title: No ancient DNA damage in Actinobacteria from the Neanderthal bone.
abstract: 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.
  
  
  RESULTS
  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
  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.
authors: Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden.
authors: Katarzyna
authors: K
authors: Zaremba-Niedźwiedzka
authors: Siv G E
authors: SG
authors: Andersson
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics*; D000818:Animals; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics*; D001842:Bone and Bones / Q000382:microbiology*; D017364:Collagenases / Q000145:classification / Q000235:genetics*; D005580:Fossils; D005798:Genes, Bacterial; D020459:Genes, rRNA; D059125:Neanderthals / Q000235:genetics / Q000382:microbiology*; D010163:Paleontology; D010802:Phylogeny
chemical_list: D001426:Bacterial Proteins; D017364:Collagenases
references: Bioinformatics. 2006 Jul 1;22(13):1658-9
references: 16731699
references: Nature. 2008 Nov 20;456(7220):387-90
references: 19020620
references: BMC Bioinformatics. 2008 Sep 19;9:386
references: 18803844
references: Nat Commun. 2012 Feb 28;3:698
references: 22426219
references: Annu Rev Microbiol. 1978;32:185-219
references: 360964
references: Curr Biol. 2004 Jan 6;14(1):R9-10
references: 14711425
references: Annu Rev Microbiol. 1983;37:189-216
references: 6357051
references: Science. 2010 May 7;328(5979):710-722
references: 20448178
references: Bioinformatics. 2006 Nov 1;22(21):2688-90
references: 16928733
references: Proc Natl Acad Sci U S A. 2006 Sep 12;103(37):13578-84
references: 16938852
references: Brief Bioinform. 2008 Jul;9(4):286-98
references: 18372315
references: Nucleic Acids Res. 2004 Feb 25;32(4):1363-71
references: 14985472
references: Bioinformatics. 2008 Jul 1;24(13):1530-1
references: 18467344
references: PLoS One. 2010 Jun 25;5(6):e11147
references: 20593022
references: Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18295-300
references: 21987801
references: Nat Biotechnol. 2003 May;21(5):526-31
references: 12692562
references: PLoS One. 2012;7(3):e34131
references: 22479540
references: Nucleic Acids Res. 2007;35(21):7188-96
references: 17947321
references: BMC Microbiol. 2009 Sep 25;9:208
references: 19781086
references: Ukr Biokhim Zh. 1977 Sep-Oct;49(5):76-80
references: 411202
references: Science. 2006 Jan 20;311(5759):392-4
references: 16368896
references: PLoS Genet. 2013 Mar;9(3):e1003393
references: 23555299
references: Nature. 2002 May 9;417(6885):141-7
references: 12000953
references: Ukr Biokhim Zh. 1975 Mar-Apr;47(2):226-32
references: 1884
references: Ukr Biokhim Zh. 1977 May-Jun;49(3):80-4
references: 407689
references: Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):E746-52
references: 21876176
references: Nature. 2012 Mar 18;484(7392):101-4
references: 22425999
references: Nature. 2011 Oct 12;478(7370):506-10
references: 21993626
references: Proc Natl Acad Sci U S A. 2007 Sep 4;104(36):14401-5
references: 17728401
references: BMC Bioinformatics. 2010 Mar 08;11:119
references: 20211023
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D227-33
references: 19892822
references: Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14616-21
references: 17715061
references: Nature. 2006 Nov 16;444(7117):330-6
references: 17108958
references: Ukr Biokhim Zh. 1973 Mar-Apr;45(2):151-5
references: 4196875