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Strains, functions and dynamics in the expanded Human Microbiome Project
Open accessAbstract
The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity and enables an understanding of personalized microbiome function and dynamics.
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“Comparative genomic analyses usually test for correlations between traits.”
From A phylogenetic approach to comparative genomics (2025) · cites this paper as [77]
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“While our inherited genome is essentially stable for the lifetime of the host, the microbiome is immensely diverse (Mosca et al., 2016;Pasolli et al., 2019), dynamic (Lloyd-Price et al., 2017), and responsive to external input, enhancing its potential as a target for therapeutic intervention”
From The Microbiota-Gut-Brain Axis (2019) · cites this paper as Lloyd-Price et al., 2017
In the citing paper
“Despite the low number of samples, these results suggest that the environment has more influence on the gut microbiome than the pathological condition, which is in accordance with recent findings 22,23 .”
From Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice (2019) · cites this paper as [23]
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“Most of the bacterial communities found in the tumoral milieu are present commonly in the gut microbiome (Human Microbiome Project, 2012b; Lloyd-Price et al., 2017)”
From Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes (2019) · cites this paper as Lloyd-Price et al., 2017
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“Studies of both a baseline adult population21–23 and ‘demonstration’ populations with specific disease states established typical ranges (for some populations) of microbial membership and enzymatic repertoires across the body, combinations of metabolic functions that were either prevalent or strain-specific, and some of the host factors (such as race or ethnicity) that determine this variation.”
From The Integrative Human Microbiome Project (2019) · cites this paper as [23]
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Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
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-citationKimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 26,312
Search and clustering orders of magnitude faster than BLAST
Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098
Inference from iterative simulation using multiple sequences
Gelman, A., & Rubin, D. B. (1992) · Statistical Science · doi:10.1214/ss/1177011136 · Cited by 16,627
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
A human gut microbial gene catalogue established by metagenomic sequencing
MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,587
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858
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Metaproteomics of human microbiota: Progress and key challenges for precision medicine
Feng, Y., Liu, D., Chen, Y., Zhang, W., & He, Y. (2025) · Process Biochemistry · doi:10.1016/j.procbio.2025.05.013 · Cited by 3
Missing Mess and Strange Agencies in Online Images of Mind-Microbiome Connections
Whiteley, L., Nygaard, N., & Glerup, C. (2025) · Engaging Science Technology and Society · doi:10.17351/ests2023.1605 · Cited by 3
McDonald, J. E., Harris, R. N., Doonan, J., Carryl, S. S., Sze, M. A., McKenzie, V. J., & Gilbert, J. A. (2020) · Cambridge University Press eBooks · doi:10.1017/9781108654418.007 · Cited by 3
Microbiome Diagnostics and Interventions in Health and Disease
