Cadaver anal-swab metagenomes reveal host-structured and preservation-dependent postmortem microbial ecology

Background Postmortem microbial succession has been proposed as a biological information source for estimating the postmortem interval (PMI), yet internal body sites remain underexplored relative to skin and soil. The anal canal presents a distinct ecological starting point: an initially anaerobic, physically protected compartment shaped by the ante-mortem distal-gut microbiome. We used shotgun metagenomics to characterize how host demographics, preservation history, season, and PMI jointly structure cadaver anal-swab bacterial communities, identify candidate taxa associated with early postmortem change, and benchmark microbiome-based PMI prediction against routinely available case metadata. Results We profiled 201 adult cadaver anal swabs collected during routine forensic autopsies. Community analysis on Aitchison distance revealed a multi-factor structure in which host age (\((R^{2}=0.014)\), \((p=0.012)\)) and sex (\((R^{2}=0.010)\), \((p=0.002)\)) were statistically supported covariates, demonstrating that host-associated microbial signatures persist at this protected site after death. PMI contributed a localized community signal concentrated in the early common-support window (\((PMI\leq 3)\) days; \((R^{2}=0.025)\), \((p=0.004)\), Holm-adjusted \((p=0.011)\)), particularly among unfrozen cadavers (\((p=0.034)\)). Feature-level testing identified two detection-supported anaerobic candidates: Cloacibacillus porcorum , a mucin-degrading gut anaerobe, and Parabacteroides sp. N37, a member of a gut-associated anaerobic lineage. Two inferred metabolic pathways reached FDR support, providing hypothesis-generating functional leads. In nested cross-validation, case metadata established a statistically significant predictive baseline (MAE\,=\,0.907 log\((_{2})\) units, \((R^{2}=0.222)\), \((p<0.001)\)), driven primarily by preservation status; bacterial composition did not improve prediction beyond this baseline, clarifying that the biological signals identified here are localized and context-dependent rather than forming a single continuous microbial clock. Conclusions Cadaver anal-swab metagenomes retain host-structured microbial organization after death and harbour localized, preservation-context-dependent PMI signals. This work identifies biologically plausible anaerobic candidates for validation, establishes a metadata-anchored prediction benchmark, and provides a compositional shotgun-metagenomic reference framework for future preservation-balanced forensic microbiome studies.