Influence of 16S rRNA target region on the outcome of microbiome studies in soil and saliva samples
This work was financially supported by the Ministry of Economy and Competitiveness of Spain co-financed with European Regional Development Funds (References: CGL2015-71709-R and SAF2015-71714-R) and the fellowship PEJ2018-004702-A. The European Union also collaborated in the funding of this study (Euronanomed programme, Reference: TARBRAINFECT, and Innovative Medicines Initiative IMI2, Reference: 3TR-831434), as well as the Health Institute Carlos III as the local management institution (Reference: AC18/00008). A.S.L. and V.S.M. were supported by a fellowship from the Ministry of Education, Culture and Sport (FPU 17/05413 and FPU 16/05822), and the results presented in this article are part of A.S.L's doctoral thesis. M.O.G acknowledges for the funds received by the F.P.U. fellowship provided by University of Almeria. ; Next generation sequencing methods are widely used in evaluating the structure and functioning of microbial communities, especially those centered on 16S rRNA subunit. Since Illumina Miseq, the most used sequencing platform, does not allow the full sequencing of 16S rRNA gene, this study aims to evaluate whether the choice of different target regions might affect the outcome of microbiome studies regarding soil and saliva samples. V1V3, V3V4, V4V5 and V6V8 domains were studied, finding that while some regions showed differences in the detection of certain bacterial taxa and in the calculation of alpha diversity, especially in soil samples, the overall effect did not compromise the differentiation of any sample type in terms of taxonomic analysis at the genus level. 16S rRNA target regions did affect the detection of specific bacteria related to soil quality and development, and microbial genera used as health biomarkers in saliva. V1V3 region showed the closest similarity to internal sequencing control mock community B, suggesting it might be the most preferable choice regarding data reliability. ; European Union (EU) 3TR-831434 ; Instituto de Salud Carlos III AC18/00008 ; Ministry of Education, Culture and Sport FPU 17/05413 FPU 16/05822 ; University of Almeria ; Ministry of Economy and Competitiveness of Spain ; European Union (EU) CGL2015-71709-R SAF2015-71714-R PEJ2018-004702-A