Cited by 8,227Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesPolar Research and Ecology

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 access

Lozupone, Catherine, Knight, Rob·2005·Applied and Environmental Microbiology

DOI 10.1128/aem.71.12.8228-8235.2005PMC PMC1317376

Open this paper in CoChat — free account

Abstract

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.

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

Crossref · 10.1128/aem.71.12.8228-8235.2005

Cites

48 of 48 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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-citation
A 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

Show all 48 references

Sorted by citations

Items 401–500 of 1,061

Pyrosequencing and mid-infrared spectroscopy reveal distinct aggregate stratification of soil bacterial communities and organic matter composition
Davinic, M., Fultz, L. M., Acosta‐Martínez, V., Calderón, F. J., Cox, S. B., Dowd, S. E., Allen, V. G., Zak, J. C., & Moore‐Kucera, J. (2011) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2011.11.012 · Cited by 290
Gut Microbiota in Human Systemic Lupus Erythematosus and a Mouse Model of Lupus
Luo, X., Edwards, M. R., Mu, Q., Yu, Y., Vieson, M. D., Reilly, C. M., Ahmed, S. A., & Bankole, A. A. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.02288-17 · Cited by 290
Prolonged drought imparts lasting compositional changes to the rice root microbiome
Santos‐Medellín, C., Liechty, Z., Edwards, J. A., Nguyen, B., Huang, B. C., Weimer, B. C., & Sundaresan, V. (2021) · Nature Plants · doi:10.1038/s41477-021-00967-1 · Cited by 293
Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis
Li, H. (2015) · Annual Review of Statistics and Its Application · doi:10.1146/annurev-statistics-010814-020351 · Cited by 288
Composition Diversity and Abundance of Gut Microbiome in Prediabetes and Type 2 Diabetes
Shah, V. O., Lambeth, S. M., Carson, T., Lowe, J. R., Ramaraj, T., Leff, J. W., Luo, L., & Bell, C. J. (2015) · Journal of Diabetes and Obesity · doi:10.15436/2376-0949.15.031 · Cited by 294
Influence of gender and menopausal status on gut microbiota
Santos-Marcos, J. A., Rangel-Zuñiga, O. A., Jimenez-Lucena, R., Quintana-Navarro, G. M., Garcia-Carpintero, S., Malagon, M. M., Landa, B. B., Tena-Sempere, M., Perez-Martinez, P., Lopez-Miranda, J., et al. (2018) · Maturitas · doi:10.1016/j.maturitas.2018.07.008 · Cited by 287
Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea
Lee, O. O., Wang, Y., Yang, J., Lafi, F. F., Al-Suwailem, A. M., & Qian, P. (2010) · The ISME Journal · doi:10.1038/ismej.2010.165 · Cited by 294
Diversity in gut bacterial community of school-age children in Asia
Nakayama, J., Watanabe, K., Jiang, J., Matsuda, K., Chao, S.-H., Haryono, P., La-ongkham, O., Sarwoko, M.-A., Sujaya, I. N., Zhao, L., et al. (2015) · Scientific Reports · doi:10.1038/srep08397 · Cited by 297
Association of exposure to formula in the hospital and subsequent infant feeding practices with gut microbiota and risk of overweight in the first year of life
Forbes, J. D., Azad, M. B., Vehling, L., Tun, H. M., Konya, T. B., Guttman, D. S., Field, C. J., Lefebvre, D., Sears, M. R., Becker, A. B., et al. (2018) · JAMA Pediatrics · doi:10.1001/jamapediatrics.2018.1161 · Cited by 285
Partitioning taxon, phylogenetic and functional beta diversity into replacement and richness difference components
Cardoso, P., François Rigal, A., Carvalho, J. C., Fortelius, M., Borges, P. A. V., Podani, J., & Schmera, D. (2013) · Journal of Biogeography · doi:10.1111/jbi.12239 · Cited by 283
Reintroducing mothur: 10 Years Later
Schloss, P. D. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.02343-19 · Cited by 298
Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants
Dong, C., Wang, L., Li, Q., & Shang, Q. (2019) · PLoS ONE · doi:10.1371/journal.pone.0223847 · Cited by 304
Spatial scale drives patterns in soil bacterial diversity
O'Brien, S. L., Gibbons, S. M., Owens, S. M., Hampton‐Marcell, J., Johnston, E. R., JASTROW, J. D., Gilbert, J. A., Meyer, F., & Antonopoulos, D. A. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13231 · Cited by 293
Abundant and rare picoeukaryotic sub‐communities present contrasting patterns in the epipelagic waters of marginal seas in the northwestern P acific O cean
Wu, W., Logares, R., Huang, B., & Hsieh, C. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13606 · Cited by 284
Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome
Labus, J. S., Hollister, E. B., Jacobs, J., Kirbach, K., Oezguen, N., Gupta, A., Acosta, J., Luna, R. A., Aagaard, K., Versalovic, J., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0260-z · Cited by 284
Pyrosequencing Reveals a Highly Diverse and Cultivar-Specific Bacterial Endophyte Community in Potato Roots
Manter, D. K., Delgado, J. A., Holm, D. G., & Stong, R. A. (2010) · Microbial Ecology · doi:10.1007/s00248-010-9658-x · Cited by 283
Human gut microbiota community structures in urban and rural populations in Russia
Tyakht, A., Kostryukova, E., Popenko, A., Belenikin, M. S., Pavlenko, A. V., Larin, A. K., Karpova, I. Y., Selezneva, O. V., Semashko, T. A., Ospanova, E. A., et al. (2013) · Nature Communications · doi:10.1038/ncomms3469 · Cited by 290
Functional diversity: an overview of its history and applicability
Laureto, L. M. O., Cianciaruso, M. V., & Samia, D. S. M. (2015) · Natureza & Conservação · doi:10.1016/j.ncon.2015.11.001 · Cited by 282
Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest
Nemergut, D. R., Cleveland, C. C., Wieder, W. R., Washenberger, C. L., & Townsend, A. R. (2010) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2010.08.011 · Cited by 281
Deep sequencing reveals extensive variation in the gut microbiota of wild mosquitoes from K enya
Osei‐Poku, J., Mbogo, C. M., Palmer, W. J., & Jiggins, F. M. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05759.x · Cited by 281
The Human Intestinal Microbiome: A New Frontier of Human Biology
Hattori, M., & Taylor, T. D. (2009) · DNA Research · doi:10.1093/dnares/dsn033 · Cited by 290
Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring
Ghannam, R. B., & Techtmann, S. M. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.01.028 · Cited by 289
Food or just a free ride? A meta-analysis reveals the global diversity of the Plastisphere
Wright, R., Langille, M. G. I., & Walker, T. R. (2020) · The ISME Journal · doi:10.1038/s41396-020-00814-9 · Cited by 289
Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior
Lukić, I., Getselter, D., Oren, Z., Oron, O., Reuveni, E., Koren, O., & Elliott, E. (2019) · Translational Psychiatry · doi:10.1038/s41398-019-0466-x · Cited by 283
Sex differences in gut microbiota in patients with major depressive disorder
Chen, J.-J., Zheng, P., Liu, Y.-Y., Zhong, X.-G., Wang, H.-Y., Guo, Y.-J., & Xie, P. (2018) · Neuropsychiatric Disease and Treatment · doi:10.2147/ndt.s159322 · Cited by 272
Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures
Schloss, P. D., & Handelsman, J. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.00474-06 · Cited by 272
Postprandial remodeling of the gut microbiota in Burmese pythons
Costello, E. K., Gordon, J. I., Secor, S. M., & Knight, R. D. (2010) · The ISME Journal · doi:10.1038/ismej.2010.71 · Cited by 275
Self-citation
Characteristic Male Urine Microbiomes Associate with Asymptomatic Sexually Transmitted Infection
Nelson, D. E., Pol, B. J. V. D., Dong, Q., Revanna, K. V., Fan, B., Easwaran, S., Sodergren, E. J., Weinstock, G. M., Diao, L., & Fortenberry, J. D. (2010) · PLoS ONE · doi:10.1371/journal.pone.0014116 · Cited by 270
