Research

Recent publications

LaCourse SM, Seko E, Wood R, Bundi W, Ouma GS, Agaya J, Richardson BA, John-Stewart G, Wandiga S, Cangelosi GA. Diagnostic performance of oral swabs for non-sputum based TB diagnosis in a TB/HIV endemic setting. PLoS One. 2022 Jan 13;17(1):e0262123. PMID: 35025930.

Montaño MA, Bemer MJ, Heller KB, Meisner A, Marfatia Z, Rechkina EA, Padgett LR, Ahls CL, Rains D, Hao L, Hsiang TY, Cangelosi GA, Greninger AL, Cantera JL, Golden A, Peck RB, Boyle DS, Gale M Jr, Drain PK. Performance of anterior nares and tongue swabs for nucleic acid, Nucleocapsid, and Spike antigen testing for detecting SARS-CoV-2 against nasopharyngeal PCR and viral culture. Int J Infect Dis. 2022 Apr;117:287-294. PMID: 35149246.
        
Valinetz ED, Matemo D, Gersh JK, Joudeh LL, Mendelsohn SC, Scriba TJ, Hatherill M, Kinuthia J, Wald A, Cangelosi GA, Barnabas RV, Hawn TR, Horne DJ. Isoniazid preventive therapy and TB transcriptional signatures in people with HIV. AIDS (London, England). 2022 May. PMID: 35608118.
        
Andama, A., Whitman, G. R., Crowder, R., Reza, T. F., Jaganath, D., Mulundo, J., Kabuleta, T. N., Semitala, F., Worodria, W., Cook, C., Wood, R. C., Weigel, K., Olson, A. M., Lohmiller Shaw, J., Denkinger, C., Nahid, P., Cangelosi, G.A., and Cattamanchi, A. (2022) Accuracy of tongue swab testing using Xpert MTB-RIF Ultra for tuberculosis diagnosis. J Clin Microbiol, 2022 Jun 27:e0042122. doi: 10.1128/jcm.00421-22. Epub ahead of print. PMID: 35758702.
        
Shapiro, A. E., Olson, A. M., Kidoguchi, L., Niu, X., Ngcobo, Z., Magcaba, Z. P., Ngwane, M. W., Whitman, G. R., Weigel, K. M., Wood, R. C., Wilson, D. P. K., Drain, P. K., and Cangelosi, G. A. (2022). Complementary non-sputum diagnostic testing for tuberculosis in people with HIV by using oral swab PCR and urine lipoarabinomannan detection. J Clin Microbiol, in press.

Diener, C., Qin, S., Zhou, Y., Patwardhan, S., Tang, L., Lovejoy, J. Magis, A.T., Price, N.D., Hood, L., Gibbons, S.M. 2021. Baseline gut metagenomic functional gene signature associated with variable weight loss responses following a healthy lifestyle intervention in humans. mSystems, e009624-21, https://doi.org/10.1128/mSystems.00964-21.

Diener, C.Hoge, A.C.H., Kearney, S.M., Kusebauch, U., Patwardhan, S., Moritz, R.L., Erdman, S.E., Gibbons, S.M. 2021. Non-responder phenotype reveals apparent microbiome-wide antibiotic tolerance in the murine gut. Communications Biology, 4(316), https://doi.org/10.1038/s42003-021-01841-8.

Wilmanski, T., Diener, C., Rappaport, N., Patwardhan, S., Wiedrick, J., Lapidus, J., Earls, J.C., Zimmer, A., Glusman, G., Robinson, M., Yurkovich, J.T., Kado, D.M., Cauley, J.A., Zmuda, J., Lane, N.E., Magis, A.T., Lovejoy, J.C., Hood, L., Gibbons, S.M., Orwoll, E., Price, N.D. 2021. Gut microbiome pattern reflects healthy ageing and predicts survival in humans. Nature Metabolismhttps://doi.org/10.1038/s42255-021-00348-0.

Dutta, M., Lim, J.J., Cui, J.Y. 2022. Pregnane X Receptor and the Gut-Liver Axis: A Recent Update. Drug Metab Dispos 50:478-491. Lim was selected by Drug Metabolism and Disposition as the highlighted trainee author of the month. (https://www.aspet.org/aspet/news/news/2022/03/24/drug-metabolism-and-disposition-highlighted-trainee-author-for-the-april-2022-issue).

