2 research outputs found
The Shimmering Dam
This piece is an attempt to understand physical structures intertextually and to map mental forms and biographical fragments onto architectural objects.It stands language games and postures of articulation next to one another to produce meaning through differentiation and creative negation
Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity
Extended data is available for this paper at https://doi.org/10.1038/s41564-022-01266-x.Despite advances in sequencing, lack of standardization makes
comparisons across studies challenging and hampers insights into
the structure and function of microbial communities across multiple
habitats on a planetary scale. Here we present a multi-omics analysis of a
diverse set of 880 microbial community samples collected for the Earth
Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun
metagenomic sequence data, and untargeted metabolomics data (liquid
chromatography-tandem mass spectrometry and gas chromatography
mass spectrometry). We used standardized protocols and analytical
methods to characterize microbial communities, focusing on relationships
and co-occurrences of microbially related metabolites and microbial taxa
across environments, thus allowing us to explore diversity at extraordinary
scale. In addition to a reference database for metagenomic and
metabolomic data, we provide a framework for incorporating additional
studies, enabling the expansion of existing knowledge in the form of an
evolving community resource. We demonstrate the utility of this database
by testing the hypothesis that every microbe and metabolite is everywhere
but the environment selects. Our results show that metabolite diversity
exhibits turnover and nestedness related to both microbial communities
and the environment, whereas the relative abundances of microbially
related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain
chemistry, in particular terpenoids, in distinguishing Earth’s environments
(for example, terrestrial plant surfaces and soils, freshwater and marine
animal stool), as well as that of certain microbes including Conexibacter
woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and
Pantoea dispersa (terrestrial plant detritus). This Resource provides insight
into the taxa and metabolites within microbial communities from diverse
habitats across Earth, informing both microbial and chemical ecology, and
provides a foundation and methods for multi-omics microbiome studies of
hosts and the environment.The Samuel Freeman Charitable Trust, US National Institute of Health (NIH), US Department of Agriculture – National Institute of Food and Agriculture, the US National Science Foundation (NSF) - Center for Aerosol Impacts on Chemistry of the Environment, Crohn’s & Colitis Foundation Award (CCFA), US Department of Energy - Office of Science - Office of Biological and Environmental Research - Environmental System Science Program, Semiconductor Research Corporation and Defence Advanced Research Projects Agency (SRC/DARPA), Department of Defense, the Office of Naval Research (ONR, the Emerald Foundation, IBM Research AI through the AI Horizons Network, and the Center for Microbiome Innovation, the NIH, the Danish Council for Independent Research (DFF) , the Research Foundation – Flanders, Deutsche Forschungsgemeinschaft, the Gordon and Betty Moore Foundation. Metabolomics analyses at Pacific Northwest National Laboratory (PNNL) were supported by the Laboratory Directed Research and Development program via the Microbiomes in Transition Initiative and performed in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the US Office of Biological and Environmental Research and located at PNNL.http://www.nature.com/nmicrobiolam2023GeneticsNon