Environmental Microbial Genomics Group<br />Laboratoire Ampère . EcoleCentrale de Lyon . Université de Lyon<br />Earth Mic...
Environmental Microbial Genomics Group<br />Laboratoire Ampère . EcoleCentrale de Lyon . Université de Lyon<br />Earth Mic...
1/ Metasoil project (Terragenome consortium)<br />To sequence as in depth as possible the Rothamsted soil metagenome<br />...
1/ Metasoil project (Terragenome consortium)<br />To sequence as in depth as possible the Rothamsted soil metagenome<br />...
1/ Metasoil project (Terragenome consortium)<br />Seasonal  Samplingeffect<br />Cell lysis stringencyeffect<br />Deptheffe...
1/ Metasoil project (Terragenome consortium)<br />Seasonal  Samplingeffect<br />Cell lysis stringencyeffect<br />Deptheffe...
1/ Metasoil project (Terragenome consortium)<br />Seasonal  Samplingeffect<br />Cell lysis stringencyeffect<br />Deptheffe...
2/ Lessons from the Global ocean survey<br />36 metagenomes from the GOS (coastal and open oceans)<br />Relative distribut...
To summarize<br />*When comparing samples from the same environment:<br />      we use (in general subjectively) the same ...
To summarize<br />*When comparing samples from the same environment:<br />      we use (in general subjectively) the same ...
DNA extraction dilemma<br />Until the inverse is proved, we should consider that DNA biases are different between and amon...
Problem when using one single method<br />15 DNA extraction approaches (>99%)<br />% of positive phylogenetic probes<br />...
DNA extraction dilemma alternative <br />Until the inverse is proved, we should consider that DNA biases are different bet...
DNA extraction dilemma alternative <br />Until the inverse is proved, we should consider that DNA biases are different bet...
To summarize<br />*When comparing samples from the same environment:<br />      we use (in general subjectively) the same ...
To summarize<br />Need to define environments  at the microorganism level<br />Global sampling grid is not coherent<br />P...
As a perspective for EMP<br />Relative distribution of the function  x  among  n  ecosystems<br />Distribution in percenta...
As a perspective for EMP<br />Relative distribution of the function  x  among  n  ecosystems<br />My vision of EMP is a co...
What should be the next sensational “omic” project?<br />
What should be the next sensational “omic” project?<br />Colonizing Mars and waiting for a Martian microbiome project? <br />
What should be the next sensational “omic” project?<br />Or sequencing an alien gut    (with metadata of course)<br />
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Tom Delmont: From the Terragenome Project to Global Metagenomic Comparisons: Implications for the Earth Microbiome Project

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Tom O Delmont's talk from the Earth Microbiome Project meeting in Shenzhen

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Tom Delmont: From the Terragenome Project to Global Metagenomic Comparisons: Implications for the Earth Microbiome Project

