The Uncultured Microbial Majority
Abstract
▪ Abstract Since the delineation of 12 bacterial phyla by comparative phylogenetic analyses of 16S ribosomal RNA in 1987 knowledge of microbial diversity has expanded dramatically owing to the sequencing of ribosomal RNA genes cloned from environmental DNA. Currently, only 26 of the approximately 52 identifiable major lineages, or phyla, within the domain Bacteria have cultivated representatives. Evidence from field studies indicates that many of the uncultivated phyla are found in diverse habitats, and some are extraordinarily abundant. In some important environments, including seawater, freshwater, and soil, many biologically and geochemically important organisms are at best only remotely related to any strain that has been characterized by phenotype or by genome sequencing. Genome sequence information that would allow ribosomal RNA gene trees to be related to broader patterns in microbial genome evolution is scant, and therefore microbial diversity remains largely unexplored territory.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
Scientists estimate that, to date, less than 1% of microbial life has been successfully cultivated.
“Scientists estimate that, to date, less than 1% of microbial life has been successfully cultivated (e.g., grown in the laboratory) (Rappé and Giovannoni, 2003).”
From The Astrobiology Primer v2.0 (2016) · cites this paper as Rappé and Giovannoni, 2003
Cites
Woese, C. R. (1987) · Microbiological Reviews · doi:10.1128/mr.51.2.221-271.1987 · Cited by 5,042 · see citing works
Prokaryotes: The unseen majority
Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6578 · Cited by 4,871 · see citing works
Proterozoic Ocean Chemistry and Evolution: A Bioinorganic Bridge?
Anbar, A. D., & Knoll, A. H. (2002) · Science · doi:10.1126/science.1069651 · Cited by 1,191 · see citing works
Zengler, K., Toledo, G., Rappé, M., Elkins, J., Mathur, E. J., Short, J. M., & Keller, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252630999 · Cited by 796 · see citing works
Self-citationHow good are deep phylogenetic trees?
Philippe, H., & Laurent, J. (1998) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(98)80028-2 · Cited by 324 · see citing works
Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton
Suzuki, M. T., Béjà, O., Taylor, L. T., & DeLong, E. F. (2001) · Environmental Microbiology · doi:10.1046/j.1462-2920.2001.00198.x · Cited by 167 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227 · see citing works
Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine
Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.02.017 · Cited by 3,358 · see citing works
The contribution of species richness and composition to bacterial services
Bell, T., Newman, J. A., Silverman, B. W., Turner, S. L., & Lilley, A. K. (2005) · Nature · doi:10.1038/nature03891 · Cited by 950 · see citing works
The oral microbiome: Role of key organisms and complex networks in oral health and disease
Sedghi, L., DiMassa, V., Harrington, A., Lynch, S. V., & Kapila, Y. L. (2021) · Periodontology 2000 · doi:10.1111/prd.12393 · Cited by 755 · see citing works
Wolfe, B. E., Button, J. E., Santarelli, M., & Dutton, R. J. (2014) · Cell · doi:10.1016/j.cell.2014.05.041 · Cited by 648 · see citing works
On the rocks: the microbiology of Antarctic Dry Valley soils
Cary, S. C., McDonald, I. R., Barrett, J. E., & Cowan, D. A. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2281 · Cited by 580 · see citing works
Benzodiazepines: use, abuse, and consequences.
Woods, J. H., Katz, J. L., & Winger, G. (1992) · Pharmacological Reviews · doi:10.1016/s0031-6997(25)00468-5 · Cited by 560 · see citing works
Mailing, L. J., Allen, J. M., Buford, T. W., Fields, C. J., & Woods, J. A. (2019) · Exercise and Sport Sciences Reviews · doi:10.1249/jes.0000000000000183 · Cited by 521 · see citing works
Actinomycetes: Still a source of novel antibiotics
Genilloud, O. (2017) · Natural Product Reports · doi:10.1039/c7np00026j · Cited by 465 · see citing works
Next-generation sequencing: insights to advance clinical investigations of the microbiome
Wensel, C. R., Pluznick, J. L., Salzberg, S. L., & Sears, C. L. (2022) · Journal of Clinical Investigation · doi:10.1172/jci154944 · Cited by 437 · see citing works
Mapping the Tree of Life: Progress and Prospects
Pace, N. R. (2009) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00033-09 · Cited by 286 · see citing works
Siegl, A., Kamke, J., Hochmuth, T., Piel, J., Richter, M., Liang, C., Dandekar, T., & Hentschel, U. (2011) · The ISME Journal · doi:10.1038/ismej.2010.95 · Cited by 276 · see citing works
Kohl, K. D., Amaya, J., Passement, C. A., Dearing, M. D., & McCue, M. D. (2014) · FEMS Microbiology Ecology · doi:10.1111/1574-6941.12442 · Cited by 249 · see citing works
Global distribution and diversity of marine <i>Verrucomicrobia</i>
Freitas, S., Hatosy, S., Fuhrman, J. A., Huse, S. M., Mark Welch, D. B., Sogin, M. L., & Martiny, A. C. (2012) · The ISME Journal · doi:10.1038/ismej.2012.3 · Cited by 236 · see citing works
Microbiology of the Red Sea (and other) deep‐sea anoxic brine lakes
Antunes, A., Ngugi, D. K., & Stingl, U. (2011) · Environmental Microbiology Reports · doi:10.1111/j.1758-2229.2011.00264.x · Cited by 173 · see citing works
Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections
PALLEN, M. J. (2014) · Parasitology · doi:10.1017/s0031182014000134 · Cited by 126 · see citing works
Domagal-Goldman, S. D., Wright, K. E., Domagal-Goldman, S. D., Wright, K. E., Adamala, K., Arina de la Rubia, L., Bond, J., Dartnell, L. R., Goldman, A. D., Lynch, K., et al. (2016) · Astrobiology · doi:10.1089/ast.2015.1460 · Cited by 136 · see citing works
“Scientists estimate that, to date, less than 1% of microbial life has been successfully cultivated (e.g., grown in the laboratory) (Rappé and Giovannoni, 2003).”
