Faculty Profile


  • PhD, Crop and Soil Sciences, Michigan State University, USA, 2004.
  • BS, Agricultural Sciences, Aristotle University of Thessaloniki, Greece, 1999.

Dr. Kostas Konstantinidis joined the Georgia Institute of Technology as an Assistant Professor in November 2007. He received his BS in Agriculture Sciences from the Aristotle University of Thessaloniki (Greece) in 1999. He continued his studies at the Center for Microbial Ecology at Michigan State University (East Lansing, MI) under the supervision of Prof. James M. Tiedje, where he obtained a PhD in 2004. His PhD studies were fully supported by the Bouyoukos Fellowship program and were devoted in advancing our understanding of the ecology and physiology of soil bacteria through the comparative analysis of their whole-genome sequences. This research resulted in a NSF-funded project to advance the species definition for prokaryotes, which also fostered a short post-doc position at the Center for Microbial Ecology. He then moved to MIT and the laboratory of Prof. Edward DeLong to get trained on innovating metagenomic techniques. His work at MIT provided important new insights into the complexity and function of oceanic microbial communities as well as how life is adapting in the deep and cold Oceans. His research interests are at the interface of genomics and computational biology in the context of microbial ecology with the overarching goal to broaden understanding of the genetic and metabolic potential of the microbial world. Advancing our knowledge on these issues is essential for a better understanding of the microbes that power, by and large, the biogeochemical cycles that sustain life on Earth and cause or control important diseases in humans and animals. He is a member of the American Society for Microbiology (ASM), the International Society for Microbial Ecology (ISME) and the Association of Environmental Engineering and Science Professors (AEESP).


  • Environmental microbiology and genomics
  • Computational approaches for studying the ecology and evolution of microorganisms
  • Development of genomic and proteomic techniques to investigate and quantify in-situ important microbial-mediated processes
  • Population and single-cell genomics
  • Assessing the extent and value of biodiversity within natural assemblages of Bacteria and Archaea
  • Biotechnological applications of microbial functional diversity
  • Environmental relevance of microbial diseases


  • 2016: CEE Interdisciplinary Research Award.
  • 2014: CEE Research Innovation Award.
  • 2014: Kavli Frontiers of Science Fellow.
  • 2013: CEE Excellence in Research Program Development Award.
  • 2012: Appointed to the Carlton S. Wilder Junior Chair in Environmental Engineering.
  • 2012: Recipient of the Sigma Xi Young Faculty Research Award (Sigma Xi’s Georgia Tech Branch).
  • 2011: Recipient of the CEE Faculty Research Excellence Award (Georgia Tech)
  • 2010: Recipient of the International Skerman Award for Microbial Taxonomy (www.wfcc.info).
  • 2010: Nominated for the Packard Fellowships for Science and Engineering by the Georgia Institute of Technology (www.packard.org).
  • 2007: Distinguished Scientist Abroad Award. Hellenic National Defense General Staff, Athens, Greece.
  • 2000-2003: Recipient of the Bouyoukos Fellowship.


