The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Bayesian community-wide culture-independent microbial source tracking
Open accessAbstract
Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments. We applied SourceTracker to microbial surveys from neonatal intensive care units (NICUs), offices and molecular biology laboratories, and provide a database of known contaminants for future testing.
Overview
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
Verification
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.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Breiman, L. (2001) · Machine Learning · doi:10.1023/a:1010933404324 · Cited by 133,538
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Self-citationUniFrac: 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
Self-citationGriffiths, T. L., & Steyvers, M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307752101 · Cited by 6,049
Lauber, C. L., Hamady, M., Knight, R., & Fierer, N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00335-09 · Cited by 4,063
Self-citationBacterial Community Variation in Human Body Habitats Across Space and Time
Costello, E. K., Lauber, C. L., Hamady, M., Fierer, N., Gordon, J. I., & Knight, R. (2009) · Science · doi:10.1126/science.1177486 · Cited by 3,231
Self-citation
Cited by
Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice
Ridaura, V. K., Faith, J. J., Rey, F. E., Cheng, J., Duncan, A. E., Kau, A. L., Griffin, N. W., Lombard, V., Henrissat, B., Bain, J. R., et al. (2013) · Science · doi:10.1126/science.1241214 · Cited by 3,788
Self-citationDavis, N. M., Proctor, D. M., Holmes, S. P., Relman, D. A., & Callahan, B. J. (2018) · Microbiome · doi:10.1186/s40168-018-0605-2 · Cited by 3,493
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
Salter, S. J., Cox, M. J., Turek, E. M., Calus, S. T., Cookson, W. O., Moffatt, M. F., Turner, P., Parkhill, J., Loman, N. J., & Walker, A. W. (2014) · BMC Biology · doi:10.1186/s12915-014-0087-z · Cited by 3,463
Current understanding of the human microbiome
Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R. (2018) · Nature Medicine · doi:10.1038/nm.4517 · Cited by 2,609
Self-citationA communal catalogue reveals Earth's multiscale microbial diversity
Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., et al. (2017) · Nature · doi:10.1038/nature24621 · Cited by 2,684
Self-citationThe Placenta Harbors a Unique Microbiome
Aagaard, K., Ma, J., Antony, K. M., Ganu, R., Petrosino, J., & Versalovic, J. (2014) · Science Translational Medicine · doi:10.1126/scitranslmed.3008599 · Cited by 2,494
Best practices for analysing microbiomes
Knight, R., Vrbanac, A., Taylor, B. C., Aksenov, A., Callewaert, C., Debelius, J., Gonzalez, A., Kosciolek, T., McCall, L.-I., McDonald, D., et al. (2018) · Nature Reviews Microbiology · doi:10.1038/s41579-018-0029-9 · Cited by 2,030
Self-citationGeller, L. T., Barzily-Rokni, M., Danino, T., Jonas, O. H., Shental, N., Nejman, D., Gavert, N., Zwang, Y., Cooper, Z. A., Shee, K., et al. (2017) · Science · doi:10.1126/science.aah5043 · Cited by 1,817
RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach
Poore, G. D., Kopylova, E., Zhu, Q., Carpenter, C., Fraraccio, S., Wandro, S., Kosciolek, T., Janssen, S., Metcalf, J., Song, S. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2095-1 · Cited by 989
Self-citationRetractedChu, D. M., Ma, J., Prince, A. L., Antony, K. M., Seferovic, M. D., & Aagaard, K. M. (2017) · Nature Medicine · doi:10.1038/nm.4272 · Cited by 1,063
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer
Dominguez-Bello, M. G., De Jesus-Laboy, K. M., Shen, N., Cox, L. M., Amir, A., Gonzalez, A., Bokulich, N. A., Song, S. J., Hoashi, M., Rivera-Vinas, J. I., et al. (2016) · Nature Medicine · doi:10.1038/nm.4039 · Cited by 1,014
Self-citationGut bacteria that prevent growth impairments transmitted by microbiota from malnourished children
Blanton, L. V., Charbonneau, M. R., Salih, T., Barratt, M. J., Venkatesh, S., Ilkaveya, O., Subramanian, S., Manary, M. J., Trehan, I., Jorgensen, J. M., et al. (2016) · Science · doi:10.1126/science.aad3311 · Cited by 735
