The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
No Ancient DNA Damage in Actinobacteria from the Neanderthal Bone
Open accessAbstract
BACKGROUND: The Neanderthal genome was recently sequenced using DNA extracted from a 38,000-year-old fossil. At the start of the project, the fraction of mammalian and bacterial DNA in the sample was estimated to be <6% and 9%, respectively. Treatment with restriction enzymes prior to sequencing increased the relative proportion of mammalian DNA to 15%, but the large majority of sequences remain uncharacterized. PRINCIPAL FINDINGS: Our taxonomic profiling of 3.95 Gb of Neanderthal DNA isolated from the Vindija Neanderthal Vi33.16 fossil showed that 90% of about 50,000 rRNA gene sequence reads were of bacterial origin, of which Actinobacteria accounted for more than 75%. Actinobacteria also represented more than 80% of the PCR-amplified 16S rRNA gene sequences from a cave sediment sample taken from the same G layer as the Neanderthal bone. However, phylogenetic analyses did not identify any sediment clones that were closely related to the bone-derived sequences. We analysed the patterns of nucleotide differences in the individual sequence reads compared to the assembled consensus sequences of the rRNA gene sequences. The typical ancient nucleotide substitution pattern with a majority of C to T changes indicative of DNA damage was observed for the Neanderthal rRNA gene sequences, but not for the Streptomyces-like rRNA gene sequences. CONCLUSIONS/SIGNIFICANCE: Our analyses suggest that the Actinobacteria, and especially members of the Streptomycetales, contribute the majority of sequences in the DNA extracted from the Neanderthal fossil Vi33.16. The bacterial DNA showed no signs of damage, and we hypothesize that it was derived from bacteria that have been enriched inside the bone. The bioinformatic approach used here paves the way for future studies of microbial compositions and patterns of DNA damage in bacteria from archaeological bones. Such studies can help identify targeted measures to increase the relative amount of endogenous DNA in the sample.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Actinobacteria were the most common microbes in the dinosaur bone based on 16S rRNA amplicon sequencing.
“The fact that Actinobacteria were the most common microbes in the dinosaur bone based on 16S rRNA amplicon sequencing is reminiscent of the results from a 38 ka Neanderthal bone, where the majority of detected DNA sequences derived from non-ancient Actinobacteria (Zaremba-Niedźwiedzka and Andersson, 2013).”
From Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities (2019) · cites this paper as Zaremba-Niedźwiedzka and Andersson, 2013
The Results (Taxonomic Compositions; page unavailable) report that Actinobacteria accounted for 74%–95% of bacterial rRNA reads from the Neanderthal bone, supporting the comparison with the dinosaur bone. The Results (Substitution Patterns; page unavailable) found no ancient-DNA damage signal in the Streptomyces-like reads, but explicitly did not assess substitution patterns for the other bacteria. Thus, the paper does not establish that all of the predominant Actinobacteria were non-ancient. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Prodigal: prokaryotic gene recognition and translation initiation site identification
Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,692
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Li, W.-Z., & Godzik, A. (2006) · Bioinform. · doi:10.1093/bioinformatics/btl158 · Cited by 10,996
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,714
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682
A draft sequence of the Neandertal genome
Green, R. E., Krause, J., Briggs, A. W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M. H.-Y., et al. (2010) · Science · doi:10.1126/science.1188021 · Cited by 4,318
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
Darling, A. E., Mau, B., & Perna, N. T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0011147 · Cited by 3,848
Recent developments in the MAFFT multiple sequence alignment program
Katoh, K., & Toh, H. (2008) · Briefings in Bioinformatics · doi:10.1093/bib/bbn013 · Cited by 3,629
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R. L., Wilke, A., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-386 · Cited by 3,565
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2)
Bentley, S. D., Chater, K. F., Cerdeño-Tárraga, A. M., Challis, G. L., Thomson, N. R., James, K., Harris, D. E., Quail, M. A., Kieser, H. M., Harper, D., et al. (2002) · Nature · doi:10.1038/417141a · Cited by 3,226
MEROPS: the peptidase database
Rawlings, N. D., & Barrett, A. J. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.325 · Cited by 2,278
Ikeda, H., Ishikawa, J., Hanamoto, A., SHINOSE, M., Kikuchi, H., Shiba, T., Sakaki, Y., Hattori, M., & Ōmura, S. (2003) · Nature Biotechnology · doi:10.1038/nbt820 · Cited by 1,238