The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism
Weger, B. D., Gobet, C., Yeung, J., Martin, E., Jimenez, S., Betrisey, B., Foata, F., Berger, B., Balvay, A., Foussier, A., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2018.09.023 · Cited by 269
Short-Term Temporal Variability in Airborne Bacterial and Fungal Populations
Fierer, N., Liu, Z. Z., Rodríguez-Hernández, M., Knight, R. D., Henn, M. R., & Hernandez, M. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01467-07 · Cited by 268
Self-citation
The Bamboo-Eating Giant Panda Harbors a Carnivore-Like Gut Microbiota, with Excessive Seasonal Variations
Xue, Z., Zhang, W., Wang, L., Hou, R., Zhang, M. H., Fei, L., Zhang, X., Huang, H., Bridgewater, L. C., Jiang, Y., et al. (2015) · mBio · doi:10.1128/mbio.00022-15 · Cited by 270
Colonization Characteristics of Bacterial Communities on Plastic Debris Influenced by Environmental Factors and Polymer Types in the Haihe Estuary of Bohai Bay, China
Li, W., Zhang, Y., Wu, N., Zhao, Z., Wei‐an, X., Ma, Y., & Niu, Z. (2019) · Environmental Science & Technology · doi:10.1021/acs.est.9b03659 · Cited by 266
Legacy effects of soil moisture on microbial community structure and N2O emissions
Banerjee, S., Helgason, B. L., Wang, L., Winsley, T. J., Ferrari, B. C., & Siciliano, S. D. (2015) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2015.12.004 · Cited by 266
Ecological and evolutionary factors underlying global and local assembly of denitrifier communities
Jones, C. M., & Hallin, S. (2010) · The ISME Journal · doi:10.1038/ismej.2009.152 · Cited by 268
The pathogen Batrachochytrium dendrobatidis disturbs the frog skin microbiome during a natural epidemic and experimental infection
Jani, A. J., & Briggs, C. J. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412752111 · Cited by 273
Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis
Yildiz, S., Mazel-Sanchez, B., Kandasamy, M., Manicassamy, B., & Schmolke, M. (2018) · Microbiome · doi:10.1186/s40168-017-0386-z · Cited by 264
Elevated atmospheric CO 2 affects soil microbial diversity associated with trembling aspen
Lesaulnier, C., Papamichail, D., McCorkle, S. M., Ollivier, B., Skiena, S., Taghavi, S., Zak, D. R., & van der Lelie, D. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01512.x · Cited by 264
Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects
Nguyen, T. T., Kosciolek, T., Maldonado, Y., Daly, R. E., Martin, A. S., McDonald, D., Knight, R., & Jeste, D. V. (2019) · Schizophrenia Research · doi:10.1016/j.schres.2018.09.014 · Cited by 260
Self-citation
Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers
Mira‐Pascual, L., Cabrera‐Rubio, R., Ocon, S. M., Costales, P., Parra, A., Suárez, A., Morís, F., Rodrigo, L., Mira, Á., & Collado, M. C. (2014) · Journal of Gastroenterology · doi:10.1007/s00535-014-0963-x · Cited by 269
Bacterial Succession on the Leaf Surface: A Novel System for Studying Successional Dynamics
Redford, A. J., & Fierer, N. (2009) · Microbial Ecology · doi:10.1007/s00248-009-9495-y · Cited by 264
Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning
Dini‐Andreote, F., Silva, M. D. C. P. E., Triadó–Margarit, X., Casamayor, E. O., van Elsas, J. D., & Salles, J. F. (2014) · The ISME Journal · doi:10.1038/ismej.2014.54 · Cited by 261
Dog and human inflammatory bowel disease rely on overlapping yet distinct dysbiosis networks
Vázquez‐Baeza, Y., Hyde, E. R., Suchodolski, J. S., & Knight, R. D. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.177 · Cited by 262
Self-citation
Statistical Analysis of Metagenomics Data
Calle, M. L. (2019) · Genomics & Informatics · doi:10.5808/gi.2019.17.1.e6 · Cited by 274
Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils
Gou, M., Hu, H., Zhang, Y. J., Wang, J., Hayden, H. L., Tang, Y., & He, J. (2017) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2017.09.028 · Cited by 260
