Eisen Lab Blog

How about this? Wash your hands. Please. (Nice video from SLV Health)

Saw this news story a while ago: Videos help spread word of bacteria, other health issues | Deseret News but only just got to watching the video from Salt Lake Valley Health. 

I note – my post originally said “Wash you hands” and my 6 year old daughter was snooping at my computer and said “Daddy, it says ‘wash you hands’ not ‘wash your hands.'” Well, I think I found a new blog editor.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Opening up one’s eyes to other fields (cross-posting from #microBEnet)

Cross-posting this: Opening up one’s eyes to other fields which I posted originally on the microBEnet blog.

I spend most of my time working on biology.  I like to think I cover lots of breadth within biology and I probably do – microbes, evolution, ecology, human health, pathogens, symbioses, forensics, genomics, bioinformatics, and more.  But nothing like really looking at other fields to realize how narrowly focused one is.

And that is what has happened to me since I took on the “microBEnet” project trying to foster communications and collaborations on microbiology of the built environment. I now pay much more attention to anything that might have a connection to “Building Science” in one way or another.  Not only did I just go to an Indoor Air meeting, but I keep discovering more and more stuff right near home that I was not aware of before.  For example – I just got sent this news link from Aaron Darling in my lab: UC Davis News & Information :: History of sciences in architecture subject of Mellon Foundation winner’s study.  Previously, I would definitely not have been paying much attention to architecture and history of science.  But now seeing other people at UC Davis working on the Built Environment just makes me think about how I can build connections with them and talk to them about buildings (and other built environments) and possibly, one day, about the microbes that are in them.

Which brings me to another story.  At the Indoor Air meeting earlier in the week in Austin, Texas, when heading to the conference center I got into a conversation with someone looking for the registration desk.  After showing her where to go she asked where I was from and I said “UC Davis.”  And it turns out – she was too.  Turns out, this was Deborah Bennett, who I had heard mentioned the evening before but had not heard the whole name.  I just knew someone else at the meeting was from Davis.   Deborah is at the UC Davis School of Public Health and works on some really interesting stuff.  And since UC Davis is so big (some 2500 or so faculty I think) – it is not always easy or simple to find people even if you might have a connection to them.

So anyway, just a little commentary on how I find it fascinating to see for the first what was in a way right before my eyes.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Fun with Ligercat: pubmed word clouds

I have been having enormous fun over the last hour playing with LigerCat.  I was searching for ways to build tag clouds for papers in Pubmed and this came up: LigerCat: Using “MeSH Clouds” from Journal, Article, or Gene Citations to Facilitate the Identification of Relevant Biomedical Literature.   And they have a web site to do searches: LigerCat Literature and Genomics Resource Catalogue

So, of course, like many others, the first thing I did was search for myself:

Eisen JA

http://ligercat.ubio.org/articles/1365086.cloud

I then repeated the search, but excluded articles from the SIGS journals, since I have about 100 of those articles that are in essence “Genome sequencing reports”:

http://ligercat.ubio.org/articles/1365087.cloud

So this was fun. So then I played around with a variety of other searches

Phylogenomics

http://ligercat.ubio.org/articles/1364022.cloud

Indoor Microbiology

http://ligercat.ubio.org/articles/1365091.cloud

University of California[Affiliation] Davis[Affiliation]

http://ligercat.ubio.org/articles/1365093.cloud

Haloarchaea

http://ligercat.ubio.org/articles/1365095.cloud

Wolbachia

http://ligercat.ubio.org/articles/1365097.cloud

GFAJ-1

http://ligercat.ubio.org/articles/1365099.cloud

Some things did not work for some reason(microbiome, metagenomic) but overall this is a useful quick way to get a feel for topics covered in some area.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Quick update (pics, twitter feed) on #IndoorAir2011 in Austin, TX #microBEnet

Here are some pics from my trip to the Indoor Air 2011 meeting. I am going to post more detail about the meeting later.

