CEE Faculty Profile

Kostas T. Konstantinidis

Carlton S. Wilder Junior Faculty Professorship & Associate Professor

Articles

  1. C. Luo , L. M. Rodriguez-R*, and Konstantinos T. Konstantinidis. A user's guide to quantitative and comparative analysis of metagenomic datasets. Methods in Enzymology (2013). 531:525-47.
  2. M. Tandukar, S. Oh*, U. Tezel, K. T. Konstantinidis, and S. G. Pavlostathis. Long-term Exposure to Benzalkoniun Chloride Disinfectants Results in Change of Microbial Community Structure and Increased Antimicrobial Resistance. Environmental Science & Technology (2013). Sep 3;47(17):9730-8.
  3. N. DeLeon-Rodriguez*, T. Lathem, L. M. Rodriguez-R*, J. M. Barazesh*, B. E. Anderson, A. J. Beyersdorf, L. D. Ziemba, M. Bergin, A. Nenes, and K. T. Konstantinidis. Reply to Smith and Griffin: Methods, air flows, and conclusions are robust in the DeLeon-Rodriguez et al. study. PNAS (2013). June 4; 110(23):E2085.
  4. S. A. Solonenko, J. C. Ignacio-Espinoza, A. Alberti, C. Cruaud, S. Hallam, K. Konstantinidis, G. Tyson, P. Wincker, and M. B. Sullivan. Sequencing platform and library preparation choices impact viral metagenomes. BMC Genomics (2013). May 10;14:320.
  5. S. Oh*, M. Tandukar, S. G. Pavlostathis, P. S. G. Chain, and K. T. Konstantinidis, Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics1. Environmental Microbiology (2013). Oct;15(10):2850-64.
  6. M. R. Weigand*, H. Ryu, L. Bozcek, K. T. Konstantinidis, J. W. Santo Domingo. Draft genome sequence of Catellicoccus marimammalium, a novel species commonly found in gull feces. Genome Announcements (2013). Jan;1(1).
  7. N. DeLeon-Rodriguez*, T. Lathem, L. M. Rodriguez-R*, J. M. Barazesh*, B. E. Anderson, A. J. Beyersdorf, L. D. Ziemba, M. Bergin, A. Nenes, and K. T. Konstantinidis. The microbiome of the upper troposphere: species composition and prevalence, effects of tropical storms, and atmospheric implications. PNAS (2013). 12; 110(7):2575-2580. (This paper received worldwide attention and was highlighted by NPR, National Geographic, Amazing Planet, U.S. News & World Report, among numerous other media)
  8. R. A Sanford, D. D. Wagner, Q. Wu , J. C. Chee-Sanford, S. H. Thomas, C. Cruz-García, G. Rodríguez, A. Massol-Deyá, K. K. Krishnani, K. Ritalahti, K. T. Konstantinidis, and F. E. Loeffler. Unexpected Non-Denitrifier Nitrous Oxide Reductase Gene Diversity and Abundance in Soils. PNAS. (2012). 109(48):19709-14.
  9. S. Oh*, S. Buddenborg, D. R. Yoder-Himes, J. Tiedje, and K. T. Konstantinidis. Genomic Diversity of Escherichia Isolates from Diverse Habitats. PLoS ONE (2012). 7(10):e47005.
  10. X. Lin, S. Green, M. M. Tfaily, O. Prakash, K. T. Konstantinidis, J. E. Corbett, J. P. Chanton, W. T. Cooper, and J. E. Kostka. Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the Glacial Lake Agassiz Peatland. Applied and Environmental Microbiology (2012). 78(19):7023-31.
  11. D. D. Wagner, L. A. Hug, J. K. Hatt, M. A. Spitzmiller, E. Padilla-Crespo, K. M. Ritalahti, E. A. Edwards, K. T. Konstantinidis, and F. E. Löffler. Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae. BMC Genomics (2012). 13(1):200.
  12. A. Caro-Quintero., K. M. Ritalahti, K. D. Cusick, F. E. Loffler, and K. T. Konstantinidis. The chimeric genome of Sphaerochaeta: nonspiral spirochetes that break with the prevalent dogma in spirochete biology. mBio (2012). 3(3): e00025-12.
  13. F. E. Löffler, J. Yan, K. M. Ritalahti, L. Adrian, E. A. Edwards, K. T. Konstantinidis, J. A. Müller, H. Fullerton, S. H. Zinder, and A. M. Spormann AM. Dehalococcoides mccartyi gen. nov., sp. nov., obligate organohalide-respiring anaerobic bacteria, relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidetes classis nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol (2012). In press.
  14. A. Caro-Quintero*, J. Deng, J. Auchtung, I. Brettar, M. Höfle, James M. Tiedje, and K. T. Konstantinidis. Genome sequencing of five Shewanella baltica strains recovered from the oxic-anoxic interface of the Baltic Sea. Journal of Bacteriology (2012). 194(5):1236.
  15. C. Luo*, D. Tsementzi*, N. Kyrpides, T. Read, and K. T. Konstantinidis. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE (2012). 7(2): e30087.
  16. A. Caro-Quintero* and K. T. Konstantinidis. Bacterial species may exist, metagenomics reveal. Environmental Microbiology (2012). 14(2):347-55. (Rated “Must read” by the Faculty of 1000).
  17. C. Luo*, D. Tsementzi*, N. Kyrpides, and K. T. Konstantinidis. Individual genome assembly from complex community short-read metagenomic datasets. The ISME Journal (2012). 6(4):898-901.
  18. S. Oh*, A. Caro-Quintero*, D. Tsementzi*, N. Deleon-Rodriguez*, C. Luo, R. Poretsky, and K. T. Konstantinidis. Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Applied and Environmental Microbiology (2011). 77(17):6000- 11.
  19. C. Luo*, S. Walk, D. M. Gordon, M. Feldgarden, J. M. Tiedje, and K. T. Konstantinidis. Genome sequencing of environmental E. coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci USA, (2011). 108(17):7200-5.
