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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
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Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.
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“the prediction of bacterial gene functions based on 16S rRNA gene sequences using PICRUSt 27 revealed some functional diversity among the 3 groups in accordance with the difference in gut microbiota composition (Figure IIIH in the online-only Data Supplement).”
From Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis (2018) · cites this paper as [27]
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Cites
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-citationSearch and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
APE: analyses of phylogenetics and evolution in R language
Paradis, E., Claude, J., & Strimmer, K. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg412 · Cited by 11,335
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.03006-05 · Cited by 10,891
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 5,144
Self-citationKEGG for integration and interpretation of large-scale molecular data sets
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., & Tanabe, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr988 · Cited by 4,848
A genomic perspective on protein families.
Tatusov, R., Koonin, E., & Lipman, D. (1997) · Science · doi:10.1126/science.278.5338.631 · Cited by 3,777
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R. L., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR ampliconsPreprint
Haas, B. J., Gevers, D., Earl, A. M., Feldgarden, M., Ward, D. V., Giannoukos, G., Ciulla, D., Tabbaa, D., Highlander, S. K., Sodergren, E. J., et al. (2011) · Genome Research · doi:10.1101/gr.112730.110 · Cited by 3,527
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Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742
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Yoon, S.-H., Ha, S. M., Kwon, S., Lim, J., Kim, Y.-S., Seo, H., & Chun, J. (2016) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.001755 · Cited by 7,733
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Douglas, G. M., Maffei, V. J., Zaneveld, J. R., Yurgel, S. N., Brown, J. R., Taylor, C. M., Huttenhower, C., & Langille, M. G. I. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0548-6 · Cited by 6,709
Self-citationCryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286
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Nguyen, N., Song, Z., Bates, S. T., Branco, S., Tedersoo, L., Menke, J., Schilling, J. S., & Kennedy, P. G. (2015) · Fungal ecology · doi:10.1016/j.funeco.2015.06.006 · Cited by 4,668
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Parks, D. H., Tyson, G. W., Hugenholtz, P., & Beiko, R. G. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu494 · Cited by 4,246
Self-citationParada, A. E., Needham, D. M., & Fuhrman, J. A. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13023 · Cited by 4,212
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Lynch, S. V., & Pedersen, O. (2016) · New England Journal of Medicine · doi:10.1056/nejmra1600266 · Cited by 3,637
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Sampson, T. R., Debelius, J. W., Thron, T., Janssen, S., Shastri, G. G., Ilhan, Z. E., Challis, C., Schretter, C. E., Rocha, S., Gradinaru, V., et al. (2016) · Cell · doi:10.1016/j.cell.2016.11.018 · Cited by 3,622
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Louca, S., Parfrey, L. W., & Doebeli, M. (2016) · Science · doi:10.1126/science.aaf4507 · Cited by 3,580
The Treatment-Naive Microbiome in New-Onset Crohn’s Disease
Gevers, D., Kugathasan, S., Denson, L. A., Vázquez-Baeza, Y., Van Treuren, W., Ren, B., Schwager, E., Knights, D., Song, S. J., Yassour, M., et al. (2014) · Cell Host & Microbe · doi:10.1016/j.chom.2014.02.005 · Cited by 3,220
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Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., Bell, J. T., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.053 · Cited by 3,164
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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
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Vogt, N. M., Kerby, R. L., Dill-McFarland, K. A., Harding, S. J., Merluzzi, A. P., Johnson, S. C., Carlsson, C. M., Asthana, S., Zetterberg, H., Blennow, K., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-13601-y · Cited by 2,137
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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-citationDhariwal, A., Chong, J., Habib, S. M., King, I. L., Agellon, L. B., & Xia, J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx295 · Cited by 1,946
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Buffie, C. G., Bucci, V., Stein, R. R., McKenney, P. T., Ling, L., Gobourne, A., No, D., Liu, H., Kinnebrew, M., Viale, A., et al. (2015) · Nature · doi:10.1038/nature13828 · Cited by 1,872