Dasgupta, N., Srivastava, A., Rao, A., Murugkar, V., Shroff, R., & Das, G. (2021) · Springer eBooks · doi:10.1007/978-981-16-3156-6_10 · Cited by 3
Patient-derived pathogenic microbe deposition enhances exposure risk in pediatric clinics
Wang, W., Qiu, Z., Li, H., Wu, X., Cui, Y., Xie, L., Chang, B., Li, P., Zeng, H., & Ding, T. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.171703 · Cited by 3
Ancient DNA and paleoproteomic analysis on Roman Imperial-era individuals from Histria, Romania
Wright, S., Rayfield, K. M., Singleton, R. R., Hughes, K., Soficaru, A., Creţu, C., Huang, L., Wu, S., Reinberger, K. L., Rabinowitz, A., et al. (2024) · Journal of Archaeological Science Reports · doi:10.1016/j.jasrep.2024.104510 · Cited by 5
Lei, S., Khan, I., Zhang, X., Chen, T., Xie, X., Zheng, X., Jianye, Z., & Li, Z. (2024) · BMC Oral Health · doi:10.1186/s12903-024-04603-0 · Cited by 3
Uniform bacterial genetic diversity along the gut
Wasney, M., Briscoe, L., Wolff, R., Ghezzi, H., Tropini, C., & Garud, N. R. (2026) · Nature Communications · doi:10.1038/s41467-026-70705-8 · Cited by 3
Gut-host Crosstalk: Methodological and Computational Challenges
Ivanov, I. V. (2020) · Digestive Diseases and Sciences · doi:10.1007/s10620-020-06105-9 · Cited by 3
Yang, Y., Wang, X., Xie, K., Zhu, C., Chen, N., & Chen, T. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.06.015 · Cited by 3
A tensor decomposition model for longitudinal microbiome studies
Ma, S., & Li, H. (2023) · The Annals of Applied Statistics · doi:10.1214/22-aoas1661 · Cited by 3
Human Endogenous Natural Products
Bai, Y., Zhang, L., & Lei, X. (2021) · Fortschritte der Chemie Organischer Naturstoffe/Fortschritte der Chemie organischer Naturstoffe/Progress in the chemistry of organic natural products · doi:10.1007/978-3-030-59444-2_4 · Cited by 3
The Gut Microbiome and Ankylosing Spondylitis
Sternes, P. R., & Brown, M. A. (2019) · Elsevier eBooks · doi:10.1016/b978-0-323-56800-5.00006-0 · Cited by 3
Vasconcelos, E. J. R., Roy, C., Geiger, J., Oney, K. M., Koo, M., Ren, S., Oakley, B. B., & Diniz, P. P. V. D. P. (2021) · BMC Veterinary Research · doi:10.1186/s12917-021-02969-9 · Cited by 3
The Oral Microbiome Bank of China
Peng, X., Zhou, X., Xu, X., Li, Y., Li, Y., Li, J., Su, X., Huang, S., Xu, J., & Liao, G. (2020) · Springer eBooks · doi:10.1007/978-981-15-7899-1_7 · Cited by 3
Macroecological dynamics of gut microbiotaPreprint
Ji, B. W., Sheth, R. U., Dixit, P. D., Tchourine, K., & Vitkup, D. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/370676 · Cited by 3
Mining the human tonsillar microbiota as autoimmune modulatorPreprint
Li, J., Li, S., Jin, J., Guo, R., Sun, X., Guo, J., Hu, F., Liu, Y., Jin, Y., Zhou, Y., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/719807 · Cited by 3
Fu, X., Norbäck, D., Li, Y., Meng, Y., Zhu, X., Yuan, Q., Wen, H., Ma’pol, A., Hashim, J. H., Hashim, Z. B., et al. (2020) · doi:10.22541/au.160279753.37398847/v1 · Cited by 3
Shahin, M., Ji, B. W., & Dixit, P. D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.18.436036 · Cited by 3
Li, W., Kielenniva, K., Kuelbs, C., Novotny, M. A., Kontiokari, T., Sarlin, S., Tejesvi, M. V., Nelson, K. E., & Tapiainen, T. (2022) · medRxiv · doi:10.1101/2022.04.08.22273642 · Cited by 3
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Mercier, B. D., Castro, D. V., & Pal, S. K. (2022) · European Urology Open Science · doi:10.1016/j.euros.2022.11.023 · Cited by 3
Duan, Q., Clegg, T., Smith, T. P., Bell, T., & Pawar, S. S. (2024) · Qeios · doi:10.32388/m1xfxl · Cited by 3
