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There is often the risk of confusing pollen grains with helminth eggs from archaeological sites. Thousands to millions of pollen grains can be recovered from archaeological burial sediments that represent past ritual, medication and environment. Some pollen grain types can be similar to parasite eggs. Such a confusion is represented by the diagnosis of enterobiasis in ancient Iran. The authors of this study confused a joint-pine (Ephedra spp.) pollen grain with a pinworm egg. This paper describes the specific Ephedra pollen morphology that can be confused with pinworm eggs.

The impact of coprolite taphonomy on parasite remains and aDNA recovery has been recognized. In general, coprolites from sites protected by geologic features such as caves and rock shelters exhibit the best preservation. In contrast, coprolites from open sites can be badly affected by taphonomic processes as shown by analyses of parasite eggs. For eggs, the impact of mites and free-living nematodes has been quantified. Mites are associated with poor pinworm egg preservation. In other studies, percolation of water through sediments has a negative impact on egg recovery. We note that dietary remains can also decompose at open sites. Through scanning electron microscopy (SEM), we present examples of screened but chemically untreated microscopic remains. “Panorama” SEM images provide an excellent visual overview of the taphonomy of dietary remains. For this study, our focus is on Southwestern coprolites as a demonstration of diversity within a single region. Examples from caves and rock shelters were examined first to describe the taphonomic challenges for protected sites. Then, attention was turned to coprolites from open sites. In general, the challenges noted for parasite preservation are seen for other microfossils. However, the preservation of lignin, sporopollenin, calcium oxalate, and siliceous microfossils is generally better than cellulose structures. These observations are relevant to the selection process of samples for aDNA analysis and immunological study. This is especially relevant for the gut microbiome since decomposer fungi and bacteria molecular signals could be recovered in metagenomic analysis.

The Skiles Mummy (SMM), a naturally mummified adult male from the late archaic period of Lower Pecos Canyonlands of South Texas, represents a unique case of care. SMM is an exceptional mummy within this region due to both the retention of a full head of hair, and having a diagnosed case of megacolon, a complication commonly associated with Chagas disease caused by Trypanosoma cruzi. Stable isotopic analysis of his hair is consistent with a diet incorporating of C4/CAM plants with some C3 plants, freshwater resources, and higher trophic level animals. However, the segments of hair most proximal to the scalp exhibited elevated δ15N values. Data from previous research indicate starvation and malnutrition can cause δ15N values to rise. The presence of large fecal boluses in the digestive tract suggest peristalsis ceased in the last four to five months of life, and this, together with results from coprolite analysis, indicate he would not have been able to adequately absorb protein and nutrients during this time. His condition would have rendered him immobile. Following Tilley's index of care, someone would have had to bring him food resources, as well as attending to his daily needs.

Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces., Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts. This work was supported by the US National Institutes of Health R01GM089886 (to Christina Warinner and Cecil Lewis), the Deutsche Forschungsgemeinschaft EXC 2051 #390713860 (to Christina Warinner), and the Max Planck Society. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Pinworms infected Ancestral Pueblo populations since early periods of occupation on the Colorado Plateau. The high prevalence of pinworm found in these populations was correlated with the habitation style developments through time. However, in previous studies, Turkey Pen Cave, an early occupation site, and Salmon Ruins, a late occupation site, exhibited prevalences that were anomalously low, suggesting that these sites were outliers. Alternatively, it is possible that the previous quantification method was not successful in detecting the real prevalence and eggs per gram, which led to inexact interpretations. The aims of this study were to verify if previous pinworm prevalences for Turkey Pen Cave and Salmon Ruins were underestimated. In addition, new analyses were added to the data set. Two latrines from Aztec Ruins, a Pueblo III occupation never studied before, were sampled and studied. We applied the pathoecology concept and descriptive/comparative parasitological statistical parameters. Human coprolites were weighed and rehydrated along with introduced exotic Lycopodium tablets and screened through 250-μm mesh. Parasite eggs and Lycopodium spores were quantified and eggs per gram were estimated for each sample. Parasitological statistical parameters were calculated at Quantitative Parasitology 3.0 software. Pinworm was the only parasite recovered in all sites. The prevalences observed in early and late occupation sites refute previous correlation with habitation style. This study indicates that the previously estimated prevalences were underestimated, which interfered in the accurate interpretation on Ancestral Pueblo pinworm infection. This study reveals a new paleoparasitological panorama of pinworm infection in Ancestral Pueblo populations.

