Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation
Next generation sequencing (NGS) has unlocked access to the wide range of non-cultivable microorganisms, including those present in the ancient past. The study of microorganisms from ancient sources (palaeomicrobiology) using DNA sequencing now provides a unique opportunity to examine ancient microb...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2020-06-01
|
| Series: | Frontiers in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fevo.2020.00040/full |
| _version_ | 1818284093970841600 |
|---|---|
| author | Luis A. Arriola Alan Cooper Alan Cooper Laura S. Weyrich Laura S. Weyrich Laura S. Weyrich |
| author_facet | Luis A. Arriola Alan Cooper Alan Cooper Laura S. Weyrich Laura S. Weyrich Laura S. Weyrich |
| author_sort | Luis A. Arriola |
| collection | DOAJ |
| description | Next generation sequencing (NGS) has unlocked access to the wide range of non-cultivable microorganisms, including those present in the ancient past. The study of microorganisms from ancient sources (palaeomicrobiology) using DNA sequencing now provides a unique opportunity to examine ancient microbial genomic content, explore pathogenicity, and understand microbial evolution in greater detail than ever before. As a result, current studies have focused on reconstructing the evolutionary history of a number of human pathogens involved in ancient and historic pandemic events. These studies have opened the door for a variety of future palaeomicrobiology studies, which can focus on commensal microorganisms, species from non-human hosts, information from host-genomics, and the use of bacteria as proxies for additional information about past human health, behavior, migration, and culture. Here, we describe the origin and the historical and recent advances in the field of palaeomicrobiology, review some of the most notable ancient pathogenic microorganism studies, and provide perspectives on how NGS and whole genome information from ancient microorganisms contributes to our understanding of bacterial evolution on a broader scale. We conclude by exploring the application of newly developed tools in palaeomicrobiology and discussing how future studies can improve our current understanding of non-pathogenic microbes. |
| first_indexed | 2024-12-13T00:47:20Z |
| format | Article |
| id | doaj.art-ed08339b3834446495d8b94158d8c6b4 |
| institution | Directory Open Access Journal |
| issn | 2296-701X |
| language | English |
| last_indexed | 2024-12-13T00:47:20Z |
| publishDate | 2020-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-ed08339b3834446495d8b94158d8c6b42022-12-22T00:05:01ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2020-06-01810.3389/fevo.2020.00040505769Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and AdaptationLuis A. Arriola0Alan Cooper1Alan Cooper2Laura S. Weyrich3Laura S. Weyrich4Laura S. Weyrich5Australian Centre for Ancient DNA, School of Biomedical Sciences, University of Adelaide, Adelaide, SA, AustraliaAustralian Centre for Ancient DNA, School of Biomedical Sciences, University of Adelaide, Adelaide, SA, AustraliaSouth Australian Museum, Adelaide, SA, AustraliaAustralian Centre for Ancient DNA, School of Biomedical Sciences, University of Adelaide, Adelaide, SA, AustraliaCentre for Australian Biodiversity and Heritage, School of Biological Sciences, University of Adelaide, Adelaide, SA, AustraliaDepartment of Anthropology and The Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United StatesNext generation sequencing (NGS) has unlocked access to the wide range of non-cultivable microorganisms, including those present in the ancient past. The study of microorganisms from ancient sources (palaeomicrobiology) using DNA sequencing now provides a unique opportunity to examine ancient microbial genomic content, explore pathogenicity, and understand microbial evolution in greater detail than ever before. As a result, current studies have focused on reconstructing the evolutionary history of a number of human pathogens involved in ancient and historic pandemic events. These studies have opened the door for a variety of future palaeomicrobiology studies, which can focus on commensal microorganisms, species from non-human hosts, information from host-genomics, and the use of bacteria as proxies for additional information about past human health, behavior, migration, and culture. Here, we describe the origin and the historical and recent advances in the field of palaeomicrobiology, review some of the most notable ancient pathogenic microorganism studies, and provide perspectives on how NGS and whole genome information from ancient microorganisms contributes to our understanding of bacterial evolution on a broader scale. We conclude by exploring the application of newly developed tools in palaeomicrobiology and discussing how future studies can improve our current understanding of non-pathogenic microbes.https://www.frontiersin.org/article/10.3389/fevo.2020.00040/fullancient DNApathogensmicrobiomemicrobiotagenomicscommensals |
| spellingShingle | Luis A. Arriola Alan Cooper Alan Cooper Laura S. Weyrich Laura S. Weyrich Laura S. Weyrich Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation Frontiers in Ecology and Evolution ancient DNA pathogens microbiome microbiota genomics commensals |
| title | Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation |
| title_full | Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation |
| title_fullStr | Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation |
| title_full_unstemmed | Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation |
| title_short | Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation |
| title_sort | palaeomicrobiology application of ancient dna sequencing to better understand bacterial genome evolution and adaptation |
| topic | ancient DNA pathogens microbiome microbiota genomics commensals |
| url | https://www.frontiersin.org/article/10.3389/fevo.2020.00040/full |
| work_keys_str_mv | AT luisaarriola palaeomicrobiologyapplicationofancientdnasequencingtobetterunderstandbacterialgenomeevolutionandadaptation AT alancooper palaeomicrobiologyapplicationofancientdnasequencingtobetterunderstandbacterialgenomeevolutionandadaptation AT alancooper palaeomicrobiologyapplicationofancientdnasequencingtobetterunderstandbacterialgenomeevolutionandadaptation AT laurasweyrich palaeomicrobiologyapplicationofancientdnasequencingtobetterunderstandbacterialgenomeevolutionandadaptation AT laurasweyrich palaeomicrobiologyapplicationofancientdnasequencingtobetterunderstandbacterialgenomeevolutionandadaptation AT laurasweyrich palaeomicrobiologyapplicationofancientdnasequencingtobetterunderstandbacterialgenomeevolutionandadaptation |