Lim, J.J., Dutta, M., Dempsey, J.L., Lehmler, H.J., MacDonald, J., Bammler, T., Walker, C., Kavanagh, T.J., Gu, H., Mani, S., Cui, J.Y. 2021. Neonatal Exposure to BPA, BDE-99, and PCB Produces Persistent Changes in Hepatic Transcriptome Associated With Gut Dysbiosis in Adult Mouse Livers. Toxicol Sci 184:83-103. https://pubmed.ncbi.nlm.nih.gov/34453844/.

Zhang, A., Matsushita, M., Zhang, L., Wang, H., Shi, X., Gu, H., Xia, Z., Cui, J.Y. 2021 Cadmium exposure modulates the gut-liver axis in an Alzheimer's disease mouse model. Commun Biol 4:1398. Featured in the NIEHS Environmental Factor Newsletter as Paper of the Month. https://www.nature.com/articles/s42003-021-02898-1

Weigel KM, Olson AM, Cangelosi GA (2021). Steady-state pre-rRNA analysis to investigate the functional microbiome. Curr Protoc. 2021 Jul;1(7):e209. PMID: 34314573.

Berke EM, Newman LM, Jemsby S, Hyde B, Bhalla N, Sheils NE, Oomman N, Reppas J, Verma P, Cangelosi GA (2021). Pooling in a Pod: A Strategy for COVID-19 Testing to Facilitate a Safe Return to School. Public Health Rep. September 2021 Sep. PMID: 34487461.

Andama, A., Whitman, G. R., Crowder, R., Reza, T. F., Jaganath, D., Mulundo, J., Kabuleta, T. N., Semitala, F., Worodria, W., Cook, C., Wood, R. C., Weigel, K., Olson, A. M., Lohmiller Shaw, J., Denkinger, C., Nahid, P., Cangelosi, G.A., and Cattamanchi, A. (2022) Accuracy of tongue swab testing using Xpert MTB-RIF Ultra for tuberculosis diagnosis. medRxiv, 2022.2002.2017.22271147 [Submitted to J Clin Microbiol].

Brian D Williamson, James P Hughes, and Amy D Willis. A multiview model for relative and absolute microbial abundances. Biometrics, 2021.

David S Clausen and Amy D Willis. Evaluating Replicability in Microbiome Data. Biostatistics, In Press, 2022.

Pauline Trinh, David S Clausen and Amy D Willis. happi: a Hierarchical Approach to Pangenomics Inference. bioRxiv.

Miller, A.**, S. Ebelt, K. Levy.‡ In Press. Combined Sewer Overflows and Gastrointestinal Illness in Atlanta, 2002 to 2013: Evaluating the Impact of Infrastructure Improvements. Environmental Health Perspectives  130(5): 057009-1- 057009-13.

Lee, G.O., J.N.S. Eisenberg, J. Uruchima*, G. Vasco, S.M. Smith**, A. VanEngen, C. Victor**, E. Reynolds, R. MacKay**, K.J. Jesser**, N. Castro, M. Calvopiña, K. Konstantinidis, G. Trueba, William Cevallos, K. Levy‡. 2021. Gut microbiome, enteric infections, and child growth across a rural-urban gradient: A prospective cohort study protocol. BMJ Open11: e046241.

Soto-Giron, M.J.*, Peña Gonzalez, A.*, J. K. Hatt, L. Montero*, M. Páez*, E. Ortega*, S. Smith**, W. Cevallos, G. Trueba, K. Konstantinidis‡, K. Levy‡. 2021. Gut microbiome response to acute diarrheal disease across a rural-to-urban gradient in northern Ecuador. American Journal of Tropical Medicine and Hygiene 104(6): 2275-2285. [‡co-corresponding authors]

Meziti, A.*, L. Rodriguez-R, J. Hatt, A. Peña-Gonzalez*, K. Levy, K. Konstantinidis. 2021. How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample. Applied and Environmental Microbiology 26;87(6):e02593-20.

Bold text: Gibbons Lab members

 

Key presentations

Dr. Gerard Cangelosi

SelectBIO Diagnostics Conference, San Diego, CA, October 2019.

