How microbial ancient DNA, found in association with human remains, can be interpreted

Microbial community types and signature-like soil bacterial patterns from fortified prehistoric hills of Thuringia (Germany)

16S rRNA profiling has been applied for the investigation of bacterial communities of surface soil samples from forest-covered areas of ten prehistorical ramparts from different parts of Thuringia. Besides the majority bacterial types that are present in all samples, there could be identified bacteria that are highly abundant in some places and absent or low abundant in others. These differences are mainly related to the acidity of substrate and distinguish the communities of lime stone hills from soils of sand/quartzite and basalt hills. Minority components of bacterial communities show partially large differences that cannot be explained by the pH of the soil or incidental effects, only. They reflect certain relations between the communities of different places and could be regarded as a kind of signature-like patterns. Such relations had also been found in a comparison of the data from ramparts with formerly studied 16S rRNA profiling from an iron-age burial field. The observations are supporting the idea that a part of the components of bacterial communities from soil samples reflect their ecological history and can be understood as the “ecological memory” of a place. Probably such memory effects can date back to prehistoric times and might assist in future interpretations of archaeological findings on the prehistoric use of a place, on the one hand. On the other hand, the genetic profiling of soils of prehistoric places contributes to the evaluation of anthropogenic effects on the development of local soil bacterial diversity.

Environmental Microbial Forensics and Archaeology of Past Pandemics

The development of paleomicrobiology with new molecular techniques such as metagenomics is revolutionizing our knowledge of microbial evolution in human history. The study of microbial agents that are concomitantly active in the same biological environment makes it possible to obtain a picture of the complex interrelations among the different pathogens and gives us the perspective to understand the microecosystem of ancient times. This research acts as a bridge between disciplines such as archaeology, biology, and medicine, and the development of paleomicrobiology forces archaeology to broaden and update its methods. This chapter addresses the archaeological issues related to the identification of cemeteries from epidemic catastrophes (typology of burials, stratigraphy, topography, paleodemography) and the issues related to the sampling of human remains for biomolecular analysis. Developments in the field of paleomicrobiology are described with the example of the plague. Because of its powerful interdisciplinary features, the paleomicrobiological study of Yersinia pestis is an extremely interesting field, in which paleomicrobiology, historical research, and archeology are closely related, and it has important implications for the current dynamics of epidemiology.

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.

THE PROCESS OF Leishmania INFECTION - DISEASE AND NEW PERSPECTIVES OF PALEOPARASITOLOGY

Species of the genus Leishmania (Kinetoplastida, Trypanosomatidae) are causative agents of leishmaniasis, a complex disease with variable clinical spectrum and epidemiological diversity, constituting, in some countries, a serious public health problem. The origin and evolution of leishmaniasis has been under discussion regarding some clinical and parasitological aspects. After the introduction of paleoparasitology, molecular methods and immunodiagnostic techniques have been applied allowing the recovery of parasite remains, as well as the diagnosis of past infections in humans and other hosts. The dating of archaeological samples has allowed the parasitological analysis in time and space. This manuscript presents the state of the art of leishmaniasis and prospects related to paleoparasitology studies and their contribution to the evolutionary and phylogenetic clarification of parasites belonging to the genus Leishmania, and the leishmaniasis caused by them.

Malaria detection in the field of paleopathology: a meta-analysis of the state of the art

An integrative literature review was conducted to identify the current state of the art regarding malaria research in human remains and to identify novel methods to test for malaria infections in archaeological samples. This review was comprised of two surveys. The first survey established methods used currently to detect malaria in human remains from archaeological contexts. The second survey identified diagnostic approaches in the field of medicine. Techniques in medicine that could have applications with samples from archaeological contexts, such as preserved soft tissue and skeletal remains, are presented.