Cox, L. M., Yamanishi, S., Sohn, J., Alekseyenko, A. V., Leung, J. M., Cho, I., Kim, S. G., Li, H., Gao, Z., Mahana, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.05.052 · Cited by 1,859
Early infancy microbial and metabolic alterations affect risk of childhood asthma
Arrieta, M., Stiemsma, L. T., Dimitriu, P. A., Thorson, L., Russell, S., Yurist‐Doutsch, S., Kuzeljevic, B., Gold, M. J., Britton, H. M., Lefebvre, D. L., et al. (2015) · Science Translational Medicine · doi:10.1126/scitranslmed.aab2271 · Cited by 1,832
Chong, J., Liu, P., Zhou, G., & Xia, J. (2020) · Nature Protocols · doi:10.1038/s41596-019-0264-1 · Cited by 1,708
De Filippis, F., Pellegrini, N., Vannini, L., Jeffery, I. B., La Storia, A., Laghi, L., Serrazanetti, D. I., Di Cagno, R., Ferrocino, I., Lazzi, C., et al. (2016) · Gut · doi:10.1136/gutjnl-2015-309957 · Cited by 1,638
Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens
Pritchard, L., Glover, R. H., Humphris, S. N., Elphinstone, J. G., & Toth, I. K. (2015) · Analytical Methods · doi:10.1039/c5ay02550h · Cited by 1,597
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Self-citationKostic, A. D., Gevers, D., Siljander, H., Vatanen, T., Hyötyläinen, T., Hämäläinen, A., Peet, A., Tillmann, V., Pöhö, P., Mattila, I. M., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.01.001 · Cited by 1,198
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Fujimura, K. E., Sitarik, A. R., Havstad, S. L., Lin, D. L., Levan, S., Fadrosh, D. W., Panzer, A. R., LaMere, B. J., Rackaityte, E., Lukacs, N. W., et al. (2016) · Nature Medicine · doi:10.1038/nm.4176 · Cited by 1,198
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 1,142
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Carmody, R. N., Gerber, G. K., Luevano, J. M., Gatti, D. M., Somes, L., Svenson, K. L., & Turnbaugh, P. J. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2014.11.010 · Cited by 1,103
Collado, M. C., Rautava, S., Aakko, J., Isolauri, E., & Salminen, S. (2016) · Scientific Reports · doi:10.1038/srep23129 · Cited by 1,098
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Toju, H., Peay, K., Yamamichi, M., Narisawa, K., Hiruma, K., Naito, K., Fukuda, S., Ushio, M., Nakaoka, S., Onoda, Y., et al. (2018) · Nature Plants · doi:10.1038/s41477-018-0139-4 · Cited by 1,106
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Taberlet, P., Bonin, A., Zinger, L., & Coissac, É. (2018) · doi:10.1093/oso/9780198767220.001.0001 · Cited by 1,122
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Chen, C., Song, X., Wei, W., Zhong, H., Dai, J., Lan, Z., Li, F., Yu, X., Feng, Q., Wang, Z., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00901-0 · Cited by 1,010
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Deschasaux, M., Bouter, K. E., Prodan, A., Levin, E., Groen, A. K., Herrema, H., Tremaroli, V., Bakker, G. J., Attaye, I., Pinto-Sietsma, S.-J., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0160-1 · Cited by 695
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Coker, O. O., Dai, Z., Nie, Y., Zhao, G., Cao, L., Nakatsu, G., Wu, W. K., Wong, S. H., Chen, Z., Sung, J. J. Y., et al. (2018) · Gut · doi:10.1136/gutjnl-2017-314281 · Cited by 695
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-citationMicrobiome Helper: a Custom and Streamlined Workflow for Microbiome Research
Comeau, A., Douglas, G. M., & Langille, M. G. I. (2017) · mSystems · doi:10.1128/msystems.00127-16 · Cited by 703
Self-citationLiu, P., Wu, L., Peng, G., Han, Y., Tang, R., Ge, J., Zhang, L., Jia, L., Yue, S., Zhou, K., et al. (2019) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2019.05.008 · Cited by 669
Li, G., Xie, C., Lu, S., Nichols, R. G., Tian, Y., Li, L., Patel, D., Ma, Y., Brocker, C. N., Yan, T., et al. (2017) · Cell Metabolism · doi:10.1016/j.cmet.2017.08.019 · Cited by 667
Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice
Bárcena, C., Valdés-Mas, R., Mayoral, P., Garabaya, C., Durand, S., Rodríguez, F., Fernández-García, M. T., Salazar, N., Nogacka, A. M., Garatachea, N., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0504-5 · Cited by 661
An introduction to the analysis of shotgun metagenomic data
Sharpton, T. J. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00209 · Cited by 705
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Lee, M., & Chang, E. B. (2021) · Gastroenterology · doi:10.1053/j.gastro.2020.09.056 · Cited by 645
Nagpal, R., Neth, B. J., Wang, S., Craft, S., & Yadav, H. (2019) · EBioMedicine · doi:10.1016/j.ebiom.2019.08.032 · Cited by 653
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Newbold, C. J., de la Fuente, G., Belanche, A., Ramos-Morales, E., & McEwan, N. R. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01313 · Cited by 637
Bacterial community dynamics are linked to patterns of coral heat tolerance
Ziegler, M., Seneca, F., Yum, L. K., Palumbi, S. R., & Voolstra, C. R. (2017) · Nature Communications · doi:10.1038/ncomms14213 · Cited by 626
