Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
Open accessAbstract
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances in sequencing throughput and computational techniques that allow for the cultivation-independent recovery of genomes from metagenomes. Here, we report the reconstruction of 7,903 bacterial and archaeal genomes from >1,500 public metagenomes. All genomes are estimated to be ≥50% complete and nearly half are ≥90% complete with ≤5% contamination. These genomes increase the phylogenetic diversity of bacterial and archaeal genome trees by >30% and provide the first representatives of 17 bacterial and three archaeal candidate phyla. We also recovered 245 genomes from the Patescibacteria superphylum (also known as the Candidate Phyla Radiation) and find that the relative diversity of this group varies substantially with different protein marker sets. The scale and quality of this data set demonstrate that recovering genomes from metagenomes provides an expedient path forward to exploring microbial dark matter.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Svartstrom et al. (2017) assembled 99 microbial genomes from the moose rumen, Stewart et al. (2018) assembled 913 microbial genomes from the rumen of cattle, and Parks et al. (2017) assembled over 8,000 novel microbial genomes from 1,500 public datasets, some of which originated from the rumen.
“Subsequently, Svartstrom et al. (2017) assembled 99 microbial genomes from the moose rumen, Stewart et al. (2018) assembled 913 microbial genomes from the rumen of cattle, and Parks et al. (2017) assembled over 8,000 novel microbial genomes from 1,500 public datasets, some of which originated from the rumen.”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Parks et al., 2017
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074 · see citing works
Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 20,966 · see citing works
Self-citationParks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works
Self-citationProdigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,426 · see citing works
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
Lowe, T. M., & Eddy, S. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.5.955 · Cited by 11,120 · see citing works
Database resources of the National Center for Biotechnology Information: update
Wheeler, D. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh073 · Cited by 10,691 · see citing works
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975 · see citing works
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,649 · see citing works
Pfam: the protein families database
Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148 · see citing works
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp077 · Cited by 5,602 · see citing works
McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,010 · see citing works
Self-citationLeinonen, R., Sugawara, H., & Shumway, M. F. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1019 · Cited by 2,760 · see citing works
The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624 · see citing works
Self-citationYarza, P., Yilmaz, P., Pruesse, E., Glöckner, F. O., Ludwig, W., SCHLEIFER, K. H., Whitman, W. B., Euzéby, J. P., Amann, R., & Rossello-Mora, R. A. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3330 · Cited by 2,563 · see citing works
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
Hugenholtz, P., Goebel, B. M., & Pace, N. R. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.18.4765-4774.1998 · Cited by 2,429 · see citing works
Self-citationCommunity structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417 · see citing works
Self-citationInsights into the phylogeny and coding potential of microbial dark matter
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., et al. (2013) · Nature · doi:10.1038/nature12352 · Cited by 2,394 · see citing works
Self-citationA new view of the tree of life
Hug, L. A., Baker, B. J., Anantharaman, K., Brown, C. T., Probst, A. J., Castelle, C. J., Butterfield, C. N., Hernsdorf, A. W., Amano, Y., Ise, K., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.48 · Cited by 2,039 · see citing works
Anvi’o: an advanced analysis and visualization platform for ‘omics data
Eren, A. M., Esen, Ö. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015) · PeerJ · doi:10.7717/peerj.1319 · Cited by 1,823 · see citing works
Infernal 1.0: inference of RNA alignments
Nawrocki, E. P., Kolbe, D. L., & Eddy, S. R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp157 · Cited by 1,428 · see citing works
Sequencing depth and coverage: key considerations in genomic analyses
Sims, D., Sudbery, I. M., Ilott, N. E., Heger, A., & Ponting, C. P. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3642 · Cited by 1,403 · see citing works
Single-cell genome sequencing: current state of the science
Gawad, C., Koh, W., & Quake, S. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2015.16 · Cited by 1,334 · see citing works
Complex archaea that bridge the gap between prokaryotes and eukaryotes
Spang, A., Saw, J. H., Jørgensen, S. L., Zaremba-Niedzwiedzka, K., Martijn, J., Lind, A. E., van Eijk, R., Schleper, C., Guy, L., & Ettema, T. J. G. (2015) · Nature · doi:10.1038/nature14447 · Cited by 1,324 · see citing works
Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., & Nielsen, P. H. (2013) · Nature Biotechnology · doi:10.1038/nbt.2579 · Cited by 1,253 · see citing works
Self-citationUnusual biology across a group comprising more than 15% of domain Bacteria
Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H., & Banfield, J. F. (2015) · Nature · doi:10.1038/nature14486 · Cited by 1,216 · cited 7× · see citing works
“Cyanobacteria (48) Thermotogae (11) Acetothermia (10) Dictyoglomi Coprothermo.”