Proteomic scrutiny of nasal microbiomes: implications for the clinic
Zhu, K., Jin, Y., Zhao, Y., He, A., Wang, R., & Cao, C. (2024) · Expert Review of Proteomics · doi:10.1080/14789450.2024.2323983 · Cited by 2
Pilling, O. A., Sundararaman, S. A., Brisson, D., & Beiting, D. P. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012418 · Cited by 2
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Rosales, S. M., Bouchard, P. I., Olmstead, E. M., & Parthasarathy, R. (2025) · mSphere · doi:10.1128/msphere.00698-24 · Cited by 2
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Hushpulian, D. M., Nikulin, S. V., Zakhariants, A. A., Сергеевич, С. С., & Tishkov, V. I. (2024) · Applied Biochemistry and Microbiology · doi:10.1134/s0003683824700261 · Cited by 2
Roos, M., Bunga, S., Tan, A., Maissy, E. S., Skola, D., Richter, A., Whittaker, D. S., Desplats, P., Zarrinpar, A., Conrad, R., et al. (2025) · mSystems · doi:10.1128/msystems.00167-25 · Cited by 2
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Godoy‐Vitorino, F. (2025) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph22091322 · Cited by 2
Comprehensive safety assessment of the probiotic Streptococcus salivarius OSTIA SALI-10
Marks, C. B., Oveisi, M., Choi, Y. H. K., Glogauer, M., & Barbour, A. (2025) · Food and Chemical Toxicology · doi:10.1016/j.fct.2025.115741 · Cited by 2
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Wei, L., Yue, P., Mao, J., & Hu, Q. (2025) · Current Microbiology · doi:10.1007/s00284-025-04516-3 · Cited by 2
Peng, L., Yu, S., Dong, Y., Gu, H., Li, Z., Ai, C., Zhang, L., & Wu, X. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1639811 · Cited by 2
DHYANESH, R., SHREE, N., I., J., ALBERT, K. S., M., S. S., & S., V. P. (2025) · International Journal of Applied Pharmaceutics · doi:10.22159/ijap.2026v18i2.56700 · Cited by 2
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Llirós, M., Buxó, M., Virolés, S., Pujolassos, M., Serra, I., Martínez, J. C., Lluansí, A., Bahí, A., Calle, M. L., & Aldeguer, X. (2026) · Scientific Reports · doi:10.1038/s41598-026-42368-4 · Cited by 2
Li, D., Li, Y., Wang, X., Feng, Y., Liu, Y., Yang, C., Zhang, W., Wen, X., Liu, Z., Yin, W., et al. (2026) · npj Biofilms and Microbiomes · doi:10.1038/s41522-026-00954-4 · Cited by 2
Sprenger, G. A., Gee, J. E., Elrod, M. G., Weiner, Z. P., & Gulvik, C. A. (2026) · Microbiology Spectrum · doi:10.1128/spectrum.02926-25 · Cited by 2
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武法贵, Chen, Y., Ni, X., Yi, T., & Tan, S. (2026) · Frontiers in Medicine · doi:10.3389/fmed.2026.1810114 · Cited by 2
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Parolini, C., & Amedei, A. (2026) · Frontiers in Bioscience-Landmark · doi:10.31083/fbl47174 · Cited by 2
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Nemenman, I. M., & Mehta, P. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2526777123 · Cited by 3
Thompson, K. N., Ma, S., Bhosle, A., Nickols, W. A., Shen, J., Ghazi, A. R., Dang, N. H., Zhang, Y., Nzabarushimana, É., Kim, H., et al. (2026) · Gastroenterology · doi:10.1053/j.gastro.2026.06.023 · Cited by 2
Self-citationMa, Z. S., & Taylor, R. A. J. (2026) · Physics of Life Reviews · doi:10.1016/j.plrev.2026.08.001 · Cited by 2
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Ma, S., & Li, H. (2022) · Methods in molecular biology · doi:10.1007/978-1-0716-2986-4_11 · Cited by 2
Dissemination of Intestinal Microbiota by Migratory Birds across Geographical Borders
Kenzaka, T. (2019) · IntechOpen eBooks · doi:10.5772/intechopen.82707 · Cited by 2
