Publications

See citation statistics for Dr. Konstantinidis on Google Scholar. And on Web of Science.

Papers

The following list is in reverse chronological order. (updated December 2021)

  1. Toward shotgun metagenomic approaches for microbial source tracking sewage spills based on laboratory mesocosms. B. G. Lindner, B. Suttner, K. J. Zhu, R. E. Conrad, L. M. Rodriguez-R, J. K. Hatt, J. Brown, and K. T. Konstantinidis. Water Research. In press. 2021.
  2. Microbial Diversity in a Military Impacted Lagoon (Vieques, Puerto Rico) and description of “Candidatus Biekebacterium resiliens” gen. nov., sp. nov. comprising a new bacterial family. L. Dávila-Santiago, N. DeLeon-Rodriguez, K. LaSanta-Pagána, J. K. Hatt, Z. Kurtb, A. Massol-Deyá, and K. T. Konstantinidis. Syst Appl Microbiol. 45(1):126288. 2021.
  3. Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations. R. E. Conrad, T. Viver, J. F. Gago, J. K. Hatt, R. Rosselló-Móra, and K. T. Konstantinidis. ISME J. In press. 2021.
  4. Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling. S. Karthikeyan, L. H. Orellana, E. R. Johnston, J. K. Hatt, F. E. Löffler, H. L. Ayala-Del-Río, G. González, and K. T. Konstantinidis. Appl Environ Microbiol. 87(12):e0054621. 2021.
  5. Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. Z. Wang, D. Tsementzi, T. C. Williams, D. L. Juarez, S. K. Blinebry, N. S. Garcia, B. K. Sienkiewicz, K. T. Konstantinidis, Z. I. Johnson, and D. E. Hunt DE. ISME J. 15(1):19-28. 2021.
  6. A genomic catalog of Earth’s microbiomes. S. Nayfach, S. Roux, R. Seshadri, D. Udwary, N. Varghese, F. Schulz, D. Wu, D. Paez-Espino, I. M. Chen, M. Huntemann, K. Palaniappan, J. Ladau, S. Mukherjee, T. B. K. Reddy, T. Nielsen, E. Kirton, J. P. Faria, J. N. Edirisinghe, C. S. Henry, S. P. Jungbluth, D. Chivian, P. Dehal, E. M. Wood-Charlson, A. P. Arkin, S. G. Tringe, A. Visel, K. T. Konstantinidis; IMG/M Data Consortium, T. Woyke, N. J. Mouncey, N. N. Ivanova, N. C. Kyrpides, and E. A. Eloe-Fadrosh. Nat Biotechnol. 39(4):499-509. 2021.
  7. Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions. J. Shan, R. A. Sanford, J. Chee-Sanford, S. K. Ooi, F. E. Löffler, K. T. Konstantinidis, and W. H. Yang WH. Glob Chang Biol. 27(12):2669-2683. 2021.
  8. A novel, divergent alkane monooxygenase (alkB) clade involved in crude oil biodegradation. S. Karthikeyan, J. K. Hatt, M. Kim, J. C. Spain, M. Huettel, J. E. Kostka, and K. T. Konstantinidis. Environ Microbiol Rep. 13(6):830-840. 2021.
  9. Impact of an Urban Sanitation Intervention on Enteric Pathogen Detection in Soils. D. Capone, D. Berendes, O. Cumming, D. Holcomb, J. Knee, K. T. Konstantinidis, K. Levy, R. Nalá, B. B. Risk, J. Stewart, and J. Brown. Environ Sci Technol. 55(14):9989-10000. 2021.
  10. Solar salterns as model systems to study the units of bacterial diversity that matter for ecosystem functioning. K. T. Konstantinidis, T. Viver, R. E. Conrad, S. N. Venter, and R. Rossello-Mora R. Curr Opin Biotechnol. 73:151-157. 2021.
  11. Gut microbiome, enteric infections and child growth across a rural-urban gradient: protocol for the ECoMiD prospective cohort study. G. O. Lee, J. N. S. Eisenberg, J. Uruchima, G. Vasco, S. M. Smith, A. Van Engen, C. Victor, E. Reynolds, R. MacKay, K. J. Jesser, N. Castro, M. Calvopiña, K. T. Konstantinidis, W. Cevallos, G. Trueba, and K. Levy. BMJ Open. 11(10):e046241. 2021.
  12. Changes in the Vaginal Microbiome and Associated Toxicities Following Radiation Therapy for Gynecologic Cancers. D. Tsementzi, R. Meador, T. Eng, P. Patel, J. Shelton, J. Arluck, I. Scott, M. Dolan, N. Khanna, K. T. Konstantinidis, and D. W. Bruner. Front Cell Infect Microbiol. 11:680038. 2021.
  13. Oil Spills in Beach Sands Selects for Generalist, not Specialist Microbial Degraders. P. Heritier-Robbins, L. M. Rodriguez-R, S. Karthikeyan, J. Hatt, M. Kim, M. Huettel, J. E. Kostka, and K. T. Konstantinidis. ISME J. 15(11):3418-3422. 2021.
  14. Metagenomic insights into the effect of sulfate on enhanced biological phosphorus removal. N. Matsuuraa, Y. Masakke, S. Karthikeyan, S. Kanazawa, R. Honda, R. Yamamoto-Ikemoto, and K. T. Konstantinidis. Appl Microbiol Biotechnol. 105(5):2181-2193. 2021.
  15. The influence of alfalfa-switchgrass intercropping on microbial community structure and function. G. Cha, K. A. Meinhardt, L. H. Orellana, J. K. Hatt, D. A. Stahl, and K. T. Konstantinidis. Environ Microbiol. 23(11):6828-6843. 2021.
  16. Bacteria make a living breathing the nitro-heterocyclic insensitive munitions compound 3-2 nitro-1,2,4-triazol-5-one (NTO). C. L. Madeira, O. Menezes, D. Park, K. V. Jog, J. K. Hatt, S. Gavazza, M. J. Krzmarzick, R. Sierra-Alvarez, J. C. Spain, K. T. Konstantinidis, and J. A. Field. Environ Sci Technol. 55(9):5806-5814. 2021.
  17. Transcriptomic and rRNA:rDNA Signatures of Environmental versus Enteric Enterococcus faecalis Isolates under Oligotrophic Freshwater Conditions. B. Suttner, B. G. Lindner, M. Kim, R. E. Conrad, L. M. Rodriguez-R, L. H. Orellana, E. R. Johnston, J. K. Hatt, K. J. Zhu, J. Brown, and K. T. Konstantinidis. Microbiol Spectr. 9(2):e0081721. 2021.