Coprolites have been a source of study for archeologists due to several reasons: they not only provide information on the life and nutritional habits of ancient individuals but also on their health. In this paper, we processed 10 coprolites collected at La Cueva de Los Muertos Chiquitos (600–800 CE), Rio Zape, Mexico, with acetolysis solution for pollen analysis. The number of pollen grains/gram of each coprolite sample was quantified along with the macroscopic remains of these samples. The main food item ingested by the population was maize, followed by Agave. Squash blossoms were also part of their food source determined by the presence of pollen grains. In macroremains, we identified rodent bones, plant seeds, and Agave fibers. The macroscopic analysis of the samples fits with the analysis of smaller remains, giving an idea of the meal represented by each coprolite analyzed. We relate these results to previous microbiome studies of coprolite samples from the same archeological site and provide a discussion on the relevancy of studying macro- and microremains that can be applied to microbiome interpretation analysis.

Lagoa Santa recorded ~12,500 years of non-continuous human occupation in cavities and open air sites. For the early- and middle Holocene occupations, lithic technology, zooarchaeology, osteological markers and multi-isotopic analyses indicate groups of foragers with low mobility and a subsistence strategy focused on gathering plant foods and hunting small and mid-sized animals but no megafauna. A high frequency of caries is observed among women. Lithics include small flakes and cores of quartz. Artefacts like projectile points and axe blades occur marginally. Funerary rituals included primary burials (10.3–10.6 cal kyBP), reduction of the body followed by secondary burial (9.4–9.6 cal kyBP) and pits filled with disarticulated and fragmented bones of a single individual (~8.2–8.6 cal kyBP). Rock art abounds, including the oldest securely dated case of South America (10.5 cal kyBP). Representations include animals, filiform anthropomorphs, geometric motifs, manioc’s tubers and semi-lunar axes. Similar styles are found over a large area of Brazil. Ancient DNA extracted from several early Holocene skeletons indicates they are entirely nested within past and present Native American genetic diversity. Pottery arrives during the late Holocene with undecorated vessels of varying sizes (0.2–417 L), tubular pipes, spindle whorls, highly polished axes and ritual semi-lunar axes (Aratu-Sapucai-Una Tradition). In the site ‘Vereda III’, more than 3,000 in situ sherds indicate repeated use for ritual feasts centred on fermented beverages: (maize?). Polychrome pottery occurring in low frequency testify to the late presence of Tupi-speaking groups. During the colonial period, Lagoa Santa housed large haciendas for cattle and agriculture, resulting in the formation of large farms with thousands of enslaved people. Stub-stemmed earthenware pipes from the nineteenth century, an important element of African diasporic identities, were produced in the region.

Ancient parasite studies depend on the recovery of parasite remains from archaeological material. Collection strategies, sample processing, and the use of parasitological techniques are essential to perform the analyses without loss of microremains and also to interpret the data obtained by correlating with the archaeological information. Together with the methods of analyses, the identification and differentiation between these microremains and others commonly observed in the processed samples, such as pollen grains, plant spores, fungi spores, and others, are essential so that no misdiagnosis occurs, resulting in misinterpretation of the health situation of an ancient population. All ancient parasite studies require an evaluation and discussion of taphonomy, based on the factors identified in each archaeological site. Paleoparasitology does not only require the identification of parasite remains in samples, but it involves a set of strategies, meticulous training, and application of multiple concepts in order to clarify the infection/disease process in ancient populations. In this chapter, the importance of paleoparasitology is discussed, and strategies and recommendations on sample collection, sample processing, use of parasitological techniques, and researcher training are presented. Taphonomic aspects related to experimental studies in specific sites are discussed. This chapter aims to orient those interested in the field and guide the community toward establishing principles of preservation applicable in all types of archaeological remains in which eggs can be recovered.