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Yoshida, N., Emoto, T., Yamashita, T., Watanabe, H., Hayashi, T., Tabata, T., Hoshi, N., Hatano, N., Ozawa, G., Sasaki, N., et al. (2018) · Circulation · doi:10.1161/circulationaha.118.033714 · Cited by 619
Zhao, Z., Ning, J., Bao, X.-Q., Shang, M., Ma, J., Li, G., & Zhang, D. (2021) · Microbiome · doi:10.1186/s40168-021-01107-9 · Cited by 616
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Bolnick, D. I., Snowberg, L. K., Hirsch, P. E., Lauber, C. L., Org, E., Parks, B. W., Lusis, A. J., Knight, R. D., Caporaso, J. G., & Svanbäck, R. (2014) · Nature Communications · doi:10.1038/ncomms5500 · Cited by 605
Self-citationChassaing, B., Van de Wiele, T., De Bodt, J., Marzorati, M., & Gewirtz, A. T. (2017) · Gut · doi:10.1136/gutjnl-2016-313099 · Cited by 590
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Rosa, P. S. L., Warner, B. B., Zhou, Y., Weinstock, G. M., Sodergren, E. J., Hall-Moore, C. M., Stevens, H. J., Bennett, W. E., Shaikh, N., Linneman, L. A., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1409497111 · Cited by 586
Zaneveld, J., Burkepile, D. E., Shantz, A. A., Pritchard, C. E., McMinds, R., Payet, J. P., Welsh, R. M., Correa, A. M. S., Lemoine, N. P., Rosales, S., et al. (2016) · Nature Communications · doi:10.1038/ncomms11833 · Cited by 589
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Wu, J., Peters, B. A., Dominianni, C., Zhang, Y., Pei, Z., Yang, L., Ma, Y., Purdue, M. P., Jacobs, E. J., Gapstur, S. M., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2016.37 · Cited by 572
Feng, X., Wang, Q., Sun, Y., Zhang, S., & Wang, F. (2021) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2021.127364 · Cited by 548
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Metcalf, J. L., Xu, Z. Z., Weiss, S. J., Lax, S. M., Treuren, W. V., Hyde, E. R., Song, S. J., Amir, A., Larsen, P. E., Sangwan, N., et al. (2015) · Science · doi:10.1126/science.aad2646 · Cited by 577
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Ainsworth, T. D., Krause, L., Bridge, T. C. L., Torda, G., Raina, J., Zakrzewski, M., Gates, R. D., Padilla‐Gamiño, J. L., Spalding, H. L., Smith, C. M., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.39 · Cited by 547
Zarrinpar, A., Chaix, A., Xu, Z. Z., Chang, M. W., Marotz, C. A., Saghatelian, A., Knight, R., & Panda, S. (2018) · Nature Communications · doi:10.1038/s41467-018-05336-9 · Cited by 546
Self-citationDai, Z., Coker, O. O., Nakatsu, G., Wu, W. K. K., Zhao, L., Chen, Z., Chan, F. K. L., Kristiansen, K., Sung, J. J. Y., Wong, S. H., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0451-2 · Cited by 545
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Carlson, A. L., Xia, K., Azcarate-Peril, M. A., Goldman, B. D., Ahn, M., Styner, M. A., Thompson, A. L., Geng, X., Gilmore, J. H., & Knickmeyer, R. C. (2018) · Biological Psychiatry · doi:10.1016/j.biopsych.2017.06.021 · Cited by 541
Bile Acid-Activated Receptors, Intestinal Microbiota, and the Treatment of Metabolic Disorders
Fiorucci, S., & Distrutti, E. (2015) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2015.09.001 · Cited by 539
Metadata
- Authors
- Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., Beiko, R. G., & Huttenhower, C.
- Affiliations
- Dalhousie University (CA)
- Oregon State University (US)
- Argonne National Laboratory (US)
- University of Colorado Boulder (US)
- University of Minnesota (US)
- Harvard University (US)
- Florida International University (US)
- Howard Hughes Medical Institute (US)
- Broad Institute (US)
- Corresponding author
- Huttenhower, Curtis
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2013-08-25
- Volume
- 31
- Issue
- 9
- Pages
- 814-821
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC3819121
- OpenAlex
- W2110300022
- Cited by
- 9,116
- References
- 49
- Citations by year
- 2026: 420 · 2025: 552 · 2024: 736 · 2023: 743 · 2022: 1094 · 2021: 1216 · 2020: 1171 · 2019: 1037 · 2018: 882 · 2017: 528 · 2016: 392 · 2015: 216 · 2014: 112 · 2013: 6
- FWCI
- 108.48
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Florida International University Digital Commons (Florida International University) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Crohn's and Colitis Foundation
- National Institutes of Health
- Canadian Institutes of Health Research
- National Human Genome Research Institute (U01HG004866, R01HG005969, R01HG004872)
- National Institute of General Medical Sciences (T32GM008759, T32GM080177, T32GM142607)
- National Institute of Diabetes and Digestive and Kidney Diseases (P01DK078669)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- PICRUSt, 16S rRNA, ancestral state reconstruction, Human Microbiome Project, reference genome, host-associated microbiota, environmental microbiota
- MeSH terms
- Bacteria, Genes, Bacterial, Genetic Markers, Humans, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Metagenomics, High-Throughput Nucleotide Sequencing, Microbiota
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