The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Open accessAbstract
We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.
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.
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?
The cited source says what the claim attributes to it.
In the citing paper
“Our results show that the multiple sequence alignment (MSA) obtained from BLS (Fig. 1b and Methods) improves microbial phylogeny inference compared to other alignment methods and enables improved UniFrac26 effect size estimation for many variables known to be important to human digestive health.”
From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [26]
In the citing paper
“Principal Coordinates Unweighted UniFrac analysis 20 showed separation of ileum and colon samples along the first component, whereas the two rooms clearly separated along PC2 on Food A (Fig1A and B).”
From The composition of the gut microbiota shapes the colon mucus barrier (2015) · cites this paper as [20]
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
Ecological Diversity and Its Measurement
Magurran, A. E. (1988) · Springer eBooks · doi:10.1007/978-94-015-7358-0 · Cited by 11,493
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,714
Measuring biological diversity
Magurran, A. E. (2004) · Choice Reviews Online · doi:10.5860/choice.42-1547 · Cited by 6,617
Obesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176
Self-citationA Molecular View of Microbial Diversity and the Biosphere
Pace, N. R. (1997) · Science · doi:10.1126/science.276.5313.734 · Cited by 2,797
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis
von Wintzingerode, F., Göbel, U. B., & Stackebrandt, E. S. (1997) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.1997.tb00351.x · Cited by 2,085
The RDP (Ribosomal Database Project)
Maidak, B. L., Olsen, G. J., Larsen, N. E., Overbeek, R., McCaughey, M. J., & Woese, C. R. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.109 · Cited by 2,018
The Uncultured Microbial Majority
Rappé, M. S., & Giovannoni, S. J. (2003) · Annual Review of Microbiology · doi:10.1146/annurev.micro.57.030502.090759 · Cited by 2,017
Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity
Hughes, J. B., Hellmann, J. J., Ricketts, T. H., & Bohannan, B. J. M. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.10.4399-4406.2001 · Cited by 1,337
The RDP-II (Ribosomal Database Project)
Maidak, B. L. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.173 · Cited by 1,180
Cited by
Sorted by citations
Items 301–400 of 1,061
Intestinal Microbial Ecology in Premature Infants Assessed with Non–Culture-Based Techniques
Mshvildadze, M., Neu, J., Shuster, J. J., Theriaque, D. W., Li, N., & Mai, V. (2009) · The Journal of Pediatrics · doi:10.1016/j.jpeds.2009.06.063 · Cited by 367
Bacterial colonization and succession in a newly opened hospital
Lax, S. M., Sangwan, N., Smith, D. P., Larsen, P. E., Handley, K. M., Richardson, M., Guyton, K. L., Krezalek, M. A., Shogan, B. D., DeFazio, J. R., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aah6500 · Cited by 367
Self-citationSimilarity of the dog and human gut microbiomes in gene content and response to diet
Coelho, L. P., Kultima, J. R., Costea, P. I., Fournier, C., Pan, Y., Czarnecki-Maulden, G. L., Hayward, M. R., Forslund, S. K., Schmidt, T., Descombes, P., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0450-3 · Cited by 380
Gut microbiome composition may be an indicator of preclinical Alzheimer’s disease
Ferreiro, A. L., Choi, J., Ryou, J., Newcomer, E. P., Thompson, R., Bollinger, R. M., Hall-Moore, C. M., Ndao, I. M., Sax, L., Benzinger, T. L. S., et al. (2023) · Science Translational Medicine · doi:10.1126/scitranslmed.abo2984 · Cited by 384