Various samples of human viscera fragments, sponges, and cloth were collected from embalming jars belonging to members of the Medici family of Florence. One jar was labeled with the name Vittoria della Rovere, who died in March of 1694. This jar contained viscera fragments that were identified as a section of collapsed intestine. The intestine of the Vittoria della Rovere sample contained a large concentration of pollen belonging to the Myrtaceae family. The Myrtaceae pollen was sometimes observed in clusters during analysis, which is indicative of purposeful ingestion of flowers, buds, or a substance derived from floral structures. Thus, the high concentrations and clustering of Myrtaceae pollen grains recovered from this sample are reflective of dietary or medicinal practices. Scanning electron microscopy indicated that the pollen was from cloves, Syzygium aromaticum. It is most likely that Vittoria della Rovere consumed cloves for medicinal or culinary reasons shortly before death.

Russia, both as the USSR and the Russian federation, provided a source of parasitological theory for decades. A key figure in Russian parasitology was Yevgeny Pavlovsky. He developed the nidus concept of Pavlovsky provided the conceptual basis for the field of pathoecology. He also coined the term "Paleoparasitology". Pathoecology is a foundation concept in archaeological parasitology. Paleoparasitology, as defined by Pavlovsky, is an avenue for understanding of host parasite evolution over very long time periods. These contributions are not fully recognized internationally. Similarly, the long history of Russian paleontological and archaeological investigations are not fully known. Most recently, discoveries from archaeological sites show that a pattern of zoonotic infection prevailed among archaeological populations in central Russia. This included a case of apparent host switching of beef tapeworm infection to reindeer. This latter discovery raises the possibility that archaeological parasitology can contribute to the new Stockholm Paradigm of ecological fitting, host switching, and emergent disease. This review covers all of the parasitological discoveries from ancient Russia and illustrates how Russian models and discoveries defined parasitological theory in the past and present.

For archaeological studies it is always necessary to consider taphonomic factors that could have influenced in ancient material preservation. Parasite eggs are usually highly degraded in ancient sites dated from all periods of time and taphonomic factors are mentioned to explain absence and low quantity of eggs found. In this study, we compare parasite egg recovery of three Great House latrines: two from Aztec Ruins (Rooms 219 and 225) and one from Salmon Ruins. We compared through statistical regression the recovery of eggs with the abundance of two classes of decomposers: mites and nematodes. These microorganisms have relation with nematode larvae and parasites remains degradation, respectively, mostly in moist environments. Pinworm was the only parasite found in the sites studied. Prevalences were 32.8% at Salmon Ruins, 72.7% at Aztec Ruins Room 225 and 14.3% at Room 219. Egg preservation was considered good at Salmon Ruins and Aztec Ruins Room 225. At Room 219, the eggs were badly preserved and there was a significant statistical correlation with mites (multiple r (18) = 0.64/ P = 0.002 ). This correlation could indicate that mites could be involved in preservation, and consequently that pinworm prevalence in this latrine is underestimated. Abiotic factors such as humidity could have possibly favored the biological relation. Considering the extreme egg degradation at Room 219, it is not possible to strictly compare parasite data with other Ancestral Pueblo sites, even with Room 225, located at the same site. Room 225 prevalence is the highest found in Ancestral Pueblo sites until now. Taphonomic analysis shows that decomposers operated at different levels of severity, despite the latrines' close location.

