Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing
By R. Ranjan, A. Rani, Ahmed A. Metwally, H. McGee, D. Perkins. Biochemical and Biophysical Research Communications - BBRC, 2015
837 citations recorded by the source corpus.
The human microbiome has emerged as a major player in regulating human health and disease. Translation studies of the microbiome have the potential to indicate clinical applications such as fecal transplants and probiotics. However, one major issue is accurate identification of microbes constituting the microbiota. Studies of the microbiome have frequently utilized sequencing of the conserved 16S ribosomal RNA (rRNA) gene. We present a comparative study of an alternative approach using shotgun whole genome sequencing (WGS). In the present study, we analyzed the human fecal microbiome compiling a total of 194.1×106 reads from a single sample using multiple sequencing methods and platforms. Specifically, after establishing the reproducibility of our methods with extensive multiplexing, we compared: 1) The 16S rRNA amplicon versus the WGS method, 2) the Illumina HiSeq versus MiSeq platforms, 3) the analysis of reads versus de novo assembled contigs, and 4) the effect of shorter versus longer reads. Our study demonstrates that shotgun whole genome sequencing has multiple advantages compared with the 16S amplicon method including enhanced detection of bacterial species, increased detection of diversity and increased prediction of genes. In addition, increased length, either due to longer reads or the assembly of contigs, improved the accuracy of species detection.
Subfields: Food Science, Infectious Diseases, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/fb6ad7be971e66dc0f6aa1510d66c78dd408a7b8
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Food Science
In Molecular Biology
Citations in the corpus
- Microbial Biodiversity and Bioremediation Assessment Through Omics Approaches (2020, background): “A major share of the microorganisms in the environment is non-culturable under laboratory conditions (Rashid and Stingl, 2015).”