Ancient Metagenomic Studies: Considerations for the Wider Scientific Community
ABSTRACT Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computat...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2021-12-01
|
| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.01315-21 |
| _version_ | 1828138550088957952 |
|---|---|
| author | Clio Der Sarkissian Irina M. Velsko Anna K. Fotakis Åshild J. Vågene Alexander Hübner James A. Fellows Yates |
| author_facet | Clio Der Sarkissian Irina M. Velsko Anna K. Fotakis Åshild J. Vågene Alexander Hübner James A. Fellows Yates |
| author_sort | Clio Der Sarkissian |
| collection | DOAJ |
| description | ABSTRACT Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field. |
| first_indexed | 2024-04-11T18:38:11Z |
| format | Article |
| id | doaj.art-0be74e2895004f2f947b34cdc1fb101a |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-04-11T18:38:11Z |
| publishDate | 2021-12-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-0be74e2895004f2f947b34cdc1fb101a2022-12-22T04:09:08ZengAmerican Society for MicrobiologymSystems2379-50772021-12-016610.1128/msystems.01315-21Ancient Metagenomic Studies: Considerations for the Wider Scientific CommunityClio Der Sarkissian0Irina M. Velsko1Anna K. Fotakis2Åshild J. Vågene3Alexander Hübner4James A. Fellows Yates5Centre for Anthropobiology and Genomics of Toulouse, UMR5288, CNRS, University Toulouse 3 Paul Sabatier, Toulouse, FranceDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyCenter for Evolutionary Hologenomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DenmarkSection for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DenmarkDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyDepartment of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, GermanyABSTRACT Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions & Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.https://journals.asm.org/doi/10.1128/msystems.01315-21ancient metagenomicsancient DNAarchaeogenomicspaleogeneticsarchaeologymicrobiome |
| spellingShingle | Clio Der Sarkissian Irina M. Velsko Anna K. Fotakis Åshild J. Vågene Alexander Hübner James A. Fellows Yates Ancient Metagenomic Studies: Considerations for the Wider Scientific Community mSystems ancient metagenomics ancient DNA archaeogenomics paleogenetics archaeology microbiome |
| title | Ancient Metagenomic Studies: Considerations for the Wider Scientific Community |
| title_full | Ancient Metagenomic Studies: Considerations for the Wider Scientific Community |
| title_fullStr | Ancient Metagenomic Studies: Considerations for the Wider Scientific Community |
| title_full_unstemmed | Ancient Metagenomic Studies: Considerations for the Wider Scientific Community |
| title_short | Ancient Metagenomic Studies: Considerations for the Wider Scientific Community |
| title_sort | ancient metagenomic studies considerations for the wider scientific community |
| topic | ancient metagenomics ancient DNA archaeogenomics paleogenetics archaeology microbiome |
| url | https://journals.asm.org/doi/10.1128/msystems.01315-21 |
| work_keys_str_mv | AT cliodersarkissian ancientmetagenomicstudiesconsiderationsforthewiderscientificcommunity AT irinamvelsko ancientmetagenomicstudiesconsiderationsforthewiderscientificcommunity AT annakfotakis ancientmetagenomicstudiesconsiderationsforthewiderscientificcommunity AT ashildjvagene ancientmetagenomicstudiesconsiderationsforthewiderscientificcommunity AT alexanderhubner ancientmetagenomicstudiesconsiderationsforthewiderscientificcommunity AT jamesafellowsyates ancientmetagenomicstudiesconsiderationsforthewiderscientificcommunity |