Analysis of the intestinal microbiota using SOLiD 16SrRNA gene sequencing and SOLiD shotgun sequencing. human gut metagenome

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 more suitable in the context of reference-guided projects. To investigate the performance of SOLiD sequencing in a metagenomic context, we compared taxonomic profiles of SOLiD mate-pair sequencing reads with the Sanger paired reads and 454 single reads. All the sequences are obtained from the bacterial 16S rRNA gene that 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 the SOLiD technique to study the composition of the intestinal microbiota and the existing microbial metabolism. By analyzing the shotgun data we found that the microbiota composition of 16S rRNA gene sequences obtained using Sanger, 454 and SOLiD sequencing provide comparable results. However, with SOLiD sequences we obtained more resolution down to the species level. In addition, with the shotgun data we are able to identify the functional profile using SEED and KEGG. 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 medical studies.