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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Obesity alters gut microbial ecology

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A Molecular View of Microbial Diversity and the Biosphere

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Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis

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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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Characterization of the skin fungal microbiota in patients with atopic dermatitis and in healthy subjects

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Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

Miller, C. S., Handley, K. M., Wrighton, K. C., Frischkorn, K. R., Thomas, B. C., & Banfield, J. F. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056018 · Cited by 210

Contrasting denitrifier communities relate to contrasting N2O emission patterns from acidic peat soils in arctic tundra

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Contrasting elevational diversity patterns between eukaryotic soil microbes and plants

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Microbiota fingerprints lose individually identifying features over time

Wilkins, D. E., Leung, M. H. Y., & Lee, P. K. H. (2017) · Microbiome · doi:10.1186/s40168-016-0209-7 · Cited by 207

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

Stahringer, S. S., Clemente, J. C., Corley, R. P., Hewitt, J., Knights, D., Walters, W. A., Knight, R., & Krauter, K. S. (2012) · Genome Research · doi:10.1101/gr.140608.112 · Cited by 180

The antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse

Morgan, A. P., Crowley, J. J., Nonneman, R. J., Quackenbush, C. R., Miller, C. N., Ryan, A. K., Bogue, M. A., Paredes, S. H., Yourstone, S., Carroll, I. M., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0115225 · Cited by 197

Biogeography of anaerobic ammonia-oxidizing (anammox) bacteria

Sonthiphand, P., Hall, M., & Neufeld, J. D. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00399 · Cited by 206

Breast tissue, oral and urinary microbiomes in breast cancer

Wang, H., Altemus, J. B., Niazi, F., Green, H., Calhoun, B. C., Sturgis, C. D., Grobmyer, S. R., & Eng, C. (2017) · Oncotarget · doi:10.18632/oncotarget.21490 · Cited by 199

Differential metabolic effects of oral butyrate treatment in lean versus metabolic syndrome subjects

Bouter, K. E. C., Bakker, G. J., Levin, E., Hartstra, A. V., Kootte, R. S., Udayappan, S. D., Katiraei, S., Bahler, L., Gilijamse, P. W., Tremaroli, V., et al. (2018) · Clinical and Translational Gastroenterology · doi:10.1038/s41424-018-0025-4 · Cited by 208

Exosome‐like nanoparticles from Mulberry bark prevent DSS‐induced colitis via the AhR/COPS8 pathway

Sriwastva, M. K., Deng, Z., Wang, B., Teng, Y., Kumar, A., Sundaram, K., Mu, J., Lei, C., Dryden, G. W., Xu, F., et al. (2022) · EMBO Reports · doi:10.15252/embr.202153365 · Cited by 203

Freshwater Perkinsea and marine-freshwater colonizations revealed by pyrosequencing and phylogeny of environmental rDNA

Bråte, J., Logares, R., Berney, C., Ree, D. K., Klaveness, D., Jakobsen, K. S., & Shalchian‐Tabrizi, K. (2010) · The ISME Journal · doi:10.1038/ismej.2010.39 · Cited by 204

Unraveling the Fecal Microbiota and Metagenomic Functional Capacity Associated with Feed Efficiency in Pigs

Yang, H., Huang, X., Fang, S., He, M., Zhao, Y., Wu, Z., Yang, M. J., Zhang, Z., Chen, C., & Huang, L. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01555 · Cited by 214

Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract

Zhang, L., Wu, W., Lee, Y. K., Xie, J., & Zhang, H. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00048 · Cited by 193

Exercise Is More Effective at Altering Gut Microbial Composition and Producing Stable Changes in Lean Mass in Juvenile versus Adult Male F344 Rats

Mika, A., Van Treuren, W., González, A., Herrera, J. J., Knight, R., & Fleshner, M. (2015) · PLOS ONE · doi:10.1371/journal.pone.0125889 · Cited by 197

Deep Sequencing Analyses of Low Density Microbial Communities: Working at the Boundary of Accurate Microbiota Detection

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Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children

Dannemiller, K. C., Gent, J. F., Leaderer, B. P., & Peccia, J. (2015) · Indoor Air · doi:10.1111/ina.12205 · Cited by 194

