Zoonotic and human parasites of inhabitants of Cueva de los Muertos Chiquitos, Rio Zape Valley, Durango, Mexico

Recovering ancient parasites from Andean herbivores: test of the Mini-FLOTAC technique in archaeological samples

The optimization of techniques for recovering parasitic remains is key in paleoparasitology. The Mini-FLOTAC technique (MF) is based on passive flotation and is used for diagnosis of parasites and was never tested on ancient samples. Our objective was to assess the effectiveness of MF in paleoparasitology, aiming at improving the techniques for the recovery of parasitic remains in order to upgrade the interpretative potential of the paleoparasitological evidence. Three techniques were tested: MF, spontaneous sedimentation (SS), and centrifugation-sucrose flotation (CF) testing camelid and goat coprolites. Statistical tests were performed with the R software. Our result displayed that, in the case of SAC samples, MF recovered less number of parasitic species than SS, but obtained a greater number of positive samples for protozoa. For goat samples, MF recovered a higher number of positive samples and parasitic species than SS, added that it was the technique that recovered a greater number of parasite structures. Therefore, results vary according to the zoological origin of the samples and the parasitic species recorded. We suggest starting using MF on ancient samples as a complementary method to those traditionally used in paleoparasitology. It is important to highlight that MF was a simple and faster way. The incorporation of reliable quantitative techniques opens the door to a new way of analyzing archaeological remains, deepening the study of the parasite-host relationships and its evolution through time with an epidemiological approach. Although further studies are needed, our results suggest the complementarity of these techniques in future paleoparasitological studies.

Paleoparasitology research on ancient helminth eggs and larvae in the Republic of Korea

Paleoparasitology is a discipline that applies existing conventional and molecular techniques to study parasites found in ancient ruins. This review focuses on the history of the discovery of parasites (mostly helminth eggs and larvae) in archaeological soil samples and mummies in Korea from the Three Kingdoms Period to the Joseon Dynasty (100 BCE-1910 CE). We also briefly review important milestones in global paleoparasitology. The helminth species reported so far in Korea included Ascaris lumbricoides, Trichuris trichiura, Strongyloides stercoralis (larva), Trichostrongylus sp. (larva), Paracapillaria philippinensis (syn. Capillaria philippinensis), Enterobius vermicularis, Fasciola hepatica, dicrocoeliids, Paragonimus westermani, Clonorchis sinensis, Metagonimus yokogawai, Pygidiopsis summa, Gymnophalloides seoi, Isthmiophora hortensis, Dibothriocephalus nihonkaiensis (syn. Diphyllobothrium nihonkaiense), and Taenia spp. tapeworms. The findings obtained by Korean paleoparasitologists/archaeologists have brought about deep insight into the status of helminthic infections in Korea's past populations. Continued paleoparasitological research is essential for further understanding of ancient parasites and parasitic diseases in Korea.

Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review

Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.

Reconstruction of ancient microbial genomes from the human gut

Loss of gut microbial diversity^1–6 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.

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

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.

Pre-Columbian zoonotic enteric parasites: An insight into Puerto Rican indigenous culture diets and life styles

The pre-Columbian Huecoid and Saladoid cultures were agricultural ethnic groups that supplemented their diets by fishing, hunting and scavenging. Archaeological deposits associated to these cultures contained a variety of faunal osseous remains that hinted at the cultures' diets. The present study identified zoonotic parasites that may have infected these two cultures as a result of their diets. We used metagenomic sequencing and microscopy data from 540-1,400 year old coprolites as well as the zooarchaeological data to recreate the possible interactions between zoonotic parasites and their hosts. Microscopy revealed Diphyllobothrium spp. and Dipylidium caninum eggs along with unidentified cestode and trematode eggs. DNA sequencing together with functional prediction and phylogenetic inference identified reads of Cryptosporidium spp., Giardia intestinalis and Schistosoma spp. The complimentary nature of the molecular, microscopy and zooarchaeology data provided additional insight into the detected zoonotic parasites' potential host range. Network modeling revealed that rodents and canids living in close proximity to these cultures were most likely the main source of these zoonotic parasite infections.

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces

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.

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

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.

Intestinal parasites at the Late Bronze Age settlement of Must Farm, in the fens of East Anglia, UK (9th century B.C.E.)