Sinclair, L., Osman, O. A., Bertilsson, S., & Eiler, A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0116955 · Cited by 385
Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments
Berg, M., Stenuit, B. A., Ho, J., Wang, A., Parke, C. D., Knight, M., Alvarez‐Cohen, L., & Shapira, M. (2016) · The ISME Journal · doi:10.1038/ismej.2015.253 · Cited by 355
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics
Escobar‐Zepeda, A., de León, A. V., & Sánchez‐Flores, A. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00348 · Cited by 397
Altered Mucosal Microbiome Diversity and Disease Severity in Sjögren Syndrome
de Paiva, C. S., Jones, D. B., Stern, M. E., Bian, F., Moore, Q. L., Corbiere, S., Streckfus, C. F., Hutchinson, D. S., Ajami, N. J., Petrosino, J. F., et al. (2016) · Scientific Reports · doi:10.1038/srep23561 · Cited by 371
Fachi, J. L., Felipe, J. D. S., Pral, L. P., da Silva, B. K., Corrêa, R. O., de Andrade, M. C. P., da Fonseca, D. M., Basso, P. J., Câmara, N. O. S., de Sales e Souza, É. L., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.054 · Cited by 364
Bacteria from Diverse Habitats Colonize and Compete in the Mouse Gut
Seedorf, H., Griffin, N. W., Ridaura, V. K., Reyes, A., Cheng, J., Rey, F. E., Smith, M. I., Simon, G. M., Scheffrahn, R. H., Woebken, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.008 · Cited by 364
Self-citationBajer, L., Kverka, M., Kostovčík, M., Mačinga, P., Dvořák, J., Stehlíková, Z., Březina, J., Wohl, P., Špičák, J., & Drastich, P. (2017) · World Journal of Gastroenterology · doi:10.3748/wjg.v23.i25.4548 · Cited by 376
Smith, C. C. R., Snowberg, L. K., Caporaso, J. G., Knight, R. D., & Bolnick, D. I. (2015) · The ISME Journal · doi:10.1038/ismej.2015.64 · Cited by 343
Self-citationKers, J. G., & Saccenti, E. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.796025 · Cited by 359
Kim, M., Morrison, M., & Yu, Z. (2010) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2010.10.020 · Cited by 393
Towards diagnostic guidelines for biofilm-associated infections
Hall‐Stoodley, L., Stoodley, P., Kathju, S., Høiby, N., Moser, C. E., Costerton, J. W., Moter, A., & Bjarnsholt, T. (2012) · FEMS Immunology & Medical Microbiology · doi:10.1111/j.1574-695x.2012.00968.x · Cited by 366
Molecular cartography of the human skin surface in 3D
Bouslimani, A., Porto, C., Rath, C. M. B., Wang, M., Guo, Y., González, A., Berg-Lyons, D., Ackermann, G. L., Christensen, G. J. M., Nakatsuji, T., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1424409112 · Cited by 365
Self-citationRethinking microbial diversity analysis in the high throughput sequencing era
Lemos, L. N., Fulthorpe, R. R., Triplett, E. W., & Roesch, L. F. W. (2011) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2011.03.014 · Cited by 373
Cui, E., Wu, Y., Zuo, Y., & Chen, H. (2015) · Bioresource Technology · doi:10.1016/j.biortech.2015.12.030 · Cited by 352
Yan, M., Pamp, S. J., Fukuyama, J., Hwang, P. H., Cho, D.-Y., Holmes, S., & Relman, D. A. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.11.005 · Cited by 351
Microbiota regulate social behaviour via stress response neurons in the brain
Wu, W., Adame, M. D., Liou, C.-W., Barlow, J. T., Lai, T.-T., Sharon, G., Schretter, C. E., Needham, B. D., Wang, M., Tang, W., et al. (2021) · Nature · doi:10.1038/s41586-021-03669-y · Cited by 351
Short-Term Effect of Antibiotics on Human Gut Microbiota
Panda, S., khader, I. E., Casellas, F., Vivancos, J., Cors, M. G., Santiago, A., Cuenca, S., Guarner, F., & Manichanh, C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0095476 · Cited by 364
