Microbial Genomics Journal / Project Club

We will be meeting on Fridays at 9am in the Morrill II 319 (OEB seminar room).

Overview - The topics/software covered may include

* Preparing proposals for DOE's Community Sequencing Program (or other
similar national programs)
* The JGI genome annotation system
* Work flows for analyzing amplicon and metagenomic Illumina seq data
* Emerging sequencing technology
* Experimental evolution and genome resequencing
* Comparative genomics

Schedule

Sep 7 - Organizational meeting
Sep 14 - No meeting
Sep 21 - Eric - Current and near future sequencing technology

http://www.jgi.doe.gov/sequencing/education/current-technology.html
http://www.pacificbiosciences.com/aboutus/video-gallery/index.html
http://en.wikipedia.org/wiki/Next-generation_sequencing#New_sequencing_m...
http://www.nanoporetech.com/

Sep 28 - Kelly

The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. Stand Genomic Sci. 2009 Jul 20;1(1):63-7.

Oct 5 - Jesus

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. Hemme et al. J Bacteriol. 2010 Dec;192(24):6494-6. Epub 2010 Oct 1.

Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2. J Bacteriol. 2012 Jun;194(12):3290-1. Brown SD, Lamed R, Morag E, Borovok I, Shoham Y, Klingeman DM, Johnson CM, Yang Z, Land ML, Utturkar SM, Keller M, Bayer EA.

Oct 12 - Amy

Genomic and physiological characterization of the Verrucomicrobia isolate Diplosphaera colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes. Wertz JT, Kim E, Breznak JA, Schmidt TM, Rodrigues JL. Appl Environ Microbiol. 2012 Mar;78(5):1544-55. Epub 2011 Dec 22.

Oct 19 - James

Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast. Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews-Pfannkoch C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA 3rd. Nucleic Acids Res. 2012 Aug 31.

Oct 26 - Josie

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Floudas et al. Science. 2012 Jun 29;336(6089):1715-9.

Nov 2 - Xyrus

Alternative processing of scrambled genes generates protein diversity in the ciliate Chilodonella uncinata.
Katz LA, Kovner AM. J Exp Zool B Mol Dev Evol. 2010 Sep 15;314(6):480-8.

Nov 9 - Joanne

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Li GW, Oh E, Weissman JS. Nature. 2012 Mar 28;484(7395):538-41.

Nov 16 - Farah

Ecology. How bacterial lineages emerge. Papke RT, Gogarten JP. Science. 2012 Apr 6;336(6077):45-6. No abstract available. This is a comment on

Population genomics of early events in the ecological differentiation of bacteria.
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ.
Science. 2012 Apr 6;336(6077):48-51. doi: 10.1126/science.1218198.

Nov 23 (Thanksgiving Break)

Nov 30 - William

Evidence of cellulose metabolism by the giant panda gut microbiome. Zhu L, Wu Q, Dai J, Zhang S, Wei F. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17714-9. Epub 2011 Oct 17.

Dec 7 - Grace

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics. Andreote FD, Jimènez DJ, Chaves D, Dias ACF, Luvizotto DM, et al. (2012) PLoS ONE 7(6): e38600. doi:10.1371/journal.pone.0038600

Dec 14 - Colby

Possible Reading List

Short genome publications

Complete Genome Sequence of Clostridium clariflavum DSM 19732. Izquierdo JA, Goodwin L, Davenport KW, Teshima H, Bruce D, Detter C, Tapia R, Han S, Land M, Hauser L, Jeffries CD, Han J, Pitluck S, Nolan M, Chen A, Huntemann M, Mavromatis K, Mikhailova N, Liolios K, Woyke T, Lynd LR. Stand Genomic Sci. 2012 Mar 19;6(1):104-15. Epub 2012 Mar 12.

Complete genome sequence of "Enterobacter lignolyticus" SCF1. Deangelis KM, D'Haeseleer P, Chivian D, Fortney JL, Khudyakov J, Simmons B, Woo H, Arkin AP, Davenport KW, Goodwin L, Chen A, Ivanova N, Kyrpides NC, Mavromatis K, Woyke T, Hazen TC. Stand Genomic Sci. 2011 Oct 15;5(1):69-85. Epub 2011 Sep 23.

Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313. Feinberg L, Foden J, Barrett T, Davenport KW, Bruce D, Detter C, Tapia R, Han C, Lapidus A, Lucas S, Cheng JF, Pitluck S, Woyke T, Ivanova N, Mikhailova N, Land M, Hauser L, Argyros DA, Goodwin L, Hogsett D, Caiazza N. J Bacteriol. 2011 Jun;193(11):2906-7. Epub 2011 Apr 1.

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. Hemme et al. J Bacteriol. 2010 Dec;192(24):6494-6. Epub 2010 Oct 1.

Genome sequences of three species in the family Planctomycetaceae. Guo M, Han X, Jin T, Zhou L, Yang J, Li Z, Chen J, Geng B, Zou Y, Wan D, Li D, Dai W, Wang H, Chen Y, Ni P, Fang C, Yang R. J Bacteriol. 2012 Jul;194(14):3740-1.

Draft genome sequences for Clostridium thermocellum wild-type strain YS and derived cellulose adhesion-defective mutant strain AD2. Brown SD, Lamed R, Morag E, Borovok I, Shoham Y, Klingeman DM, Johnson CM, Yang Z, Land ML, Utturkar SM, Keller M, Bayer EA. J Bacteriol. 2012 Jun;194(12):

Complete genome sequence of Acidaminococcus intestini RYC-MR95, a Gram-negative bacterium from the phylum Firmicutes. D'Auria G, Galán JC, Rodríguez-Alcayna M, Moya A, Baquero F, Latorre A. J Bacteriol. 2011 Dec;193(24):7008-9.

Longer genome publications

The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing. Kuwahara T, Ogura Y, Oshima K, Kurokawa K, Ooka T, Hirakawa H, Itoh T, Nakayama-Imaohji H, Ichimura M, Itoh K, Ishifune C, Maekawa Y, Yasutomo K, Hattori M, Hayashi T. DNA Res. 2011 Aug;18(4):291-303. doi: 10.1093/dnares/dsr022. Epub 2011 Jul 26.

Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence. Fonknechten N, Chaussonnerie S, Tricot S, Lajus A, Andreesen JR, Perchat N, Pelletier E, Gouyvenoux M, Barbe V, Salanoubat M, Le Paslier D, Weissenbach J, Cohen GN, Kreimeyer A. BMC Genomics. 2010 Oct 11;11:555.

Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation. Prakash T, Oshima K, Morita H, Fukuda S, Imaoka A, Kumar N, Sharma VK, Kim SW, Takahashi M, Saitou N, Taylor TD, Ohno H, Umesaki Y, Hattori M. Cell Host Microbe. 2011 Sep 15;10(3):273-84. doi: 10.1016/j.chom.2011.08.007.

The genome of th17 cell-inducing segmented filamentous bacteria reveals extensive auxotrophy and adaptations to the intestinal environment. Sczesnak A, Segata N, Qin X, Gevers D, Petrosino JF, Huttenhower C, Littman DR, Ivanov II. Cell Host Microbe. 2011 Sep 15;10(3):260-72. doi: 10.1016/j.chom.2011.08.005.

The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Seedorf H, Fricke WF, Veith B, Brüggemann H, Liesegang H, Strittmatter A, Miethke M, Buckel W, Hinderberger J, Li F, Hagemeier C, Thauer RK, Gottschalk G. Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2128-33. Epub 2008 Jan 24.

Clostridium phytofermentans Genome and Transcriptome: A Window on the Direct Conversion of Plant Biomass to Fuels. Petit et al.

Genome resequencing

Population level analysis of evolved mutations underlying improvements in biofuel production by Clostridium phytofermentans. Mukherjee et al.

Comparative genomics and evolution

The bacterial pan-genome:a new paradigm in microbiology. Mira A, Martín-Cuadrado AB, D'Auria G, Rodríguez-Valera F. Int Microbiol. 2010 Jun;13(2):45-57. Review.

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Floudas et al. Science. 2012 Jun 29;336(6089):1715-9.

The emergence and early evolution of biological carbon-fixation. Braakman R, Smith E. PLoS Comput Biol. 2012;8(4):e1002455. Epub 2012 Apr 19.

A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem. Takami H, Noguchi H, Takaki Y, Uchiyama I, Toyoda A, Nishi S, Chee GJ, Arai W, Nunoura T, Itoh T, Hattori M, Takai K. PLoS One. 2012;7(1):e30559. Epub 2012 Jan 27.

