Matthieu Le Bailly

Amoebiasis distribution in the past: first steps using an immunoassay technique

The identification of parasites in ancient human faeces is compromised by differential preservation of identifiable parasite structures. However, protein molecules can survive the damage of the environment and can be detected even after centuries. In this paper it is shown that is possible to detect copro-antigen of Entamoeba histolytica in historic and prehistoric human faecal remains, using a commercially available enzyme immunoassay (ELISA) kit. The kit uses monoclonal antibody-peroxidase conjugate specific for E. histolytica adhesin. A total of 90 specimens of desiccated faeces found in mummies and ancient organic sediment from South America, North America, Africa, and Europe were examined. The ELISA detected 20 positive samples, dated to about 5300 years before present to the 19th Century ad. The positive samples are from archaeological sites in Argentina, USA, France, Belgium, and Switzerland. The detection of protozoan antigen using immunoassays is a reliable tool for the studies of intestinal parasites in the past.

Viruses in a 14th-century coprolite

ABSTRACT Coprolites are fossilized fecal material that can reveal information about ancient intestinal and environmental microbiota. Viral metagenomics has allowed systematic characterization of viral diversity in environmental and human-associated specimens, but little is known about the viral diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite from a closed barrel in a Middle Ages site in Belgium using electron microscopy and metagenomics. Viruses that infect eukaryotes, bacteria, and archaea were detected, and we confirmed the presence of some of them by ad hoc suicide PCR. The coprolite DNA viral metagenome was dominated by sequences showing homologies to phages commonly found in modern stools and soil. Although their phylogenetic compositions differed, the metabolic functions of the viral communities have remained conserved across centuries. Antibiotic resistance was one of the reconstructed metabolic functions detected.

Polyphasic Analysis of a Middle Ages Coprolite Microbiota, Belgium

Paleomicrobiological investigations of a 14th-century coprolite found inside a barrel in Namur, Belgium were done using microscopy, a culture-dependent approach and metagenomics. Results were confirmed by ad hoc PCR – sequencing. Investigations yielded evidence for flora from ancient environment preserved inside the coprolite, indicated by microscopic observation of amoebal cysts, plant fibers, seeds, pollens and mold remains. Seventeen different bacterial species were cultured from the coprolite, mixing organisms known to originate from the environment and organisms known to be gut inhabitants. Metagenomic analyses yielded 107,470 reads, of which known sequences (31.9%) comprised 98.98% bacterial, 0.52% eukaryotic, 0.44% archaeal and 0.06% viral assigned reads. Most abundant bacterial phyla were Proteobacteria, Gemmatimonadetes, Actinobacteria and Bacteroidetes. The 16 S rRNA gene dataset yielded 132,000 trimmed reads and 673 Operational Taxonomic Units. Most abundant bacterial phyla observed in the 16 S rRNA gene dataset belonged to Proteobacteria, Firmicutes, Actinobacteria and Chlamydia. The Namur coprolite yielded typical gut microbiota inhabitants, intestinal parasites Trichuris and Ascaris and systemic pathogens Bartonella and Bordetella. This study adds knowledge to gut microbiota in medieval times.

A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites.

Human gastrointestinal parasites are good indicators for hygienic conditions and health status of past and present individuals and communities. While microscopic analysis of eggs in sediments of archeological sites often allows their taxonomic identification, this method is rarely effective at the species level, and requires both the survival of intact eggs and their proper identification. Genotyping via PCR-based approaches has the potential to achieve a precise species-level taxonomic determination. However, so far it has mostly been applied to individual eggs isolated from archeological samples. To increase the throughput and taxonomic accuracy, as well as reduce costs of genotyping methods, we adapted a PCR-based approach coupled with next-generation sequencing to perform precise taxonomic identification of parasitic helminths directly from archeological sediments. Our study of twenty-five 100 to 7,200 year-old archeological samples proved this to be a powerful, reliable and efficient approach for species determination even in the absence of preserved eggs, either as a stand-alone method or as a complement to microscopic studies.

Past Intestinal Parasites

This chapter aims to provide some key points for researchers interested in the study of ancient gastrointestinal parasites. These few pages are dedicated to my colleague and friend, Prof. Adauto Araújo (1951-2015), who participated in the writing of this chapter. His huge efforts in paleoparasitology contributed to the development and promotion of the discipline during more than 30 years.

Paleoparasitological investigations on the Neolithic lakeside settlement of La Draga (Lake Banyoles, Spain)

Paleoparasitological analyses were conducted on samples from the Neolithic lakeside settlement of La Draga in Spain (5320–4980 BC). Conventional microscopic analysis revealed the presence of tapeworms (genus Taenia/Echinoccocus and Diphyllobothrium), roundworms (genus Trichuris, Capillaria, and Ascaris), rumen fluke (genus Paramphistomum), and Acanthocephalan (genus Macracanthorhynchus). In addition, genetic analysis demonstrated the presence of the lancet liver fluke (Dicrocoelium dendriticum) and the human pinworm (Enterobius vermicularis) at the site. These results represent the first parasitological data from a Neolithic lakeside settlement related to the Cardial Pottery Culture. Some parasites are comparable with those retrieved from Neolithic lakeside sites studied in France, Germany, and Switzerland, which stem from and are posterior to the Linear Band Keramic Culture. However, some taxa were identified here for the first time during the Neolithic period, or represent the oldest mention of these parasites. This new paleoparasitological contribution reinforces our knowledge of intestinal parasites in Neolithic populations and provides new data on their history.

Archaeological occurrences and historical review of the human amoeba, Entamoeba histolytica, over the past 6000years.

Understanding parasite history and the evolution of host/parasite relationships is one of the most important aspects of paleoparasitology. Within the framework of this research topic, this paper focuses on the human pathogenic amoeba, Entamoeba histolytica. The compilation of all the available archaeological data concerning this parasite leads to a first glimpse of the history of this parasite of current medical importance. Paleoparasitological investigation into this parasite uses immunological techniques and shows that the modern strain of E. histolytica has been present in Western Europe since at least the Neolithic period (3700yearsBCE), and could have originated in the Old World. The appearance of the modern amoeba strain in the pre-Columbian Americas and the Middle East around the 12th century CE gives rise to hypotheses as to how human migrations (Atlantic or Pacific routes) contributed to the diffusion of this pathogen, resulting in its current distribution. This compilation proves that parasites are valuable proxies for studying past human and animal migrations, and should be given more consideration in the future.

A First Case of Human Trichuriasis from a Roman Lead Coffin in France

A paleoparasitological study was carried out on 2 lead coffins recovered from the Roman site of Jaunay-Clan (near Poitiers, France). For the first time, this particular type of burial gave positive parasitological results, and eggs of the whipworm Trichuris trichiura were identified in 1 individual. In the present case, thanatomorphose associated with funerary practices may explain the scarcity of the recovered eggs. However, human whipworm has now been observed in 9 individuals dated to the Roman period. The very high frequency of Trichuris sp. eggs in Roman archaeological sites (up to 80%) suggests that fecal peril, hygiene, and waste management were problematic during this period. Finally, due to the fact that very few analyses have been conducted on human bodies dated to the Roman period, more analyses must be performed in the future to provide further information about diseases in the Roman world.

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.