Charlson, E. S., Diamond, J. M., Bittinger, K., Fitzgerald, A. S., Yadav, A., Haas, A. R., Bushman, F. D., & Collman, R. G. (2012) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201204-0693oc · Cited by 348
Rausch, P., Rehman, A., Künzel, S., Häsler, R., Ott, S. J., Schreiber, S., Rosenstiel, P. C., Franke, A., & Baines, J. F. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1106408108 · Cited by 351
Convergence of gut microbiomes in myrmecophagous mammals
Delsuc, F., Metcalf, J. L., Parfrey, L. W., Song, S. J., González, A., & Knight, R. D. (2013) · Molecular Ecology · doi:10.1111/mec.12501 · Cited by 350
Self-citationIntestinal epithelial vitamin D receptor deletion leads to defective autophagy in colitis
Wu, S., Zhang, Y., Lu, R., Xia, Y., Zhou, D., Petrof, E. O., Claud, E. C., Chen, D., Chang, E. B., Carmeliet, G., et al. (2014) · Gut · doi:10.1136/gutjnl-2014-307436 · Cited by 353
Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization
Chang, H.-W., Yan, D., Singh, R., Liu, J., Lu, X., Uçmak, D., Lee, K. M., Afifi, L., Fadrosh, D. W., Leech, J. M., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0533-1 · Cited by 363
Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes
Dunn, R. R., Fierer, N., Henley, J. B., Leff, J., & Menninger, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064133 · Cited by 354
Intestinal microbiota associated with differential feed conversion efficiency in chickens
Stanley, D., Denman, S. E., Hughes, R. J., Geier, M. S., Crowley, T. M., Chen, H., Haring, V. R., & Moore, R. J. (2012) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-011-3847-5 · Cited by 312
Jalanka-Tuovinen, J., Salojärvi, J., Salonen, A., Immonen, O., Garsed, K., Kelly, F. M., Zaitoun, A., Palva, A., Spiller, R. C., & de Vos, W. M. (2014) · Gut · doi:10.1136/gutjnl-2013-305994 · Cited by 340
Zhao, N., Chen, J., Carroll, I. M., Ringel-Kulka, T., Epstein, M. P., Zhou, H., Zhou, J. J., Ringel, Y., Li, H., & Wu, M. C. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.04.003 · Cited by 306
Gajardo, K., Rodiles, A., Kortner, T. M., Krogdahl, Å., Bakke, A. M., Merrifield, D. L., & Sørum, H. R. (2016) · Scientific Reports · doi:10.1038/srep30893 · Cited by 350
Meta-analysis To Define a Core Microbiota in the Swine Gut
Holman, D. B., Brunelle, B. W., Trachsel, J., & Allen, H. K. (2017) · mSystems · doi:10.1128/msystems.00004-17 · Cited by 360
Strickland, M. S., Osburn, E. D., Lauber, C. L., Fierer, N., & Bradford, M. A. (2008) · Functional Ecology · doi:10.1111/j.1365-2435.2008.01515.x · Cited by 337
Integrated biogeography of planktonic and sedimentary bacterial communities in the Yangtze River
Liu, T., Zhang, A., Wang, J., Liu, S., Jiang, X., Dang, C., Ma, T., Liu, S., Chen, Q., Xie, S., et al. (2018) · Microbiome · doi:10.1186/s40168-017-0388-x · Cited by 332
Reshaping the gut microbiome with bacterial transplantation and antibiotic intakePreprint
Manichanh, C., Reeder, J., Gibert, P., Varela, E., Llopis, M., Antolı́n, M., Guigó, R., Knight, R. D., & Guarner, F. (2010) · Genome Research · doi:10.1101/gr.107987.110 · Cited by 338
Self-citationComparative Gut Microbiota of 59 Neotropical Bird Species
Hird, S. M., Sánchez, C., Carstens, B. C., & Brumfield, R. T. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01403 · Cited by 342
Angelberger, S., Reinisch, W., Makristathis, A., Lichtenberger, C., Dejaco, C., Papay, P., Novacek, G., Trauner, M., Loy, A., & Berry, D. (2013) · American Journal of Gastroenterology · doi:10.1038/ajg.2013.257 · Cited by 330
