Microbiology and immunology
in the national interest

About our group

The Microbiology/Immunology Group is part of the Biosciences and Biotechnology Division within the Physical and Life Sciences Directorate at Lawrence Livermore National Laboratory.

We are a diverse group of scientists with expertise in microbiology, virology, immunology, infectious disease pathogenesis, and microbiome science.

We conduct research on clinical and environmental host–pathogen interactions, vaccine and therapeutic design, viral evolution, and microbial communities. Our projects prioritize application spaces critical to the national interest, including biothreat viruses and bacteria, rapid responses to emerging disease, and military medicine.

Mission: Perform leading-edge microbiology and immunology research to fill knowledge gaps and deliver technology products that serve vital national needs.

Vision: Maintain and expand an innovative, flexible portfolio of multidisciplinary research that integrates LLNL’s biomedical, computational, and bioengineering capabilities for an improved national capacity to address emerging needs in infectious disease and microbe–human dynamics.

We address our mission space through capabilities in:

  • Comparative genomics and metagenomics
  • Next-generation sequencing and bioinformatics
  • Animal models
  • In vitro assay design, development, and application
  • Integration with high-performance computing simulations and machine learning

In the news

Our team

Team

Our publications

2023

Coccidioidomycosis Osteoarticular Dissemination | J. Fungi
B.M. Moni, B.L. Wise, G.G. Loots, D.R. Weilhammer

Evaluation of 6-OxP-CD, an Oxime-based cyclodextrin as a viable medical countermeasure against nerve agent poisoning: Experimental and molecular dynamic simulation studies on its inclusion complexes with cyclosarin, soman and VX | PLoS One
E.Y. Lau, H.A. Enright, V. Lao, M.A. Malfatti, B.P. Mayer, A.M. Williams, C.A. Valdez

Improved chemical synthesis, identification and evaluation of prospective centrally active oxime antidotes for the treatment of nerve agent exposure | Tetrahedron
C.A. Valdez, D. Lam, V. Lao, A. Subramanian, H.A. Enright, M.A. Malfatti, N.A. Be, M.L. Dreyer

Targeted metagenomic assessment reflects critical colonization in battlefield injuries | Microbiol. Spectr.
C.R. Kok, N. Mulakken, J.B. Thissen, S.F. Grey, A. Avila-Herrera, M.M. Upadhyay, F.A. Lisboa, S. Mabery, E.A. Elster, S.A. Schobel, N.A. Be

2022

Domestic Dogs as Sentinels for West Nile Virus but not Aedes-borne Flaviviruses, Mexico | Emerg. Infect. Dis.
E. Davila, N.A. Fernández-Santos, J.G. Estrada-Franco, L. Wei, J.A. Aguilar-Durán, M. de J. López-López, R. Solís-Hernández, R. García-Miranda, D.D. Velázquez-Ramírez, J. Torres-Romero, S. Arellano Chávez, R. Cruz-Cadena, R. Navarro-López, A.A. Pérez de León, C. Guichard-Romero, E. Martin, W. Tang, M. Frank, M. Borucki, M.J. Turell, A. Pauvolid-Corrêa, M.A. Rodríguez-Pérez, H. Ochoa-Díaz-López, S.A. Hamer, G.L. Hamer

Large-scale application of free energy perturbation calculations for antibody design | Scientific Reports
F. Zhu, F.A. Bourguet, W.F.D. Bennett, E.Y. Lau, K.T. Arrildt, B.W. Segelke, A.T. Zemla, T.A. Desautels, and D.M. Faissol

MAVS mediates a protective immune response in the brain to Rift Valley fever virus | PLOS Pathogens
N.R. Hum, F.A. Bourguet, A. Sebastian, D. Lam, A.M. Phillips, K.R. Sanchez, A. Rasley, G.G. Loots, and D.R. Weilhammer

Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds | Sci. Rep.
A. Avila-Herrera, J.B. Thissen, N. Mulakken, S.A. Schobel, M.D. Morrison, X. Zhou, S.F. Grey, F.A. Lisboa, D. Unselt, S. Mabery, M.M. Upadhyay, C.J. Jaing, E.A. Elster, N.A. Be

Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples | Viruses
J. Kimbrel, J. Moon, A. Avila-Herrera, J.M. Martí, J. Thissen, N. Mulakken, S.H. Sandholtz, T. Ferrell, C. Daum, S. Hall, B. Segelke, K.T. Arrildt, S. Messenger, D.A. Wadford, C. Jaing, J.E. Allen, M.K. Borucki

SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection | Viruses
J. McGowan, M. Borucki, H. Omairi, M. Varghese, S. Vellani, S. Chakravarty, S. Fan, S. Chattopadhyay, M. Siddiquee, J.B. Thissen, N. Mulakken, J. Moon, J. Kimbrel, A.K. Tiwari, R.T. Taylor, D.W. Kang, C. Jaing, R. Chakravarti, S. Chattopadhyay

Tailored approach to study Legionella infection using a lattice light sheet microscope (LLSM) | Biomed Opt. Express
X. Yi, H. Miao, J.K. Lo, M.M. Elsheikh, T.H. Lee, C. Jiang, Y. Zhang, B.W. Segelke, K.W. Overton, P.T. Bremer, T.A. Laurence

2021

A Survey of Preclinical Studies Evaluating Nanoparticle-Based Vaccines Against Non-Viral Sexually Transmitted Infections | Front. Pharmacol.
A. Abisoye-Ogunniyan, M. Carrano, D.R. Weilhammer, S.F. Gilmore, N.O. Fischer, S. Pal, L.M. de la Maza, M.A. Coleman, A. Rasley

Development of a CNS-permeable reactivator for nerve agent exposure: an iterative, multi-disciplinary approach | Sci. Rep.
B.J. Bennion, M.A. Malfatti, N.A. Be, H.A. Enright, S. Hok, C.L. Cadieux, T.S. Carpenter, V. Lao, E.A. Kuhn, M.W. McNerney, F.C. Lightstone, T.H. Nguyen, C.A. Valdez

Development of potent and effective synthetic SARS-CoV-2 neutralizing nanobodies | mAbs
M.A. Stefan, Y.K. Light, J.L. Schwedler, P.R. McIlroy, C.M. Courtney, E.A. Saada, C.E. Thatcher, A.M. Phillips, F.A. Bourguet, C.M. Mageeney, S.A. McCloy, N.M. Collette, O.A. Negrete, J.S. Schoeniger, D.R. Weilhammer, B. Harmon

Discovery of Small-Molecule Inhibitors of SARS-CoV-2 Proteins Using a Computational and Experimental Pipeline | Front. Mol. Biosci.
E.Y. Lau, O.A. Negrete, W.F.D. Bennett, B.J. Bennion, M. Borucki, F. Bourguet, A. Epstein, M. Franco, B. Harmon, S. He, D. Jones, H. Kim, D. Kirshner, V. Lao, J. Lo, K. McLoughlin, R. Mosesso, D.K. Murugesh, E.A. Saada, B. Segelke, M.A. Stefan, G.A. Stevenson, M.W. Torres, D.R. Weilhammer, S. Wong, Y. Yang, A. Zemla, X. Zhang, F. Zhu, J.E. Allen, F.C. Lightstone

Performance of three-dimensional printed nasopharyngeal swabs for COVID-19 testing | MRS Bulletin
A. Tooker, M.L. Moya, D.N. Wang, D. Freeman, M. Borucki, E. Wheeler, G. Larsen, M. Shusteff, E.B. Duoss, C.M. Spadaccini Tooker

Quantitative Fit Evaluation of N95 Filtering Facepiece Respirators and Coronavirus Inactivation Following Heat Treatment | Ann. Work Expo. and Health
T.L. Massey, M.K. Borucki, S.Y. Paik, K.W. Fuhrer, M. Bora, S.R. Kane, R.M. Haque, S.H. Baxamusa

Shotgun Immunoproteomic Approach for the Discovery of Linear B-Cell Epitopes in Biothreat Agents Francisella tularensis and Burkholderia pseudomallei | Front. Immunol.
P. D’haeseleer, N.M. Collette, V. Lao, B.W. Segelke, S.S. Branda, M. Franco

The Eco-Bio-Social Factors That Modulate Aedes aegypti Abundance in South Texas Border Communities | Insects
J.G. Juarez, S.M. Garcia-Luna, M.C.I. Medeiros, K.L. Dickinson, M.K. Borucki, M. Frank, I. Badillo-Vargas, L.F. Chaves, G.L. Hamer

2020

Cell fusing agent virus (Flavivirus) infection in Aedes aegypti in Texas: seasonality, comparison by trap type, and individual viral loads | Arch. Virol.
E. Martin, W. Tang, C. Briggs, H. Hopson, J.G. Juarez, S.M. Garcia-Luna, M.W. de Valdez, I.E. Badillo-Vargas, M.K. Borucki, M. Frank, G.L. Hamer

Characterization of Bacillus anthracis Spore Proteins Using a Nanoscaffold Vaccine Platform | Front. Immunol.
D.R. Weilhammer, A.D. Dunkle, T. Boone, S.F. Gilmore, M. Khemmani, S.K.G. Peters, P.D. Hoeprich, N.O. Fischer, C.D. Blanchette, A. Driks, A. Rasley

Countermeasures for Preventing and Treating Opioid Overdose | Clin. Pharmacol. Ther.
C.P. France, G.P. Ahern, S. Averick, A. Disney, H.A. Enright, B. Esmaeli-Azad, A. Federico, L.R. Gerak, S.M. Husbands, B. Kolber, E.Y. Lau, V. Lao, D.R. Maguire, M.A. Malfatti, G. Martinez, B.P. Mayer, M. Pravetoni, N. Sahibzada, P. Skolnick, E.Y. Snyder, N. Tomycz, C.A. Valdez

Crewmember microbiome may influence microbial composition of ISS habitable surfaces | PLoS One
A Avila-Herrera, J Thissen, C Urbaniak, NA Be, DJ Smith, F Karouia, S Mehta, K Venkateswaran, C. Jaing

High Rate of Non-Human Feeding by Aedes aegypti Reduces Zika Virus Transmission in South Texas | Viruses
M.F. Olson, M.L. Ndeffo-Mbah, J.G. Juarez, S. Garcia-Luna, E. Martin, M.K. Borucki, M. Frank, J.G. Estrada-Franco, M.A. Rodríguez-Pérez, N.A. Fernández-Santos, G.J. Molina-Gamboa, S.D. Carmona Aguirre, B.L. Reyes-Berrones, L.J. Cortés-De la Cruz, A. García-Barrientos, R.E. Huidobro-Guevara, R.M. Brussolo-Ceballos, J. Ramirez, A. Salazar, L.F. Chaves, I.E. Badillo-Vargas, G.L. Hamer

Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere | Sci. Rep.
C. Jaing, J. Thissen, M. Morrison, M.B. Dillon, S.M. Waters, G.T. Graham, N.A. Be, P. Nicoll, S. Verma, T. Caro, D.J. Smith

Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo | Viruses
N.M. Collette, V.H.I. Lao, D.R. Weilhammer, B. Zingg, S.D. Cohen, M. Hwang, L.L. Coffey, S.L. Grady, A.T. Zemla, M.K. Borucki

Two Sides of a Coin: a Zika Virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors | J. Virol.
D. Lemos, J.B. Stuart, W. Louie, A. Singapuri, A.L. Ramírez, J. Watanabe, J. Usachenko, R.I. Keesler, C. Sanchez-San Martin, T. Li, C. Martyn, G. Oliveira, S. Saraf, N.D. Grubaugh, K.G. Andersen, J. Thissen, J. Allen, M. Borucki, K.A. Tsetsarkin, A.G. Pletnev, C.Y. Chiu, K.K.A. Van Rompay, L.L. Coffey