  18. The Reliability of Metagenome-Assembled Genomes (MAGs) in Representing Natural Populations: Insights from Comparing MAGs against Isolate Genomes Derived from the Same Fecal Sample. A. Meziti, L. M. Rodriguez-R, J. K. Hatt, A. Peña-Gonzalez, K. Levy, and K. T. Konstantinidis. Appl Environ Microbiol. 87(6):e02593-20. 2021.
  19. Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes. L. Ramírez-Fernández, L. H. Orellana, E. R. Johnston, K. T. Konstantinidis, and J. Orlando. Sci Total Environ. 788:147693. 2021.
  20. Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. M. J. Soto-Girón, A. Peña-Gonzalez, J. K. Hatt, L. Montero, M. Páez, E. Ortega, S. Smith, W. Cevallos, G. Trueba, K. T. Konstantinidis, and K. Levy. Am J Trop Med Hyg. 104(6):2275-85. 2021.
  21. Microbial taxonomy run amok. R. A. Sanford, K. G. Lloyd, K. T. Konstantinidis, and F. E. Löffler. Trends in Microbiology. 29(5):394-404. 2021.
  22. Hidden Diversity within Common Protozoan Parasites Revealed by a Novel Genomotyping Scheme. M. H. Seabolt, K. T. Konstantinidis, and D. M. Roellig. Appl Environ Microbiol. 87(6):e02275-20. 2021.
  23. Reply to: “Re-evaluating the evidence for a universal genetic boundary among microbial species”. L. M. Rodriguez-R, C. Jain, S. Aluru, and K. T. Konstantinidis. Nat Commun. 12(1):4060. 2021.
  24. Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones. C. A. Ruiz-Perez, A. D. Bertagnolli, D. Tsementzi, T. Woyke, F. J. Stewart, and K. T. Konstantinidis. Syst Appl Microbiol. 44(2):126185. 2021.
  25. Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. Z. Wang, D. Tsementzi, T. C. Williams, D. L. Juarez, S. K. Blinebry, N. S. Garcia, B. K. Sienkiewicz, K. T. Konstantinidis, Z. I. Johnson, D. E. Hunt. ISME J. 15(1):19-28. 2021.
  26. MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. C. A. Ruiz-Perez, R. E. Conrad, and K. T. Konstantinidis. BMC Bioinformatics. 22(1):11. 2021.
  27. Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs. A. Meziti, E. Nikouli, J. K. Hatt, K. T. Konstantinidis, and K. A. Kormas. Environ Microbiol. 23(7):3710-3726. 2021.
  28. Non-denitrifier nitrous oxide reductases dominate marine biomes. A. D. Bertagnolli, K. T. Konstantinidis, and F. J. Stewart. Environ Microbiol. Reports. 12(6):681-692. 2020.
  29. Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps. T. Viver, R. E. Conrad, L. H. Orellana, M. Urdiain, J. E. González-Pastor, J. K. Hatt, R. Amann, J. Antón, K. T. Konstantinidis, and R. Rosselló-Móra. ISME J. 15(4):1178-1191. 2020.
  30. The Role of the Gut Microbiome in Resisting Norovirus Infection as Revealed by a Human Challenge Study. N. V. Patin, A. Peña-Gonzalez, J. K. Hatt, C. Moe, A. Kirby, and K. T. Konstantinidis. mBio. 11(6):e02634-20. 2020.
  31. Using flow cytometry and light-induced fluorescence to characterize the variability and characteristics of bioaerosols in springtime in Metro Atlanta, Georgia. A. Negron, N. DeLeon-Rodriguez, S. M. Waters, L. D. Ziemba, B. Anderson, M. Bergin, K. T. Konstantinidis, and A. Nenes. Atmos. Chem. Phys. 20, 1817–1838. 2020.
  32. A genomic catalog of Earth’s microbiomes. S. Nayfach, S. Roux, R. Seshadri, D. Udwary, N. Varghese, S. Schulz, D. Wu, D. Paez-Espino, I. M. Chen, M. Huntemann, K. Palaniappan, J. Ladau, S. Mukherjee, T. B. K. Reddy, T. Nielsen, E. Kirton, J. P. Faria, J. N. Edirisinghe, C. S. Henry, S. P. Jungbluth, D. Chivian, P. Dehal, E. M. Wood-Charlson, A. P. Arkin, S. G. Tringe, A. Visel, IMG/M Data Consortium (Konstantinidis is part of the Consortium), T. Woyke, N. J. Mouncey, N. N. Ivanova, N. C. Kyrpides, E. A. Eloe-Fadrosh. Nat. Biotechnol. 39(4):499-509. 2020.
  33. Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming. X. Guo, Q. Gao, M. Yuan, G. Wang, X. Zhou, J. Feng, Z. Shi, L. Hale, L. Wu, A. Zhou, R. Tian, F. Liu, B. Wu, L. Chen, C. G. Jung, S. Niu, D. Li, X. Xu, L. Jiang, A. Escalas, L. Wu, Z. He, J.D. Van Nostrand, D. Ning, X. Liu, Y. Yang, E. A. G. Schuur, K. T. Konstantinidis, J. R. Cole, C. R. Penton, Y. Luo, J. M. Tiedje, and J.  Zhou. Nat. Commun. 11(1):4897. 2020.
  34. A novel droplet digital PCR human mtDNA assay for fecal source tracking. K. Zhu, B. Suttner, A. Pickering, K. T. Konstantinidis, J. Brown. Water Res. 183:116085. 2020.
  35. Integrated Omics Elucidate the Mechanisms Driving the Rapid Biodegradation of Deepwater Horizon Oil in Intertidal Sediments Undergoing Oxic-Anoxic Cycles. S. Karthikeyan, M. Kim, P. Heritier-Robbins, J. K. Hatt, J. C. Spain, W. A. Overholt, M. Huettel, J. E. Kostka, and K. T. Konstantinidis. Environ Sci Technol. 54(16):10088-10099. 2020.
  36. Roadmap for naming uncultivated Archaea and Bacteria. A. E. Murray, J. Freudenstein, S. Gribaldo, R. Hatzenpichler, P. Hugenholtz, P. Kämpfer, K. T. Konstantinidis, C. E. Lane,…[another 50 authors]…, F. P. Wang, P. Yarza, B. P. Hedlund, and A. L. Reysenbach. Nat. Microbiol. 5(8):987-994. 2020.
  37. Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria. X. Tao, J. Feng, Y. Yang, G. Wang, R. Tian, F. Fan, D. Ning, C. T. Bates, L. Hale, M. M. Yuan, L. Wu, Q. Gao, J. Lei, E. A. G. Schuur, J. Yu, R. Bracho, Y. Luo, K. T. Konstantinidis, E. R. Johnston, J. R. Cole, C. R. Penton, J. M. Tiedje, and J. Zhou. Microbiome. 8(1):84. 2020.
  38. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. R. M. Rodriguez-R, D. Tsementzi, C. Luo, and K. T. Konstantinidis. Environ Microbiol. 22(8):3394-3412. 2020.
