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.

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 digitalcommons.unl.edu

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 macro remains, we identified rodent bones, digitalcommons.unl.edu

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.

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