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Vanni, C. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1099-2_8 · Cited by 2
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Galeota-Sprung, B., Bhatt, A. S., & de la Fuente‐Núñez, C. (2025) · Trends in Genetics · doi:10.1016/j.tig.2024.12.004 · Cited by 2
deepBreaks identifies and prioritizes genotype–phenotype associations using machine learning
Baghbanzadeh, M., Dawson, T., Sayoldin, B., Frazer, S. A., Oakley, T. H., Crandall, K. A., & Rahnavard, A. (2025) · Scientific Reports · doi:10.1038/s41598-025-25580-6 · Cited by 2
Appanna, V. D. (2018) · Springer eBooks · doi:10.1007/978-981-10-7684-8_4 · Cited by 2
Gu, X., Yu, T., Guo, T., & Kong, J. (2021) · Future Microbiology · doi:10.2217/fmb-2020-0269 · Cited by 2
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Aguinaldo, R. D., Solano, G. A., Pontiveros, M. J., & Balolong, M. P. (2021) · IEEE Region 10 Conference (TENCON) · doi:10.1109/tencon54134.2021.9707181 · Cited by 2
expam—high-resolution analysis of metagenomes using distance trees
Solari, S. M., Young, R. B., Marcelino, V. R., & Forster, S. C. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac591 · Cited by 2
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Zeng, M., Li, S., Lv, Q., Wang, X., Qadeer, A., & Mahmoud, M. H. (2024) · Frontiers in Veterinary Science · doi:10.3389/fvets.2024.1403920 · Cited by 2
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ROSENBERG, E. B. (2021) · The microbiomes of humans, animals, plants, and the environment · doi:10.1007/978-3-030-65317-0_5 · Cited by 2
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Fernández-Rodríguez, A., Gónzález‐Candelas, F., & Arora, N. (2021) · Springer eBooks · doi:10.1007/978-3-030-62155-1_12 · Cited by 2
Huang, W., & Zhang, W. (2020) · Springer eBooks · doi:10.1007/978-981-15-3895-7_10 · Cited by 2
Skillings, D., & Hooks, K. B. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-409548-9.10877-2 · Cited by 2
Mahmoudabadi, G., Homyk, K., Catching, A., Foley, H. B., Tadmor, A. D., Mahmoudabadi, A., Cheung, A., & Phillips, R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/516864 · Cited by 2
Lafargue, P. (2021) · UWE Research Repository (UWE Bristol) · Cited by 2
Wolf, P. G., Cowley, E. S., Breister, A. M., Matatov, S., Lucio, L., Polak, P., Ridlon, J. M., Gaskins, H. R., & Anantharaman, K. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.01.450790 · Cited by 2
Su, F., Liu, Z., Zou, L., Xu, X., Luo, Q., Li, H., Jia, W., Tang, M., Huang, Y., Zhao, Y., et al. (2020) · doi:10.21203/rs.2.20234/v1 · Cited by 2
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Anari, S. S. (2020) · doi:10.18174/532136 · Cited by 2
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Schroer, H. W., Beghini, F., Garay, J. A. R., Christakis, N. A., & Bosch, D. E. (2026) · mSystems · doi:10.1128/msystems.00305-26 · Cited by 1
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Hu, A., Yang, L., & Yan, J. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00548-4 · Cited by 1
Awad, N., Larson, P. J., Sissoko, C. A., Bond, L. L., & Dion, G. R. (2025) · Scientific Reports · doi:10.1038/s41598-025-11468-y · Cited by 1
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Mallick, H., Bardhan, M., Dagli, C. S., Liu, Z., & Gao, J. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-22376-1.00010-6 · Cited by 2
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Zhang, Y., Li, F., Zhang, X., Zhang, D., & Wang, W. (2025) · Animals · doi:10.3390/ani15182724 · Cited by 1
