{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T23:47:13Z","timestamp":1788479233441,"version":"build-2803163510"},"reference-count":41,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2025,4,6]],"date-time":"2025-04-06T00:00:00Z","timestamp":1743897600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Natural Science Foundation of China","award":["82371896"],"award-info":[{"award-number":["82371896"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Microbiota have emerged as a promising tool for estimating the post-mortem interval (PMI) in forensic investigations. The role of oral and nasal microbiota in cadaver decomposition is crucial; however, their distribution across human cadavers at different PMIs remains underexplored. In this study, we collected 88 swab samples from the oral and nasal cavities of 10 healthy volunteers and 34 human cadavers. Using 16S rRNA gene sequencing, we conducted comprehensive analyses of the alpha diversity, beta diversity, and relative abundance distribution to characterize the microbial communities in both healthy individuals and cadavers at varying PMIs and under different freezing conditions. Random forest models identified Firmicutes, Proteobacteria, Bacteroidota, Actinobacteriota, and Fusobacteriota as potential PMI-associated biomarkers at the phylum level for both the oral and nasal groups, along with genus-level biomarkers specific to each group. These biomarkers exhibited nonlinear changes over increasing PMI, with turning points observed on days 5, 12, and 22. The random forest inference models demonstrated that oral biomarkers at both the genus and phylum levels achieved the lowest mean absolute error (MAE) values in the training dataset (MAE = 2.16 days) and the testing dataset (MAE = 5.14 days). Additionally, freezing had minimal impact on the overall phylum-level microbial composition, although it did affect the relative abundance of certain phyla. At the genus level, significant differences in microbial biomarkers were observed between frozen and unfrozen cadavers, with the oral group showing greater stability compared to the nasal group. These findings suggest that the influence of freezing should be considered when using genus-level microbial data to estimate PMIs. Overall, our results highlight the potential of oral and nasal microbiota as robust tools for PMI estimation and emphasize the need for further research to refine predictive models and explore the environmental factors shaping microbial dynamics.<\/jats:p>","DOI":"10.3390\/ijms26073432","type":"journal-article","created":{"date-parts":[[2025,4,7]],"date-time":"2025-04-07T11:24:39Z","timestamp":1744025079000},"page":"3432","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Unveiling the Forensic Potential of Oral and Nasal Microbiota in Post-Mortem Interval Estimation"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-2271-6858","authenticated-orcid":false,"given":"Ji","family":"Chen","sequence":"first","affiliation":[{"name":"Institute of Forensic Science, Fudan University, Shanghai 200032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Wei","sequence":"additional","affiliation":[{"name":"Institute of Forensic Science, Fudan University, Shanghai 200032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Yang","sequence":"additional","affiliation":[{"name":"Ministry of Education\u2019s Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China"},{"name":"Key Laboratory of Forensic Evidence and Science Technology, Institute of Forensic Science, Ministry of Public Security, Shanghai 200042, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanan","family":"Liu","sequence":"additional","affiliation":[{"name":"Ministry of Education\u2019s Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China"},{"name":"Key Laboratory of Forensic Evidence and Science Technology, Institute of Forensic Science, Ministry of Public Security, Shanghai 200042, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yurong","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Fudan University, Shanghai 200438, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Han","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Forensic Science, Fudan University, Shanghai 200032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianye","family":"Zeng","sequence":"additional","affiliation":[{"name":"Institute of Forensic Science, Fudan University, Shanghai 200032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Forensic Science, Fudan University, Shanghai 200032, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3984-9728","authenticated-orcid":false,"given":"Suhua","family":"Zhang","sequence":"additional","affiliation":[{"name":"Institute of Forensic Science, Fudan University, Shanghai 200032, China"},{"name":"Ministry of Education\u2019s Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,4,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/j.forsciint.2006.05.017","article-title":"Estimation of the time since death","volume":"165","author":"Henssge","year":"2007","journal-title":"Forensic Sci. Int."