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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ftmdpi:oai:mdpi.com:/2073-4425/9/9/436/ 2023-08-20T04:09:11+02:00 Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf Giada Ferrari Heidi E. L. Lischer Judith Neukamm Enrique Rayo Nicole Borel Andreas Pospischil Frank Rühli Abigail S. Bouwman Michael G. Campana agris 2018-08-31 application/pdf https://doi.org/10.3390/genes9090436 EN eng Multidisciplinary Digital Publishing Institute Microbial Genetics and Genomics https://dx.doi.org/10.3390/genes9090436 https://creativecommons.org/licenses/by/4.0/ Genes; Volume 9; Issue 9; Pages: 436 ancient DNA Mammuthus primigenius microbiome environmental DNA DNA contamination Text 2018 ftmdpi https://doi.org/10.3390/genes9090436 2023-07-31T21:42:17Z 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 MDPI Open Access Publishing Genes 9 9 436 |
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MDPI Open Access Publishing |
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ftmdpi |
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English |
topic |
ancient DNA Mammuthus primigenius microbiome environmental DNA DNA contamination |
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ancient DNA Mammuthus primigenius microbiome environmental DNA DNA contamination Giada Ferrari Heidi E. L. Lischer Judith Neukamm Enrique Rayo Nicole Borel Andreas Pospischil Frank Rühli Abigail S. Bouwman Michael G. Campana Assessing Metagenomic Signals Recovered from Lyuba, a 42,000-Year-Old Permafrost-Preserved Woolly Mammoth Calf |
topic_facet |
ancient DNA Mammuthus primigenius microbiome environmental DNA DNA contamination |
description |
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 |
Giada Ferrari Heidi E. L. Lischer Judith Neukamm Enrique Rayo Nicole Borel Andreas Pospischil Frank Rühli Abigail S. Bouwman Michael G. Campana |
author_facet |
Giada Ferrari Heidi E. L. Lischer Judith Neukamm Enrique Rayo Nicole Borel Andreas Pospischil Frank Rühli Abigail S. Bouwman Michael G. Campana |
author_sort |
Giada Ferrari |
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 |
Multidisciplinary Digital Publishing Institute |
publishDate |
2018 |
url |
https://doi.org/10.3390/genes9090436 |
op_coverage |
agris |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
Genes; Volume 9; Issue 9; Pages: 436 |
op_relation |
Microbial Genetics and Genomics https://dx.doi.org/10.3390/genes9090436 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/genes9090436 |
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Genes |
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9 |
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9 |
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436 |
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