Little is known about the types of intestinal parasites that infected people living in prehistoric Britain. The Late Bronze Age archaeological site of Must Farm was a pile-dwelling settlement located in a wetland, consisting of stilted timber structures constructed over a slow-moving freshwater channel. At excavation, sediment samples were collected from occupation deposits around the timber structures. Fifteen coprolites were also hand-recovered from the occupation deposits; four were identified as human and seven as canine, using fecal lipid biomarkers. Digital light microscopy was used to identify preserved helminth eggs in the sediment and coprolites. Eggs of fish tapeworm (Diphyllobothrium latum and Diphyllobothrium dendriticum), Echinostoma sp., giant kidney worm (Dioctophyma renale), probable pig whipworm (Trichuris suis) and Capillaria sp. were found. This is the earliest evidence for fish tapeworm, Echinostoma worm, Capillaria worm and the giant kidney worm so far identified in Britain. It appears that the wetland environment of the settlement contributed to establishing parasite diversity and put the inhabitants at risk of infection by helminth species spread by eating raw fish, frogs or molluscs that flourish in freshwater aquatic environments, conversely the wetland may also have protected them from infection by certain geohelminths.

Recovering parasites from mummies and coprolites: an epidemiological approach

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.

Reestablishing rigor in archaeological parasitology

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.

Assessing the Archaeoparasitological Potential of Quids As a Source Material for Immunodiagnostic Analyses

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.

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.

Insights from paleomicrobiology into the indigenous peoples of pre-colonial America - a review

This review investigates ancient infectious diseases in the Americas dated to the pre-colonial period and considers what these findings can tell us about the history of the indigenous peoples of the Americas. It gives an overview, but focuses on four microbial pathogens from this period: Helicobacter pylori, Mycobacterium tuberculosis, Trypanosoma cruzi and Coccidioides immitis, which cause stomach ulceration and gastric cancer, tuberculosis, Chagas disease and valley fever, respectively. These pathogens were selected as H. pylori can give insight into ancient human migrations into the Americas, M. tuberculosis is associated with population density and urban development, T. cruzi can elucidate human living conditions and C. immitis can indicate agricultural development. A range of methods are used to diagnose infectious disease in ancient human remains, with DNA analysis by polymerase chain reaction one of the most reliable, provided strict precautions are taken against cross contamination. The review concludes with a brief summary of the changes that took place after European exploration and colonisation.

Cryptosporidium parvum Among Coprolites from La Cueva de los Muertos Chiquitos (600-800 CE), Rio Zape Valley, Durango, Mexico

:  In the present study, 90 coprolites from La Cueva de los Muertos Chiquitos (CMC) were subjected to enzyme-linked immunosorbent assay (ELISA) tests for 3 diarrhea-inducing protozoan parasites, Entamoeba histolytica , Giardia duodenalis , and Cryptosporidium parvum , to determine whether these parasites were present among the people who utilized this cave 1,200-1,400 yr ago. These people, the Loma San Gabriel, developed as a culture out of the Archaic Los Caracoles population and lived throughout much of present-day Durango and Zacatecas in Mexico. The Loma San Gabriel persisted through a mixed subsistence strategy of hunting-gathering and agricultural production. The results of ELISA testing were negative for both E. histolytica and G. duodenalis across all coprolites. A total of 66/90 (∼73% prevalence) coprolites tested positive or likely positive for C. parvum . The high prevalence of C. parvum among CMC coprolites contributes to our growing knowledge of the pathoecology among the Loma San Gabriel who utilized CMC. Herein, we report the successful recovery of C. parvum coproantigens from prehistoric coprolites. The recovery of these coproantigens demonstrates the existence of C. parvum in Mesoamerica before European contact in the 1400s.

Echinostomes in Felid Coprolites from Brazil

The first record of Echinostoma (Trematoda: Echinostomatidae) in coprolites was from a mummified human body in Minas Gerais State, Brazil. The finding raised questions on this parasite's incidence in prehistoric populations and the natural hosts of each species in remote times. Echinostomes occur worldwide and, despite the wide range of hosts, there is no record of Echinostomatidae in felines in Brazil. This study reports the finding of Echinostomatidae eggs in felid coprolites in the Furna do Estrago Archaeological Site, located in Pernambuco State in the Brazilian semiarid. Despite the possibility of false parasitism, the finding expands the distribution of this Digenea in remote times and raises the hypothesis of other cases of echinostomiasis in pre-Colombian populations.

