Bioinformatics tools for enviromental diagnostics

Abstract

Traditionally, the detection and identification of microorganisms in water samples is done by culture-dependent methods, but these do not allow the detection of all microorganisms. High-throughput sequencing now makes possible to determine the whole microbiome and the viral diversity of water samples. A 16S ribosomal RNA subunit gene-based method was used to study the bacterial diversity of 24 reclaimed water samples. The phyla Patescibacteria, Bacteroidetes, Proteobacteria, Epsilonbacteraeota or Campylobacteria and Verrucomicrobia dominated the microbiomes of the studied samples. The results provide insight into the complex microbial community of reclaimed water, highlighting the potential environmental and health risks associated with its use. A set of ten sewage samples was analysed for low-frequency variants within the SARS CoV-2 genome. The method used was able to distinguish multiple SNPs belonging to different SARS-Cov-2 variants within the same wastewater sample. In addition, several mutations of the Gamma variant (P.1, Brazil) were detected before it was considered a Variant of Concern (VOC). The use of qRT-PCR in conjunction with wastewater sequencing methods has shown the potential to quantify the amount of SARS-Cov-2 present in a sample, and to identify specific mutations or single nucleotide polymorphisms (SNPs) to track SARS-Cov-2 variants. Thanks to the use of bioinformatics approaches such as those used in this study, it has been shown that the analysis of sequences presents in water samples (reclaimed, wastewater...) should play a key role in environmental decision-making and, increasingly, in the field of public health. Stressing the importance of including these new technologies in the future regulations to improve the quality control of water.