UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

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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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Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

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Captivity humanizes the primate microbiome

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Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases

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Unraveling the processes shaping mammalian gut microbiomes over evolutionary time

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Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice

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Differences in gut microbiota profile between women with active lifestyle and sedentary women

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Chapter 12: Human Microbiome Analysis

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Alterations in the Gut Microbiota Associated with HIV-1 Infection

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Characterizing the avian gut microbiota: membership, driving influences, and potential function

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Soil microbial community response to drying and rewetting stress: does historical precipitation regime matter?

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Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

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Supervised classification of human microbiota

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Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

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Infant gut microbiota and food sensitization: associations in the first year of life

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Human milk microbiota profiles in relation to birthing method, gestation and infant gender

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Biodiversity and species competition regulate the resilience of microbial biofilm community

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Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat

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Bacterial Communities Associated with the Surfaces of Fresh Fruits and Vegetables

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Bacterial community structures are unique and resilient in full-scale bioenergy systems

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Global diversity in the human salivary microbiomePreprint

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Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples

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A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities

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Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

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Microbial shifts in the aging mouse gut

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Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA

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Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels

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Application of multivariate statistical techniques in microbial ecology

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Environmental and anthropogenic controls over bacterial communities in wetland soils

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Biogeography of bacterial communities exposed to progressive long-term environmental change

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Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.)

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Altered Gut Microbiota in a Mouse Model of Alzheimer’s Disease

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Strong host preference of ectomycorrhizal fungi in a Tasmanian wet sclerophyll forest as revealed by DNA barcoding and taxon‐specific primers

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Temporal variability is a personalized feature of the human microbiome

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Changes in assembly processes in soil bacterial communities following a wildfire disturbance

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Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

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Bacterial Community Mapping of the Mouse Gastrointestinal Tract

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Bacterial diversity at different stages of the composting process

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Extreme Dysbiosis of the Microbiome in Critical Illness

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Community differentiation of the cutaneous microbiota in psoriasis

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Phylogenetic structure in tropical hummingbird communities

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A Compositional Look at the Human Gastrointestinal Microbiome and Immune Activation Parameters in HIV Infected Subjects

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Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade

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Disordered Microbial Communities in the Upper Respiratory Tract of Cigarette Smokers

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The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis

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Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea‐predominant irritable bowel syndrome

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Low-Dose Penicillin in Early Life Induces Long-Term Changes in Murine Gut Microbiota, Brain Cytokines and Behavior

Leclercq, S., Mian, F. M., Stanisz, A. M., Bindels, L. B., Cambier, E., Ben-Amram, H., Koren, O., Forsythe, P., & Bienenstock, J. (2017) · Nature Communications · doi:10.1038/ncomms15062 · Cited by 434

Altered gut microbiota and activity in a murine model of autism spectrum disorders

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Metagenomic analyses reveal antibiotic-induced temporal and spatial changes in intestinal microbiota with associated alterations in immune cell homeostasis

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Viral and microbial community dynamics in four aquatic environments

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Effects of organic–inorganic compound fertilizer with reduced chemical fertilizer application on crop yields, soil biological activity and bacterial community structure in a rice–wheat cropping system

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Early-life gut microbiome composition and milk allergy resolution

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A wellness study of 108 individuals using personal, dense, dynamic data clouds

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Meta-analyses of studies of the human microbiota

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Alterations in Gut Microbiome Composition and Barrier Function Are Associated with Reproductive and Metabolic Defects in Women with Polycystic Ovary Syndrome (PCOS): A Pilot Study

Lindheim, L., Bashir, M., Münzker, J., Trummer, C., Zachhuber, V., Leber, B., Horvath, A., Pieber, T. R., Gorkiewicz, G., Stadlbauer, V., et al. (2017) · PLOS ONE · doi:10.1371/journal.pone.0168390 · Cited by 416

Structural modulation of gut microbiota during alleviation of type 2 diabetes with a Chinese herbal formula

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Bacterial Community Structure in the Drinking Water Microbiome Is Governed by Filtration Processes

Pinto, A. J., Xi, C., & Raskin, L. M. (2012) · Environmental Science & Technology · doi:10.1021/es302042t · Cited by 420

Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies

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Responses of gut microbiota to diet composition and weight loss in lean and obese mice

Ravussin, Y., Koren, O., Spor, A., LeDuc, C., Gutman, R., Stombaugh, J., Knight, R., Ley, R. E., & Leibel, R. L. (2012) · Obesity · doi:10.1038/oby.2011.111 · Cited by 406

Vaginal microbiome transplantation in women with intractable bacterial vaginosis

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Insight into how organic amendments can shape the soil microbiome in long-term field experiments as revealed by network analysis

Ling, N., Zhu, C., Xue, C., Chen, H., Duan, Y., Peng, C., Guo, S., & Shen, Q. (2016) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2016.05.005 · Cited by 412

Mucins and the Microbiome

Hansson, G. C. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-011520-105053 · Cited by 435

The microbial metabolite trimethylamine N-oxide promotes antitumor immunity in triple-negative breast cancer

Wang, H., Rong, X., Zhao, G., Zhou, Y., Xiao, Y., Ma, D., Jin, X., Wu, Y., Yan, Y., Yang, H., et al. (2022) · Cell Metabolism · doi:10.1016/j.cmet.2022.02.010 · Cited by 411

Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans

Ha, C. W. Y., Martin, A., Sepich‐Poore, G. D., Shi, B., Wang, Y., Gouin, K. H., Humphrey, G., Sanders, K., Ratnayake, Y., Chan, K. S. L., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.009 · Cited by 415

Caenorhabditis elegans responses to bacteria from its natural habitats

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Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome

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Rules of Engagement: Interspecies Interactions that Regulate Microbial Communities

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Rumen Microbiome from Steers Differing in Feed Efficiency

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The human microbiome in evolution

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Cervical Microbiome and Cytokine Profile at Various Stages of Cervical Cancer: A Pilot Study

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Exposure to a social stressor disrupts the community structure of the colonic mucosa-associated microbiota

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Gut microbial diversity in women with polycystic ovary syndrome correlates with hyperandrogenism

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A meta-analysis of changes in bacterial and archaeal communities with time

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Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics

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Ancient and modern environmental DNA

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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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