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Roy, D., Tomo, S., Purohit, P., and Setia, P. (2021). Microbiome in Death and Beyond: Current Vistas and Future Trends. Front. Ecol. Evol., 9.","DOI":"10.3389\/fevo.2021.630397"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Tozzo, P., Amico, I., Delicati, A., Toselli, F., and Caenazzo, L. (2022). Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review. Diagnostics, 12.","DOI":"10.3390\/diagnostics12112641"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2273","DOI":"10.1111\/1462-2920.15000","article-title":"Predicting postmortem interval based on microbial community sequences and machine learning algorithms","volume":"22","author":"Liu","year":"2020","journal-title":"Environ. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Matuszewski, S. (2021). Post-Mortem Interval Estimation Based on Insect Evidence: Current Challenges. Insects, 12.","DOI":"10.3390\/insects12040314"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"102251","DOI":"10.1016\/j.jflm.2021.102251","article-title":"Role of molecular techniques in PMI estimation: An update","volume":"83","author":"Sangwan","year":"2021","journal-title":"J. Forensic Leg. Med."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Tozzo, P., Scrivano, S., Sanavio, M., and Caenazzo, L. (2020). The Role of DNA Degradation in the Estimation of Post-Mortem Interval: A Systematic Review of the Current Literature. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21103540"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Maiese, A., Scatena, A., Costantino, A., Di Paolo, M., La Russa, R., Turillazzi, E., Frati, P., and Fineschi, V. (2021). MicroRNAs as Useful Tools to Estimate Time Since Death. A Systematic Review of Current Literature. Diagnostics, 11.","DOI":"10.3390\/diagnostics11010064"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.forsciint.2017.10.033","article-title":"Estimation of the late postmortem interval using FTIR spectroscopy and chemometrics in human skeletal remains","volume":"281","author":"Wang","year":"2017","journal-title":"Forensic Sci. Int."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Schmidt, V.M., Zelger, P., Woess, C., Pallua, A.K., Arora, R., Degenhart, G., Brunner, A., Zelger, B., Schirmer, M., and Rabl, W. (2022). Application of Micro-Computed Tomography for the Estimation of the Post-Mortem Interval of Human Skeletal Remains. Biology, 11.","DOI":"10.3390\/biology11081105"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Hyde, E.R., Haarmann, D.P., Lynne, A.M., Bucheli, S.R., and Petrosino, J.F. (2013). The living dead: Bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0077733"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e01104","DOI":"10.7554\/eLife.01104","article-title":"A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system","volume":"2","author":"Metcalf","year":"2013","journal-title":"eLife"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Cl\u00e1udia-Ferreira, A., Barbosa, D.J., Saegeman, V., Fern\u00e1ndez-Rodr\u00edguez, A., Dinis-Oliveira, R.J., Freitas, A.R., and on behalf of the MR CLEAN Registry Investigators (2023). The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations. Microorganisms, 11.","DOI":"10.3390\/microorganisms11102509"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/s00414-013-0872-1","article-title":"The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing","volume":"128","author":"Pechal","year":"2014","journal-title":"Int. J. Leg. Med."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1007\/s12024-023-00733-z","article-title":"Microbiology and postmortem interval: A systematic review","volume":"20","author":"Moitas","year":"2024","journal-title":"Forensic Sci. Med. Pathol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Wang, Z., Zhang, F., Wang, L., Yuan, H., Guan, D., and Zhao, R. (2022). Advances in artificial intelligence-based microbiome for PMI estimation. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1034051"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"102904","DOI":"10.1016\/j.fsigen.2023.102904","article-title":"Exploring postmortem succession of rat intestinal microbiome for PMI based on machine learning algorithms and potential use for humans","volume":"66","author":"Li","year":"2023","journal-title":"Forensic Sci. Int. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Yang, F., Zhang, X., Hu, S., Nie, H., Gui, P., Zhong, Z., Guo, Y., and Zhao, X. (2023). Changes in Microbial Communities Using Pigs as a Model for Postmortem Interval Estimation. Microorganisms, 11.","DOI":"10.3390\/microorganisms11112811"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Janaway, R.C., Percival, S.L., and Wilson, A.S. (2009). Decomposition of Human Remains. Microbiology and Aging, Humana Press.","DOI":"10.1007\/978-1-59745-327-1_14"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3451","DOI":"10.1111\/jam.15771","article-title":"Estimation of the post-mortem interval by modelling the changes in oral bacterial diversity during decomposition","volume":"133","author":"Zhao","year":"2022","journal-title":"J. Appl. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1111\/omi.12191","article-title":"Dynamics of the oral microbiota as a tool to estimate time since death","volume":"32","author":"Quijada","year":"2017","journal-title":"Mol. Oral. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Dong, K., Xin, Y., Cao, F., Huang, Z., Sun, J., Peng, M., Liu, W., and Shi, P. (2019). Succession of oral microbiota community as a tool to estimate postmortem interval. Sci. Rep., 9.","DOI":"10.1038\/s41598-019-49338-z"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Johnson, H.R., Trinidad, D.D., Guzman, S., Khan, Z., Parziale, J.V., DeBruyn, J.M., and Lents, N.H. (2016). A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval. PLoS ONE, 11.","DOI":"10.1371\/journal.pone.0167370"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Iancu, L., Bonicelli, A., and Procopio, N. (2024). Decomposition in an extreme cold environment and associated microbiome-prediction model implications for the postmortem interval estimation. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1392716"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"102686","DOI":"10.1016\/j.fsigen.2022.102686","article-title":"Microbial DNA in human nucleic acid extracts: Recoverability of the microbiome in DNA extracts stored frozen long-term and its potential and ethical implications for forensic investigation","volume":"59","author":"Sguazzi","year":"2022","journal-title":"Forensic Sci. Int. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Ogbanga, N., Nelson, A., Gino, S., Wescott, D.J., Mickleburgh, H.L., Gocha, T.P., and Procopio, N. (2023). The impact of freezing on the post-mortem human microbiome. Front. Ecol. Evol., 11.","DOI":"10.3389\/fevo.2023.1151001"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2076","DOI":"10.1038\/s41396-018-0157-2","article-title":"Temporal dynamics of microbiota before and after host death","volume":"12","author":"Preiswerk","year":"2018","journal-title":"ISME J."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/mBio.00129-10","article-title":"Comparative analyses of the bacterial microbiota of the human nostril and oropharynx","volume":"1","author":"Lemon","year":"2010","journal-title":"mBio"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Bassis, C.M., Tang, A.L., Young, V.B., and Pynnonen, M.A. (2014). The nasal cavity microbiota of healthy adults. Microbiome, 2.","DOI":"10.1186\/2049-2618-2-27"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1007\/s00414-014-1128-4","article-title":"Initial insights into bacterial succession during human decomposition","volume":"129","author":"Hyde","year":"2015","journal-title":"Int. J. Leg. Med."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1038\/s41597-024-03518-3","article-title":"16S rRNA, metagenomics and 2bRAD-M sequencing to decode human thanatomicrobiome","volume":"11","author":"Huang","year":"2024","journal-title":"Sci. Data"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1126\/science.aad2646","article-title":"Microbial community assembly and metabolic function during mammalian corpse decomposition","volume":"351","author":"Metcalf","year":"2016","journal-title":"Science"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Hyde, E.R., Metcalf, J.L., Bucheli, S.R., Lynne, A.M., and Knight, R. (2017). Microbial communities associated with decomposing corpses. Forensic Microbiology, Wiley.","DOI":"10.1002\/9781119062585.ch10"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/s41579-023-00963-6","article-title":"The oral microbiome: Diversity, biogeography and human health","volume":"22","author":"Baker","year":"2024","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Pechal, J.L., Schmidt, C.J., Jordan, H.R., and Benbow, M.E. (2018). A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition. Sci. Rep., 8.","DOI":"10.1038\/s41598-018-23989-w"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.bjm.2016.10.005","article-title":"Microbial interactions: Ecology in a molecular perspective","volume":"47","author":"Braga","year":"2016","journal-title":"Braz. J. Microbiol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1111\/j.0006-341X.2002.00531.x","article-title":"Estimating the number of species in a stochastic abundance model","volume":"58","author":"Chao","year":"2002","journal-title":"Biometrics"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6941.2003.tb01040.x","article-title":"Using ecological diversity measures with bacterial communities","volume":"43","author":"Hill","year":"2003","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_41","first-page":"18","article-title":"Classification and Regression by randomForest","volume":"2\u20133","author":"Liaw","year":"2007","journal-title":"R J."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/7\/3432\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:11:06Z","timestamp":1760029866000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/7\/3432"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,6]]},"references-count":41,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,4]]}},"alternative-id":["ijms26073432"],"URL":"https:\/\/doi.org\/10.3390\/ijms26073432","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,4,6]]}}}