Mark Liles

Publications with green marking on the journal name are available as PDF files. To view the pdf files, you need to have installed "Acrobat Reader". Other papers are available as a reprint request by mail.

You have requested access to material protected by copyright. We considered your request as reprint request as is common in the scientific community. When you download a PDF, you agree to download one copy for personal and scientific use only. Commercial use or duplication is not allowed unless a permission from the copyright owner is granted.

Publications in scientific journals


  1. Hossain, M. J., Ran, C., Liu, K., Ryu, C. M., Rasmussen-Ivey, C. R., Williams, M. A., Hassna, M. K., Choi, S.-K., Jeong, H., Newman, M., Kloepper, J. W. and Liles, M. R. 2015 Deciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum. Frontiers in Plant Science 6


  2. Zhou, J., Sun, D., Childers, A., McDermott, T.R., Wang, Y., and Liles, M.R. 2014 Three novel virophage genomes discovered from Yellowstone Lake metagenomes. Journal of Virology doi: 10.1128/JVI.03039-14

  3. Hossain, M.J., Beaz-Hidalgo, R., Figueras, M.J., and Liles, M.R. 2014 Draft Genome Sequences of Two Novel Aeromonas Species Recovered in Association with Cyanobacterial Blooms. Genome Announcements vol. 2 no. 6 e01181-14, doi: 10.1128/genomeA.01181-14

  4. Figueras, M.J., Beaz-Hidalgo, R., Hossain, M.J., Liles, M.R. 2014 The taxonomic affiliation of new genomes should be verified using the average nucleotide identity and multilocus phylogenetic analysis. Genome Announcements vol. 2 no. 6. e00927-14, doi: 10.1128/genomeA.00927-14.

  5. Hanson, L., Liles, M.R., Hossain, M.J., Griffin, M. and Hemstreet, W. 2014 Motile Aeromonas Septicemia In: Fish Health Section Blue Book 2014 Edition, section 1.2.9. American Fisheries Society-Fish Health Section, Bethesda, Maryland.

  6. Wang, L., Nasrin, S., Liles, M.R., and Yu, Z. 2014 Use of bacterial artificial chromosomes in metagenomic studies, pp. 1-12. In: The Encyclopedia of Metagenomics, Edited by Nelson, K,Highlander, S, Rodriguez-Valera, F, White BA. Berlin Heidelberg: Springer-Verlag.

  7. Chander, Y., Koelbl, J., Puckett, J., Moser, M.J., Liles, M.R., Carrias, A., Mead, D.A., and Schoenfeld, T.W. 2014 OmniAmp DNA polymerase, a novel thermostable viral enzyme for LAMP. Frontiers in Microbiology 5:1-11, doi: 10.3389/fmicb.2014.00395.

  8. Hossain, M.J., Sun, D., McGarey, D.J., Wrenn, S., Alexander, L.M., Martino, M.E., Xing, Y., Terhune, J.S., and Liles, M.R. 2014 An Asian origin of virulent Aeromonas hydrophila responsible for disease epidemics in United States-farmed catfish. mBio 5(3):e00848-14. doi:10.1128/mBio.00848-14.

  9. Zhou, Z., Yao, B., Romero, J., Waines, P., Ringø, E., Emery, M., Liles, M. R. and Merrifield, D. L. 2014 Methodological Approaches Used to Assess Fish Gastrointestinal Communities, in Aquaculture Nutrition: Gut Health, Probiotics and Prebiotics (eds D. Merrifield and E. Ringø), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9781118897263.ch5


  10. Hossain, M.J., Waldbieser, G.C., Sun, D., Capps, N.K., Hemstreet, W.B., Griffin, M.J., Khoo, L., Goodwin, A.E., Sonstegard, T., Schroeder, S., Hayden, K., Newton, J.C., Terhune, J.S., and Liles, M.R. 2013 Implication of lateral genetic transfer in the emergence of Aeromonas hydrophila isolates of epidemic outbreaks in channel catfish. PLOS ONE 8: e80943. doi:10.1371/journal.pone.0080943

  11. Looper, J.K., Cotto, A., Kim, B.-Y., Lee, M.-K., Liles, M.R., Chadhain, S.M., and Son, A. 2013 Microbial community analysis of Deepwater Horizon oil-spill impacted sites along the Gulf coast using functional and phylogenetic markers. Environmental Science: Processes and Impacts, 15(11):2068-79.