  39. The Great Oxidation Event expanded the genetic repertoire of arsenic metabolism and cycling. S. C. Chen, G. X. Sun, Y. Yan, K. T. Konstantinidis, S. Y. Zhang, Y. Deng, X. M. Li, H. L. Cui, F. Musat, D. Popp, B. P. Rosen, and Y. G. Zhu. Proc Natl Acad Sci USA. 117(19):10414-10421. 2020.
  40. Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women. D. Tsementzi, A. Pena-Gonzalez, J. Bai, Y. J. Hu, P. Patel, J. Shelton, M. Dolan, J. Arluck, N. Khanna, L. Conrad, I. Scott, T. Y. Eng, K. T. Konstantinidis, and D. W. Bruner. Cancer Med. 9(11):3714-3724. 2020.
  41. New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters. S. Campanaro, L. Treu, L. M. Rodriguez-R, A. Kovalovszki, R. M. Ziels, I. Maus, X. Zhu, P. G. Kougias, A. Basile, G. Luo, A. Schlüter, K. T. Konstantinidis, and I. Angelidaki. Biotechnol. Biofuels. 13:25. 2020.
  42. Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes. S. Karthikeyan, R. M. Rodriguez-R, P. Heritier-Robbins, J. K. Hatt, M. Huettel, J. E. Kostka, and K. T. Konstantinidis. Environ Microbiol. 22(6):2094-2106. 2020.
  43. Opinion: Response to concerns about the use of DNA sequences as types in the nomenclature of prokaryotes. R. Rossello-Mora, K. T. Konstantinidis, I. Sutcliffe, and W. Whitman. Syst Appl Microbiol. 43(2):126070. 2020.
  44. Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes. P. Dam, L. M. Rodriguez-R, C. Luo, J. Hatt, D. Tsementzi, K. T. Konstantinidis, and E. O. Voit. Sci Rep. 10(1):2423. 2020.
  45. Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy. K. T. Konstantinidis, R. Rosselló-Móra, and R. Amann. Environ Microbiol. 22(3):819-822. 2020.
  46. Giant virus diversity and host interactions through global metagenomics. F. Schulz, S. Roux, D. Paez-Espino, S. Jungbluth, D. A. Walsh, V. J. Denef, K. D. McMahon, K. T. Konstantinidis, E. A. Eloe-Fadrosh, N. C. Kyrpides, and T. Woyke. Nature. 578(7795):432-436. 2020.
  47. Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community. J. Feng, C. Wang, J. Lei, Y. Yang, Q. Yan, X. Zhou, X. Tao, D. Ning, M. M. Yuan, Y. Qin, Z. J. Shi, X. Guo, Z. He, J. D. Van Nostrand, L. Wu, R. G. Bracho-Garillo, C. R. Penton, J. R. Cole, K. T. Konstantinidis, Y. Luo, E. A. G. Schuur, J. M. Tiedje, and J. Zhou. Microbiome. 8(1):3. 2020.
  48. Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations. B. J. Suttner, E. R. Johnston, L. H. Orellana, L. M. Rodriguez-R, J. K. Hatt, D. Carychao, M. Q. Carter, M. B. Cooley, and K. T. Konstantinidis. Appl Environ Microbiol. 86(6):e02525-19. 2020.
  49. Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils. J. Feng, C. R. Penton, Z. He, J. D. Van Nostrand, M. M. Yuan, L. Wu, C. Wang, Y. Qin, Z. J. Shi, X. Guo, E. A. G. Schuur, Y. Luo, R. Bracho, K. T. Konstantinidis, J. R. Cole, J. M. Tiedje, Y. Yang, and J. Zhou. mBio. 10(1). pii: e02521-18. 2019.
  50. “Candidatus Macondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments. “Candidatus Macondimonas diazotrophica”, a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments. S. Karthikeyan, L. M. Rodriguez-R, P. Heritier-Robbins, M. Kim, W. A. Overholt, J. C. Gaby, J. K. Hatt, J. C. Spain, R. Rosselló-Móra, M. Huettel, J. E. Kostka, and K. T. Konstantinidis. ISME J. 13(8):2129-2134. 2019.
  51. Drinking Water Microbiome Project: Is it Time? N. M. Hull, F. Ling, A. J. Pinto, M. Albertsen, H. G. Jang, P. Y. Hong, K. T. Konstantinidis, M. LeChevallier, R. R. Colwell, and W. T. Liu. Trends Microbiol. 27(8):670-677. 2019.
  52. Consent insufficient for data release-Response. R. I. Amann, S. Baichoo, B. J. Blencowe, P. Bork, M. Borodovsky, C. Brooksbank, P. S. G. Chain, R. R. Colwell, […another 10 authors in alphabetic order], K. T. Konstantinidis, N. C. Kyrpides, C. E. Mason CE, […another 10 authors in alphabetic order], and I. Xenarios. Science. 3;364(6439):446. 2019.
  53. First description of two moderately halophilic and psychrotolerant Mycoplasma species isolated from cephalopods and proposal of Mycoplasma marinum sp. nov. and Mycoplasma todarodis sp. nov. A. S. Ramírez, O. M. Vega-Orellana, T. Viver, J. B. Poveda, R. S. Rosales, C. G. Poveda, J. Spergser, M. P. Szostak, M. J. Caballero, L. Ressel, J. M. Bradbury, M. Mar Tavío, S. Karthikeyan*, R. Amann, K. T. Konstantinidis, and R. Rossello-Mora. Syst Appl Microbiol. 42(4):457-467. 2019.
  54. Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus “Candidatus Fonsibacter” and proposal of Ca. Fonsibacter lacus sp. nov. D. Tsementzi, L. M. Rodriguez-R, C. A. Ruiz-Perez, A. Meziti, J. K. Hatt, and K. T. Konstantinidis. Syst Appl Microbiol. 42(4):495-505. 2019.
  55. Prevalence of viral photosynthesis genes along a freshwater to saltwater transect in Southeast USA. C. A. Ruiz-Perez, D. Tsementzi, J. K. Hatt, M. B. Sullivan, and K. T. Konstantinidis. Environ Microbiol Rep. 11(5):672-689. 2019.
  56. Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths. E. R. Johnston, J. K. Hatt, Z. He, L. Wu, X. Guo, Y. Luo, E. A. G. Schuur, J. M. Tiedje, J. Zhou, and K. T. Konstantinidis. Proc Natl Acad Sci U S A. 116(30):15096-15105. 2019.
  57. Decomposition of sediment-oil-agglomerates in a Gulf of Mexico sandy beach. I. Bociu, B. Shin, W. B. Wells, J. E. Kostka, K. T. Konstantinidis, and M. Huettel. Sci Rep. 9(1):10071. 2019.