Quantifying Phylogenetic Beta Diversity: Distinguishing between ‘True’ Turnover of Lineages and Phylogenetic Diversity Gradients
Leprieur, F., Albouy, C. P., de Bortoli, J., Cowman, P. F., Bellwood, D. R., & Mouillot, D. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042760 · Cited by 259
Chronic nitrogen additions fundamentally restructure the soil fungal community in a temperate forest
Morrison, E. W., Frey, S. D., Sadowsky, J., van Diepen, L. T. A., Thomas, W. K., & Pringle, A. (2016) · Fungal ecology · doi:10.1016/j.funeco.2016.05.011 · Cited by 260
Microbiome–metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model
Mao, S., Huo, W., & Zhu, W. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.12724 · Cited by 257
Bacterial and fungal community structure in Arctic tundra tussock and shrub soils
Wallenstein, M. D., McMahon, S. K., & Schimel, J. P. (2007) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2006.00260.x · Cited by 261
Caenorhabditis elegans as a Model for Microbiome Research
Zhang, F., Berg, M. J., Dierking, K., Félix, M., Shapira, M., Samuel, B. S., & Hinrich Schulenburg, Y. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00485 · Cited by 257
Evidence for the functional significance of diazotroph community structure in soil
Hsu, S.-F., & Buckley, D. H. (2008) · The ISME Journal · doi:10.1038/ismej.2008.82 · Cited by 258
Stability of peatland carbon to rising temperatures
Wilson, R. M., Hopple, A. M., Tfaily, M., Sebestyen, S. D., Schadt, C. W., Pfeifer‐Meister, L. E., Medvedeff, C. A., McFarlane, K. J., Kostka, J. E., Kolton, M., et al. (2016) · Nature Communications · doi:10.1038/ncomms13723 · Cited by 256
HLA-B27 and Human β2-Microglobulin Affect the Gut Microbiota of Transgenic Rats
Lin, P., Bach, M., Asquith, M. J., Lee, A., Akileswaran, L., Stauffer, P., Davin, S., Pan, Y., Cambronne, E. D., Dorris, M. L., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0105684 · Cited by 261
Self-citation
Phylogenetic Beta Diversity Metrics, Trait Evolution and Inferring the Functional Beta Diversity of Communities
Swenson, N. G. (2011) · PLoS ONE · doi:10.1371/journal.pone.0021264 · Cited by 253
Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest
Barberán, A., McGuire, K. L., Wolf, J. A., Jones, F. A., Wright, S. J., Turner, B. L., Essene, A., Hubbell, S. P., Faircloth, B. C., & Fierer, N. (2015) · Ecology Letters · doi:10.1111/ele.12536 · Cited by 262
High-fat diet modifies the PPAR-γ pathway leading to disruption of microbial and physiological ecosystem in murine small intestine
Tomas, J., Mulet, C., Saffarian, A., Cavin, J., Ducroc, R. A., Regnault, B., Tan, C. K., Duszka, K., Burcelin, R., Wahli, W., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1612559113 · Cited by 260
Warming enhances old organic carbon decomposition through altering functional microbial communities
Cheng, L., Zhang, N., Yuan, M., Xiao, J., Qin, Y., Deng, Y., Tu, Q., Xue, K., Nostrand, J. D. V., Wu, L., et al. (2017) · The ISME Journal · doi:10.1038/ismej.2017.48 · Cited by 252
Solar treatment (H2O2, TiO2-P25 and GO-TiO2 photocatalysis, photo-Fenton) of organic micropollutants, human pathogen indicators, antibiotic resistant bacteria and related genes in urban wastewater
Moreira, N. F. F., Narciso‐da‐Rocha, C., Polo-López, M. I., Pastrana‐Martínez, L. M., Faria, J. L., Manaia, C. M., Fernández‐Ibañez, P., Nunes, O. C., & Silva, A. M. T. (2018) · Water Research · doi:10.1016/j.watres.2018.01.064 · Cited by 253
Application of organic fertilizer improves microbial community diversity and alters microbial network structure in tea (Camellia sinensis) plantation soils
Gu, S., Hu, Q., Cheng, Y., Bai, L., Liu, Z., Xiao, W., Gong, Z., Wu, Y., Feng, K., Deng, Y., et al. (2019) · Soil and Tillage Research · doi:10.1016/j.still.2019.104356 · Cited by 256