  12. Davis, R., Hossain, M.J., Liles, M.R., and Panizzi, P. 2013 Complete Genome Sequence of Staphylococcus aureus Tager 104, a ST49 ancestor. Genome Announcements, vol. 1 no. 5 e00706-13.

  13. Tekedar, H., Waldbieser, G., Karsi, A., Liles, M., Griffin, M., Vamenta, S., Sonstegard, T., Hossain, M., Schroeder, S., Khoo, L., and Lawrence, M. 2013 Complete genome sequence of channel catfish epidemic isolate Aeromonas hydrophila ML09-119. Genome Announcements vol. 1 no. 5 e00755-13.

  14. Zheng, H., Chatfield, C.H., Liles, M.R., and Cianciotto, N.P. 2013 Secreted Pyomelanin of Legionella pneumophila Promotes Bacterial Iron Uptake and Growth Under Iron-Limiting Conditions. Infection and Immunity, 81(11):4182-91.

  15. Griffin, M.J., Goodwin, A.E., Merry, G., Williams, M.A., Liles, M.R., and Waldbieser, G. 2013 Rapid quantitative detection of Aeromonas hydrophila strains responsible for an epidemic in channel catfish. Journal of Veterinary Diagnostic Investigation 25: 473-481

  16. Morrow, K.M., Liles, M.R., Paul, V., Moss, A., and Chadwick, N.E. 2013 Bacterial shifts associated with coral-macroalgal competition in three Caribbean regions. Marine Ecology Progress Series, 488:103-117.

  17. Ashby, D., Brady, S.F., Cowan, D.A., Doemer, J., Edwards, E.A., Fiebig, K., Martens, E.C., McCormac, D., Mead, D.A., Miyazaki, K., Moreno-Hagelsieb, G., O’Gara, F., Reid, A., Rose, D.R., Simonet, P., Sjöling, S., Smalla, K., Streit, W.R., Tedman-Jones, J., Valla, S., Wellington, E.M.H., Wu, C.C., Liles, M.R., Neufeld, J.D., Sessitsch, A., and Charles, T.C. 2013 Meeting Report: 1st International Functional Metagenomics Workshop May 7–8, 2012, St. Jacobs, Ontario, Canada. Standards in Genomic Sciences, 8(1).

  18. Wu, Y., Wang, K., Buschle-Diller, G., and Liles, M.R. 2013 Fiber formation by dehydration-induced aggregation of albumin. Journal of Applied Polymer Science, DOI: 10.1002/APP.38771.

  19. Wang, X., Liles, M.R., and Son, Ahjeong. 2013 Quantification of E. coli O157:H7 in soils using an inhibitor-resistant NanoGene assay. Soil Biology and Biochemistry, 58:9-15.


  20. Morrow, K. M., Ritson-Williams, R., Ross, C., Liles, M. R., and Paul, V. J. 2012 Macroalgal extracts induce bacterial assemblage shifts and sublethal tissue stress in Caribbean corals. PLoS One 7: e44859

  21. Morrow, K.M., Ritson-Williams, R., Ross, C., Liles, M.R., and Paul, V. 2012 Allelochemicals produced by Caribbean macroalgae alter coral-bacterial communities and tissue stress responses in situ. PLoS ONE 7(9): e44859. doi:10.1371/journal.pone.0044859.

  22. Ran, C., Carrias, A., Williams, M.A., Capps, N., Dan, B.C.T, Newton, J.C., Kloepper, J.W., Ooi, E.L., Browdy, C.L., Terhune, J.S., and Liles, M.R. 2012 Identification of Bacillus strains for biological control of catfish pathogens. PLoS ONE 7: e45793. doi:10.1371/journal.pone.0045793.

