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The Statistical Analysis of Compositional Data

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Factors influencing the composition of the intestinal microbiota in early infancy

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Exposure to Environmental Microorganisms and Childhood Asthma

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Human Intestinal Lumen and Mucosa-Associated Microbiota in Patients with Colorectal Cancer

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Oral Microbiota Changes Contribute to Autism Spectrum Disorder in Mice

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Subacute ruminal acidosis phenotypes in periparturient dairy cows differ in ruminal and salivary bacteria and in the in vitro fermentative activity of their ruminal microbiota

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Human Milk Oligosaccharides Reduce Murine Group B Streptococcus Vaginal Colonization with Minimal Impact on the Vaginal Microbiota

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Association of Human Intestinal Microbiota with Lifestyle Activity, Adiposity, and Metabolic Profiles in Thai Children with Obesity

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Multi-omic Analysis of the Gut Microbiome in Rats with Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy

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Active Peptide AR-9 From Eupolyphaga sinensis Reduces Blood Lipid and Hepatic Lipid Accumulation by Restoring Gut Flora and Its Metabolites in a High Fat Diet–Induced Hyperlipidemia Rat

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Grain, Gluten, and Dietary Fiber Intake Influence Gut Microbial Diversity: Data from the Food and Microbiome Longitudinal Investigation

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Development of gut mycobiome in infants and young children: a prospective cohort study

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Microbiota Predict Infections and Acute Graft-Versus-Host Disease After Pediatric Allogeneic Hematopoietic Stem Cell Transplantation

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Zearalenone attenuates colitis associated colorectal tumorigenesis through Ras/Raf/ERK pathway suppression and SCFA-producing bacteria promotion

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Topsoil and subsoil bacterial community assemblies across different drainage conditions in a mountain environment

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Subgingival Microbiome Colonization and Cytokine Production during Early Dental Implant Healing

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The Proteome of Pancreatic Cancer‐Derived Exosomes Reveals Signatures Rich in Key Signaling Pathways

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Ground beef microbiome changes with antimicrobial decontamination interventions and product storage

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Metritis and the uterine disease microbiome are associated with long-term changes in the endometrium of dairy cows

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Influence of host phylogeny, geographical location and seed harvesting diet on the bacterial community of globally distributed Pheidole ants

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Applications of weighted association networks applied to compositional data in biology

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Meta-analysis cum machine learning approaches address the structure and biogeochemical potential of marine copepod associated bacteriobiomes

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A rarefaction-based extension of the LDM for testing presence–absence associations in the microbiome

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Partial Substitution of Meat with Insect (Alphitobius diaperinus) in a Carnivore Diet Changes the Gut Microbiome and Metabolome of Healthy Rats

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Cervicovaginal microbiome dynamics after taking oral probiotics

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Enterococcus faecium are associated with the modification of gut microbiota and shrimp post-larvae survival

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Effects of a Low-Carbohydrate, High-Protein Diet on Gut Microbiome Composition in Insulin-Resistant Individuals With Chronic Spinal Cord Injury: Preliminary Results From a Randomized Controlled Trial

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Fresh Versus Frozen Stool for Fecal Microbiota Transplantation—Assessment by Multimethod Approach Combining Culturing, Flow Cytometry, and Next-Generation Sequencing

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Microbiome signatures in Acropora cervicornis are associated with genotypic resistance to elevated nutrients and heat stress

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Impact of Putative Probiotics on Growth, Behavior, and the Gut Microbiome of Farmed Arctic Char (Salvelinus alpinus)

Knobloch, S., Skírnisdóttir, S., Dubois, M., Kolypczuk, L., Leroi, F., Leeper, A., Passerini, D., & Marteinsson, V. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.912473 · Cited by 22

Bacterial extracellular vesicles in the microbiome of first-pass meconium in newborn infants

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Supplementation of polyphenol-rich grapes attenuates colitis, colitis-associated colon cancer, and disease-associated dysbiosis in mice, but fails to mitigate colitis in antibiotic-treated mice

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Effects of land-use intensity, grazing and fire disturbances on soil bacterial and fungal communities in subtropical wetlands

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Effects of Pesticide Intake on Gut Microbiota and Metabolites in Healthy Adults