ARB: A Software Environment for Sequence Data
Westram, R., Bader, K. C., Pruesse, E., Kumar, Y., Meier, H., Glöckner, F. O., & Ludwig, W. (2011) · Wiley eBooks · doi:10.1002/9781118010518.ch46 · Cited by 1,064
Goodfellow, M., & Williams, S. T. (1983) · Annual Review of Microbiology · doi:10.1146/annurev.mi.37.100183.001201 · Cited by 1,022
Patterns of damage in genomic DNA sequences from a neandertal
Briggs, A. W., Stenzel, U., Johnson, P. L. F., Green, R. E., Kelso, J., Prüfer, K., Meyer, M., Krause, J., Ronan, M. T., Lachmann, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704665104 · Cited by 981
MEROPS: the peptidase database
Rawlings, N. D., Barrett, A. J., & Bateman, A. G. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp971 · Cited by 974
Analysis of one million base pairs of Neanderthal DNA
Green, R. E., Krause, J., Ptak, S. E., Briggs, A. W., Ronan, M. T., Simons, J. F., Du, L., Egholm, M., Rothberg, J. M., Paunović, M., et al. (2006) · Nature · doi:10.1038/nature05336 · Cited by 758
Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA
Poinar, H. N., Schwarz, C., Qi, J., Shapiro, B., MacPhee, R. D. E., Buigues, B., Tikhonov, A., Huson, D. H., Tomsho, L. P., Auch, A. F., et al. (2005) · Science · doi:10.1126/science.1123360 · Cited by 638
A draft genome of Yersinia pestis from victims of the Black Death
Bos, K. I., Schuenemann, V. J., Golding, G. B., Burbano, H. A., Waglechner, N., Coombes, B. K., McPhee, J. B., DeWitte, S. N., Meyer, M., Schmedes, S., et al. (2011) · Nature · doi:10.1038/nature10549 · Cited by 619
Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA
Sawyer, S., Krause, J., Guschanski, K., Savolainen, V., & Pääbo, S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0034131 · Cited by 489
New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
Keller, A., Graefen, A., Ball, M., Matzas, M., Boisguerin, V., Maixner, F., Leidinger, P., Backes, C., Khairat, R., Forster, M., et al. (2012) · Nature Communications · doi:10.1038/ncomms1701 · Cited by 437
Sequencing the nuclear genome of the extinct woolly mammoth
Miller, W., Drautz, D. I., Ratan, A., Pusey, B. N., Qi, J., Lesk, A. M., Tomsho, L. P., Packard, M., Zhao, F., Sher, A. V., et al. (2008) · Nature · doi:10.1038/nature07446 · Cited by 353
Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment
Lomstein, B. A., Langerhuus, A. T., D'Hondt, S. L., Jørgensen, B. B., & Spivack, A. J. (2012) · Nature · doi:10.1038/nature10905 · Cited by 334
Ancient bacteria show evidence of DNA repair
Johnson, S. S., Hebsgaard, M. B., Christensen, T. R., Mastepanov, M., Nielsen, R., Munch, K., Brand, T., Gilbert, M. T. P., Zuber, M. T., Bunce, M., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706787104 · Cited by 292
Schuenemann, V. J., Bos, K. I., DeWitte, S. N., Schmedes, S. E., Jamieson, J., Mittnik, A., Forrest, S., Coombes, B. K., Wood, J. W., Earn, D. J. D., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105107108 · Cited by 260
Long-term persistence of bacterial DNA
Willerslev, E., Hansen, A. J., Rønn, R., Brand, T. B., Barnes, I., Wiuf, C., Gilichinsky, D., Mitchell, D., & Cooper, A. (2004) · Current Biology · doi:10.1016/j.cub.2003.12.012 · Cited by 232
Carbon and nitrogen assimilation in deep subseafloor microbial cells
Morono, Y., Terada, T., Nishizawa, M., Ito, M., Hillion, F., Takahata, N., Sano, Y., & Inagaki, F. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1107763108 · Cited by 218
Child, A. M. (1995) · Journal of Archaeological Science · doi:10.1006/jasc.1995.0018 · Cited by 204
PatMaN: rapid alignment of short sequences to large databases
Prüfer, K., Stenzel, U., Dannemann, M., Green, R. E., Lachmann, M., & Kelso, J. F. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn223 · Cited by 202
Stiller, M., Green, R. E., Ronan, M., Simons, J. F., Du, L., He, W., Egholm, M., Rothberg, J. M., Keates, S. G., Ovodov, N. D., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605327103 · Cited by 199
Glass, E. M., & Meyer, F. (2011) · Wiley eBooks · doi:10.1002/9781118010518.ch37 · Cited by 196
Formation, Properties, and Germination of Actinomycete Spores
Ensign, J. C. (1978) · Annual Review of Microbiology · doi:10.1146/annurev.mi.32.100178.001153 · Cited by 169
Microbial Taphonomy of Archaeological Bone
Child, A. M. (1995) · Studies in Conservation · doi:10.1179/sic.1995.40.1.19 · Cited by 149
Guy, L., Nystedt, B., Toft, C., Zaremba-Niedźwiedzka, K., Berglund, E., Granberg, F., Näslund, K., Eriksson, A.-S., & Andersson, S. G. E. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003393 · Cited by 105
Self-citationVisualization of ribosomal RNA operon copy number distribution
Rastogi, R., Wu, M., Dasgupta, I., & Fox, G. E. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-208 · Cited by 69
[Hydrolysis of the collagen from calf hide by a crystalline protease of Streptomyces griseus].
