Quantifying the bias introduced by the use of different targeted regions of the 16S rRNA gene for the characterization of microbial communities using amplicon-sequencing

IBARBALZ, F.M.; PEREZ, M.V.; FIGUEROLA, E.L.M.; ERIJMAN, L.

Rosario

Congreso; 4to. Congreso Argentino de Bioinformática y Biología Computacional (4CAB2C) y 4ta. Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SolBio); 2013

Asociacion Argentina de Bioinformatica y Biologia Computacional

The aim of this work was to assess the degree of dissimilarity among communities that would overcome the bias introduced by the use of primer sets targeting different 16S rRNA regions. We hypothesized that a transition from 16S region-based clustering to composition-based clustering would occur within a gradient of communities with gradually increasing dissimilarity. To test this hypothesis, we performed 454 pyrosequencing of a series of twelve monthly samples from activated sludge taken from a sewage treatment plant (STP) located in the northern suburbs of Buenos Aires, Argentina. Additionally, two activated sludge samples from a different STP located in the southern suburbs of Buenos Aires were also included in the analysis. DNA amplification was performed using two pairs of universal primers, targeting the V1-V3 regions (E. coli 8-534 position) and the V4 region (E. coli 563-924 position). We showed that V1-V3 and the V4 region of the 16S rRNA can reach similar estimation of alpha diversity, but fail in providing an appropriate representation of beta diversity due to the biases introduced by the unequal amplification of the different community members. These results highlight the need to combine different strategies for the study of complex microbial ecosystems.