  58. Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon. L. Hale, W. Feng, H. Yin, X. Guo, X. Zhou, R. Bracho, E. Pegoraro, C. R. Penton, L. Wu, J. Cole, K. T. Konstantinidis, Y. Luo, J. M. Tiedje, E. A. G. Schuur, and J. Zhou. ISME J. 13(12):2901-2915. 2019.
  59. Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities. T. Viver, L H. Orellana, S. Díaz, M. Urdiain, M. D. Ramos-Barbero, J. E. González-Pastor, A. Oren, J. K. Hatt, R. Amann, J. Antón, K. T. Konstantinidis, and R. Rosselló-Móra. Environ Microbiol. 21(11):4300-4315. 2019.
  60. Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota. L. H. Orellana, T. Ben Francis, K. Krüger, H. Teeling, M. C. Müller, B. M. Fuchs, K. T. Konstantinidis, and R. I. Amann. ISME J. 13(12):3024-3036. 2019.
  61. The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content. R. A. Beinart, C. Luo, K. T. Konstantinidis, F. J. Stewart, and P. R. Girguis. Front Microbiol. 10:1818. 2019.
  62. Comparative Genomics and Phylogenomic Analysis of the Genus Salinivibrio. R. R. de la Haba, C. López-Hermoso, C. Sánchez-Porro, K. T. Konstantinidis, and A. Ventosa A. Front Microbiol. 10:2104. 2019.
  63. Metagenomic signatures of gut infection caused by different Escherichia coli pathotypes.  Peña-Gonzalez A, M. J. Soto-Girón, S. Smith, J. Sistrunk, L. Montero, M. Páez, E. Ortega, J. K. Hatt, W. Cevallos, G. Trueba, K. Levy, and K. T. Konstantinidis. Appl Environ Microbiol. pii: AEM.01820-19. 2019.
  64. Genomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica. L. J. Deng, J. M. Auchtung, K. T. Konstantinidis, I. Brettar, M. G. Höfle, and J. M. Tiedje. mSystems. 4(5). pii: e00560-19. 2019.
  65. Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer. L. H. Orellana, J. K. Hatt, R. Iyer, K. Chourey, R. L. Hettich, J. C. Spain, W. H. Yang, J. C. Chee-Sanford, R. A. Sanford, F. E. Löffler, and K. T. Konstantinidis KT. Sci Rep. 9(1):17630. 2019.
  66. Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment. B. Shin B, M. Kim, K. Zengler, K. J. Chin, W. A. Overholt, L. M. Gieg, K. T. Konstantinidis, and J. E. Kostka. Sci Rep. 9(1):1239. 2019.
  67. Toward unrestricted use of public genomic data. R. I. Amann, S. Baichoo, B. J. Blencowe, P. Bork, M. Borodovsky, C. Brooksbank, P. S. G. Chain, R. R. Colwell, […another 10 authors in alphabetic order], K. T. Konstantinidis, N. C. Kyrpides, C. E. Mason CE, […another 10 authors in alphabetic order], and I. Xenarios. Science. 25;363(6425):350-352. 2019.
  68. Moving the cataloguing of the “uncultivated majority” forward. K. T. Konstantinidis, R. Rosselló-Móra, and R. Amann. Systematic & Applied Microbiology. Jan;42(1):3-4. 2019.
  69. Phosphate addition increases tropical forest soil respiration primarily by deconstraining microbial population growth. E. R. Johnston, M. Kim, J. K. Hatt, J. R. Phillips, Q. Yao, Y. Song, T. C. Hazen, M. A Mayes, and K. T. Konstantinidis. Soil Biology and Biochemistry. 130: 43-54. 2019.
  70. Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient.  A. Meziti, D. Tsementzi, L. M. Rodriguez-R, J. K. Hatt, H. Karayanni, K. A. Kormas, and K. T. Konstantinidis. ISME J. 13(3):767-779. 2018.
  71. Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics. S. Y. Zhang, D. Tsementzi, J. K. Hatt, A. Bivins, N. Khelurkar, J. Brown, S. N. Tripathi, and K. T. Konstantinidis. Environmental Microbiology. 13(3):767-779. 2018.
  72. imGLAD: accurate detection and quantification of target organisms in metagenomes. J. C. Castro, L. M. Rodriguez-R, W. T. Harvey, M. R. Weigand, J. K. Hatt, M. Q. Carter, and K. T. Konstantinidis. PeerJ. 6:e5882. 2018.
  73. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. C. Jain, L. M. Rodriguez-R, A. M. Phillippy, K. T. Konstantinidis, and S. Aluru. Nat Commun. 9(1):5114. 2018.
  74. Genomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains.  A. Pena-Gonzalez, L. M. Rodriguez-R., C. K. Marston, J. E. Gee, C. A. Gulvik, C. B. Kolton, E. Saile, M. Frace, A. R. Hoffmaster, and K. T. Konstantinidis. mSystems. 3(4). pii: e00065-18. 2018.
  75. More replenishment than priming loss of soil organic carbon with additional carbon input.  J. Liang, Z. Zhou, C. Huo, Z. Shi, J. R. Cole, L. Huang, K. T. Konstantinidis, X. Li, B. Liu, Z. Luo, C. R. Penton, E. A. G. Schuur, J. M. Tiedje, Y. P. Wang, L. Wu, J. Xia, J. Zhou, and Y. Luo. Nat Commun. 9(1):3175. 2018.
  76. Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria. S. Ganesh, A. D. Bertagnolli, L. A. Bristow, C. C. Padilla, N. Blackwood, M. Aldunate, A. Bourbonnais, M. A. Altabet, R. R. Malmstrom, T. Woyke, O. Ulloa, K. T. Konstantinidis, B. Thamdrup, and F. J. Stewart. ISME J. 12(11):2706-2722. 2018.
  77. Widely used benzalkonium chloride disinfectants can promote antibiotic resistance.  M. Kim, M. R. Weigand, S. Oh, J. K. Hatt, R. Krishnan, U. Tezel, S. G. Pavlostathis, and K. T. Konstantinidis. Applied & Environmental Microbiology. pii: AEM.01201-18. 2018.
  78. The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level. L. M. Rodriguez-R., S. Gunturu, W. T. Harvey, R. Rosselló-Mora, J. M. Tiedje, J. R. Cole, and K. T.  Konstantinidis. Nucleic Acids Research. 46(W1):W282-W288. 2018.
  79. Biotic responses buffer warming-induced soil organic carbon loss in Arctic tundra. J. Liang, J. Xia, Z. Shi, L. Jiang, S. Ma, X. Lu, M. Mauritz, S. M. Natali, E. Pegoraro, C. R. Penton, C. Plaza, V. G. Salmon, G. Celis, J. R. Cole, K. T. Konstantinidis, J. M. Tiedje, J. Zhou, E. A. G. Schuur, and Y. Luo. Global Chang Biology. 24(10):4946-4959. 2018.
