Parasitism of prehistoric humans and companion animals from Antelope Cave, Mojave County, northwest Arizona

Previously, we reported a tick recovered from Antelope Cave in extreme northwest Arizona. Further analyses of coprolites from Antelope Cave revealed additional parasitological data from coprolites of both human and canid origin. A second tick was found. This site is the only archaeological locality where ticks have been recovered. We also discovered an acanthocephalan in association with Enterobius vermicularis eggs in the same coprolite. This association shows that the coprolite was deposited by a human. This discovery expands our knowledge of the range of prehistoric acanthocephalan infection. In addition, findings from canid coprolites of Trichuris vulpis are reported. This is the first published discovery of T. vulpis from a North American archaeological context. The close association of dogs with humans at Ancestral Puebloan (Anasazi) sites raises the potential that zoonotic parasites were transferred to the human population. The archaeological occupation is associated with the Ancestral Pueblo culture 1,100 yr ago.     

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.     

The finding of Enterobius vermicularis eggs in pre-Columbian human coprolites

Enterobius vermicularis eggs were found in human coprolites collected in the archaeological site of Caserones, Tarapaca Valley, Chile, dating from 400 BC to 800 AD. The human pinworm had already been found in other pre-historic archaeological sites in America, and its introduction in this continent is discussed.     

Trichuris sp. from 1,040 +/- 50-year-old Cervidae coprolites from the archaeological site Furna do Estrago, Pernambuco, Brazil

We present results of the paleoparasitological analysis of Cervidae coprolites that were recovered from the archaeological site Furna do Estrago, Pernambuco, Brazil. Trichuris sp. eggs were recovered from the coprolite samples dated 1,040 ± 50 years before present. This is the first record of Trichuris sp. in semiarid Cervidae, unexpectedly recorded in archaeological material.     

A molecular analysis of ground sloth diet through the last glaciation

DNA was extracted from five coprolites, excavated in Gypsum Cave, Nevada and radiocarbon dated to approximately 11 000, 20 000 and 28 500 years BP. All coprolites contained mitochondrial DNA sequences identical to a DNA sequence determined from a bone of the extinct ground sloth Nothrotheriops shastensis. A 157-bp fragment of the chloroplast gene for the large subunit of the ribulosebisphosphate carboxylase (rbcL) was amplified from the boluses and several hundred clones were sequenced. In addition, the same DNA fragment was sequenced from 99 plant species that occur in the vicinity of Gypsum Cave today. When these were compared to the DNA sequences in GenBank, 69 were correctly (two incorrectly) assigned to taxonomic orders. The plant sequences from the five coprolites as well as from one previously studied coprolite were compared to rbcL sequences in GenBank and the contemporary plant species. Thirteen families or orders of plants that formed part of the diet of the Shasta ground sloth could be identified, showing that the ground sloth was feeding on trees as well as herbs and grasses. The plants in the boluses further indicate that the climate 11 000 years BP was dryer than 20 000 and 28 500 years BP. However, the sloths seem to have visited water sources more frequently at 11 000 BP than at earlier times.     

A tick from a prehistoric Arizona coprolite

Ticks have never been reported in archaeological analyses. Here, we present the discovery of a tick from a coprolite excavated from Antelope Cave in extreme northwest Arizona. Dietary analysis indicates that the coprolite has a human origin. This archaeological occupation is associated with the Ancestral Pueblo culture (Anasazi). This discovery supports previous hypotheses that ticks were a potential source of disease and that ectoparasites were eaten by ancient people.     

Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures

Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.     