https://picasaweb.google.com/s/c/bin/slideshow.swf

If you want some information about what happened at the meeting, best place right now is probably twitter

http://widgets.twimg.com/j/2/widget.js
new TWTR.Widget({ version: 2, type: ‘search’, search: ‘#IndoorAir2011’, interval: 6000, title: ”, subject: ‘Indoor Air 2011’, width: 250, height: 300, theme: { shell: { background: ‘#8ec1da’, color: ‘#ffffff’ }, tweets: { background: ‘#ffffff’, color: ‘#444444’, links: ‘#1985b5’ } }, features: { scrollbar: true, loop: false, live: true, hashtags: true, timestamp: true, avatars: true, toptweets: true, behavior: ‘all’ } }).render().start();

Also see the microBEnet blog which has some recent posts on this.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Worst new omicsword, perhaps ever, the Dispensome #awful #badomics #reallybad #uggh

Well, I do not even have any idea what to say. I got pointed to this paper: PLoS Genetics: Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis by KamounLab on twitter. The authors of the paper include colleagues at the DOE-Joint Genome Institute so it is possible that they are baiting me to get some attention. But YHGTBFKM – the dispensome? Defined by them as “The dispensable chromosomes collectively comprise the dispensome and showed extreme plasticity during sexual reproduction.” Now, I have seen my share of bad omics words (and which I write about often with, for example, my Worst New Omics Word Award and Bad Omics Word of the Day). But this is the first case where the word, and the excessive use of it in the paper is distracting (as suggested by KamounLab) to the science. Is this word really necessary? Could they not just say “dispensable chromosomes” (which I note, I might still have problems with since they would only be known as dispensable under certain conditions)? But “dispensome” is unnecessary, distracting, and, well, not a good word. Thus in this case I have decided to not even give them an award per se but to simply say that I think this is possibly the worst omics word I have ever seen. I note – I am not criticizing the science (nor endorsing it mind you) they did here. But the word, oh the word. It hurts me. It really does.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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I like this pic of me so much it gets a whole post – "Apple Love" by Rhonda Roman

Apple Love by Rhonda Roman
 So a few Saturday’s ago I was at the Davis Farmer’s Market and Steve Smit from Mt. Moriah Farm’s showed me this pic that a photographer had given him.  Steve is one of my favorite people anywhere.  I don’t know why really.  But I go to the Farmer’s Market many times just to see him/buy stuff from him.  He is funny, warm, interesting, social, etc.  And apparently a photographer caught one of our interactions from earlier this year.  

Fortunately, she put her name on the back of the picture and a little googling and I found her photo collection on flickr.  Her name is Rhonda Roman and I really like her collections there.  But in particular I love this picture she took of me and Steven and others at the Market.  It captures everything really about my interactions with Steve.  Thanks Rhonda.  A picture is worth way way more than 1000 words.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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#UCDavis to partner with the Beijing Genome Institute (BGI)

Well, it is now formal so I guess I can post about it here.  UC Davis is officially developing a genomics partnership with the Beijing Genomics Institute (BGI).