  80. Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity. L. M. Rodriguez-R, S. Gunturu, J. M. Tiedje, J. R. Cole, and K. T. Konstantinidis.  mSystems. 3(3). pii: e00039-18. 2018.
  81. Genomic and Transcriptomic Insights into How Bacteria Withstand High Concentrations of Benzalkonium Chloride Biocides. M. Kim, J. K. Hatt, M. R. Weigand, R. Krishnan, S. G. Pavlostathis, and K. T. Konstantinidis. Applied & Environmental Microbiology. 84(12). pii: e00197-18. 2018.
  82. Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis. D. Tsementzi, J. Castro Gordillo, M. Mahagna, Y. Gottlieb, and K. T. Konstantinidis. Environmental Microbiology. 20(5):1751-1764. 2018.
  83. Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones.   E. Cardenas, L. H. Orellana, K. T. Konstantinidis, and W. W. Mohn.  Scientific Reports. 8(1):3142. 2018.
  84. Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano. T. Viver, L. Orellana, P. González-Torres, S. Díaz, M. Urdiain, M. E. Farías, V. Benes, P. Kaempfer, A. Shahinpei, M. Ali Amoozegar, R. Amann, J. Antón, K. T. Konstantinidis, and R. Rosselló-Móra. Systematic & Applied Microbiology. 41(3):198-212. 2018.
  85. How much do rRNA gene surveys underestimate extant bacterial diversity? L. M. Rodriguez-R, J. C. Castro, N. C. Kyrpides, J. R. Cole, J. M. Tiedje, and K. T. Konstantinidis. Applied & Environmental Microbiology. 84(6). pii: e00014-18. 2018.
  86. Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization.  L. H. Orellana, J. C. Chee-Sanford, R. A. Sanford, F. E. Löffler, and K. T. Konstantinidis. Applied & Environmental Microbiology. 84 (2), e01646-17. 2018.
  87. Divergence in gene regulation contributes to sympatric speciation of Shewanella baltica strains. J. Deng, J. Auchtung, K. T. Konstantinidis, A. Caro-Quintero, I. Brettar, M. Höfle, and J. M. Tiedje. Applied & Environmental Microbiology. 02015-17. 2018.
  88. Reply to the commentary “Uncultivated microbes – in need of their own nomenclature?”. K. T. Konstantinidis, R. Rosselló-Móra, and R. Amann. ISME J. 12(3):653-654. 2018.
  89. Microbial functional diversity covaries with permafrost thaw‐induced environmental heterogeneity in tundra soil.  M. M. Yuan, J. Zhang, K. Xue, L. Wu, Y. Deng, J. Deng, L. Hale, X. Zhou, Z. He, Y. Yang, J. D. Van Nostrand, E. A. G. Schuur, K. T. Konstantinidis, C. R. Penton, J. R. Cole, J. M. Tiedje, Y. Luo, and J. Zhou. Global Change Biology. 24(1):297-307. 2018.
  90. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.   R. M. Bowers, N. C. Kyrpides, R. Stepanauskas, M. Harmon-Smith, […], K. T Konstantinidis, […], D. H. Parks, A. M. Eren, J. F. Banfield, T. Woyke, Genome Standards Consortium. Nature Biotechnology. 35 (8), 725. 2017. 
  91. Uncultivated microbes in need of their own taxonomy.   K. T. Konstantinidis, R. Rosselló-Móra, and R. Amann.  ISME J. 11(11):2399-2406. 2017. 
  92. Draft Genome Sequence of Bacillus cereus LA2007, a Human-pathogenic Isolate Harboring Anthrax-like Plasmids. A. Pena-Gonzalez, C. K. Marston, L. M. Rodriguez-R, C. B. Kolton, J. Garcia-Diaz, A. Theppote, M. Frace, K. T. Konstantinidis, and A. R. Hoffmaster. Genome Announc. 5(16). 2017. 
  93. The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa.  T. Viver, L. Orellana, J. Hatt, M. Urdiain, M. Richter, J. Antón, R. Amann, M. Avian, K. T. Konstantinidis, R. Rosselló-Móra. Environmental Microbiology. 19(8):3039-3058. 2017. 
  94. Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem.  Y. Wang, J. K. Hatt, D. Tsementzi, L. M. Rodriguez-R, C. A. Ruiz-Pérez, M. R. Weigand, H. Kizer, G. Maresca, R. Krishnan, R. Poretsky, J. C. Spain, and K. T. Konstantinidis. Applied & Environmental Microbiology. 03321-16. 2017. 
  95. Warming enhances old organic carbon decomposition through altering functional microbial communities.  C. Lei, N. Zhang, M. Yuan, J. Xiao, Y. Qin, Y. Deng, Q. Tu, K. Xue, J. D Van Nostrand, L. Wu, Z. He, X. Zhou, M. B. Leigh, K. T Konstantinidis, E. A. G. Schuur, Y. Luo, J. M. Tiedje and J. Zhou.ISME J. 11 (8), 1825. 2017.
  96. Candidatus Dichloromethanomonas elyunquensis gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family. S. Kleindienst, S. A. Higgins, D. Tsementzi, G. Chen, K. T. Konstantinidis, E. E. Mack, and F.E. Loffler. Systematic & Applied Microbiology. 40 (3), 150-159. 2017.
  97. Metagenomics of two severe foodborne outbreaks provides diagnostic signatures and signs of co-infection not attainable by traditional methods. A. D. Huang, C. Luo, A. Pena-Gonzalez, M. R. Weigand, C. Tarr, and K. T. Konstantinidis. Applied & Environmental Microbiology. 83 (3), e02577-16. 2017.
  98. Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe. X. Zhang, E. R. Johnston, L. Li, K. T. Konstantinidis, and X. Han. ISME J. 11 (4), 885. 2017.
  99. ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets. L. H. Orellana, L. M. Rodriguez-R, and K. T. Konstantinidis. Nucleic Acids Research. 45 (3), e14-e14. 2016.
  100. A Rieske-type Oxygenase of Pseudomonas sp. BIOMIG1 converts Benzalkonium Chlorides to Benzyldimethyl Amine. E. Ertekin, K. T. Konstantinidis, and U. Tezel. Environ Science & Technol. 51(1):175-181. 2016.
  101. Meeting report: GenBank microbial genomic taxonomy workshop (12-13 May, 2015). S. Federhen, R. Rossello-Mora, H-P. Klenk, B. J. Tindall, K. T. Konstantinidis, W. B. Whitman, D. Brown, D. Labeda, D. Ussery, and G. M. Garrity. Standards in Genomic Sciences. 11:1. 2016.
  102. Dynamic models of the complex microbial metapopulation of lake mendota. P. Dam, L. L. Fonseca, K. T. Konstantinidis, and E. O. Voit. NPJ Systems Biology And Applications. 2:16007. 2016.
