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Cheddar flavor can change when the membership of its starter-culture community changes. In a year-long cheddar-making experiment, the presence or absence of particular bacteria altered which organisms grew, how they exchanged metabolic resources, and the resulting profile of flavor-related compounds. The key lesson is not that one species has a fixed “flavor job,” but that strain combinations and interactions matter.
The study by Chrats Melkonian and colleagues, published in Nature Communications on 21 December 2023, examined a defined commercial starter culture containing Streptococcus thermophilus and several Lactococcus groups. Its findings apply to the tested culture and experimental cheesemaking and milk-fermentation conditions, not automatically to every cheddar, factory, starter blend, or home recipe. Read the primary paper.
What question did the cheddar study ask?
Cheese microbiology often describes individual organisms by the reactions they can perform: acid production, protein breakdown, citrate metabolism, or formation of aroma compounds. Those capabilities are useful, but a cheese starter is a community rather than a collection of isolated cultures. One organism can change the nutrients available to another, alter its growth rate, or redirect a shared precursor into a different end product.
Melkonian and colleagues asked whether changing community membership would change cheddar formation itself. Instead of comparing unrelated commercial cheeses, they worked with one defined starter system and deliberately omitted selected strains or groups. That design allowed the investigators to connect a change in membership with changes in bacterial growth and in measured metabolites and flavor-related compounds.
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The work combined several kinds of evidence:
- Genomic information to identify the organisms and their metabolic potential.
- Genome-scale metabolic modelling to examine possible exchanges and pathway changes between community members.
- Metatranscriptomics to determine which genes and pathways were active under the tested conditions.
- Measurements of metabolites and flavor-related compounds during the cheesemaking and controlled milk-fermentation experiments.
Using these approaches together matters because a genome can show what a strain is capable of, while transcript measurements and chemical assays show what the community actually did in the experiment.
How the experimental starter community was organized
The main experiment ran for a year and used a commercial culture with a deliberately defined composition. The published counts describe the study design, not the make-up of all cheddar cultures.
| Community component | Amount in the studied starter | How it was used in the design |
|---|---|---|
| Streptococcus thermophilus | One strain | Its presence was tested in relation to the growth and metabolism of Lactococcus members. |
| Major Lactococcus lactis strains | Two strains | Individual major strains were excluded in follow-up controlled milk fermentations. |
| Major Lactococcus cremoris strain | One strain | Its contribution to flavor-compound formation was examined through omission experiments. |
| Additional Lactococcus strains | Blend of 21 strains | These formed part of the broader community whose membership could be selectively changed. |
Selected strains or groups were omitted during cheesemaking, and separate milk fermentations excluded individual major Lactococcus strains. This is an important distinction from a simple “add one microbe, get one flavor” test: the investigators were studying a community under controlled changes in membership.
S. thermophilus helped Lactococcus grow
The strongest community-level result was that S. thermophilus supported Lactococcus growth in the studied system. Integrated genomic, transcriptional, modelling, and chemical analyses pointed to a nutrient interaction rather than a merely coincidental co-occurrence.
The authors concluded that proteolytic activity by S. thermophilus relieved a nitrogen limitation faced by Lactococcus. In practical terms, protein breakdown by the S. thermophilus member made nitrogen-containing resources more available in a form that helped the Lactococcus population. The analysis also linked that relief of nitrogen stress to de novo nucleotide biosynthesis in Lactococcus.
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Nucleotides are required for essential cellular processes, including the production and maintenance of genetic material. The finding therefore describes a chain of effects: one organism changes the nutrient environment, the partner can invest in nucleotide production, and the partner’s growth and activity can influence the chemical mixture from which flavor develops. It is an example of a community interaction shaping the trajectory of fermentation.
This does not mean that S. thermophilus universally benefits every Lactococcus strain, or that adding it to any starter will produce the same result. The evidence comes from the particular strains, proportions, milk fermentations, and cheddar process examined in the paper.
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Closely related bacteria did not behave as interchangeable parts. The study found that Lactococcus lactis strains interacted with S. thermophilus differently from one another. A species name can therefore hide functionally important variation: two strains assigned to the same species may consume, release, or redirect different metabolites, and may respond differently to the same neighbor.
This result cautions against statements such as “L. lactis creates a particular flavor” without specifying the strain and conditions. In this experiment, the relevant unit was often a strain pairing or a complete community, not a species in isolation. Removing one strain could also alter the opportunities available to the remaining organisms, so the outcome of an omission cannot be read as a universal ranking of “good” and “bad” bacteria.
L. cremoris constrained buttery aroma compounds
The study identified a distinct role for the major Lactococcus cremoris strain. Its presence limited the formation of diacetyl and acetoin in the tested system. Both compounds can contribute buttery notes, but excessive amounts can produce an off-flavor. A community that controls their accumulation may therefore produce a more balanced aroma than one in which their formation proceeds unchecked.
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The proposed explanation involves citrate metabolism. The paper attributes the control to citrate being rerouted toward α-ketoglutarate. That rerouting changes how carbon flows through the community’s metabolic network and leaves less of the relevant pathway output directed toward diacetyl and acetoin formation under the studied conditions.
