Posts Tagged ‘Metagenomics’

Exploring the Mycorrhizal Genomes

September 9th, 2012

 

I hope you are wrapping up a good summer. I’m touching base to update you on our Mycorrhizal Genomics Initiative (MGI).

The list of taxa of mycorrhizal fungi for the first series of analyses aiming to identify symbiotic traits has now been “frozen”. Thanks to Igor Grigoriev’s JGI team, this list includes an outstanding series of annotated genomes and transcriptomes from ectomycorrhizal, ericoid and orchid symbionts:

  • Amanita muscaria Koide
  • Hebeloma cylindrosporum h7  (v2.0),
  • Laccaria bicolor (v2.0),
  • Oidiodendron maius Zn,
  • Paxillus involutus,
  • Paxillus rubicundulus,
  • Piloderma croceum F 1598,
  • Pisolithus microcarpus 441,
  • Pisolithus tinctorius 270,
  • Scleroderma citrinum FougA,
  • Sebacina vermifera MAFF 305830,
  • Suillus luteus UH-Slu-Lm8-n1,
  • Tulasnella calospora AL13/4D,

In addition, the following available transcriptomes will also be mined for symbiotic-related features:

  • Cenococcum geophilum
  • Cortinarius glaucopus,
  • Laccaria amethystina 08-1,
  • Lactarius quietus,
  • Meliniomyces bicolor,
  • Meliniomyces variabilis, and
  • Tricholoma matsutake 945.

Finally, we will add the unpublished genomes of five saprotrophic agaricomycotina (including leaf-litter species) that we will use for identifying potential common genomic features in litter-borne and mycorrhizal fungi:

  • Jaapia argillacea MUCL-33604,
  • Hydnomerulium pinastri MD-312,
  • Plicaturopsis crispa FD-325 SS-3,
  • Hypholoma sublateritium FD-334 SS-4, and
  • Gymnopus luxurians FD-317 M1

JGI has (or will soon) publicly released the web portals with the annotation for the above-mentioned fungal species. Visit the JGI Mycocosm database. In addition, we have released web sites for the corresponding transcriptome annotation at the Mycorhiza Genomics Initiative portal [restricted].

To make good use of this tremendous genomic resource, we are organizing the 2nd MGI Workshop at the INRA-Nancy center in Champenoux (France), on November 13-14, 2012. The aim of the workshop is to bring together the consortium teams for discussing our findings. The format of the workshop will be roughly equally split between informal presentations summarizing the current findings and brainstorming about how to take advantage of the genome sequences to inform our understanding of symbiosis and fungal biology.

On the following days, we will organize a New Phytologist Workshop entitled ‘ Bridging Mycorrhizal Genomics, Metagenomics & Forest Ecology‘. The workshop will also take place at INRA-Nancy over two days (Thursday 15 & Friday 16 November). The aim is to bring together a small group of MGI PI’s, fungal biologists and ecologists (20-25 attendees) to explore the future use of mycorrhizal genomes in order to both maximize the efficacy with which the community utilizes these technological breakthroughs in biology, ecology, phylogenetics, and forestry.

Photo: Larch Bolete (Suillus grevellei) (Boletales), a close relative of the sequenced slippery Jack (Suillus luteus) (© F Martin).

DOE JGI 2012 Community Sequencing Program Portfolio

November 4th, 2011

Trillions Served: Massive, Complex Projects Dominate DOE JGI 2012 Community Sequencing Program Portfolio.

‘The 2012 Community Sequencing Program (CSP) call invited researchers to submit proposals for projects that advance capabilities in fields such as plant-microbe interactions, microbes involved in carbon capture and greenhouse gas emission, and metagenomics—the characterization of complex collections of microbes from particular environmental niches. The total allocation for the coming year’s CSP portfolio will exceed 30 trillion bases (terabases or Tb), a 100-fold increase compared with just two years ago, when just a third of a terabase was allocated to more than 70 projects. This amounts to the equivalent of at least 10,000 human genomes in data …’ Read more

 

Photo:  The boreal forest, one of the ecosystem investigated by the CSP 2012 program. Denali Natl Park, Alaska  (© F Martin)

