Share This Author
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.
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
It is shown that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
This work sequences a diverse array of 25 environmental samples and three known “mock communities” at a depth averaging 3.1 million reads per sample to demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature.
Toward an ecological classification of soil bacteria.
Survey, experimental, and meta-analytical results suggest that certain bacterial phyla can be differentiated into copiotrophic and oligotrophic categories that correspond to the r- and K-selected categories used to describe the ecological attributes of plants and animals.
The diversity and biogeography of soil bacterial communities.
- N. Fierer, R. B. Jackson
- Environmental ScienceProceedings of the National Academy of Sciences…
- 17 January 2006
Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in this study.
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
- C. Lauber, M. Hamady, R. Knight, N. Fierer
- Biology, MedicineApplied and Environmental Microbiology
- 5 June 2009
The results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.
Bacterial Community Variation in Human Body Habitats Across Space and Time
- E. Costello, C. Lauber, M. Hamady, N. Fierer, J. Gordon, R. Knight
- Environmental ScienceScience
- 18 December 2009
The results indicate that the microbiota, although personalized, varies systematically across body habitats and time; such trends may ultimately reveal how microbiome changes cause or prevent disease.
Soil bacterial and fungal communities across a pH gradient in an arable soil
Soils collected across a long-term liming experiment were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria, and both the relative abundance and diversity of bacteria were positively related to pH.
Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns
- M. Dominguez-Bello, E. Costello, R. Knight
- Medicine, BiologyProceedings of the National Academy of Sciences
- 21 June 2010
It is found that in direct contrast to the highly differentiated communities of their mothers, neonates harbored bacterial communities that were undifferentiated across multiple body habitats, regardless of delivery mode.