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Earthworm-Driven Changes in Soil Chemico-Physical Properties, Soil Bacterial Microbiota, Tree/Tea Litter Decomposition, and Plant Growth in a Mesocosm Experiment with Two Plant Species

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Fungal Hyphosphere Microbiomes Are Distinct from Surrounding Substrates and Show Consistent Association Patterns

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Oral supplementation of nicotinamide riboside alters intestinal microbial composition in rats and mice, but not humans

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Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data

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Association of probable post-traumatic stress disorder with dietary pattern and gut microbiome in a cohort of women

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Remote effects of kidney drug transporter OAT1 on gut microbiome composition and urate homeostasis

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Practical considerations for sampling and data analysis in contemporary metagenomics-based environmental studies

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A novel normalization and differential abundance test framework for microbiome data

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Effect of Cyberlindnera jadinii yeast as a protein source on intestinal microbiota and butyrate levels in post-weaning piglets

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Tick Microbiomes in Neotropical Forest Fragments Are Best Explained by Tick-Associated and Environmental Factors Rather than Host Blood Source

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Implications of taxonomic bias for microbial differential-abundance analysisPreprint

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Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater

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Inhibition of Rumen Protozoa by Specific Inhibitors of Lysozyme and Peptidases in vitro

Park, T., Mao, H., & Yu, Z. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02822 · Cited by 24

Gut Dysbiosis in Chagas Disease. A Possible Link to the Pathogenesis

de Souza-Basqueira, M., Ribeiro, R., de Oliveira, L. C., Moreira, C. H. V., Martins, R. C. R., Franco, D. C., Amado, P. P. P., Mayer, M. P. A., & Sabino, É. C. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00402 · Cited by 21

Spatial distribution of microbial communities among colonies and genotypes in nursery-reared Acropora cervicornis

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Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures

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A Multi-Omics Approach Reveals New Signatures in Obese Allergic Asthmatic Children

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Influence of the cold bottom water on taxonomic and functional composition and complexity of microbial communities in the southern Yellow Sea during the summer

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Early Gut Fungal and Bacterial Microbiota and Childhood Growth

Schei, K., Simpson, M. R., Avershina, E., Rudi, K., Øien, T., Júlíusson, P. B., Underhill, D. M., Salamati, S., & Ødegård, R. A. (2020) · Frontiers in Pediatrics · doi:10.3389/fped.2020.572538 · Cited by 21

Delayed Gut Colonization Shapes Future Allergic Responses in a Murine Model of Atopic Dermatitis

Arildsen, A. W., Zachariassen, L. F., Krych, Ł., Hansen, A. K., & Hansen, C. H. F. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.650621 · Cited by 23

Intestinal mucositis precedes dysbiosis in a mouse model for pelvic irradiation

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Massive Survey on Bacterial–Bacteriophages Biodiversity and Quality of Natural Whey Starter Cultures in Trentingrana Cheese Production

Mancini, A., Cid-Rodríguez, M., Zago, M., Cologna, N., Goss, A., Carafa, I., Tuohy, K. M., Merz, A., & Franciosi, E. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.678012 · Cited by 21

Longitudinal patterns in the skin microbiome of wild, individually marked frogs from the Sierra Nevada, California

Ellison, S., Knapp, R. A., & Vredenburg, V. T. (2021) · ISME Communications · doi:10.1038/s43705-021-00047-7 · Cited by 21

Characterization of the gut microbiota among Veterans with unique military-related exposures and high prevalence of chronic health conditions: A United States-Veteran Microbiome Project (US-VMP) study

Stanislawski, M. A., Stamper, C. E., Stearns‐Yoder, K. A., Hoisington, A. J., Brostow, D. P., Forster, J. E., Postolache, T. T., Lowry, C. A., & Brenner, L. A. (2021) · Brain Behavior & Immunity - Health · doi:10.1016/j.bbih.2021.100346 · Cited by 23

Metataxonomic and Metabolic Impact of Fecal Microbiota Transplantation From Patients With Pancreatic Cancer Into Germ-Free Mice: A Pilot Study

Genton, L., Lazarević, V., Stojanović, O., Spiljar, M., Djaafar, S., Koessler, T., Dutoit, V., Gaïa, N., Mareschal, J., Macpherson, A. J., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.752889 · Cited by 25

