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Irina Marie Velsko


Department of Archaeogenetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig

phone: +49 (0) 341 3550 806
e-mail: irina_marie_velsko@[>>> Please remove the text! <<<]eva.mpg.de

Research Interests
Research Experience

Research Interests

I am interested in ecology and evolution of the oral microbiome, and how the oral microbiome interacts with the host. I earned my BA in Biology from the University of California, Santa Barbara, College of Creative Studies in 2010, and my PhD from the University of Florida College of Medicine in 2014. I was awarded an NIH F31 pre-doctoral fellowship to support my research to demonstrate a causal association between periodontal disease and atherosclerosis, which sparked my interest in host responses to polymicrobial infections. As a postdoc I have lead projects broadly covering oral microbiology and host responses, both wet lab and computational, working with model organisms, clinical samples, and ancient biomolecules. My projects have applied varied techniques including in vivo infection modeling, in vitro biofilm growth, immune cell stimulation, bacterial genomics, and (ancient) oral microbiome metagenomics, proteomics, and metabolomics.

I am currently leading the ancient dental calculus and oral microbiome research arm of the Microbiome Group headed by Dr. Christina Warinner at the Max Planck Institute of Evolutionary Anthropology (MPI-EVA) Department of Archaeogenetics in Leipzig, Germany. I have developed and implemented standardized protocols for oral microbiome data processing and analysis, leading to publications that have set fundamental groundwork for ancient microbiome research. Here my research has focused on understanding coevolution of the oral microbiome with the host throughout human history, how cultural and social transitions affect the microbiome, and how this in turn has affected oral health. In addition, I have supervised undergraduate, masters, and PhD students at Clemson University and MPI-EVA, participated in open data initiatives within the field of ancient metagenomics, and been an active with public outreach in science.


2010-2014PhD in Biomedical Sciences, University of Florida, Gainesville, FL, USA
2006-2010BA in Biology, University of California, Santa Barbara, Santa Barbara, CA, USA

Research Experience

2021 June-presentPost-doctoral Research Associate
Max Plank Institute for Evolutionary Anthropology, Dept. of Archaeogenetics
2018 Sept-2021 JunePost-doctoral Research Associate 
Max Plank Institute for the Science of Human History, Dept. of Archaeogenetics
2016 Dec-2018 AugPost-doctoral Research Associate 
Clemson University, Department of Biological Sciences
2015-2016 NovPost-doctoral Research Associate 
University of Oxford, School of Archaeology, RLAHA
2015 Jan-2015 NovPost-doctoral Fellow 
University of Florida, Department of Periodontology 
2010 Aug-2014 DecPre-doctoral Fellow 
University of Florida, Departments of Oral Biology and Periodontology



Borry, M., Forsythe, A., Andrades Valtueña, A., Hübner, A., Ibrahim, A., Quagliariello, A., White, A. E., Kocher, A., Vågene, Å. J., Bartholdy, B. P., Spurīte, D., Ponce-Soto, G. Y., Neumann, G., Huang, I.-T., Light, I., Velsko, I. M., Jackson, I., Frangenberg, J., Serrano, J. G., Fumey, J., Özdoğan, K. T., Blevins, K. E., Daly, K. G., Lopopolo, M., Moraitou, M., Michel, M., van Os, M., Bravo-Lopez, M. J., Sarhan, M. S., Dagtas, N. D., Oskolkov, N., Smith, O. S., Lebrasseur, O., Rozwalak, P., Eisenhofer, R., Wasef, S., Ramachandran, S. L., Vanghi, V., Warinner, C. G., & Fellows Yates, J. A. (2023). Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research, 12: 926.
Open Access    DOI    BibTeX   Endnote   

Velsko, I. M., Gallois, S., Stahl, R., Henry, A. G., & Warinner, C. (2023). High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration. Molecular Ecology, 32(14), 3872-3891.
Open Access    DOI    BibTeX   Endnote   