For more on this breaking news see

Not much detail there I know – but in essence the plan is to build a partnership between UC Davis and BGI with BGI provided genomics and informatics expertise and capabilities and Davis providing biological expertise and diversity (of course, Davis has some genomics chops too and BGI does some biology but you probably get the point). 
For those who do not know, BGI is a relative newcomer on the block in terms of large scale genomics research institutes.  But by being new they have had a massive advantage in a way in that they are really the first to be developed as a “Second-generation Genome Center” having been built / developed with the new second generation sequencing systems at its core.  Thus while other large centers around the world have tried to adapt to the new second generation sequencing systems, BGI started from scratch and could build it’s enterprise around the new systems.  
I am excited about the possible connections with BGI though I confess I do not know a whole lot about the plans.  There have been lots of whisperings here at Davis about building a partnership with BGI and people have been a bit nervous about word getting out too early.  So, though I have heard some details I have not been an active part of the discussions.  However, whatever the plans are I am looking forward to interactions with BGI.  They are really pushing the frontiers of genome sequencing in many ways.  And despite the moans and groans from many people, I do not think genome sequencing is on a downward slope in any way.  For example, as a tool in studying microbes, genome sequencing still has many many years of use – after all there are hundreds of millions of microbial species that have yet to be studied and each one has lots of intraspecific diversity (e.g., across geography) to be characterized.  
And as a UC Davis faculty member I think BGI picked a great place to work with.  Davis has an almost unprecedented diversity of faculty working on some area in the life sciences – and these faculty come from across campus from the College of Biological Sciences, School of Medicine, Viticulture and Enology, School of Veterinary Medicine, College of Agriculture and Environmental Sciences, College of Engineering, School of Nursing, and College of Letters and Sciences.  In fact, you could say – in a way – UC Davis is a campus more dedicated to Life Sciences than almost any other place in the world.  
This development is just one of many that make me impressed with the new UC Davis Administration.    Ever since Chancellor Katehi came on board I have been pleased with almost every major initiative and development and administrative hire on campus.  Sure – the budget cuts from the California government hurt.  But in challenging times, you need great leadership.  And we certainly have it at UC Davis these days.  And if you think I am just sucking up, you should read some of the things I wrote about our previous administration.  I really am impressed here.  
I do not know what will happen with the BGI – UC Davis partnership.  Right now it is just a plan.  But I will do what I can to help it succeed and I am looking forward to interactions with BGI and the bright future at UC Davis. 
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Off to #IndoorAir 2011 in Austin, TX – to discuss and promote http://microbe.net #microBEnet

Well, off to Austin for a meeting I would not have imagined going to a few years ago. Indoor Air 2011. Why am I going? Because a few years ago I began to discuss studying the microbiology of the built environment with Paula Olsiewski, from the Alfred P. Sloan Foundation. You see, the Sloan Foundation has a new program in this area “The Indoor Environment“. Eventually, after much discussion I applied for a grant in their program. My grant is a bit unusual (for me and for others probably) in that it focuses on communication, coordination, networking, collaboration, etc.
My project is called “microBEnet” – which stands for “microbiology of the Built Environment network”. The BE is purposefully capitalized to emphasize the Built Environment part and we figure, since microbes are small, the m should be lower case. For more on the project see: Microbiology of the Built Environment Network | Site for the microBEnet project. As part of this project, a collaborator (Hal Levin) and I are doing many activities and I will post more about them over time. Among our activities are a new blog, and a diversity of resources.

Which brings me to Indoor Air 2011.  We are also starting to organize or help organize some meetings and workshops to bring together the various folks who might be interested in microbiology of the built environment.  And for Indoor Air we have helped the meeting organizer Rich Corsi plan some sessions on microbiology of the built environment.  The sessions take place Wednesday and Thursday and should be great.   Looking forward to going to Austin, maybe seeing some friends at UT and nearby (hint hint Dr. Hillis, Sheril K, etc) and learning about the built environment.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Apparently, my own local paper hates my blog

I mean, I knew evolution was controversial and that I can be a bit snarky at times.  But does my own local paper -the Davis Enterprise have to have a whole article about how they hate me and my blog?

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Crosspost from http://microBE.net: New, massive volumes on #metagenomics coming out soon

For those interested in microbial diversity and/or metagenomics there are two volumes that are coming out soon that are of interest:

Edited by Frans J. de Bruijn these two volumes are the most comprehensive coverage of metagenomics out there right now. The chapters are almost overwhelming (full disclosure, I have two chapters in here – both of which are republications of Open Access papers I have published on metagenomics).  See below for full chapter lists.

