Analysis of ancient DNA from coprolites: a perspective with random amplified polymorphic DNA-polymerase chain reaction approach

Gastrointestinal parasite burden in 4th-5th c. CE Florence highlighted by microscopy and paleogenetics

The study of ancient parasites, named paleoparasitology, traditionally focused on microscopic eggs disseminated in past environments and archaeological structures by humans and other animals infested by gastrointestinal parasites. Since the development of paleogenetics in the early 1980s, few paleoparasitological studies have been based on the ancient DNA (aDNA) of parasites, although such studies have clearly proven their utility and reliability. In this paper, we describe our integrative approach for the paleoparasitological study of an ancient population from Florence in Italy, dated to the 4th-5th c. CE. The first stage consisted in the study of sediment samples from the pelvic area of 18 individuals under light microscopy. This allowed us to detect Ascarid-type eggs belonging very probably to the human-infesting roundworm Ascaris lumbricoides. Ten subsamples were selected corresponding to five individuals, and we extracted their whole DNA following sediment aDNA protocols. A targeted approach allowed us to detect two nematodes and one trematode aDNA fragments, namely Ascaris sp., Trichuris trichiura, and Dicrocoelium dendriticum. Among the five individuals tested for microscopic eggs and aDNA, three of them showed the remains of eggs (only Ascarid-type), but all of them tested positive to the presence of at least one parasite aDNA. Microscopic diagnosis first guided our research for the selection of promising samples while the targeted aDNA approach significantly improved our knowledge in terms of parasitic diversity and frequency in this population subgroup. These results enabled us to discuss the possible impact of latent parasitism in this past population at the time of an epidemic, as suggested in Florence. In particular, the singular case of D. dendriticum detection is discussed in light of the present-day scarcity of genuine human infections. Nevertheless, actual infections are known in the paleoparasitological record, and food habits may have led to false parasitism in this historical context. aDNA leaching from overlying strata may also explain this detection. This study strongly pleads for a systematic integrative approach combining microscopy and aDNA in paleoparasitology.

Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus

Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace

This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.

Mummy studies and the bioarchaeology of care

The bioarchaeology of care is a framework through which researchers can begin to infer the level of care an individual may have required based on the presence of paleopathological evidence. To date, all of the research that has employed the framework has been based on evidence derived from skeletal material. This special issue was organized in order to highlight how the analysis of mummified soft tissue, as well as other sources of data commonly associated with mummified remains, such as coprolites and intestinal contents, has the potential to provide valuable insight into the reconstruction of care in the past.

First Paleogenetic Evidence of Probable Syphilis and Treponematoses Cases in the Brazilian Colonial Period

Despite interest in the origins of syphilis, paleopathological analysis has not provided answers, and paleogenetic diagnosis remains a challenge. Even venereal syphilis has low infectivity which means there are few circulating bacteria for most of the individual's life. Human remains recovered from the Nossa Senhora do Carmo Church (17th to 19th centuries) and the Praça XV Cemetery (18th to 19th centuries), Rio de Janeiro, Brazil, were subjected to Treponema paleogenetic analysis. Historical data point to endemic treponemal infections in the city, including venereal syphilis. Based on the physiopathology of Treponema pallidum infection, 25 samples, mostly from skull remains of young adults, with no visible paleopathological evidence of treponematoses, were analyzed. PCR with three molecular targets, tpp47, polA, and tpp15, were applied. Ancient DNA tpp15 sequences were recovered from two young adults from each archaeological site and revealed the polymorphism that characterizes T. p. subsp. pallidum in a female up to 18 years old, suggesting a probable case of syphilis infection. The results indicated that the epidemiological context and the physiopathology of the disease should be considered in syphilis paleogenetic detection. The findings of Treponema sp. aDNA are consistent with historical documents that describe venereal syphilis and yaws as endemic diseases in Rio de Janeiro. Data on the epidemiological characteristics of the disease and its pathophysiology offer new perspectives in paleopathology.

