My research group has an interest in three primary areas:

1) Metagenomic Analysis of Microbial Assemblages. We use a microbial community genomic approach (a.k.a.“metagenomic”) to study complex microbial assemblages in different environments. The research topics include expression of natural products (enzymes, metabolites) encoded by environmental metagenomes. In particular, we focus on expression of biosynthetic gene clusters obtained from soil metagenomes in order to characterize bioactive metabolites that can inhibit the growth of multidrug-resistant pathogens.

2) Biological control of disease using beneficial microorganisms. We have identified probiotic bacteria, particularly within the genus Bacillus, that can prevent and control disease in aquaculture farmed fish and in agriculturally important plants. We are investigating the natural products produced by these probiotics that can enhance growth performance of the animal or plant host, or inhibit the growth of pathogenic microorganisms. We also are investigatings ways to enhance the metabolism of these probiotics to enhance their in situ beneficial activities.

3) Pathogenesis and control of virulent Aeromonas hydrophila. Our studies have led to the development of diagnostic methods and a vaccine for a virulent strain of Aeromonas hydrophila that is responsible for severe epidemic outbreaks of disease in farmed fish in the United States, China and other countries. Our lab studies the pathogenesis of disease and the control of disease using both biological control agents and an attenuated vaccine. We are also helping the worldwide community of aquaculture researchers track the distribution and spread of virulent Aeromonas hydrophila.

• Pereira, Alinne, Francesco S. Moen, Beatrice Severance, and Mark R. Liles. (2023) Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment. Frontiers in Microbiology 14: 1114548. https://doi.org/10.3389/fmicb.2023.1114548

• Xu, T., Rasmussen-Ivey, C.R., Moen, F.S. , Fernández-Bravo, A., Lamy, B., Beaz-Hidalgo, R.,  Khan, C.D., Escarpulli, G.C., Yasin, I.S., Figueras, M.J., Sayuti, M.A., Karim, M.M., Mazharul, K.M., Le, T.T.T., Thao, N.H.P., Addo, S., Duodu, S., Ali, S., Latif, T., Mey, S., Thay, S., and Liles, M.R. (2023) A global survey of hypervirulent Aeromonas hydrophila (vAh)  identified vAh strains in the lower Mekong River basin and diverse opportunistic pathogens from farmed fish and other environmental sources. Microbiology Spectrum. https://doi.org/10.1128/spectrum.03705-22
• Afroj, S., Brannen, A. D., Nasrin, S., Al Mouslem, A., Hathcock, T., Maxwell, H., Rasmussen-Ivey, C., Sandage, M.J., Davis, E., Panizzi, P., Wang, C. and Liles, M. R. (2021). Bacillus velezensis AP183 inhibits Staphylococcus aureus biofilm formation and proliferation in murine and bovine disease models. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.746410
• Pereira, A., Sandoval-Powers, M., Monsma, S., Zhou, J., Santos, S.R., Mead, D.A., and Liles, M.R. (2020) Discovery of novel biosynthetic gene cluster diversity from a soil metagenomic library. Frontiers in Microbiology, vol. 11, Open access article link

• Barger, P.C., Liles, M.R., Beck, B.H. and Newton, J.C. (2020) Differential Production and Secretion of Potentially Toxigenic Extracellular Proteins from Hypervirulent Aeromonas hydrophila Under Biofilm and Planktonic Culture. BMC Microbiology, DOI: 10.21203/rs.3.rs-70188/v2

• Barger, P.C., Liles, M.R. and Newton, J.C. (2020) Type II Secretion Is Essential for Virulence of the Emerging Fish Pathogen, Hypervirulent Aeromonas hydrophila. Frontiers in Veterinary Science. https://doi.org/10.3389/fvets.2020.574113

• Thurlow, C.M., Hossain, M.J., Heiss, C., Sun, D., Foshee, L., Wang, Z., Azadi, P., Newton, J.C., Terhune, J.S., Saper, M.A., and Liles, M.R. (2019) The gfc operon is involved in the formation of the O antigen capsule in Aeromonas hydrophila and contributes to virulence in channel catfish. Aquaculture, https://doi.org/10.1016/j.aquaculture.2019.734334

• Hassan, M.K., McInroy, J.A., Jones, J., Shantharaj, D., Liles, M.R. and Kloepper, J.W. (2019) Pectin-rich amendment enhances soybean growth and nodulation mediated by Bacillus velezensis strains. Plants, 8(5).

• Thurlow, C.M., Williams, M.A., Carrias, A., Ran, C., Newman, M., Tweedie, J., Allison, E., Jescovitch, L.N., Terhune, J.S. and Liles, M.R. (2019) Bacillus velezensis AP193 exerts probiotic effects in channel catfish (Ictalurus punctatus) and reduces aquaculture pond eutrophication. Aquaculture, 503:347-356.

• Wang, E., Yuan, Z., Wang, K., Gao, D., Liu, Z. and Liles, M.R. (2019) Consumption of florfenicol-medicated feed alters the composition of the channel catfish intestinal microbiota including enriching the relative abundance of opportunistic pathogens. Aquaculture, 501:111-118.

• Li, Y., Liles, M.R. and Halanych, K. (2018) Endosymbiont genomes yield clues of tubeworm success. ISME Journal, 12: 2785–2795.

• Nasrin, S., Ganji, S., Kakirde, K.S., Jacob, M.R., Wang, M., Rao, R.R., Cobine, P.A., Khan, I.A., Wu, C.C., Mead, D.A., Li, X.-C. and Liles, M.R. (2018) Chloramphenicol derivatives with antibacterial activity identified by functional metagenomics. Journal of Natural Products, 81(6):1321-1332.

• Lewin, A., Zhou, J., Pham, V.T.T., Haugen, T., Zeiny, M.E., Aarstad, O., Liebl, W., Wentzel, A. and Liles, M.R. (2017) Novel Archaeal Thermostable Cellulases from an Oil Reservoir Metagenome. Applied Microbiology and Biotechnology, 7:183.

• Rasmussen-Ivey, C., Hossain, M.J., Odom, S.E., Terhune, J.S., Hemstreet, W.G., Shoemaker, C.A., Zhang, D., Xu, D., Griffin, M.J., Liu, Y., Figueras, M.J., Santos, S.R., Newton, J.C. and Liles, M.R. (2016) Classification of a hypervirulent Aeromonas hydrophila pathotype responsible for epidemic outbreaks in warm-water fishes. Frontiers in Microbiology DOI: 10.3389/fmicb.2016.01615

• Rasmussen-Ivey, C., Figueras, M.J., McGarey, D. and Liles, M.R. (2016) Virulence factors of Aeromonas hydrophila: In the wake of reclassification. Frontiers in Microbiology 7:1337.

• Fasina, Y.O., Newman, M.M., Stough, J.M. and Liles, M.R. (2016) Effect of Clostridium perfringens infection and antibiotic administration on microbiota in the small intestine of broiler chickens. Poultry Science 95:247-260.

• Hassan, M.K., Choi, S.K., Jeong, H., Newman, M., Kloepper, J.W., and Liles, M.R. (2015) Deciphering the conserved genetic loci implicated in disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum strains. Frontiers in Plant Science 6:631.

• Ravu, R.R., Jacob, M.R., Chen, X., Wang, M., Nasrin, S., Kloepper, J.W., Liles, M.R., Mead, D.A., Khan, I.A., and Li, X.-C. (2015) Bacillusin A, A Potent Antibacterial Macrodiolide from Bacillus amyloliquefaciens AP183. Journal of Natural Products 78:924-928.

• 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:e00848-14.

• 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

• 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.

• 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.

For a complete list of peer-reviewed publications (>100) please see my Google Scholar Page