Evaluating different approaches that test whether microbial communities have the same structure

Schloss, P. D. (2008) · The ISME Journal · doi:10.1038/ismej.2008.5 · Cited by 197

The occupant as a source of house dust bacteria

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Development of Ruminal and Fecal Microbiomes Are Affected by Weaning But Not Weaning Strategy in Dairy Calves

Meale, S. J., Li, S., Azevedo, P. A., Derakhshani, H., Plaizier, J. C., Khafipour, E., & Steele, M. A. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00582 · Cited by 212

Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

Miho, E., Yermanos, A., Weber, C. R., Berger, C. T., Reddy, S. T., & Greiff, V. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.00224 · Cited by 189

Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale

Bokulich, N. A., Bamforth, C. W., & Mills, D. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035507 · Cited by 197

Patterns of fungal diversity and composition along a salinity gradient

Mohamed, D. J., & Martiny, J. B. H. (2010) · The ISME Journal · doi:10.1038/ismej.2010.137 · Cited by 194

PyCogent: a toolkit for making sense from sequence

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Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

Thorsen, J., Brejnrod, A., Mortensen, M. S., Rasmussen, M. A., Stokholm, J., Al‐Soud, W. A., Sørensen, S. J., Bisgaard, H. F., & Waage, J. (2016) · Microbiome · doi:10.1186/s40168-016-0208-8 · Cited by 194

Temperature and soil moisture control microbial community composition in an arctic–alpine ecosystem along elevational and micro-topographic gradients

Frindte, K., Pape, R., Werner, K. A., Löffler, J., & Knief, C. (2019) · The ISME Journal · doi:10.1038/s41396-019-0409-9 · Cited by 195

Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella , and fimbriae-encoding bacteria

Olm, M. R., Bhattacharya, N., Crits‐Christoph, A., Firek, B., Baker, R. W., Song, Y. S., Morowitz, M. J., & Banfield, J. F. (2019) · Science Advances · doi:10.1126/sciadv.aax5727 · Cited by 195

Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden

Olsson, L. M., Boulund, F., Nilsson, S., Khan, M. T., Gummesson, A., Fagerberg, L., Engstrand, L. G., Perkins, R., Uhlén, M., Bergström, G. M. L., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.03.002 · Cited by 200

Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm

Bartram, A. K., Jiang, X., Lynch, M. D. J., Masella, A. P., Nicol, G. W., Dushoff, J. G., & Neufeld, J. D. (2013) · FEMS Microbiology Ecology · doi:10.1111/1574-6941.12231 · Cited by 195

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

Mackenzie, B. W., Waite, D. W., & Taylor, M. W. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00130 · Cited by 200

Influence of tree shape and evolutionary time‐scale on phylogenetic diversity metrics

Mazel, F., Davies, T. J., Gallien, L., Renaud, J., Groussin, M., Münkemüller, T., & Thuiller, W. (2015) · Ecography · doi:10.1111/ecog.01694 · Cited by 194

Host genotype and gut microbiome modulate insulin secretion and diet-induced metabolic phenotypes

Kreznar, J. H., Keller, M. P., Traeger, L. L., Rabaglia, M. E., Schueler, K. L., Stapleton, D. S., Zhao, W., Vivas, E. I., Yandell, B. S., Broman, A. T., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.01.062 · Cited by 177

Effects of long‐term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach

Lentendu, G., Wubet, T., Chatzinotas, A., Wilhelm, C., Buscot, F., & Schlegel, M. (2014) · Molecular Ecology · doi:10.1111/mec.12819 · Cited by 195

Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles

Allegretti, J. R., Kearney, S. M., Li, N., Bogart, E., Bullock, K. H., Gerber, G. K., Bry, L., Clish, C. B., Alm, E. J., & Korzenik, J. R. (2016) · Alimentary Pharmacology & Therapeutics · doi:10.1111/apt.13616 · Cited by 198

A global comparison of the microbiome compositions of three gut locations in commercial pigs with extreme feed conversion ratios

Quan, J., Cai, G., Ye, J., Yang, M. J., Ding, R., Wang, X., Zheng, E., Fu, D., Li, S., Zhou, S., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-22692-0 · Cited by 202

Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans

David, L. A., Weil, A. A., Ryan, E. T., Calderwood, S. B., Harris, J. B., Chowdhury, F., Begum, Y. A., Qadri, F., LaRocque, R. C., & Turnbaugh, P. J. (2015) · mBio · doi:10.1128/mbio.00381-15 · Cited by 187

A comparative study of composting the solid fraction of dairy manure with or without bulking material: Performance and microbial community dynamics

Zhong, X.-Z., Ma, S., Wang, S.-P., Wang, T., Sun, Z.-Y., Tang, Y., Deng, Y., & Kida, K. (2017) · Bioresource Technology · doi:10.1016/j.biortech.2017.09.116 · Cited by 191

Gut microbiome composition is associated with temperament during early childhood

Christian, L. M., Galley, J. D., Hade, E. M., Schoppe-Sullivan, S., Kamp Dush, C., & Bailey, M. T. (2015) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2014.10.018 · Cited by 191

Gut Microbial Community Structure and Complications After Kidney Transplantation

Lee, J. R., Muthukumar, T., Dadhania, D. M., Toussaint, N. C., Ling, L., Pamer, E. G., & Suthanthiran, M. (2014) · Transplantation · doi:10.1097/tp.0000000000000370 · Cited by 191

Interactions between multiple helminths and the gut microbiota in wild rodents

Kreisinger, J., Bastien, G., Hauffe, H. C., Marchesi, J. R., & Perkins, S. E. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0295 · Cited by 202

Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development

Pfeiffer, S., Mitter, B., Oswald, A., Schloter-Hai, B., Schloter, M., Declerck, S., & Sessitsch, A. (2016) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw242 · Cited by 188

Commensals Suppress Intestinal Epithelial Cell Retinoic Acid Synthesis to Regulate Interleukin-22 Activity and Prevent Microbial Dysbiosis

Grizotte-Lake, M., Zhong, G. G., Duncan, K., Kirkwood, J. S., Iyer, N. R., Smolenski, I., Isoherranen, N., & Vaishnava, S. (2018) · Immunity · doi:10.1016/j.immuni.2018.11.018 · Cited by 195

Forensic analysis of the microbiome of phones and shoes

Lax, S. M., Hampton‐Marcell, J., Gibbons, S. M., Colares, G. B., Smith, D. P., Eisen, J. A., & Gilbert, J. A. (2015) · Microbiome · doi:10.1186/s40168-015-0082-9 · Cited by 190

Hypothesis testing and statistical analysis of microbiome

Xia, Y., & Sun, J. (2017) · Genes & Diseases · doi:10.1016/j.gendis.2017.06.001 · Cited by 206

Structural and functional profiles of the gut microbial community in polycystic ovary syndrome with insulin resistance (IR-PCOS): a pilot study

Zeng, B., Lai, Z., Sun, L., Zhang, Z., Yang, J., Li, Z., Lin, J., & Zhang, Z. (2018) · Research in Microbiology · doi:10.1016/j.resmic.2018.09.002 · Cited by 196

Microbial Transplantation With Human Gut Commensals Containing CutC Is Sufficient to Transmit Enhanced Platelet Reactivity and Thrombosis Potential

Skye, S. M., Zhu, W., Romano, K. A., Guo, C.-J., Wang, Z., Jia, X., Kirsop, J., Haag, B., Lang, J. M., DiDonato, J. A., et al. (2018) · Circulation Research · doi:10.1161/circresaha.118.313142 · Cited by 189

Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China

Zhang, M., Ma, W., Zhang, J., He, Y., & Wang, J. (2018) · Scientific Reports · doi:10.1038/s41598-018-32219-2 · Cited by 188

Molecular analysis of gut microbiota in obesity among Indian individuals

Patil, D. P., Dhotre, D. P., Chavan, S. G., Sultan, A., Jain, D. S., Lanjekar, V. B., Gangawani, J., Shah, P. S., Todkar, J., Shah, S. S., et al. (2012) · Journal of Biosciences · doi:10.1007/s12038-012-9244-0 · Cited by 189