Brain evolution, the determinates of food choice, and the omnivore's dilemma

A coevolutionary paradigm using a biocultural perspective can help to unravel the complex interactions that led to the contemporary pattern of eating. Evolutionary history helps to understand the adaptation of diet and its nutritional implications. Anatomical and behavioral changes linked to changing dietary patterns in the Paleolithic resulted in an adaptive framework that affects modern diet. The evolution of an expanding brain, a shrinking large intestine, and lengthening small intestine necessitated a demand for nutritionally dense foods. The key to these changes is an understanding of the response to the omnivore's dilemma. Omnivores in their search for new items to feed their varied diet (neophilia) have a challenge when they fear (neophobia) novel items that may be poisonous and can cause death. The inborn mechanism initiates palate fatigue (sensory-specific satiety) ensuring a variety of foods will be eaten. Variety will limit the impact of toxins ingested and provide a more balanced diet. The development of cuisine, a momentous event in history, mediated the conflict, and changed the course of human evolution. The cuisine, a biocultural construct, defines which items found in nature are edible, how these products are transformed into food, the flavors used to add a sensory dimension to foods, and rules of eating or etiquette. Etiquette defines how, when, and with whom we eat. Patterns of eating in the modern setting are the end product of the way that Homo sapiens evolved and resolved the omnivore's dilemma. Control of fire and cooking expanded the range of available foods by creating a class of foods that are "predigested." An essential element to the evolution of the human diet was the transition to agriculture as the primary mode of subsistence. The Neolithic revolution dramatically narrowed the dietary niche by decreasing the variety of available foods, with the shift to intensive agriculture creating a dramatic decline in human nutrition. The recent industrialization of the world food system has resulted in a nutritional transition in which developing nations are simultaneously experiencing undernutrition and obesity. In addition, an abundance of inexpensive, high-density foods laden with sugar and fats is available to a population that expends little energy to obtain such large numbers of calories. Furthermore, the abundant variety of ultraprocessed foods overrides the sensory-specific satiety mechanism leading to overconsumption.

Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations

The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.

Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects

Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17(th) to the 19(th) century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity ≥ 95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17(th) century to the early 18(th) century.

Molecular characterization of a pre-Columbian mummy and in situ coprolite

The history of Homo sapiens dispersal around the world and inherent interpopulation contacts and conflicts has given rise to several transitions in his relationships with the natural world, with the final result of changes in the patterns of infectious disease (McMichael [2001] Ecosystem Health 7:107-115). Of particular interest, in this context, is the contact between Amerindians and Europeans that started at the end of the 15th century, and the resulting exchange of microbes. We successfully recovered ancient DNA from a pre-Columbian mummy from Cuzco (Peru), radiocarbon-dated to 980-1170 AD, for which consistent mtDNA amplifications and sequences were obtained. The analysis of mtDNA revealed that the mummy's haplogroup was characteristic of Native American populations. We also investigated a sample of feces directly isolated from the intestines of the mummy, using a polymerase chain reaction system designed to detect the broadest spectrum of bacterial DNAs. The analysis of results, following a criterion of "paleoecological consistency" (Rollo and Marota [1998] Philos. Trans. R. Soc. Lond. [Biol.] 354: 111-119), demonstrated that some vestiges of the original microbial flora of the feces were preserved. In particular, we were able to identify the DNA of Haemophylus parainfluenzae, thus suggesting that this recently recognized pathogen was present in precontact Native Americans.

Geologically ancient DNA: fact or artefact?

Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication criteria for work with geologically ancient DNA.

