Presence and function
A species list tells you who's there. A functional gene tells you what they can do.
Two organisms with the same name do not always carry the same genes — which is why naming a community and describing what it can do are different measurements.
Most microbiome testing answers one question: which organisms are present, and in what proportion. That is a taxonomic question, and it is useful. It is also incomplete, because bacteria within a single named species differ in which genes they carry — the shared core is smaller than the name suggests. So knowing a species is present does not establish that a particular capability is present with it. A functional test asks the second question directly: is the gene that performs this reaction here? OraPath targets narG, part of the enzyme that reduces nitrate to nitrite, rather than inferring that capacity from a species list.
Taxonomy and function are different questions
Taxonomy asks who is present. Function asks what the community is capable of doing. They are related — organisms carry the genes — but they are not interchangeable, and a test answers whichever one it was designed around.
Most consumer microbiome reports answer the first. That is a real answer. It is simply not the same answer as the second.
How species are identified from DNA
Identification works by reading a stretch of DNA and matching it to a reference. Marker gene sequencing amplifies one gene present in all bacteria — commonly 16S rRNA — and sorts reads by how that gene varies. Shotgun sequencing reads everything present and assigns fragments to organisms. Targeted assays go the other way: a primer pair is designed for one known sequence, and the assay reports whether it was there.
All three identify by sequence. What differs is how much they read and how specific the answer is.
Genes vary within a species
This is the part that makes function a separate question. Two isolates carrying the same species name can differ substantially in gene content — the genes every member shares are a subset of the genes the species as a whole can have.
Which means a species name is a reasonable guide to capability and not a guarantee of it. If the capability is what you care about, the gene is the thing to look for.
Carrying a gene and using it are not the same
A gene has to be transcribed and translated before anything happens, and bacteria regulate that constantly in response to conditions — what is available, what the neighbors are doing, how much oxygen there is.
So detecting a gene establishes capacity: the community can perform the reaction. How much it performs at any moment is governed by the conditions around it, which is the next section.
Functional pathways
Functions often run across several organisms rather than inside one. A product of one becomes the substrate of another, and the community accomplishes together what no single member does alone.
That is part of why community-level function is worth measuring at the level of the function: the capability can be present in a community whose individual members would not each look capable on a species list.
Nitrate reduction as the worked example
Dietary nitrate is concentrated into saliva and reduced to nitrite by bacteria on the tongue — a step human cells do not perform efficiently. Downstream conversion yields nitric oxide.
The organisms that carry out the reduction span several genera. No single species defines the capability, which makes it a clean case for measuring the function rather than the roster. The pathway is set out in full on the nitric oxide page.
narG
narG encodes the alpha subunit of respiratory nitrate reductase — the catalytic part of the enzyme that performs the conversion.
Detecting it establishes that the genetic machinery for that reaction is present in the sample. Not that a related organism is present. That the machinery is.
Why OraPath targets the gene directly
Inferring capability from a species list requires an assumption: that the organisms detected carry the gene. Given how much gene content varies within a species, that assumption is doing real work, and it is unnecessary when the gene can be targeted.
This is a choice about method, not a ranking of methods. A targeted assay answers a bounded question precisely and cannot find what it was not designed to look for; an untargeted one surveys broadly and reports proportions rather than quantities. The trade is set out on the method comparison page.
Reading a narG result
A detection means the capacity is present in your community, at the level reported.
How much of that capacity is being used is shaped by several things at once. Dietary nitrate is the substrate — without it arriving, capacity has nothing to act on. Saliva flow delivers it and clears the surface. The low-oxygen depth of the tongue coating is where the reduction happens, so what disturbs that surface changes conditions. And periodontal disease has been associated with reduced nitrate-reduction capacity, which puts the rest of the community in the picture too.
Capacity and activity are both real, and they are measured differently.
Species and function read together
Neither answer replaces the other. The species side says which organisms are present and how much of each — which is what the periodontal and caries research is written about. The functional side says what the community can do, independent of who is doing it.
A panel that reports both lets one be read against the other, which is the reason to carry both.
Where the research is
Where the relevant findings sit.
Gene content varies between members of the same bacterial species.
narG encodes the alpha subunit of respiratory nitrate reductase.
Oral bacteria across several genera reduce nitrate to nitrite; human cells do not perform this step efficiently.
Detecting a gene establishes that the genetic capacity is present, not how much of it is being expressed.
Community function can be described from the genes a community carries, not only from which organisms are named in it.
Nitrate-reduction capacity is reduced in periodontitis.
How closely the genetic capacity present in a community tracks the activity actually occurring in it.
In context
Diet
Capacity acts on a substrate. Dietary nitrate is what the nitrate-reducing capacity has to work with.
The rest of the community
Functions run across organisms. What surrounds a capability shapes whether it is exercised.
Conditions on the surface
Oxygen, saliva flow and what disturbs the tongue all change the setting the reaction happens in.
The clinical exam
A gene detection describes a community's capability. What is happening in the tissue is established by an examination.
How OraPath measures this
The Oral Balance Test reports both kinds of result on the same panel. Twelve targets are organisms, named and quantified. Four are narG gene detections, reported as a functional capacity rather than as a species count.
Each is reported at its own Detection Level, a semi-quantitative scale set out in full on the Detection Level page.
Measure what your community can do.
Curious what your oral microbiome looks like? The Oral Balance Test measures targeted organisms and microbial functions from a saliva sample processed in our Norman, Oklahoma laboratory.
Common questions
What is narG?
A gene encoding the alpha subunit of respiratory nitrate reductase — the catalytic part of the enzyme that reduces nitrate to nitrite. Detecting it indicates the community carries the machinery for that reaction.
What is the difference between presence and function?
Presence says which organisms are there. Function says what the community is capable of. Because gene content varies within a species, the first does not establish the second.
Why not just identify the species that reduce nitrate?
The capability spans several genera and varies between members of the same species, so a species list is an inference about capability. Targeting the gene measures it.
Does detecting narG mean my body is making nitric oxide?
It means the capacity is present at the level reported. How much is used depends on dietary nitrate, saliva flow, conditions on the tongue and the surrounding community.
Do other microbiome tests measure function?
Shotgun metagenomic sequencing can describe functional gene content across a whole community. Marker gene sequencing generally infers function from taxonomy instead. The methods answer different questions.
Is a gene test better than a species test?
They answer different questions, and the Balance Test carries both — twelve organism targets and four narG detections.
References
- Rosier BT, Takahashi N, Zaura E, Krom BP, Marsh PD. The importance of nitrate reduction for oral health. J Dent Res. 2022;101(8):887–897.
- Rosier BT, Moya-Gonzalvez EM, Corell-Escuin P, et al. Nitrate reduction capacity of the oral microbiota is impaired in periodontitis. Int J Oral Sci. 2024;16:3.
- Rosier BT, Buetas E, Moya-Gonzalvez EM, et al. Nitrate as a potential prebiotic for the oral microbiome. ISME J. 2020;14:2459–2469.
- Hezel MP, Weitzberg E. The oral microbiome and nitric oxide homeostasis. Free Radic Biol Med. 2015;105:48–57.
- Wang J, Qi J, Zhao H, et al. Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease. Sci Rep. 2013;3:1843.
- Kilian M, Chapple ILC, Hannig M, et al. The oral microbiome — an update for oral healthcare professionals. Clin Microbiol Infect. 2016;22:657–666.
Laboratory developed test · for adjunctive clinical use · not FDA cleared.