Insights into the biodiversity of the gut microbiota of broiler chickens

Mancabelli, L., Ferrario, C., Milani, C., Mangifesta, M., Turroni, F., Duranti, S., Lugli, G. A., Viappiani, A., Ossiprandi, M. C., van Sinderen, D., et al. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13363 · Cited by 193

Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees

Müller, H., Berg, C., Landa, B. B., Auerbach, A. K., Moissl‐Eichinger, C., & Berg, G. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00138 · Cited by 192

Metagenomics: Facts and Artifacts, and Computational Challenges

Wooley, J., & Ye, Y. (2010) · Journal of Computer Science and Technology · doi:10.1007/s11390-010-9306-4 · Cited by 198

Monitoring Seasonal Changes in Winery-Resident Microbiota

Bokulich, N. A., Ohta, M., Richardson, P. M., & Mills, D. A. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066437 · Cited by 198

Comparative studies of the composition of bacterial microbiota associated with the ruminal content, ruminal epithelium and in the faeces of lactating dairy cows

Liu, J., Zhang, M., Zhang, R., Zhu, W., & Mao, S. (2016) · Microbial Biotechnology · doi:10.1111/1751-7915.12345 · Cited by 188

NG-Tax, a highly accurate and validated pipeline for analysis of 16S rRNA amplicons from complex biomes

Ramiro‐Garcia, J., Hermes, G. D. A., Giatsis, C., Sipkema, D., Zoetendal, E. G., Schaap, P. J., & Smidt, H. (2016) · F1000Research · doi:10.12688/f1000research.9227.1 · Cited by 187

Microbiome and its relation to gestational diabetes

Cortez, R. V., Taddei, C. R., Sparvoli, L. G., Angelo, A. G. S., Padilha, M., Mattar, R., & Daher, S. (2018) · Endocrine · doi:10.1007/s12020-018-1813-z · Cited by 187

Life history strategies of soil bacterial communities across global terrestrial biomes

Piton, G., Allison, S., Bahram, M., Hildebrand, F., Martiny, J. B. H., Treseder, K. K., & Martiny, A. C. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01465-0 · Cited by 193

Gut Microbiota Condition the Therapeutic Efficacy of Trastuzumab in HER2-Positive Breast Cancer

Di Modica, M., Gargari, G., Regondi, V., Bonizzi, A., Arioli, S., Belmonte, B., De Cecco, L., Fasano, E., Bianchi, F., Bertolotti, A., et al. (2021) · Cancer Research · doi:10.1158/0008-5472.can-20-1659 · Cited by 184

Characterizing the microbiota across the gastrointestinal tract of a Brazilian Nelore steer

de Oliveira, M. N. V., Jewell, K. A., Freitas, F. S., Benjamin, L. A., Tótola, M. R., Borges, A. C., Moraes, C. A., & Suen, G. (2013) · Veterinary Microbiology · doi:10.1016/j.vetmic.2013.02.013 · Cited by 184

Characterization of the Active Microbiotas Associated with Honey Bees Reveals Healthier and Broader Communities when Colonies are Genetically Diverse

Mattila, H. R., Ríos, D., Walker-Sperling, V. E. K., Roeselers, G., & Newton, I. L. G. (2012) · PLoS ONE · doi:10.1371/journal.pone.0032962 · Cited by 188

Comparative Ocular Microbial Communities in Humans with and without Blepharitis

Lee, S. H., Oh, D. H., Jung, J. Y., Kim, J. C., & Jeon, C. O. (2012) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.12-9922 · Cited by 188

Gut microbiome contributes to impairment of immunity in pulmonary tuberculosis patients by alteration of butyrate and propionate producers

Maji, A., Misra, R., Dhakan, D. B., Gupta, V., Mahato, N. K., Saxena, R., Mittal, P., Thukral, N., Sharma, E., Singh, A., et al. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.14015 · Cited by 191

MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities

Cao, K. L., Costello, M., Lakis, V., Bartolo, F., Chua, X., Brazeilles, R., & Rondeau, P. (2016) · PLoS ONE · doi:10.1371/journal.pone.0160169 · Cited by 188

Gut microbiome variation modulates the effects of dietary fiber on host metabolism

