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Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

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NATURE REVIEWS MICROBIOLOGY
卷 16, 期 10, 页码 629-645

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NATURE PUBLISHING GROUP
DOI: 10.1038/s41579-018-0076-2

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  1. Lawrence Berkeley National Laboratory's Genomes-to-Watershed Scientific Focus Area
  2. US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231]
  3. DOE [DOE-SC10010566]
  4. Sloan Foundation Deep Life [G-2016-20166041]
  5. Innovative Genomics Institute at the University of California, Berkeley
  6. Chan Zuckerberg Biohub
  7. DOE Joint Genome Institute, a DOE Office of Science User Facility [DE-AC02-05CH11231]

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Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.

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