UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

Ecological Diversity and Its Measurement

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ARB: a software environment for sequence data

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Measuring biological diversity

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The RDP (Ribosomal Database Project)

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The Uncultured Microbial Majority

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Counting the Uncountable: Statistical Approaches to Estimating Microbial Diversity

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The RDP-II (Ribosomal Database Project)

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Endolithic Microbial Ecosystems

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Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12

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Chronic Repression of mTOR Complex 2 Induces Changes in the Gut Microbiota of Diet-induced Obese Mice

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Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month

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Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling

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D-Tryptophan From Probiotic Bacteria Influences the Gut Microbiome and Allergic Airway Disease

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Altered enteric microbiota ecology in interleukin 10-deficient mice during development and progression of intestinal inflammation

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Plant nitrogen uptake drives rhizosphere bacterial community assembly during plant growth

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Host-genotype dependent gut microbiota drives zooplankton tolerance to toxic cyanobacteria

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Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics

Leung, M. H. Y., Wilkins, D. E., Li, E. K. T., Kong, F. K. F., & Lee, P. K. H. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.02244-14 · Cited by 175

Betel nut chewing, oral premalignant lesions, and the oral microbiome

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Transfer of environmental microbes to the skin and respiratory tract of humans after urban green space exposure

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Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing

Qian, P., Wang, Y., Lee, O. O., Lau, S. C. K., Yang, J., Lafi, F. F., Al-Suwailem, A. M., & Wong, T. Y. H. (2010) · The ISME Journal · doi:10.1038/ismej.2010.112 · Cited by 174

Microbiome Assembly across Multiple Body Sites in Low-Birthweight Infants

Costello, E. K., Carlisle, E. M., Bik, E. M., Morowitz, M. J., & Relman, D. A. (2013) · mBio · doi:10.1128/mbio.00782-13 · Cited by 175

Sampling locality is more detectable than taxonomy or ecology in the gut microbiota of the brood-parasitic Brown-headed Cowbird ( Molothrus ater )

Hird, S. M., Carstens, B. C., Cardiff, S. W., Dittmann, D. L., & Brumfield, R. T. (2014) · PeerJ · doi:10.7717/peerj.321 · Cited by 169

A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition

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Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods

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Bacterial communities in penile skin, male urethra, and vaginas of heterosexual couples with and without bacterial vaginosis

Zozaya, M., Ferris, M. J., Siren, J. D., Lillis, R., Myers, L., Nsuami, M. J., Eren, A. M., Brown, J. M., Taylor, C. M., & Martin, D. H. (2016) · Microbiome · doi:10.1186/s40168-016-0161-6 · Cited by 171

Host mitochondria influence gut microbiome diversity: A role for ROS

Yardeni, T., Tanes, C., Bittinger, K. L., Mattei, L. M., Schaefer, P. M., Singh, L. N., Wu, G. D., Murdock, D. G., & Wallace, D. C. (2019) · Science Signaling · doi:10.1126/scisignal.aaw3159 · Cited by 172

Recent and emerging innovations in Salmonella detection: a food and environmental perspective

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The Potential Effect of Oral Microbiota in the Prediction of Mucositis During Radiotherapy for Nasopharyngeal Carcinoma

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Investigation of bacterial diversity in the feces of cattle fed different diets1

Kim, M.-H., Kim, J., Kuehn, L. A., Bono, J. L., Berry, E. D., Kalchayanand, N., Freetly, H. C., Benson, A. K., & Wells, J. E. (2013) · Journal of Animal Science · doi:10.2527/jas.2013-6841 · Cited by 176

Primate vaginal microbiomes exhibit species specificity without universal Lactobacillus dominance

Yıldırım, S., Yeoman, C. J., Janga, S. C., Thomas, S. M., Ho, M., Leigh, S. R., Microbiome, P., White, B. A., Wilson, B. A., & Stumpf, R. M. (2014) · The ISME Journal · doi:10.1038/ismej.2014.90 · Cited by 169

Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

Pepe‐Ranney, C., Campbell, A., Koechli, C., Berthrong, S. T., & Buckley, D. H. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00703 · Cited by 179

Microbial community compositional analysis for membrane bioreactor treating antibiotics containing wastewater

Zhu, Y., Wang, Y., Jiang, X., Zhou, S., Wu, M. T., Pan, M., & Chen, H. (2017) · Chemical Engineering Journal · doi:10.1016/j.cej.2017.05.073 · Cited by 169

Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture

Yun, Y., Srinivas, G., Kuenzel, S., Linnenbrink, M., Alnahas, S., Bruce, K. D., Steinhoff, U., Baines, J. F., & Schaible, U. E. (2014) · PLoS ONE · doi:10.1371/journal.pone.0113466 · Cited by 168