Archaeoparasitology provides a unique perspective on the health and habits of ancient cultures through the identification of parasite remains in archaeological materials. We identified eggs of the human whipworm, Trichuris trichiura, in coprolites recovered from Late Archaic (1926–1751 cal. BCE) and Ancestral Puebloan (1039–1163 cal. CE) sites in Chaco Canyon, New Mexico. Our findings represent the earliest record of T. trichiura in North America, the first record of the species from Chaco Canyon, and the first record of a macroparasite from a Late Archaic site (Atlatl Cave) on the Colorado Plateau. T. trichiura is common in the global archaeoparasitology record, but until now it was not known to have infected Ancestral Puebloans. Environmental barriers to transmission and lack of contact with infected Mesoamerican cultures have previously been used to explain the absence of this species from the Southwest. The new evidence of T. trichiura presented here raises questions about the cultural context which led to the arrival and persistence of this parasite in both a Late Archaic cave and an Ancestral Puebloan great house at Chaco Canyon. We propose that the moisture requirements of T. trichiura transmission may have been met through anthropogenic modification of the local environment, and that the presence of this species at Chaco Canyon suggests contact with infected Mesoamerican cultures. We also report the presence of the pinworm, Enterobius vermicularis, and unidentified larval nematodes in the Chaco Canyon archaeological record.

One hundred coprolites excavated from La Cueva de los Muertos Chiquitos (600–800 CE) in the Rio Zape Valley of present-day Durango, Mexico, were examined for the presence of helminth eggs utilizing standard archaeoparasitological techniques. Eggs of the human pinworm (Enterobius vermicularis) were recovered from 34 of the 100 coprolites examined. Eggs of parasites were photographed and measured before egg concentration values were calculated for each positive sample. Egg concentration values demonstrated an overdispersed pattern of distribution among the samples (66% uninfected, 25% less than 100 eggs/g, 8% between 100 and 500 eggs/g, and 1% more than 500 eggs/g). Given that only 5% of infected hosts in modern cases of human enterobiasis pass the eggs of parasites in their stools, the recovery of E. vermicularis eggs in 34% of the coprolites supports the conclusion that virtually all of the individuals utilizing the site during the coprolite depositional time frame likely were infected with this parasite. These data are discussed in light of other studies of prehistoric human enterobiasis.

Intestinal contents were sampled from a spontaneously enhanced mummy from the Sepulcher of the Priests of the Piraino Mother Church in the Province of Messina, Sicily. This adult male mummy, Piraino 1, is an unidentified religious dignitary dating from the late-18th to mid-19th centuries. Immunological and molecular diagnostics were used to test for common and clinically significant parasites. A morphological diagnosis of Trichuris trichiura (whipworm) was confirmed genetically. A previously undetected Enterobius vermicularis (pinworm) infection was also identified genetically. These data indicate that the Piraino 1 individual was simultaneously infected with multiple intestinal parasite species indicative of poor hygiene. This study also emphasizes the importance of utilizing multiple diagnostic techniques to detect pathogens from archaeological contexts.

Archaeological parasitology originated in the mid-twentieth century with interdisciplinary teams of specialists directed by archaeologists. The goals of such studies were detailed analyses of dietary, medicinal, and environmental factors that shaped the patterns of infection. By the 1970s, a cadre of unique coprolite analysts was trained to analyze macroscopic and microscopic remains for integrated reconstructions of the cultural determinants of parasitism. During these first phases of research, diagnostic rigor was maintained by direct training of specialists in parasitology and archaeology sub-disciplines including archaeobotany and archaeopalynology. Near the end of the twentieth century, however, "paleoparasitology" was defined as a separate field focusing on defining parasite distribution through time and space. Ironically, this focus resulted in an increase in misdiagnosis, especially prominent after 2000. Paleoparasitology does not explicitly include other specialized studies in it research design. Thus, dietary, environmental and medicinal inferences have been neglected or lost as samples were destroyed solely for the purpose of parasitological analysis. Without ancillary archaeological studies, paleoparasitology runs the risk of separation from archaeological context, thereby reducing its value to the archaeologists who recover samples for analysis.

