Microbial Metagenomics, Metatranscriptomics, and Metaproteomics

<p>SECTION I. PREPARATION AND GENOMIC ANALYSES OF SINGLE CELLS FROM NATURAL POPULATIONS</p> <p>1. In-solution fluorescence in situ hybridization (FISH) for single cell genome preparation</p> <p>2. Ribosomal RNA-&shy;‐targeted magnetic cell separation for targeted metagenomic analysis</p> <p>3. Genomic characterization of uncultivated symbiont populations using FACs and genome amplification.</p> <p>4. Microfluidic Cell separation from complex microbial communities for single cell genome analysis</p> <p>5. Assessing the abundance of active/damage cells and using cell sorting to determine their composition.</p> <p>SECTION II. MICROBIAL COMMUNITY GENOMICS – SAMPLING, LIBRARY PREPARATION, AND SEQUENCING</p> <p>6. Preparation of BAC libraries from marine microbial community DNA.</p> <p>7. Preparation of fosmid libraries and functional metagenomic analysis of microbial community DNA</p> <p>8. Preparation of metagenomic libraries from naturally occurring marine phage.</p> <p>9. Preparation and metatranscriptomic analyses of host-&shy;‐microbe systems.</p> <p>10. Massively multiplexed ribosomal RNA tag sequencing on the Illumina Mi Seq platform</p> <p>SECTION III. MICROBIAL COMMUNITY TRANSCRIPTOMICS -&shy;‐ SAMPLING, SAMPLE PREPARATION, AND SEQUENCING</p> <p>11. Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton.</p> <p>12. Simultaneous extraction of metabolites, RNA, DNA, and proteins from the same sample</p> <p>13. Utilization of quantitative internal standards for microbial community metatranscriptomics</p> <p>14. Informatics workflows for phytoplankton metatranscriptomics</p> <p>15. Sample processing and cDNA preparation for microbial metatranscriptomics in complex soil communities</p> <p>SECTION IV. MICROBIAL COMMUNITY PROTETOMICS -&shy;‐ SAMPLING, SAMPLE PREPARATION, AND SPECTRAL ANALYSIS AND INTERPRETATION.</p> <p>16. Sample preparation and processing for planktonic microbial community protetomics.</p> <p>17. Bioinformatic analysis of microbial metaproteomic datasets</p> <p>18. Sample handling, mass spectrometry and spectra-&shy;‐peptide matching for microbial metatproteomic analyses</p> <p>SECTION V. MICROBIAL COMMUNITY "OMICS" – DATABASES, COMPUTATIONAL ANALYSES, COMPARATIVE ANALYSES, AND STATISTICS</p> <p>19. Microbial community analysis using Megan</p> <p>20. Microbial community analysis on the MG-&shy;‐RAST platform.</p> <p>21. Analysis/assembly of shotgun-re-sequenced genomes.</p> <p>22. Computational methods for high-&shy;‐throughput comparative analyses of natural microbial communities</p> <p>23. Microbial community analysis using QIIME</p> <p>24. Genome assembly from fosmid metagenomic library sequences</p> <p>25. Qualitative and quantitative analyses of metagenomic datasets</p> <p>26. Assembling full length rRNA genes from short read metagenomic sequence datasets using EMIRGE</p>