A multi-omics perspective on the biology and evolution of the genus Macrococcus
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Date
2020-04-05
Authors
Mazhar, Shahneela
Journal Title
Journal ISSN
Volume Title
Publisher
University College Cork
Published Version
Abstract
The Gram-positive genus Macrococcus currently comprises eleven species;
Macrococcus bovicus, Macrococcus carouselicus, Macrococcus equipercicus,
Macrococcus brunensis, Macrococcus hajekii, Macrococcus lamae, Macrococcus
goetzii, Macrococcus bohemicus, Macrococcus epidermidis, Macrococcus canis, and
Macrococcus caseolyticus that are commonly isolated from animal skin and their meat
and milk products. The species of this genus are evolutionarily closely related to the
species of Staphylococcus. In contrast to staphylococcal species, macrococci are
generally thought to be avirulent. However, new evidence suggests the emergence of
the species M. caseolyticus as a potential new pathogen. Additionally, genomic
insights into the genomes of some members of this genus demonstrate the potential
for these organisms to serve as reservoirs of methicillin resistance determinants.
Considering that strains of the M. caseolyticus species have been associated with
flavour development in dairy and fermented meat products, further investigation of
this fascinating genus, and the species within it, is warranted. Therefore, this thesis
aimed to explore genus-wide genomic diversity and distribution of antimicrobial
resistance along with examining the role of M. caseolyticusin the flavour development
of fermented dairy products, paying particular attention to the safety of this organism
in the food system.
During this thesis work, a rapid PCR-based method was developed to isolate and
establish a strain collection of M. caseolyticus and M. canis from diverse sources. The
13 strains isolated in this study were investigated using phylogenetic analysis based
on partial 16S rRNA and ctaC gene, revealed DPC7161T
strain to form a separate
branch from all the known members of the genus. A polyphasic approach based on the
combination of genomic, phenotypic, and chemotaxonomic characteristics were used
to identify the taxonomic position of DPC7161T. The results from this analysis
suggested that strain DPC7161T represents a novel species of the genus Macrococcus
with the name Macrococcus linguae sp. nov, proposed. Further comparative genomics
analysis suggested that M. goetzii and M. canis species are composed of two distinct
subspecies: M. canis subsp. canis subsp. nov., M. canis subsp. bovinus subsp. nov., M.
goetzii subsp. goetzii subsp. nov, and M. goetzii subsp. corkensis subsp. nov. After a
thorough taxonomic characterisation of strain collection, six strains belonging to the
M. caseolyticus species were further investigated using a systems wide approach integrating the enzymatic, metabolic and genomic data to unravel their flavour
forming potential. The enzymatic analysis has identified highly active cell wall bound
proteases driving extensive casein hydrolysis associated with dairy-derived strains of
M. caseolyticus. Finally, pan-genomic analysis revealed considerable genetic diversity
within the genus Macrococcus. The presence of antimicrobial resistance genes on
genomic islands associated with mobile genetic elements suggests horizontal gene
transfer as a key driver in the spread of antimicrobial resistance genes across the
members of this genus. Overall, this thesis presents the genomic and metabolic
diversity within the genus Macrococcus and the potential application of M.
caseolyticus in flavour diversification.
Description
Keywords
Macrococcus , Methicillin resistance , Evolution , Staphylococcus , Comparative genomics , Mobile genetic elements , Horizontal gene transfer
Citation
Mazhar, S. 2020. A multi-omics perspective on the biology and evolution of the genus Macrococcus. PhD Thesis, University College Cork.