Metatranscriptomics of Forest Soil Ecosystems

October 29th, 2011

 

Forest soils (including litter, humus and coarse woody debris) host diverse microbial communities that impact tree health and productivity, and which play pivotal roles in terrestrial carbon sequestration, and biogeochemical cycles. Among these microbial communities, fungi are undoubtly major players. Traditionally, they have been divided into discrete ecological guilds, such as leaf litter-decomposers, humus saprobes, white- and brown-rot wood decayers, parasites and mycorrhizal symbionts. However, the actual functional properties of individual species, and the synergistic effects among them, are often obscure. Moreover, the basic biodiversity of the vast majority of soil systems (e.g., boreal forests and subartic taiga) remains unexplored using high-throughput DNA barcoding approaches.

We hypothesize that firm distinctions between fungi commonly labeled mycorrhizal, wood decomposer, humus and litter saprobes are, in some instances, unwarranted, and that crucial ecosystem processes, such as carbon sequestration, wood and litter decay and trophic mutualism, can only be understood in the context of interactions among multiple species representing a functional continuum. The number of available fungal genomes has expanded dramatically in recent months, and this provides unprecedented opportunities to study the functional (and taxonomic) diversity of soil communities.

Within the framework of the DOE Joint Genome Institute Community Sequencing Program, we have therefore embarked in a challenging large-scale metatranscriptomics project to explore the interaction of forest trees with communities of soil fungi, including ectomycorrhizal symbionts that dramatically affect tree growth, and saprotrophic soil fungi impacting carbon sequestration in forests. We are going to sequence the metatranscriptome of soil fungi (i.e., wood decayers, litter and humus saprotrophs, and ectomycorrhizal symbionts) in woody debris, litter/humus, rhizosphere and ectomycorrhizal roots of ecosystems representative of major Earth biomes, the boreal, temperate and mediterranean forests.

Metatranscriptome samples. A range of forest ecosystems has been selected on the basis of their ecological importance and the availability of metadata linked to these forest sites. In contrast to agricultural soils, forest soils, in particular those of boreal forests with low pH values, are characterised by strong vertical stratification due to the resulting absence of fauna causing mixing. This provides a spatial structure for evaluation of hypotheses concerning functional attributes of taxa occupying spatially distinct horizons.

Sampling will be conducted on selected stands in long-term observatories (LTOs) or national survey sites:

  • Boreal forests: Bonanza Creek (Alaska) and Siljansfors (Sweden).
  • Temperate forests: DOE long term studies at Duke Forest, the post-fire stands at the Bitterroot National Forest and Michigan maple N-deposition sites (USA), a forest-woodland-grassland transect in Rollainville (France), and the Breuil-Chenue plantation (France).
  • Mediterranean forests at Puéchabon near Montpellier (France) and at Aspurz south-western Pyrenees (Spain).

For these soil samples, we will run: (1) Tag-encoded FLX-titanium amplicon pyrosequencing (TEFAP) of the fungal rDNA ITS to survey the existing communities and (2) RNA-Seq of soil samples. For this cDNA profiling, we will sequence ~110Gbp per site for a total of 1 terabase using Illumina HiSeq PE chemistry. Reads produced by RNA-Seq will be used to reconstruct de novo the different fungal metatranscriptomes (best case scenario). In addition, we will use Illumina fragment recruitment, a process of aligning sequencing reads to reference genomes. Metatranscriptomic reads will thus be aligned to the >100 genomes of soil fungi available in the JGI MycoCosm. To improve this crucial step, we also propose the gDNA sequencing and RNA-Seq of the 25 most abundant fungal species harvested on the studied sites to serve as the foundation for a reference database for metagenomics of fungi and for a comprehensive survey of the potential soil fungal metabolome. We will annotate the fungal genomes/transcriptomes and soil fungal metagenomes with all these characteristics and will compare the different metagenomes in terms of these characteristics.

These experimental datasets will provide a mechanistic insight into the fungal communities’ structural organization and functioning in forests. In addition, the present metagenomic data will give a comprehensive picture of the organization of the tree-associated microbiome in terms of metabolic pathways, subsystems, molecular functions and biological processes.