Berry, D., Schwab, C., Milinovich, G. J., Reichert, J., Mahfoudh, K. B., Decker, T., Engel, M., Hai, B., Hainzl, E., Heider, S., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.39 · Cited by 337
Yu, E. W.-Y., Gao, L., Stastka, P., Cheney, M. C., Mahabamunuge, J., Soto, M. T., Ford, C. B., Bryant, J. A., Henn, M. R., & Hohmann, E. L. (2020) · PLoS Medicine · doi:10.1371/journal.pmed.1003051 · Cited by 346
Long-term maintenance of species-specific bacterial microbiota in the basal metazoan Hydra
Fraune, S., & Bosch, T. C. G. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0703375104 · Cited by 331
Epibacterial community patterns on marine macroalgae are host‐specific but temporally variable
Lachnit, T., Meske, D. S., Wahl, M., Harder, T., & Schmitz, R. A. (2010) · Environmental Microbiology · doi:10.1111/j.1462-2920.2010.02371.x · Cited by 343
Tipping elements in the human intestinal ecosystem
Lahti, L., Salojärvi, J., Salonen, A., Scheffer, M., & de Vos, W. M. (2014) · Nature Communications · doi:10.1038/ncomms5344 · Cited by 336
Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome
Maier, T. V., Lucio, M., Lee, L. H., VerBerkmoes, N. C., Brislawn, C. J., Bernhardt, J., Lamendella, R., McDermott, J. E., Bergeron, N., Heinzmann, S. S., et al. (2017) · mBio · doi:10.1128/mbio.01343-17 · Cited by 316
Self-citationChassaing, B., Ley, R. E., & Gewirtz, A. T. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.08.033 · Cited by 326
Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone
Ganesh, S., Parris, D. J., DeLong, E. F., & Stewart, F. J. (2013) · The ISME Journal · doi:10.1038/ismej.2013.144 · Cited by 324
Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data
Rosa, P. S. L., Brooks, J. P., Deych, E., Boone, E. L., Edwards, D., Wang, Q., Sodergren, E. J., Weinstock, G. M., & Shannon, W. D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0052078 · Cited by 325
Microbial Biogeography of Public Restroom Surfaces
Flores, G. E., Bates, S. T., Knights, D., Lauber, C. L., Stombaugh, J., Knight, R. D., & Fierer, N. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028132 · Cited by 343
Self-citationAirway microbiome dynamics in exacerbations of chronic obstructive pulmonary disease
Huang, Y. J., Sethi, S., Murphy, T., Nariya, S., Boushey, H. A., & Lynch, S. V. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.00035-14 · Cited by 323
Zhou, X., Baumann, R., Gao, X., Mendoza, M., Singh, S., Sand, I. K., Xia, Z., Cox, L. M., Chitnis, T., Yoon, H., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.021 · Cited by 326
Self-citationIt's all relative: analyzing microbiome data as compositions
Gloor, G. B., Wu, J. R., Pawlowsky-Glahn, V., & Egozcue, J. J. (2016) · Annals of Epidemiology · doi:10.1016/j.annepidem.2016.03.003 · Cited by 323
Bile acid is a significant host factor shaping the gut microbiome of diet-induced obese mice
Zheng, X., Huang, F., Zhao, A., Lei, S., Zhang, Y., Xie, G., Chen, T., Qu, C., Rajani, C., Dong, B., et al. (2017) · BMC Biology · doi:10.1186/s12915-017-0462-7 · Cited by 323
Liu, X., Shao, L., Liu, X., Ji, F., Mei, Y., Cheng, Y., Liu, F., Yan, C., Li, L., & Ling, Z. (2018) · EBioMedicine · doi:10.1016/j.ebiom.2018.12.034 · Cited by 329
Comparative analyses of the bacterial microbiota of the human nostril and oropharynx
Lemon, K. P., Klepac-Ceraj, V., Schiffer, H. K., Brodie, E. L., Lynch, S. V., & Kolter, R. (2010) · mBio · doi:10.1128/mbio.00129-10 · Cited by 322
Gerassy-Vainberg, S., Blatt, A., Danin‐Poleg, Y., Gershovich, K., Sabo, E., Nevelsky, A., Daniel, S., Dahan, A., Ziv, O., Dheer, R., et al. (2017) · Gut · doi:10.1136/gutjnl-2017-313789 · Cited by 331
