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02 Predictive microbiology · shelf life

FoodSpan

The only module that computes shelf life from metagenomic microbiological panels: all the informative power of the classic panel, plus the granularity of knowing which specific species sit behind each label.

From each species it derives its metabolic capabilities and, with its kinetics, the forecast of spoilage or of a safety problem. Not how much a count rises: which organism spoils the product, by which route and when.

The rule that orders the module
A shelf-life study starts from the finished product.
The first control's counts are taken on what comes off the line: the lethality of the treatment is already built into that figure. What has been measured is not modelled again.
4
primary models, with the anchored predictive one governing the verdict
10,000
Monte Carlo iterations per product, with a percentile band
17
report sections, none below 300 words
P95
a conservative shelf life and a 95% interval by default, not a loose number
01 What it answers

Two questions. Never just one.

A shelf-life study that delivers a single number, without separating safety from quality, is not defensible before an auditor. The declared shelf life is the minimum of the three axes, always naming which one rules and which agent governs it.
Eje 1 · Seguridad
Does it support pathogen growth?
For chilled ready-to-eat products the governing pathogen is Listeria monocytogenes. Growth potential δ = log10 N(final) − log10 N(initial): with δ ≤ 0.5 the product does not support growth; above that, the dynamic limit of 100 cfu/g at end of shelf life applies.
EURL Lm TGD v4 (2021) · Reg (CE) 2073/2005 mod. Reg (UE) 2024/2895
Eje 2 · Calidad
When does it become unacceptable?
Governed by the specific spoilage organism reaching its rejection level — Photobacterium phosphoreum around 10⁷–10⁸ in modified-atmosphere fish, for example. The SSO is named per track, never by majority across products.
Gram & Dalgaard · SSO resolved on the limiting track
Eje 3 · Sensorial
When does the panel reject it?
Time to rejection by the sensory panel, treated as its own series and tested against the microbiology only after removing the shared temporal trend.
ISO 16779 · tiempo-a-rechazo
Explicit precedence
The shortest axis wins. In a tie, safety over sensory over quality — for the same number, the axis with the greater regulatory consequence is named. The verdict carries every candidate, not only the winner: the question "and what about the other number?" is answered without recomputing anything on the side.
Two things that are not conflated
Growth potential δ — describes the MATRIX
The process does not move it. It is always computed from the EURL reference. A lethal step does not launder a permissive matrix: at 6 °C, pH 7 and aw 0.99 the pathogen crosses 100 cfu/g again whatever happens.
Time to 100 cfu/g — describes the LOAD
Here the process does rule: it sets the level you start from. A product may still permit growth and yet not reach the limit within its shelf life. The report keeps them separate.
02 How it works

A mechanistic model anchored in the data.

The curve is not characterised by regression over three points: a literature-validated model is anchored and corrected with the observations, bounded to its horizon of validity. That is the answer to "few points, badly spread".
01 Cardinal secondary model
Le Marc–Coroller over Rosso CPM, in the Mejlholm–Dalgaard family: temperature, NaCl and aw, pH, eight undissociated organic acids, dissolved CO₂ by Henry's law, smoke phenols, nitrite and their interactions. The hurdles — modified atmosphere, vacuum, acidification, salting, curing, fermentation — enter here as γ on μ, which is where they are physically correct.
02 Primary model and anchoring
Baranyi–Roberts with the observations as anchor and correction, not as regression material. The empirical fit remains a supporting estimator; the anchored predictive engine is what signs the number.
03 Acceptability band
Ross's Bf/Af (1996) and Oscar's APZ Performance Index (2005), with a different asymmetric band for pathogen and for spoilage organism: underestimating a pathogen and underestimating a spoiler do not cost the same.
04 Veredicto
Decision tree aligned with EFSA BIOHAZ (2018), with a term-by-term gamma breakdown and consultable references. Every rejection states its reason.
05 Incertidumbre
Monte Carlo at ten thousand iterations with a percentile band. The 95% interval is delivered along with a conservative shelf life at the 95th percentile — what the auditor asks is not the number, it is how wrong it can be.
06 Muestreo escaso
With few points, μ is not extracted from the exponential phase: the theoretical curve anchored at N0 is tested against the observations by residual pattern inside the band. Extrapolation stays bounded to the model's horizon of validity, never open-ended.
03 Suspicion about the reading

Dead DNA is not corrected. It is declared.