Intestinal lamina propria dendritic cells maintain T cell homeostasis but do not affect commensalism

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Evidence for a distinct gut microbiome in kidney stone formers compared to non-stone formers

Stern, J. M., Moazami, S., Qiu, Y., Kurland, I. J., Chen, Z., Agalliu, I., Burk, R. D., & Davies, K. P. (2016) · Urolithiasis · doi:10.1007/s00240-016-0882-9 · Cited by 168

Fungal and bacterial growth in floor dust at elevated relative humidity levels

Dannemiller, K. C., Weschler, C. J., & Peccia, J. (2016) · Indoor Air · doi:10.1111/ina.12313 · Cited by 167

Distinct soil bacterial communities along a small-scale elevational gradient in alpine tundra

Shen, C., Ni, Y., Liang, W., Wang, J., & Chu, H. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00582 · Cited by 167

Gut bacteria in children with autism spectrum disorders: challenges and promise of studying how a complex community influences a complex disease

Krajmalnik‐Brown, R., Lozupone, C., Kang, D., & Adams, J. B. (2015) · Microbial Ecology in Health and Disease · doi:10.3402/mehd.v26.26914 · Cited by 175

Species sorting and seasonal dynamics primarily shape bacterial communities in the Upper Mississippi River

Staley, C. M., Gould, T. J., Wang, P., Phillips, J., Cotner, J. B., & Sadowsky, M. J. (2014) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2014.10.012 · Cited by 167

Impact of combined β-glucanase and xylanase enzymes on growth performance, nutrients utilization and gut microbiota in broiler chickens fed corn or wheat-based diets

Munyaka, P. M., Nandha, N. K., Kiarie, E. G., Nyachoti, C. M., & Khafipour, E. (2015) · Poultry Science · doi:10.3382/ps/pev333 · Cited by 167

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species‐specificity

Manirajan, B. A., Ratering, S., Rusch, V., Schwiertz, A., Geißler-Plaum, R., Cardinale, M., & Schnell, S. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13524 · Cited by 167

Global-Scale Structure of the Eelgrass Microbiome

Fahimipour, A. K., Kardish, M. R., Eisen, J. A., Lang, J., Green, J. L., & Stachowicz, J. J. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.03391-16 · Cited by 166

Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community

Pang, Z., Dong, F., Liu, Q., Lin, W., Hu, C., & Yuan, Z. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.627569 · Cited by 167

Biogeographical differences in the influence of maternal microbial sources on the early successional development of the bovine neonatal gastrointestinal tract

Yeoman, C. J., Ishaq, S. L., Bichi, E., Olivo, S. K., Lowe, J., & Aldridge, B. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-21440-8 · Cited by 168

Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms

Landa, M., Blain, S., Christaki, U., Monchy, S., & Obernosterer, I. (2015) · The ISME Journal · doi:10.1038/ismej.2015.105 · Cited by 167

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

Amend, A. S., Barshis, D. J., & Oliver, T. A. (2011) · The ISME Journal · doi:10.1038/ismej.2011.193 · Cited by 167

Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny

Chang, Q., Luan, Y., & Sun, F. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-118 · Cited by 170

Tissue-Associated Bacterial Alterations in Rectal Carcinoma Patients Revealed by 16S rRNA Community Profiling

Thomas, A. M., Jesus, E. C., Lopes, A., Aguiar, S., Begnami, M. D., Rocha, R. M., Carpinetti, P. A., Camargo, A. A., Hoffmann, C., Freitas, H. C., et al. (2016) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2016.00179 · Cited by 136

Assessment of bacterial profiles in aged, home-made Sichuan paocai brine with varying titratable acidity by PacBio SMRT sequencing technology

Cao, J., Yang, J., Hou, Q., Xu, H., Zheng, Y., Zhang, H., & Zhang, L. (2017) · Food Control · doi:10.1016/j.foodcont.2017.02.006 · Cited by 166

An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men

Armstrong, A. J. S., Shaffer, M., Nusbacher, N. M., Griesmer, C., Fiorillo, S. P., Schneider, J. M., Neff, C. P., Li, S. X., Fontenot, A. P., Campbell, T., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0580-7 · Cited by 165

Structural modulation of the gut microbiota and the relationship with body weight: compared evaluation of liraglutide and saxagliptin treatment

Wang, L., Li, P., Tang, Z., Yan, X., & Feng, B. (2016) · Scientific Reports · doi:10.1038/srep33251 · Cited by 165

Fumarole-Supported Islands of Biodiversity within a Hyperarid, High-Elevation Landscape on Socompa Volcano, Puna de Atacama, Andes