Fragmented remains of pseudoscorpions belonging to the family Cheiridiidae (Arachnida, Pseudoscorpiones) were recovered from Ychsma polity (c. AD 1000–1475) burial sediments from Pachacamac, Peru. Sediments from 21 burials were examined following rehydration in 0.5% trisodium phosphate for 48 h and subsequent screening through a 250 μm mesh. Materials larger than 250 μm were surveyed for the presence of arthropods. A total of two samples contained pseudoscorpion fragments, which were collected and quantified to determine the minimal number of pseudoscorpions present per gram of each sample. Following quantification, pseudoscorpion specimens were imaged utilizing confocal laser scanning microscopy (CLSM) to assist with identification efforts. Specimens have morphological characteristics consistent with those found in members of the pseudoscorpion family Cheiridiidae. Members of this family have not been previously described from archaeological materials recovered from Peru, and the implications of pseudoscorpions as members of the archaeological corpocenosis have not been fully interpreted. Herein, we report the first recovery of pseudoscorpions from archaeological materials at Pachacamac, and discuss the significance of their roles in the archaeological corpocenosis.

The study of coprolites has been a theme of archaeology in the American Southwest. A feature of archaeoparasitology on the Colorado Plateau is the ubiquity of pinworm infection. As a crowd parasite, this ubiquity signals varying concentrations of populations. Our recent analysis of coprolite deposits from 2 sites revealed the highest prevalence of infection ever recorded for the region. For Salmon Ruins, the deposits date from AD 1140 to 1280. For Aztec Ruins, the samples can be dated by artifact association between AD 1182-1253. Both sites can be placed in the Ancestral Pueblo III occupation (AD 1100-1300), which included a period of cultural stress associated with warfare. Although neither of these sites show evidence of warfare, they are typical of large, defensible towns that survived this time of threat by virtue of large populations in stonewalled villages with easily accessible water. We hypothesize that the concentration of large numbers of people promoted pinworm infection and, therefore, explains the phenomenal levels of infection at these sites.

Prevotella copri is a common inhabitant of the human gut. Interest in P. copri has gathered pace due to conflicting reports on whether it is beneficial or detrimental to health. In a cross-continent meta-analysis exploiting >6,500 available metagenomes supported by new isolate sequencing and recovery of high-quality genomes from metagenomes, we obtained >1,000 P. copri genomes. This 100-fold increase over existing isolate genomes allowed the genetic and global population structure of P. copri to be explored at an unprecedented depth. We demonstrate P. copri is not a monotypic species, but encompasses four distinct clades (>10% inter-clade vs. P. copri complex, comprising clades A, B, C and D. We show the complex is near ubiquitous in non-Westernised populations (95.4% versus 29.6% in Westernised populations), where all four clades are typically co-present within an individual (61.6% of the cases), in contrast to Westernised populations (4.6%). Genomic analysis of the complex reveals substantial and complementary functional diversity, including the potential for utilisation of complex carbohydrates, suggestive that multi-generational dietary modifications may be a driver for the reduced P. copri prevalence in Westernised populations. Analysis of ancient stool microbiomes highlights a similar pattern of P. copri presence consistent with modern non-Westernised populations, allowing us to estimate the time of clade delineation to pre-date human migratory waves out of Africa. Our analysis reveals P. copri to be far more diverse than previously appreciated and this diversity appears to be underrepresented in Western-lifestyle populations.

Objectives Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases. Methods In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP). Results Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA. Conclusions These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.

Forensic archaeology investigations must adhere to state laws. First, the state has a coroner’s physician arrangement to adapt to the fact that each county attorney acts as that county’s coroner. The county attorney employs forensic specialists to provide him/her with the expertise to act as the coroner. Second, the Nebraska Unmarked Human Burial Sites and Skeletal Remains Protection Act mandates the assistance of an archaeologist at the discovery site of skeletal remains. Since the establishment of the University of Nebraska – Lincoln Forensic Science Program, faculty have been involved in investigations. This chapter reviews these arrangements through time and presents some recent cases.