BackgroundInfluentialMetaHIT Consortium, Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2939 · Cited by 1,184 · see citing works
Stoddard, S. F., Smith, B. J., Hein, R., Roller, B. R. K., & Schmidt, T. M. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1201 · Cited by 1,096 · see citing works
Anantharaman, K., Brown, C., Hug, L., Sharon, I., Castelle, C., Probst, A., Thomas, B., Singh, A., Wilkins, M., Karaoz, U., et al. (2016) · Nature Communications · doi:10.1038/ncomms13219 · Cited by 1,040 · see citing works
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N., Kunin, V., Goodwin, L., Wu, M., Tindall, B. J., et al. (2009) · Nature · doi:10.1038/nature08656 · Cited by 998 · see citing works
Self-citationThe TIGRFAMs database of protein families
Haft, D. H. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg128 · Cited by 984 · see citing works
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4458 · Cited by 873 · see citing works
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics
Evans, P. N., Parks, D. H., Chadwick, G. L., Robbins, S. J., Orphan, V. J., Golding, S. D., & Tyson, G. W. (2015) · Science · doi:10.1126/science.aac7745 · Cited by 785 · see citing works
Self-citationA Catalog of Reference Genomes from the Human Microbiome
The Human Microbiome Jumpstart Reference Strains Consortium, Nelson, K. E., Weinstock, G. M., Highlander, S. K., Worley, K. C., Creasy, H. H., Wortman, J. R., Rusch, D. B., Mitreva, M., Sodergren, E., et al. (2010) · Science · doi:10.1126/science.1183605 · Cited by 702 · see citing works
Microbial species delineation using whole genome sequences
Varghese, N. J., Mukherjee, S., Ivanova, N., Konstantinidis, K. T., Mavrommatis, K., Kyrpides, N. C., & Pati, A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv657 · Cited by 693 · see citing works
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla
Wrighton, K. C., Thomas, B. C., Sharon, I., Miller, C. S., Castelle, C. J., VerBerkmoes, N. C., Wilkins, M. J., Hettich, R. L., Lipton, M. S. W., Williams, K. H., et al. (2012) · Science · doi:10.1126/science.1224041 · Cited by 643 · see citing works
Marcy, Y., Ouverney, C., Bik, E. M., Lösekann, T., Ivanova, N., Martín, H. G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D. A., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704662104 · Cited by 632 · see citing works
Self-citationMethylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
Vanwonterghem, I., Evans, P. N., Parks, D. H., Jensen, P. D., Woodcroft, B. J., Hugenholtz, P., & Tyson, G. W. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.170 · Cited by 537 · see citing works
Self-citationCastelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.01.014 · Cited by 536 · see citing works
An archaeal origin of eukaryotes supports only two primary domains of life
Williams, T. A., Foster, P. G., Cox, C. J., & Embley, T. M. (2013) · Nature · doi:10.1038/nature12779 · Cited by 519 · see citing works
RefSeq microbial genomes database: new representation and annotation strategy
Tatusova, T. A., Ciufo, S. A., Fedorov, B., O’Neill, K. E., & Tolstoy, I. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1274 · Cited by 483 · see citing works