南京汤山驼子洞鬣狗粪化石的孢粉分析

南京汤山驼子洞洞穴堆积中鬣狗粪化石含有相对丰富的孢粉,推测草食性哺乳动物食用带有孢粉的植物后,经鬣狗的猎杀、摄食、消化和排泄,孢粉较好地保存在鬣狗粪中,形成粪化石,成为洞穴地层的组成部分。虽然鬣狗粪化石中的孢粉含量不及湖沼相地层中丰富,但有几种植物的花粉保存较好且相对集中,如Pinus,Tsuga,Quercus,Carpinus,Artemisia,Cyperaceae,Polygonum,Polypodiaceae出现的频率较高。孢粉组合揭示早更新世南京地区植被主要是草原或森林-草地,气候凉干或半干旱半湿润,可以和地层中脊椎动物群反映的自然环境相互印证。在研究洞穴古环境的代用指标中,堆积物中的鬣狗粪化石中包含的孢粉是比较好的研究对象,对环境有一定的指示意义。     

The steroids of 2000-year-old human coprolites.

Six samples of human coprolites, some more than 2,000 years old, were analyzed for fecal steroid composition. Despite this very lengthy period of storage, the fecal steroids of coprolites were remarkably similar to those of stool samples collected today. The sterol nucleus was clearly rather stable under the dry environmental conditions of the Nevada Caves. The steroid content (microgram/g dried weight) of coprolite was low in comparison to that of modern man. The bile acid/cholesterol and plant sterol/cholesterol ratios of the coprolite, however, were similar to these ratios of the stools of modern man. In the six coprolites, an average 73% of the neutral steroids was digitonin-precipitable. This precipitate was composed of cholesterol and three plant sterols (campesterol, stigmasterol, and beta-sitosterol) and their bacteria-modified products. A portion of the neutral steroids had been converted to products tentatively identified as epimers of these steroids. Individual bile acids were identified in the coprolite. The bile acid composition of the coprolite was similar to that of the stool of modern man.     

Microbial Communities in Pre-Columbian Coprolites

The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures.     

A palaeoparasitological analysis of rodent coprolites from the Cueva Huenul 1 archaeological site in Patagonia (Argentina)

The aim of the present study was to examine the parasite fauna present in rodent coprolites collected from Cueva Huenul 1 (CH1), northern Neuquén (Patagonia, Argentina), an archaeological site that provides stratified sequences of archaeological and palaeontological remains dating from the Late Pleistocene/Early Holocene Transition to the Late Holocene period. Twenty rodent coprolites collected from different sedimentary units from the site, with ages ranging from 13.844 ± 75-1.416 ± 37 years BP, were examined for parasites. Each coprolite was processed as a whole: rehydrated, homogenised, spontaneously sedimented and examined using light microscopy. The coprolites and the eggs of any parasites present were described, measured and photographed. In all, 158 parasite eggs were found in 10 coprolites. The faeces were positive for Viscachataenia quadrata Denegri, Dopchiz, Elissondo & Beveridge and Monoecocestus sp. Beddard (Cestoda: Anoplocephalidae) and for Heteroxynema (Cavioxyura) viscaciae Sutton & Hugot (Nematoda: Oxyuridae). The coprolites examined were tentatively attributed to Lagidium viscacia Molina (Mammalia, Rodentia, Caviomorpha, Chinchillidae). The life cycles of these parasites are discussed.     

Applying modern analogs to understand the pollen content of coprolites

Most scientists working with coprolites from archaeological contexts assume that human fecal specimens reflect the mixing of the pollen ingested during the period in which the contribution to the coprolite, 19 to 37.5 h, was ingested, that the amount of pollen in a fecal sample directly reflects the amount of pollen originally ingested during that interval, and that differences between the amounts of pollen in different fecal specimens reflect differences in the quantities of pollen ingested at different times. These assumptions were tested and found wanting in an experiment in which two persons sequentially ate separate quantities of 15 pollen types in meals over a four-day interval. The pollen was retrieved and analyzed from feces produced during those four days and five days of subsequent fecal production. Pollen ingested first appeared in relatively small amounts, usually the day after it was ingested. Its concentration per gram of sample then increased rapidly and remained high over a one to three day interval relative to the amounts in previous and subsequent fecal specimens deposited. When pollen concentrations declined some pollen was retained in the gastrointestinal system and much lower concentrations per gram of sample of each type continued to appear in fecal samples for several days. These relatively low pollen concentrations appeared in fecal samples approximately twice as often as did higher concentrations. Our results indicate that comparatively high pollen concentrations can be used to determine that a given pollen type was ingested, but comparisons between pollen concentrations of the same pollen type in different fecal specimens or between different pollen types in the same fecal specimen, cannot be used to determine whether different amounts of pollen were ingested, or what was the relative amount of each ingested. Because pollen concentrations per gram of sample varied widely with time since ingestion, percentages of given pollen types did not occur in predictable patterns and could actually increase as the concentration of the pollen type decreases. Hence, percentages should not be used in coprolite pollen analysis. The experimental results also suggest that variations in the pollen content of different portions of a coprolite are meaningful only in terms of the overall pattern of a sequential group of coprolites.     

