomics. , 2012, Journal of microbiological methods.

[23]  J. D. Buck.  Physiological effects of heterologous expression of proteorhodopsin photosystems , 2012 .

[24]  E. Kanaya,et al.  Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach , 2011, Applied and Environmental Microbiology.

[25]  J. V. van Elsas,et al.  The great screen anomaly—a new frontier in product discovery through functional metagenomics , 2011, Applied Microbiology and Biotechnology.

[26]  Trevor C. Charles,et al.  Open resource metagenomics: a model for sharing metagenomic libraries , 2011, Standards in genomic sciences.

[27]  Marcus Taupp,et al.  The art and design of functional metagenomic screens. , 2011, Current opinion in biotechnology.

[28]  Mark R Liles,et al.  Gram negative shuttle BAC vector for heterologous expression of metagenomic libraries. , 2011, Gene.

[29]  Uwe Sauer,et al.  From good old biochemical analyses to high-throughput omics measurements and back. , 2011, Current opinion in biotechnology.

[30]  Gabriel Moreno-Hagelsieb,et al.  Open resource metagenomics , 2011 .

[31]  W. Kelly,et al.  Heterologous production of thiostrepton A and biosynthetic engineering of thiostrepton analogs. , 2011, Molecular bioSystems.

[32]  Yongping Huang,et al.  Microbiome of Fungus-Growing Termites: a New Reservoir for Lignocellulase Genes , 2010, Applied and Environmental Microbiology.

[33]  J. Doré,et al.  Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. , 2010, Genome research.

[34]  M. Liles,et al.  Size Does Matter: Application-driven Approaches for Soil Metagenomics. , 2010, Soil biology & biochemistry.

[35]  J. Handelsman,et al.  Metagenomic Analysis of Apple Orchard Soil Reveals Antibiotic Resistance Genes Encoding Predicted Bifunctional Proteins , 2010, Applied and Environmental Microbiology.

[36]  F. Rodríguez-Valera,et al.  Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing , 2010, The ISME Journal.

[37]  G. Church,et al.  A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion , 2010, Molecular systems biology.

[38]  I. Hope,et al.  Escherichia coli MW005: lambda Red-mediated recombineering and copy-number induction of oriV-equipped constructs in a single host , 2010, BMC biotechnology.

[39]  S. Brady,et al.  Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria , 2010, Applied and Environmental Microbiology.

[40]  D. Mead,et al.  Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli , 2009, Nucleic acids research.

[41]  Karl-Erich Jaeger,et al.  Novel tools for the functional expression of metagenomic DNA. , 2010, Methods in molecular biology.

[42]  Tao Zhang,et al.  Gene cloning and characterization of a novel esterase from activated sludge metagenome , 2009, Microbial cell factories.

[43]  T. Uchiyama,et al.  Functional metagenomics for enzyme discovery: challenges to efficient screening. , 2009, Current opinion in biotechnology.

[44]  S. Hallam,et al.  Extraction of high molecular weight genomic DNA from soils and sediments. , 2009, Journal of visualized experiments : JoVE.

[45]  T. Thomas,et al.  Phylogenetic screening of a bacterial, metagenomic library using homing endonuclease restriction and marker insertion , 2009, Nucleic acids research.

[46]  René L. Warren,et al.  Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules , 2009, Proceedings of the National Academy of Sciences.

[47]  Wolfgang Liebl,et al.  A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles. , 2009, Systematic and applied microbiology.

[48]  J. Gilbert,et al.  Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing , 2009, The ISME Journal.

[49]  R. Daniel,et al.  Rapid Identification of Genes Encoding DNA Polymerases by Function-Based Screening of Metagenomic Libraries Derived from Glacial Ice , 2009, Applied and Environmental Microbiology.

[50]  Heather K. Allen,et al.  Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil , 2009, The ISME Journal.

[51]  Uwe Völker,et al.  A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species. , 2009, FEMS microbiology letters.

[52]  Colin Hill,et al.  Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome , 2008, Proceedings of the National Academy of Sciences.

[53]  J. Handelsman,et al.  Recovery, Purification, and Cloning of High-Molecular-Weight DNA from Soil Microorganisms , 2008, Applied and Environmental Microbiology.

[54]  Peer Bork,et al.  Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer , 2007, Science.

[55]  Natalia N. Ivanova,et al.  Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite , 2007, Nature.

[56]  H. Suenaga,et al.  Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. , 2007, Environmental microbiology.

[57]  S. Brady.  Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules , 2007, Nature Protocols.

[58]  Junjian Z. Chen,et al.  DNA supercoiling suppresses real-time PCR: a new approach to the quantification of mitochondrial DNA damage and repair , 2007, Nucleic acids research.

[59]  T. Oh,et al.  Isolation and Characterization of a Novel Lipase from a Metagenomic Library of Tidal Flat Sediments: Evidence for a New Family of Bacterial Lipases , 2006, Applied and Environmental Microbiology.

[60]  E. Delong,et al.  Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior , 2006, Science.

[61]  Philip L Bond,et al.  A wide host-range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase. , 2005, Environmental microbiology.

[62]  Heather K. Allen,et al.  Intracellular Screen To Identify Metagenomic Clones That Induce or Inhibit a Quorum-Sensing Biosensor , 2005, Applied and Environmental Microbiology.

[63]  Joern Hopke,et al.  Genetically Modified Bacterial Strains and Novel Bacterial Artificial Chromosome Shuttle Vectors for Constructing Environmental Libraries and Detecting Heterologous Natural Products in Multiple Expression Hosts , 2004, Applied and Environmental Microbiology.

[64]  W. Szybalski,et al.  Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones. , 2002, Genome research.

[65]  F. Graham,et al.  A helper-dependent system for adenovirus vector production helps define a lower limit for efficient DNA packaging , 1997, Journal of virology.

[66]  J. Tiedje,et al.  DNA recovery from soils of diverse composition , 1996, Applied and environmental microbiology.

[67]  W. Vahjen,et al.  Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast , 1993, Applied and environmental microbiology.

[68]  D. Figurski,et al.  Precise deletions in large bacterial genomes by vector-mediated excision (VEX). The trfA gene of promiscuous plasmid RK2 is essential for replication in several gram-negative hosts. , 1993, Journal of molecular biology.

[69]  B. Birren,et al.  Stable propagation of cosmid sized human DNA inserts in an F factor based vector. , 1992, Nucleic acids research.

[70]  D. Helinski,et al.  Replication of the broad-host-range plasmid RK2: direct measurement of intracellular concentrations of the essential TrfA replication proteins and their effect on plasmid copy number , 1990, Journal of bacteriology.

[71]  D. Lilley.  DNA supercoiling. , 1986, Biochemical Society transactions.