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https://doi.org/10.1186/1471-2164-14-S5-S16
Title: | Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing | Authors: | Mitra, S Förster-Fromme, K Damms-Machado, A Scheurenbrand, T Biskup, S Huson, D.H Bischoff, S.C |
Keywords: | DNA RNA RNA 16S bacterial RNA RNA 16S Actinobacteria Article Bacteroidetes Clostridiales controlled study DNA extraction DNA sequence feces analysis Firmicutes Fusobacteria gene sequence intestine flora Lactobacillus Listeria metagenomics microbial community microbial metabolism microbiome Neisseria next generation sequencing nonhuman Proteobacteria pyrosequencing RNA sequence Sanger sequencing Verrucomicrobia article comparative study DNA sequence feces genetics human metagenome methodology microbiology microflora Feces Humans Metagenome Metagenomics Microbiota RNA, Bacterial RNA, Ribosomal, 16S Sequence Analysis, DNA |
Issue Date: | 2013 | Citation: | Mitra, S, Förster-Fromme, K, Damms-Machado, A, Scheurenbrand, T, Biskup, S, Huson, D.H, Bischoff, S.C (2013). Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics 14 : S16. ScholarBank@NUS Repository. https://doi.org/10.1186/1471-2164-14-S5-S16 | Rights: | Attribution 4.0 International | 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. © 2013 Mitra et al. | Source Title: | BMC Genomics | URI: | https://scholarbank.nus.edu.sg/handle/10635/181583 | ISSN: | 14712164 | DOI: | 10.1186/1471-2164-14-S5-S16 | Rights: | Attribution 4.0 International |
Appears in Collections: | Elements Staff Publications |
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