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This article is part of the supplement: Twelfth International Conference on Bioinformatics (InCoB2013): Computational Biology

Open Access Research

Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing

Suparna Mitra1*, Karin Förster-Fromme2, Antje Damms-Machado2, Tim Scheurenbrand4, Saskia Biskup4, Daniel H Huson3 and Stephan C Bischoff2*

Author Affiliations

1 Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551

2 Department of Nutritional Medicine, University of Hohenheim, Stuttgart, Germany

3 Center for Bioinformatics, University of Tübingen, Tübingen, Germany

4 CeGaT GmbH, Tübingen, Germany

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BMC Genomics 2013, 14(Suppl 5):S16  doi:10.1186/1471-2164-14-S5-S16

Published: 16 October 2013

Abstract

Background

Metagenomics seeks to understand microbial communities and assemblages by DNA sequencing. Technological advances in next generation sequencing technologies are fuelling a rapid growth in the number and scope of projects aiming to analyze complex microbial environments such as marine, soil or the gut. Recent improvements in longer read lengths and paired-sequencing allow better resolution in profiling microbial communities. While both 454 sequencing and Illumina sequencing have been used in numerous metagenomic studies, SOLiD sequencing is not commonly used in this area, as it is believed to be more suitable in the context of reference-guided projects.

Results

To investigate the performance of SOLiD sequencing in a metagenomic context, we compared taxonomic profiles of SOLiD mate-pair sequencing reads with Sanger paired reads and 454 single reads. All sequences were obtained from the bacterial 16S rRNA gene, which was amplified from microbial DNA extracted from a human fecal sample. Additionally, from the same fecal sample, complete genomic microbial DNA was extracted and shotgun sequenced using SOLiD sequencing to study the composition of the intestinal microbiota and the existing microbial metabolism. We found that the microbiota composition of 16S rRNA gene sequences obtained using Sanger, 454 and SOLiD sequencing provide results comparable to the result based on shotgun sequencing. Moreover, with SOLiD sequences we obtained more resolution down to the species level. In addition, the shotgun data allowed us to determine a functional profile using the databases SEED and KEGG.

Conclusions

This study shows that SOLiD mate-pair sequencing is a viable and cost-efficient option for analyzing a complex microbiome. To the best of our knowledge, this is the first time that SOLiD sequencing has been used in a human sample.

Keywords:
Metagenomics; Intestinal Microbiota; Next-Generation Sequencing; SOLiD Mate-Pair Sequencing; Human Fecal Sample