Order from Amazon:

Volume I: Metagenomics and Complementary Approached

  • 1. Introduction (Frans J. de Bruijn).
  • Background Chapters.
    • 2. DNA reassociation yields broad-scale information on metagenome complexity and microbial diversity (V. Torsvik).
    • 3. Diversity of 23S rRNA genes within individual prokaryotic genomes (Zhiheng Pei).
    • 4. Use of the rRNA operon and genomic repetitive sequences for the identification of bacteria (A. Nascimento).
    • 5. Use of different PCR primer-based strategies for characterization of natural microbial communities (James Prosser).
    • 6. Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plants Astragalus luteolus and Astragalus ernestii in Sichuan, China (Xiaoping Zhang).
    • 7. Amplified rDNA restriction analysis (ARDRA)for identification and phylogenetic placement of 16S-rDNA clones (Menachim Sklarz).
    • 8. Clustering-based peak alignment algorithm for objective and quantitative analysis of DNA fingerprinting data (Satoshi Ishii).
  • The Species Concept.
    • 9. Population genomics informs our understanding of the bacterial species concept (Margaret Riley).
    • 10. Genome analysis of Streptococcus agalactiae: Implication for the microbial “pan-genome” (Rino Rappuoli).
    • 11. Metagenomic insights into bacterial species (Kostas Konstantinidis).
    • 12. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology (Erko Stackebrandt).
    • 13. Metagenomic Approaches for the Identification of Microbial Species (David Ward).
  • Metagenomics.
    • 14. Microbial Ecology in the age of metagenomics (Jianping Xu).
    • 15. The enduring legacy of small rRNA in microbiology (Susan Tringe).
    • 16. Pitfalls of PCR-based rRNA gene sequence analysis:  an update on some parameters (Erko Stackebrandt).
    • 17. Empirical testing of 16S rRNA gene PCR primer pairs reveals variance in target specificity and efficacy not suggested by in silico analysis (Sergio Morales and Bill Holben).
    • 18. The impact of next-generation sequencing technologies on (meta)genomics (George Weinstock).
    • 19. Accuracy and quality of massively parallel DNA pyrosequencing (Susan Huse and David Mark Welch).
    • 20. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes (Jonathan Eisen).
    • 21. Comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library (C. Manischan).
    • 22. Metagenomic libraries for functional screeing (Svein Valla).
    • 23. GC Fractionation Allows Comparative Total Microbial Community  Analysis, Enhances Diversity Assessment, and Facilitates of Minority Populations of Bacteria (Bill Holben).
    • 24. Enriching plant microbiota for a metagenomic library construction (Ying Zeng).
    • 25. Towards Automated Phylogenomic Inference (Wu and Eisen).
    • 26. Integron first gene cassettes: a target to find adaptive genes in metagenomes (Christine Cagnon).
    • 27. High-resolution metagenomics: assessing specific functional types in complex microbial communities (Christoserdova).
    • 28. Gene-targeted –metagenomics (GT-metagenomics) to explore the extensive diversity of genes of interest in microbial communities (J. Tiedje).
    • 29. Phylogenetic screening of metagenomic libraries using homing endonuclease restriction and marker insertion (Torsten Thomas).
    • 30. ArrayOme- & tRNAcc-facilitated mobilome discovery: comparative genomics approaches for identifying rich veins of novel bacterial DNA sequences (Hong-Yu OU).
    • 31. Sequence-Based Characterization of Microbiomes by Serial Analysis of Ribosomal Sequence Tags (SARST) (Zhongtang Yu).
  • Consortia and Databases.
    • 32. The metagenomics of plant pathogen-suppressive soils (J.D. Van Elsas).
    • 33. Soil Metagenomic Exploration of the Rare Biosphere (Pascal Simonet and Timothy Vogel).
    • 34. The BIOSPAS consortium: Soil Biology and agricultural production (Luis Wall).
    • 35. The Human Microbiome Project (George Weinstock).
    • 36. The Ribosomal Database Project: sequences and Software for high-throughput rRNA analysis (J. R. Cole, G. M. Garrity and Jim Tiedje).
    • 37. The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes (Folker Meyer).
    • 38. The EBI Metagenomics Archive, Integration and Analysis resource (Apweiler).
  • Computer Assisted Analysis.
    • 39. Comparative metagenome analysis using MEGAN (Suparna Mitra and Daniel Huson).
    • 40. Phylogenetic binning of metagenome sequence samples (Alice C. McHardy).
