Recently, scientists of the University medical center in Netherlands highlighted that WGS provides more accurate results, in terms of taxa prediction and abundance estimation, in comparison to those of 16S. They showed that distinct taxonomy assignment algorithms produce similar results when using WGS data and that using 16S data for metagenomic investigations can lead to conclusions that are incorrect.
https://www.fsigenetics.com/article/S1872-4973(20)30028-4/fulltext
At MetaGenoPolis, we have an integrated WGS pipeline to perform exhaustive and high-resolution microbiome analysis with Metagenomic Species Pan-genomes (MSPs). MSPs capture and distinguish not only the core genes but also the accessory genes of microbial species. This work provides a gut microbiome composition at strain-level and its inter-individual variability opening the way to a better understanding of the link between the microbiota and diseases.
https://academic.oup.com/bioinformatics/article/35/9/1544/5106712
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