Freedberg, D. E., Toussaint, N. C., Chen, S. P., Ratner, A. J., Whittier, S., Wang, T. C., Wang, H. H., & Abrams, J. A. (2015) · Gastroenterology · doi:10.1053/j.gastro.2015.06.043 · Cited by 322
A phylogenetic transform enhances analysis of compositional microbiota data
Silverman, J. D., Washburne, A., Mukherjee, S., & David, L. A. (2017) · eLife · doi:10.7554/elife.21887 · Cited by 321
Taxonomic structure and functional association of foxtail millet root microbiome
Jin, T., Wang, Y., Huang, Y., Xu, J. H., Zhang, P., Wang, N., Liu, X., Chu, H., Liu, G., Jiang, H., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix089 · Cited by 319
Zhou, Y., Xu, Z. Z., He, Y., Yang, Y., Liu, L., Lin, Q., Nie, Y., Li, M., Zhi, F., Liu, S., et al. (2018) · mSystems · doi:10.1128/msystems.00188-17 · Cited by 327
Self-citationq2-longitudinal: Longitudinal and Paired-Sample Analyses of Microbiome Data
Bokulich, N. A., Dillon, M. R., Zhang, Y., Rideout, J. R., Bolyen, E. K., Li, H., Albert, P. S., & Caporaso, J. G. (2018) · mSystems · doi:10.1128/msystems.00219-18 · Cited by 331
Gacias, M., Gaspari, S., Santos, P.-M. G., Tamburini, S., Andrade, M., Zhang, F., Shen, N., Tolstikov, V., Kiebish, M. A., Dupree, J. L., et al. (2016) · eLife · doi:10.7554/elife.13442 · Cited by 308
16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain
Emery, D. C., Shoemark, D. K., Batstone, T. E., Waterfall, C. M., Coghill, J. A., Cerajewska, T. L., Davies, M., West, N. X., & Allen, S. J. (2017) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2017.00195 · Cited by 317
Middelbos, I. S., Boler, B. M. V., Qu, A., White, B. A., Swanson, K. S., & Fahey, G. C., Jr. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009768 · Cited by 343
Seasonal Community Succession of the Phyllosphere Microbiome
Copeland, J. K., Yuan, L., Layeghifard, M., Wang, P. W., & Guttman, D. S. (2015) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi-10-14-0331-fi · Cited by 317
Cano-Gamez, K., Soskic, B., Roumeliotis, T. I., So, E., Smyth, D. J., Baldrighi, M., Willé, D., Nakic, N., Esparza-Gordillo, J., Larminie, C. G. C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15543-y · Cited by 274
Hakozaki, T., Richard, C., Elkrief, A., Hosomi, Y., Benlaïfaoui, M., Mimpen, I., Terrisse, S., Derosa, L., Zitvogel, L., Routy, B., et al. (2020) · Cancer Immunology Research · doi:10.1158/2326-6066.cir-20-0196 · Cited by 316
Uribe-Herranz, M., Rafail, S., Beghi, S., Gil-de-Gómez, L., Verginadis, I., Bittinger, K., Pustylnikov, S., Pierini, S., Perales-Linares, R., Blair, I. A., et al. (2019) · Journal of Clinical Investigation · doi:10.1172/jci124332 · Cited by 316
Ubeda, C., Lipuma, L., Gobourne, A., Viale, A., Leiner, I., Equinda, M., Khanin, R., & Pamer, E. G. (2012) · Journal of Experimental Medicine · doi:10.1084/jem.20120504 · Cited by 310
Mack, I., Cuntz, U., Grämer, C., Niedermaier, S., Pohl, C., Schwiertz, A., Zimmermann, K., Zipfel, S., Enck, P., & Penders, J. (2016) · Scientific Reports · doi:10.1038/srep26752 · Cited by 313
Maternal IgG and IgA Antibodies Dampen Mucosal T Helper Cell Responses in Early Life
Koch, M. A., Reiner, G. L., Lugo, K. A., Kreuk, L. S. M., Stanbery, A. G., Ansaldo, E., Seher, T. D., Ludington, W. B., & Barton, G. M. (2016) · Cell · doi:10.1016/j.cell.2016.04.055 · Cited by 315
Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., & Singh, U. (2013) · PLoS ONE · doi:10.1371/journal.pone.0053838 · Cited by 314
Heart Failure is Associated with Depletion of Core Intestinal Microbiota
Luedde, M., Winkler, T., Heinsen, F., Rühlemann, M. C., Spehlmann, M. E., Bajrovic, A., Lieb, W., Franke, A., Ott, S. J., & Frey, N. (2017) · ESC Heart Failure · doi:10.1002/ehf2.12155 · Cited by 317
The Human Microbiome and Its Potential Importance to Pediatrics
