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The University of Sydney Page 1
Caries and the oral
microbiome
Presented byDr Christina AdlerSchool of Dentistry, Faculty of Medicine and Health
The University of Sydney Page 2
Microbiome
The University of Sydney Page 3
Oral microbiome
– Ubiquitous
– Diverse
– Ecosystem
– Dental caries
– Periodontal disease
– Systemic health
Plaque
SalivaTongue
Firmicutes
Actinobacteria
Bacteroidetes
Proteobacteria
Fusobacteria
Other
Mucosa
The University of Sydney Page 4
Multifactorial Nature of Caries
The University of Sydney Page 5
Changing concepts in
caries microbiology
The University of Sydney Page 6
Bacterial CultureCloning and Sequencing
Next Generation Sequencing
Single Species Non-Specific/Multiple
Species
Ecology
The University of Sydney Page 7
Loesche WJ: Clinical and microbiological aspects of chemotherapeutic agents used according to the specific plaque hypothesis. J Dent Res
1979, 58(12):2404-2412.
Specific plaque hypothesis
Culture Technique
Streptococcus mutans
Specific plaque hypothesis
Evidence S. mutans caries
– S. mutans could induce caries in
animals fed a high sucrose diet
– S. mutans is highly aciduric
– S. mutans is ‘sticky’
The University of Sydney Page 8
Specific plaque hypothesis
S. mutans vaccine
– 30+ years
– Protein
– DNA
– Experimental and animal evidence (Hamada, 1991, Oral passive immunization against dental
caries in rats by use of hen egg yolk antibodies specific for
cell-associated glucosyltransferase of Streptococcus mutans)
– Lack of clinical evidence in humans
The University of Sydney Page 9
Evidence against S. mutans in caries
1. Culture methods can only identify ~50% of bacteria
2. The bacteria S. mutans is ubiquitous in the oral cavity
3. The bacteria S. mutans is not always present in biofilms
associated with caries
4. Other aciduric bacteria involved in carious lesions
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Non-specific plaque hypothesis
Overall activity of total plaque
microbiota
Genetic methods
– Extract DNA
– Amplify a gene (16S rRNA
gene)
– Clone and sequence
– Identify bacteria, fungi, viruses
and archea
The University of Sydney Page 11
Gross EL, et al: Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol 2010, 48(11):4121-4128.
Non-specific plaque hypothesis
– Multiple caries associated
species
– Supported the findings from
culture studies
– Revealing a greater
diversity
– Caries a polymicobial
disease
– Did not correlate the
bacteria with environment
The University of Sydney Page 12
Takahashi N, Nyvad B: The role of bacteria in the caries process: ecological perspectives. J Dent Res 2011, 90(3):294-303.
Ecological plaque hypothesis
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Ecological plaque hypothesis - Oral microbiome
Next Generation Sequencing
High bacterial diversity
600 – 4200 bacterial species
(Kejiser et al., JDR, 2008,Yang et al., ISME, 2012,
Zaura et al., BMC Microbiology, 2009)
High inter-individual variation
High site specific diversity
The University of Sydney Page 14
Caries oral microbiome
No ‘caries specific’ taxa (Belda et al., ISME,
2012, Yang et al., ISME, 2012)
Changes in overall oral microbiota
composition
Varied by caries stage
Changes in function
– Health associated with
antibacterial functions
– Caries with mixed acid
fermentation
The University of Sydney Page 15
Kilian M, et al: The oral microbiome - an update for oral healthcare professionals. British Dental Journal 2016, 221(10):657-666.
Caries oral microbiome evolution
The University of Sydney Page 16
Hunter-gatherer200, 000 – 10, 000 years
Agriculturist10, 000 – 200/150
years
Industrialisation200/150 years – today
The University of Sydney Page 17
Past dietary change
Adler CJ, et al: Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nature Genetics 2013, 45(4):450-455, 455e451.
Cornejo OE, Lefebure T, Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ et al: Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Molecular Biology and Evolution 2013, 30(4):881-893.
Kianoush N, Adler CJ, Nguyen KA, Browne GV, Simonian M, Hunter N: Bacterial profile of dentine caries and the impact of pH on bacterial population diversity. PloS One 2014, 9(3):e92940.
The University of Sydney Page 19
Gaps in knowledge
Outstanding Questions
Host genetics versus
environment?
Function versus composition?
Immunisation and antimicrobials
to prevent caries?
Relationship of bacteria to fungi
and viruses?
The University of Sydney Page 20
Childhood caries oral
microbiome study
The University of Sydney Page 21
Right to Left: Associate Professor Toby Hughes and Professor Grant Townsend, The University of Adelaide,
Genetic and environmental influences on the oral
microbiome in childhood
To determine how host genetic and
environmental factors drive
variation in composition of the
developing oral microbiome,
leading to either dental decay or
oral health in childhood
NHMRC, APP1062911, 2015-
2019
Adler C (CIA), Hughes T (CIB),
Townsend G (CIC), Arora M (CID)
The University of Sydney Page 22
Study population
– Twin cohort (MZ and DZ)
– 400 individuals
– Longitudinal (3 months - 10 years
of age)
– Australia wide
– Oral health assessment:
International Caries Detection and
Assessment System
– Oral biofilm samples
– Survey data
The University of Sydney Page 23
~5 months (edentulous)
Question 1: Health versus caries
– 400 Children, ~50% health
and ~50% caries
– Biofilm: hard and soft tissue
– 3 time points
– 2 samples per time point
– Total samples ~2400
– 16S, ITS Illumina and
metagenomics
– Causation1-2 years (deciduous)
7-9 years (mixed)
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Question 2: Genetic and environmental influences
– Twins: MZ and DZ
– Structural Equation
Modelling
A = Additive genetic
C = Common environment
E = Unique environment
– Longitudinal
The University of Sydney Page 25
Question 2: Genetic and environmental influences
– Prenatal: Pre-eclampsia, twin-to-
twin transfusion syndrome, mothers’
drinking during pregnancy,
placental type and parental age
at conception
– Neonatal: Type of birth, birth
weight, early feeding practices
and smoke exposure
– Early childhood/childhood: Diet,
oral hygiene, medications and BMI
The University of Sydney Page 26
Fechney JM, Browne GV, Prabhu N, Irinyi L, Meyer W, Hughes T, Bockmann M, Townsend G, Salehi H, Adler CJ: Preliminary study of the oral mycobiome of children with and without dental caries. Journal of
Oral Microbiology 2019, 11(1):1536182.
Caries mycobiome (fungi)
Core Differential abundance
The University of Sydney Page 27
Interaction between fungi and bacteria
The University of Sydney Page 28
Translational potential
1. Prevention
Identification of high risk individuals
Informing when preventative measures are required
Development of early detection methods - Biomarkers
2. Treatment - Oral biofilm modulation
Antimicrobial development
Probiotics development and testing
The University of Sydney Page 29
Acknowledgements - Thanks for listening!
Investigators: Assoc. Prof. Toby Hughes, Prof. Grant
Townsend, Ms. Gina Browne, Ms. Michelle Bockmann,
Assoc. Prof Jacqui Norris and Prof. Richard Malik
Cohort: Big thank you to the Twins and their Families!
Funding: NHMRC, APP1062911, 2015-2019, NHMRC
APP1147383, 2018-2020
The University of Sydney Page 30
X Morgan et al. Trends in Genetics 29, 51-58 (2013) doi:10.1016/j.tig.2012.09.005
