Literature DB >> 29234139

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

Donovan H Parks1, Christian Rinke1, Maria Chuvochina1, Pierre-Alain Chaumeil1, Ben J Woodcroft1, Paul N Evans1, Philip Hugenholtz2, Gene W Tyson3.   

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 However, these are in fact unpublished, low-quality metagenome-assembled genomes (MAGs) obtained from Richmond Mine, California.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.

Entities:  

Year:  2018        PMID: 29234139     DOI: 10.1038/s41564-017-0083-5

Source DB:  PubMed          Journal:  Nat Microbiol        ISSN: 2058-5276            Impact factor:   17.745


  15 in total

1.  Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean.

Authors:  Tom O Delmont
Journal:  Proc Natl Acad Sci U S A       Date:  2021-11-16       Impact factor: 11.205

2.  Cyanuric Acid Biodegradation via Biuret: Physiology, Taxonomy, and Geospatial Distribution.

Authors:  Kelly G Aukema; Lambros J Tassoulas; Serina L Robinson; Jessica F Konopatski; Madison D Bygd; Lawrence P Wackett
Journal:  Appl Environ Microbiol       Date:  2020-01-07       Impact factor: 4.792

Review 3.  Syntrophic propionate-oxidizing bacteria in methanogenic systems.

Authors:  Maria Westerholm; Magdalena Calusinska; Jan Dolfing
Journal:  FEMS Microbiol Rev       Date:  2022-03-03       Impact factor: 16.408

4.  Mixing of meteoric and geothermal fluids supports hyperdiverse chemosynthetic hydrothermal communities.

Authors:  Daniel R Colman; Melody R Lindsay; Eric S Boyd
Journal:  Nat Commun       Date:  2019-02-08       Impact factor: 14.919

5.  Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface.

Authors:  Lianna Poghosyan; Hanna Koch; Adi Lavy; Jeroen Frank; Maartje A H J van Kessel; Mike S M Jetten; Jillian F Banfield; Sebastian Lücker
Journal:  Environ Microbiol       Date:  2019-06-10       Impact factor: 5.491

6.  Genome size evolution in the Archaea.

Authors:  Siri Kellner; Anja Spang; Pierre Offre; Gergely J Szöllősi; Celine Petitjean; Tom A Williams
Journal:  Emerg Top Life Sci       Date:  2018-12-14

7.  Taxogenomics and Systematics of the Genus Pantoea.

Authors:  James T Tambong
Journal:  Front Microbiol       Date:  2019-10-30       Impact factor: 5.640

8.  Molecular Analysis of Bacterial Isolates From Necrotic Wheat Leaf Lesions Caused by Xanthomonas translucens, and Description of Three Putative Novel Species, Sphingomonas albertensis sp. nov., Pseudomonas triticumensis sp. nov. and Pseudomonas foliumensis sp. nov.

Authors:  James T Tambong; Renlin Xu; Suzanne Gerdis; Greg C Daniels; Denise Chabot; Keith Hubbard; Michael W Harding
Journal:  Front Microbiol       Date:  2021-05-19       Impact factor: 5.640

9.  Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f.

Authors:  Michael L Chen; Eric D Becraft; Maria Pachiadaki; Julia M Brown; Jessica K Jarett; Josep M Gasol; Nikolai V Ravin; Duane P Moser; Takuro Nunoura; Gerhard J Herndl; Tanja Woyke; Ramunas Stepanauskas
Journal:  Front Microbiol       Date:  2020-03-12       Impact factor: 5.640

10.  A global metagenomic map of urban microbiomes and antimicrobial resistance.

Authors:  David Danko; Daniela Bezdan; Evan E Afshin; Sofia Ahsanuddin; Chandrima Bhattacharya; Daniel J Butler; Kern Rei Chng; Daisy Donnellan; Jochen Hecht; Katelyn Jackson; Katerina Kuchin; Mikhail Karasikov; Abigail Lyons; Lauren Mak; Dmitry Meleshko; Harun Mustafa; Beth Mutai; Russell Y Neches; Amanda Ng; Olga Nikolayeva; Tatyana Nikolayeva; Eileen Png; Krista A Ryon; Jorge L Sanchez; Heba Shaaban; Maria A Sierra; Dominique Thomas; Ben Young; Omar O Abudayyeh; Josue Alicea; Malay Bhattacharyya; Ran Blekhman; Eduardo Castro-Nallar; Ana M Cañas; Aspassia D Chatziefthimiou; Robert W Crawford; Francesca De Filippis; Youping Deng; Christelle Desnues; Emmanuel Dias-Neto; Marius Dybwad; Eran Elhaik; Danilo Ercolini; Alina Frolova; Dennis Gankin; Jonathan S Gootenberg; Alexandra B Graf; David C Green; Iman Hajirasouliha; Jaden J A Hastings; Mark Hernandez; Gregorio Iraola; Soojin Jang; Andre Kahles; Frank J Kelly; Kaymisha Knights; Nikos C Kyrpides; Paweł P Łabaj; Patrick K H Lee; Marcus H Y Leung; Per O Ljungdahl; Gabriella Mason-Buck; Ken McGrath; Cem Meydan; Emmanuel F Mongodin; Milton Ozorio Moraes; Niranjan Nagarajan; Marina Nieto-Caballero; Houtan Noushmehr; Manuela Oliveira; Stephan Ossowski; Olayinka O Osuolale; Orhan Özcan; David Paez-Espino; Nicolás Rascovan; Hugues Richard; Gunnar Rätsch; Lynn M Schriml; Torsten Semmler; Osman U Sezerman; Leming Shi; Tieliu Shi; Rania Siam; Le Huu Song; Haruo Suzuki; Denise Syndercombe Court; Scott W Tighe; Xinzhao Tong; Klas I Udekwu; Juan A Ugalde; Brandon Valentine; Dimitar I Vassilev; Elena M Vayndorf; Thirumalaisamy P Velavan; Jun Wu; María M Zambrano; Jifeng Zhu; Sibo Zhu; Christopher E Mason
Journal:  Cell       Date:  2021-05-26       Impact factor: 41.582

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.