Johnson, C. L., & Versalovic, J. A. (2012) · PEDIATRICS · doi:10.1542/peds.2011-2736 · Cited by 317
The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites
Ursell, L. K., Clemente, J. C., Rideout, J. R., Gevers, D., Caporaso, J. G., & Knight, R. D. (2012) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2012.03.010 · Cited by 320
Self-citationLiu, J., Sui, Y., Yu, Z., Shi, Y., Chu, H., Jin, J., Liu, X., & Wang, G. (2015) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2015.01.009 · Cited by 310
Dynamics of Gut Microbiota in Autoimmune Lupus
Zhang, H., Liao, X., Sparks, J. B., & Luo, X. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.02676-14 · Cited by 308
Kieffer, D. A., Piccolo, B. D., Vaziri, N. D., Liu, S., Lau, W. L., Khazaeli, M., Nazertehrani, S., Moore, M. E., Marco, M. L., Martin, R. J., et al. (2016) · American Journal of Physiology-Renal Physiology · doi:10.1152/ajprenal.00513.2015 · Cited by 308
Burrello, C., Garavaglia, F., Cribiù, F. M., Ercoli, G., Lopez, G., Troisi, J., Colucci, A., Guglietta, S., Carloni, S., Guglielmetti, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07359-8 · Cited by 315
Shakya, M., Gottel, N., Castro, H. F., Yang, Z. K., Gunter, L. E., Labbé, J., Muchero, W., Bonito, G. M., Vilgalys, R. J., Tuskan, G. A., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0076382 · Cited by 317
LotuS: an efficient and user-friendly OTU processing pipeline
Hildebrand, F., Tadeo, R., Voigt, A. Y., Bork, P., & Raes, J. (2014) · Microbiome · doi:10.1186/2049-2618-2-30 · Cited by 321
Endothelial TLR4 and the microbiome drive cerebral cavernous malformations
Tang, A. T., Choi, J. P., Kotzin, J. J., Yang, Y., Hong, C. C., Hobson, N., Girard, R., Zeineddine, H. A., Lightle, R., Moore, T., et al. (2017) · Nature · doi:10.1038/nature22075 · Cited by 306
Kleiman, S. C., Watson, H. J., Bulik-Sullivan, E. C., Huh, E. Y., Tarantino, L. M., Bulik, C. M., & Carroll, I. M. (2015) · Psychosomatic Medicine · doi:10.1097/psy.0000000000000247 · Cited by 303
Bowers, R. M., Lauber, C. L., Wiedinmyer, C., Hamady, M., Hallar, A. G., Fall, R., Knight, R. D., & Fierer, N. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.00447-09 · Cited by 322
Self-citationExposure of Soil Microbial Communities to Chromium and Arsenic Alters Their Diversity and Structure
Sheik, C. S., Mitchell, T. W., Rizvi, F. Z., Rehman, Y., Faisal, M., Hasnain, S., McInerney, M. J., & Krumholz, L. R. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040059 · Cited by 301
Haro, C., Montes-Borrego, M., Rangel-Zúñiga, O. A., Alcala-Diaz, J. F., Gómez-Delgado, F., Pérez‐Martínez, P., Delgado‐Lista, J., Quintana‐Navarro, G. M., Tinahones, F. J., Landa, B. B., et al. (2015) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2015-3351 · Cited by 309
Allali, I., Arnold, J. W., Roach, J., Cadenas, M. B., Butz, N., Hassan, H. M., Koci, M., Ballou, A., Mendoza, M., Ali, R., et al. (2017) · BMC Microbiology · doi:10.1186/s12866-017-1101-8 · Cited by 298
Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque
Yasuda, K., Oh, K., Ren, B., Tickle, T. L., Franzosa, E. A., Wachtman, L. M., Miller, A. D., Westmoreland, S. V., Mansfield, K. G., Vallender, E. J., et al. (2015) · Cell Host & Microbe · doi:10.1016/j.chom.2015.01.015 · Cited by 298
Mutlu, E., Comba, I. Y., Cho, T., Engen, P. A., Yazıcı, C., Soberanes, S., Hamanaka, R. B., Niğdelioğlu, R., Meliton, A. Y., Ghio, A. J., et al. (2018) · Environmental Pollution · doi:10.1016/j.envpol.2018.04.130 · Cited by 309
Kolton, M., Gräber, E. R., Tsehansky, L., Elad, Y., & Cytryn, E. J. (2016) · New Phytologist · doi:10.1111/nph.14253 · Cited by 303