Branco-de-Almeida, L., Velsko, I. M., de Oliveira, I., de Oliveira, R., & Shaddox, L. (2023). Impact of treatment on host responses in young individuals with periodontitis. Journal of Dental Research, 102(5), 473-488.
DOI    BibTeX   Endnote   

Klapper, M., Hübner, A., Ibrahim, A., Wasmuth, I., Borry, M., Haensch, V. G., Zhang, S., Al-Jammal, W. K., Suma, H., Fellows Yates, J. A., Frangenberg, J., Velsko, I. M., Chowdhury, S., Herbst, R., Bratovanov, E. V., Dahse, H.-M., Horch, T., Hertweck, C., González Morales, M. R., Straus, L. G., Vilotijevic, I., Warinner, C., & Stallforth, P. (2023). Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science, 380(6645), 619-624.
DOI    BibTeX   Endnote   

Wegner, C.-E., Stahl, R., Velsko, I. M., Hübner, A., Fagernäs, Z., Warinner, C., Lehmann, R., Ritschel, T., Totsche, K. U., & Küsel, K. (2023). A glimpse of the paleome in endolithic microbial communities. Microbiome, 11(1): 210.
Open Access    DOI    BibTeX   Endnote   


Dimopoulos, E. A., Carmagnini, A., Velsko, I. M., Warinner, C., Larson, G., Frantz, L. A. F., & Irving-Pease, E. K. (2022). HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data. PLoS Computational Biology, 18(9): e1010493.
Open Access    DOI    BibTeX   Endnote   

Velsko, I. M., Semerau, L., Inskip, S. A., García-Collado, M. I., Ziesemer, K., Ruber, M. S., de Enrich, L. B. L., García, J. M. M., Valle, D. G., Ruiz, A. C. P., Salazar-García, D. C., Hoogland, M. L. P., & Warinner, C. (2022). Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology. PNAS Nexus, 1(4).
Open Access    DOI    BibTeX   Endnote   

Fagernäs, Z., Salazar-García, D. C., Haber Uriarte, M., Avilés Fernández, A., Henry, A. G., Lomba Maurandi, J., Ozga, A. T., Velsko, I. M., & Warinner, C. G. (2022). Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation. FEMS Microbes, 3: xtac006.
Open Access    DOI    BibTeX   Endnote   


Warinner, C. G., Velsko, I. M., & Fellows Yates, J. A. (2021). Reply to Ben-Dor et al.: Oral bacteria of Neanderthals and modern humans exhibit evidence of starch adaptation. Proceedings of the National Academy of Sciences, 118: e2112526118.
DOI    BibTeX   Endnote   

Fellows Yates, J. A., Andrades Valtueña, A., Vågene, A. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-López, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., & Warinner, C. G. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 8: 31.
Open Access    DOI    BibTeX   Endnote   

Fellows Yates, J. A., Velsko, I. M., Aron, F., Posth, C., Hofman, C. A., Austin, R. M., Parker, C. E., Mann, A. E., Nägele, K., Arthur, K. W., Arthur, J. W., Bauer, C. C., Crevecoeur, I., Cupillard, C., Curtis, M. C., Dalén, L., Díaz-Zorita Bonilla, M., Díez Fernández-Lomana, J. C., Drucker, D. G., Escribano Escrivá, E., Francken, M., Gibbon, V. E., González Morales, M. R., Grande Mateu, A., Harvati, K., Henry, A. G., Humphrey, L., Menéndez, M., Mihailović, D., Peresani, M., Rodríguez Moroder, S., Roksandic, M., Rougier, H., Sázelová, S., Stock, J. T., Straus, L. G., Svoboda, J., Teßmann, B., Walker, M. J., Power, R. C., Lewis, C. M., Sankaranarayanan, K., Guschanski, K., Wrangham, R. W., Dewhirst, F. E., Salazar-García, D. C., Krause, J., Herbig, A., & Warinner, C. G. (2021). The evolution and changing ecology of the African hominid oral microbiome. Proceedings of the National Academy of Sciences, 118(20): e2021655118.
Open Access    DOI    BibTeX   Endnote   

