Revisiting the subgingival microbiota: Towards an ecological risk scale for periodontology

What matters is not only the composition of each group but also their combination: certain proportions align with clinical health, others with periodontitis, and some with the previously defined microbial patterns. These complexes can be considered fundamental ecological units of the subgingival biofilm. Their relative abundance may define the commensal or pathogenic nature of the ecosystem.

Furthermore, some taxa are tightly associated with a single complex and may serve as core markers; others act as boundary taxa and could signal ecological transitions.

The microbial risk scale: a new diagnostic dimension

This framework opens the door to a third diagnostic axis: microbial risk. This axis can complement staging and grading by positioning the patient's microbiota within a dynamic ecological landscape:

• Are there consistent markers of health or disease? → Complexes.
• Is the ecosystem stable or tipping? → Boundary taxa.
• Does the profile follow a typical disease path or indicate an alternative route? → Patterns.

These questions reframe diagnosis as anticipatory—using microbiota profiling to estimate risk before irreversible damage occurs. Notably, one microbial pattern (Pattern D) was associated with disease but lacked P. gingivalis, the classical keystone pathogen, suggesting the existence of alternative disease trajectories that may involve other bacterial kingdoms or provide evidence of host specificities.

From sequencing to practice: making the leap

Sequencing is unlikely to become a routine diagnostic tool in the immediate future, but innovation is narrowing the gap. Advances in multiplex quantitative polymerase chain reaction (qPCR), lab-on-chip systems, and AI-assisted platforms are making molecular microbiota profiling more accessible. These tools may soon support risk stratification, monitoring, and personalized interventions in periodontal care.

In the meantime, our findings foster the use of phase-contrast microscopy as a powerful and underused diagnostic surrogate. With minimal equipment, clinicians can observe morphotypes and motility—key indicators of the ecosystem’s state. For instance, Complex 10, linked to periodontitis, includes nine Treponema species, easily recognised as motile and spiralled bacteria under the microscope. This contrasts with the sessile morphologies observed in health-associated complexes.

Future directions: towards ecological and precision medicine

These insights contribute to the emergence of predictive, ecological medicine—where diagnosis is no longer just retrospective but also guides early, personalized prevention. These tools can be used for the early follow-up of therapy because shifts in the microbiota might precede healing. We are currently working on:

• Refining the patterns by analysing the non-bacterial microbiota in the samples: parasites, fungi, archaea, and viruses.
• Building innovative diagnosis tools for immediate, molecular-based multiplexed biomarker analysis of periodontal risk to use at the clinic.
• Developing image-recognition algorithms for microscope-based risk estimation.

Our results can also guide microbiota-based interventions beyond diagnosis:

• Seeding with core taxa associated with health as controlled microbiota grafts for preventive intervention or as adjuvants during periodontal treatment.
• Targeting core taxa associated with disease to limit damage.
• Controlling boundary taxa to prevent the evolution towards disease.

Above all, we aim to codevelop these tools with clinicians because diagnostic and therapeutic tools only change practice when they are trusted, used, and compatible with real-world care.

We invite clinicians, researchers, and partners to join this effort. Together, we can move beyond damage assessment and towards the early detection of imbalance, where the microbiota becomes not just a trace of past disease but also a guide to preserving health.