    • 41. Gene prediction in metagenomic fragments with Orphelia: A large scale machine learning approach (Katharina Hoff).
    • 42. Binning metagenomic sequences using seeded GSOm (Sen-Lin Tang).
    • 43. Iterative read mapping and assembly allows the use of a more distant reference in metagenomic assembly (Bas E. Dutilh).
    • 44. Ribosomal RNA identification in metagenomic and metatranscriptomic datasets (Li).
    • 45. SILVA: comprehensive databases for quality checked and aligned ribosomal RNA sequence data compatible with ARB (Frank Gloeckner).
    • 46. ARB; a software environment for sequence data (Wolfgang Ludwig).
    • 47. The Phyloware Project: A software framework for phylogenomic virtue (Daniel Frank).
    • 48. Metasim- A sequencing simulator for genomics and metagenomics (Daniel Richter).
    • 49. ClustScan: an integrated program package for the detection and semi-automatic annotation of secondary metabolite clusters in genomic and metagenomic DNA datasets (Daslav Hranueli).
    • 50. MetaGene; Prediction of prokaryotic and phage genes in metagenomic sequences (Noguchi).
    • 51. primers4clades, a web server to design lineage-specific PCR primers for gene-targeted metagenomics (Pablo Vinuesa).
    • 52. A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes (Y. Ye).
    • 53. ESPRIT: estimating species richness using large collections of 16S rRNA data (Yijun Sun).
  • Complementary Approaches.
    • 54. (Meta) genomics approaches in systems biology (Manuel Ferrer).
    • 55. Towards “focused metagenomics”: a case study combining DNA stable-isotope probing, multiple displacement amplification and metagenomics (J. Colin Murrell).
    • 56. Galbraith, E. A., D. A. Antonopoulos, K. E. Nelson, and B. A. White . Suppressive subtractive hybridization reveals extensive horizontal transfer in the rumen metagenome (Bryan White).
  • Microarrays.
    • 57. GeoChip: A high throughout metagenomics technology for dissecting microbial community functional structure (J. Zhou).
    • 58. Phylogenetic microarrays (PhyloChips) for analysis of complex microbial communities (Eoin Brodie).
    • 59. Phenomics and Phenotype MicroArrays: Applications Complementing Metagenomics (Barry Bochner).
    • 60. Microbial persistence in low biomass, extreme environments: The great unknown (Kasthuri Venkateswaran).
    • 61. Application of phylogenetic oligonucleotide microarrays in microbial analysis (Nian Wang).
  • Metatranscriptomics.
    • 62. Isolation of mRNA from environmental microbial communities for metatranscriptomic analyses (P. Schenk).
    • 63. Comparative day/night metatrancriptomic analysis of microbial communities in the North Pacific subtropical gyre (Rachel Poretski).
    • 64. The “double RNA” approach to simultaneously assess the structure and function of environmental microbial communities by meta-transcriptomics (Tim Urich and Christa Schleper).
    • 65. Soil eukaryotic diversity, a metatranscriptomic approach (Marmeisse).
  • Metaproteomics.
    • 66. Proteomics for the analysis of environmental stress responses in prokaryotes Ksenia Groh, Victor Nesatyy and Marc Suter).
    • 67. Microbial community proteomics (Paul Wilmes).
    • 68. Synchronicity between population structure and proteome profiles: A metaproteomic  analysis of Chesapeake Bay bacterial communities (Feng Chen).
    • 69. High-Throughput Cyanobacterial Proteomics: Systems-level Proteome Identification and Quantitation   (Phillip Wright).
    • 70. Protein Expression Profile of an Environmentally Important Bacterial Strain: the Chromate Response of Arthrobacter sp. strain FB24 (K. Henne).
  • Metabolomics.
    • 71. The small molecule dimension: Mass spectrometry based metabolomics, enzyme assays, and imaging (Trent R. Northen).
    • 72. Metabolomics: high resolution tools offer to follow bacterial growth on a molecular level (Lucio Marianna and Philipp Schmitt-Kopplin).
    • 73. Metabolic profiling of plant tissues by electrospray mass spectrometry (Heather Walker).
    • 74. Metabolite identification, pathways and omic integration using online databases and tools (Matthew Davey).
  • Single cell analysis.
    • 75. Application of cytomics to separate natural microbial communities by their physiological properties (Susann Müller).
    • 76. Capturing microbial populations for environmental genomics (A. Pernthaler/Wendeberg).
    • 77. Microscopic single-cell isolation and multiple displacement amplification of genomes from uncultured prokaryotes (Peter Westermann).