Costello, E. K., Halloy, S. R. P., Reed, S. C., Sowell, P., & Schmidt, S. K. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01469-08 · Cited by 167

Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota

Yan, W., Sun, C., Zheng, J., Wen, C., Ji, C., Zhang, D., Chen, Y., Hou, Z., & Yang, N. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02126 · Cited by 165

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

Hassler, H. B., Probert, B., Moore, C. P., Lawson, E., Jackson, R. W., Russell, B. T., & Richards, V. P. (2022) · Microbiome · doi:10.1186/s40168-022-01295-y · Cited by 191

Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill

Bik, H. M., Halanych, K. M., Sharma, J., & Thomas, W. K. (2012) · PLoS ONE · doi:10.1371/journal.pone.0038550 · Cited by 164

Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease

Khanna, S., Vázquez‐Baeza, Y., González, A., Weiss, S. J., Schmidt, B. A., Pedrogo, D. A. M., Rainey, J. F., Kammer, P. P., Nelson, H., Sadowsky, M. J., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0269-3 · Cited by 163

Bacterial Composition and Diversity in Breast Milk Samples from Mothers Living in Taiwan and Mainland China

Li, S.-W., Watanabe, K., Hsu, C.-C., Chao, S.-H., Yang, Z.-H., Lin, Y.-J., Chen, C.-C., Cao, Y.-M., Huang, H., Chang, C.-H., et al. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00965 · Cited by 164

Sex Differences in the Gut Microbiota as Potential Determinants of Gender Predisposition to Disease

Santos-Marcos, J. A., Haro, C., Vega‐Rojas, A., Alcala-Diaz, J. F., Molina‐Abril, H., Leon‐Acuña, A., López-Moreno, J., Landa, B. B., Tena‐Sempere, M., Pérez‐Martínez, P., et al. (2019) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201800870 · Cited by 171

Supplementation with Sodium Butyrate Modulates the Composition of the Gut Microbiota and Ameliorates High-Fat Diet-Induced Obesity in Mice

Fang, W., Xue, H., Chen, X., Chen, K., & Ling, W. (2019) · Journal of Nutrition · doi:10.1093/jn/nxy324 · Cited by 168

Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome

Hodkinson, B. P., Gottel, N., Schadt, C. W., & Lutzoni, F. M. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02560.x · Cited by 167

Pyrosequencing as a tool for better understanding of human microbiomes

Siqueira, J. F., Jr., FOUAD, A. F., & Rôças, I. N. (2012) · Journal of Oral Microbiology · doi:10.3402/jom.v4i0.10743 · Cited by 184

Gut microbiota composition is associated with environmental landscape in honey bees

Jones, J. C., Fruciano, C., Hildebrand, F., Toufalilia, H. A., Balfour, N. J., Peer Bork, B., Engel, P., Ratnieks, F. L. W., & Hughes, W. O. H. (2017) · Ecology and Evolution · doi:10.1002/ece3.3597 · Cited by 163

Crypt- and Mucosa-Associated Core Microbiotas in Humans and Their Alteration in Colon Cancer Patients

Saffarian, A., Mulet, C., Regnault, B., Amiot, A., Nhieu, J. T. V., Ravel, J., Sobhani, I., Sansonetti, P. J., & Pédron, T. (2019) · mBio · doi:10.1128/mbio.01315-19 · Cited by 167

Dietary heme induces gut dysbiosis, aggravates colitis, and potentiates the development of adenomas in mice

Constante, M., Fragoso, G., Calvé, A., Samba-Mondonga, M., & Santos, M. M. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01809 · Cited by 161

Inflammation-associated microbiota in pediatric eosinophilic esophagitis

Benitez, A., Hoffmann, C., Muir, A. B., Dods, K. K., Spergel, J. M., Bushman, F. D., & Wang, M. (2015) · Microbiome · doi:10.1186/s40168-015-0085-6 · Cited by 162

Microbial composition affects the functioning of estuarine sediments

Reed, H. E., & Martiny, J. B. H. (2012) · The ISME Journal · doi:10.1038/ismej.2012.154 · Cited by 162

Seawater transfer alters the intestinal microbiota profiles of Atlantic salmon (Salmo salar L.)