Entomological investigations of material from embalming jars found in the San Lorenzo Basilica of Florence, Italy, reveals information concerning the mortuary and embalming practices of the Medici family during the 17th and 18th centuries. The analysis of samples from these jars demonstrated the presence of mid- to late colonizers, Hydrotaea capensis (Diptera: Muscidae) and Conicera tibialis (Diptera: Phoridae), among the human remains and embalming materials within the jars. The presence of puparia and absence of adult flies suggests that some of the jars may have been initially left open to the surrounding environment and later closed. The lack of dipteran remains from sepsids, piophilids, and fannids was not surprising as materials in the jars were not likely to attract these types of flies. Spider beetles, likely Ptinus dubius and Ptinus subpilosus (Coleoptera: Ptinidae), were recovered from the embalming jars, indicating that insects also had access to embalming jar contents after drying. The absence of dermestid beetles, which are extremely common on dried remains, supports the interpretation that these jars could have been made unavailable at some point after embalming. These analyses provide an interesting case for insect colonization into embalming jars and give more information regarding mortuary practices.

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.

Paleopathologists have begun exploring the pathoecology of parasitic diseases in relation to diet and environment. We are summarizing the parasitological findings from a mummy in the site of Lapa do Boquete, a Brazilian cave in the state of Minas Gerais. These findings in context of the archaeology of the site provided insights into the pathoecology of disease transmission in cave and rockshelter environments. We are presenting a description of the site followed by the evidence of hookworm, intestinal fluke, and Trypanosoma infection with resulting Chagas disease in the mummy discovered in the cave. These findings are used to reconstruct the transmission ecology of the site.

In the present study, quids from La Cueva de los Muertos Chiquitos (CMC) were subjected to ELISA tests for 2 protozoan parasites, Toxoplasma gondii (n=45) and Trypanosoma cruzi (n=43). The people who occupied CMC, the Loma San Gabriel, lived throughout much of present-day Durango and Zacatecas in Mexico. The known pathoecology of these people puts them into at-risk categories for the transmission of T. gondii and T. cruzi. Human antibodies created in response to these 2 parasites can be detected in modern saliva using ELISA kits intended for use with human serum. For these reasons, quids were reconstituted and subjected to ELISA testing. All test wells yielded negative results. These results could be a factor of improper methods because there is no precedence for this work in the existing literature. The results could equally be a simple matter of parasite absence among those people who occupied CMC. A final consideration is the taphonomy of human antibodies and whether or not ELISA is a sufficient method for recovering antibodies from archaeological contexts. An additional ELISA test targeting secretory IgA (sIgA) was conducted to further examine the failure to detect parasite-induced antibodies from quids. Herein, the methods used for quid preparation and ELISA procedures are described so that they can be further developed by future researchers. The results are discussed in light of the potential future of quid analysis.

Due to paleoparasitology's relatively late beginnings, the fundamental data necessary for any reasonably complete understanding of parasitic infection patterns in Korean history remains insufficient. Especially with respect to ancient samples dating to before the Joseon Dynasty (1392–1910 CE), few cases have been analyzed by parasitological techniques. In the present study, we therefore undertook a series of paleoparasitological examinations of archaeological samples from the ancient Silla Kingdom (57 BCE–935 CE). Specifically, in soil samples obtained from shell midden and mountain top fortress sites, we observed Ascaris lumbricoides , Trichuris trichiura , Dicrocoelid and Taenia sp. eggs. The results of our current investigation of strata and samples from the prosperous first-millennium era of the Silla Kingdom are encouraging for a comprehensive understanding of the parasitic infection patterns in the earlier days of Korean history that could not be obtained by any previous studies.