Volume 2: Metagenomics in Different Habitats

  • 1. Introduction (Frans J. de Bruijn).
  • Viral Genomes.
    • 2. Viral metagenomics (Shannon Williamson).
    • 3. Methods in Viral Metagenomics (Thurber).
    • 4. Metagenomic contrasts of viruses in soil and aquatic environments (Eric Wommack).
    • 5. Biodiversity and biogeography of phages in modern stromatolites and thromolites (Christelle Desnues).
    • 6. Assembly of Viral Metagenomes from Yellowstone Hot Springs Reveals Phylogenetic Relationships and Host Co-Evolution (Thomas Schoenfeld).
    • 7. Next-generation sequencing and metagenomic analysis; a universal diagnostic tool in plant pathology (Ian Adams).
    • 8. Direct Metagenomic Detection of Viral Pathogens in Human Specimens Using an Unbiased High-throughput Sequencing Approach (T. Nakaya).
  • The Soil Habitat.
    • 9. Soil based Metagenomics (R. Daniel).
    • 10. Methods in Metagenomic DNA, RNA and Protein Isolation from Soil (P. Gunasharan).
    • 11. Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications (Mark Liles).
    • 12. Application of PCR-DGGE and metagenome walking to retrieve full-length functional genes from soil (Morimoto).
    • 13. Actinobacterial diversity associated with Antarctic Dry Valley mineral soils (Cowan).
    • 14. Targetting major soil-borne bacterial lineages using large-insert metaenomic approaches (G. Kowalchuk).
    • 15. Novelty and uniqueness patterns of rare members of the soil biosphere (M. Elshahed).
    • 16. Extensive phylogenetic analysis of a soil bacterial community illustrates extreme taxon evenness and the effects of amplicon length, degree of coverage, and DNA fractionation on classification and ecological parameters (Holben WE).
    • 17. The Antibiotic Resistance: Origins, Diversity, and Future Prospects (Gerard Wright).
  • The Digestive Tract.
    • 18. Functional Intestinal Metagenomics (Michael Kleerebezem).
    • 19. Assessment and improvement of methods for microbial DNA preparation from fecal Samples (M. Hattori).
    • 20. Role of dysbiosis in inflammatory bowel diseases (Johan Dicksved).
    • 21. Culture independent analysis of the human gut microbiota and its activities (Kieran Tuohi).
    • 22. Complete genome of an uncultured endowsymbiont coupling nitrogen fixation to cellulolysis with protest cells in termite gut (Hongo).
    • 23. Cloning and identification of genes encoding acidic cellulases from metagenomes of buffalo rumen (Feng).
  • Marine and Lakes.
    • 24. Microbial diversity in the deep seas and the underexplored “rare biosphere” (David Mark Welsch and Susan Huse).
    • 25. Bacterial Community Structure and Dynamics in a Seasonally Anoxic Fjord (Steven J. Hallam).
    • 26. Adaptation to nutrient availability in marine microorganisms by gene gain and loss (A. Martini).
    • 27. Detection of large numbers of novel sequences in the metatranscriptomes of complex marine microbial communities (Jack Gilbert).
    • 28. Metagenomic approach studying the taxonomic and functional diversity of the bacterial community in a lacustrine ecosystem (Didier Debroas).
    • 29. Metagenomics of the marine subsurface: the first glimpse from the Peru Margin, ODP Site 122 (Jennifer Biddle).
    • 30. A targeted metagenomic approach to determine the ‘population genome’ of marine Synechoccus (D. J. Scanlan).