  23. Morrow, K.M., Moss, A., Chadwick, N.E., and Liles, M.R. 2012 Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability. Applied and Environmental Microbiology 78: 6438-6449

  24. Hossain, M.J., Rahman, K.S., Terhune, J.S., and Liles, M.R. 2012 An Outer Membrane Porin Protein Modulates Phage Susceptibility in Edwardsiella ictaluri. Microbiology 158: 488-497

  25. Carrias, A., Ran, C., Terhune, J., and Liles, M.R. 2012 Biological agents for control of disease in aquaculture, pp. 353-393. In: Infectious Diseases in Aquaculture, S. Austin (Ed.). London: Woodhead Publishing.


  26. George, I.F., Hartmann, M., Liles, M.R., and Agathos, S.N. 2011 Recovery of as-yet-uncultured soil Acidobacteria on dilute solid media. Applied and Environmental Microbiology 77: 8184-8188

  27. Zhou, P., Hussain, S.K., Liles, M.R., Arias, C.R., Backert, S., Kieninger, J., and Oyarzabal, O.A. 2011 Simplified Enrichment Protocol for the Isolation of Campylobacter spp. from Retail Broiler Meat. BMC Microbiology 11: 175

  28. Parsley, L.C., Goode, A.M., Becklund, K., George, I., Linneman, J., Lopanik, N.B., Goodman, R.M., and Liles, M.R. 2011 Polyketide synthase pathways identified from a metagenomic library are derived from soil Acidobacteria. FEMS Microbiology Ecology 78: 176-187

  29. Parsley, L.C., Wu, C., Mead, D., Goodman, R.M., and Liles, M.R. 2011 Soil Microbial DNA Purification Strategies for Multiple Metagenomic Applications. In: Handbook of Molecular Microbial Ecology, F. J. de Bruijn (Ed.). Hoboken, N.J.: John Wiley and Sons, Inc.

  30. Aakvik, T., Lale, R., Liles, M.R., and Valla, S. 2011 Metagenomic libraries for functional screening. In: Handbook of Molecular Microbial Ecology, F. J. de Bruijn (Ed.). Hoboken, N.J.: John Wiley and Sons, Inc. 4

  31. Wommack, K.E., Srinivasiah, S., Liles, M.R., Bhavsar, J., Bench, S., and Polson, S. 2011 Phages across the biosphere: Contrasts of viruses in soil and aquatic environments. In: Handbook of Molecular Microbial Ecology, F. J. de Bruijn (Ed.). Hoboken, N.J.: John Wiley and Sons, Inc.

  32. Sudini, H., Arias, C., Liles, M. R., Bowen, K., and Huettel, R. 2011 Exploring soil bacterial communities in different peanut cropping sequences using multiple molecular approaches. Phytopathology 101: 819-827

  33. Carrias, A., Welch, T.J., Waldbieser, G.C., Mead, D.A., Terhune, J.S., and Liles, M.R. 2011 Comparative genomic analysis of bacteriophages specific to the channel catfish pathogen Edwardsiella ictaluri. Virology Journal 8:6, doi:10.1186/1743-422X-8-6.

  34. Kakirde, K.S., Wild, J., Godiska, R., Mead, D., Wiggins, A., Szybalski, W., and Liles, M.R. 2011 Gram-negative shuttle BAC vector for heterologous expression of metagenomic libraries. Gene 475: 57-62

  35. Morrow, K.M., Paul, V.J., Liles, M.R., and Chadwick, N.E 2011 Allelochemicals produced by Caribbean macroalgae and cyanobacteria have species-specific effects on reef coral microorganisms. Coral Reefs 30: 309-320


  36. Kakirde, K.S., Parsley, L.C., and Liles, M.R. 2010 Size Does Matter: Application-driven Approaches for Soil Metagenomics. Soil Biology and Biochemistry 42: 1911-1923

  37. Sudini, H., Arias, C., Liles, M.R., Bowen, K., and Huettel, R. 2010 Comparison of soil fungal community structure in different peanut rotation sequences using RISA in relation to aflatoxin producing fungi. Phytopathology, 101(1):52-7.

