Human Coprolites as a Source for Paleomicrobiology

The Technological Advance and Application of Coprolite Analysis

Coprolites (mummified or fossilized feces), belonging to the group of ichnofossils, are fossilized remains of feces produced by animals. Various types of data from coprolites provide detailed evidence of the producer’s condition, like diet, intestinal microbiome, virus infection and parasites diseases. In addition, the palaeoenvironment information relevant to producers’ ecological niche can be drawn from taphonomy details the coprolites mirrored. At present, the phylogenetic clues of the producer’s population can be determined by advanced molecular biotechnologies. With the integration of multiple methods and techniques, coprolite has been widely accepted as an ideal material to study the diet, evolution, and palaeoenvironment of producers. In this paper, we reviewed the history of coprolite research, enumerated and interpreted the data recovered from coprolites, and explained their research value to palaeocoprology and evolutionary biology. Finally, we summarized the current directions of coprolite research and looked into its future prospects.

Paleomicrobiology of the human digestive tract: A review

The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.

Assessing the Parasitic Burden in a Late Antique Florentine Emergency Burial Site

Excavation (2008–2014) carried out under the Uffizi Gallery (Florence, Italy) led to the discovery of 75 individuals, mostly buried in multiple graves. Based on Roman minted coins, the graves were preliminarily dated between the second half of the 4th and the beginning of the 5th centuries CE. Taphonomy showed that this was an emergency burial site associated with a catastrophic event, possibly an epidemic of unknown etiology with high mortality rates. In this perspective, paleoparasitological investigations were performed on 18 individuals exhumed from 9 multiple graves to assess the burden of gastrointestinal parasitism. Five out of eighteen individuals (27.7%) tested positive for ascarid-type remains; these are considered as “decorticated” Ascaris eggs, which have lost their outer mammillated coat. Roundworms (genus Ascaris) commonly infest human populations under dire sanitary conditions. Archaeological and historical evidence indicates that Florentia suffered a period of economic crisis between the end of 4th and the beginning of the 5th centuries CE, and that the aqueduct was severely damaged at the beginning of the 4th century CE, possibly during the siege of the Goths (406 CE). It is more than plausible that the epidemic, possibly coupled with the disruption of the aqueduct, deeply affected the living conditions of these individuals. A 27.7% frequency suggests that ascariasis was widespread in this population. This investigation exemplifies how paleoparasitological information can be retrieved from the analysis of sediments sampled in cemeteries, thus allowing a better assessment of the varying frequency of parasitic infections among ancient populations.

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

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