Characterizing the postmortem human bone microbiome from surface-decomposed remains

PLoS One. 2020 Jul 8;15(7):e0218636. doi: 10.1371/journal.pone.0218636. eCollection 2020.

Abstract

Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anthropology
  • Ascomycota / genetics
  • Ascomycota / isolation & purification
  • Autopsy
  • Bacteroidetes / genetics
  • Bacteroidetes / isolation & purification
  • Bone and Bones / microbiology*
  • DNA / chemistry
  • DNA / metabolism
  • Humans
  • Male
  • Microbiota*
  • Proteobacteria / genetics
  • Proteobacteria / isolation & purification
  • RNA, Ribosomal, 16S / chemistry
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / metabolism
  • Tooth / microbiology

Substances

  • RNA, Ribosomal, 16S
  • DNA

Grants and funding

This project was supported by Award No. 2010-DN-BX-K229, awarded by the National Institute of Justice, Office of Justice Programs, U.S. Department of Justice (DOJ) to AZM, JMD, and JD and Award 1549726, awarded by the National Science Foundation (NSF), to JMD. DOJ and NSF had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Bode Cellmark Forensics provided support in the form of salary for JD, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section. The opinions, findings, and conclusions or recommendations expressed in this manuscript are those of the authors and do not necessarily reflect those of the DOJ, NSF or Bode Cellmark Forensics.