52nd Union World Conference on Lung Health (virtual), October 2021.

Symposium on Environmental Risks for Nontuberculous Mycobacterial Lung Infections, Fort Collins, CO, June 2022.

Environmental Risks for Nontuberculous Mycobacterial Lung Infections Symposium, Colorado Mycobacteria Conference 2022, Fort Collins, CO. June 2022
        
McGill Summer Institutes in Global Health, Advanced TB Diagnostics Course (virtual). June 2022

Dr. Julia Cui

2021 Invites speaker and Toxicology Early Career Award lecture on gut microbiome and hepatic xenobiotic metabolism at the Experimental Biology National annual meeting on gut microbiome and hepatic xenobiotic metabolism.

2021 Invited speaker at NIH/NIEHS Xenobiotics and Microbiome Workshop on the gut-liver axis.

2019 Invited speaker at the Gordon Research Conference on gut microbiome and drug metabolism.

Dr. Sean Gibbons

The State of the Microbiome, A Conversation with Jack Gilbert, Seattle Town Hall, 2021 https://www.youtube.com/watch?v=3sSPX2M2Uoc

ISB Research Roundtable Event on the Gut Microbiome and Nutrition, 2021 https://www.youtube.com/watch?v=Hl4JyILiM7k

ESCAIDE Conference talk, 2019 https://www.youtube.com/watch?v=7_UkfFT3io4

Invited to present at meetings:

International Society of Microbiota, 8th Annual Meeting on Targeting Microbiota 2021 (Paris/Virtual)

American Society for Microbiology and American Society for Nutrition Joint Meeting, Nutrition 2020 (Virtual)

Microbiome Drug Development Summit, 2022 (Boston)

Dr. Amy Willis

2022 Keynote speaker at Purdue Applied Microbiome Sciences Symposium; West Lafayette, Indiana.

2022 Plenary lecturer at Having IMPACTT: Advancing Microbiome Research; Canmore, Alberta, Canada

2022 Keynote speaker at Bioc2022; Seattle, WA.

Dr. Karen Levy

Invited to be a keynote speaker at the International Symposium on Zoonoses Research. German Research Platform for Zoonoses. October 2022.

Invited talk at ID Week. Symposium on Impact of climate change on infectious diseases in children. October 2022.

 

Trainee highlights

 

Dr. Christian Diener

Write-up of Dr. Diener's recent paper on predicting weight loss responses based on the composition of the human gut microbiome: https://gibbons.isbscience.org/news/2021/09/14/can-you-lose-weight-ask-your-microbiome/

Brief abstract: Recent human feeding studies have shown how the baseline taxonomic composition of the gut microbiome can determine responses to dietary interventions, but the exact functional determinants underlying this phenomenon remain unclear. In this study, we set out to better understand interactions between baseline BMI, metabolic health, diet, gut microbiome functional profiles, and subsequent weight changes in a human cohort that underwent a healthy lifestyle intervention. Overall, our results suggest that the microbiota may influence host weight loss responses through variable bacterial growth rates, dietary energy harvest efficiency, and immunomodulation.

Joe Lim

Joe Lim is a second-year PhD student in the Cui lab and a NIEHS T32 (Environmental Pathology/Toxicology) trainee. His research focuses on understanding how early life exposure to persistent organic pollutants impact the long-term metabolic changes in liver cell types, as well as the interactions between the gut microbiome. He utilizes single cell transcriptomics, metagenomics, metabolomics, imaging, genetically engineered animal models and computational biology to determine how the gut microbiome impacts the metabolic functions of liver cells from exposures to environmental toxicants. His long-term goal is to mitigate adverse health effects from exposures that occur during critical developmental time windows. Joe has published five peer-reviewed manuscripts with Dr. Cui and has won several research awards, including a Best Platform Presentation Award in the 2020 Pacific Northwest Association of Toxicologists annual research conference, the Russell L. Castner Endowed Student Research Award (2021), the Highlighted Trainee Author of the Month by the journal Drug Metabolism and Disposition (2022), and the National Society of Toxicology Young Soo Choi Student Scholar Award (2022). 

Alyssa Miller

Alyssa Miller is a PhD student in the Levy lab.  Here is her recent recent EHP paper: https://ehp.niehs.nih.gov/doi/10.1289/EHP11525