Oral Microbiome in health

This set of vocabulary flashcards covers the foundational concepts of the oral microbiome, including sequencing technologies, the process of microbial succession, and the definitions of health and disease states within the microbial community.

Integrative metabolism

Putting together our and our microbes metabolisms

Holobiont

The host organism and all its symbiotic microbial residents. Definition geared more towards coevolution

Microbiome

All microorganisms in a particular habitat and their collective genomes. Microbiome is not the same thing as microbiota

Close vs open ended techniques

Closed = specific target sequence and specific primers. Metagenomics is open ended

Sanger sequencing

Only one sequence at a time, high accuracy ($99.99\%$) and long reads up to $1,500\,bp$.

Next generation sequencing (NGS)

Millions of fragments can be sequenced in one run (high throughput), lower accuracy (98.5-99%), shorter reads ($80$ to $600\,bp$). Platforms are Illumina and PacBio

Human microbiome project (HMP)

A comprehensive characterization of the microbiome in 18 sites of the human body, 9 of which are located in the mouth.

16S rRNA gene

A gene present in all bacteria with sequences that differ from one bacteria to another, used to identify microbial community composition. This is considered targeted sequencing

ITS

A genetic marker used specifically for the identification and study of fungi.

Metagenome sequencing

Community DNA sequences. “Functional potential”

Metatranscriptome sequencing

Community mRNA sequencing. “Function”

Integrative Human Microbiome Project (iHMP)

Looks at the association between microbiome and major diseases

Primary nutrient source in the oral cavity

Saliva, also GCF

Microbial succession

Every newcoming species modifies the environment to allow even more species to colonize.

Pioneer species

The initial microorganisms that colonize the oral cavity, primarily comprising Streptococcus species which are Gram-positive aerobes. This also includes actinomyces

Autogenic succession

Microbial succession caused by microbial factors, such as the generation of new nutrients (lactate, peptides), modifying attachment sites, and changing pH.

Allogenic succession

Microbial succession caused by non-microbial factors, such as the eruption of teeth, placement of dental appliances, or dietary shifts.

Climax community

The final, stable, and diverse microbial community established at the end of the succession process.

Secondary colonizers

gram negative anerobes (prevotella, fusobacterium)

Ecological succession

Early aerobic environment gets reduced (oxygen used up), secondary colonization by anaerobic species

Capnophilic

Microorganisms that thrive in or require high concentrations of carbon dioxide ($CO_2$).

Mature dental plaque

see photo

microbial complexes in plaque

red = disease causing

The principal bacterial genera found in the oral cavity

see photo

Streptococcus

gram positive, cocci, facultative aerobe. Most abundant group in oral cavity. There are some streptococci that are strict anaerobes

Rothia

gram positive, rods, facultative aerobe. Associated with health

Actinomyces

gram positive, rods, facultative aerobe. Associated with health

Lactobacillus

gram positive, rods, facultative aerobe

Eubacterium

gram positive, rods, anaerobic. Associated with disease

Propionibacterium

gram positive, rods, anaerobic.

Neisseria

gram negative, cocci, facultative aerobe. Associated with health

Veillonella

gram negative, cocci, anaerobic. Associated with health

Haemophilus

gram negative, rods, facultative or capnophilic

capnocytophaga

gram negative, rods, facultative or capnophilic

Aggregatibacter actinomycetemcomitans

gram negative, rods, facultative or capnophilic. Associated with periodontal disease.

Fusobacterium

gram negative, rods, anaerobic. Associated with health

Prevotella

gram negative, rods, anaerobic. Associated with disease

Porphyromonas

gram negative, rods, anaerobic. Associated with disease.

Don’t stain gram positive or negative

spirochetes

Dominant flora in subgingival plaque

steptococcus and actinomyces

Betadiversity (PCA plots)

see photo

Core Microbiome

Microbial species that are found in the majority of the population.