  • S. Kleindienst, S. A. Higgins, D. Tsementzi*, G. Chen, K. T. Konstantinidis, E. E. Mack, and F.E. Löffler. 'Candidatus Dichloromethanomonas elyunquensis' gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. Systematic and Applied Microbiology. In press.
  • L. H. Orellana*, L. M. Rodriguez-R*, and K. T. Konstantinidis. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets. Nucleic Acids Research (2016). In press.
  • X. Zhang, E. R. Johnston*, L. Li, K. T. Konstantinidis, and X. Han. Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe. ISME J (2016). In press.
  • A. D. Huang, C. Luo*, A. Pena-Gonzalez*, M. R. Weigand*, C. Tarr, and K. T. Konstantinidis. Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods. Applied & Environmental Microbiology (2016). In press.
  • E. Ertekin, K. T. Konstantinidis, and U. Tezel. A Rieske-type Oxygenase of Pseudomonas sp. BIOMIG1 converts Benzalkonium Chlorides to Benzyldimethyl Amine. Environ Science & Technol (2016). In press.
  • K. Konstantinidis and E. Stackebrandt. Defining taxonomic ranks. In The Prokaryotes. M.Dworkin et al (Eds.). New York: Springer-Verlag. pg. 229-254. 2013.
  • K. T. Konstantinidis. Metagenomic insights into bacterial species. In Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats. Frans J. de Bruijn editor. John Wiley & Sons, Inc. Hoboken, New Jersey, USA. 2011.
  • J. Cole, K. T. Konstantinidis, R. J. Farris, and J. M. Tiedje. Microbial diversity and phylogeny: extending from rRNAs to genomes. In Environmental Molecular Biology. WT. Liu and J. Jansson (eds). Horizon Scientific Press. Norwich, UK. 2009.
  • K. T. Konstantinidis, and J. M. Tiedje. Microbial diversity and genomics. In Microbial Functional Genomics. J. Zhou, D. K. Thompson, Y. Xu, and J. M. Tiedje (eds.) John Wiley & Sons. Hoboken, New Jersey, 2004, pg. 21-46.
  • K. Konstantinidis. Pesticide residues in cucumber crops in Northern Greece (in Greek). In Integrated management of disease and pest of plants. Aristotle University of Thessaloniki, 2000. (Book series on sustainable agriculture sponsored by the European Union).
  • Konstantinidis K. T., and J. M. Tiedje. 2004. Modeling DNA microarray performance for genetic studies. 104th American Society for Microbiology, General Meeting, May 23-27, 2004, New Orleans, LA, USA.
  • Konstantinidis K. T., and J. M. Tiedje. 2004. Genomic insights to advance the bacterial species concept. Genomes 2004, April 14-17, Hinxton Cambridgeshire, UK.
  • Konstantinidis K. T., and J. M. Tiedje. 2004. Trends between gene content and genome size in prokaryotic species. 102nd American Society for Microbiology, General Meeting, May 18-22, 2003, Washington, DC, USA.
  • Konstantinidis K. T., N. Isaacs, S. Simpson, D. Long, and T. L. Marsh. 2001. Characterization of copper-resistant bacteria from a contaminated superfund site. 101st American Society for Microbiology, General Meeting, May 20-24, 2001, Orlando, Fl, USA.
  • N. DeLeon*, A. Negron, N. Matthew, A. Bougiatoioti, S.M. Waters*, A. Nenes, and K. T. Konstantinidis. Bacterial phenotypes: Implications for cloud condensation. Astrobiology Science Conference. June 15-19, 2015. Chicago, IL, USA.
  • A. Pena-Gonzalez*, J. K. Hatt, M.R. Weigand*, G. Trueba, W. Cevallos, J. Eisenberg, K. T. Konstantinidis and K. Levy. Effect of diarrheal disease and biogeographic factors in shaping the gut microbiota composition of individuals from Northern Coastal Ecuador. In the 115th American Society for Microbiology, General Meeting. May 30-June 2, 2015. New Orleans, Louisiana, USA.
  • M. R. Weigand*, A. Pena-Gonzalez*, T. B. Shirey, R. G. Broeker, M. K. Ishaq, K. T. Konstantinidis and B. H. Raphael. Genome-based discrimination between Group I Clostridium botulinum and Clostridium sporogenes strains: implications for bacterial taxonomy. In the 115th American Society for Microbiology, General Meeting. May 30-June 2, 2015. New Orleans, Louisiana, USA.
  • A. Huang, M. R. Weigand*, A. Pena-Gonzalez*, K. T. Konstantinidis and C. L. Tarr. Metagenomic Pathogen Detection and Gut microbiome Response to Foodborne Illness. In the International Conference on Emerging Infectious Diseases, ICEID. August 24-26, 2015. Atlanta, GA, USA
  • A. Huang, M. R. Weigand*, A. Pena-Gonzalez*, K. T. Konstantinidis and C. L. Tarr. Metagenomic Pathogen Detection and Gut microbiome Response to Acute Foodborne Salmonella infection. In the Sequencing, Finishing and Analysis in the Future Meeting, SFAF. May 27-29, 2015. Santa Fe, NM, USA.