Tsyperovich, A. S., & Mishunin, I. F. (1973) · PubMed · Cited by 2
[Hydrolysis of insoluble collagen of bull bones by Streptomyces griseus crystalline protease].
Myshunin, I. F., Tsyperovych, O. S., & Kuznetsova, I. M. (1975) · PubMed · Cited by 1
[Age difference of bone collagen in hydrolysis by Streptomyces griseus protease].
Hf, K., & Te, K. (1977) · PubMed · Cited by 1
Gf, K., & Tf, K. (1977) · PubMed · Cited by 1
Flagged first, then by citations
Cited by
Sorted by citations
Neandertal and Denisovan DNA from Pleistocene sediments
Slon, V., Hopfe, C., Weiß, C. L., Mafessoni, F., de la Rasilla, M., Lalueza-Fox, C., Rosas, A., Soressi, M., Knul, M. V., Miller, R., et al. (2017) · Science · doi:10.1126/science.aam9695 · Cited by 465
Diagenesis of archaeological bone and tooth
Kendall, C., Eriksen, A., Kontopoulos, I., Collins, M. J., & Turner‐Walker, G. (2017) · Palaeogeography Palaeoclimatology Palaeoecology · doi:10.1016/j.palaeo.2017.11.041 · Cited by 366
Warinner, C., Speller, C., Collins, M. J., & Lewis, C. M. (2015) · Journal of Human Evolution · doi:10.1016/j.jhevol.2014.10.016 · Cited by 178
Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens
Weiß, C. L., Schuenemann, V. J., Devos, J., Shirsekar, G. S., Reiter, E., Gould, B. A., Stinchcombe, J. R., Krause, J., & Burbano, H. A. (2016) · Royal Society Open Science · doi:10.1098/rsos.160239 · Cited by 133
Selective enrichment of damaged DNA molecules for ancient genome sequencing
Gansauge, M.-T., & Meyer, M. (2014) · Genome Research · doi:10.1101/gr.174201.114 · Cited by 118
Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures
Cano, R. J., Rivera-Perez, J., Toranzos, G. A., Santiago-Rodríguez, T. M., Narganes-Storde, Y. M., Chanlatte-Baik, L., García-Roldán, E., Bunkley-Williams, L., & Massey, S. E. (2014) · PLoS ONE · doi:10.1371/journal.pone.0106833 · Cited by 77
Saitta, E. T., Liang, R., Lau, M. C., Brown, C. M., Longrich, N. R., Kaye, T. G., Novak, B. J., Salzberg, S. L., Norell, M. A., Abbott, G. D., et al. (2019) · eLife · doi:10.7554/elife.46205 · Cited by 67
Shotgun microbial profiling of fossil remains
Sarkissian, C. S. I. D., Ermini, L., Jónsson, H., Alekseev, A. N., Crubézy, É., Shapiro, B., & Orlando, L. (2014) · Molecular Ecology · doi:10.1111/mec.12690 · Cited by 63
Eriksen, A., Nielsen, T. K., Matthiesen, H., Carøe, C., Hansen, L. H., Gregory, D., Turner‐Walker, G., Collins, M. J., & Gilbert, M. T. P. (2020) · PLoS ONE · doi:10.1371/journal.pone.0240512 · Cited by 48
Metagenomic Analysis Reveals Presence of Treponema denticola in a Tissue Biopsy of the Iceman
Maixner, F., Thomma, A., Cipollini, G., Stefanie Widder, A., Rattei, T., & Zink, A. (2014) · PLoS ONE · doi:10.1371/journal.pone.0099994 · Cited by 36
Thiel, V., Blumenberg, M., Kiel, S., Leefmann, T., Liebenau, K., Lindgren, J., Sjövall, P., Treude, T., & Zilla, T. (2013) · Organic Geochemistry · doi:10.1016/j.orggeochem.2013.12.006 · Cited by 24
Exploring DNA degradation in situ and in museum storage through genomics and metagenomics
Eriksen, A., Rodríguez, J. A., Seersholm, F. V., Hollund, H., Gotfredsen, A. B., Collins, M. J., Grønnow, B., Pedersen, M. W., Gilbert, M. T. P., & Matthiesen, H. (2025) · Communications Biology · doi:10.1038/s42003-025-07616-9 · Cited by 15
Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Weiß, C. L., Gansauge, M.-T., Aximu‐Petri, A., Meyer, M., & Burbano, H. A. (2020) · BMC Genomics · doi:10.1186/s12864-020-06820-7 · Cited by 11
Towards predicting the geographical origin of ancient samples with metagenomic data
