title: Natural mummification of the human gut preserves bacteriophage DNA.
abstract: The natural mummification process of the human gut represents a unique opportunity to study the resulting microbial community structure and composition. While results are providing insights into the preservation of bacteria, fungi, pathogenic eukaryotes and eukaryotic viruses, no studies have demonstrated that the process of natural mummification also results in the preservation of bacteriophage DNA. We characterized the gut microbiome of three pre-Columbian Andean mummies, namely FI3, FI9 and FI12, and found sequences homologous to viruses. From the sequences attributable to viruses, 50.4% (mummy FI3), 1.0% (mummy FI9) and 84.4% (mummy FI12) were homologous to bacteriophages. Sequences corresponding to the Siphoviridae, Myoviridae, Podoviridae and Microviridae families were identified. Predicted putative bacterial hosts corresponded mainly to the Firmicutes and Proteobacteria, and included Bacillus, Staphylococcus, Clostridium, Escherichia, Vibrio, Klebsiella, Pseudomonas and Yersinia. Predicted functional categories associated with bacteriophages showed a representation of structural, replication, integration and entry and lysis genes. The present study suggests that the natural mummification of the human gut results in the preservation of bacteriophage DNA, representing an opportunity to elucidate the ancient phageome and to hypothesize possible mechanisms of preservation.
authors.affiliation: Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA tasantia@calpoly.edu.
authors.forename: Tasha M
authors.initials: TM
authors.lastname: Santiago-Rodriguez
authors.affiliation: Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa 56126, Italy Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy.
authors.forename: Gino
authors.initials: G
authors.lastname: Fornaciari
authors.affiliation: Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Luciani
authors.affiliation: Molecular Research LP (MR DNA), Shallowater, TX 79363, USA.
authors.forename: Scot E
authors.initials: SE
authors.lastname: Dowd
authors.affiliation: Department of Biology, University of Puerto Rico, San Juan 00932, Puerto Rico.
authors.forename: Gary A
authors.initials: GA
authors.lastname: Toranzos
authors.affiliation: Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.
authors.forename: Isolina
authors.initials: I
authors.lastname: Marota
authors.affiliation: Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA 93407, USA Department of Biology, California Polytechnic State University, San Luis Obispo, CA 93407, USA.
authors.forename: Raul J
authors.initials: RJ
authors.lastname: Cano
mesh_terms: D000293:Adolescent; D000328:Adult; D001419:Bacteria / Q000821:virology*; D001435:Bacteriophages / Q000145:classification / Q000235:genetics*; D004279:DNA, Viral / Q000302:isolation & purification*; D005260:Female; D041981:Gastrointestinal Tract / Q000821:virology*; D006801:Humans; D008297:Male; D009106:Mummies / Q000821:virology*; D055815:Young Adult
chemical_list: D004279:DNA, Viral
keywords: ancient microbiomes; bacteriophages; microbiome; mummy; phageome; virome