Beyond ancient microbial DNA: Nonnucleotidic Biomolecules For Paleomicrobiology

Abstract

Identifying the causes of past epidemics depends on the specific detection of pathogens in buried individuals; this field of research is known as paleomicrobiology, an emerging field that has benefited from technological advances in microbiology. For almost 15 years, the detection, identification, and characterization of microbes in ancient environmental and human specimens emerged on the basis of ancient DNA (aDNA) analyses. aDNA limitations due to potential contamination by modern DNA and altered aDNA led to the development of alternative methods for the detection and characterization of nonnucleotidic biomolecules, including mycolic acids (of ancient mycobacteria) and proteins. Accordingly, immunohistochemistry, immunochromatography, and enzyme-linked immunosorbent assay techniques have been developed for the specific detection of microbes from ancient human and environmental specimens. Protein analysis by mass spectrometry, a standard for ancient animal identification, has also recently emerged as a technique for ancient mycobacteria detection, while immuno-PCR is yet another promising technique. As with aDNA, strict protocols must be enforced to ensure authenticity of the data. Here we review the analysis of nonnucleotidic biomolecules from ancient microbes and the ability of these analyses to complement aDNA analyses, which opens new opportunities for identification of ancient microbes as well as new avenues to potentially resolve controversies regarding the cause of some historical pandemics and study the coevolution of microbes and hosts.

Ancient pathogens in museal dry bone specimens: analysis of paleocytology and aDNA

“…Even if treponemal aDNA does not survive the decay process, the pathogen envelope remains stainable and thus detectable. The positive outcome of this study corresponds with Tran et al [80], emphasizing the value of non-nucleotide structures for paleopathology. Assuming dedicated working conditions, the quality of a stained smear containing a spirochete implies evidence of a treponematosis.…”

“…Ancient non-nucleotidic biomolecules can retain integrity through the decay process and their chemical character may therefore remain detectable [80]. Reports are available on the microscopic detection of fungi [13], bacteria [22], human DNA [28], and a multitude of normal human cells [10,16,42,72,76] deriving from human skeletal remains.…”

Plague: History and contemporary analysis

“…The plague in Athens does not seem to be related to Y. pestis but instead to Salmonella typhi. 5 The plague that prevailed at the beginning of the Roman Empire under the Antonine emperors has not been explained. The Justinian plague (starting in 541) is the first confirmed plague pandemic.…”

Mycolic Acids as Markers of Osseous Tuberculosis in the Neolithic Skeleton from Kujawy Region (Central Poland)

“…Despite its advantages, aDNA analysis, using spoligotyping and sequencing techniques, faces a number of research limitations -most importantly, it is prone to the contamination of ancient material with environmental DNA, leading to false-positive results (Tran et al 2011). Moreover, aDNA-based identification of microorganisms in ancient specimens might be limited by chemical modifications and fragmentation of nucleic acids during postmortem degradation.…”