Paleomicrobiology of Humans

There are several scenarios regarding how burial sites in archaeological contexts are discovered. We will focus on two scenarios according to the degree of historical knowledge regarding the studied sector. The excavation may be performed in a known funeral place or a highly suspected place (e.g., the interior or immediate exterior space in a religious monument or a parish cemetery). Also, the excavation of unexpected graves or graves discovered by chance may occur in places that had unknown or forgotten funeral purposes.

As early researchers in paleomicrobiology, we have used its techniques to study the plague, generating controversy after the publication of our initial results ( 1 ). The controversy has allowed us to respond and propose new approaches to understanding plague pandemics. Our conclusion is that the plague was related to outbreaks of lice, not to rat fleas, because fleas cannot explain epidemics of this magnitude ( 1 ).

Paleomicrobiology is a part of general microbiology that aims to describe microbial flora (including bacteria, archaea, viruses, parasites, and microscopic fungi) in older specimens; it includes the retrospective diagnosis of infectious and tropical diseases ( 1 , 2 ). There is no precise numerical definition of an old specimen; we consider as paleomicrobiological specimens any specimen older than 100 years, while the study of more recent samples may be called meso-microbiology. Also, we will consider in this chapter only animal and human specimens, excluding inanimate environmental specimens. The initial works of paleopathology, which used molecular biology techniques based on PCR, highlighted the possibility of the contamination of old samples by contemporary human DNA, casting doubt on the validity of PCR-based work for the detection of human and microbial ancient DNA (aDNA). These doubts, arising in the field of human aDNA, were then relayed to the field of paleomicrobiology by colleagues not practicing microbiology and without microbiological knowledge, who simply derived doubts from their observations of old human DNA. In fact, microbial contamination of an ancient specimen can take place in situ from the surrounding flora, which can be either ancient flora contemporary with the sample or flora from operators at the time of excavation and storage of the old material or during laboratory manipulations, which is modern contamination. Contamination can occur with whole organisms or biomolecules of interest, such as nucleic acids or proteins or mycolic acids ( Fig. 1 ). Indeed, several methods are now used for discovering microbes in ancient specimens beyond the now-conventional aDNA analyses ( 2 ).

It is generally now known that the emergence of antibiotic resistance in bacteria is an ancient biological event, meaning that the existence of resistance genes predates our present-day use of antibiotics. In other words, antibiotic resistance is not a modern phenomenon. These findings have been made possible by emerging fields, such as paleomicrobiology, and paleo-environmental studies of ancient biological samples, deep subsurface environments, and isolated pristine environments that are free of contemporary sources (contemporary antibiotic compounds or genes) ( 1 ). Paleomicrobiology has been employed to gain insight into ancient infections, such as the Black Death and Justinian’s plague, and has shown evidence of the involvement of bacteria in these pandemics ( 2 , 3 ).

Paleopathology is the most recent discipline among the sciences of the past; it studies traces of diseases that can be recognized in animal and human remains from ancient times. This research field is located at the interface of medicine, anthropology, and archaeology. Since its beginning in the late 19th century, paleopathology has developed a specific interest in the origin and evolution of infectious diseases affecting human populations. Since the mid 1990s, thanks to the introduction of PCR into the field, the studies of past human infections have undergone a significant revival, evolving from the analysis of ancient writings and bones to that of ancient molecules, allowing evidence-based diagnosis. The goal of this chapter is to provide some examples of an integrative approach that combines these three sources of data for reconstructing the history of human infections.

Tuberculosis remains one of the world’s deadliest communicable diseases. In 2014, tuberculosis developed in an estimated 9.6 million people, and 1.5 million died of the disease ( 1 ). The principal causative organism is Mycobacterium tuberculosis, an obligate pathogen that is a member of the M. tuberculosis complex (MTBC), a group of closely related organisms that primarily infect different animal hosts. Tuberculosis may involve every organ in the body, but the most common clinical presentation is pulmonary disease, in which transmission is via infectious aerosols released from the lungs of an infected person. In the alveolus of the lung, inhaled tubercle bacilli are ingested by macrophages and are normally contained by the host immune response. This leads to granuloma formation and eventually to calcified lesions. Swallowing infected sputum can cause intestinal tuberculosis. Transmission can occur via direct contact in cases of scrofula (skin tuberculosis). In addition, ingestion of milk or food from an infected animal can cause human infection with Mycobacterium bovis or other members of the MTBC. However, subsequent transmission of these animal MTBC lineages from person to person is rare. M. tuberculosis can survive and grow within macrophages, so that it is able to evade the host immune system. An active cell-mediated immune response is required to contain and kill the tubercle bacilli, so any underlying conditions that reduce its efficiency increase susceptibility to tuberculosis. One-third of the global population is estimated to have latent tuberculosis infection. These individuals do not have active disease but may develop it in the near or remote future, a process called tuberculosis reactivation. The lifetime risk for reactivation is estimated to be 5% to 10%, with tuberculosis developing in the majority of cases within the first 5 years after initial infection. However, the risk is considerably higher in the presence of predisposing factors ( 2 ).

The study of ancient parasites, paleoparasitology, is an area of parasitology that evolved as a research field combining archaeology, anthropology, biology, and health sciences ( 1 ). It aims to detect parasite traces in ancient samples and to study parasitism evolution over time and space ( 2 ). This research field covers the study of parasites in humans and other animal remains recovered from archaeological and paleontological sites.

Smallpox, the infectious disease caused by species of the variola virus (VARV), is probably one of the most terrible diseases to have affected human populations over the past hundreds of years. Its dissemination was significantly related to global population growth and the movement of people across regions and continents. The geographical origin of the disease remains a matter of debate; hypotheses suggest the Indus Valley or Egypt and the Near East, regions that had high population densities 3,000 to 4,000 years ago ( 1 , 2 ). The latter hypothesis was recently refined by Babkin and Babkina ( 3 ), who suggested that the initial spread of the virus in humans could have occurred in the Horn of Africa (Kingdom of the Queen of Sheba). In this region, active trade expeditions overlapped with the distribution areas of several animal poxvirus hosts (including the naked-soled gerbil) and the introduction of the domesticated camel as a new potential host. The disease spread from these regions to the west and east, with historical reports suggesting epidemics in China and Europe as early as the 1st or 2nd century CE, with a subsequent progressive emergence of the virus in western Africa ( 4 ). During the 16th century, smallpox was a significant cause of death in Europe. The smallpox agent was also exported to South America during this time and passed over both American continents ( 5 , 6 ). As noted by Fenner et al., smallpox was a major global endemic disease by the mid-18th century, with the exception of Australia ( 4 ). Only the variolation and vaccination campaigns initiated more than two centuries ago reduced dramatically the spread and impact of the disease in contemporary populations.

Lice (Insecta, Phthiraptera) are permanent obligate parasites of birds and mammals. Approximately 4,900 species of lice are recorded and distributed into four suborders: chewing or biting lice, including Rhynchophthirina, Ischnocera, and Amblycera, and sucking lice, Anoplura ( 1 ).