Patterns of microbial colonization of human bone from surface-decomposed remains

Abstract

46Microbial colonization of bone is an important mechanism of post-mortem skeletal degradation. 47However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It 48 is unknown if microbial communities vary in abundance or composition between bone element types, 49which could help explain patterns of human DNA preservation. The goals of the present study were to (1) 50identify the types of microbes capable of colonizing different human bone types and (2) relate microbial 51 abundances, diversity, and community composition to bone type and human DNA preservation. DNA 52 extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial 53 loading and microbial community composition and structure. Random forest models were applied to 54 predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant 55 bacterial bone colonizers were from the phyla Proteobacteria (36%), Actinobacteria (23%), Firmicutes 56 (13%), Bacteroidetes (12%), and Planctomycetes (4.4%). Eukaryotic bone colonizers were from 57Ascomycota (40%), Apicomplexa (21%), Annelida (19%), Basidiomycota (17%), and Ciliophora (14%). 58Bacterial loading was not a significant predictor of human DNA concentration in two out of three 59individuals. Random forest models were minimally successful in identifying microbes related to patterns 60 of DNA preservation, complicated by high variability in community structure between individuals and 61 body regions. This work expands on our understanding of the types of microbes capable of colonizing 62human bone and contributing to human skeletal DNA degradation. 63 64

Dissecting the Microbial Community Structure of Internal Organs During the Early Postmortem Period in a Murine Corpse Model

“…The possible reason may be that the locations of the liver and kidney are near the intestine of the body. Thermus, dominant in the heart, liver, and kidney samples, was found in the human postmortem skeleton, which was due to the greater duration of exposure to environmental uctuations [51]. Based on the comparison of alpha diversity, a lower observed ASV value was observed in the brain than in the other organs (P < 0.05, Fig.…”

Bone biodeterioration—The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community

“…Thirdly, based on previous studies on collagenase producing bacteria [ 49 , 50 ] we specifically investigated all the bones for the genera Bacillus , Pseudomonas , Bacteroides and Clostridium , along with the Alcaligenaceae family. The Firmicutes genus Bacillus was only present in the sediment at the terrestrial sand environment, as well as at very low abundance in the bones from that environment.…”

“…They have been found across a wide range of salinity and temperature gradients, and it is suggested that they are anaerobic, and capable of fermenting carbohydrates and proteinaceous substrates [ 59 ]. Observations from previous studies [ 14 , 49 ] exploring the microbial communities within degrading bones have found that the community predominantly consists of the phyla Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, as well to a lesser degree Acidobacteria and Planctomycetes. These studies were done on bones from whole cadavers, however, we find some similarities in the community structure, as across all four environments we find that members of these phyla are the main contributors to the microbial community ( Fig 1 , S10 Fig ).…”

“…We also observed an increase in relative abundance for the Proteobacterial family Alcaligenaceae, although in general at a lower relative abundance than that of Streptomyces and Streptosporangium . However, previous research has shown that members of the Alcaligenaceae are capable of producing collagenase and can use bone as a substrate [ 10 , 49 ]. Although these observations may be interesting in terms of implying which bacteria acts in terms of the bone diagenesis process, given the dynamic nature of many bacterial species' genomes, and the limited taxonomic resolution of metabarcoding data, future studies using shotgun sequenced metagenome data would be needed to clarify the relevance of our observations.…”

Deciphering a marine bone degrading microbiome reveals a complex community effort

“…Differential microbial colonization of the spongy cancellous bone tissue over the cortical compact bone has also been observed in the terrestrial environment and has been related to easier access to the red marrow (88) although a priming effect linked to the differential composition of the bone cannot be ruled out. Complex microbial mats form preferentially on the epiphysis of the long bones and this area is normally covered with hyaline cartilage (89) which was not removed before deployment.…”