The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations
Ying, S., Zeng, D.-N., Chi, L., Tan, Y., Galzote, C., Cardona, C., Lax, S. M., Gilbert, J. A., & Quan, Z. (2015) · PLoS ONE · doi:10.1371/journal.pone.0141842 · Cited by 258
Evaluating the core microbiota in complex communities: A systematic investigation
Astudillo‐García, C., Bell, J. J., Webster, N. S., Glasl, B., Jompa, J., Montoya, J. M., & Taylor, M. W. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13647 · Cited by 258
Evolutionary Biology Needs Wild Microbiomes
Hird, S. M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00725 · Cited by 255
The Cockroach Origin of the Termite Gut Microbiota: Patterns in Bacterial Community Structure Reflect Major Evolutionary Events
Dietrich, C., Köhler, T., & Brune, A. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.04206-13 · Cited by 253
Gut microbial ecology of lizards: insights into diversity in the wild, effects of captivity, variation across gut regions and transmission
Kohl, K. D., Brun, A., Magallanes, M. E., Brinkerhoff, J., Laspiur, A., Acosta, J. C., Caviedes‐Vidal, E., & Bordenstein, S. R. (2016) · Molecular Ecology · doi:10.1111/mec.13921 · Cited by 258
A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology
Williamson, I., Arnold, J. W., Samsa, L. A., Gaynor, L. T., DiSalvo, M., Cocchiaro, J. L., Carroll, I. M., Azcárate-Peril, M. A., Rawls, J. F., Allbritton, N. L., et al. (2018) · Cellular and Molecular Gastroenterology and Hepatology · doi:10.1016/j.jcmgh.2018.05.004 · Cited by 259
Data analysis for 16S microbial profiling from different benchtop sequencing platforms
Pylro, V. S., Roesch, L. F. W., Morais, D., Clark, I. M., Hirsch, P. R., & Tótola, M. R. (2014) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2014.08.018 · Cited by 247
Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy
Nuriel‐Ohayon, M., Neuman, H., Oren, Z., Belogolovski, A., Barsheshet, Y., Bloch, N., Uzan-Yulzari, A., Lahav, R., Peretz, A., Frishman, S., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.075 · Cited by 255
Histone deacetylase 3 coordinates commensal-bacteria-dependent intestinal homeostasis
Alenghat, T., Osborne, L. C., Saenz, S. A., Kobuley, D. E., Ziegler, C. G. K., Mullican, S. E., Choi, I., Grunberg, S., Sinha, R., Wynosky-Dolfi, M. A., et al. (2013) · Nature · doi:10.1038/nature12687 · Cited by 255
Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection
Weingarden, A. R., González, A., Vázquez‐Baeza, Y., Weiss, S. J., Humphry, G., Berg-Lyons, D., Knights, D., Unno, T., Bobr, A., Kang, J., et al. (2015) · Microbiome · doi:10.1186/s40168-015-0070-0 · Cited by 252
Self-citation
Mucosal Barrier Depletion and Loss of Bacterial Diversity are Primary Abnormalities in Paediatric Ulcerative Colitis
Alipour, M., Zaidi, D., Valcheva, R. S., Jovel, J., Martínez, I., Sergi, C. M., Walter, J., Mason, A. L., Wong, G. K., Dieleman, L. A., et al. (2015) · Journal of Crohn s and Colitis · doi:10.1093/ecco-jcc/jjv223 · Cited by 257
Microbiota-mediated inflammation and antimicrobial defense in the intestine
Caballero, S., & Pamer, E. G. (2015) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032713-120238 · Cited by 238
Succession and Replacement of Bacterial Populations in the Caecum of Egg Laying Hens over Their Whole Life
Videnska, P., Sedlář, K., Lukač, M., Faldynová, M., Dávidová‐Geržová, L., Čejková, D., Šišák, F., & Rychlı́k, I. (2014) · PLoS ONE · doi:10.1371/journal.pone.0115142 · Cited by 247
A Hidden Pitfall in the Preparation of Agar Media Undermines Microorganism Cultivability
Tanaka, T., Kawasaki, K., Daimon, S., Kitagawa, W., Yamamoto, K., Tamaki, H., Tanaka, M., Nakatsu, C. H., & Kamagata, Y. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.02741-14 · Cited by 255