  103. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. L. M. Rodriguez-R, and K. T. Konstantinidis. PeerJ Preprints. 2016.
  104. Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming. K. Xue, M. Yuan, Z. Shi, Y. Qin, Y. Deng, L. Cheng, L. Wu, Z. He, J. D. Van Nostrand, R. Bracho, S. Natali, E. A. G. Schuur, C. Luo, K. T. Konstantinidis, Q. Wang, J. R. Cole, J. M. Tiedje, Y. Luo, and J. Zhou. Nature Climate Change. 6:595-600. 2016.
  105. Temperature sensitivity of organic matter decomposition of permafrost-region soils during laboratory incubations. R. Bracho, S. Natali, E. Pegoraro, K. G. Crummer, C. Schadel, G. Celis, L. Hale, L. Wu, H. Yin, J. M. Tiedje, K. T. Konstantinidis, Y. Luo, J. Zhou, and E. A. Schuur. Soil Biology and Biochemistry. 97:1-14. 2016. 2016.
  106. SAR11 bacteria linked to ocean anoxia and nitrogen loss. D. Tsementzi, J. Wu, S. Deutsch, S. Nath, L. M. Rodriguez-R, A. S. Burns, P. Ranjan, N. Sarode, R. P. Malmstrom, C. C. Padilla, B. K. Stone, L. A. Bristow, M. Larsen, J. B. Glass, B. Thamdrup, T. Woyke, K. T. Konstantinidis, and F. J. Stewart. Nature. 536:179-183. 2016.
  107. Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections. M. J. Soto-Giron, L. M. Rodriguez-R, C. Luo, M. Elk, H. Ryu, J. Hoelle, J. W. Santo Domingo, and K. T. Konstantinidis. Applied Environmental Microbiology. 82:2872-2883. 2016.
  108. Anthropogenic effects on bacterial diversity and function along a river-to-estuary gradient in Northwest Greece revealed by metagenomics. A. Meziti, D. Tsementzi, K. A. Kormas, H. Karayanni, and K. T. Konstantinidis. Environmental Microbiology. 18(12):4640-4652. 2016.
  109. Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium. S. Kleindienst, S. A. Higgins, D. Tsementzi, K. T. Konstantinidis, E. E. Mack, and F. E. Loffler. Genome Announcements. 4. 2016. 2016.
  110. Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem. E. R. Johnston, L. M. Rodriguez-R, C. Luo, M. M. Yuan, L. Wu, Z. He, E. A. Schuur, Y. Luo, J. M. Tiedje, J. Zhou, and K. T. Konstantinidis. Frontiers in Microbiology. 7:579. 2016. 2016.
  111. Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils. S. A. Higgins, A. Welsh, L. H. Orellana, K. T. Konstantinidis, J. C. Chee-Sanford, R. A. Sanford, C. W. Schadt, and F. E. Loffler. Applied & Environmental Microbiology. 82:2919-2928. 2016.
  112. Similar Microbial Consortia and Genes Are Involved in the Biodegradation of Benzalkonium Chlorides in Different Environments. E. Ertekin, J. K. Hatt, K. T. Konstantinidis, and U. Tezel. Environ Science & Technology. 50:4304-4313. 2016. 2016.
  113. 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 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. Int J Syst Evol Microbiol. Feb;63(Pt 2):625-35. 2015.
  114. Methods for estimating temperature sensitivity of soil organic matter based on incubation data: A comparative evaluation. J. Liang, D. Li, Z. Shi, J. M Tiedje, J. Zhou, E. A. G. Schuur, K. T Konstantinidis, and Y. Luo. Soil Biology and Biochemistry. 80:127-135. 2015. 2016.
  115. Microbial species delineation using whole genome sequences. N. J. Varghese, S. Mukherjee, N. Ivanova, K. T. Konstantinidis, K. Mavrommatis, N. C. Kyrpides, and A. Pati. Nucleic Acids Res. Aug 18;43(14):6761-71. 2015.
  116. Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy. M. R. Weigand, A. Pena-Gonzalez, T. B. Shirey, R. G. Broeker, M. K. Ishaq, K. T. Konstantinidis, and B. H. Raphael. Applied and Environmental Microbiology. Aug 15;81(16):5420-9. 2015.
  117. Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill. L. M. Rodriguez-R, W. A. Overholt, C. Hagan, M. Huettel, J. E. Kostka, and K. T. Konstantinidis. ISME J. Sep;9(9):1928-40. 2015.
  118. Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal. K. T. Konstantinidis and R. Rosselló-Móra. Syst Appl Microbiol. Jun;38(4):223-30. 2015.
  119. Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification. M. Vital, B. Chai, B. Østman, J. Cole, K. T. Konstantinidis, and J. M. Tiedje. ISME J. May;9(5):1130-40. 2015.
  120. Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria. A. Caro-Quintero and K. T. Konstantinidis. ISME J. Mar 17;9(4):958-67. 2015.
  121. Evaluation of metatranscriptomic protocols and application to the study of planktonic freshwater microbial communities. D. Tsementzi, R. Poretsky, C. Luo, L. Rodriguez, and K. T. Konstantinidis. Environmental Microbiology Reports. (6), 640-655. 2014.
  122. Microbial community degradation of widely used quaternary ammonium disinfectants. S. Oh, Z. Kurt, D. Tsementzi, M. R. Weigand, M. Kim, J. K. Hatt, M. Tandukar, S. G. Pavlostathis, J. C. Spain, and K. T. Konstantinidis. Applied and Environmental Microbiology. Oct;80(19):5892-900. 2014.
  123. Detecting nitrous oxide reductase (NosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle.  L. H. Orellana, L. M. Rodriguez-R., S. Higgins, J. C. Chee-Sanford, R. A. Sanford, K. M. Ritalahti, F. E. Löffler, and K. T. Konstantinidis. mBio. Jun 3;5(3):e01193-14. 2014.
  124. Estimating coverage in metagenomic data sets and why it matters. L. M. Rodriguez-R and K. T. Konstantinidis. ISME J. Nov;8(11):2349-51. 2014.
  125. Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. R. Poretsky, L. M. Rodriguez-R, C. Luo, D. Tsementzi, and K. T. Konstantinidis. PLoS One. Apr 8;9(4):e93827. 2014.
  126. Bypassing cultivation to identify bacterial species. L. M. Rodriguez-R, and K. T. Konstantinidis. ASM Microbe Magazine. March issue. 2014.
  127. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. C. Luo, L. M. Rodriguez-R, and K. T. Konstantinidis. Nucleic Acids Res. Apr;42(8):e73. 2014.
  128. Genome sequencing reveals the environmental origin of enterococci and potential biomarkers for water quality monitoring. M. R. Weigand, N. J. Ashbolt, K. T. Konstantinidis, and J. Santodomingo. Environmental Science and Technology. Apr 1;48(7):3707-14. 2014.