Tuberculosis in post-contact Native Americans of Brazil: Paleopathological and paleogenetic evidence from the Tenetehara-Guajajara

Tuberculosis (TB) has been described in Native American populations prior to the arrival of European explorers, and in Brazilian populations dating from the Colonial Period. There are no studies demonstrating TB infection in native Brazilians, and the history and epidemiological scenario of TB in Brazil is still unknown. The aim of this study was to verify the presence of TB infection among the native Tenetehara-Guajajara population from Maranhão State, Brazil, 210 ± 40 years ago. A Tenetehara-Guajajara skeleton collection was submitted to paleopathological analysis, and rib bone samples (n = 17) were used for paleogenetic analysis based on Mycobacterium tuberculosis complex (MTC) targets. Porotic hyperostosis and cribra orbitalia were found in 10 and 13 individuals, respectively. Maternal ancestry analysis revealed Native American mtDNA haplogroups A and C1 in three individuals. Three samples showed osteological evidence suggestive of TB. katG and mtp40 sequences were detected in three individuals, indicating probable TB infection by two MTC lineages. Tuberculosis infection in the Tenetehara-Guajajara population since the 18th century points to a panorama of the disease resulting, most probably, from European contact. However, the important contribution of African slaves in the population of Maranhão State, could be also considered as a source of the disease. This study provides new data on TB during the Brazilian Colonial Period. This is the first report integrating paleopathological and paleogenetic data for the study of TB in Brazil.

First record of the nematode Libyostrongylus dentatus Hoberg, Lloyd & Omar, 1995 (Trichostrongylidae) in ostriches (Struthio camelus Linnaeus, 1758) (Struthionidae) outside the Americas

Background

Libyostrongylus douglassii, Libyostrongylus dentatus and Libyostrongylus magnus are nematodes that infect ostriches. The first species has been identified in ostriches from Africa, Europe, Americas and Oceania. Although the natural range of ostriches is Africa, L. dentatus was first described in birds from the USA and later identified in Brazil, where co-infections with L. douglassii have been commonly reported. Libyostrongylus magnus is known from the original description only. There are a few reports on infections with L. douglassii in ostriches from Africa and all farmed birds examined are from the southern region of the continent. The aim of this report was to verify Libyostrongylus spp. infections in wild ostriches from Ethiopia. Fecal samples from ostriches, Struthio molybdophanes, were collected and submitted to coproculture. Infective larvae were identified to the species level based on general morphology and morphometry. In addition, phylogenetic analysis of the first and second internal transcribed spacer (ITS1 and ITS2) of the nuclear ribosomal DNA was performed.

Results

Infective larvae from Ethiopian ostriches had the morphological characteristics of L. dentatus. Confidence interval estimate for sheath tail length from Ethiopian Libyostrongylus sp. isolates overlapped one for Brazilian L. dentatus. Neighbor-joining and Maximum Likelihood phylogenetic trees based on sequences of the ITS1 and ITS2 regions revealed that the Ethiopian samples belong to the L. dentatus species clade. Monospecific infections with L. dentatus were confirmed in Ethiopian wild ostriches, opposed to the co-infections typically found in the Americas.

Conclusions

To our knowledge, this is the first record of L. dentatus from African ostriches, the region from which this parasite originated.

Ancient human mitochondrial DNA and radiocarbon analysis of archived quids from the Mule Spring Rockshelter, Nevada, USA

Chewed and expectorated quids, indigestible stringy fibers from the roasted inner pulp of agave or yucca root, have proven resilient over long periods of time in dry cave environments and correspondingly, although little studied, are common in archaeological archives. In the late 1960s, thousands of quids were recovered from Mule Spring Rockshelter (Nevada, USA) deposits and stored without consideration to DNA preservation in a museum collection, remaining unstudied for over fifty years. To assess the utility of these materials as repositories for genetic information about past inhabitants of the region and their movements, twenty-one quids were selected from arbitrary excavation depths for detailed analysis. Human mitochondrial DNA sequences from the quids were amplified by PCR and screened for diagnostic single nucleotide polymorphisms. Most detected single nucleotide polymorphisms were consistent with recognized Native American haplogroup subclades B2a5, B2i1, C1, C1c, C1c2, and D1; with the majority of the sample set consistent with subclades C1, C1c, and C1c2. In parallel with the DNA analysis, each quid was radiocarbon dated, revealing a time-resolved pattern of occupancy from 347 to 977 calibrated years before present. In particular, this dataset reveals strong evidence for the presence of haplogroup C1/C1c at the Southwestern edge of the US Great Basin from ~670 to 980 cal YBP, which may temporally correspond with the beginnings of the so-called Numic Spread into the region. The research described here demonstrates an approach which combines targeted DNA analysis with radiocarbon age dating; thus enabling the genetic analysis of archaeological materials of uncertain stratigraphic context. Here we present a survey of the maternal genetic profiles from people who used the Mule Spring Rockshelter and the historic timing of their utilization of a key natural resource.