Human ectoparasites, including lice, have been recovered from a wide range of archaeological materials. The human head louse, Pediculus humanus capitis, has been identified from mummies and sediments for decades. Louse eggs are the body part most commonly encountered and therefore the most frequently quantified. Typically, several types of microscopy are applied for egg documentation. For studies in which quantification of infestation is a goal, counting is done with the naked eye or with the aid of handheld lenses. For determination and stage classification, stereomicroscopy is commonly used. For more detailed examination of microstructure, light microscopy, scanning electron microscopy (SEM), and confocal laser scanning microscopy (CLSM) can be employed. In most reports, researchers use two or more techniques to accomplish interrelated goals. Automontage microscopy is used to document prehistoric arthropods with good success. Herein, we report the results of a combination of SEM and automontage microscopy to document lice and eggs recovered from South American mummies. This combined approach allows for simultaneous examination of internal and external characteristics. Thirty automontage composite images of 2 adult lice and 16 eggs showed that egg internal morphologies were easily examined showing the within-egg anatomy of emergent nymphs. SEM imaging of 9 lice and 129 eggs was completed. In the case of two adults and several eggs, SEM imaging was accomplish after automontage image capture of the same specimens. This one-to-one image comparison of SEM and automontage shows that transmitted light of automontage reveals egg internal structures and details of the adult lice. SEM allows for high magnification examination of egg, nymph and adult microstructures. We conclude that automontage imaging followed by SEM results in efficient graphic documentation of rare louse specimens.

Paleoparasitological analysis of shaft feature sediments, such as latrines and wells, has a long trajectory. Recovery of parasite eggs in ideal preservation has long been achieved through palynological processing. However, most laboratories are not equipped for this method. We experimented with abbreviated pollen processing with the goal of presenting a safe method that could be employed in most labs. Soil samples from latrines are processed using a formalized method derived from palynological studies to assess a) the efficacy of the method and b) determine the array of taphonomic changes affecting egg morphology. Results demonstrated the efficacy of the palynological processing in recovering eggs and preserving their morphology unaltered. In addition, two simplified techniques are also tested, and the results compared to further comprehend how laboratory procedures affect egg morphology. Results from the simplified methods also confirm their effectiveness as well as offering a viable alternative to non-specialized labs to facilitate future research. A second goal was to assess the numbers of degraded eggs that researchers can expect from archaeological soils. In recent years, there has been an increased reporting of degraded parasite eggs from archaeological contexts, particularly of eggs of Ascaris lumbricoides. Researchers have been reporting the finding of “decorticated” ascarid eggs, a process in which such eggs lose the diagnostic outer layer of the shells. We quantify the preservation types for these species and found that decorticated eggs are very rare. Although these data are cautionary, we advance that researchers who find only decorticated eggs are likely to make misdiagnoses. We also quantify eggs of Trichuris trichiura and assess taphonomic changes altering their morphology. This paper considers preservation aspects to determine what researchers can expect to find with regard to egg degradation of A. lumbricoides and T. trichiura from archaeological sediments.

In Spring of 2012, the partially undressed and skeletonized remains of a homeless adult Hispanic male was found in a fairly open wooded area in Nebraska. The remains showed evidence of extensive pathologies, which included healed traumas and surgeries. Examination of the decedent's medical records revealed that he had a history of kidney and liver problems, alcohol abuse, several traumas including a major head injury that necessitated a craniotomy, and radiological features of neurocysticercosis. The autologous bone flap, which was replaced after the craniotomy, had resorbed significantly away from the edges of the injury. Death was variously attributed to craniocerebral injury with hypothermia sequel to blunt force trauma most probably due to a fall. The manner of death was ruled as an accident. This study makes use of the forensic evidence and medical records to examine the possibility that the unique combination of failed cranioplasty, hypothermia, and neurocysticercosis may have contributed to the victim's death. Other potential causes of death are considered.

Experimental studies show that pollen resides in the intestinal tract for a minimum of seven days to at least 21 days. Because of this long residence time, pollen analysis is an important avenue of forensic research. Pollen provides evidence of the environment of the decedent as well as foods and medicine. We analyzed a coprolite recovered from a Korean mummy. The decedent was a high-ranking general who lived during the 16th or 17th centuries. Twenty pollen types were recovered. These ranged from 100 s to 10,000 s of pollen grains per gram of coprolite. Importantly, comparison of the coprolite pollen spectrum to modern aeropalynology studies of Korea suggests that the general died in winter between middle November to late February. Economic pollen types were most abundant. Economic refers to dietary, medicinal, spice, and beverage types. Dietary pollen types include pollen from Oryza (rice), Eriogonum (buckwheat), Brassicaceae (mustard family), and Solanaceae (tomato-chile pepper family). Pollen consistent with dandelion is present and may represent its use as food. Tens of thousands of grains from water plants, bur-reed or cattail, dominate the pollen spectrum. We believe that this was introduced with water. The large numbers of water-related pollen suggest that the general consumed broth, tea, or soup for a considerable time before death.

