Evidence map›Paper›PMID 29234139›Full record

ArticleNature microbiology2018

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.

Donovan H Parks, Christian Rinke, Maria Chuvochina, Pierre-Alain Chaumeil, Ben J Woodcroft, Paul N Evans, Philip Hugenholtz, Gene W Tyson

Abstract readPublished Erratum
PubMed Publisher
In one paragraph

Article in Nature microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Capturing clinically relevantMicrobial genomics · 2024
    Article
  5. Article
  6. Article
  7. Review
  8. Article
  9. Discovery of nondiazotrophicProceedings of the National Academy of Sciences of the United States of America · 2021
    Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Review
  18. Article
  19. Taxogenomics and Systematics of the GenusFrontiers in microbiology · 2019
    Article
  20. Genome size evolution in the Archaea.Emerging topics in life sciences · 2018
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Donovan H ParksAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
Christian RinkeAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
Maria ChuvochinaAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
Pierre-Alain ChaumeilAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
Ben J WoodcroftAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
Paul N EvansAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
Philip HugenholtzAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia. p.hugenholtz@uq.edu.au.
Gene W TysonAustralian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia. g.tyson@uq.edu.au.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In the original version of this Article, the authors stated that the archaeal phylum Parvarchaeota was previously represented by only two single-cell genomes (ARMAN-4_'5-way FS' and ARMAN-5_'5-way FS'). However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California. In addition, the authors overlooked two higher-quality published Parvarchaeota MAGs from the same habitat, ARMAN-4 (ADCE00000000) and ARMAN-5 (ADHF00000000) (B. J. Baker et al., Proc. Natl Acad. Sci. USA 107, 8806-8811; 2010). The ARMAN-4 and ARMAN-5 MAGs are estimated to be 68.0% and 76.7% complete with 3.3% and 5.6% contamination, respectively, based on the archaeal-specific marker sets of CheckM. The 11 Parvarchaeota genomes identified in our study were obtained from different Richmond Mine metagenomes, but are highly similar to the ARMAN-4 (ANI of ~99.7%) and ARMAN-5 (ANI of ~99.6%) MAGs. The highest-quality uncultivated bacteria and archaea (UBA) MAGs with similarity to ARMAN-4 and ARMAN-5 are 82.5% and 83.3% complete with 0.9% and 1.9% contamination, respectively. The Parvarchaeota represents only 0.23% of the archaeal genome tree and addition of the ARMAN-4 and ARMAN-5 MAGs do not change the conclusions of this Article, but do impact the phylogenetic gain for this phylum. This has now been corrected in all versions of the Article. An updated version of Fig. 5 has also been used to replace the previous version, with the row for Parvarchaeota removed, and Supplementary Table 15 and Supplementary Table 17 have both been replaced to reflect the availability of the two additional Parvarchaeota genomes. In addition, the Methods incorrectly stated that all metagenomes identified as being from studies where MAGs had previously been recovered were excluded from consideration. Metagenomes from studies where MAGs had previously been recovered were retained if the UBA MAGs provided appreciable improvements in genome quality or phylogenetic diversity. All versions of the Article have been updated to indicate the retention of such metagenomes.

Identifiers

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.