Bozzi, D., Neuenschwander, S., Dávalos, D. I. C., da Mota, B. S., Schroeder, H., Moreno-Mayar, J. V., Allentoft, M. E., & Malaspinas, A. (2024) · Scientific Reports · doi:10.1038/s41598-023-40246-x · Cited by 10
Liebenau, K., Kiel, S., Vardeh, D., Treude, T., & Thiel, V. (2015) · Organic Geochemistry · doi:10.1016/j.orggeochem.2015.09.005 · Cited by 9
Eriksen, A., Puetz, L., Rocha, C. D. S., Nielsen, T. K., Hansen, L. H., & Gilbert, M. T. P. (2020) · STAR Science & Technology of Archaeological Research · doi:10.1080/20548923.2020.1738115 · Cited by 6
Inayah, M. N., Lestari, Y., & Meryandini, A. (2022) · HAYATI Journal of Biosciences · doi:10.4308/hjb.29.3.389-398 · Cited by 3
Haidău, C., Bulzu, P., Mirea, I. C., Năstase-Bucur, R., & Moldovan, O. T. (2023) · Geomicrobiology Journal · doi:10.1080/01490451.2023.2227625 · Cited by 1
Milanesi, C., Vignani, R., Scali, M., Faleri, C., Cresti, M., Donne, M. D., Canci, A., Friziero, M., Sebastiani, A., & Sajjadi, S. M. S. (2022) · Archaeological Discovery · doi:10.4236/ad.2023.111001
Additional file 3 of Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Weiß, C. L., Gansauge, M.-T., Aximu‐Petri, A., Meyer, M., & Burbano, H. A. (2020) · Figshare · doi:10.6084/m9.figshare.12569444
Additional file 4 of Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Weiß, C. L., Gansauge, M.-T., Aximu‐Petri, A., Meyer, M., & Burbano, H. A. (2020) · Figshare · doi:10.6084/m9.figshare.12569450
Additional file 5 of Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Weiß, C. L., Gansauge, M.-T., Aximu‐Petri, A., Meyer, M., & Burbano, H. A. (2020) · Figshare · doi:10.6084/m9.figshare.12569453
Additional file 1 of Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Weiß, C. L., Gansauge, M.-T., Aximu‐Petri, A., Meyer, M., & Burbano, H. A. (2020) · Figshare · doi:10.6084/m9.figshare.12569432
Additional file 2 of Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Weiß, C. L., Gansauge, M.-T., Aximu‐Petri, A., Meyer, M., & Burbano, H. A. (2020) · Figshare · doi:10.6084/m9.figshare.12569438
Histological and metagenomic analysis of microbial communities in archaeological human bones
Kaptan, D., Elvers, A. C. F., Knudsen, A. K., Schroeder, H., & Hollund, H. (2026) · PLoS ONE · doi:10.1371/journal.pone.0340244
Metadata
- Authors
- Zaremba-Niedźwiedzka, K., & Andersson, S. G. E.
- Affiliations
- Uppsala University (SE)
- Corresponding author
- Andersson, Siv G. E.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2013-05-03
- Volume
- 8
- Issue
- 5
- Pages
- e62799
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3643900
- OpenAlex
- W2126686241
- Cited by
- 26
- References
- 39
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 1 · 2023: 1 · 2022: 2 · 2020: 8 · 2019: 1 · 2018: 1 · 2017: 2 · 2016: 1 · 2015: 2 · 2014: 4 · 2013: 1
- FWCI
- 1.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Uppsala University Publications (Uppsala University) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Knut och Alice Wallenbergs Stiftelse
- Vetenskapsrådet
- Max-Planck-Institut für Evolutionäre Anthropologie
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- Neanderthal DNA, actinobacteria, Streptomyces, rRNA gene sequences, bacterial contamination, cave deposits, endogenous DNA
- MeSH terms
- Animals, Bacterial Proteins, Bone and Bones, Fossils, Genes, Bacterial, Paleontology, Phylogeny, Collagenases, Genes, rRNA, Actinobacteria, Neanderthals
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