High-resolution coproecology: using coprolites to reconstruct the habits and habitats of New Zealand's extinct upland moa (Megalapteryx didinus)

Knowledge about the diet and ecology of extinct herbivores has important implications for understanding the evolution of plant defence structures, establishing the influences of herbivory on past plant community structure and composition, and identifying pollination and seed dispersal syndromes. The flightless ratite moa (Aves: Dinornithiformes) were New Zealand's largest herbivores prior to their extinction soon after initial human settlement. Here we contribute to the knowledge of moa diet and ecology by reporting the results of a multidisciplinary study of 35 coprolites from a subalpine cave (Euphrates Cave) on the South Island of New Zealand. Ancient DNA analysis and radiocarbon dating revealed the coprolites were deposited by the extinct upland moa (Megalapteryx didinus), and span from at least 6,368±31 until 694±30 (14)C years BP; the approximate time of their extinction. Using pollen, plant macrofossil, and ancient DNA analyses, we identified at least 67 plant taxa from the coprolites, including the first evidence that moa fed on the nectar-rich flowers of New Zealand flax (Phormium) and tree fuchsia (Fuchsia excorticata). The plant assemblage from the coprolites reflects a highly-generalist feeding ecology for upland moa, including browsing and grazing across the full range of locally available habitats (spanning southern beech (Nothofagus) forest to tussock (Chionochloa) grassland). Intact seeds in the coprolites indicate that upland moa may have been important dispersal agents for several plant taxa. Plant taxa with putative anti-browse adaptations were also identified in the coprolites. Clusters of coprolites (based on pollen assemblages, moa haplotypes, and radiocarbon dates), probably reflect specimens deposited at the same time by individual birds, and reveal the necessity of suitably large sample sizes in coprolite studies to overcome potential biases in diet interpretation.     

Determination of prehistoric use of arrowhead (Sagittaria,Alismataceae) in the Great Basin of North America by scanning electron microscopy

Analyses of human coprolites from Dryden Cave, Nevada, indicated that the prehistoric population that inhabited the rockshelter included locally available herbs in their diet. Plant epidermal tissue remains have been identified as fragments from roots ofSagittaria (Alismataceae), a genus of semi-aquatic monocots. Other remains from the coprolites included fish bones, freshwater diatoms, seeds, and pollen. This assemblage supports the hypothesis that this prehistoric population principally exploited the available lacustrine resources of the area; comparisons with other archaeological sites suggests that this pattern had an extremely long history of development in the Great Basin.     

Cryptosporidium,Giardia, and Cyclospora in ancient Peruvians

Twenty-two coprolites of human origin, collected from excavations along the north-central coast of Peru, were examined using fluorescent microscopy for the presence of fecal parasites, with emphasis on Cryptosporidium sp., Giardia sp., and Cyclospora sp. Three samples were positive. One coprolite dated between ca. 2,375 and 1,525 BC contained Giardia sp. cysts. This coprolite corresponded to the Peruvian preceramic period. Another positive coprolite ca. AD 770-830 corresponded to Epoch 3 of the Middle Horizon and contained Cryptosporidium sp. oocysts. The third positive coprolite (corresponding to the Middle Horizon. ca. AD 500-900) contained Giardia sp. cysts. This report demonstrates that Giardia sp. and Cryptosporidium sp. were present in Peruvian coastal populations for at least 4,300 and 1,100 BP.     