Dehler, C. E., Secombes, C. J., & Martín, S. (2017) · Scientific Reports · doi:10.1038/s41598-017-13249-8 · Cited by 166

A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Lappan, R. J., Imbrogno, K., Sikazwe, C. T., Anderson, D. R., Mok, D., Coates, H. L. C., Vijayasekaran, S., Bumbak, P., Blyth, C. C., Jamieson, S. E., et al. (2018) · BMC Microbiology · doi:10.1186/s12866-018-1154-3 · Cited by 165

An in vivo assessment of the cholesterol-lowering efficacy of Lactobacillus plantarum ECGC 13110402 in normal to mildly hypercholesterolaemic adults

Costabile, A., Buttarazzi, I., Kolida, S., Quercia, S., Baldini, J., Swann, J. R., Brigidi, P., & Gibson, G. R. (2017) · PLOS ONE · doi:10.1371/journal.pone.0187964 · Cited by 161

Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies

Sullam, K. E., Rubin, B. E., Dalton, C. M., Kilham, S. S., Flecker, A. S., & Russell, J. A. (2015) · The ISME Journal · doi:10.1038/ismej.2014.231 · Cited by 160

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features

Burns, K. N., Kluepfel, D. A., Strauss, S. L., Bokulich, N. A., Cantù, D., & Steenwerth, K. L. (2015) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2015.09.002 · Cited by 172

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem

Gibbons, S. M., Lekberg, Y., Mummey, D. L., Sangwan, N., Ramsey, P. W., & Gilbert, J. A. (2017) · mSystems · doi:10.1128/msystems.00178-16 · Cited by 180

Microbiota-Induced TNF-like Ligand 1A Drives Group 3 Innate Lymphoid Cell-Mediated Barrier Protection and Intestinal T Cell Activation during Colitis

Castellanos, J. G., Woo, V., Viladomiu, M., Putzel, G., Lima, S. F., Diehl, G. E., Marderstein, A. R., Gandara, J. A., Perez, A. R., Withers, D. R., et al. (2018) · Immunity · doi:10.1016/j.immuni.2018.10.014 · Cited by 161

The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile

Molinero, N., Ruíz, L., Milani, C., Gutiérrez‐Díaz, I., Sánchez, B., Mangifesta, M., Segura, J., Rodríguez, M. I. C., Campelo, A. B., García-Bernardo, C., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0712-8 · Cited by 168

Gut Microbiota Dysbiosis and Increased Plasma LPS and TMAO Levels in Patients With Preeclampsia

Wang, J., Gu, X., Yang, J., Wei, Y., & Zhao, Y. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00409 · Cited by 161

Anaerobic bacterial fermentation products increase tuberculosis risk in antiretroviral-drug-treated HIV patients.

Segal, L. N., Clemente, J. C., Li, Y., Ruan, C., Cao, J., Danckers, M., Morris, A., Tapyrik, S., Wu, B. G., Diaz, P., et al. (2017) · Cell Host & Microbe · doi:10.1016/j.chom.2017.03.003 · Cited by 160

Patterns of benthic bacterial diversity in coastal areas contaminated by heavy metals, polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs)

Quero, G. M., Cassin, D., Botter, M., Perini, L. T., & Luna, G. M. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01053 · Cited by 160

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

Kearns, P. J., Angell, J. H., Howard, E. M., Deegan, L. A., Stanley, R. H. R., & Bowen, J. L. (2016) · Nature Communications · doi:10.1038/ncomms12881 · Cited by 162

Estimating diversity in networked ecological communities

Willis, A. D., & Martin, B. D. (2020) · Biostatistics · doi:10.1093/biostatistics/kxaa015 · Cited by 168

High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy

Lee, H., Jeong, S. E., Kim, P. J., Madsen, E. L., & Jeon, C. O. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00639 · Cited by 159

Molecular methods for pathogen and microbial community detection and characterization: Current and potential application in diagnostic microbiology

Sibley, C. D., Peirano, G., & Church, D. L. (2012) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2012.01.011 · Cited by 163

Biogeography and habitat modelling of high-alpine bacteria

King, A. J., Freeman, K. R., McCormick, K. F., Lynch, R. C., Lozupone, C., Knight, R. D., & Schmidt, S. K. (2010) · Nature Communications · doi:10.1038/ncomms1055 · Cited by 163

Adaptively Evolving Bacterial Communities for Complete and Selective Reduction of Cr(VI), Cu(II), and Cd(II) in Biocathode Bioelectrochemical Systems

Huang, L., Wang, Q., Jiang, L., Zhou, P., Quan, X., & Logan, B. E. (2015) · Environmental Science & Technology · doi:10.1021/acs.est.5b00191 · Cited by 159

Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers

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Depth matters: effects of precipitation regime on soil microbial activity upon rewetting of a plant-soil system

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Description

Chen, J., Chen, M. J., Yes, L., & No, N. (2014)

The UniFrac significance test generates different outputs given semantically equivalent inputs

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A method for comparing multiple bacterial community structures from 16S rDNA clone library sequences.

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