Palaeoparasitology and palaeogenetics: review and perspectives for the study of ancient human parasites

While some species of parasites can be identified to species level from archaeological remains using microscopy (i.e.Enterobius vermicularis,Clonorchis sinensis), others can only be identified to family or genus level as different species produce eggs with similar morphology (i.e.Tæniasp. andEchinococcussp.). Molecular and immunological approaches offer the possibility to provide more precise determination at the species level. They can also identify taxa when classic parasite markers such as eggs or cysts have been destroyed over time. However, biomolecules can be poorly preserved and modern reference DNA is available only for a limited number of species of parasites, leading to the conclusion that classic microscopic observation should be combined with molecular analyses. Here we present a review of the molecular approaches used over the past two decades to identify human pathogenic helminths (Ascarissp.,Trichurissp.,E. vermicularis,Fasciolasp. etc.) or protists (Giardiasp.,Trypanosomasp.,Leishmaniasp. etc.). We also discuss the prospects for studying the evolution of parasites with genetics and genomics.

Temporal and Spatial Distribution of Enterobius vermicularis (Nematoda: Oxyuridae) in the Prehistoric Americas

Investigations of Enterobius sp. infection in prehistory have produced a body of data that can be used to evaluate the geographic distribution of infection through time in the Americas. Regional variations in prevalence are evident. In North America, 119 pinworm positive samples were found in 1,112 samples from 28 sites with a prevalence of 10.7%. Almost all of the positive samples came from agricultural sites. From Brazil, 0 pinworm positive samples were found in 325 samples from 7 sites. For the Andes region, 22 pinworm positive samples were found in 411 samples from 26 sites for a prevalence of 5.3%. Detailed analyses of these data defined several trends. First, preagricultural sites less frequently show evidence of infection compared to agricultural populations. This is especially clear in the data from North America, but is also evident in the data from South America. Second, there is an apparent relationship between the commonality of pinworms in coprolites and the manner of constructing villages. These analyses show that ancient parasitism has substantial value in documenting the range of human behaviors that influence parasitic infections.

Human Coprolites as a Source for Paleomicrobiology

The paleomicrobiology of coprolites, which are fossilized fecal materials, has already yielded data about various organisms, including micro-eukaryotes, bacteria, and archaea, thus expanding our comprehension of ancient human dietary habits, gut microbiota, and intestinal and systemic infections. This mini-review briefly describes previous works and summarizes the main techniques used in handling coprolites and the findings obtained about ancient gut microbiota. Past intestinal and systemic infections are outlined.

Evidence of Helminth Infection in Guanche Mummies: Integrating Paleoparasitological and Paleogenetic Investigations

The Guanches, ancient inhabitants of the Canary Islands, Spain, practiced mummification of their dead. A paleoparasitological and paleogenetic analysis was conducted on mummified bodies (n = 6) (AD 1200, Cal BP 750) belonging to the Guanche culture from Gran Canaria Island. Coprolite and sediment samples (n = 19) were removed from below the abdominal region or sacral foramina. The samples were rehydrated in 0.5% trisodium phosphate solution for 72 hr at 4 C, and the paleoparasitological investigation was conducted by spontaneous sedimentation method and microscopic examination. The results revealed the presence of well-preserved eggs of Ascaris sp., Trichuris trichiura , Enterobius vermicularis , and hookworms. Ancient DNA was extracted from sediment samples to elucidate the ancestry of the mummies and for molecular detection of Ascaris sp. infection. Results of paleogenetic analysis demonstrated Ascaris sp. infection using 2 molecular targets, cytb and nad1. The mtDNA haplotypes U6b, U6b1, and HV were identified, which confirmed records of Guanche ancestry. The excellent preservation of Guanche mummies facilitated the paleoparasitological and paleogenetic study, the results of which contribute to our knowledge of Guanche culture and their health status.

