Genomics of Microbes and Microbiomes Overview

2016-12-15

Listed below is a brief overview of the talk and the papers referenced throughout the talk.

Recently, the NHGRI published a series on Current Topics in Genome Analysis. One of the talks was of special interest to me, Genomics of Microbes and Microbiomes by Julie Segre.

Topic 1 Bacterial Diversity Studies with 16S rRNA Sequencing

Important issues to consider in experiment:

• Study design?
• Sequencing platform?
• 16S rRNA region?
• Number of reads?
• Hidden technical issues?
• Analysis tools?
• Visualize data?
• Comparison to previous studies?
• What information will yield testable hypothesis?

Describing diversity:

• richeness - number of OTUs
• evenness - Shannon equitability index
• Shannon diversity index - accounts for both richness and evenness of OTUs

Papers:

• Peterson, Daniel A., et al. “Metagenomic Approaches for Defining the Pathogenesis of Inflammatory Bowel Diseases” Cell Host & Microbe 3.6 (2008): 417-427.
• Siqueira, José F., Ashraf F. Fouad, and Isabela N. Roˆcas. “Pyrosequencing as a tool for better understanding of human microbiomes.” Journal of Oral Microbiology 4 (2012).
• Kong, Heidi H. “Skin microbiome: genomics-based insights into the diversity and role of skin microbes.” Trends in Molecular Medicine 17.6 (2011): 320-328.
• Castillo, Marisol, et al. “Quantification of total bacteria, enterobacteria and lactobacilli populations in pig digesta by real-time PCR.” Veterinary Microbiology 114.1 (2006): 165-170.
• Kozich, James J., et al. “Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.” Applied and environmental Microbiology 79.17 (2013): 5112-5120.
• Caporaso, J. Gregory, et al. “Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.” The ISME Journal 6.8 (2012): 1621-1624.
• Fadrosh, Douglas W., et al. “An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform.” Microbiome 2.1 (2014): 1.
• Conlan, Sean, Heidi H. Kong, and Julia A. Segre. “Species-level analysis of DNA sequence data from the NIH Human Microbiome Project.” PloS One 7.10 (2012): e47075.
• Ravel, Jacques, et al. “Vaginal microbiome of reproductive-age women.” Proceedings of the National Academy of Sciences 108.Supplement 1 (2011): 4680-4687.
• Wang, Qiong, et al. “Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy.” Applied and Environmental Microbiology 73.16 (2007): 5261-5267.
• Quast, Christian, et al. “The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.” Nucleic Acids Research 41.D1 (2013): D590-D596.
• Ludwig, Wolfgang, et al. “ARB: a software environment for sequence data.” Nucleic Acids Research 32.4 (2004): 1363-1371.
• Haas, Brian J., et al. “Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.” Genome Research 21.3 (2011): 494-504.
• Jumpstart Consortium Human Microbiome Project Data Generation Working Group. “Evaluation of 16S rDNA-based community profiling for human microbiome research.” PloS One 7.6 (2012): e39315.
• Grice, Elizabeth A., and Julia A. Segre. “The human microbiome: our second genome.” Annual Review of Genomics and Human Genetics 13 (2012): 151.
• Oh, Julia, et al. “Shifts in human skin and nares microbiota of healthy children and adults.” Genome Medicine 4.10 (2012): 1.
• Ley, Ruth E., et al. “Obesity alters gut microbial ecology.” Proceedings of the National Academy of Sciences of the United States of America 102.31 (2005): 11070-11075.
• Scharschmidt, Tiffany C., et al. “Matriptase-deficient mice exhibit ichthyotic skin with a selective shift in skin microbiota.” Journal of Investigative Dermatology 129.10 (2009): 2435-2442.
• Hamady, Micah, and Rob Knight. “Microbial community profiling for human microbiome projects: Tools, techniques, and challenges.” Genome Research 19.7 (2009): 1141-1152.
• Kuczynski, Justin, et al. “Experimental and analytical tools for studying the human microbiome.” Nature Reviews Genetics 13.1 (2012): 47-58.

Topic 2 Fungal Diversity

• Grice, Elizabeth A., et al. “Topographical and temporal diversity of the human skin microbiome.” Science 324.5931 (2009): 1190-1192.
• Findley, Keisha, et al. “Topographic diversity of fungal and bacterial communities in human skin.” Nature 498.7454 (2013): 367-370.

Topic 3 Bacterial Genomes

Need to consider similar issues as 16S rRNA, but also the following:

• Existing reference genome?
• Sequencing depth?

Papers:

• Hunt, Martin, et al. “A comprehensive evaluation of assembly scaffolding tools.” Genome Biology 15.3 (2014): 1.
• Tettelin, Hervé, et al. “Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial ‘pan-genome’.” Proceedings of the National Academy of Sciences of the United States of America 102.39 (2005): 13950-13955.
• Krzywinski, Martin, et al. “Circos: an information aesthetic for comparative genomics.” Genome Research 19.9 (2009): 1639-1645.

Topic 4 Metagenomics

Databases:

• KEGG
• MetaCyc
• the Gene Ontology
• eggNOG

Goals:

• Who’s there and abundance?
• Function?
  • Genes
  • Pathways
  • Strains
• Recover genomes?
• Novel pathogenic organisms?

Papers:

• Hugenholtz, Philip, and Gene W. Tyson. “Microbiology: metagenomics.” Nature 455.7212 (2008): 481-483.
• Warnecke, Falk, et al. “Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite.” Nature 450.7169 (2007): 560-565.
• Hess, Matthias, et al. “Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.” Science 331.6016 (2011): 463-467.
• Segata, Nicola, et al. “Metagenomic microbial community profiling using unique clade-specific marker genes.” Nature Methods 9.8 (2012): 811-814.
• Sunagawa, Shinichi, et al. “Metagenomic species profiling using universal phylogenetic marker genes.” Nature Methods 10.12 (2013): 1196-1199.
• Abubucker, Sahar, et al. “Metabolic reconstruction for metagenomic data and its application to the human microbiome.” PLoS Comput Biol 8.6 (2012): e1002358.
• Human Microbiome Project Consortium. “Structure, function and diversity of the healthy human microbiome.” Nature 486.7402 (2012): 207-214.
• Ghai, Rohit, et al. “New abundant microbial groups in aquatic hypersaline environments.” Scientific Reports 1 (2011).
• Karlsson, Fredrik H., et al. “Gut metagenome in European women with normal, impaired and diabetic glucose control.” Nature 498.7452 (2013): 99-103.
• Oh, Julia, et al. “Biogeography and individuality shape function in the human skin metagenome.” Nature 514.7520 (2014): 59-64.
• Zhu, Ana, et al. “Inter-individual differences in the gene content of human gut bacterial species.” Genome Biology 16.1 (2015): 1.
• Naccache, Samia N., et al. “A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.” Genome Research 24.7 (2014): 1180-1192.
• Wilson, Michael R., et al. “Actionable diagnosis of neuroleptospirosis by next-generation sequencing.” New England Journal of Medicine 370.25 (2014): 2408-2417.

Topic 4 Sequencing Technology

Illumina MiSeq dominates, but PacBio gives long reads for reference genomes. There may be talk of MinION from Oxford Nanopore in teh future for long read sequencing.

• Byrd, Allyson L., and Julia A. Segre. “Adapting Koch’s postulates.” Science 351.6270 (2016): 224-226.