Abstract
Humans host complex microbial communities believed to contribute to health maintenance and, when in imbalance, to the development of diseases. Determining the microbial composition in patients and healthy controls may thus provide novel therapeutic targets. For this purpose, high-throughput, cost-effective methods for microbiota characterization are needed. We have employed 454-pyrosequencing of a hyper-variable region of the 16S rRNA gene in combination with sample-specific barcode sequences which enables parallel in-depth analysis of hundreds of samples with limited sample processing. In silico modeling demonstrated that the method correctly describes microbial communities down to phylotypes below the genus level. Here we applied the technique to analyze microbial communities in throat, stomach and fecal samples. Our results demonstrate the applicability of barcoded pyrosequencing as a high-throughput method for comparative microbial ecology.
Highlights
The human gastrointestinal tract is populated by complex communities of microorganisms, which outnumber the eukaryotic host cells by one order of magnitude [1]
The gut microbiota play important roles in extracting nutrients from the diet [2,3], regulating host fat storage [4], stimulating intestinal epithelium renewal [5], and directing the maturation of the immune system [6]. Keeping these communities in balance is most likely crucial for health maintenance, and perturbation of microbial composition has been hypothesized to be involved in a range of diseases, within and outside the gut [7,8]
The most extensive surveys of human microbial ecology have been performed on colonic microbiota (e.g. [9,10,11]), whereas less has been reported from upper gastro-intestinal tract habitats
Summary
The human gastrointestinal tract is populated by complex communities of microorganisms, which outnumber the eukaryotic host cells by one order of magnitude [1]. The gut microbiota play important roles in extracting nutrients from the diet [2,3], regulating host fat storage [4], stimulating intestinal epithelium renewal [5], and directing the maturation of the immune system [6]. Keeping these communities in balance is most likely crucial for health maintenance, and perturbation of microbial composition has been hypothesized to be involved in a range of diseases, within and outside the gut [7,8]. Developed methods based on microarray technology [17,18] hold promise for large-scale studies, but they do not capture novel sequences
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