Sharon, I., Morowitz, M. J., Thomas, B. C., Costello, E. K., Relman, D. A., & Banfield, J. F. (2012) · Genome Research · doi:10.1101/gr.142315.112 · Cited by 474 · see citing works
Genome Project Standards in a New Era of Sequencing
Chain, P. S. G., Grafham, D. V., Fulton, R. S., FitzGerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., et al. (2009) · Science · doi:10.1126/science.1180614 · Cited by 400 · see citing works
Self-citationSchloss, P. D. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000844 · Cited by 393 · see citing works
GroopM: an automated tool for the recovery of population genomes from related metagenomes
Imelfort, M., Parks, D. H., Woodcroft, B. J., Dennis, P. G., Hugenholtz, P., & Tyson, G. W. (2014) · PeerJ · doi:10.7717/peerj.603 · Cited by 310 · see citing works
Self-citationSmall Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla
Kantor, R. S., Wrighton, K. C., Handley, K. M., Sharon, I., Hug, L. A., Castelle, C. J., Thomas, B. C., & Banfield, J. F. (2013) · mBio · doi:10.1128/mbio.00708-13 · Cited by 307 · see citing works
An Expanded Genomic Representation of the Phylum Cyanobacteria
Soo, R. M., Skennerton, C. T., Sekiguchi, Y., Imelfort, M., Paech, S. J., Dennis, P. G., Steen, J. A., Parks, D. H., Tyson, G. W., & Hugenholtz, P. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu073 · Cited by 290 · see citing works
Self-citationConStrains identifies microbial strains in metagenomic datasets
Luo, C., Knight, R. D., Siljander, H., Knip, M., Xavier, R. J., & Gevers, D. (2015) · Nature Biotechnology · doi:10.1038/nbt.3319 · Cited by 267 · see citing works
IMG/M 4 version of the integrated metagenome comparative analysis system
Markowitz, V. M., Chen, I.-M. A., Chu, K., Szeto, E., Palaniappan, K., Pillay, M., Ratner, A., Huang, J., Pagani, I., Tringe, S. G., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt919 · Cited by 264 · see citing works
The bright side of microbial dark matter: lessons learned from the uncultivated majority.
Solden, L., Lloyd, K., & Wrighton, K. (2016) · Current Opinion in Microbiology · doi:10.1016/j.mib.2016.04.020 · Cited by 253 · see citing works
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Mukherjee, S., Seshadri, R., Varghese, N. J., Eloe‐Fadrosh, E. A., Meier‐Kolthoff, J. P., Göker, M., Coates, R. C., Hadjithomas, M., Pavlopoulos, G. A., Páez-Espino, D., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3886 · Cited by 246 · see citing works
Self-citationLazar, C. S., Baker, B. J., Seitz, K. W., Hyde, A. S., Dick, G. J., Hinrichs, K., & Teske, A. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13142 · Cited by 244 · see citing works
The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures
Strous, M., Kraft, B., Bisdorf, R., & Tegetmeyer, H. E. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00410 · Cited by 226 · see citing works
The MG-RAST metagenomics database and portal in 2015
Wilke, A., Bischof, J., Gerlach, W., Glass, E. M., Harrison, T., Keegan, K. P., Paczian, T., Trimble, W. L., Bagchi, S., Grama, A. Y., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1322 · Cited by 209 · see citing works
Reconstructing 16S rRNA genes in metagenomic data
