The impact of the gut microbiota on human health: an integrative view.

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Published in Cell on March 16, 2012

Authors

Jose C Clemente1, Luke K Ursell, Laura Wegener Parfrey, Rob Knight

Author Affiliations

1: Department of Chemistry & Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA.

Associated clinical trials:

Microbiome Changes in Severe Burns (Microbiome) | NCT03130868

Nutritional Intake and Gut Microbiome | NCT03388411

Malaria Birth Cohort (MBC) | NCT04050566

Comparison of the Permanent Skin Flora of Children Who Had Bathing With Two Different Products | NCT04845672

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The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol (2012) 2.17

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Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics (2011) 2.15

Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci U S A (2011) 2.05

Microbial biogeography of public restroom surfaces. PLoS One (2011) 2.04

Advancing our understanding of the human microbiome using QIIME. Methods Enzymol (2013) 2.04

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol (2012) 2.01

Pan-genome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proc Natl Acad Sci U S A (2011) 1.96

Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell Host Microbe (2012) 1.93

Microbiota restoration: natural and supplemented recovery of human microbial communities. Nat Rev Microbiol (2010) 1.89