Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf

• Main Authors: Ferrari, Giada, Lischer, Heidi, Neukamm, Judith, Rayo, Enrique, Borel, Nicole, Pospischil, Andreas, Rühli, Frank, Bouwman, Abigail, Campana, Michael
• Format: Article in Journal/Newspaper
• Language: English
• Published: MDPI Publishing 2018
• Subjects: Institute of Veterinary Pathology; Institute of Evolutionary Medicine; Evolution in Action: From Genomes to Ecosystems; 610 Medicine & health; permafrost
• Online Access: https://www.zora.uzh.ch/id/eprint/153441/; https://www.zora.uzh.ch/id/eprint/153441/1/genes-09-00436.pdf; https://doi.org/10.5167/uzh-153441; https://doi.org/10.3390/genes9090436

The reconstruction of ancient metagenomes from archaeological material, and their implication in human health and evolution, is one of the most recent advances in paleomicrobiological studies. However, as for all ancient DNA (aDNA) studies, environmental and laboratory contamination need to be specifically addressed. Here we attempted to reconstruct the tissue-specific metagenomes of a 42,000-year-old, permafrost-preserved woolly mammoth calf through shotgun high-throughput sequencing. We analyzed the taxonomic composition of all tissue samples together with environmental and non-template experimental controls and compared them to metagenomes obtained from permafrost and elephant fecal samples. Preliminary results suggested the presence of tissue-specific metagenomic signals. We identified bacterial species that were present in only one experimental sample, absent from controls, and consistent with the nature of the samples. However, we failed to further authenticate any of these signals and conclude that, even when experimental samples are distinct from environmental and laboratory controls, this does not necessarily indicate endogenous presence of ancient host-associated microbiomic signals.