Letter | Published:

Unusual biology across a group comprising more than 15% of domain Bacteria

Nature volume 523, pages 208211 (09 July 2015) | Download Citation

This article has been updated


A prominent feature of the bacterial domain is a radiation of major lineages that are defined as candidate phyla because they lack isolated representatives. Bacteria from these phyla occur in diverse environments1 and are thought to mediate carbon and hydrogen cycles2. Genomic analyses of a few representatives suggested that metabolic limitations have prevented their cultivation2,3,4,5,6. Here we reconstructed 8 complete and 789 draft genomes from bacteria representing >35 phyla and documented features that consistently distinguish these organisms from other bacteria. We infer that this group, which may comprise >15% of the bacterial domain, has shared evolutionary history, and describe it as the candidate phyla radiation (CPR). All CPR genomes are small and most lack numerous biosynthetic pathways. Owing to divergent 16S ribosomal RNA (rRNA) gene sequences, 50–100% of organisms sampled from specific phyla would evade detection in typical cultivation-independent surveys. CPR organisms often have self-splicing introns and proteins encoded within their rRNA genes, a feature rarely reported in bacteria. Furthermore, they have unusual ribosome compositions. All are missing a ribosomal protein often absent in symbionts, and specific lineages are missing ribosomal proteins and biogenesis factors considered universal in bacteria. This implies different ribosome structures and biogenesis mechanisms, and underlines unusual biology across a large part of the bacterial domain.

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Change history

  • 29 January 2016

    Extended Data Table 1 was corrected on 25 January 2016


Primary accessions


Sequence Read Archive

Data deposits

DNA and RNA sequences have been deposited in the NCBI Sequence Read Archive under accession number SRP050083, and genome sequences have been deposited in NCBI BioProject under accession number PRJNA273161 (first versions described here). Genomes are also available through ggKbase: http://ggkbase.berkeley.edu/CPR-complete-draft/organisms. ggKbase is a ‘live data’ site, thus annotations and genomes may be improved after publication.


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We thank J. Cate and S. Moore for input into the ribosomal protein analysis, J. Doudna and E. Nawrocki for suggestions on the rRNA insertion analysis, and M. Markillie and R. Taylor for assistance with RNA sequencing. Research was supported by the US Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research under award number DE-AC02-05CH11231 (Sustainable Systems Scientific Focus Area and DOE-JGI) and award number DE-SC0004918 (Systems Biology Knowledge Base Focus Area). L.A.H. was partially supported by a Natural Sciences and Engineering Research Council postdoctoral fellowship. DNA sequencing was conducted at the DOE Joint Genome Institute, a DOE Office of Science User Facility, via the Community Science Program. RNA sequencing was performed at the DOE-supported Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory.

Author information


  1. Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA

    • Christopher T. Brown
  2. Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA

    • Laura A. Hug
    • , Brian C. Thomas
    • , Itai Sharon
    • , Cindy J. Castelle
    • , Andrea Singh
    •  & Jillian F. Banfield
  3. School of Earth Sciences, The Ohio State University, Columbus, Ohio 43210, USA

    • Michael J. Wilkins
  4. Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA

    • Michael J. Wilkins
    •  & Kelly C. Wrighton
  5. Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA

    • Kenneth H. Williams
    •  & Jillian F. Banfield
  6. Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA

    • Jillian F. Banfield


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Samples and geochemical measurements were taken by M.J.W., K.C.W. and K.H.W. B.C.T. assembled the metagenome data. I.S. implemented the ABAWACA algorithm. C.T.B. and J.F.B. binned the data and carried out the ESOM binning validation. J.F.B. closed and curated the complete genomes. C.T.B., L.A.H. and B.C.T. conducted the rRNA gene insertion analysis. C.T.B. and L.A.H. performed phylogenetic analyses. M.J.W. and K.C.W. conducted the RNA sequencing. C.T.B. carried out the 16S rRNA gene copy number, primer binding and transcript analyses. C.T.B. and J.F.B. carried out the ribosomal protein analyses. C.T.B., L.A.H., C.J.C. and J.F.B. conducted the metabolic analysis. A.S. and B.C.T. provided bioinformatics support. C.T.B. and J.F.B. drafted the manuscript. All authors reviewed the results and approved the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jillian F. Banfield.

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