Ancient human microbiomes

Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.

Molecular paleoparasitological hybridization approach as effective tool for diagnosing human intestinal parasites from scarce archaeological remains

Paleoparasitology is the science that uses parasitological techniques for diagnosing parasitic diseases in the past. Advances in molecular biology brought new insights into this field allowing the study of archaeological material. However, due to technical limitations a proper diagnosis and confirmation of the presence of parasites is not always possible, especially in scarce and degraded archaeological remains. In this study, we developed a Molecular Paleoparasitological Hybridization (MPH) approach using ancient DNA (aDNA) hybridization to confirm and complement paleoparasitological diagnosis. Eight molecular targets from four helminth parasites were included: Ascaris sp., Trichuris trichiura, Enterobius vermicularis, and Strongyloides stercoralis. The MPH analysis using 18th century human remains from Praça XV cemetery (CPXV), Rio de Janeiro, Brazil, revealed for the first time the presence E. vermicularis aDNA (50%) in archaeological sites of Brazil. Besides, the results confirmed T. trichiura and Ascaris sp. infections. The prevalence of infection by Ascaris sp. and E. vermicularis increased considerably when MPH was applied. However, a lower aDNA detection of T. trichiura (40%) was observed when compared to the diagnosis by paleoparasitological analysis (70%). Therefore, based on these data, we suggest a combination of Paleoparasitological and MPH approaches to verify the real panorama of intestinal parasite infection in human archeological samples.

Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular Approach

This paper reports an approach to the identification of prehistoric parasitic infection, which integrates traditional morphological methods with molecular methods. The approach includes the strengths of each method while mitigating the limitations. Demonstrating the efficacy of this approach, we provide a case study from a 1,400 year old desiccated fecal sample from La Cueva de los Muertos Chiquitos, archaeological site, near Rio Zape, Durango, Mexico. Traditionally prepared microscope slides were processed via microscopy and tentative ascarids were identified. Information regarding the parasites' developmental stage was recorded. DNA was then extracted directly from the slide material. From this DNA extract, a small segment of the 18S ribosomal RNA gene variant that is specific to Ascaris, and its phylogenetically close relatives, was targeted for PCR amplification and sequencing. Phylogenetic analysis of the DNA sequence best matched a member of physalopterids, rather than ascarids, with a single exception of a match to Contracaecum spiculigerum. Subsequent extractions, amplifications and sequencing of the original rehydrated coprolite material confirmed these results. The C. spiculigerum sequence represented a phylogenetic anomaly and subsequent analysis determined the sequence was an error in the BLAST database, likely attributable to misidentification of juvenile specimens prior to sequencing and submission. Physaloptera are a difficult genus to identify morphologically and can carry major health burdens. They may be underreported in humans, in part, because of morphological similarities to the more common human parasites belonging to ascarids. We conclude that integrating traditional morphological methods with molecular methods can help resolve this issue, in both contemporary and prehistoric populations.

Paleoparasitological results from XVIII century human remains from Rio de Janeiro, Brazil

Paleoparasitological studies of the Brazilian colonial period are scarce. A paleoparasitological analysis was performed on human remains from the archeological site Praça XV Cemetery in Rio de Janeiro, dating from the early 18th to 19th Centuries. The samples were obtained from the Institute of the Brazilian Archaeology collection, and showed evidence of washing and brushing. Sediments were extracted from sacral foramina by scraping. Sediments from skulls were used as negative paleoparasitological controls. Spontaneous sedimentation method was performed prior to microscopic analysis. The results revealed that 8 of 10 individuals were infected with intestinal helminths and/or protozoa. Eggs of the nematodes Trichuris sp. and Ascaris sp. as well as a single taeniid egg were found. Protozoa cysts suggestive of Entamoeba sp. were also observed. Trichuris sp. was the most frequent and abundant parasite, found in 70% of individuals (26 eggs). The study showed the importance of analysis of sediment from human remains preserved in museum or scientific collections, even those subjected to a curating procedure. The levels of infection revealed here should be considered underestimations. This is the first paleoparasitological study from Rio de Janeiro city for the Brazilian colonial period and the first report of human Taenia sp. in the New World.

