{
  "abstract": "Microbial spoilage of packaged meat is driven by complex microbial succession and related metabolic activity, yet conventional shelf-life assessment is mainly based on shelf-life studies relying on culturing and sensory analysis. In routine quality assurance, results are obtained retrospectively, and they are only indirectly linked to the metabolic activity related to sensory deterioration. Functional, time informative approaches that capture the active metabolic state of the spoilage microbiome and predict the rate of spoilage are lacking. We developed a censoring-aware Gaussian process (CAGP) framework to model longitudinal pathway expression profiles from broiler meat metatranscriptomes collected over consecutive storage days at 4 or 6{degrees}C. Samples were annotated using odor-based sensory scores defining fresh, early-spoilage, and late-spoilage phases. Because observed zeros in pathway-level data may reflect non-detection rather than true absence, the model treats low values as left-censored observations below a detection threshold while estimating smooth temporal trajectories with uncertainty. In leave-one-out prediction within the 4{degrees}C time series, predicted sampling days differed from the true days by an average of 0.43 days, and predicted spoilage phases agreed with the sensory classification. Trajectories learned at 4{degrees}C also transferred to an independent 6{degrees}C time series at the spoilage-phase level, suggesting that shared functional spoilage programs are preserved despite temperature-dependent changes in spoilage rate. Cross-entropy ranking further identified pathway modules carrying time- and phase-informative signals across temperatures. Overall, this framework provides a probabilistic approach for linking metatranscriptomic functional dynamics to sensory spoilage progression, supporting shelf-life assessment beyond retrospective microbial enumeration. Microbial spoilage of packaged meat is driven by complex microbial succession and related metabolic activity. The current tools to assess product quality and determine shelf life do not fully serve food manufacturers. Functional time informative approaches that capture the active metabolic state of the spoilage microbiome and predict the rate of spoilage are lacking. We developed a censoring-aware Gaussian process (CAGP) framework to model longitudinal pathway expression profiles of broiler meat spoilage microbiomes. We used two series of metatranscriptomic data generated in our previous study of samples stored either at 4 or 6{degrees}C. The samples had also been annotated with odor-based sensory scores defining fresh, early-spoilage, and late-spoilage phases. The 4{degrees}C time series were used to develop and evaluate the temporal prediction framework, while the independent 6{degrees}C series were used to assess whether the functional spoilage trajectories learned at 4{degrees}C could generalize across temperature conditions. The CAGP models smooth temporal trajectories of pathway activity while accounting for uncertainty and for observed zero values that may arise from non-detection rather than true biological absence. In this framework, zeros are treated as left-censored observations below a soft detection threshold. Within the 4{degrees}C time series, leave-one-replicate-out (LORO) and leave-one-day-out (LODO) analyzes predicted the sampling time of held-out samples with mean absolute errors of 0.43 and 0.78 days, respectively. In the LORO analysis, predicted spoilage phases also largely agreed with the sensory classification. When trajectories learned at 4{degrees}C were applied to the independent 6{degrees}C samples, the predicted samples retained their temporal ordering along the spoilage trajectory, suggesting the preservation of shared functional spoilage programs despite temperature-dependent differences in spoilage rates. Cross-entropy ranking further identified pathway modules carrying time- and phase-informative signals across temperatures. Overall, this framework provides a probabilistic approach for linking metatranscriptomic functional dynamics to sensory spoilage progression, supporting shelf-life assessment beyond retrospective microbial enumeration.",
  "abstract_shown": true,
  "affiliations": [
    "Helsingin yliopisto"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "E. Nushi"
    },
    {
      "name": "J. Manninen"
    },
    {
      "name": "P. Johansson"
    },
    {
      "name": "A. Honkela"
    },
    {
      "name": "J. Björkroth"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3y47f2zmzk4jb.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.06.11.731636",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.06.11.731636v2.full",
  "id": "3y47f2zmzk4jb",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.06.11.731636v2",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.06.11.731636v2.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-06-11",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/3y47f2zmzk4jb.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T00:20:36Z",
      "native_id": "10.64898/2026.06.11.731636",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.06.11.731636v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Censoring-aware Gaussian process modeling identifies time informative functional dynamics associated with spoilage status of modified atmosphere packaged broiler meat",
  "title_text": "Censoring-aware Gaussian process modeling identifies time informative functional dynamics associated with spoilage status of modified atmosphere packaged broiler meat",
  "type": "preprint",
  "updated_at": "2026-11-04T00:21:02Z",
  "url": "https://research.draconitic.com/paper/3y47f2zmzk4jb",
  "venue": "bioRxiv",
  "versions": []
}