Bacterial whole-genome sequencing for establishment of reference sequences, comparative genomics, biomarker discovery and characterization of novel taxa.
[eng] Bacteria are the most ubiquitous and widely distributed organisms and play major roles in almost any environment. Therefore, studying and understanding their biology is essential to secure the well-being of the planet and humanity. This can be done by determining, analyzing, and characterizing...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2023 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/688942 |
| Acceso en línea: | http://hdl.handle.net/10803/688942 |
| Access Level: | acceso abierto |
| Palabra clave: | Microbiologia i Biomedicina 579 61 |
| Sumario: | [eng] Bacteria are the most ubiquitous and widely distributed organisms and play major roles in almost any environment. Therefore, studying and understanding their biology is essential to secure the well-being of the planet and humanity. This can be done by determining, analyzing, and characterizing their genome sequences, which has been facilitated thanks to the development of high-throughput DNA sequencing technologies. In this thesis, whole-genome sequencing methodologies were used for establishing bacterial reference genome sequences, including those of the type strains of species within three selected taxa (Papers I, II, III, IV, VI and VIII): Stutzerimonas balearica (formerly, Pseudomonas balearica), a marine bacterium with capacities for degrading aromatic compounds; species of the genus Streptococcus, which encompasses well-known commensal species as well as major human pathogens; and of the family Enterobacteriaceae, an ecologically diverse and taxonomically complex group of bacteria, members of which can be found in many different environments and also can cause an extensive range of diseases in humans. The different methodologies utilized in the studies of this thesis reflect the marked evolution of high-throughput DNA sequencing technologies that has occurred in the last years; this includes the capacity for determining highly accurate complete genome sequences, using the latest long-read sequencing technologies. These developments have led to vast amounts of publicly available genome sequence data, which are essential for downstream studies, such as those described in Papers VI – VIII. However, not everything is positive (“All that glitters is not gold”) about the databases of whole-genome sequences, and Paper V warns users of publicly available genome sequences about the presence of “false” type strain genome sequences and the importance of performing quality controls on the sequence data used in research studies. Subsequently, in Paper VI, the genome sequences determined in Papers I and II were used in combination with publicly available genome sequences to perform a comparative genomic study for elucidating the genomic diversity of S. balearica and its potential for biodegradation of aromatic compounds. Genome sequence data also facilitated the establishment of a strategy for detecting additional strains of S. balearica, based on 16S rRNA gene signature nucleotide positions and sequence similarities for determining the habitats of the species. In Paper VII, hundreds of genome sequences of the Mitis-Group of the genus Streptococcus allowed the determination of a biomarker gene specific for the human pathogen Streptococcus pneumoniae and the establishment of a PCR-based species-specific assay for differentiating S. pneumoniae from closely-related species, which has often hindered accurate identification. In Paper VIII, whole-genome sequencing, in combination with publicly available type strain genome sequences, enabled the confirmation that a clinical isolate of the family Enterobacteriaceae, which was not able to be further identified at clinical laboratories, represents a novel genus and species (Scandinavium goeteborgense) within the family Enterobacteriaceae (Scandinavium goeteborgense) and to accurately determine its taxonomic position. The specific contributions of this thesis exemplify and demonstrate that the latest developments of high-throughput DNA sequencing and whole-genome sequencing have certainly pushed the limits of microbiology and life sciences to a next level, in which we can establish solid grounds for down-stream research and applications and explore the genomic insights of bacteria with extremely high resolution. |
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