In the field of archaeological parasitology, researchers have long documented the distribution of parasites in archaeological time and space through the analysis of coprolites and human remains. This area of research defined the origin and migration of parasites through presence/absence studies. By the end of the 20th century, the field of pathoecology had emerged as researchers developed an interest in the ancient ecology of parasite transmission. Supporting studies were conducted to establish the relationships between parasites and humans, including cultural, subsistence, and ecological reconstructions. Parasite prevalence data were collected to infer the impact of parasitism on human health. In the last few decades, a paleoepidemiological approach has emerged with a focus on applying statistical techniques for quantification. The application of egg per gram (EPG) quantification methods provide data about parasites’ prevalence in ancient populations and also identify the pathological potential that parasitism presented in different time periods and geographic places. Herein, we compare the methods used in several laboratories for reporting parasite prevalence and EPG quantification. We present newer quantification methods to explore patterns of parasite overdispersion among ancient people. These new methods will be able to produce more realistic measures of parasite infections among people of the past. These measures allow researchers to compare epidemiological patterns in both ancient and modern populations.

In the present study, the abdominal contents of 10 mummies from beneath the Dominican Church of the Holy Spirit in Vilnius, Lithuania, were examined for the presence of helminth parasites using standard archaeoparasitological techniques. Of the mummies examined, only one individual presented with evidence of parasitism. This individual was infected with both Trichuris trichiura and Ascaris lumbricoides (5,222 parasite eggs/gram). The conditions of many of the T. trichiura eggs suggest that a fortuitously embedded female whipworm decomposed within the individual's gut to release the eggs, as opposed to the eggs actually being passed by the adult helminth. This study highlights a taphonomic issue unique to mummies by demonstrating the differential preservation of parasite eggs existing in various stages of development. Whenever one is not dealing with parasite eggs that have already been passed by the host, as is the case when analyzing intestinal tissues, one must understand that some types of parasite eggs may not be fully formed. It is imperative, as demonstrated by our findings, that researchers have the knowledge to recognize under-developed intestinal helminth eggs in addition to fully formed intestinal helminth eggs from mummy source materials. Together, these findings demonstrate the persistence of these helminth parasites in Europe during the 18th and 19th centuries and represent the first archaeoparasitological evidence from mummies in Vilnius, Lithuania.

Paleoparasitology is the application of conventional or molecular investigative techniques to archeological sam- ples in order to reveal parasitic infection patterns among past populations. Although pioneering studies already have report- ed key paleoparasitological findings around the world, the same sorts of studies had not, until very recently, been conduct- ed in sufficient numbers in Korea. Mummified remains of individuals dating to the Korean Joseon Dynasty actually have proved very meaningful to concerned researchers, owing particularly to their superb preservation status, which makes them ideal subjects for paleoparasitological studies. Over the past several years, our study series on Korean mummies has yield- ed very pertinent data on parasitic infection patterns prevailing among certain Joseon Dynasty populations. In this short re- view, we summarized the findings and achievements of our recent paleoparasitological examinations of Joseon mummies and discussed about the prospects for future research in this vein.

Summary Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations., Graphical Abstract, Highlights • P. copri is not a monotypic species but composed of four distinct clades • The P. copri complex is more prevalent in populations with non-Westernized lifestyles • P. copri clades are frequently co-present within non-Westernized individuals • Ancient stool samples suggest Westernization leads to P. copri underrepresentation, Tett et al. find that the intestinal microbe Prevotella copri encompasses four distinct clades constituting the P. copri complex. The complex is prevalent in non-Westernized populations where co-presence of all clades is commonly observed within individuals. Analysis of ancient stool samples supports Westernization as contributing to reduced P. copri prevalence.