The mouth microbiome: plaque, caries and gums, explained
The mouth microbiome is the community of bacteria living on teeth, gums, tongue and cheeks. On teeth it forms plaque — a structured biofilm held together by sugars the bacteria make themselves. In balance it protects; when sugar is frequent or cleaning is rare, acid-making species take over, enamel dissolves and gums inflame.
Written by: Magnus Larsen · Microbiologist · Science bloggerPublished: Facts checked: What the mouth microbiome is
The mouth is the only place where the body offers microbes a surface that never sheds: tooth enamel. Skin flakes off, the gut lining renews, but a tooth stays. So bacteria build on it. First come the pioneers that stick to the saliva film; then others attach to them; then the whole community wraps itself in a matrix of sticky sugars — glucans — made from the sucrose we eat. That structure is plaque. It is a biofilm, a city with walls, not a smear of dirt.
Inside a biofilm, bacteria behave differently from free-floating cells. They share food, resist rinses and survive doses of antiseptic that would kill them alone. This is why brushing — mechanical disruption — outperforms most mouthwashes.
The three questions people ask
Why do I get cavities when I brush? Caries is not a hygiene failure alone. It is a chemistry of frequency: each sugar exposure lets acid-producing species drop the pH at the enamel surface, and saliva needs time to buffer it back. Frequent snacking beats good brushing.
Are bleeding gums serious? Bleeding is the immune system responding to plaque at the gum line. Early on, it is reversible. Left alone, the community below the gum shifts toward anaerobes that live on inflamed tissue, and the bone that holds the tooth slowly recedes.
Do mouth bacteria affect the rest of me? Some species from inflamed gums are found in arterial plaques, in the placenta and in colon tumours. Whether they travel as cause or as passenger is still being worked out.
What the science can and cannot say yet
It can say: plaque is a biofilm; sugar frequency drives caries; gum inflammation is a conversation between bacteria and immune cells, and it is reversible early; mechanical cleaning works because it breaks the matrix.
It cannot yet say: whether treating gums prevents heart disease, which probiotic strains reliably colonise the mouth, or how much of the "oral–systemic link" is causal rather than shared risk. Trials are short, and outcomes are mostly surrogate markers.
Read the encyclopedia of bacteria for the species named here, and the news list for what changed this month.