Segal, L. N., Clemente, J. C., Tsay, J.-C. J., Koralov, S. B., Keller, B. C., Wu, B. G., Li, Y., Shen, N., Ghedin, E., Morris, A., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.31 · Cited by 685
Self-citationPathogens and host immunity in the ancient human oral cavity
Warinner, C., Rodrigues, J. F. M., Vyas, R., Trachsel, C., Shved, N., Grossmann, J., Radini, A., Hancock, Y., Tito, R. Y., Fiddyment, S., et al. (2014) · Nature Genetics · doi:10.1038/ng.2906 · Cited by 618
Interconnected microbiomes and resistomes in low-income human habitats
Pehrsson, E. C., Tsukayama, P., Patel, S., Mejía-Bautista, M., Sosa-Soto, G., Navarrete, K. M., Calderon, M., Cabrera, L., Hoyos-Arango, W., Bertoli, M. T., et al. (2016) · Nature · doi:10.1038/nature17672 · Cited by 607
Subsistence strategies in traditional societies distinguish gut microbiomes
Obregon-Tito, A. J., Tito, R. Y., Metcalf, J., Sankaranarayanan, K., Clemente, J. C., Ursell, L. K., Zech Xu, Z., Van Treuren, W., Knight, R., Gaffney, P. M., et al. (2015) · Nature Communications · doi:10.1038/ncomms7505 · Cited by 587
Self-citationSegal, L. N., Alekseyenko, A. V., Clemente, J. C., Kulkarni, R., Wu, B., Chen, H., Berger, K. I., Goldring, R. M., Rom, W. N., Blaser, M. J., et al. (2013) · Microbiome · doi:10.1186/2049-2618-1-19 · Cited by 482
Translocation and dissemination of commensal bacteria in post-stroke infection
Stanley, D., Mason, L. J., Mackin, K. E., Srikhanta, Y. N., Lyras, D., Prakash, M. D., Nurgali, K., Venegas, A., Hill, M. D., Moore, R. J., et al. (2016) · Nature Medicine · doi:10.1038/nm.4194 · Cited by 464
Extreme Dysbiosis of the Microbiome in Critical Illness
McDonald, D., Ackermann, G., Khailova, L., Baird, C., Heyland, D., Kozar, R., Lemieux, M., Derenski, K., King, J., Vis-Kampen, C., et al. (2016) · mSphere · doi:10.1128/msphere.00199-16 · Cited by 426
Self-citationOrlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411
Saint-Antoine IBD Network, Sokol, H., Landman, C., Seksik, P., Berard, L., Montil, M., Nion-Larmurier, I., Bourrier, A., Le Gall, G., Lalande, V., et al. (2020) · Microbiome · doi:10.1186/s40168-020-0792-5 · Cited by 378
Ancient and modern environmental DNA
Pedersen, M. W., Overballe-Petersen, S., Ermini, L., Sarkissian, C. D., Haile, J., Hellstrom, M., Spens, J., Thomsen, P. F., Bohmann, K., Cappellini, E., et al. (2015) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2013.0383 · Cited by 329
Haifer, C., Paramsothy, S., Kaakoush, N. O., Saikal, A., Ghaly, S., Yang, T., Luu, L. D. W., Borody, T. J., & Leong, R. W. (2022) · The Lancet Gastroenterology & Hepatology · doi:10.1016/s2468-1253(21)00400-3 · Cited by 285
Sbihi, H., Boutin, R. C., Cutler, C., Suen, M., Finlay, B. B., & Turvey, S. E. (2019) · Allergy · doi:10.1111/all.13812 · Cited by 199
Velsko, I. M., Fellows Yates, J. A., Aron, F., Hagan, R. W., Frantz, L. A. F., Loe, L., Martinez, J. B. R., Chaves, E., Gosden, C., Larson, G., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0717-3 · Cited by 170
Gomez-Arango, L. F., Barrett, H. L., McIntyre, H. D., Callaway, L. K., Morrison, M., & Nitert, M. D. (2017) · Scientific Reports · doi:10.1038/s41598-017-03066-4 · Cited by 168
Seto, C. T., Jeraldo, P., Orenstein, R., Chia, N., & DiBaise, J. K. (2014) · Microbiome · doi:10.1186/2049-2618-2-42 · Cited by 163
Faecal microbiota transplantation for Clostridioides difficile: mechanisms and pharmacology
Khoruts, A., Staley, C., & Sadowsky, M. J. (2021) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-020-0350-4 · Cited by 155
The lung tissue microbiota of mild and moderate chronic obstructive pulmonary disease
Pragman, A. A., Lyu, T., Baller, J. A., Gould, T. J., Kelly, R. F., Reilly, C. S., Isaacson, R. E., & Wendt, C. H. (2018) · Microbiome · doi:10.1186/s40168-017-0381-4 · Cited by 150
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
