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.

FIG 1

Transmission electron microscopy of negatively stained viral particles. (A) Overview of stained viral particles, which vary in size and shape, isolated from the Middle Ages coprolite. (B to E) A representative virion (B) and virus-like particles (C to E) with icosahedral nucleocapsids and a long filament tail characteristic of Siphoviridae bacteriophages.

FIG 2

(A) The proportion of known and unknown reads (in percent). Reads were defined as “unknown” if they lacked homology to the nonredundant NCBI database according to a BLASTN search (E value, <1e−5) and as “known” otherwise. (B) Relative abundance of viral families. The relative abundance of identified viral families was estimated using the GAAS software.

FIG 3

Relative abundance of hits to known bacteriophages. The relative abundance of hits to known bacteriophages was estimated using the GAAS software. The hosts of the bacteriophages that were also identified in a previous study on the bacterial community associated with this specimen (Appelt et al., unpublished data) are noted to the right with dots.

FIG 4

Comparison between the modern human stool viromes and the coprolite virome. Principal component (PCO) analysis was used to compare the viral metagenomes associated with the coprolite (highlighted in red) to those associated with modern human stool samples (S1 to S21) at the taxonomic (A) and functional (B) levels.