The point is not that diacetyl or acetoin are inherently desirable or undesirable. Their sensory effect depends on concentration and on the rest of the cheese’s chemical profile. The result shows why a flavor target cannot be managed by maximizing one aroma compound alone: a strain that suppresses a buttery compound may be preventing an imbalance rather than removing a wanted character.
What changed when members were omitted?
Omission experiments provide a useful way to interpret the paper’s central contrast. When a selected member was removed, the investigators measured both community behavior and chemistry. The resulting profiles were not identical across all omissions. Some removals changed the metabolic landscape substantially; others had smaller effects.
That pattern supports three conclusions:
- Community membership is causal in the tested system. Changing who was present changed growth and measured metabolites or flavor-related compounds.
- Effects are uneven. A strain can be influential even when a close relative has a different or less visible effect.
- Interactions are conditional. The consequence of removing a member depends on which partners remain and on the fermentation environment.
Lead researcher Chrats Melkonian described the observation this way in a report by Chemistry World: “When we did the experiment, it was obvious that part of the community clearly benefited from the presence of another member – Streptococcus thermophilus – and also the metabolic profile was significantly different when we removed specific members of the community, but not others.” The full report is available from Chemistry World.
Why this is more than a list of flavor-producing microbes
A list of microbial capabilities treats fermentation as an inventory: one organism makes acid, another releases peptides, and another makes an aroma molecule. The paper instead presents flavor formation as an interacting network. Growth changes the available substrates; substrate use changes the chemical environment; and those changes feed back into which organisms can remain active.
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Bart Weimer, identified in the Chemistry World report as a microbiologist at the University of California, Davis, summarized the broader significance: “An extensive literature base exists for the individual biochemistry but this work brings together the bacterial communication that are at play in the complex metabolic landscape that leads to the overall cheese flavour profiles.” The value of the study is therefore its integration of community behavior with chemical output, rather than a claim that it has identified a single universal cheddar-flavor organism.
What the findings mean for cheesemaking decisions
For a cheesemaker or culture developer, the study suggests a more precise way to think about starter selection. The relevant question is not simply whether a culture contains a species associated with cheddar, but whether the specific strains are compatible and whether their interactions produce the desired balance of acidification, growth, and aroma compounds.
- Evaluate complete communities. A strain that performs well alone may behave differently when neighboring strains alter its nutrient supply or pathway use.
- Track strain identity. Closely related L. lactis strains should not be assumed to be functionally interchangeable.
- Measure aroma balance. Diacetyl and acetoin can contribute buttery notes, yet excessive formation can be an off-flavor. A target should specify the desired level and context, not merely “more” or “less.”
- Interpret omissions carefully. Removing a member can reveal an interaction in one community, but it does not prove that the same removal will behave identically in another starter or plant.
- Use process-specific validation. The findings came from a year-long cheddar experiment and controlled milk fermentations. A culture intended for a different temperature profile, milk composition, aging schedule, or cheese style needs its own validation.
The study used a commercial starter culture, but it did not test home cheesemaking kits, compare suppliers, or show that a household process can reproduce the year-long experiment. Anyone trying a recipe at home should treat the paper as an explanation of microbial ecology, not as a guaranteed formula for matching its flavor profile.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.What the study does not establish
The evidence has clear boundaries. It does not establish that every cheddar depends on S. thermophilus for Lactococcus growth, that every L. cremoris strain suppresses diacetyl and acetoin, or that any one omission will improve flavor in a different culture. It also does not provide a consumer product comparison or a universal sensory scale for the compounds measured.
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The primary paper discloses that several authors were current or former employees of Chr. Hansen A/S, a supplier of microbial cultures for food fermentation. That disclosure is relevant context when assessing the work; it does not by itself determine whether a particular finding is correct, and the conclusions should be read against the methods and evidence reported in the paper.
How to read the result without oversimplifying it
A useful mental model is to treat a starter culture as a small ecosystem. First, identify the organisms and strains that are present. Next, ask what each member makes available or removes. Then examine whether those exchanges alter growth. Finally, connect the changed growth pattern to measured metabolites and flavor compounds.
Applied to this study, that sequence looks like this:
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- Exchange: S. thermophilus proteolysis changed nitrogen availability for Lactococcus.
- Growth response: the relieved nitrogen limitation supported de novo nucleotide biosynthesis in Lactococcus and helped its growth.
- Flavor pathway: the presence of L. cremoris redirected citrate toward α-ketoglutarate and limited diacetyl and acetoin formation.
- Strain dependence: different L. lactis strains did not all interact with S. thermophilus in the same way.
This chain explains why the article’s title is about a “bacterial community,” not a single bacterium. Flavor emerges from the interaction of membership, metabolism, and process conditions.
Bottom line for cheddar flavor
In the defined starter culture studied by Melkonian and colleagues, bacterial neighbors changed both growth and flavor chemistry. S. thermophilus helped Lactococcus by easing nitrogen limitation through proteolytic activity, while L. cremoris constrained diacetyl and acetoin formation through citrate rerouting. Because closely related strains behaved differently, the safest conclusion is specific: cheddar flavor depends on the particular community and conditions, not on species names alone.
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