  38. Parsley, L.C., Consuegra, E.J., Kakirde, K.S., Land, A.M., Harper, W.F., and Liles, M.R. 2010 Identification of diverse antimicrobial resistance determinants encoded on bacterial, plasmid, and bacteriophage metagenomes from an activated sludge microbial community. Applied and Environmental Microbiology 76: 3753-3757

  39. Parsley, L.C., Consuegra, E.J., Thomas, S.J., Bhavsar, J., Land, A.M., Bhuiyan, N.N., Mazher, M.A., Waters, R.J., Wommack, K.E., Harper, W.F., and Liles, M.R. 2010 A census of the viral metagenome within an activated sludge microbial assemblage. Applied and Environmental Microbiology 76: 2673-2677

  40. Parsley, L.C., Newman, M. and Liles, M.R. 2010 Fluorescence in situ hybridization of bacterial cell suspensions. Cold Spring Harbor Protocols, doi: 10.1101/pdb.prot5493.

  41. Newman, M.M., Feminella, J.W., and Liles, M.R. 2010 Purification of genomic DNA from environmental sources for use in a polymerase chain reaction. Cold Spring Harbor Protocols, doi:10.1101/pdb.prot5383.

  42. Liles, M.R., Turkmen, O., Manske, B.F., Zhang, M., Rouillard, J.M., George, I.F., Balser, T., Billor, N., and Goodman, R.M. 2010 A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria reveals a lineage-specific distribution in a soil clay fraction. Soil Biology and Biochemistry, 42(5):739-747.


  43. Schoenfeld, T., Liles, M.R., Wommack, K.E., Polson, S.W., Godiska, R., and Mead, D. 2009 Functional viral metagenomics and the next generation of molecular tools. Trends in Microbiology 18: 20-29

  44. George, I.F., Liles, M.R., Hartmann, M., Ludwig, W., Goodman, R.M., and Agathos, S. N. 2009 Changes in soil Acidobacteria communities after 2,4,6-trinitrotoluene contamination. FEMS Microbiology Letters 296: 159-166

  45. Liles, M. R., Williamson, L. L., Rodbumrer, J., Parsley, L., Torsvik, V., Goodman, R. M., and Handelsman, J. 2009 Isolation and cloning of high molecular weight metagenomic DNA from soil microorganisms. Cold Spring Harbor Protocols, doi:10.1101/pdb.prot5271.


  46. Walakira, J., Carrias, A., Hossain, M.J., Jones, E., Terhune, J.S., and Liles, M.R. 2008 Identification and characterization of bacteriophages specific to the catfish pathogen Edwardsiella ictaluri. Journal of Applied Microbiology 105: 2133-2142

  47. Srinivasiah, S., Bhavsar, J., Thapar, K., Liles, M. R., Shoenfeld, T., and Wommack, K.E. 2008 Phages across the biosphere: Contrasts of viruses in soil and aquatic environments. Research in Microbiology 159: 349-357

  48. Liles, M. R., Williamson, L. L., Rodbumrer, J., Torsvik, V., Goodman, R. M., and Handelsman, J. 2008 Recovery, purification, and cloning of high molecular weight genomic DNA from soil microorganisms. Applied and Environmental Microbiology 74: 3302-3305


  49. Shi, J., Aono, S., Lu, W., Ouellette, A.J., Hu, X., Ji, Y., Wang, L., Lenz, S., Van Ginkel, F., Liles, M.R., Dykstra, C., Morrison, E.E., and Elson, C.O. 2007A novel role for defensins in intestinal homeostasis: regulation of IL-1 secretion, Journal of Immunology, 179(2):1245-1253.


  50. Sabree, Z.L., Bergendahl, V., Liles, M.R., Goodman, R.M., Handelsman, J., and Burgess, D. 2006 Identification and characterization of the Acidobacterium capsulatum major sigma factor. Gene, 376:144-151.