Characterization of the Fecal Microbiota Using High-Throughput Sequencing Reveals a Stable Microbial Community during Storage
Carroll, I. M., Ringel‐Kulka, T., Siddle, J. P., Klaenhammer, T. R., & Ringel, Y. (2012) · PLoS ONE · doi:10.1371/journal.pone.0046953 · Cited by 241
Denitrifying Bacteria from the Genus Rhodanobacter Dominate Bacterial Communities in the Highly Contaminated Subsurface of a Nuclear Legacy Waste Site
Green, S. J., Prakash, O., Jasrotia, P., Overholt, W. A., Cardenas, E., Hubbard, D., Tiedje, J. M., Watson, D. B., Schadt, C. W., Brooks, S. C., et al. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.06435-11 · Cited by 246
Litter quality versus soil microbial community controls over decomposition: a quantitative analysis
Cleveland, C. C., Reed, S. C., Keller, A. B., Nemergut, D. R., O’Neill, S., Ostertag, R., & Vitousek, P. M. (2013) · Oecologia · doi:10.1007/s00442-013-2758-9 · Cited by 244
The sponge microbiome project
Moitinho‐Silva, L., Nielsen, S. J., Amir, A., González, A., Ackermann, G. L., Cerrano, C., Astudillo‐García, C., Easson, C., Sipkema, D., Liu, F., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix077 · Cited by 240
Self-citation
Enrichment of beneficial bacteria in the skin microbiota of bats persisting with white-nose syndrome
Lemieux‐Labonté, V., Simard, A., Willis, C. K. R., & Lapointe, F. (2017) · Microbiome · doi:10.1186/s40168-017-0334-y · Cited by 254
Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes
Adams, R. I., Bhangar, S., Pasut, W., Arens, E. A., Taylor, J. W., Lindow, S. E., Nazaroff, W. W., & Bruns, T. D. (2015) · PLoS ONE · doi:10.1371/journal.pone.0128022 · Cited by 260
A guide to the application of Hill numbers to DNA‐based diversity analyses
Alberdi, A., & Gilbert, M. T. P. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13014 · Cited by 255
Structural and Functional Dysbiosis of Fecal Microbiota in Chinese Patients With Alzheimer's Disease
Ling, Z., Zhu, M., Yan, X., Cheng, Y., Shao, L., Liu, X., Jiang, R., & Wu, S. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.634069 · Cited by 252
Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data.
McMurdie, P. J., & Holmes, S. (2012) · PubMed · Cited by 244
Phylogenetic and functional alpha and beta diversity in temperate and tropical tree communities
Swenson, N. G., Erickson, D. L., Mi, X., Bourg, N. A., Forero‐Montaña, J., Ge, X., Howe, R. W., Lake, J. K., Liu, X., Ma, K., et al. (2012) · Ecology · doi:10.1890/11-0402.1 · Cited by 241
Acute dextran sulfate sodium (DSS)‐induced colitis promotes gut microbial dysbiosis in mice
Munyaka, P. M., Rabbi, M. F., Khafipour, E., & Ghia, J. (2016) · Journal of Basic Microbiology · doi:10.1002/jobm.201500726 · Cited by 249
Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes
Logares, R., Tesson, S. V. M., Canbäck, B., Pontarp, M., Hedlund, K., & Rengefors, K. (2018) · Environmental Microbiology · doi:10.1111/1462-2920.14265 · Cited by 239
MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge
Nierychlo, M., Andersen, K. S., Xu, Y., Green, N., Jiang, C., Albertsen, M., Dueholm, M. S., & Nielsen, P. H. (2020) · Water Research · doi:10.1016/j.watres.2020.115955 · Cited by 244
Diet strongly influences the gut microbiota of surgeonfishes
Miyake, S., Ngugi, D. K., & Stingl, U. (2014) · Molecular Ecology · doi:10.1111/mec.13050 · Cited by 254
The Impact of Breastfeeding on Nasopharyngeal Microbial Communities in Infants
Biesbroek, G., Bosch, A. A. T. M., Wang, X., Keijser, B. J. F., Veenhoven, R. H., Sanders, E. A. M., & Bogaert, D. (2014) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201401-0073oc · Cited by 247
Influence of Plant Polymers on the Distribution and Cultivation of Bacteria in the Phylum Acidobacteria
Eichorst, S. A., Kuske, C. R., & Schmidt, T. M. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.01080-10 · Cited by 247