    • 31. Diversity and role of bacterial integron/gene cassette metagenome in extreme marine environments (Hosam Easa Elsaied and Akihiko Maruyama).
  • Other Habitats.
    • 32. The Olavius algarvensis metagenome revisited: lessons learned from the analysis of the low diversity microbial consortium of a gutless marine worm (Nicole Dubulier).
    • 33. Microbiome diversity in human saliva (Ivan Nasidze).
    • 34. Approaches to understanding population level functional diversity in a microbial community (D. Bhaya).
    • 35. A functional metagenomic approach for discovering nickel resistance genes from the rhizosphere of an acid mine drainage environment (JOSE Gonzales –Pastor).
    • 36. The Microbiome of Leaf-cutter Ant Fungus Gardens (Garret Suen).
    • 37. Diversity of archaea in terrestrial hot springs and role In ammonia oxidation (Chuanlun Zhang).
    • 38. Colinization of nascent, deep-sea hydrothermal vents by a novel Archaeal and Nanoarchaeal assemblage (S. Craig Cary).
    • 39. Analysis of the Metagenome from a biogas-producing microbial Community by means of Bioinformatucs Methods (Andreas Schlueter).
    • 40. Amplicon pyrosequencing analysis of endosymbiont population structure (Colleen Kavahagh).
    • 41. Investigative bacterial diversity along alkaline hot spring thermal gradients by barcoded pyrosequencing (Scott Miller and Michael Welzer).
    • 42. Genetic characterization of microbial communities living at the surface of building stones (J. C. Salvado).
    • 43. Novel aromatic degradation pathway genes and their organization as revealed by metagenomic analysis (Kentaro).
    • 44. Functional screening of a wide host-range metagenomic library from a wastewater treatment plant yields a novel alcohol/aldehyde dehydrogenase (Wexler).
    • 45. Aromatic hydrocarbon degradation genes from chronically polluted Subantarctic marine sediments (H. M. Dionisi).
    • 46. Isolation and characterization if alkane hydroxylases from a metagenomic llibrary of Pacific deep-sea sediment  (Fengping Wang).
  • Biocatalysts and Natural Products.
    • 47. Emerging Fields in Functional Metagenomics and its Industrial Relevance  – Overcoming Limitations and Redirecting the Search for Novel Biocatalysts (Wolfgang Streit).
    • 48. Carboxylesterases and Lipases from Metagenomes (Chow and Wolfgang Streit).
    • 49. Expanding small molecule functional megenomics through parallel screening of broad host-range cosmid environmental DNA libraries in diverse Proteobacteria (Sean Brady).
    • 50. Biomedicinals from the microbial metagenomes of marine invertebrates (Walter Dunlap).
    • 51. Molecular characterization of TEM-type beta-Lactamases identified in Cold-seep sediments of Edison Seamount (South of Lihir Island).
    • 52. Identification of Novel Bioactive Compounds from the Metagenome of the Marine (David Lejon).
    • 53. Functional Viral Metagenomics and the Development of New Enzymes for DNA and RNA Amplification and Sequencing (Thomas Schoenfeld).
  • Summary.
    • 54. Future of metagenomics, metatranscriptomics, metabolomics, metaproteomics and single cell analysis: A perspective (J. Tiedje).
    • 55. Darwin in the 21st Century: Natural Selection, Molecular Biology, and Species Concepts (Francisco Ayala).
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–