After a listericidal step, DNA from inactivated cells persists for weeks: that is precisely where a molecular count most overestimates the viable load. The rule does not touch the number — that would be manufacturing it: it issues a confidence verdict and says what would confirm it.

The sensory↔microbiology correlation is decided on the residuals after removing the temporal trend from both series: the raw correlation is explained by the shared clock, not by a relation between them. It requires the correct physical sign — more load, worse score — and significance p ≤ 0.05.

Three independent lines of evidence of active metabolism
01
Cultivo
Culture in the same indicator group — direct evidence of viability.
02
Crecimiento
Residual DNA does not multiply: it degrades. If the series grows, there is metabolism.
03
Symptom
A correlated organoleptic sign, with the correct physical sign and significant.
What is not done
Growth in the series is measured by fitted slope, never by maximum minus first, and with a threshold above measurement noise. A positive correlation is not a "better correlation" for having a larger magnitude: it is physically impossible, and it confirms nothing.
04 Verified on a real study

Eight products, four time points, one conclusion per product.

Ready-to-eat seafood dishes treated by high pressure, sampled at 0, 45, 75 and 90 days at 2 °C. The output unit is the product: eight shelf lives, not one average.
8
Ready-to-eat seafood products
Treated by high pressure, each with its own series and its own shelf-life study.
31,8 d
Worst-case shelf life
Governed by the real data, bounded to the sampled range.
32–46 d
Range across products
Eight numbers, not one average that describes none of them.
δ 0,06
Does not support growth
Far below 0.5. Modulated by the high-pressure hurdles.
The difference between the crumb with and without preservative — 45.9 against 31.8 days — was not assumed: it came out of the data, bounded to the sampled range. When the product diverges from the reference cardinal value, the observation rules. And where no specific spoilage organism has been identified, the executive summary writes a dash, not an invented pathogen.
05 Where it fits

The panel goes in at the top. The shelf life comes out at the bottom.

OmniOta Antes
Raw reads from any platform through to taxonomy. It is what turns an aggregated label into a list of named species.
reads → taxonomy
DeLorean Antes
Relative abundances into reportable absolute units, with copy-number correction and food-matrix calibration.
abundancias → CFUeq/g
FoodSpan Aquí
Per-product kinetics, three decision axes and the dossier. The output unit is the product, in days from manufacture.
CFUeq/g → shelf life
A DeLorean analysis is a snapshot of a single observation time: one condition, several products. FoodSpan stacks N analyses — one per time point — and builds the product × time matrix. Each product carries its own food matrix, and the storage temperature is locked: an inconsistency between analyses blocks the import.
06 The deliverable

A dossier an auditor cannot break open.

The prose of each section is written as chained connective narrative with verified DOIs. The tables, the figures and the arithmetic of the decision do not go through it: they are deterministic, and numbers are not drafted.

An automated audit reviews the emitted HTML — length, thin sections, captioned figures, verified citations — before it goes out.

17
Sections
None may be left at three lines: 300 words minimum, verified.
8,900
Target words
Above the minimum required by the in-house scientific report specification.
4
Languages
Spanish, English, French and German, scaffolding and prose included.
Q1
Automated audit
Length, thin sections, captioned figures and verified citations, over the emitted HTML.
07 Technical sheet
In
DeLorean analyses in CFUeq/g — one per observation time — the product's physicochemical characteristics (pH, aw, preservatives), declared treatment and packaging, storage temperature and date of manufacture.
Out
Shelf life per product in days from manufacture, with limiting axis and agent named, a curve with observed anchors and retrospective and prospective zones, every decision candidate, and the full report ready for audit.
Output unit
The product, never the study. A shelf-life study is a multi-product container and a comparator: eight products are eight shelf lives.
Escenarios
What would happen if — a weaker hurdle, thermal abuse, a new preservative, a switch to modified atmosphere — over the same mix of observed and predicted.
Limit · lethality
The lethality of the treatment is not modelled here: it is already built into the finished-product count. Modelling heat penetration, cold spot or D/z is thermal process validation — another authority and another module.
Limit · scope
When the safety axis does not apply, the conclusion rests on the validated process and the operator's batch records. Both are verification of the self-control system and fall outside the scope of a shelf-life study. That limit is stated in the report, not hidden.
Limit · nature of the data
CFUeq/g is a calibrated culture equivalent, not a plate count. In silico does not replace a challenge test: it extends it and contextualises it with the real product.

Bring your panels. We return the dossier.

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