The Microbial Ecology of the Paediatric Oral Microbiome in Healthy and Sleep Disorder Breathers

Author: Jessica Carlson-Jones

Carlson-Jones, Jessica, 2019 The Microbial Ecology of the Paediatric Oral Microbiome in Healthy and Sleep Disorder Breathers, Flinders University, College of Science and Engineering

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The human body is colonised by an array of microorganisms that are involved in maintaining overall health and wellbeing. Disruption to these beneficial microbial communities is linked to the progression of numerous disease states. Regarded as the gateway to the body, the oral cavity has become a site for numerous taxonomic studies investigating microbial links between health and disease. Within the oral cavity are different microhabitats that support the colonisation of different bacterial communities. However, little is known about the absolute microbial abundance dynamics within and between these microhabitats, and whether they are different in disease states. Used as a tool for monitoring microbial dynamics in environmental studies, flow cytometry enables the rapid enumeration of bacteria and viruses within a community. In chapters 2, 3 and 4 of this thesis we demonstrate that flow cytometry can be used on medical samples to count bacteria and viruses within niches of the human body. We establish that the upper respiratory tract, specifically the sinuses and oral cavity, are colonised by ‘high’ numbers of microbes and that these counts are not homogeneous in their distribution spatially and among individuals. In addition, chapters 3 and 4 also establish that the microbial communities in the healthy paediatric oral cavity significantly increase in absolute abundance during sleep by counts of up to 100 million. In sleep disorder breathers (SDB), this microbial dynamic is predicted to be different as variations in sleeping patterns are suspected to change oral environmental conditions. Chapter 5 presents the first study to identify, using flow cytometry, a significant difference in the absolute microbial abundances, specifically in viruses, between microhabitats in the healthy and sleep disorder breathers’ oral cavities. Chapter 6 characterises the relative taxonomic distribution of the microhabitats of the healthy paediatric oral cavity and shows for the first time that these bacterial communities significantly shift during sleep, specifically in anaerobic genera of bacteria. Finally, chapter 7 shows that paediatric sleep disorder breathers have significantly different oral taxonomic profiles than healthy paediatric participants, specifically at the tip of the tongue after sleep. Overall, this thesis highlights the potential value in high frequency time series of healthy and SDB oral microbiomes. Here we show that the paediatric oral microbial communities significantly shift in abundance over time, suggesting of a highly dynamic community. Therefore, there is the need for careful interpretation when identifying shifts in oral microbial composition between health states. This thesis suggests the need for future microbial related research in paediatric SDB with a particular focus on the oral microbiome to determine if there is a causal relation between the microbial communities present and the health condition.

Keywords: Oral microbiome, sleep disorder breathing, flow cytometry, bacteria, viruses, 16S, sleep

Subject: Biological Sciences thesis

Thesis type: Doctor of Philosophy
Completed: 2019
School: College of Science and Engineering
Supervisor: Jim Mitchell