  20. C. Luo*, and K. T. Konstantinidis. Phosphorus-related gene content is similar in Prochlorococcus populations from the North Pacific and North Atlantic Oceans. Proc Natl Acad Sci USA (2011). 108(16):E62-3.
  21. A. Caro-Quintero., J. Deng, J. Auchtung, I. Brettar, M. Hofle, J. Klappenbach, and K. T. Konstantinidis. Unprecedented levels of horizontal gene transfer among spatially cooccurring Shewanella bacteria from the Baltic Sea. The ISME Journal (2011). 5(1):131- 40.
  22. S. Oh*, D. R. Yoder-Himes, J. Tiedje, and K. T. Konstantinidis. Evaluating the performance of oligonucleotide microarrays for strains of increasing genetic divergence to the reference strain. Applied and Environmental Microbiology (2010). 76(9):2980-8.
  23. D. R. Yoder-Himes, K. T. Konstantinidis, J. M. Tiedje. Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. PLoS ONE (2010). 5(1):e8724.
  24. K. T. Konstantinidis, M. H. Serres, M. F. Romine, J. L. M. Rodrigues, J. Auchtung, L.-A. McCue, M. S. Lipton, A. Obraztsova, C. S. Giometti, K. H. Nealson, J. K. Fredrickson, and J. M. Tiedje. Comparative systems biology across an evolutionary gradient within the Shewanella genus. PNAS (2009). 106(37):15909-14.
  25. A. Caro-Quintero*, G. P. Rodriguez-Castaño, and K. T. Konstantinidis. Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species. Journal of Bacteriology (2009). 191(18):5824-31.
  26. K. T. Konstantinidis, J. Braff, D. M. Karl, and E. F. Delong. Comparative metagenomic analysis of a microbial community from 4000 m at Station ALOHA in the North Pacific Subtropical Gyre. Applied and Environmental Microbiology (2009). 75(16):5345-55.
  27. K. T. Konstantinidis, and E. F. DeLong. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. The ISME Journal (2008). 2(10):1052-65.
  28. V. D. Pham, K. T. Konstantindis, T. Palden, and E. F. DeLong. Vertical Phyloecology of North Pacific Bacterioplankton. Environmental Microbiology (2008). 10(9):2313 – 2330.
  29. V. I. Rich, K. Konstantinidis, and E. F. Delong. Design and testing of 'genome-proxy' microarrays to profile marine microbial communities. Environmental Microbiology (2008). 10(2):506-21.
  30. W. Song, F. S. Juhn, D. Q. Naiman, K. T. Konstantinidis, T. S. Gardner, and M. J. Ward. Predicting sigma (28) promoters in eleven Shewanella genomes. FEMS Microbiol Letters (2008), 283(2):223-30.
  31. K. T. Konstantinidis, and J. M. Tiedje. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Current Opinion in Microbiology (2007). 10(5):504-9.
  32. J. Goris, K. T. Konstantinidis, T. Coenye, P. Vandamme, and J. M. Tiedje. DNA-DNA hybridization values and their relation to whole genome sequence. International Journal of Systematic and Evolutionary Microbiology (2007). 57(Pt 1):81-91.
  33. S. J. Hallam, K. T. Konstantinidis, N. Putnam, C. Schleper, Y. Watanabe, J. Sugahara, C. Preston, J. dela Torre, P. M. Richardson, and E. F. DeLong. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. PNAS (2006). 103(48):18296-301.
  34. K. T. Konstantinidis, A. Ramette, and J. M. Tiedje. The bacterial species definition in the genomic era. Philos Trans R Soc Lond B Biol Sci. (2006). 361(1475):1929-40.
  35. P. S. G. Chain, V. J. Denef, K. T. Konstantinidis…and 25 more authors. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73 M bp genome shaped for versatility. PNAS (2006). 103(42):15280-7.
  36. K. T. Konstantinidis, A. Ramette, and J. M. Tiedje. Toward a more robust assessment of intra-species diversity using fewer genetic markers. Applied and Environmental Microbiology (2006). 72(11):7286-93.
  37. K. T. Konstantinidis, and J. M. Tiedje. Towards a genome-based taxonomy for Prokaryotes. Journal of Bacteriology (2005). 187(18):6258-64.
  38. K. T. Konstantinidis, and J. M. Tiedje. Genomic insights that advance the species concept for prokaryotes. PNAS (2005). 102(7):2567-72.
  39. E. Kolker E, A. F. Picone…K. T. Konstantinidis…and 28 more authors. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. PNAS (2005). 102(6):2099-104.
  40. K. T. Konstantinidis, and J. M. Tiedje. Trends between gene content and genome size in prokaryotic species with larger genomes. PNAS (2004). 101(9):3160-5.
  41. K. T. Konstantinidis, N. Isaacs, S. Simpson, D. Long, and T. L. Marsh. 2003. Microbial diversity and resistance to copper in metal contaminated lake sediment. Microbial Ecology (2003). 45(2): 191-202.

Books

  1. K. Konstantinidis and E. Stackebrandt. Defining taxonomic ranks. In The Prokaryotes. M.Dworkin et al (Eds.). New York: Springer-Verlag. To appear in 2013.
  2. 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.
  3. 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.
  4. 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.
  5. 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).

Proceedings

  1. 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.
  2. Konstantinidis K. T., and J. M. Tiedje. 2004. Genomic insights to advance the bacterial species concept. Genomes 2004, April 14-17, Hinxton Cambridgeshire, UK.
  3. 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.
  4. 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.