Purcell, E., Dowling, P., O’Gorman, P., & Bazou, D. (2025) · Blood Reviews · doi:10.1016/j.blre.2025.101360 · Cited by 1
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Zheng, W., Wu, C., Wang, Y., Yan, X., Han, W., Liu, X., He, C., Chen, X., Zhou, X., Zhang, L., et al. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117143 · Cited by 1
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Merkesvik, J., Lindstad, L. J., Umu, Ö. C. O., Sandholm, R. M., Rosa, S. L. L., Hvidsten, T. R., Pope, P. B., & Westereng, B. (2026) · Applied and Environmental Microbiology · doi:10.1128/aem.00140-26 · Cited by 1
Ni, Z., Xie, J., Zhang, Z., Zhang, K., Ding, J., Chang, M., Su, Y., Zhang, Y., Yao, M., Wang, C., et al. (2026) · iMeta · doi:10.1002/imt2.70148 · Cited by 1
Deng, Z., Huang, Y., Cao, K.-X., Peng, Z., Refaie, A., Khalil, M. M., Zhao, L., Guan, L. L., & Sun, L. (2026) · Microbiome · doi:10.1186/s40168-026-02461-2 · Cited by 1
Wang, H., Xu, J., Liang, K., Tian, Y., Cui, Z., & Zhang, J. (2026) · British Journal of Pharmacology · doi:10.1111/bph.70565 · Cited by 1
He, T., Zhang, S., Chen, J., Zheng, X., Zhao, J., Li, H., Mao, J., Luo, J., Zheng, J., Ma, D., et al. (2026) · iMetaOmics. · doi:10.1002/imo2.70133 · Cited by 1
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Stefanis, C., Tsigalou, C., Bezirtzoglou, I., Voidarou, C. C., & Stavropoulou, E. (2025) · Microorganisms · doi:10.3390/microorganisms13040725 · Cited by 1
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Enck, P., & Mazurak, N. (2019) · Zeitschrift für Gastroenterologie · doi:10.1055/a-0901-2558 · Cited by 1
Dehnow, A. H., & Krishna, M. S. (2020) · Advances in Zoology and Botany · doi:10.13189/azb.2020.080202 · Cited by 1
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Gitomer, S. A., & Ramakrishnan, V. R. (2020) · Springer eBooks · doi:10.1007/978-3-030-50330-7_1 · Cited by 1
Metadata
- Authors
- Lloyd-Price, J., Mahurkar, A., Rahnavard, G., Crabtree, J., Orvis, J., Hall, A. B., Brady, A., Creasy, H. H., McCracken, C., Giglio, M. G., McDonald, D., Franzosa, E. A., Knight, R., White, O., & Huttenhower, C.
- Affiliations
- University of Maryland, Baltimore (US)
- Broad Institute (US)
- University of California San Diego (US)
- Corresponding author
- Huttenhower, Curtis
- ORCID
- Venue
- Nature
- Published
- 2017-09-20
- Volume
- 550
- Issue
- 7674
- Pages
- 61-66
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC5831082
- OpenAlex
- W2756958651
- Cited by
- 1,267
- References
- 70
- Citations by year
- 2026: 91 · 2025: 126 · 2024: 150 · 2023: 108 · 2022: 165 · 2021: 195 · 2020: 160 · 2019: 168 · 2018: 91 · 2017: 10
- FWCI
- 47.89
- Type
- journal article
- Language
- en
- Update notices
- erratum (2017-10-12)
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- National Institutes of Health
- National Human Genome Research Institute (U54HG004969, U54HG003079, U01HG004866, U01HG006537, R01HG004872, U54HG004968, U54HG004973)
- National Institute of Allergy and Infectious Diseases (U54AI084844)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK102557, P30DK043351)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- human microbiome, metagenomics, Human Microbiome Project, microbial diversity, strain identification, phylogenetic diversity, functional profiling, pathway enrichment, temporal dynamics
- MeSH terms
- Humans, National Institutes of Health (U.S.), Organ Specificity, Phylogeny, Time Factors, United States, Metagenome, Molecular Sequence Annotation, Spatio-Temporal Analysis, Microbiota, Datasets as Topic
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