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

Retroviral DNA Sequences as a Means for Determining Ancient Diets.

For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host's diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures

Archeological sites and coprolite samples in the present study.

<p>Panel (A) shows the deposits of the Saladoid and Huecoid groups in Vieques, Puerto Rico, from which the coprolite samples were collected. (B) Representative coprolite from the Sorcé, Vieques archaeological site.</p

Primers in the present study included those for human and dog Bacteroides, universal primers for the 16S rRNA of bacteria and archaea, and the ITS region of fungi.

<p>Primers in the present study included those for human and dog Bacteroides, universal primers for the 16S rRNA of bacteria and archaea, and the ITS region of fungi.</p

SIMPER Analysis of Bacterial taxa impacting clustering of Huecoid and Saladoid Coprolite.

*<p>Total Average dissimilarity = 65.75.</p

R Statistics for Coprolites from Saladoid and Huecoid Archaeological Sites in Vieques.

<p>R Statistics for Coprolites from Saladoid and Huecoid Archaeological Sites in Vieques.</p

MDS analysis of the Saladoid and Huecoid coprolite samples from Vieques, Puerto Rico.

<p>MDS analysis of the Saladoid and Huecoid coprolite samples from Vieques, Puerto Rico.</p

Cumulative number of unique TRF peaks accumulating with sample intensity.

<p>Values were calculated from the average of unique bands resulting from 50 permutations of random ordering.</p

Presence of DNA, proteins and lipids in the coprolite samples.

<p>Detection of the macromolecules was determined using specific cytochemical staining.</p

SIMPER Analysis of fungal taxa impacting clustering of Huecoid and Saladoid Coprolite.

<p>SIMPER Analysis of fungal taxa impacting clustering of Huecoid and Saladoid Coprolite.</p