Sequencing of new fungal species will be performed in concert with existing large-scale genome studies (e.g., the 1000 Fungal Genomes project), so as to minimize unnecessary redundancies. As such we recognize that this project represents a large effort and great challenge in defining the microbiome of important forest ecosystems and a group of micro-organisms, the soil fungi.

The Consortium: Scott BAKER, Dan CULLEN, Roger FINLAY, David HIBBETT, Igor GRIGORIEV, Cheryl KUSKE, Roland MARMEISSE, Francis MARTIN, Antonio PISABARRO, Joey SPATAFORA, Jan STENLID & Rytas VILGALYS

Image (top): Denali Ntl Park, Alaska (© F Martin)

International Human Microbiome Congress in Paris

October 23rd, 2011

The next International Human Microbiome Congress, organized by the European consortium MetaHIT will take place in Paris, March 19-21, 2012 at the Palais Brongniart.

Darkness Visible: Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

October 20th, 2011

At the Jacques Monod Conference on Integrated Ecological Genomics, scientists from the USA and Europe met in Roscoff earlier this week to discuss how to bridge metagenomics, functional genomics, evolution biology and microbial ecology for a better understanding of marine, soil and gut ecosystems. The meeting was very exciting hosting top-notch speakers: Eugene Koonin, Mary Ann Moran, Tim Vogel, Julia Vorholt, Peter Young, Philippe Vandenkoornuyse, Puri Lopez-Garcia, Antje Boetius, Folker Meyer, Laurence Garzarek, Gurvan Michel, Oded Beja, Patrick Forterre, Forest Rohwer and Rotem Sorek, amongst others.

As a soil microbiologist, I enjoyed very much the presentations on metagenomics of ‘exotic’ ecosystems, such as the Chilean upwelling, the Deap Sea and the seafloor. I’m so envious of those guys from the Tara Oceans Expedition collecting samples throughout the world seas (see Map below).

If you want to learn more about the ‘Microbial Ecology of the Dark Ocean above, at, and below the Seafloor‘, visit Beth Orcutt amazing web site ‘Microbes Are Awesome‘ and read:

Zinger et al. (2011) Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems. PLoS One 6: e24570.

Orcutt et al. (2010) Microbial Ecology of the Dark Ocean above, at, and below the Seafloor. Microbiology & Molecular Biology Reviews 75: 361–422.

Karsenti E, Acinas SG, Bork P, Bowler C, De Vargas C, et al. (2011) A Holistic Approach to Marine Eco-Systems Biology. PLoS Biol 9: e1001177. doi:10.1371/journal.pbio.1001177.

Poretsky, R. S., S. Gifford, J. Rinta-Kanto, M. Vila-Costa, and M. A. Moran. 2009. Analyzing gene expression from marine microbial communities using environmental transcriptomics. Journal of Visualized Experiments 24, e1086, doi: 10.3791/1086.

Thx Philippe & Oded

Image: © CNRS-Roscoff

 

28th NPS

July 15th, 2011

EMBO Metagenomics Workshop

June 19th, 2011

Sequencing the Fungal Tree of Life

April 24th, 2011

Last week, a paper of mine has been published online March 14, 2011 in New Phytologist. I enjoyed drafting this letter titled ‘Sequencing the fungal tree of life (fToL)’ with other long-time DOE JGI fungal genomics collaborators. Since I think it is pretty cool, I would like to  further discuss our on-going fToL projects dealing with comparative genomics of soil fungi and metagenomics of forest soils discussed in this paper.

As you may know, forest soils host diverse microbial communities that impact tree health and productivity, and which play pivotal roles in terrestrial carbon cycling and sequestration, and biogeochemical cycles.

Amongst these microbial communities, soil fungi are undoubtly major players. Traditionally, they have been divided into discrete ecological guilds, such as leaf litter-decomposers, white- and brown-rot wood decayers, parasites and ectomycorrhizal (ECM) symbionts. However, the actual functional properties of individual species, and the synergistic effects among them, are often obscure. Moreover, the basic biodiversity of the vast majority of soil systems (e.g., boreal forests and subartic taiga)  remains unexplored using modern high-throughput DNA barcoding approaches.

