Natural mummification of the human gut preserves bacteriophage DNA.
Identifieur interne : 000049 ( Main/Exploration ); précédent : 000048; suivant : 000050Natural mummification of the human gut preserves bacteriophage DNA.
Auteurs : Tasha M. Santiago-Rodriguez [États-Unis] ; Gino Fornaciari [Italie] ; Stefania Luciani [Italie] ; Scot E. Dowd [États-Unis] ; Gary A. Toranzos [Porto Rico] ; Isolina Marota [Italie] ; Raul J. Cano [États-Unis]Source :
- FEMS microbiology letters [ 1574-6968 ] ; 2016.
English descriptors
- KwdEn :
- MESH :
- chemical , isolation & purification : DNA, Viral.
- classification : Bacteriophages.
- genetics : Bacteriophages.
- virology : Bacteria, Gastrointestinal Tract, Mummies.
- Adolescent, Adult, Female, Humans, Male, Young Adult.
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.
DOI: 10.1093/femsle/fnv219
PubMed: 26564967
Affiliations:
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Santiago-Rodriguez</name><affiliation wicri:level="2"><nlm: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.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>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</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Fornaciari, Gino" sort="Fornaciari, Gino" uniqKey="Fornaciari G" first="Gino" last="Fornaciari">Gino Fornaciari</name><affiliation wicri:level="4"><nlm: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.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>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</wicri:regionArea><orgName type="university">Université de Pise</orgName><placeName><settlement type="city">Pise</settlement><region type="region" nuts="2">Toscane</region></placeName></affiliation></author><author><name sortKey="Luciani, Stefania" sort="Luciani, Stefania" uniqKey="Luciani S" first="Stefania" last="Luciani">Stefania Luciani</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032</wicri:regionArea><wicri:noRegion>Camerino 62032</wicri:noRegion></affiliation></author><author><name sortKey="Dowd, Scot E" sort="Dowd, Scot E" uniqKey="Dowd S" first="Scot E" last="Dowd">Scot E. 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Toranzos</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, University of Puerto Rico, San Juan 00932, Puerto Rico.</nlm:affiliation><country xml:lang="fr">Porto Rico</country><wicri:regionArea>Department of Biology, University of Puerto Rico, San Juan 00932</wicri:regionArea><wicri:noRegion>San Juan 00932</wicri:noRegion></affiliation></author><author><name sortKey="Marota, Isolina" sort="Marota, Isolina" uniqKey="Marota I" first="Isolina" last="Marota">Isolina Marota</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino 62032</wicri:regionArea><wicri:noRegion>Camerino 62032</wicri:noRegion></affiliation></author><author><name sortKey="Cano, Raul J" sort="Cano, Raul J" uniqKey="Cano R" first="Raul J" last="Cano">Raul J. Cano</name><affiliation wicri:level="2"><nlm: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.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>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</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author></analytic><series><title level="j">FEMS microbiology letters</title><idno type="eISSN">1574-6968</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adolescent</term><term>Adult</term><term>Bacteria (virology)</term><term>Bacteriophages (classification)</term><term>Bacteriophages (genetics)</term><term>DNA, Viral (isolation & purification)</term><term>Female</term><term>Gastrointestinal Tract (virology)</term><term>Humans</term><term>Male</term><term>Mummies (virology)</term><term>Young Adult</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Viral</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Bacteriophages</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteriophages</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Bacteria</term><term>Gastrointestinal Tract</term><term>Mummies</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adolescent</term><term>Adult</term><term>Female</term><term>Humans</term><term>Male</term><term>Young Adult</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><affiliations><list><country><li>Italie</li><li>Porto Rico</li><li>États-Unis</li></country><region><li>Californie</li><li>Texas</li><li>Toscane</li></region><settlement><li>Pise</li></settlement><orgName><li>Université de Pise</li></orgName></list><tree><country name="États-Unis"><region name="Californie"><name sortKey="Santiago Rodriguez, Tasha M" sort="Santiago Rodriguez, Tasha M" uniqKey="Santiago Rodriguez T" first="Tasha M" last="Santiago-Rodriguez">Tasha M. Santiago-Rodriguez</name></region><name sortKey="Cano, Raul J" sort="Cano, Raul J" uniqKey="Cano R" first="Raul J" last="Cano">Raul J. Cano</name><name sortKey="Dowd, Scot E" sort="Dowd, Scot E" uniqKey="Dowd S" first="Scot E" last="Dowd">Scot E. Dowd</name></country><country name="Italie"><region name="Toscane"><name sortKey="Fornaciari, Gino" sort="Fornaciari, Gino" uniqKey="Fornaciari G" first="Gino" last="Fornaciari">Gino Fornaciari</name></region><name sortKey="Luciani, Stefania" sort="Luciani, Stefania" uniqKey="Luciani S" first="Stefania" last="Luciani">Stefania Luciani</name><name sortKey="Marota, Isolina" sort="Marota, Isolina" uniqKey="Marota I" first="Isolina" last="Marota">Isolina Marota</name></country><country name="Porto Rico"><noRegion><name sortKey="Toranzos, Gary A" sort="Toranzos, Gary A" uniqKey="Toranzos G" first="Gary A" last="Toranzos">Gary A. Toranzos</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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