Ancient DNA

In the past two decades, ancient DNA research has progressed from the retrieval of small fragments of mitochondrial DNA from a few late Holocene specimens, to large-scale studies of ancient populations, phenotypically important nuclear loci, and even whole mitochondrial genome sequences of extinct species. However, the field is still regularly marred by erroneous reports, which underestimate the extent of contamination within laboratories and samples themselves. An improved understanding of these processes and the effects of damage on ancient DNA templates has started to provide a more robust basis for research. Recent methodological advances have included the characterization of Pleistocene mammal populations and discoveries of DNA preserved in ancient sediments. Increasingly, ancient genetic information is providing a unique means to test assumptions used in evolutionary and population genetics studies to reconstruct the past. Initial results have revealed surprisingly complex population histories, and indicate that modern phylogeographic studies may give misleading impressions about even the recent evolutionary past. With the advent and uptake of appropriate methodologies, ancient DNA is now positioned to become a powerful tool in biological research and is also evolving new and unexpected uses, such as in the search for extinct or extant life in the deep biosphere and on other planets.

Parasitism, the diversity of life, and paleoparasitology

The parasite-host-environment system is dynamic, with several points of equilibrium. This makes it difficult to trace the thresholds between benefit and damage, and therefore, the definitions of commensalism, mutualism, and symbiosis become worthless. Therefore, the same concept of parasitism may encompass commensalism, mutualism, and symbiosis. Parasitism is essential for life. Life emerged as a consequence of parasitism at the molecular level, and intracellular parasitism created evolutive events that allowed species to diversify. An ecological and evolutive approach to the study of parasitism is presented here. Studies of the origin and evolution of parasitism have new perspectives with the development of molecular paleoparasitology, by which ancient parasite and host genomes can be recovered from disappeared populations. Molecular paleoparasitology points to host-parasite co-evolutive mechanisms of evolution traceable through genome retrospective studies.

An introduction to reproduction in pharaonic Egypt

Reproductive science is a new-born medical speciality compared with other specialities such as surgery or dentistry. However, infertility and obstetrical complications commonly diagnosed in the 20th century have a history as old as medicine itself. In an attempt to distance themselves from the African and Middle-Eastern roots of our culture, the European intellectuals of the 18th and 19th century have written the history of the democratic world starting with the Greco-Roman period. Egyptian medicine has influenced the medicine of neighbouring civilisations, including the culture of ancient Greece and its influence spread onward, thereby affecting Western civilisation. The aim of this review is to give credit to these early researchers, who often concluded with extremely accurate observations and to present their colourful and sometimes controversial contribution to our knowledge of reproductive anatomy, physiology and pathology.

Analysis of bacterial DNA in skin and muscle of the Tyrolean iceman offers new insight into the mummification process

About 80 sequences (16s ribosomal RNA gene) of bacterial DNA in samples of skin and muscle taken directly from the Tyrolean iceman (3350-3100 years B.C.) or recovered during the 1992 archaeological expedition at the Alpine site were analyzed to obtain clues to the natural mummification process that allowed the corpse of the Neolithic shepherd/hunter to be preserved for more than 5,000 years. The investigation was made more complex by the fact that the surface of the mummy had been swabbed with phenol soon after the discovery (September 19, 1991). Our results show that no trace of microbial DNA is left on the actual surface of the body, while the untreated skin still bears the remains of large numbers of bacteria belonging to the genera Sphingomonas, Afipia, Curtobacterium, Microbacterium, Agromyces, and others. Compared to the untreated skin, the iceman's muscle is also very rich in bacterial DNA. However, this DNA comes, with few exceptions, from the species Clostridium algidicarnis. The sharp difference in the bacterial DNA composition of skin and muscle suggests that the remains of the original cadaveric microflora of the latter have not disappeared during the iceman's taphonomic history. On the other hand, the massive presence of C. algidicarnis, a cold-adapted sporigenous, the DNA of which was previously (Ubaldi et al. [1998] Am. J. Phys. Anthropol. 107:285-295) found in the soft tissue of a naturally desiccated Andean mummy, indicates that the hypothesis that the iceman's corpse underwent rapid dehydration by the effect of a warm wind (föhn) is no longer plausible. The results best fit with the hypothesis (Bereuter et al. [1997] Chem. Eur. J. 7:1032-1038) that the body was first covered by snow and ice, and then underwent thawing and, finally, desiccation.