Yuan, C., Lei, J., Cole, J. R., & Sun, Y. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv231 · Cited by 156 · see citing works
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
Eloe-Fadrosh, E., Páez-Espino, D., Jarett, J., Dunfield, P., Hedlund, B., Dekas, A., Grasby, S., Brady, A., Dong, H.-L., Briggs, B., et al. (2016) · Nature Communications · doi:10.1038/ncomms10476 · Cited by 151 · see citing works
Vanwonterghem, I., Jensen, P., Rabaey, K., & Tyson, G. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13382 · Cited by 145 · see citing works
Self-citationヒト口腔からの微量の培養されないTM7微生物の単一細胞遺伝分析による生物学的「不明な物体」の詳細な分析
Marcy, Y., Ouverney, C., Elisabeth, M. B., Tina, L., Ivanova, N., Garcia, M. H., Szeto, E., Darren, P., Hugenholtz, P., David, A. R., et al. (2007) · Cited by 138 · see citing works
Self-citationShepherd, J., & Ibba, M. (2015) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuv004 · Cited by 127 · see citing works
A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres
Rahman, N. A., Parks, D. H., Vanwonterghem, I., Morrison, M., Tyson, G. W., & Hugenholtz, P. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01469 · Cited by 122 · see citing works
Self-citationSRAdb: query and use public next-generation sequencing data from within R
Zhu, Y. J., Stephens, R. M., Meltzer, P. S., & Davis, S. R. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-19 · Cited by 103 · see citing works
Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
Kyrpides, N. C., Woyke, T., Eisen, J. A., et al. (2013) · Standards in Genomic Sciences · doi:10.4056/sigs.5068949 · Cited by 94 · see citing works
Whitman, W. B., Woyke, T., Klenk, H., Zhou, Y., Lilburn, T., Beck, B. J., Vos, P. D., Vandamme, P. A. R., Eisen, J. A., Garrity, G. M., et al. (2015) · Standards in Genomic Sciences · doi:10.1186/s40793-015-0017-x · Cited by 75 · see citing works
Self-citationSekiguchi, Y., Ohashi, A., Parks, D. H., Yamauchi, T., Tyson, G. W., & Hugenholtz, P. (2015) · PeerJ · doi:10.7717/peerj.740 · Cited by 75 · see citing works
Self-citationYeoh, Y. K., Sekiguchi, Y., Parks, D., & Hugenholtz, P. (2015) · Molecular biology and evolution · doi:10.1093/molbev/msv281 · Cited by 73 · see citing works
Self-citationA catalogue of 136 microbial draft genomes from Red Sea metagenomes
Haroon, M. F., Thompson, L., Parks, D. H., Hugenholtz, P., & Stingl, U. (2016) · Scientific Data · doi:10.1038/sdata.2016.50 · Cited by 64 · see citing works
Self-citationSczyrba, A., Hofmann, P., Belmann, P., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/099127 · Cited by 53 · see citing works
Database resources of the National Center for Biotechnology Information
Sayers, E. W., Barrett, T., Benson, D. A., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp382 · Cited by 49 · see citing works
Editorial: Microbiotechnology Based Surfactants and Their Applications
Rahman, P. K. S. M., & Sekhon, K. K. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01344 · Cited by 11 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Hugenholtz, P., Sharshewski, A. & Parks, D. H. in Microbial Evolution (ed. Ochman, H.) 55-65 (Cold Spring Harbor Laboratory Press, New York, 2016).
