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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and 1565057 to R.K. Partial support was also provided by the following: grants NIH U54CA143925 (J.G.C. and T.P.) andExpand
Structure, Function and Diversity of the Healthy Human Microbiome
TLDR
The Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far, finding the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. Expand
The treatment-naive microbiome in new-onset Crohn's disease.
TLDR
Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD. Expand
Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy
TLDR
It is indicated that host-microbial interactions that impact host metabolism can occur and may be beneficial in pregnancy and when transferred to germ-free mice, T3 microbiota induced greater adiposity and insulin insensitivity compared to T1. Expand
Using QIIME to Analyze 16S rRNA Gene Sequences from Microbial Communities
TLDR
The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities. Expand
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
TLDR
QIIME 2 provides new features that will drive the next generation of microbiome research, including interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science. Expand
Advancing our understanding of the human microbiome using QIIME.
TLDR
This chapter demonstrates the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. Expand
Moving pictures of the human microbiome
TLDR
The largest human microbiota time series analysis to date is presented, covering two individuals at four body sites over 396 timepoints and finds that despite stable differences between body sites and individuals, there is pronounced variability in an individual's microbiota across months, weeks and even days. Expand
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
TLDR
The value of characterizing vertebrate gut microbiomes to understand host evolutionary histories at a supraorganismal level is illustrated by shotgun sequencing of microbial community DNA and targeted sequencing of bacterial 16S ribosomal RNA genes. Expand
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
TLDR
It is demonstrated that periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts, and integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. Expand
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