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QIIME allows analysis of high-throughput community sequencing data
An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
An obesity-associated gut microbiome with increased capacity for energy harvest
- P. Turnbaugh, R. Ley, M. Mahowald, V. Magrini, E. Mardis, J. Gordon
- Biology, MedicineNature
- 21 December 2006
It is demonstrated through metagenomic and biochemical analyses that changes in the relative abundance of the Bacteroidetes and Firmicutes affect the metabolic potential of the mouse gut microbiota and indicates that the obese microbiome has an increased capacity to harvest energy from the diet.
Microbial ecology: Human gut microbes associated with obesity
It is shown that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet.
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 R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
A core gut microbiome in obese and lean twins
The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
Obesity alters gut microbial ecology.
- R. Ley, F. Bäckhed, P. Turnbaugh, C. Lozupone, R. Knight, J. Gordon
- BiologyProceedings of the National Academy of Sciences…
- 2 August 2005
Analysis of the microbiota of genetically obese ob/ob mice, lean ob/+ and wild-type siblings, and their ob/+ mothers, all fed the same polysaccharide-rich diet, indicates that obesity affects the diversity of the gut microbiota and suggests that intentional manipulation of community structure may be useful for regulating energy balance in obese individuals.
Evolution of Mammals and Their Gut Microbes
It is indicated that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.
Structure, Function and Diversity of the Healthy Human Microbiome
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.
Defining the core Arabidopsis thaliana root microbiome
The pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants is reported to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages.
The Human Microbiome Project
- P. Turnbaugh, R. Ley, M. Hamady, C. Fraser-Liggett, R. Knight, J. Gordon
- 17 October 2007
A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.