Publications by authors named "Judith Neukamm"

8 Publications

  • Page 1 of 1

Comparison of target enrichment strategies for ancient pathogen DNA.

Biotechniques 2020 12 2;69(6):455-459. Epub 2020 Nov 2.

Institute for Archaeological Sciences, Archaeo- & Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany.

In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods - array-based hybridization capture and in-solution capture using either RNA or DNA baits - have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of and from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits.
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http://dx.doi.org/10.2144/btn-2020-0100DOI Listing
December 2020

Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox.

Philos Trans R Soc Lond B Biol Sci 2020 11 5;375(1812):20190572. Epub 2020 Oct 5.

Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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http://dx.doi.org/10.1098/rstb.2019.0572DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7702794PMC
November 2020

New ancient Eastern European genomes illuminate the dispersal of plague in Europe.

Philos Trans R Soc Lond B Biol Sci 2020 11 5;375(1812):20190569. Epub 2020 Oct 5.

Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.

, the causative agent of plague, has been prevalent among humans for at least 5000 years, being accountable for several devastating epidemics in history, including the Black Death. Analyses of the genetic diversity of ancient strains of have shed light on the mechanisms of evolution and the spread of plague in Europe. However, many questions regarding the origins of the pathogen and its long persistence in Europe are still unresolved, especially during the late medieval time period. To address this, we present four newly assembled genomes from Eastern Europe (Poland and Southern Russia), dating from the fifteenth to eighteenth century AD. The analysis of polymorphisms in these genomes and their phylogenetic relationships with other ancient and modern strains may suggest several independent introductions of plague into Eastern Europe or its persistence in different reservoirs. Furthermore, with the reconstruction of a partial genome from rat skeletal remains found in a Polish ossuary, we were able to identify a potential animal reservoir in late medieval Europe. Overall, our results add new information concerning transmission and its evolutionary history in Eastern Europe. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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http://dx.doi.org/10.1098/rstb.2019.0569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7702796PMC
November 2020

2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.

BMC Biol 2020 08 28;18(1):108. Epub 2020 Aug 28.

Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.

Background: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging.

Results: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed.

Conclusions: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.
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http://dx.doi.org/10.1186/s12915-020-00839-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456089PMC
August 2020

Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe.

Curr Biol 2020 Oct 13;30(19):3788-3803.e10. Epub 2020 Aug 13.

Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany; Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP), University of Tübingen, Tübingen, Germany. Electronic address:

Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15 century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and yaws-causing T. pallidum subspecies were already present in Northern Europe in the early modern period. We also discovered a previously unknown T. pallidum lineage recovered as a sister group to yaws- and bejel-causing lineages. These findings imply a more complex pattern of geographical distribution and etiology of early treponemal epidemics than previously understood.
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http://dx.doi.org/10.1016/j.cub.2020.07.058DOI Listing
October 2020

Ongoing tissue changes in an experimentally mummified human leg.

Anat Rec (Hoboken) 2020 12 27;303(12):3085-3095. Epub 2019 Dec 27.

Institute of Evolutionary Medicine, Faculty of Medicine, University of Zurich, Zurich, Switzerland.

Artificial mummification has been used since antiquity and is best known from ancient Egypt. Despite ancient Egyptian mummies being studied for several decades, the mummification techniques of that time are not well understood. Modern mummification experiments involving animal and human tissues have contributed additional insights relevant to a broad field of research. In the current study, we present follow-up results of an experiment on artificial mummification, which began in 2009. A human leg was artificially mummified and monitored for almost a year with histological, molecular, and radiological techniques. Since then, it has remained in a dry, natron salt blend for 9 years. The current analyses show further progression of dehydration and tissue alterations, as well as DNA degradation, suggesting an ongoing process. Our results add new insights into the mechanisms of tissue mummification. Taking into account that the process is still ongoing, further research is required, including a re-evaluation of the human leg in the future.
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http://dx.doi.org/10.1002/ar.24333DOI Listing
December 2020

Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear.

Sci Rep 2019 08 15;9(1):10700. Epub 2019 Aug 15.

Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.

The cave bear (Ursus spelaeus) is one of the Late Pleistocene megafauna species that faced extinction at the end of the last ice age. Although it is represented by one of the largest fossil records in Europe and has been subject to several interdisciplinary studies including palaeogenetic research, its fate remains highly controversial. Here, we used a combination of hybridisation capture and next generation sequencing to reconstruct 59 new complete cave bear mitochondrial genomes (mtDNA) from 14 sites in Western, Central and Eastern Europe. In a Bayesian phylogenetic analysis, we compared them to 64 published cave bear mtDNA sequences to reconstruct the population dynamics and phylogeography during the Late Pleistocene. We found five major mitochondrial DNA lineages resulting in a noticeably more complex biogeography of the European lineages during the last 50,000 years than previously assumed. Furthermore, our calculated effective female population sizes suggest a drastic cave bear population decline starting around 40,000 years ago at the onset of the Aurignacian, coinciding with the spread of anatomically modern humans in Europe. Thus, our study supports a potential significant human role in the general extinction and local extirpation of the European cave bear and illuminates the fate of this megafauna species.
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http://dx.doi.org/10.1038/s41598-019-47073-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6695494PMC
August 2019

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

Genes (Basel) 2018 Aug 31;9(9). Epub 2018 Aug 31.

Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland.

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.
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http://dx.doi.org/10.3390/genes9090436DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162753PMC
August 2018