Cited by
Sorted by citations
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018) · Nature Communications · doi:10.1038/s41467-018-07641-9 · Cited by 5,748 · see citing works
Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab776 · Cited by 2,402 · see citing works
Self-citationBeghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works
Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works
Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023) · Nature Methods · doi:10.1038/s41592-023-01940-w · Cited by 1,705 · see citing works
Self-citationA unified catalog of 204,938 reference genomes from the human gut microbiome
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367 · see citing works
Self-citationA new genomic blueprint of the human gut microbiota
Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314 · see citing works
Fusobacterium nucleatum — symbiont, opportunist and oncobacterium
Brennan, C. A., & Garrett, W. S. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0129-6 · Cited by 1,205 · see citing works
Unified rational protein engineering with sequence-based deep representation learning
Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M., & Church, G. M. (2019) · Nature Methods · doi:10.1038/s41592-019-0598-1 · Cited by 1,131 · see citing works
Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869 · see citing works
New insights from uncultivated genomes of the global human gut microbiome
Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737 · see citing works
GToTree: A user-friendly workflow for phylogenomics
Lee, M. D. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz188 · Cited by 552 · see citing works
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen
Stewart, R. D., Auffret, M. D., Warr, A., Wiser, A. H., Press, M. O., Langford, K. W., Liachko, I., Snelling, T. J., Dewhurst, R. J., Walker, A. W., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03317-6 · Cited by 559 · see citing works
Huws, S. A., Creevey, C. J., Oyama, L. B., Mizrahi, I., Denman, S. E., Popova, M., Muñoz-Tamayo, R., Forano, E., Waters, S. M., Hess, M., et al. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02161 · Cited by 487 · see citing works
The person-to-person transmission landscape of the gut and oral microbiomes
Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449 · see citing works
Microbial abundance, activity and population genomic profiling with mOTUs2
Milanese, A., Mende, D. R., Paoli, L., Salazar, G., Ruscheweyh, H.-J., Cuenca, M., Hingamp, P., Alves, R., Costea, P. I., Coelho, L. P., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08844-4 · Cited by 446 · see citing works
Accurate and complete genomes from metagenomes
Chen, L.-X., Anantharaman, K., Shaiber, A., Eren, A. M., & Banfield, J. F. (2020) · Genome Research · doi:10.1101/gr.258640.119 · Cited by 401 · see citing works
Gut Microbiome Dysbiosis and Immunometabolism: New Frontiers for Treatment of Metabolic Diseases
Belizário, J. E., Faintuch, J., & Garay-Malpartida, M. (2018) · Mediators of Inflammation · doi:10.1155/2018/2037838 · Cited by 341 · see citing works
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303 · see citing works
A rooted phylogeny resolves early bacterial evolution
Coleman, G. A., Davín, A. A., Mahendrarajah, T. A., Szánthó, L. L., Spang, A., Hugenholtz, P., Szöllősi, G. J., & Williams, T. A. (2021) · Science · doi:10.1126/science.abe0511 · Cited by 285 · see citing works
Self-citationPhylogenomics provides robust support for a two-domains tree of life
Williams, T. A., Cox, C. J., Foster, P. G., Szöllősi, G. J., & Embley, T. M. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-1040-x · Cited by 274 · see citing works
Genomes OnLine database (GOLD) v.7: updates and new features
Mukherjee, S., Stamatis, D., Bertsch, J., Ovchinnikova, G., Katta, H. Y., Mojica, A., Chen, I.-M. A., Kyrpides, N. C., & Reddy, T. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky977 · Cited by 230 · see citing works
Beresford-Jones, B. S., Forster, S. C., Stares, M. D., Notley, G., Viciani, E., Browne, H. P., Boehmler, D. J., Soderholm, A. T., Kumar, N., Vervier, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.003 · Cited by 194 · see citing works
Delmont, T. O., Gaia, M., Hinsinger, D. D., Frémont, P., Vanni, C., Fernandez-Guerra, A., Eren, A. M., Kourlaiev, A., d'Agata, L., Clayssen, Q., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100123 · Cited by 173 · see citing works
Multiple levels of the unknown in microbiome research