We hypothesize that firm distinctions between fungi commonly labeled ECM, parasite, wood decomposer, litter saprotroph are, in some instances, unwarranted, and that crucial ecosystem processes, such as carbon sequestration, litter decay and mutualism, can only be understood in the context of interactions among multiple species representing a functional continuum.

Thanks to the DOE JGI launched Fungal Genomic Program, the number of available fungal genomes has expanded dramatically in recent months (see my previous post ‘Crunching Fungal Genomes at High Speed‘), and this provides unprecedented opportunities to study the functional (and taxonomic) diversity of soil communities. We — David Hibbett, Dan Cullen, Roger Finlay, Cheryl Kuske, Rytas Vilgalys and others — have taken this opportunity to set up a series of projects to elucidate physiological processes taking place along the ‘saprotrophism/mutualism’ continuum encompassing decaying woody debris, soil hyphal networks and ECM symbiosis on major forest ecosystems, using comparative genomics and metatranscriptomic approaches.

As described in the New Phytologist paper, these complementary projects should provide valuable opportunities to investigate two major aspects of the interactions between trees, ECM symbionts and wood/litter decayers, and their role in carbon and nutrient cycling:

  • By studying the transcriptional regulation of genes coding for secreted enzymes, such as plant cell wall polysaccharide degrading enzymes, we would gain a more holistic picture of enzyme secretion and subsequent organic matter turnover than has subsequently been possible.
  • By focusing on transcriptional regulation of fungal genes involved in resource exchange across the ECM/plant and ECM/saprotroph interfaces, we would obtain a better understanding of how mycorrhizal symbiont and the wood decayer communities are altered by changes in nutrient availability.

More exciting times ahead!!!

Another post on this fToL paper: DOE JGI Science Highlights: Toward a Genomic Encyclopedia of Fungi.

F. Martin, D. Cullen, D. Hibbett, A. Pisabarro, J. W. Spatafora, S. E. Baker and I. V. Grigoriev (2011) Sequencing the fungal tree of life. New Phytologist, DOI: 10.1111/j.1469-8137.2011.03688.x

Photo: State Forest of Champenoux © F Martin

There might be at least one other, previously hidden, domain of life

April 3rd, 2011

Environmental metagenomics is currently generating massive streams of  DNA sequences from almost all ecosystems, including our human body. Most of these new sequences are coded by the genomes of unknown organisms, but belonging to the three major domains of life: Archaea, Bacteria and the Eukaryota. In a recent paper published in PLoS One, Jonathan Eisen and his colleagues mined the vast amount of sequences generated by Craig Venter’s Global Ocean Sampling (GOS) circumnavigation around the world seas and oceans. They sought to address a single, but crucial, question: Are there sequences encoded by this metagenomic data set that represent novel lineages that branch closer to the base of the tree of life (ToL) than any known phylogenetic marker sequences?

They developed an automated screening system (STAP) for detecting ss-rRNA genes that branch very deeply in the ToL (see Jonathan’s blog post discussing this novel approach). It appeared that rRNA genes in metagenomic data sets were not ideally suited for finding phylogenetically very deep branches of the ToL. Due to these difficulties, they used two genes called RecA and RpoB to answer this question. RecA is involved in DNA recombination. RpoB is involved in translating DNA into RNA. Both, like the genes for ribosomal RNA, are old and ubiquitous. When they constructed phylogenetic trees that tracked the evolutionary relationships between all the RecAs and all the RpoBs found in the GOS DNA samples, they discovered clades that did not fit with any known sequences in the databases. Some of these novel gene subfamilies were, nevertheless, similar enough to known branches to be accounted for as ‘known unknowns’. But both RecA and RpoB had one branch (subfamily) that really was an ‘unknown unknown’. Neither of these branches fits in the existing ToL. Assuming the sequences are in fact real, they may belong to some as-yet-unknown group of viruses (e.g. cyanophages). More excitingly, they may come from a new (i.e., fourth) major branch of cellular organisms on the ToL. I liked the fact that the authors do not overinterpret their results and call for additional analyses to support their speculation. Additional metagenomics and phylogenetics analyses are undoubtly required to confirm the existence of these deeply branching lineages.

Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, et al. (2011) Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees.PLoS ONE 6: e18011. doi:10.1371/journal.pone.0018011

Phylogenetic approaches to metagenomic analysis by Jonathan Eisen (slide presentation at Keystone Symposium).

Cartoon: © The Economist: A new domain of life. Plenty more bugs in the sea.

 

Faire parler l’invisible

March 30th, 2011

For those reading french, I recommend this BIOFUTUR special issue dedicated to environmental genomics. I coordinated this series of paper describing recent metagenomics studies  of various ecosystems, including oceans and forest and agrosystem soils, but also buffalo dropping!!! .

Bacterial Community Variation in Human Body Habitats Across Space and Time

March 27th, 2011

Personally, my favorite talk at the last 6th Annual DOE JGI Users Meeting at Walnut Creek was Rob Knight‘s contribution on ‘Spatially and Temporally Resolved Studies of the Human Microbiome‘. Rob was creative and integrative. Displaying the biogeography of bacterial communities on the human body using UniFrac and QUIME was astounding.

A series of large-scale sequencing analyses of  the variable region 2 (V2) of the bacterial 16S ribosomal RNA (rRNA) gene conducted by Rob and his collaborators have shown that the community composition is mainly determined by body habitat (gut, mouth, skin, hair, nostril, …). Within these ecological niches, interpersonal variability is striking, whereas individuals exhibit minimal temporal variability. Several skin locations harbor more diverse communities than the gut and mouth, and skin locations (e.g. your different face zones) varie in their community assembly patterns. These results indicate that our microbiota, although personalized, varies systematically across body habitats and time. According to Rob, these trends may ultimately reveal how microbiome changes cause or prevent disease. For more details, read their recent papers, including Costello et al. (2009).

Let’s do it on the bacterial communities associated with trees.

Fig. 16S rRNA gene surveys reveal hierarchical partitioning of human-associated bacterial diversity. Communities clustered using PCoA of the unweighted UniFrac distance matrix. Each point corresponds to a sample colored by body habitat (from Costello et al. 2009).

Costello et al. (2009). Bacterial Community Variation in Human Body Habitats Across Space and Time. Science 326, 1694-1697.

Caporaso et al.(2010)QIIME allows analysis of high-throughput community sequencing data. Nature Methods doi:10.1038/nmeth.f.303

BGI Joins Earth Microbiome Project

March 22nd, 2011

A GenomeWeb Daily News Post

BGI (Beijing Genomics Institute) will provide a range of services and support for the Earth Microbiome Project (EMP), an effort to sample, sequence, and analyze microbial communities from all over the globe.

The multi-disciplinary EMP effort, the largest sequencing project yet undertaken, will conduct metagenomics studies of 200,000 samples of microbes from soil, air, sea, and freshwater systems from around the world to produce a global Gene Atlas.

BGI said today that it will lead the effort to identify sample collections in Asia, and it will provide DNA extraction, amplification, sequence library construction, and sequencing for metagenomics projects. The Shenzhen, China-based institute also will use its computational resources to develop the bioinformatics pipeline that will provide the analysis framework for the vast amount of data the EMP will produce.

The EMP effort also includes Argonne National Laboratory, the University of Chicago, the University of Colorado-Boulder, Lawrence Berkley National Laboratory, and the US Department of Energy’s Joint Genome Institute. BGI also said that it will host the First International Earth Microbiome Project Conference in Shenzhen this June.

See also:

 

    Metagenomics Tutorials

    March 3rd, 2011

    stFor those in the lab and elsewhere willing to follow recent tutorials on metagenomics tools:

    – METAREP Human Microbiome Project Virtual Jamboree Tutorial: presented at the Human Microbiome Project (HMP) Virtual Jamboree by Johannes Goll on January 19, 2011.

    – “Climbing Mt. Metagenome“: – a talk Titus Brown gave at JGI on assembling very large, diverse metagenomes.

