35 Result(s)
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J. Gregory Caporaso
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Article
Open AccessCabozantinib and nivolumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial
Supplementation with CBM588, a bifidogenic live bacterial product, has been associated with improved clinical outcomes in persons with metastatic renal cell carcinoma (mRCC) receiving nivolumab and ipilimumab....
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Open AccessEnvironmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border
We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs. 8.4%). This investigation assessed differences in microbial dust composition in relation to...
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Open AccessOligofructose improves small intestinal lipid-sensing mechanisms via alterations to the small intestinal microbiota
Upper small intestinal dietary lipids activate a gut-brain axis regulating energy homeostasis. The prebiotic, oligofructose (OFS) improves body weight and adiposity during metabolic dysregulation but the exact...
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Article
Open AccessLeptospira in river and soil in a highly endemic area of Ecuador
Leptospira are shed into the environment via urine of infected animals. Rivers are thought to be an important risk factor for transmission to humans, though much is unknown about the types of environment or chara...
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Article
Open AccessSpecies abundance information improves sequence taxonomy classification accuracy
Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linear...
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Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
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Article
Open AccessLong-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota
Many studies have reported abnormal gut microbiota in individuals with Autism Spectrum Disorders (ASD), suggesting a link between gut microbiome and autism-like behaviors. Modifying the gut microbiome is a pot...
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Article
Open AccessNext steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017
The National Cancer Institute (NCI) sponsored a 2-day workshop, “Next Steps in Studying the Human Microbiome and Health in Prospective Studies,” in Bethesda, Maryland, May 16–17, 2017. The workshop brought tog...
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Open AccessCurrent progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018
The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its f...
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Species-level functional profiling of metagenomes and metatranscriptomes
Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious map**, and often...
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Qiita: rapid, web-enabled microbiome meta-analysis
Multi-omic insights into microbiome function and composition typically advance one study at a time. However, in order for relationships across studies to be fully understood, data must be aggregated into meta-...
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Best practices for analysing microbiomes
Complex microbial communities shape the dynamics of various environments, ranging from the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies and data analysis have provided ...
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Open AccessOptimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
Taxonomic classification of marker-gene sequences is an important step in microbiome analysis.
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Current understanding of the human microbiome
Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of...
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Open AccessMicrobiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study
Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and ...
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Open AccessKeemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets
Bioinformatics software often requires human-generated tabular text files as input and has specific requirements for how those data are formatted. Users frequently manage these data in spreadsheet programs, wh...
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Open Accessghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fung...
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Protocol
Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon Environments
Interest in the microbiology of hydrocarbon-rich environments has increased rapidly in recent years, with applications ranging from oil spill cleanup to reservoir management. Modern techniques for reading out ...
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Open AccessErratum to: Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