Thomas, A. M., & Segata, N. (2019) · BMC Biology · doi:10.1186/s12915-019-0667-z · Cited by 176 · see citing works
Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000436 · Cited by 152 · see citing works
Evolution of resilience in protein interactomes across the tree of life
Zitnik, M., Sosič, R., Feldman, M. W., & Leskovec, J. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1818013116 · Cited by 130 · see citing works
Muñoz-Gómez, S. A., Susko, E., Williamson, K., Eme, L., Slamovits, C. H., Moreira, D., López-García, P., & Roger, A. J. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-021-01638-2 · Cited by 111 · see citing works
An estimate of the deepest branches of the tree of life from ancient vertically evolving genes
Moody, E. R., Mahendrarajah, T. A., Dombrowski, N., Clark, J. W., Petitjean, C., Offre, P., Szöllősi, G. J., Spang, A., & Williams, T. A. (2022) · eLife · doi:10.7554/elife.66695 · Cited by 95 · see citing works
Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea
Martinez-Gutierrez, C. A., & Aylward, F. O. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab254 · Cited by 95 · see citing works
Tamburini, F. B., Maghini, D., Oduaran, O. H., Brewster, R., Hulley, M. R., Sahibdeen, V., Norris, S. A., Tollman, S., Kahn, K., Wagner, R. G., et al. (2022) · Nature Communications · doi:10.1038/s41467-021-27917-x · Cited by 88 · see citing works
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition
Taib, N., Megrian, D., Witwinowski, J., Adam, P., Poppleton, D., Borrel, G., Beloin, C., & Gribaldo, S. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01299-7 · Cited by 82 · see citing works
New technologies for developing phage-based tools to manipulate the human microbiome
Khan Mirzaei, M., & Deng, L. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2021.04.007 · Cited by 53 · see citing works
Alexander, H., Hu, S. K., Krinos, A. I., Pachiadaki, M., Tully, B. J., Neely, C. J., & Reiter, T. (2021) · doi:10.1101/2021.07.25.453713 · Cited by 67 · see citing works
Richardson, L. J., Rawlings, N. D., Salazar, G. A., Almeida, A., Haft, D. R., Ducq, G., Sutton, G. G., & Finn, R. D. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1013 · Cited by 36 · see citing works
Tomofuji, Y., Kishikawa, T., Maeda, Y., Ogawa, K., Otake-Kasamoto, Y., Kawabata, S., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100219 · Cited by 35 · see citing works
Ladeira, R., Tap, J., & Derrien, M. (2023) · Microbiome Research Reports · doi:10.20517/mrr.2023.01 · Cited by 19 · see citing works
Parker, C. W., Senko, J. M., Auler, A. S., Sasowsky, I. D., Schulz, F., Woyke, T., & Barton, H. A. (2022) · Scientific Reports · doi:10.1038/s41598-022-21365-3 · Cited by 12 · see citing works
A multi-modal deep language model for contaminant removal from metagenome-assembled genomes
Zou, B., Wang, J., Ding, Y., Zhang, Z., Huang, Y., Fang, X., Cheung, K. C., See, S., & Zhang, L. (2024) · Nature Machine Intelligence · doi:10.1038/s42256-024-00908-5 · Cited by 9 · see citing works
- Authors
- Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W.
- Affiliations
- The University of Queensland (AU)
- Corresponding author
- Hugenholtz, Philip
- Tyson, Gene W.
- ORCID
- Venue
- Nature Microbiology
- Published
- 2017-09-11
- Volume
- 2
- Issue
- 11
- Pages
- 1533-1542
- ISSN
- 2058-5276 (ISSN-L)
- OpenAlex
- W2753961085
- Cited by
- 1,882
- References
- 70
- Citations by year
- 2026: 146 · 2025: 173 · 2024: 214 · 2023: 217 · 2022: 290 · 2021: 271 · 2020: 251 · 2019: 184 · 2018: 125 · 2017: 6 · 2016: 1
- FWCI
- 63.52
- Type
- journal article
- Language
- en
- Update notices
- correction (2017-12-12)
- Open access
- hybrid
- doi.org
- Locations
- Nature Microbiology (publishedVersion, cc-by)
- PubMed (publishedVersion)
- QUT ePrints (Queensland University of Technology) (submittedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, cc-by)
- VBN Forskningsportal (Aalborg Universitet) (submittedVersion)
- Funders
- U.S. Department of Energy (DESC0010580)
- Australian Research Council (DE170100428, DE160100248, FL150100038)
- Biological and Environmental Research (DE-SC0010580)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
- Keywords
- metagenome-assembled genomes, microbial dark matter, Candidate Phyla Radiation, Patescibacteria, genome completeness, microbial diversity
- MeSH terms
- Archaea, Bacteria, Phylogeny, Genome, Bacterial, Sequence Analysis, DNA, Genome, Archaeal, Metagenome, Metagenomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