  129. Do airborne microbes matter for atmospheric chemistry and cloud formation? K. T. Konstantinidis. Environmental Microbiology. Jun;16(6):1482-4. 2014.
  130. Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. C. Luo, L. M. Rodriguez-R, E. R. Johnston, L. Wu, L. Cheng, K. Xue, Q. Tu, Y. Deng, Z. He, J. Z. Shi, M. M. Yuan, R. A. Sherry, D. Li, Y. Luo, E. A. Schuur, P. Chain, J. M. Tiedje, J. Zhou, and K. T. Konstantinidis. Applied and Environmental Microbiology. Mar;80(5):1777-86. 2013.
  131. Stability, genotypic and phenotypic diversity of Shewanella baltica in the redox transition zone of the Baltic Sea. J. Deng, I. Brettar, C. Luo, J. Auchtung, K. T. Konstantinidis, J. L. Rodrigues, M. Hofle, and J. M. Tiedje. Environmental Microbiology. Jun;16(6):1854-66. 2014.
  132. A User’s Guide to Quantitative and Comparative Analysis of Metagenomic Datasets. C. Luo, L. M. Rodriguez-R, and K. T. Konstantinidis. Methods Enzymol. 531:525-47. 2013.
  133. Nonpareil: A redundancy-based approach to assess the level of coverage in metagenomic datasets. L. M. Rodriguez-R, and K. T. Konstantinidis. Bioinformatics. Mar 1;30(5):629-35. 2014.
  134. Long-term Exposure to Benzalkoniun Chloride Disinfectants Results in Change of Microbial Community Structure and Increased Antimicrobial Resistance. M. Tandukar, S. Oh, U. Tezel, K. T. Konstantinidis, and S. G. Pavlostathis. Environ Sci Technol. Sep 3;47(17):9730-8. 2013.
  135. Reply to Smith and Griffin: Methods, air flows, and conclusions are robust in the DeLeon-Rodriguez et al. study. 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. Proc Natl Acad Sci U S A. June 4; 110(23):E2085. 2013.
  136. Sequencing platform and library preparation choices impact viral metagenomes. S. A. Solonenko, J. C. Ignacio-Espinoza, A. Alberti, C. Cruaud, S. Hallam, K. Konstantinidis, G. Tyson, P. Wincker, and M. B. Sullivan. BMC Genomics. May 10; 14:320. 2013.
  137. Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics. S. Oh, M. Tandukar, S. G. Pavlostathis, P. S. Chain, and K. T. Konstantinidis. Environmental Microbiology. Oct;15(10):2850-64. 2013.
  138. Draft Genome Sequence of Catellicoccus marimammalium, a Novel Species Commonly Found in Gull Feces. M. R. Weigand, H. Ryu, L. Bozcek, K. T. Konstantinidis, and J. W. Santo Domingo. Genome Announc. Jan;1(1). pii: e00019-12. 2013.
  139. Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications. 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. Proc Natl Acad Sci U S A. Feb 12; 110(7):2575-2580. 2013. This paper received worldwide attention and was highlighted by NPR, National Geographic, Amazing Planet, U.S. News & World Report, among numerous other media.
  140. Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. 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. M. Ritalahti, S. Nissen, K. T. Konstantinidis, F. E. Löffler. Proc Natl Acad Sci U S A. Nov 27;109(48):19709-14. 2012.
  141. Genomic diversity of Escherichia isolates from diverse habitats. S. Oh, S. Buddenborg, D. R. Yoder-Himes, J. M. Tiedje, and K. T. Konstantinidis. PLoS ONE. 7(10):e47005. 2012.
  142. Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the glacial lake agassiz peatland. 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. Applied and Environmental Microbiology. Oct;78(19):7023-31. 2012.
  143. Genomic determinants of organohalide-respiration in Geobacter lovleyi, an unusual member of the Geobacteraceae. D. D. Wagner, L . A. Hug, J. K. Hatt, M. R. Spitzmiller, E. Padilla-Crespo, K. M. Ritalahti, E. A. Edwards, K. T. Konstantinidis, and F. E. Löffler. BMC Genomics. May 22;13(1):200. 2012.
  144. The chimeric genome of Sphaerochaeta: nonspiral spirochetes that break with the prevalent dogma in spirochete biology. A. Caro-Quintero, K. M. Ritalahti, K. D. Cusick, F. E. Löffler, and K. T. Konstantinidis mBio. May 15;3(3). 2012.
  145. Genome sequencing of five Shewanella baltica strains recovered from the oxic-anoxic interface of the Baltic Sea. A. Caro-Quintero , J. Deng, J. Auchtung, I. Brettar, M. Höfle, James M. Tiedje, and K. T. Konstantinidis. Journal of Bacteriology. Mar;194(5):1236. 2012.
  146. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. C. Luo , D. Tsementzi , N. Kyrpides, T. Read, and K. T. Konstantinidis. PLoS ONE. 7(2):e30087. 2012.
  147. Bacterial species may exist, metagenomics reveal. A. Caro-Quintero and K. T. Konstantinidis. Environmental Microbiology. Feb;14(2):347-55. 2012. Rated “Must read” by the Faculty of 1000.
  148. Individual genome assembly from complex community short-read metagenomic datasets. C. Luo, D. Tsementzi, N. Kyrpides, and K. T. Konstantinidis. ISME J. Apr;6(4):898-901. 2012.
  149. Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. S. Oh, A. Caro-Quintero, D. Tsementzi, N. Deleon-Rodriguez, C. Luo, R. Poretsky, and K. T. Konstantinidis. Applied and Environmental Microbiology. Sep;77(17):6000-11. 2011.
  150. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. C. Luo, S. T. Walk, D. M. Gordon, M. Feldgarden, J. M. Tiedje, and K. T. Konstantinidis. Proc Natl Acad Sci U S A. Apr 26;108(17):7200-5. 2011.
  151. Phosphorus-related gene content is similar in Prochlorococcus populations from the North Pacific and North Atlantic Oceans. C. Luo, and T. K. Konstantinidis. Proc Natl Acad Sci U S A. Apr 19;108(16):E62-3. 2011.
  152. Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea. A. Caro-Quintero, J. Deng, J. Auchtung, I. Brettar, M. Hoefle, and K. T. Konstantinidis. ISME J. Jan;5(1):131-40. 2011.
  153. Evaluating the performance of oligonucleotide microarrays for strains of increasing genetic divergence to the reference strain. S. Oh, D. R. Yoder-Himes, J. Tiedje, and K. T. Konstantinidis. Applied and Environmental Microbiology. May;76(9):2980-8. 2010.
  154. Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics. D. R. Yoder-Himes, K. T. Konstantinidis, J. M. Tiedje. PLoS ONE. Jan 15;5(1):e8724. 2010.