Mycobacterium tuberculosis complex detection in human remains: tuberculosis spread since the 17th century in Rio de Janeiro, Brazil

Paleogenetic analysis for tuberculosis (TB) was conducted on bone and sediment samples dating from the 17th to 19th centuries from the archeological site of Nossa Senhora do Carmo Church in Rio de Janeiro, Brazil. Forty samples were analyzed, corresponding to 32 individuals from 28 burials, 22 of primary type and 6 of secondary type. The samples were collected following strict paleogenetic investigation guidelines and submitted to ancient DNA (aDNA) extraction. In order to detect TB infection, aDNA hybridizations with the molecular targets of Mycobacterium tuberculosis complex (MTC) IS6110 and IS1081 were applied. Additionally, the ancestry of individuals was assessed by human mitochondrial DNA (mtDNA) analysis of hypervariable segment I (HVS-I) sequence polymorphisms. The results of aDNA hybridizations demonstrated varying levels of MTC intensity in 17/32 individuals (53.1%), using the IS6110 target. The IS1081 MTC target showed lower sensitivity, confirming TB positivity in 10/32 (31.2%) individuals. The mtDNA analysis allowed the recovery of HVS-I sequences in 23/32 individuals (71.8%). The majority of these individuals (21/23, 91.3%) were of European ancestry, especially in primary burials. Haplogroups U, J, V, T, K, N, H and R, were identified with haplogroup U being the most frequent at 6/23 (26.1%). African and Amerindian mtDNA haplogroups were observed in two individuals in secondary burials. In spite of the ecclesiastic and aristocratic bias of the population of the study, human ancestry analysis revealed the prominent contribution of Europeans in the introduction or spread of TB in the New World.

Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: new scenery of ascariasis in pre-Colombian South America times

Paleoparasitological studies using microscopy showed that Ascarisand Trichuris trichiura are the human intestinal parasites most found in archaeological sites. However, in pre-Columbian South American archaeological sites, Ascaris is rare. In this work we standardized a molecular methodology for Ascaris diagnosis directly from ancient DNA retrieved from coprolites. Using cythochrome b gene (142 bp) target, ancient DNA sequences were retrieved from South American samples, negative by microscopy. Moreover, the methodology applied was sensitive enough to detect ancient DNA extracted from 30 Ascaris eggs from an European coprolite. These results revealed a new scenery for the paleodistribution of Ascaris in South America.

Paleoparasitological remains revealed by seven historic contexts from "Place d'Armes", Namur, Belgium

Human occupation for several centuries was recorded in the archaeological layers of "Place d'Armes", Namur, Belgium. Preventive archaeological excavations were carried out between 1996/1997 and seven historical strata were observed, from Gallo-Roman period up to Modern Times. Soil samples from cesspools, latrines, and structures-like were studied and revealed intestinal parasite eggs in the different archaeological contexts. Ascaris lumbricoides, A. suum, Trichuris trichiura, T. suis. Taenia sp., Fasciola hepatica, Diphyllobothrium sp., Capillaria sp. and Oxyuris equi eggs were found. Paleoparasitology confirmed the use of structures as latrines or cesspit as firstly supposed by the archaeologists. Medieval latrines were not only used for rejection of human excrements. The finding of Ascaris sp. and Trichuris sp. eggs may point to human's or wild swine's feces. Gallo-Roman people used to eat wild boar. Therefore, both A. suum and T. suis, or A. lumbricoides and T. trichuris, may be present, considering a swine carcass recovered into a cesspit. Careful sediment analysis may reveal its origin, although parasites of domestic animals can be found together with those of human's. Taenia sp. eggs identified in latrine samples indicate ingestion of uncooked beef with cysticercoid larvae. F. hepatica eggs suggest the ingestion of raw contaminated vegetables and Diphyllobothrium sp. eggs indicate contaminated fresh-water fish consumption. Ascaris sp. and Trichuris sp. eggs indicate fecal-oral infection by human and/or animal excrements.