Agave Chewing and Dental Wear: Evidence from Quids

Agave quid chewing is examined as a potential contributing behavior to hunter-gatherer dental wear. It has previously been hypothesized that the contribution of Agave quid chewing to dental wear would be observed in communities wherever phytolith-rich desert succulents were part of subsistence. Previous analysis of coprolites from a prehistoric agricultural site, La Cueva de los Muertos Chiquitos in Durango, Mexico, showed that Agave was a consistent part of a diverse diet. Therefore, quids recovered at this site ought to be useful materials to test the hypothesis that dental wear was related to desert succulent consumption. The quids recovered from the site were found to be largely derived from chewing Agave. In this study, the quids were found to be especially rich in phytoliths, and analysis of dental casts made from impressions left in the quids revealed flat wear and dental attrition similar to that of Agave-reliant hunter-gatherers. Based on evidence obtained from the analysis of quids, taken in combination with results from previous studies, it is determined that Agave quid chewing was a likely contributing factor to dental wear in this population. As such, our method provides an additional avenue of dental research in areas where quids are present.

Palaeoparasitology - Human Parasites in Ancient Material

Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases.

Trichuris trichiura in a post-Colonial Brazilian mummy

Trichuris trichiura is a soil-transmitted helminth which is prevalent in warm, moist, tropical and subtropical regions of the world with poor sanitation. Heavy whipworm can result either in Trichuris dysenteric syndrome - especially in children - or in a chronic colitis. In heavy infections, worms can spread proximally and may cause ileitis. Here we provide first microscopic evidence for a T. trichiura adult worm embedded in the rectum of a post-Colonial Brazilian adult mummy. During Colonial and post-Colonial times, many European chroniclers described a parasitic disease named Maculo whose symptomatology coincides with heavy helminthiasis. Based on our findings and on comparison of ancient textual evidence with modern description of heavy whipworm, we feel confident in considering that the two syndromes are expressions of the same pathological condition.

A retrospective examination of paleoparasitology and its establishment in the Journal of Parasitology

Volume 95 (2009) of the Journal of Parasitology represented a significant benchmark in the history of paleoparasitology when it received on the cover formal recognition as a topical area for publication. This retrospective examination chronicles the emergence of paleoparasitology, from its origins as an adjunct contribution to the study of prehistoric human populations to its modern expression as a sub-disciplinary interest. The aim of paleoparasitology is to elucidate the temporal and spatial dimensions of parasitism from the fossil record of human and non-human host populations.

Lutz's spontaneous sedimentation technique and the paleoparasitological analysis of sambaqui (shell mound) sediments

Parasite findings in sambaquis (shell mounds) are scarce. Although the 121 shell mound samples were previously analysed in our laboratory, we only recently obtained the first positive results. In the sambaqui of Guapi, Rio de Janeiro, Brazil, paleoparasitological analysis was performed on sediment samples collected from various archaeological layers, including the superficial layer as a control. Eggs of Acanthocephala, Ascaridoidea and Heterakoidea were found in the archaeological layers. We applied various techniques and concluded that Lutz's spontaneous sedimentation technique is effective for concentrating parasite eggs in sambaqui soil for microscopic analysis.

Paleoparasitology: the origin of human parasites

Parasitism is composed by three subsystems: the parasite, the host, and the environment. There are no organisms that cannot be parasitized. The relationship between a parasite and its host species most of the time do not result in damage or disease to the host. However, in a parasitic disease the presence of a given parasite is always necessary, at least in a given moment of the infection. Some parasite species that infect humans were inherited from pre-hominids, and were shared with other phylogenetically close host species, but other parasite species were acquired from the environment as humans evolved. Human migration spread inherited parasites throughout the globe. To recover and trace the origin and evolution of infectious diseases, paleoparasitology was created. Paleoparasitology is the study of parasites in ancient material, which provided new information on the evolution, paleoepidemiology, ecology and phylogenetics of infectious diseases.

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.

Insights from characterizing extinct human gut microbiomes

In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (∼8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.