Early Microbial Evolution: The Age of Anaerobes
Martin, W. F., & Sousa, F. L. (2016) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a018127 · Cited by 129 · see citing works
Advancements toward a systems level understanding of the human oral microbiome
McLean, J. S. (2014) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2014.00098 · Cited by 108 · see citing works
Gonzalez, A., Mouquet, N., & Loreau, M. (2009) · Biodiversity, Ecosystem Functioning, and Human Wellbeing · doi:10.1093/acprof:oso/9780199547951.003.0010 · Cited by 92 · see citing works
Advances in microbial ecosystem concepts and their consequences for ruminant agriculture
Edwards, J. E., Huws, S. A., Kim, E. J., Lee, M. R. F., Kingston-Smith, A. H., & Scollan, N. D. (2008) · animal · doi:10.1017/s1751731108002164 · Cited by 75 · see citing works
Arpaia, S., Birch, A. N. E., Kiss, J., van Loon, J. J. A., Messéan, A., Nuti, M., Perry, J. N., Sweet, J. B., & Tebbe, C. C. (2017) · Science of The Total Environment · doi:10.1016/j.scitotenv.2017.01.039 · Cited by 62 · see citing works
Yang, C., Lin, F., Li, Q., Li, T., & Zhao, J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00394 · Cited by 44 · see citing works
PANGASTUTI, A., SUWANTO, A., LESTARI, Y., & SUHARTONO, M. T. (2009) · Biodiversitas Journal of Biological Diversity · doi:10.13057/biodiv/d110203 · Cited by 24 · see citing works
O’Brien, A. M., Laurich, J. R., & Frederickson, M. E. (2024) · Evolution · doi:10.1093/evolut/qpad183 · Cited by 21 · see citing works
QSpec: online control and data analysis system for single-cell Raman spectroscopy
Ren, L., Su, X., Wang, Y., Xu, J., & Ning, K. (2014) · PeerJ · doi:10.7717/peerj.436 · Cited by 10 · see citing works
- Authors
- Rappé, M. S., & Giovannoni, S. J.
- Affiliations
- Oregon State University (US)
- Venue
- Annual Review of Microbiology
- Publisher
- Annual Reviews
- Published
- 2003-10
- Volume
- 57
- Issue
- 1
- Pages
- 369-394
- ISSN
- 0066-4227 (ISSN-L)
- 1545-3251
- OpenAlex
- W2147378425
- Cited by
- 2,017
- References
- 6
- Citations by year
- 2026: 25 · 2025: 51 · 2024: 47 · 2023: 65 · 2022: 89 · 2021: 85 · 2020: 84 · 2019: 88 · 2018: 98 · 2017: 95 · 2016: 96 · 2015: 110 · 2014: 123 · 2013: 116 · 2012: 118
- FWCI
- 6.39
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Annual Review of Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- Oregon State University
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Keywords
- uncultured bacteria, bacterial phyla, microbial diversity, 16S rRNA phylogeny, environmental DNA, bacterial culture, soil bacteria, freshwater bacteria, marine bacteria
- MeSH terms
- DNA, Bacterial, Gram-Negative Bacteria, Gram-Positive Bacteria, Phylogeny, RNA, Ribosomal, 16S, Soil Microbiology, Genetic Variation, Water Microbiology, Genome, Bacterial, Sequence Analysis, DNA, Evolution, Molecular
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