Association between Parkinson’s disease and the faecal eukaryotic microbiota

Weis, S., Meisner, A., Schwiertz, A., Unger, M. M., Becker, A., Fassbender, K. C., Schnell, S., Schäfer, K., & Egert, M. (2021) · npj Parkinson s Disease · doi:10.1038/s41531-021-00244-0 · Cited by 21

Bacterial Biofilm Thickness and Fungal Inhibitory Bacterial Richness Both Prevent Establishment of the Amphibian Fungal Pathogen Batrachochytrium dendrobatidis

Chen, M. Y., Alexiev, A., & McKenzie, V. J. (2022) · Applied and Environmental Microbiology · doi:10.1128/aem.01604-21 · Cited by 24

Additional Resistant Starch from One Potato Side Dish per Day Alters the Gut Microbiota but Not Fecal Short-Chain Fatty Acid Concentrations

DeMartino, P., Johnston, E. A., Petersen, K. H., Kris‐Etherton, P. M., & Cockburn, D. W. (2022) · Nutrients · doi:10.3390/nu14030721 · Cited by 21

Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women

Carter, K. A., Balkus, J. E., Anzala, O., Kimani, J., Hoffman, N. G., Fiedler, T. L., Mochache, V., Fredricks, D. N., McClelland, R. S., & Srinivasan, S. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.801770 · Cited by 21

Bacterial communities in the gastrointestinal tract segments of helminth-resistant and helminth-susceptible sheep

Paz, E. A., Chua, E. G., Hassan, S. U., Greeff, J. C., Palmer, D. G., Liu, S., Lamichhane, B., Sepúlveda, N., Liu, J., Tay, C. Y., et al. (2022) · Animal Microbiome · doi:10.1186/s42523-022-00172-1 · Cited by 21

A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility

Belk, A. D., Frazier, A., Fuerniss, L. K., Delmore, R. J., Belk, K. E., Borlee, B. R., Geornaras, I., Martin, J. N., & Metcalf, J. L. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02045-22 · Cited by 21

Myeloid-derived suppressor cells prevent disruption of the gut barrier, preserve microbiota composition, and potentiate immunoregulatory pathways in a rat model of experimental autoimmune encephalomyelitis

Radojević, D., Bekić, M., Gruden‐Movsesijan, A., Ilić, N., Dinić, M., Bisenić, A., Golić, N., Vučević, D., Đokić, J., & Tomić, S. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2127455 · Cited by 21

Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort

Claassen-Weitz, S., Gardner‐Lubbe, S., Xia, Y., Mwaikono, K. S., Mounaud, S. H., Nierman, W. C., Workman, L., Zar, H. J., & Nicol, M. P. (2023) · Microbiome · doi:10.1186/s40168-023-01563-5 · Cited by 20

Multi-omics analysis of hospital-acquired diarrhoeal patients reveals biomarkers of enterococcal proliferation and Clostridioides difficile infection

Bosnjak, M., Karpe, A. V., Van, T. T. H., Kotsanas, D., Jenkin, G., Costello, S. P., Johanesen, P., Moore, R. J., Beale, D. J., Srikhanta, Y. N., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-43671-8 · Cited by 22

Excess fermentation and lactic acidosis as detrimental functions of the gut microbes in treatment-naive TB patients

Yunusbaeva, M. M., Borodina, L., Terentyeva, D., Bogdanova, A. A., Zakirova, A., Bulatov, S., Altinbaev, R., Bilalov, F. S., & Yunusbayev, B. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1331521 · Cited by 20

Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

Debode, F., Caulier, S., Demeter, S., Dubois, B., Gelhay, V., Hulin, J., Muhovski, Y., Ninane, V., Rousseau, G., & Bragard, C. (2024) · EFSA Supporting Publications · doi:10.2903/sp.efsa.2024.en-8602 · Cited by 22

Systematic Evaluation of Normalization Methods for Glycomics Data Based on Performance of Network Inference

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Longitudinal Changes in Diet Cause Repeatable and Largely Reversible Shifts in Gut Microbial Communities of Laboratory Mice and Are Observed across Segments of the Entire Intestinal Tract

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The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f

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