Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf
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 speci...
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ftpubmed:oai:pubmedcentral.nih.gov:6162753 2023-05-15T17:56:56+02:00 Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf Ferrari, Giada Lischer, Heidi E. L. Neukamm, Judith Rayo, Enrique Borel, Nicole Pospischil, Andreas Rühli, Frank Bouwman, Abigail S. Campana, Michael G. 2018-08-31 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162753/ http://www.ncbi.nlm.nih.gov/pubmed/30200350 https://doi.org/10.3390/genes9090436 en eng MDPI http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162753/ http://www.ncbi.nlm.nih.gov/pubmed/30200350 http://dx.doi.org/10.3390/genes9090436 © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). CC-BY Article Text 2018 ftpubmed https://doi.org/10.3390/genes9090436 2018-10-14T00:25:31Z 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. Text permafrost PubMed Central (PMC) Genes 9 9 436 |
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Article Ferrari, Giada Lischer, Heidi E. L. Neukamm, Judith Rayo, Enrique Borel, Nicole Pospischil, Andreas Rühli, Frank Bouwman, Abigail S. Campana, Michael G. Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf |
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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. |
format |
Text |
author |
Ferrari, Giada Lischer, Heidi E. L. Neukamm, Judith Rayo, Enrique Borel, Nicole Pospischil, Andreas Rühli, Frank Bouwman, Abigail S. Campana, Michael G. |
author_facet |
Ferrari, Giada Lischer, Heidi E. L. Neukamm, Judith Rayo, Enrique Borel, Nicole Pospischil, Andreas Rühli, Frank Bouwman, Abigail S. Campana, Michael G. |
author_sort |
Ferrari, Giada |
title |
Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf |
title_short |
Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf |
title_full |
Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf |
title_fullStr |
Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf |
title_full_unstemmed |
Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf |
title_sort |
assessing metagenomic signals recovered from lyuba, a 42,000-year-old permafrost-preserved woolly mammoth calf |
publisher |
MDPI |
publishDate |
2018 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162753/ http://www.ncbi.nlm.nih.gov/pubmed/30200350 https://doi.org/10.3390/genes9090436 |
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permafrost |
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permafrost |
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162753/ http://www.ncbi.nlm.nih.gov/pubmed/30200350 http://dx.doi.org/10.3390/genes9090436 |
op_rights |
© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/). |
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CC-BY |
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https://doi.org/10.3390/genes9090436 |
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Genes |
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