Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens

Abstract

The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.

The past, present and future of ancient bacterial DNA

“…Therefore, datasets that comprise contemporary and ancient samples are apt to address the conflict in reported evolutionary rates. Bos and colleagues [36] investigated the impact of the inclusion of aDNA of increasingly larger time periods using three different Y. pestis datasets.…”

“…Therefore, datasets that comprise contemporary and ancient samples are apt to address the conflict in reported evolutionary rates. Bos and colleagues [ 36 ] investigated the impact of the inclusion of aDNA of increasingly larger time periods using three different Y. pestis datasets. The estimated mean ages were pushed further back the older the included sequences were and showed that the inclusion of Late Neolithic and Bronze Age samples decreased dating uncertainty immensely.…”

Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation

“…Investigations into human pathogens with animal or insect reservoirs would also provide key information about pathogen-host co-evolution. As we expect rates of evolution to be variable across different microbes and/or strains in specific hosts, clear attention to the calculation of evolutionary rates and how these are influenced by mis-mapping or contamination will be key (Key et al, 2017;Bos et al, 2019). Studies exploring animal microbiomes could also provide information into the health and morbidity of ancient animals, help define their interactions with humans, and even provide details about their domestication, migration, and adaptation to past environments.…”

“…The ability to interrogate a mixture of genetic material from all of the microorganisms present in a sample (the microbiome) using metagenomic approaches has also resulted in renewed interest and significant technical and analytical advances in the palaeomicrobiology field (Adler et al, 2013;Warinner et al, 2014;Harkins and Stone, 2015). By comparing ancient and modern microorganisms, researchers have now reconstructed the evolutionary history of several pathogens over extensive timescales and traced specific genomic changes that are linked to past diseases and epidemics (Anastasiou and Mitchell, 2013;Harkins and Stone, 2015;Bos et al, 2019).…”

A Significant Question in Cancer Risk and Therapy: Are Antibiotics Positive or Negative Effectors? Current Answers and Possible Alternatives

“…Ultimately, the outcome of competitive interactions between commensal members of our microbiota and potential pathogens would become a key life/death determining factor for human beings [49]. Recent methodological advances (e.g., high-throughput DNA sequencing) in paleomicrobiology [50][51][52] have allowed substantial progress in expanding our understanding on the appearance of human infectious microorganisms, their co-evolution with humans, the health conditions of past human populations, and the overall global ecological interactions across time. Accordingly, we know now that microbial pathogens, particularly bacteria, have been infecting humans for thousands of years [53][54][55].…”