THESIS
2021
1 online resource (xviii, 144 pages) : illustrations (some color), map
Abstract
Escherichia coli is widely used as one of the major fecal indicator bacteria for water quality
monitoring due to its feature of being adapted to the gastrointestinal tracts of warm-blooded
animals (primary habitats) and considered unable to survive for extended time in external
environments (secondary habitats). However, recent studies indicated the existence of six
monophyletic cryptic Escherichia clades (CI to VI) indistinguishable from E. coli sensu stricto
using conventional diagnostic methods. CI is a subspecies of E. coli and host-associated, and
CIII to V are associated with external environments. Contrarily, the evolution, habitat, and
lifestyle of the members of CII were rarely investigated. This research investigated the
evolution and ecology of the CII strains and their relat...[
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Escherichia coli is widely used as one of the major fecal indicator bacteria for water quality
monitoring due to its feature of being adapted to the gastrointestinal tracts of warm-blooded
animals (primary habitats) and considered unable to survive for extended time in external
environments (secondary habitats). However, recent studies indicated the existence of six
monophyletic cryptic Escherichia clades (CI to VI) indistinguishable from E. coli sensu stricto
using conventional diagnostic methods. CI is a subspecies of E. coli and host-associated, and
CIII to V are associated with external environments. Contrarily, the evolution, habitat, and
lifestyle of the members of CII were rarely investigated. This research investigated the
evolution and ecology of the CII strains and their relationship with other Escherichia, especially
E. coli through genomic approaches. Preliminary indications of ecological differentiation
within CII were also investigated through a combination of delta-bitscore metrics and random
forest classifier. Comparative genomics between 18 CII strains isolated from marine and
freshwater environments in Hong Kong and 42 reference strains revealed Escherichia’s genome
plasticity, with gene loss predominated as they evolve and differentiate. Generally, accelerated
gene loss related to cell adhesion in CII-VI drives their divergence from enteric Escherichia,
reflected an inclination towards extra-host lifestyle. Moreover, enteric and CII-VI strains have
genetic and functional enrichments favoring survival in gastrointestinal tract and external
environments, respectively. Homologous recombination of core genes was not only detected
within CII-VI but also between CII-VI and enteric genomes. CII is monophyletic and justifiable
as a novel Escherichia species rather than E. coli sensu stricto based on genome sequence
similarity DDH and ANI analysis. CII strains displayed genomic signatures that are consistent
with divergent adaptation to gastrointestinal and external environments. Overall, gene
degradation was more prominent in the gastrointestinal CII strains. The trained random forest
model identified predictor genes that were informative of habitat association. Functional
divergences in many of these genes were reflective of ecological divergence.
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