1 Taxonomic Classification
2 Abundance Profiles
Top 15 MAGs by Total Abundance
Figure 2a. MAGs ranked by cumulative abundance across all samples.
Sample Detection Distribution
Figure 2b. Distribution of MAGs by number of samples detected.
Abundance Heatmap (Top 30 MAGs × Top 50 Samples)
Figure 2c. Relative abundance patterns. Color intensity indicates log₁₀(abundance + 1).
2.1 Abundance Table
3 Metabolic Potential
Figure 1. Distribution of metabolic pathway genes across MAGs.
4 Methods
This database presents metagenome-assembled genomes (MAGs) recovered from soils associated with human decomposition research conducted at three U.S. anthropological facilities between 2016–2017. Below we summarize the key methodological steps relevant to the data presented in this interface.
4.1 Study Design
Three Facilities
Samples collected from Colorado Mesa University (FIRS, semi-arid), Sam Houston State University (STAFS, temperate), and University of Tennessee (ARF, temperate).
Seasonal Coverage
Three cadavers placed per season (spring, summer, fall, winter) at each facility, totaling 36 subjects across the study.
Temporal Sampling
Daily sampling over 21 days of decomposition, capturing early, active, and advanced decomposition stages.
4.2 MAG Generation
The taxonomy data in this database derives from metagenome-assembled genomes constructed through the following pipeline:
Sequencing
Shotgun metagenomic sequencing of 569 hip-adjacent soil samples on Illumina HiSeq 4000 and NovaSeq 6000 platforms. Human sequences filtered against GRCh37/hg19 reference.
Co-assembly
Metagenomes co-assembled within sites using MEGAHIT (v1.2.9) with k-min of 41. Scaffolds >2,500 bp retained for binning.
Binning & QC
Scaffolds binned into MAGs using MetaBAT2 (v2.12.1). Quality assessed with CheckM (v1.1.2). MAGs retained if >50% complete and <10% contaminated.
Dereplication
MAGs dereplicated at 99% identity using dRep (v2.6.2), yielding 257 representative genomes from 1,130 initial bins.
Taxonomy
Taxonomic classification assigned using GTDB-tk (v2.0.0, release 207). Novel taxa identified at order (n=3), family (n=9), genus (n=28), and species (n=158) levels.
4.3 Abundance Quantification
The abundance profiles displayed in this database represent normalized read counts across samples:
- Reads from each sample mapped to the dereplicated MAG set using Bowtie2 (v2.3.5) with sensitive alignment parameters
- BAM files filtered for reads mapping at ≥95% identity using BBMap (v38.90)
- Abundance calculated as Transcripts Per Million (TPM) using CoverM (v0.3.2)
- Low-abundance features filtered: minimum 50 total counts and presence in ≥6 samples required
4.4 Metabolic Annotation
The metabolic pathway data derives from functional annotation of MAG gene content:
- MAGs and co-assemblies annotated using DRAM (v1.0.0) for comprehensive functional profiling
- Gene sequences clustered at 95% identity using MMseqs2 to identify orthologous groups
- Pathway assignments based on KEGG modules and custom metabolic categories relevant to decomposition processes
- Genome-scale metabolic models constructed with CarveMe (v1.5.1) for cross-feeding and interaction analyses
4.5 Key Findings
The study identified a universal microbial decomposer network that assembles despite environmental variation. Key decomposers including Oblitimonas alkaliphila, Ignatzschineria, Wohlfahrtiimonas, and Yarrowia were phylogenetically unique and rare in non-decomposition environments. Cross-feeding interactions, particularly involving amino acid exchange, increased during active decomposition. These patterns enabled development of machine learning models capable of predicting postmortem interval within approximately ±3 days.