Introduction to microbiome - the oral microbiome in health

Superorganism

Metabolism represents an amalgamation of microbial and human attributes

Holobiont

Host organism and all its symbiotic microbial residents

Microbiome

All microorganisms in a particular habitat and their collective genomes

Bacteriome

All bacteria in a habitat & collective genome

Mycobiome

All fungi in a habitat & collective genomes

Virome

All viruses in a habitat & collective genomes

The advent of open-end molecular techniques

Metagenomics

Technological developments

Explore microbial community composition and genetic makeup

Study the cultivable and non-cultivable components simultaneously

Identify novel species

Sanger

One sequence at a time

Expensive; laborious

High accuracy

Long reads

Standard data analysis

NGS (next generation sequencing)

Millions of fragments

Cheap;easy

Lower accuracy

Short reads

Analysis of data challenging and computationally demanding

Targeted sequencing (marker - gene sequencing)

16S rRNA → bacteriome

ITS —> mycobiome

(Least specific out the three)

Pros of targeted sequencing

Economical, bioinformatics analysis not demanding, host sequences excluded

Cons of targeted sequencing

Kingdom/domain specific, PCR biases/sequencing errors, low taxonomic resolution

Metagenome sequencing

Community DNA sequences

Pros of metagenome sequencing

High taxonomic resolution, all microbial kingdoms can be assessed simultaneously, study whole community genetic makeup up; functional potential

Metagenome sequencing

Community DNA sequences

Metatranscriptome sequencing

Community mRNA sequences (most specific)

Pros of metatranscriptome

High taxonomic resolution, all microbial kingdoms can be assessed simultaneously, activity-based species abundance, study whole community function

Cons of metatranscriptome

Costly, requires depletion of host sequences, bioinformatics analysis analysis challenging

Unique features of oral cavity as a microbial habitat

Dorsum of the tongue - accumulation of bacteria

Teeth - nonshedding

Nutrients (food, saliva, GCF) - bacteria below the gum

Oral cavity as a microbial habitat - heterogeneous

Differences in key ecological factors (levels of O2, access to nutrients)

All micro-organism categories

Bacteria (most predominant), fungi, viruses, protozoa, archaea

Dental plaque - the most studied

Soft, tenacious deposit that forms on tooth surfaces and which is not readily removed by rinsing with water

Ecological stages in establishment of a microbial community

1. Transmission

2. Acquisition and colonization

3. Pioneer species

4. Microbial succession

5. Increasing species diversity

   1. Environment modification

6. Climax community

Mother

Role of; saliva, vaginal delivery and breast feeding; Shapes kids Microbiome

Oral microbial pioneers

Streptococcus

Autogenic succession

Modify or expose new attachment receptors, change local ppm or Eh, generate new nutrients

Allogenic succession

Eruption of teeth, placement of appliances, dietary shifts, antimicrobials

Key non-microbial factor

Eruption of teeth

Succession in dental plaque

Early colonizers are mainly facultative gram positives, such as Actinomyces and streptococcus

Secondary colonization

by capnophilic/anaerobic gram-negative bacteria

Capnphilic/anerobic examples

Capnocyophaga and veillonella followed by prevotella, fusobacterium and pypyromonas

Oral microbial homeostasis

Despite its diversity, once established, oral microbial communities are characterized by a high degree of stability

Microbial homeostasis results from a balance of dynamic ____ and _____ microbial interactions

Synergistic; anaagonistic

Microbial homeostasis interactions

Food chains & webs

Enzyme consortium

Environmental interactions

Sharing resistance to antimicrobial and host immune responses

Bacteriocins, organic compounds

Autoinducers

Positive effects of host-microbiome

Regulates the cardiovascular system

Supports host defense

Has anti-inflammatory properties

Provides additional metabolic potential

Has antioxidant activity

Maintains a healthy digestive tract

Confers resistance to colonization by pathogens

Dysbiosis

A disruption of microbial community homeostasis characterized by imbalanced composition, function and metabolic activity

Gram positive cocci - facultative

Mutans - S. Mutans

Salivarius

Anginosus

Mitis

Gram positive cocci - anaerobic

Anaerobic streptococci

Gram positive rods - facultative

Actinomyces, lactobacillus, rothia

Gram positve rods - anaerobic

Eubacterium, reclassified eubacterium, propionibacterium

Gram negative cocci - facultative

Neisseria

Gram negative cocci - anaerobic

Veillonella

Gram negative rods - facultative or capnophilic

Haemophilus, capnocytophaga, aggregatibacter -aggregatibacter actinomycetemomitans

Gram negative rods - anaerobic

Fusbacterium, prevotella - provotella intermeida, porphyromonas - prophyromonas gingivalis

Other bacteria

Spirochetes, oral synergistetes, TM7 (saccharibacteria)

Other microorganisms

Fungi - candida, malassezia, viruses, mycoplasma, protozoa - trichomonas tenax, entamoeba gingivalis

Subgingival dental plaque bacteria

Streptococcus, actinomyces

Oral microbiome by NGS

Advent of next generation sequencing technologies have enabled comprehensive assessment of the oral microbiome

How many species from NGS produced per individual

200-350 species

Variable composition (NGS)

Intra-individual, inter-individual, inter-ethnicity

Core microbiome

Microbial species found in majority of the population