The Cause of Death of a Child in the 18th Century Solved by Bone Microbiome Typing Using Laser Microdissection and Next Generation Sequencing

Abstract

The history of medicine abounds in cases of mysterious deaths, especially by infectious diseases, which were probably unresolved because of the lack of knowledge and of appropriate technology. The aim of this study was to exploit contemporary technologies to try to identify the cause of death of a young boy who died from a putative “infection” at the end of the 18th century, and for whom an extraordinarily well-preserved minute bone fragment was available. After confirming the nature of the sample, we used laser microdissection to select the most “informative” area to be examined. Tissue genotyping indicated male gender, thereby confirming the notary’s report. 16S ribosomal RNA sequencing showed that Proteobacteria and Actinobacteria were more abundant than Firmicutes and Bacteroidetes, and that Pseudomonas was the most abundant bacterial genus in the Pseudomonadaceae family. These data suggest that the patient most likely died from Pseudomonas osteomyelitis. This case is an example of how new technological approaches, like laser microdissection and next-generation sequencing, can resolve ancient cases of uncertain etiopathology. Lastly, medical samples may contain a wealth of information that may not be accessible until more sophisticated technology becomes available. Therefore, one may envisage the possibility of systematically storing medical samples for evaluation by future generations.

The Prenatal Microbiome: A New Player for Human Health

“…Indeed, several reports have demonstrated that microbial alterations (or dysbiosis) can be found in an increasing number of human diseases and that their entities may be associated with the severity of the phenotype or with the sensitivity to specific therapies [1,2,3,4,5,6,7,8]. Thus, even if it has not been well established yet whether the microbiome alterations are the cause or the consequence of diseases, their study is intriguing since it opens the way to the identification of novel disease-specific biomarkers, or to the development of targeted therapies aiming to manipulate the microbiome in the attempt to restore a healthy status [9,10,11,12,13,14,15,16,17]. Next generation sequencing-based approaches have assessed their reliability in metagenomic studies escalating the possibility to describe microbial communities in detailand obtain both qualitative and quantitative information [1,2,18,19].…”

The High-Throughput Analyses Era: Are We Ready for the Data Struggle?

“…These techniques have impacted every field of molecular research, escalating previously used sequencing technologies [ 11 ], and opening the way to the -omic sciences foundation [ 1 , 2 ]. Indeed, NGS methods allow the sequencing of entire genomes [ 12 , 13 , 14 , 15 ], of exomes [ 16 , 17 , 18 ], of panels of genes related to a disease of interest [ 19 , 20 , 21 ], or of a single gene [ 22 , 23 , 24 , 25 , 26 ], but can also be used to explore the entire transcriptome [ 27 , 28 , 29 ], small RNAs [ 30 , 31 , 32 ], the epigenome [ 33 , 34 ], and the microbiome [ 35 , 36 , 37 , 38 ].…”

“…In addition to the study of sequence variations at the DNA level, NGS methods can be used to study genetic variability, and the mechanisms underlying the onset of specific diseases at epigenetic, transcriptomic and metagenomic levels [ 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 ]. Indeed, several factors, other than individual genetic predisposition, such as diet, environmental factors and lifestyle, can influence the epigenome, the transcriptome and the microbiome [ 2 , 50 ].…”

“…Finally, by superseding the need of microbial cultivation, NGS-based techniques also gave a significant boost to metagenomics for the study of the microbial relationships with human physiology and pathology, and for the identification of specific microbial signatures related to a disease of interest [ 35 , 36 , 37 , 38 , 50 ]. It is now established that the human microbiome plays a role in healthy status acquisition and maintenance [ 50 , 55 ].…”

Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

“…Based on these technological advances, a plethora of studies have been carried out to characterize the microbial communities of specific environments, including human beings [ 3 , 4 , 5 , 6 , 7 , 8 , 9 ]. In particular, the mutually beneficial relationship between the microbiome and the human host has been largely investigated [ 2 , 10 , 11 , 12 , 13 , 14 ].…”