  1. 1. Environmental Microbial Genomics Group<br />Laboratoire Ampère . EcoleCentrale de Lyon . Université de Lyon<br />Earth Microbiome Project andGlobal Metagenomic Comparisons<br />8.10%<br />Functional subsystems distribution among 77 metagenomes<br />15.16%<br />Tom O. Delmont Emmanuel Prestat Pascal Simonet Timothy M. Vogel<br />
  2. 2. Environmental Microbial Genomics Group<br />Laboratoire Ampère . EcoleCentrale de Lyon . Université de Lyon<br />Earth Microbiome Project andGlobal Metagenomic Comparisons<br />8.10%<br />Functional subsystems distribution among 77 metagenomes<br />Metasoil project<br />(Terragenome)<br />Global Ocean Survey<br />15.16%<br />Tom O. Delmont Emmanuel Prestat Pascal Simonet Timothy M. Vogel<br />
  3. 3. 1/ Metasoil project (Terragenome consortium)<br />To sequence as in depth as possible the Rothamsted soil metagenome<br />A 2 million fosmid library was constructed (Libragen Company)<br /> 90 Titanium pyrosequencing runs and some HiSeq are being generated by varying different parameters<br />
  4. 4. 1/ Metasoil project (Terragenome consortium)<br />To sequence as in depth as possible the Rothamsted soil metagenome<br />A 2 million fosmid library was constructed (Libragen Company)<br /> 90 Titanium pyrosequencing runs and some HiSeq are being generated by varying different parameters<br /> -Time (years/seasons)<br /> -Spatial variations (e.g. depth)<br /> -Methodology (DNA extraction approaches)<br />To maximize the natural and methodological fluctuations of this soil metagenome(Delmont et al., 2011, AEM)<br />Our strategy to sequence a new environment:<br />Five dimensions:<br />1 for time<br />3 for space <br />1 for methodology<br />
  5. 5. 1/ Metasoil project (Terragenome consortium)<br />Seasonal Samplingeffect<br />Cell lysis stringencyeffect<br />Deptheffect<br />Relative functional<br />distribution (%)<br />Species distribution (SEED annotation) using four lyses<br />Comparison of functional distributions among metagenomes (1million reads) using MG RAST and STAMP<br />Important DNA extraction biases<br />Concept of standard deviation of distribution<br />Relative distribution (%)<br />Species<br />
  6. 6. 1/ Metasoil project (Terragenome consortium)<br />Seasonal Samplingeffect<br />Cell lysis stringencyeffect<br />Deptheffect<br />Relative functional<br />distribution (%)<br />Species distribution <br />Important methodological fluctuations<br />Concept of metagenomic variance<br />Relative distribution (%)<br />Species<br />
  7. 7. 1/ Metasoil project (Terragenome consortium)<br />Seasonal Samplingeffect<br />Cell lysis stringencyeffect<br />Deptheffect<br />Relative functional<br />distribution (%)<br />Species distribution <br />The other metagenomic variance is lacking<br /> Comparison difficult<br />Relative distribution (%)<br />Species<br />
  8. 8. 2/ Lessons from the Global ocean survey<br />36 metagenomes from the GOS (coastal and open oceans)<br />Relative distribution in percentage<br />Different times<br />Different locations<br />Only one method used<br />Do these datasets represent this environment?<br />If not DNA extraction,<br />cells filtration effect?<br />
  9. 9. To summarize<br />*When comparing samples from the same environment:<br /> we use (in general subjectively) the same method <br />
  10. 10. To summarize<br />*When comparing samples from the same environment:<br /> we use (in general subjectively) the same method <br />*When studying a new environment: <br /> use different approaches metagenomic variance (represents a global picture)<br /> Temporal, spatial and methodological variations<br />
  11. 11. DNA extraction dilemma<br />Until the inverse is proved, we should consider that DNA biases are different between and among environments<br />
  12. 12. Problem when using one single method<br />15 DNA extraction approaches (>99%)<br />% of positive phylogenetic probes<br />One DNA extraction approach (<40%)<br />(Delmont et al., 2011, AEM)<br />The diversityishighlyunderestimatedwhen<br />usingonly one DNA extraction approach<br />
  13. 13. DNA extraction dilemma alternative <br />Until the inverse is proved, we should consider that DNA biases are different between and among environments<br />1/ We cannot know how cosmopolitan are taxa with one method<br />2/ Replicates are insufficient (biases are hidden behind strong reproducibilities)<br />The most protocols we use,<br />The most species will be detected<br />The better the global picture will be<br />
  14. 14. DNA extraction dilemma alternative <br />Until the inverse is proved, we should consider that DNA biases are different between and among environments<br />1/ We cannot know how cosmopolitan are taxa with one method<br />2/ Replicates are insufficient (biases are hidden behind strong reproducibilities)<br />The most protocols we use,<br />The most species will be detected<br />Proposition:MoBio for all samples (referential protocol)-<br />Microbial ecologists send DNA samples that represent, in their point of view, the environment they study since years<br />The “tricky” DNA extraction effort could be shared by laboratories involved in EMP<br />
  15. 15. To summarize<br />*When comparing samples from the same environment:<br /> we use (in general subjectively) the same method <br />*When studying a new environment: <br /> use different approaches metagenomic variance (represents a global picture)<br /> Temporal, spatial and methodological variations<br />*When performing global metagenomic comparisons:<br /> metagenomic variance for all environments <br />the experimental design depends on the environment<br /> need to be flexible and adapted to specific problems<br />
  16. 16. To summarize<br />Need to define environments at the microorganism level<br />Global sampling grid is not coherent<br />Possible metagenomic definition of ecosystem boundaries:<br />When inter-environmental distribution differences are globally stronger than intra-environmental fluctuations (natural OR methodological)<br />
  17. 17. As a perspective for EMP<br />Relative distribution of the function x among n ecosystems<br />Distribution in percentage <br />
  18. 18. As a perspective for EMP<br />Relative distribution of the function x among n ecosystems<br />My vision of EMP is a concerted and flexible experimental design constructed with the expertise of all microbial ecologists to represent for the best microbial communities<br />Distribution in percentage <br />
  19. 19. What should be the next sensational “omic” project?<br />
  20. 20. What should be the next sensational “omic” project?<br />Colonizing Mars and waiting for a Martian microbiome project? <br />
  21. 21. What should be the next sensational “omic” project?<br />Or sequencing an alien gut (with metadata of course)<br />
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