[Obo-envo] EnvO used in latest paper by von Mering et al in Genome Research!

[Norman M. <mor...@cs...>]

"To annotate clusters in the co‐occurrence network with environmental  
information, we relied on the controlled vocabulary
maintained by the Environment Ontology project (EnvO, version 1.51, http://environmentontology.org 
)."

All,

Apologies if some of you receive multiple copies of this - but it's  
too good to miss! This amazing paper (highlighted to me by David  
Taylor from Unilever) uses 298,591 16S sequences in Greengenes as a  
data source, builds OTUs across the full dataset and then using  
ontologies looks at associations between OTUs within environments.

Fig S12 in the supplementary material is a hyperlinked document which  
allows you to zoom in on the clusters and see their associated  
phylogeny and EnvO ID!	

http://genome.cshlp.org/content/early/2010/05/10/gr.104521.109.abstract

All the best,
Norman

---

A global network of coexisting microbes from environmental and whole- 
genome sequence data.
Chaffron S, Rehrauer H, Pernthaler J, von Mering C.

Abstract:

Microbes are the most abundant and diverse organisms on Earth. In  
contrast to macroscopic organisms, their environmental preferences and  
ecological interdependencies remain difficult to assess, requiring  
laborious molecular surveys at diverse sampling sites. Here we present  
a global meta-analysis of previously sampled microbial lineages in the  
environment. We grouped publicly available 16S ribosomal RNA sequences  
into operational taxonomic units at various levels of resolution, and  
systematically searched these for co-occurrence across environments.  
Naturally occurring microbes indeed exhibited numerous, significant  
inter-lineage associations. These ranged from relatively specific  
groupings encompassing only a few lineages, to larger assemblages of  
microbes with shared habitat preferences. Many of the co-existing  
lineages were phylogenetically closely related, but a significant  
number of distant associations were observed as well. The increased  
availability of completely sequenced genomes allowed us, for the first  
time, to search for genomic correlates of such ecological  
associations. Genomes from coexisting microbes tended to be more  
similar than expected by chance, both with respect to pathway content  
and genome size, and outliers from these trends are discussed. We  
hypothesize that groupings of lineages are often ancient, and that  
they may have significantly impacted on genome evolution.

http://www.ncbi.nlm.nih.gov/pubmed/20458099