Murga-Garrido, S. M., Hong, Q., Cross, T.-W., Hutchison, E. R., Han, J. H., Thomas, S. P., Vivas, E. I., Denu, J. M., Ceschin, D. G., Tang, Z.-Z., et al. (2021) · Microbiome · doi:10.1186/s40168-021-01061-6 · Cited by 186

Complement modulates the cutaneous microbiome and inflammatory milieu

Chehoud, C., Rafail, S., Tyldsley, A. S., Seykora, J. T., Lambris, J. D., & Grice, E. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1307855110 · Cited by 184

Studying the microbiology of the indoor environment

Kelley, S. T., & Gilbert, J. A. (2013) · Genome biology · doi:10.1186/gb-2013-14-2-202 · Cited by 192

Biochar alters the soil microbiome and soil function: results of next-generation amplicon sequencing across Europe

Jenkins, J. R., Viger, M., Arnold, E. C., Harris, Z. M., Ventura, M., Miglietta, F., Girardin, C., Edwards, R. J., Rumpel, C., Fornasier, F., et al. (2017) · GCB Bioenergy · doi:10.1111/gcbb.12371 · Cited by 184

The rectal mucosa and condomless receptive anal intercourse in HIV-negative MSM: implications for HIV transmission and prevention

Kelley, C. F., Kraft, C. S., de Man, T. J., Duphare, C., Lee, H., Yang, J., Easley, K. A., Tharp, G. K., Mulligan, M. J., Sullivan, P. S., et al. (2016) · Mucosal Immunology · doi:10.1038/mi.2016.97 · Cited by 185

Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress

Naama, M., Telpaz, S., Awad, A., Ben-Simon, S., Harshuk-Shabso, S., Modilevsky, S., Rubin, E., Sawaed, J., Zelik, L., Zigdon, M., et al. (2023) · Cell Host & Microbe · doi:10.1016/j.chom.2023.01.006 · Cited by 187

Unveiling the gut microbiota composition and functionality associated with constipation through metagenomic analyses

Mancabelli, L., Milani, C., Lugli, G. A., Turroni, F., Mangifesta, M., Viappiani, A., Ticinesi, A., Nouvenne, A., Meschi, T., van Sinderen, D., et al. (2017) · Scientific Reports · doi:10.1038/s41598-017-10663-w · Cited by 182

Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota

Munyaka, P. M., Eissa, N., Bernstein, C. N., Khafipour, E., & Ghia, J. (2015) · PLoS ONE · doi:10.1371/journal.pone.0142536 · Cited by 189

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

Parfrey, L. W., Walters, W. A., Lauber, C. L., Clemente, J. C., Berg-Lyons, D., Teiling, C., Kodira, C. D., Mohiuddin, M., Brunelle, J., Driscoll, M. D., et al. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00298 · Cited by 191

Community Dynamics and Activity of Ammonia-Oxidizing Prokaryotes in Intertidal Sediments of the Yangtze Estuary

Zheng, Y., Hou, L., Newell, S. E., Liu, M., Zhou, J., Zhao, H., You, L., & Cheng, X. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.03035-13 · Cited by 183

Intestinal microbiota in infants at high risk for allergy: Effects of prebiotics and role in eczema development

Wopereis, H., Sim, K., Shaw, A., Warner, J. O., Knol, J., & Kroll, J. S. (2017) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2017.05.054 · Cited by 185

Inulin-type fructan improves diabetic phenotype and gut microbiota profiles in rats

Zhang, Q., Yu, H., Xiao, X., Hu, L., Xin, F., & Yu, X. (2018) · PeerJ · doi:10.7717/peerj.4446 · Cited by 188

Next generation sequencing for gut microbiome characterization in rainbow trout (Oncorhynchus mykiss) fed animal by-product meals as an alternative to fishmeal protein sources

Rimoldi, S., Terova, G., Ascione, C., Giannico, R., & Brambilla, F. (2018) · PLoS ONE · doi:10.1371/journal.pone.0193652 · Cited by 193

Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences

Zhang, X., Hu, B. X., Ren, H., & Zhang, J. (2018) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2018.03.158 · Cited by 179

Vitamin D metabolites and the gut microbiome in older men

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Suppression of the gut microbiome ameliorates age‐related arterial dysfunction and oxidative stress in mice

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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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