  155. Comparative systems biology across an evolutionary gradient within the Shewanella genus. 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. Proc Natl Acad Sci USA. Sep 15;106(37):15909-14. 2009. This article was featured by numerous science media and blogs including: MSNBC, R&D magazine, GenomeWed, and Eureka; and the journal Nature.
  156. Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species. A. Caro-Quintero, G. P. Rodriguez-Castaño, and K. T. Konstantinidis. Journal of Bacteriology. Sep;191(18):5824-31. 2009. This article reveals, among other important findings, that a recent claim in Science (Sheppard et al, 2008) was biased by the genes used in the analysis and that the evidence for the claim is lacking.
  157. Comparative metagenomic analysis of a microbial community from 4000 m at Station ALOHA in the North Pacific Subtropical Gyre. K. T. Konstantinidis, J. Braff, D. M. Karl, and E. F. Delong. Applied and Environmental Microbiology. Aug;75(16):5345-55. 2009. This article reveals, among other important findings, that a recent claim in Nature (Agugo et al, 2008) was biased by the genes used in the analysis and that the evidence for the claim is lacking.
  158. Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. K. T. Konstantinidis, and E. F. DeLong. ISME J. Oct. 2(10):1052-65. 2008.
  159. Vertical Phyloecology of North Pacific Bacterioplankton. V. D. Pham, K. T. Konstantindis, T. Palden, and E. F. DeLong. Environmental Microbiology. Sep.10(9):2313 – 2330. 2008.
  160. Design and testing of ‘genome-proxy’ microarrays to profile marine microbial communities. V. I. Rich, K. Konstantinidis, and E. F. Delong. Environmental Microbiology. Feb.10(2):506-21. 2008. Rated “Must read” by the Faculty of 1000.
  161. Predicting sigma (28) promoters in eleven Shewanella genomes. W. Song, F. S. Juhn, D. Q. Naiman, K. T. Konstantinidis, T. S. Gardner, and M. J. Ward. FEMS Microbiol Lett. Jun.283(2):223-30. 2008.
  162. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. K. T. Konstantinidis, and J. M. Tiedje. Current Opinion Microbiology. Oct.10(5):504-9. 2007. Invited, peer-reviewed contribution.
  163. DNA-DNA hybridization values and their relation to whole genome sequence. J. Goris, K. T. Konstantinidis, T. Coenye, P. Vandamme, and J. M. Tiedje. Int J Syst Evol Microbiol. Jan.57(Pt 1):81-91. 2007.
  164. Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. 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. Proc Natl Acad Sci USA. Nov.103(48):18296-301. 2006. This article describes the first successful attempt to derive the complete genome of an uncultivated microorganism using metagenomic approaches; it is rated “Recommended read” by the Faculty of 1000.
  165. The bacterial species definition in the genomic era. K. T. Konstantinidis, A. Ramette, and J. M. Tiedje. Philos Trans R Soc Lond B Biol Sci. Nov.361(1475):1929-40. 2006. Invited, peer-reviewed contribution.
  166. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73 M bp genome shaped for versatility. P. S. G. Chain, V. J. Denef, K. T. Konstantinidis…and 25 more authors. Proc Natl Acad Sci USA. Oct.103(42):15280-7. 2006.
  167. Toward a more robust assessment of intra-species diversity using fewer genetic markers. K. T. Konstantinidis, A. Ramette, and J. M. Tiedje. Applied and Environmental Microbiology. Nov.72(11):7286-93. 2006. Ranked in the top-twenty articles of the journal in terms of number of downloads.
  168. Towards a genome-based taxonomy for prokaryotes. K. T. Konstantinidis, and J. M. Tiedje. Journal of Bacteriology. 187(18):6258-64. 2005. Highlighted in the ASM news; J. Bacteriology featured a guest commentary on this article; ranked 2nd in terms of number of downloads.
  169. Genomic insights that advance the species concept for prokaryotes. K. T. Konstantinidis, and J. M. Tiedje. Proc Natl Acad Sci USA. 102(7):2567-72. 2005. This highly cited (>200 times) article describes a new approach for studying and cataloguing intra-species diversity. It is considered a very influential article for the new field of genomic taxonomy.
  170. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. E. Kolker E, A. F. Picone…K. T. Konstantinidis…and 28 more authors. Proc Natl Acad Sci USA. 102(6):2099-104. 2005.
  171. Trends between gene content and genome size in prokaryotic species with larger genomes. K. T. Konstantinidis, and J. M. Tiedje. Proc. Natl. Acad. Sci. USA. 101(9):3160-5. 2004. Rated “Must read” by the Faculty of 1000; three of its figures have been included in the “Biology of Microorganisms” 8th Edition by Madigan, Martinko and Parker, the most popular microbiology textbook.
  172. Microbial diversity and resistance to copper in metal contaminated lake sediment. K. T. Konstantinidis, N. Isaacs, S. Simpson, D. Long, and T. L. Marsh. Microbial Ecology. 45(2): 191-202. 2003.

Books and Book Chapters

The following list is in reverse chronological order. (updated Dec 2010)

  1. Classifying prokaryotic genomes using the Microbial Genomes Atlas (MiGA) webserver. L. M. Rodriguez-R, W. T. Harvey, R. Rosselló-Mora, J. M. Tiedje, J. R. Cole, and K. T. Konstantinidis. In Bergey’s Manual Trust. W. B. Whitman, editor. John Wiley & Sons, Inc. Hoboken, New Jersey, USA. 2020.
  2. Identification and Classification of Prokaryotes Using Whole Genome Sequences. L. M. Rodriguez-R, R. Rosselló-Mora, and K. T. Konstantinidis. In Trends in the Systematics of Bacteria and Fungi. P. Bridge, D. Smith and E. Stackebrandt (eds). CAB International. Oxfordside, UK. 2020.
  3. Defining taxonomic ranks. K. T. Konstantinidis and E. Stackebrandt. In The Prokaryotes. M.Dworkin et al (eds.). Springer-Verlag. New York, USA. 2013.
  4. Metagenomic insights into bacterial species. K. T. Konstantinidis. 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.
  5. Microbial diversity and phylogeny: extending from rRNAs to genomes. J. Cole, K. T. Konstantinidis, Ryan J. Farris, and J. M. Tiedje. Pages: 1-20. In Environmental Molecular Biology. W-T. Liu and J. Jansson (eds). Horizon Scientific Press. Norwich, UK. 2009.
  6. Microbial diversity and genomics. K. T. Konstantinidis, and J. M. Tiedje. Pages: 21-40. In Microbial Functional Genomics. J. Zhou, D. K. Thompson, Y. Xu, and J. M. Tiedje (eds.). John Wiley & Sons. Hoboken, New Jersey, USA. 2004.