  51. Liles, M.R., Williamson, L.L., Goodman, R.M., and Handelsman, J. 2004 Isolation of high molecular weight genomic DNA from soil bacteria for genomic library construction. In: Molecular Methods in Environmental Microbiology, Kowalchuk, G.A.; de Bruijn, F.J.; Head, I.M.; Akkermans, A.D.; van Elsas, J.D. (Eds.), pp. 839-852.


  52. Liles, M.R., Manske, B.F., Bintrim, S.B., Handelsman, J., and Goodman, R.M. 2003 A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Applied and Environmental Microbiology 69: 2684-2691


  53. Handelsman, J., Liles, M.R., Mann, D., Riesenfeld, C., and Goodman, R.M. 2002 Cloning the metagenome: Culture-independent access to the diversity and functions of the uncultivated microbial world. Methods in Microbiology 33: 241-255

  54. Gillespie, D.E., Brady, S.F., Bettermann, A.D., Cianciotto, N.P., Liles, M.R., Rondon, M.R., Clardy, J., Goodman, R.M., Handelsman, J. 2002 Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Applied and Environmental Microbiology 68: 4301-4306

  55. Nelson, B.P., Liles, M.R., Frederick, K.B., Corn, R.M., and Goodman, R.M. 2002 Label-free detection of 16S ribosomal RNA hybridization onto reusable DNA arrays using surface plasmon resonance imaging. Environmental Microbiology, 4(11):735-743.


  56. Nelson, B. C., Grimsrud, T. E., Liles, M. R., Goodman, R. M., and Corn, R. M. 2001 Surface plasmon resonance imaging measurements of DNA and RNA Hybridization-Adsorption onto DNA microarrays. Analytical Chemistry 73: 1-7


  57. Rondon, M.R., August, P.R., Bettermann, A.D., Brady, S.F., Grossman, T.H., Liles, M.R., Loiacono, K.A., Lynch, B.A., MacNeil, I.A., Minor, C., Tiong, C.L., Gilman, M., Osbourne, M.S., Clardy, J., Handelsman, J., and Goodman, R.M. 2000 Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Applied and Environmental Microbiology, 66 (6): 2541-2547.

  58. Liles, M. R., Scheel, T. A., and Cianciotto, N. P. 2000 Discovery of a non-classical siderophore, legiobactin, produced by strains of Legionella pneumophila. Journal of Bacteriology, 182 (3): 749-757.


  59. Liles, M. R., Edelstein, P. H., and Cianciotto, N. P. 1999 The prepilin peptidase is required for protein secretion by and the virulence of the intracellular pathogen Legionella pneumophila. Molecular Microbiology 31: 959-970


  60. Liles, M. R., Viswanathan, V. K., and Cianciotto, N. P. (1998) Identification and temperature regulation of Legionella pneumophila genes involved in type IV pilus biogenesis and type II secretion. Infection and Immunity, 66:1776-1782. 6


  61. Liles, M.R., and Cianciotto, N.P. 1996 Absence of siderophore-like activity in Legionella pneumophila supernatants. Infection and Immunity, 64: 1873-1875.


  62. Miceli, M. V., Liles, M. R., and Newsome, D. A. 1994 Evaluation of oxidative processes in human retinal pigment epithelial cells associated with retinal outer segment phagocytosis. Experimental Cell Research 214: 242-249

  63. Newsome, D. A., Miceli, M. V., Liles, M. R., Tate, D. J., and Oliver, P. D. 1994 Antioxidants in the retinal pigment epithelium. Progress in Retinal and Eye Research, 13:101-123.


  64. Liles, M. R., Oliver, P. D., and Newsome, D. A. 1991 Antioxidant enzymes in the aging human retinal pigment epithelium. Archives of Ophthalmology 109: 1285-1288


  65. Newsome, D. A., Dobard, E. P., Liles, M. R., and Oliver, P. D. 1990 Human retinal pigment epithelium contains two distinct species of superoxide dismutase. Investigative Ophthalmology and Visual Science 31: 2508-2513

Comments about the content of these pages:

Mark Liles, Ph.D.
Environmental Microbiology

Bashan Fuondation

Designed by: Juan Pablo Hernandez