The microbiome beyond the horizon of ecological and evolutionary theory
Koskella, B. L., Hall, L. J., & Metcalf, C. J. E. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0340-2 · Cited by 292
An introduction to phylosymbiosis
Lim, S. J., & Bordenstein, S. R. (2020) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2019.2900 · Cited by 298
Nemergut, D. R., Townsend, A. R., Sattin, S. R., Freeman, K. R., Fierer, N., Neff, J. C., Bowman, W. D., Schadt, C. W., Weintraub, M. N., & Schmidt, S. K. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01735.x · Cited by 297
Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants
Bokulich, N. A., & Mills, D. A. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00934-13 · Cited by 295
Microbial Diversity in the Deep Sea and the Underexplored “Rare Biosphere”
Welch, D. B. M., & Huse, S. M. (2011) · doi:10.1002/9781118010549.ch24 · Cited by 295
Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation
Crawford, P. A., Crowley, J. R., Sambandam, N., Muegge, B. D., Costello, E. K., Hamady, M., Knight, R., & Gordon, J. I. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902366106 · Cited by 278
Self-citationEun, C. S., Kim, B. K., Han, D. S., Kim, S., Kim, K. M., Choi, B. Y., Song, K. S., Kim, Y. S., & Kim, J. F. (2014) · Helicobacter · doi:10.1111/hel.12145 · Cited by 292
Minter, M. R., Hinterleitner, R., Meisel, M., Zhang, C., Leone, V., Zhang, X., Oyler-Castrillo, P., Zhang, X., Musch, M. W., Shen, X., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-11047-w · Cited by 292
Diversity and seasonal dynamics of bacterial community in indoor environment
Rintala, H., Pitkäranta, M., Toivola, M., Paulin, L. G., & Nevalainen, A. I. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-56 · Cited by 291
Skin microbiome: genomics-based insights into the diversity and role of skin microbes
Kong, H. H. (2011) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2011.01.013 · Cited by 293
Determinants of bacterial communities in C anadian agroforestry systems
Banerjee, S., Baah‐Acheamfour, M., Carlyle, C. N., Bissett, A. B., Richardson, A. E., Siddique, T., Bork, E. W., & Chang, S. X. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.12986 · Cited by 300
Tarr, A. J., Galley, J. D., Fisher, S. E., Chichlowski, M., Berg, B. M., & Bailey, M. T. (2015) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2015.06.025 · Cited by 284
Metadata
- Authors
- Lozupone, C., & Knight, R.
- Affiliations
- University of Colorado Boulder (US)
- Corresponding author
- Knight, Rob
- Venue
- Applied and Environmental Microbiology
- Publisher
- American Society for Microbiology
- Published
- 2005-12
- Volume
- 71
- Issue
- 12
- Pages
- 8228-8235
- ISSN
- 0099-2240 (ISSN-L)
- 1098-5336
- PMC
- PMC1317376
- OpenAlex
- W2170024099
- Cited by
- 8,227
- References
- 48
- Citations by year
- 2026: 311 · 2025: 420 · 2024: 500 · 2023: 564 · 2022: 681 · 2021: 832 · 2020: 766 · 2019: 654 · 2018: 676 · 2017: 607 · 2016: 508 · 2015: 401 · 2014: 363 · 2013: 281 · 2012: 210
- FWCI
- 31.33
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Applied and Environmental Microbiology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (T32-GM08759, T32GM008759, T32GM142607)
- Topics
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Polar Research and Ecology
- Keywords
- UniFrac, phylogenetic distance, microbial community comparison, 16S rRNA gene library, bacterial communities, community clustering, ordination, sea ice bacteria, marine sediment bacteria, marine bacteria
- MeSH terms
- Bacteria, Genetic Techniques, Geography, Phylogeny, RNA, Ribosomal, 16S
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