Pollen concentration analysis of Ancestral Pueblo dietary variation

Previous coprolite research on the Colorado Plateau has shown that macrofossils are a useful way of statistically demonstrating prehistoric dietary variation of Ancestral Pueblos (Anasazi). Up until now, pollen concentration from human coprolites has not been used for comparative, statistical study. We present here the statistical analysis of pollen concentration values of coprolites from two Ancestral Pueblo sites, Salmon Ruin and Antelope House. The data show that although most pollen types do not show statistically significant variation, there are some types that show how different Ancestral Pueblo populations adapted to plant resources in different environments. The analysis indicates that future work should focus more on pollen concentration analysis of coprolites.     

Cultural ecology of prehistoric parasitism on the Colorado Plateau as evidenced by coprology

The study of coprolites (desiccated feces) is recognized as a viable method for analyzing parasitism of prehistoric peoples. Eight species of helminth parasites, including nematodes, cestodes, and acanthcephalans, have been recovered from archaeological sites on the Colorado Plateau. The comparative analysis of parasitological findings illustrates the effects of changing subsistence strategies and varying life-style on prehistoric human parasitism. This comparative study is based on the analysis of coprolites recovered from one Archaic hunter-gatherer site and two Anasazi agricultural villages. Hunter-gatherers are represented by coprolites from Dust Devil Cave in south-eastern Utah. Coprolites of prehistoric agriculturalists from Antelope House in Canyon de Chelly, Arizona, and from Salmon Ruin in northwestern New Mexico were studied. The results demonstrate that helminth parasitism increased with the advent of agriculture. Between the agricultural sites, differences in patterns of excreta disposal, foraging behavior, and local ecology resulted in pronounced variations in both percentage of coprolites containing parasite remains and the number of parasite species represented.     

The science of coprolite analysis: The view from Hinds cave

This paper explores some of the new perspectives resulting from re-examination of the pollen data from my 1978 comprehensive analysis of 100 coprolites from one of the earliest identified prehistoric latrines in North America. Of particular interest are the empirical results of previously unavailable pollen concentration calculations for some of the prehistoric specimens as well as a time-series of 82 modern fecal specimens produced during an experiment yielding data on the rate of elimination of specific pollen grains from the human system. Experimental data of all sorts are needed to extend coprolite analyses and interpretations, particularly from pollen-ingestion studies conducted with more volunteers over long periods of time. Parasitological studies of human coprolites will benefit from experimental data to determine the fate of the constituents of human feces ingested by dogs. The application of specialized techniques at the microscope, such as Intensive Systematic Microscopy ([Dean, G., 1998. Finding a needle in a palynological haystack. In: Bryant, V.M., Wrenn, J.H. (Eds.), New Developments in Palynomorph Sampling, Extraction, and Analysis. Am. Assoc. of Stratigraphic Palynologists Foundation., Contribs Series No. 33, pp. 53-59]), to locate and quantify rare pollen types needs to be explored. Easy and useful ways to express the abundance of macroremains in a coprolite are also needed.     

A comparative study of gut microbiota profiles of earthworms fed in three different substrates

The gut microbiome of earthworms has a complex interdependence with the host. When the soil minerals pass through earthworm’s gut, they may affect the gut microbiota. To gain insight into the response of gut microbiota to the passed minerals, we fed earthworm (Eisenia fetida) on nutrient-poor soil and ore powder, and used high throughput sequencing to characterize the earthworm intestinal microbial community to find evidence for a core bacterial community of the E. fetida. The results showed that earthworms’ gut maintained a core microbiome that appeared in all samples. These core microbiota may play a significant role in a species’ environmental interactions. The composition of intestinal microbiomes varied with substrates. The earthworm guts from two nutrient-poor substrates had similar microbial communities and they were different from nutrient-rich substrate. Proteobacteria and Bacteroidetes were more abundant in the gut of earthworms kept on a nutrient-poor substrate such as ore powder or mineral soil than in the gut of earthworms kept in organic-rich compost soil; some of these microorganisms may help earthworms survive in nutrient-poor substrates.