Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

Abstract

The current prokaryotic taxonomy classifies phenotypically and genotypically diverse microorganisms using a polyphasic approach. With advances in the next-generation sequencing technologies and computational tools for analysis of genomes, the traditional polyphasic method is complemented with genomic data to delineate and classify bacterial genera and species as an alternative to cumbersome and error-prone laboratory tests. This review discusses the applications of sequence-based tools and techniques for bacterial classification and provides a scheme for more robust and reproducible bacterial classification based on genomic data. The present review highlights promising tools and techniques such as ortho-Average Nucleotide Identity, Genome to Genome Distance Calculator and Multi Locus Sequence Analysis, which can be validly employed for characterizing novel microorganisms and assessing phylogenetic relationships. In addition, the review discusses the possibility of employing metagenomic data to assess the phylogenetic associations of uncultured microorganisms. Through this article, we present a review of genomic approaches that can be included in the scheme of taxonomy of bacteria and archaea based on computational and in silico advances to boost the credibility of taxonomic classification in this genomic era.

Taxonomy and nomenclature of bacteria with clinical and scientific importance: current concepts for pharmacists and pharmaceutical scientists

“…E. coli species conjugate well with Salmonella and Shigella species (which are more closely related taxonomically), but not with members of the genera Proteus, Providencia or Enterobacter. Similar results were found in transformation studies on Rhizobium, Micrococcus, Bacillus and Haemophilus species, showing that transformation events more frequently occur with different species of the same genera (smaller genomic variation), compared to species of different genera (larger genomic variation) [47][48][49][50].…”

“…These methods have demonstrated that genotypic/phylogenetic relatedness does not necessary correlate well with phenotypic attributes, such as a Gram-staining pattern, microscopic morphology, oxygen-tolerance or fastidious growth characteristics [47]. These molecular methods include comparison of DNAdenaturation or melting temperatures (T m ), characterization of GC (guanine and cytosine) ratios of bacterial DNA, DNA-DNA and DNA-RNA hybridization, pulse-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), average nucleotide identity (ANI), MALDI-TOF MS, 16S rRNA gene and whole genome sequencing (WGS) and next-generation sequencing (NGS) [48][49][50]. The use of these methods in increasingly prevalent not only in classification, but also in identification thus, revolutionizing the field of microbiology in the process [48][49][50].…”

“…they are more conserved), compared to other genes coding for proteins [52,53]. Currently, various nucleic acid sequencing methods (of which, WGS and NGS are one of the most modern) represent the top-tier methods for bacterial classification and the comparison of genomic structures [48][49][50]. Nucleic acid (DNA and RNA) sequencing is another mo-lecular characteristic that helps directly compare the genomic structures.…”

“…Nucleic acid (DNA and RNA) sequencing is another mo-lecular characteristic that helps directly compare the genomic structures. The sequencing of 5S rRNA (from the 50S prokaryotic ribosomal subunit), 16S rRNA and 16S rDNA (from the 30S prokaryotic ribosomal subunit) has received the most substantial attention [47][48][49][50]. In fact, current recommendations state that for the submission of a novel species, the performance of MLST or sequencing (to characterize genomic relatedness) and the submission of a preferably full-length 16S rRNA gene sequence are recommended [47].…”

“…conjugation, transformation and transduction), which entails the transfer of plasmid DNA from one species/genus/family of bacteria to another. In reality, these properties may also be useful to characterize relations between different bacterial taxa [47][48][49][50]. E. coli species conjugate well with Salmonella and Shigella species (which are more closely related taxonomically), but not with members of the genera Proteus, Providencia or Enterobacter.…”