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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. HereExpand
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Metagenomic biomarker discovery and explanation
This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses theExpand
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Structure, Function and Diversity of the Healthy Human Microbiome
Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remainsExpand
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Metagenomic microbial community profiling using unique clade-specific marker genes
Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large dataExpand
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MetaPhlAn2 for enhanced metagenomic taxonomic profiling
 Profiling of all domains of life. Marker and quasi-marker genes are now identified not only for microbes (Bacteria and Archaea), but also for viruses and Eukaryotic microbes (Fungi, Protozoa) thatExpand
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Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment
BackgroundThe inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions ofExpand
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The treatment-naive microbiome in new-onset Crohn's disease.
Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota.Expand
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PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes
New microbial genomes are constantly being sequenced, and it is crucial to accurately determine their taxonomic identities and evolutionary relationships. Here we report PhyloPhlAn, a new method toExpand
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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
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Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.
The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of theseExpand
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