SL1 RNA gene recovery from Enterobius vermicularis ancient DNA in pre-Columbian human coprolites

Enterobius vermicularis, pinworm, is one of the most common helminths worldwide, infecting nearly a billion people at all socio-economic levels. In prehistoric populations the paleoparasitological findings show a pinworm homogeneous distribution among hunter-gatherers in North America, intensified with the advent of agriculture. This same increase also occurred in the transition from nomad hunter-gatherers to sedentary farmers in South America, although E. vermicularis infection encompasses only the ancient Andean peoples, with no record among the pre-Colombian populations in the South American lowlands. However, the outline of pinworm paleoepidemiology has been supported by microscopic finding of eggs recovered from coprolites. Since molecular techniques are precise and sensitive in detecting pathogen ancient DNA (aDNA), and also could provide insights into the parasite evolutionary history, in this work we have performed a molecular paleoparasitological study of E. vermicularis. aDNA was recovered and pinworm 5S rRNA spacer sequences were determined from pre-Columbian coprolites (4110 BC-AD 900) from four different North and South American archaeological sites. The sequence analysis confirmed E. vermicularis identity and revealed a similarity among ancient and modern sequences. Moreover, polymorphisms were identified at the relative positions 160, 173 and 180, in independent coprolite samples from Tulán, San Pedro de Atacama, Chile (1080-950 BC). We also verified the presence of peculiarities (Splicing leader (SL1) RNA sequence, spliced donor site, the Sm antigen biding site, and RNA secondary structure) which characterise the SL1 RNA gene. The analysis shows that the SL1 RNA gene of contemporary pinworms was present in pre-Columbian E. vermicularis by 6110 years ago. We were successful in detecting E. vermicularis aDNA even in coprolites without direct microscopic evidence of the eggs, improving the diagnosis of helminth infections in the past and further pinworm paleoepidemiological studies.

Palaeomicrobiology: current issues and perspectives

Palaeomicrobiology is an emerging field that is devoted to the detection, identification and characterization of microorganisms in ancient remains. Data indicate that host-associated microbial DNA can survive for almost 20,000 years, and environmental bacterial DNA preserved in permafrost samples has been dated to 400,000-600,000 years. In addition to frozen and mummified soft tissues, bone and dental pulp can also be used to search for microbial pathogens. Various techniques, including microscopy and immunodetection, can be used in palaeomicrobiology, but most data have been obtained using PCR-based molecular techniques. Infections caused by bacteria, viruses and parasites have all been diagnosed using palaeomicrobiological techniques. Additionally, molecular typing of ancient pathogens could help to reconstruct the epidemiology of past epidemics and could feed into current models of emerging infections, therefore contributing to the development of appropriate preventative measures.

Detection of Toxoplasma gondii DNA by polymerase chain reaction in experimentally desiccated tissues

Despite toxoplasmosis being a common infection among human and other warm-blooded animals worldwide, there are no findings about Toxoplasma gondii evolutionary forms in ancient populations. The molecular techniques used for amplification of genetic material have allowed recovery of ancient DNA (aDNA) from parasites contained in mummified tissues. The application of polymerase chain reaction (PCR) to paleoparasitological toxoplasmosis research becomes a promising option, since it might allow diagnosis, acquisition of paleoepidemiological data, access to toxoplasmosis information related origin, evolution, and distribution among the ancient populations. Furthermore, it makes possible the analysis of parasite aDNA aiming at phylogenetic studies. To standardize and evaluate PCR applicability to toxoplasmosis paleodiagnostic, an experimental mummification protocol was tested using desiccated tissues from mice infected with the ME49 strain cysts, the chronic infection group (CIG), or infected with tachyzoites (RH strain), the acute infection group (AIG). Tissues were subjected to DNA extraction followed by PCR amplification of T. gondii B1 gene. PCR recovered T. gondii DNA in thigh muscle, encephalon, heart, and lung samples. AIG presented PCR positivity in encephalon, lungs, hearts, and livers. Based on this results, we propose this molecular approach for toxoplasmosis research in past populations.