RNAseq

Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus. Khudyakov JI, D'haeseleer P, Borglin SE, Deangelis KM, Woo H, Lindquist EA, Hazen TC, Simmons BA, Thelen MP. Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):E2173-82. http://www.pnas.org/content/109/32/E2173.long

Phytotyping

Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons. Shepherd ML, Swecker WS Jr, Jensen RV, Ponder MA. FEMS Microbiol Lett. 2012 Jan;326(1):62-8. doi: 10.1111/j.1574-6968.2011.02434.x. Epub 2011 Nov 2.

Metagenomics

Evidence of cellulose metabolism by the giant panda gut microbiome. Zhu L, Wu Q, Dai J, Zhang S, Wei F. Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17714-9. Epub 2011 Oct 17.

Anaerobic decomposition of switchgrass by tropical soil-derived feedstock-adapted consortia. DeAngelis KM, Fortney JL, Borglin S, Silver WL, Simmons BA, Hazen TC. MBio. 2012 Feb 21;3(1). pii: e00249-11. doi: 10.1128/mBio.00249-11. Print 2012.

Metatranscriptomics

The active human gut microbiota differs from the total microbiota. Peris-Bondia F, Latorre A, Artacho A, Moya A, D'Auria G. PLoS One. 2011;6(7):e22448. Epub 2011 Jul 28.

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol. 2012 Apr 30;158(4):248-58. doi: 10.1016/j.jbiotec.2012.01.020. Epub 2012 Feb 8. Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A.

Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms. Tveit A, Schwacke R, Svenning MM, Urich T. ISME J. 2012 Sep 6. doi: 10.1038/ismej.2012.99. [Epub ahead of print]

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition. Baldrian P, Kolařík M, Stursová M, Kopecký J, Valášková V, Větrovský T, Zifčáková L, Snajdr J, Rídl J, Vlček C, Voříšková J.ISME J. 2012 Feb;6(2):248-58. doi: 10.1038/ismej.2011.95. Epub 2011 Jul 21.

Methods/Software

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Thorvaldsdóttir H, Robinson JT, Mesirov JP. Brief Bioinform. 2012 Apr 19. - http://www.broadinstitute.org/igv/

Sequencing Facilities

* UMass Deep Sequencing Core Facility - http://www.umassmed.edu/nemo/index.aspx
* UMass Amherst Genomics Resource Lab (Sanger Sequencing) - https://sites.google.com/site/umassgenomics/
* DOE Community Sequencing Program - http://www.jgi.doe.gov/CSP/
* Overview of Illumina and PacBio sequencing at JGI - http://www.jgi.doe.gov/sequencing/education/current-technology.html
* Illumina MiSeq at Dana Farber Cancer Institute - http://mbcf.dfci.harvard.edu/miseq/miseq.html/

Publishing research

Scientific Writing 101 - http://www.nature.com/nsmb/journal/v17/n2/full/nsmb0210-139.html
Scientific Publishing Dos and Don’ts for Authors and Reviewers - http://www.aai.org/About/Publications/Additional/index.html

Additional notes for the Blanchard Research Group

Be scholar in your area of research
* Actively read the emerging literature and be aware of presentations at conferences (even if you don't go)
* Set aside a time once a week to browse journals and search PubMed or Web of Knowledge
* Create an email alert using search terms at PubMed or WoK

Make high quality publishable figures and tables as you generate the data
* Figures are a big part of telling the story
* These figures are good to have ready for communicating with me
* Practice telling the story for lab meeting
* Do learn R and use R when appropriate to make figures - it will also look good on your CV
* It is hard to go back through the data and rediscovery what you knew a year ago

I do expect all graduate students to lead the publication of their manuscripts
* Do send me a draft of the manuscript in the form required by your target journal
* Not all reviewers will be experts in your area (e.g. a microcompartment paper is likely to be reviewed by at least one reviewer with no knowledge of microcompartments and a Cphy paper is likely to be reviewed by someone unfamiliar with Cphy)
* Please use Zotero (www.zotero.com) for your references so that we can share reference databases.
* Please OpenDocument format files for publication. They are default in OpenOffice, LibreOffice and NeoOffice
* The use of OpenDocument files will alleviate formating problems that result from translating Microsoft formats (there seem to be less problems translating the other direction) and facilitate editing references