Ziesemer, K. A., Mann, A. E., Sankaranarayanan, K., Schroeder, H., Ozga, A. T., Brandt, B. W., Zaura, E., Waters-Rist, A., Hoogland, M., Salazar-García, D. C., et al. (2015) · Scientific Reports · doi:10.1038/srep16498 · Cited by 148
The best practice for microbiome analysis using R
Wen, T., Niu, G., Chen, T., Shen, Q., Yuan, J., & Liu, Y.-X. (2023) · Protein & Cell · doi:10.1093/procel/pwad024 · Cited by 139
Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice
Le Bastard, Q., Ward, T., Sidiropoulos, D., Hillmann, B. M., Chun, C. L., Sadowsky, M. J., Knights, D., & Montassier, E. (2018) · Scientific Reports · doi:10.1038/s41598-018-24342-x · Cited by 134
Self-citationGut microbiome of an 11th Century A.D. pre-Columbian Andean mummy
Santiago-Rodriguez, T. M., Fornaciari, G., Luciani, S., Dowd, S. E., Toranzos, G. A., Marota, I., & Cano, R. J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0138135 · Cited by 123
Charbonnet, J. A., Rodowa, A. E., Joseph, N. T., Guelfo, J. L., Field, J. A., Jones, G. D., Higgins, C. P., Helbling, D. E., & Houtz, E. F. (2021) · Environmental Science & Technology · doi:10.1021/acs.est.0c08506 · Cited by 121
Huggins, M. A., Sjaastad, F. V., Pierson, M., Kucaba, T. A., Swanson, W., Staley, C., Weingarden, A. R., Jensen, I. J., Danahy, D. B., Badovinac, V. P., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.07.028 · Cited by 114
An intact gut microbiome protects genetically predisposed mice against leukemia
Vicente-Dueñas, C., Janssen, S., Oldenburg, M., Auer, F., González-Herrero, I., Casado-García, A., Isidro-Hernández, M., Raboso-Gallego, J., Westhoff, P., Pandyra, A. A., et al. (2020) · Blood · doi:10.1182/blood.2019004381 · Cited by 106
Petersen, C., Wankhade, U. D., Bharat, D., Wong, K., Mueller, J. E., Chintapalli, S. V., Piccolo, B. D., Jalili, T., Jia, Z., Symons, J. D., et al. (2019) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2019.01.004 · Cited by 73
Maixner, F., Sarhan, M. S., Huang, K. D., Tett, A., Schoenafinger, A., Zingale, S., Blanco-Míguez, A., Manghi, P., Cemper-Kiesslich, J., Rosendahl, W., et al. (2021) · Current Biology · doi:10.1016/j.cub.2021.09.031 · Cited by 62
Wang, N., Wu, S., Huang, L., Hu, Y., He, X., He, J., Hu, B., Xu, Y., Rong, Y., Yuan, C., et al. (2025) · Journal of Biomedical Science · doi:10.1186/s12929-025-01117-x · Cited by 62
Elkrief, A., Waters, N. R., Smith, N., Dai, A., Slingerland, J., Aleynick, N., Febles, B., Gogia, P., Socci, N. D., Lumish, M., et al. (2024) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-23-0498 · Cited by 48
Computational methods and challenges in analyzing intratumoral microbiome data
Wang, Q., Liu, Z., Ma, A., Li, Z., Liu, B., & Ma, Q. (2023) · Trends in Microbiology · doi:10.1016/j.tim.2023.01.011 · Cited by 37
Alexa, E. A., Cobo-Díaz, J. F., Renes, E., O´Callaghan, T. F., Kilcawley, K., Mannion, D., Skibinska, I., Ruiz, L., Margolles, A., Fernández-Gómez, P., et al. (2024) · Microbiome · doi:10.1186/s40168-024-01790-4 · Cited by 28
Santiago-Rodriguez, T. M., Fornaciari, A., Fornaciari, G., Luciani, S., Marota, I., Vercellotti, G., Toranzos, G. A., Giuffra, V., & Cano, R. J. (2019) · Genes · doi:10.3390/genes10040299 · Cited by 10
DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome
Zeng, W., Gautam, A., & Huson, D. H. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac584 · Cited by 7
Li, D., Van De Werfhorst, L. C., Ervin, J., Poresky, A., Steets, B., Rivers, C., Sharp, G., Smith, J., & Holden, P. A. (2023) · Environmental Pollution · doi:10.1016/j.envpol.2023.122521 · Cited by 6
Metadata
- Authors
- Knights, D., Kuczynski, J., Charlson, E. S., Zaneveld, J., Mozer, M. C., Collman, R. G., Bushman, F. D., Knight, R., & Kelley, S. T.
- Venue
- Nature Methods
- Published
- 2011-07-17
- Volume
- 8
- Issue
- 9
- Pages
- 761-763
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2054407804
- Cited by
- 1,856
- References
- 6
- FWCI
- 7.52
- Type
- journal article
- Language
- en
- Open access
- green
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
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