    See also the JVCI blog post ‘Virtual Comparative Metagenomics

    Genomics of Energy & Environment

    February 15th, 2011

    6jgiJust a reminder…that the deadline for poster/abstract submission for the 6th Annual DOE Joint Genome Institute Genomics of Energy & Environment meeting (http://go.usa.gov/g4N) is rapidly approaching: February 21.

    The meeting brings together, in JGI’s hometown of Walnut Creek, California, an international network of researchers interest in: Synthetic Biology, Ecogenomics and Ecoresilience of the Gulf Oil Spill, Hardware and Software Trends in Genomics Supercomputing, Computational Approaches to Massive Short Read Metagenomic Data Sets, Genomics of Biofuel Crops, Behavioral Genetics of Pollinating Bees, Microbiome Analyses from Humans to Shipworms, Metatranscriptomics of Marine Microbial Communities, Successful Transposable Elements Secrets, and Great Prairie Soil Metagenomics.

    Confirmed speakers: Peer Bork, (European Molecular Biology Laboratory), Ed Buckler, Cornell University, Dan Distel, Ocean Genome Legacy, Dusko Ehrlich, French National Institute for Agricultural Research (INRA), Terry Hazen, Lawrence Berkeley National Laboratory (LBNL), Scott Hodges, University of California, Santa Barbara, Tom Juenger, University of Texas at Austin, Rob Knight, University of Colorado, Ruth Ley, Cornell University, Mary Ann Moran, University of Georgia, Magnus Nordborg, Gregor Mendel Institute, Gene Robinson, University of Illinois at Urbana-Champaign, Christopher Scholin, Monterey Bay Aquarium Research Institute (MBARI), Stephan Schuster, Penn State University, Pam Silver, Harvard, Jim Tiedje, Michigan State University, Mike Thomashow, Michigan State University, Jerry Tuskan, Oak Ridge National Laboratory/DOE JGI and Katherine Yelick, National Energy Research Scientific Computing Center (NERSC).

    Workshops include:

    • Integrated Microbial Genomes (IMG)/Metagenomes data analysis systems http://img.jgi.doe.gov/
    • Mycocosm fungal genomics portal provides data access, visualization, and analysis tools for comparative genomics of fungi http://genome.jgi-psf.org/ programs/fungi/index.jsf
    • Phytozome provides data access and visualization tools for comparative plant genomics http://www.phytozome.net/
    • RNA Technologies & Analysis: a comprehensive suite for transcriptome interrogation, including RNA-Seq for expression profiling, etc.

    Soil Metagenomics 2010

    August 15th, 2010

    401px-Braunschweig-burgplatz_1Christoph Tebbe is organizing the next International Symposium on Soil Metagenomics at the Johann Heinrich von Thünen-Institute (vTI) Forum in Braunschweig (Germany) on December 08–10, 2010. An objective of this symposium is to discuss the future applications of next generation sequencing to address the complex soil ecosystems.

    Photo: © Burgplatz in Braunschweig, Germany by Matthias Prinke.

    ECOFINDERS

    May 30th, 2010

    CB055265Great news!!! To increase the understanding of the role of soil biodiversity in ecosystem functioning, the European Commission (EC) awarded €7 million to our research project ECOFINDERS. This four year project, coordinated by INRA, aims to support European Union soil policy making by providing the necessary tools to design and implement strategies for sustainable use of soils.

    The project will include:

    • Characterisation of the biodiversity of European soils and the normal operating range (NOR) according to soil types, threats, climatic zone and land use,
    • Determination of relationships between soil biodiversity, functioning and ecosystem services,
    • Quantification of the economic values of soil ecosystem services,
    • Evaluation of the impacts of human activities on soil biodiversity, functioning and services,
    • Design of policy-relevant and cost-effective indicators for monitoring soil biodiversity, functioning and ecosystem services.

    To reach this overall aim, the project will pursue the following:

    • Describe the diversity of soil organisms (microorganisms and fauna) by using nextgen sequencing,
    • Decipher their interactions through trophic food webs,
    • Determine the role played by soil organisms in soil functioning and major ecosystem services: nutrient retention, carbon storage, water retention, soil structure regulation, resistance to pests and diseases, and regulation of above-ground diversity,
    • Assess the stability and resilience of ecosystems against threats in relation to their biodiversity: soil erosion and physical degradation, decline in organic content, loss of soil biodiversity, and soil contamination.