Sarkissian, C. D., Velsko, I. M., Fotakis, A. K., Vågene, Å. J., Hübner, A., & Fellows Yates, J. A. (2021). Ancient metagenomic studies: Considerations for the wider scientific community. mSystems, 6(6), e01315-e01321.
Open Access    DOI    BibTeX   Endnote   


Velsko, I. M., Harrison, P., Chalmers, N., Barb, J., Huang, H., Aukhil, I., & Shaddox, L. (2020). Grade C molar-incisor pattern periodontitis subgingival microbial profile before and after treatment. Journal of oral microbiology, 12(1): 1814674, pp. 1-13.
DOI    BibTeX   Endnote   

Fagernäs, Z., García-Collado, M. I., Hendy, J., Hofman, C. A., Speller, C., Velsko, I. M., & Warinner, C. (2020). A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus. Journal of Archaeological Science, 118: 105135.
Open Access    DOI    BibTeX   Endnote   


Velsko, I. M., Fellows Yates, J. A., Aron, F., Hagan, R., Frantz, L. A. F., Loe, L., Martinez, J. B. R., Chaves, E., Gosden, C., Larson, G., & Warinner, C. G. (2019). Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage. Microbiome, 7(1): 102.
Open Access    DOI    BibTeX   Endnote   

Richards, V. P., Velsko, I. M., Alam, T., Zadoks, R. N., Manning, S. D., Pavinski Bitar, P. D., Hasler, H. B., Crestani, C., Springer, G., Probert, B., Town, C. D., & Stanhope, M. J. (2019). Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae. Molecular Biology and Evolution, 36(11): msz169, pp. 2572-2590.
Open Access    DOI    BibTeX   Endnote   

Kaspar, J. R., Godwin, M. J., Velsko, I. M., Richards, V. P., & Burne, R. A. (2019). Spontaneously arising streptococcus mutans variants with reduced susceptibility to chlorhexidine display genetic defects and diminished fitness. Antimicrobial Agents and Chemotherapy, 63(7): e00161-19.
DOI    BibTeX   Endnote   

Velsko, I. M., M. S. Perez, V. P. Richards. 2019. Resolving phylogenetic relationships for Streptococcus mitis and Streptococcus oralis through core and pan genome analyses. Genome Biology and Evolution, 11(4): 1077-1087. doi.org/10.1093/gbe/evz049


Velsko, I. M., B. Chakraborty, M. M. Nascimento, R. A. Burne, V. P. Richards. 2018. Species Designations Belie Phenotypic and Genotypic Heterogeneity in Oral Streptococci. mSystems, 3:e00158-18. doi.org/10.1128/ mSystems.00158-18. Preprint bioRxiv: doi.org/10.1101/375139

Velsko, I. M., L. A. F. Frantz, A. Herbig, G. Larson, C. Warinner. 2018. Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research. mySystems, 3(4):e00080-18. doi.org/10.1128/ mSystems.00080-18. *Editor’s Pick. Preprint doi.org/10.1101/260042.

Hendy, J., C. Warinner, A. Bouwman, M. Collins, S. Fiddyment, R. Fischer, R. Hagan, C. Hofman, M. Holst, E. Chaves, L. Klaus, G. Larson, M. Mackie, K. McGrath, A. Mundorff, A. Radini, H. Rao, C. Trachsel, I. Velsko, C. Speller. 2018. Proteomic Evidence of Dietary Sources in Ancient Dental Calculus. Proceedings of the Royal Society B, 285:20180977. dx.doi.org/10.1098/rspb.2018.0977

Velsko, I. M., and L. M. Shaddox. 2018. Consistent and reproducible long-term in vitro growth of health and disease-associated oral subgingival biofilms. BMC Microbiology, 18(70).  https://doi.org/10.1186/s12866-018-1212-x. Preprint bioRxiv: doi.org/10.1101/324475


Velsko, I. M., K. A. Overmyer, C. Speller, M. Collins, L. Loe, L. A. F. Frantz, J. B. Rodriguez Martinez, E. Chaves, L. Klaus, K. Sankaranarayanan, Cecil M. Lewis Jr., J. J. Coon, G. Larson, C. Warinner. 2017. The dental calculus metabolome in modern and historic samples. Metabolomics, 13(134). doi: 10.1007/s11306-017-1270-3. Preprint bioRxiv doi: doi.org/10.1101/136176

Velsko, I. M., C. Warinner. Bioarchaeology of the human microbiome. Bioarchaeology International. 2017, 1(1-2):86-99, doi: 10.5744/bi.2017.1004.   

Oral Presentations since 2018

I.  M. Velsko, A. Hübner, C. Warinner. Extensive diversity of unnamed Anaerolineaceae taxa in ancient dental calculus revealed through de novo genome assembly. 10th International Symposium on Biomolecular Archaeology, Tartu, Estonia, September 2023.  Talk MET-004. 

I. M. Velsko. Considerations for de novo ancient metagenome assembly. SPAAM5, Tartu, Estonia, September 2023. 

I. M. Velsko, C. Warinner. Distinctive Streptococcus clades characterize oral niches regardless of industrialization status and oral pathology. Applied Hologenomics Conference, Bilbao, Spain, September 2022.

I. M. Velsko. Which taxonomic classifier should I use?. Standards, Precautions, & Advancements in Ancient Metagenomics 3 (SPAAM3). Virtual Conference, September 2021.

I. M. Velsko, D. Kühnert, A. Herbig, The OMEC Consortium, C. Warinner. Tracing human evolution through oral microbiome gene content. 9th International Symposium on Biomolecular Archaeology (Virtual conference), 2021. 

I. M. Velsko. Expanding our understanding of dental plaque biofilms using unusual sources. University of Kentucky College of Dentistry. Invited talk. 28 April 2020. 

Velsko, I. M., J. A. Fellows-Yates, F. Aron, R. W. Hagen, L. A. F. Frantz, L. Loe, J. Bautista Rodriguez Martinez, E. Chaves, C. Gosden, G. Larson, C. Warinner. Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage. 5th Annual International Society for Evolution, Medicine, and Public Health Meeting, Zürich, Switzerland 2019. Session 11A.

I. M. Velsko, K. A. Overmyer, C. Speller, M. Collins, L. Loe, L. A. F. Frantz, J. B. Rodriguez Martinez, E. Chaves, L. Klaus, K. Sankaranarayanan, Cecil M. Lewis Jr., J. J. Coon, G. Larson, C. Warinner. The dental calculus metabolome in modern and historic samples. 8th International Symposium on Biomolecular Archaeology, Jena, DE 2018. Abstract # O-MIB-01.

Poster Presentations since 2018

I. M. Velsko, A. Hübner, C. Warinner. Extensive genomic diversity of uncatalogued taxa in ancient and modern oral samples revealed through de novo genome assembly. EMBL Human Microbiome, Heidelberg, Germany, September 2023. 

I. M. Velsko*, C. Warinner. Genetic drivers of dental plaque biofilm niche specialization in oral Streptococcus species. Cold Spring Harbor Laboratory Microbiome. Cold Spring Harbor, NY, USA 2022. Poster #160.

I. M. Velsko, Lena Semerau, Menno Hoogland, Sarah Inskip, Christina Warinner. Hidden impacts of industrialization on the dental calculus microbiome species composition. Ancient Biomolecules of Plants, Animals, and Microbes (Virtual Conference), Wellcome Genome Campus, UK 2021. 

I.M. Velsko, J. Fellows Yates, OMEC Consortium, C. Warinner. Ancient human microbiomes for the study of microbe-microbe and host-microbiome interactions. 5th International Symposium on Systems Biology of Microbial Infection, Jena, Germany 2019.