The microenvironment of injured murine gut elicits a local pro-restitutive microbiota
Alam, A. M., Leoni, G., Quirós, M., Wu, H., Desai, C., Nishio, H., Jones, R. M., Nusrat, A., & Neish, A. S. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2015.21 · Cited by 243
Significant Impacts of Increasing Aridity on the Arid Soil Microbiome
Neilson, J. W., Califf, K. J., Cardona, C., Copeland, A., Treuren, W. V., Josephson, K. L., Knight, R. D., Gilbert, J. A., Quade, J., Caporaso, J. G., et al. (2017) · mSystems · doi:10.1128/msystems.00195-16 · Cited by 255
Self-citation
Promises and pitfalls of using high‐throughput sequencing for diet analysis
Alberdi, A., Aizpurua, O., Bohmann, K., Gopalakrishnan, S., Lynggaard, C., Nielsen, M., & Gilbert, M. T. P. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12960 · Cited by 259
RETRACTED: Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice
Zhang, W., Xu, J., Yu, T., & Chen, Q. (2019) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2019.109131 · Cited by 247
Retracted
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome
Rühlemann, M. C., Hermes, B. M., Bang, C., Doms, S., Moitinho‐Silva, L., Thingholm, L. B., Frost, F., Degenhardt, F. C., Wittig, M., Kässens, J. C., et al. (2021) · Nature Genetics · doi:10.1038/s41588-020-00747-1 · Cited by 252
Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle
Carey, H. V., Walters, W. A., & Knight, R. D. (2012) · American Journal of Physiology-Regulatory, Integrative and Comparative Physiology · doi:10.1152/ajpregu.00387.2012 · Cited by 240
Self-citation
Mx1 reveals innate pathways to antiviral resistance and lethal influenza disease
Pillai, P. S., Molony, R. D., Martinod, K., Dong, H., Pang, I. K., Tal, M. C., Solis, A. G., Bielecki, P., Mohanty, S., Trentalange, M., et al. (2016) · Science · doi:10.1126/science.aaf3926 · Cited by 229
Bacterial diversity of water and sediment in the Changjiang estuary and coastal area of the East China Sea
Feng, B.-W., Li, X., Wang, J., Hu, Z., Meng, H., Xiang, L., & Quan, Z. (2009) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2009.00772.x · Cited by 239
Molecular-phylogenetic characterization of microbial communities imbalances in the small intestine of dogs with inflammatory bowel disease
Xenoulis, P. G., Palculict, B., Allenspach, K., Steiner, J. M., House, A. M. V., & Suchodolski, J. S. (2008) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2008.00556.x · Cited by 254
Fungi of the Murine Gut: Episodic Variation and Proliferation during Antibiotic Treatment
Dollive, S., Chen, Y., Grunberg, S., Bittinger, K. L., Hoffmann, C., Vandivier, L. E., Cuff, C. F., Lewis, J. D., Wu, G. D., & Bushman, F. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071806 · Cited by 244
Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants
Gregory, K. E., Samuel, B. S., Houghteling, P. D., Shan, G., Ausubel, F. M., Sadreyev, R. I., & Walker, W. A. (2016) · Microbiome · doi:10.1186/s40168-016-0214-x · Cited by 244
Microbiome analysis among bats describes influences of host phylogeny, life history, physiology and geography
Phillips, C. D., PHELAN, G., Dowd, S. E., McDonough, M. M., Ferguson, A. W., Hanson, J. D., Siles, L., Ordóñez‐Garza, N., Francisco, M. S., & Baker, R. J. (2012) · Molecular Ecology · doi:10.1111/j.1365-294x.2012.05568.x · Cited by 237

Authors: Lozupone, C., & Knight, R.
Affiliations: University of Colorado Boulder (US)
Corresponding author: Knight, Rob
ORCID: Lozupone, Catherine
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
DOI: 10.1128/aem.71.12.8228-8235.2005
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
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
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

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks