Please find my list of peer-reviewed publications and preprints below.
If you'd like a copy of any publication, just email me!
^ = undergraduate mentee, * = grad student mentee
Please find my list of peer-reviewed publications and preprints below.
If you'd like a copy of any publication, just email me!
^ = undergraduate mentee, * = grad student mentee
2025
28. Kelliher, JM; Johnson, LY; Rodriguez, FE; Saunders, JK; Kroger, M; Hanson, B; Robinson, AJ; Anthony, W; Van Goethem, MW; Kiledal, A; Shibl, AA; de Andrade, AA; Ettinger, CL; Gupta, CL; Robinson, CR; Zuniga, C; Sprockett, D; Machado, DT; Skoog, EJ; Oduwole, I; Rothman, JA; Prime, K; Lane, KR; Lemos, LN; Karstens, L; McCauley, M; Seyoum, MM; Elmassry, MM; Guzel, M; Longley, R; Roux, S; Pitot, TM; Eloe-Fadrosh, EA. 2025. A cost and community perspective on the barriers to microbiome data reuse. 2025. Frontiers in Bioinformatics. Here's the link!
2024
27. ^Capocchi, JK; Figueroa-Romero, C; Dunham, SJB; Faraci, G; Rothman, JA; Whiteson, KL; Seo, D-O; Holtzman, DM; Grabrucker, S; Nolan, YM; Kaddurah-Daouk, RF; Jett, DA. What does the microbiome tell us about prevention and treatment of Alzheimer's Disease / Alzheimer's Disease and Related Dementias (AD/ADRD)? 2024. The Journal of Neuroscience. Here's the link!
26. Rothman, JA; Piccerillo, HL; Dunham, SJB; Riis, JL; Granger, DA; Thomas, EA; Whiteson, KL. 2024. The salivary metabolome of children and parental caregivers in a large-scale family environment study. npj Metabolic Health and Disease. Here's the link!
25. Rothman, JA; ^Saghir, A; Zimmer-Faust, AG; Langlois, K; *Raygoza, K; Steele, JA; Griffith, JF; Whiteson, KL. 2024. Longitudinal sequencing and variant detection of SARS-CoV-2 across Southern California wastewater. Applied Microbiology. Here's the link!
24. Dunham, SJB; Avelar-Barragan, J; Rothman, JA; Adams, ED; Faraci, G; Forner, S; Kawauchi, K; Tenner, AJ; Green, K; LaFerla, F; MacGregor, G; Mapstone, M; Whiteson, KL. 2024. Sex-specific associations between AD genotype and the microbiome of human amyloid beta knock-in mice. Alzheimer's & Dementia: The Journal of the Alzheimer's Association. Here's the link!
2023
23. Rothman, JA; Riis, JL; Hamilton, KR; Blair, C; Granger, DA; Whiteson, KL. 2023. Oral microbial communities in children, caregivers, and associations with salivary biomeasures and environmental tobacco smoke exposure. mSystems. Here's the link!
Featured as part of the ASM Diversity, Equity, and Inclusivity special collection.
22. Zünd, M; Dunham, SJB; Rothman, JA; Whiteson, KL. 2023. What lies beneath? Taking the plunge into the murky waters of phage biology. mSystems. Here's the link!
Find the associated video here!
Featured as an "Editor's Choice" article.
2022
21. Rothman, JA; ^Saghir, A; Chung, S-A; *Boyajian, N; ^Dinh, T; ^Kim, J; *Saravanan, V; ^York, C; Zimmer-Faust, AG; Langlois, K; Steele, JA; Griffith, JF; Whiteson, KL. 2022. Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread antibiotic resistance genes. Water Research. Here's the link!
20. Rothman, JA; Whiteson, KL. 2022. Sequencing and variant detection of eight abundant plant-infecting tobamoviruses across Southern California wastewater. Microbiology Spectrum. Here's the link!
2021
19. Rothman, JA; Loveless, TB; Kapcia, J; *Adams, ED; Steele, JA; Zimmer-Faust, AG; Langlois, K; Wanless, D; Griffith, M; Mao, L; Chokry, J; Griffith, JF; Whiteson, KL. 2021. RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants. Applied and Environmental Microbiology. Here's the link!
Featured in National Geographic's article "One of the best tools for predicting COVID-19 outbreaks? Sewage." Here's the link!
Featured as a Spotlight article of significant interest and part of the ASM COVID-19 special collection.
18. Rothman, JA; Loope, KJ; McFrederick, QS; Wilson Rankin, E. 2021. Microbiome of the wasp Vespula pensylvanica in native and invasive populations, and associations with Moku virus. PLoS ONE. Here's the link!
2020
17. Gallagher, T; Riedel, S; Kapacia, J; Caverly, LJ; Carmody, L; Kalikin LM; Lu, J; Phan, J; Gargus, M; Kagawa, M; Leemans, SW; Rothman, JA; Grun, F; LiPuma, JJ; Whiteson, KL. 2020. LC-MS detection of antibiotic agents in sputum from persons with cystic fibrosis. Antimicrobial Agents and Chemotherapy. Here's the link!
16. Rothman, JA; Russell, KA; Leger, L; McFrederick, QS; Graystock, P. 2020. The direct and indirect effects of environmental toxicants on the health of bumble bees and their microbiomes. Proceedings of the Royal Society B. Here's the link!
15. Rothman, JA; Loveless, TB; Griffith, ML; Steele, JA; Griffith, JL; Whiteson, KL. 2020. Metagenomics of wastewater influent from Southern California wastewater treatment facilities in the era of COVID-19. Microbiology Resource Announcements. Here's the link!
14. Rothman, JA; Cox-Foster, D; *Andrikopoulos, C; McFrederick, QS. 2020. Diet breadth affects bacterial identity but not diversity in the pollen provisions of closely related polylectic and oligolectic bees. Insects. Here's the link!
2019
13. Palmer-Young, EC; Ngor, L; Nevarez, RB; Rothman, JA; Raffel, TR; McFrederick, QS. 2019. Temperature dependence of parasitic infection and gut bacterial communities in bumble bees. Environmental Microbiology.
Part of the special issue "Pathogen and Antimicrobial Resistance Ecology." Here's the link!
Featured in the Society for Applied Microbiology's magzine, "Microbiologist." Here's the link!
12. Rothman, JA; Leger, LM; Kirkwood, J; McFrederick, QS. 2019. Cadmium and selenate exposure affects the honey bee microbiome and metabolome, and bee-associated bacteria show potential for bioaccumulation. Applied and Environmental Microbiology. Here's the link!
11. Rothman, JA; Leger, LM; Graystock, P; Russell, KA; McFrederick, QS. 2019. The bumble bee microbiome increases survival of bees exposed to selenate toxicity. Environmental Microbiology.
Part of the special issue "Our Microbial Overlords." Here's the link!
10. Rubanov, A; Russell, KA; Rothman, JA; Nieh, JC; McFrederick, QS. 2019. Intensity of Nosema ceranae infection is associated with specific honey bee gut bacteria and weakly associated with gut microbiome structure. Scientific Reports. Here's the link!
9. Rothman, JA; Andrikopoulos, CJ; Cox-Foster, D; McFrederick, QS. 2019. Floral and foliar source affect the bee nest microbial community. Microbial Ecology. Here's the link!
2018
8. Carroll, MJ; Meikle, WG; McFrederick, QS; Rothman, JA; Brown, NJ; Weiss, M; Ruetz, Z; Chang, E. 2018. Pre-almond supplemental forage improves colony survival and alters queen pheromone signaling in overwintering colonies. Apidologie. Here's the link!
7. McFrederick, QS; Vuong, HQ; Rothman, JA. 2018. Lactobacillus micheneri sp. nov., Lactobacillus timberlakei sp. nov., and Lactobacillus quenuiae sp. nov., lactic acid bacteria isolated from wild bees and flowers. International Journal of Systematic and Evolutionary Microbiology. Here's the link!
6. Pennington, MJ; Rothman, JA; Jones, MB; McFrederick, QS; Gan, J; Trumble, JT. 2018. Effects of contaminants of emerging concern on Myzus persicae (Sulzer, Hemiptera: Aphididae) biology and on their host plant, Capsicum annum. Environmental Assessment and Monitoring. Here's the link!
5. Rothman, JA; Carroll, MJ; Meikle, WG; Anderson, KE; McFrederick, QS. 2018. Longitudinal effects of supplemental forage on the honey bee (Apis mellifera) microbiota and inter- and intra-colony variability. Microbial Ecology. Here's the link!
2017
4. Pennington, MJ; Rothman, JA; Dudley, SL; Jones, MB; McFrederick, QS; Gan, J; Trumble, JT. 2017. Contaminants of emerging concern affect Trichoplusia ni growth and development on artificial diets and a key host plant. Proceedings of the National Academy of Sciences USA. Here's the link!
3. Pennington, MJ; Rothman, JA; Jones, MB; McFrederick, QS; Gan, J; Trumble, JT. 2017. Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community. Scientific Reports. Here's the link!
2013
2. Biswas, A; Elmatari, D; Rothman, JA; LaMunyon, CW; Said, HM. 2013. Identification and functional characterization of the Caenorhabditis elegans riboflavin transporters rft-1 and rft-2. PLoS ONE. Here's the link!
1. Liau, W-S; Nasri, U; Elmatari, D; Rothman, JA; LaMunyon, CW. 2013. Premature Sperm Activation and Defective Spermatogenesis Caused by Loss of spe-46 Function in Caenorhabditis elegans. PLoS ONE. Here's the link!