    The 22 consortium partners will:

    • Develop and standardise phenotypic tools and procedures to measure the faunal biodiversity,
    • Design molecular methods to characterise the faunal diversity calibrated upon phenotypic traits,
    • Customise functional tools and methods to determine the functional diversity of fauna,
    • Establish high-throughput molecular assays for assessing microbial and faunal biodiversity,
    • Design, develop and establish a database aimed at mapping the European soil biodiversity and threats,
    • Establish cost-effective bioindicators to measure microbial and faunal diversity, their associated functions and the resulting ecosystem services,
    • Evaluate the economic added-value brought by these bioindicators in assessing the consequences of soil management policy for soil biodiversity and functioning,
    • Implement effective dissemination strategies to transfer the project knowledge and tools to soil stakeholders, notably but not exclusively regional, national and European policy-makers, and inform the general public about the issues associated with the sustainability of soil biodiversity.

    My lab will focus on developing 454-based genotyping to survey the microbial communities — hundreds of creeping subterranean bugs will ended up in digits. Our on-going analysis of forest soil metagenomes will likely feed this large scale multi-year project.

    You Are What You Eat

    May 22nd, 2010

    cabbage-noriA nice post from by Karen Schwarzberg and Mike Gurney at Small Things Considered (The Microbe Blog) discussing a paper recently published in Nature by Hehemann et al. which reports that, in at least one particular instance, we do harbor bacteria adapted to the traditional diet of our culture. Porphyranases are glycosyl hydrolases cleaving sulphated polysaccharides of carrageenan and agar from marine algae. These enzymes found in marine bacteria are common in Japanese—and only Japanese—intestinal microbiota. The Japanese can digest their nori (Porphyra) thanks to specific strains of Bacteroides plebeius that they host. The initial acquisition of the β-porphyranase genes by B. plebeius was likely by horizontal transfer from a marine Bacteroidetes.

    Hehemann, J., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota Nature, 464 (7290), 908-912 DOI: 10.1038/nature08937

    See also my previous post on the gut metagenomics-inspired poem from the Cuttlefish Poet at The Digital Cuttlefish‘s “You are What you Eat.”

    Photo: Cabbage Nori Rolls.© http://blog.fatfreevegan.com/2006/05/cabbage-nori-rolls.html

    Microbial genomics: meeting the challenges and fulfilling the dream

    August 15th, 2009

    Nature BiotechnologyIn the July issue of Nature Biotechnology, Nikos Kirpides from JGI published a challenging paper entitled “Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream” where he discussed the past and future of microbial genomics. More than two-thirds of the 4,800 currently reported genome projects are microbial and the number of genomes and pangenomes will tremendously increase in the years to come. Unfortunately, several underlying problems hinder additional growth of the field and, even more importantly, compromise the ability of biologists to use and interpret the available data. This includes: (i) Genome publication and data release policy violating a longstanding scientific precept, i.e. examine the actual data, (ii) bias in the selection of species for genome projects, (iii) poor funding for the maintenance of biological databases, (iv) the lack of dedicated professionals for gene catalog curation, and (v) the lack of standard in genomics. As strongly recommended by  Nikos Kirpides “a systematic and comprehensive exploration of the planet microbial world  cannot be achieved by the efforts of individual researchers but requires the establishment of effective national and international collaborations.”

    Sign-up now for Microbial Genomics & Metagenomics workshop

    August 10th, 2009

    The U.S. Department of Energy Joint Genome Institutejgi (DOE JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics September 14-18, 2009 in Walnut Creek, California. The workshop will include two days of intensive seminars and three days of hands-on tutorials. Our goal is to provide you with training in microbial genomic and metagenomic analysis and demonstrate how the cutting-edge science and technology of DOE JGI can enhance your research.

    For more information, see:

    http://www.jgi.doe.gov/meetings/mgm/index.html