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The gut microbiota and its biogeography.
G McCallum, C Tropini. (2023). Nature Reviews Microbiology. doi: 10.1038/s41579-023-00969-0
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Microbial endocrinology: the mechanisms by which the microbiota influences host sex steroids.
S Cotton, C A Clayton, C Tropini. (2023). Trends in Microbiology. doi:10.1016/j.tim.2023.03.010
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Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo.
J C Burckhardt, D H Y Chong, N Pett, C Tropini. (2023). Microbiome. 11, 65.
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An impedance-based chemiresistor for the real-time detection of gut microbiota-generated short-chain fatty acids
A Yavarinasab, S Flibotte, S Liu, C Tropini. (2023). Chemical Sensors and Actuators: B. 393, 134182
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Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota
K M Ng*, S M Pannu*, S Liu, J C Burckhardt, T Hughes, W V Treuren, J Nguyen, K Naqvi, B Nguyen, D M Pepin, C Clayton, S R Collins, C Tropini. (2023). mBio.
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The CIAMIB: a large and metabolically diverse collection of inflammation-associated bacteria from the murine gut.
E Wong, E Brownlie, K M Ng, S Kathirgamanathan, B Yu, B Merrill, KC Huang, A Martin, C Tropini, and W Navarre. (2022). e02949-21, doi: 10.1128/mbio.02949-21. mBio.
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Molecular hallmarks of heterochronic parabiosis at single cell resolution.
R Pálovics, A Keller, N Schaum, W Tan, T Fehlmann, M Borja, J Webber, A McGeever, L Bonanno, The Tabula Muris Consortium*, A O Pisco, J Karkanias, N F Neff, S Darmanis, S R Quake & T Wyss-Coray. (2022). Nature. 603, 309–314.
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How the Physical Environment Shapes the Microbiota.
C Tropini. (2021) mSystems. 6(4) e00675-2
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Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging
K M Ng, C Tropini. (2021) Journal of Visualization (JoVE). doi: 10.3791/62646
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Cause or effect? The spatial organization of pathogens and the gut microbiota in disease
Nguyen J, Pepin D, Tropini C. (2021) Microbes and Infection. 104815. doi.org/10.1016/j.micinf.2021.104815
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The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome.
Finlay BB, Amato KR, Azad M, Blaser MJ, Bosch TCG, Chu H, Dominguez-Bello MG, Ehrlich SD, Elinav E, Geva-Zatorsky N, Gros P, Guillemin K, Keck F, Korem T, McFall-Ngai MJ, Melby MK, Nichter M, Pettersson S, Poinar H, Rees T, Tropini C, Zhao L, Giles-Vernick T. Cell Host Microbe. 2021. 118(6):e2010217118.
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Bacterial species singled out from a diverse crowd.
Nguyen J, Tropini C . Nature News and Views. 2020. 588(24/31): 591-592.
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A single-cell transcriptomic atlas characterizes ageing tissues in the mouse
Tabula Muris Consortium. Nature. 583(7817):590-595. 2020. doi:10.1038/s41586-020-2496-1
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Ageing hallmarks exhibit organ-specific temporal signatures
N Schaum, B Lehallier, O Hahn, R Pálovics, S Hosseinzadeh, S E Lee, R Sit, D P Lee, P M Losada, M E Zardeneta, T Fehlmann, J T Webber, A McGeever, K Calcuttawala, H Zhang, D Berdnik, V Mathur, W Tan, A Zee, M Tan, Tabula Muris Consortium, A O Pisco, J Karkanias, N F Neff, A Keller, S Darmanis, S R Quake, T Wyss-Coray. Nature. 2020. 583(7817):596-602. doi:10.1038/s41586-020-2499-y
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Dysbiosis-induced secondary bile acid deficiency promotes intestinal inflammation
S R Sinha, Y Haileselassie, L P Nguyen, C Tropini, M Wang, L Becker, D S Sim, K Jarr, E T Spear, G Singh, H Namkoong, K Bittinger, M A Fischbach, J L Sonnenburg, A Habtezion. Cell Host & Microbe. 2020. 27(4):659-670.
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Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs
K M Ng, A Aranda-Diaz, C Tropini, M R Frankel, W Van Treuren, C T. O’Laughlin, B D Merrill, F B Yu, K M Pruss, R A Oliveira, S K Higginbottom, N F Neff, M A Fischbach, K B Xavier, J L Sonnenburg, and K C Huang. Cell Host and Microbe. 2019. 26:650-665
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Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota
Tropini C, Moss EL, Merrill BD, Ng KM, Higginbottom SK, Casavant EP, Gonzalez CG, Fremin B, Bouley DM, Elias JE, Bhatt AS, Huang KC, Sonnenburg JL. Cell. 2018. 173(7):1742-1754.e17.
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Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials
Krajina BA, Tropini C, Zhu A, DiGiacomo P, Sonnenburg JL, Heilshorn SC, Spakowitz AJ. ACS Cent Sci. 2017 Dec 27;3(12):1294-1303.
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Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library
Ursell T, Lee TK, Shiomi D, Shi H, Tropini C, Monds RD, Colavin A, Billings G, Bhaya-Grossman I, Broxton M, Huang BE, Niki H, Huang KC. BMC Biol. 2017 Feb 21;15(1):17.
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Deep Phenotypic Mapping of Bacterial Cytoskeletal Mutants Reveals Physiological Robustness to Cell Size
Shi H, Colavin A, Bigos M, Tropini C, Monds RD, Huang KC. Curr Biol. 2017 Nov 20;27(22):3419-3429.e4.
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The gut microbiome: connecting spatial organization to function
Tropini C, Earle KA, Huang KC, Sonnenburg JL. Cell Host Microbe. 2017 Apr 12;21(4):433-442.
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Your gut microbiome, deconstructed
Dodd D, Tropini C, Sonnenburg JL. Nat Biotechnol. 2015 Dec 9;33(12):1238-1240.
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High-throughput, highly sensitive analyses of bacterial morphogenesis using ultra performance liquid chromatography
Desmarais SM, Tropini C, Miguel A, Cava F, Monds RD, de Pedro MA, Huang KC. J Biol Chem. 2015 Dec 25;290(52):31090-100. doi: 10.1074/jbc.M115.661660.
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Principles of bacterial cell-size determination revealed by cell-wall synthesis perturbations
Tropini C, Lee TK, Hsin J, Desmarais SM, Ursell T, Monds RD, Huang KC. Cell Rep. 2014 Nov 20;9(4):1520-7. doi: 10.1016/j.celrep.2014.10.027.
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A dynamically assembled cell wall synthesis machinery buffers cell growth
Lee TK, Tropini C, Hsin J, Desmarais SM, Ursell TS, Gong E, Gitai Z, Monds RD, Huang KC. Proc Natl Acad Sci U S A. 2014 Mar 25;111(12):4554-9.
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Physical constraints on the establishment of intracellular spatial gradients in bacteria
Tropini C, Rabbani N, Huang KC. BMC Biophys. 2012 Aug 29;5:17.
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Interplay between the localization and kinetics of phosphorylation in flagellar pole development of the bacterium Caulobacter crescentus
Tropini C, Huang KC. PLoS Comput Biol. 2012;8(8):e1002602.
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Measuring the stiffness of bacterial cells from growth rates in hydrogels of tunable elasticity
Tuson HH, Auer GK, Renner LD, Hasebe M, Tropini C, Salick M, Crone WC, Gopinathan A, Huang KC, Weibel DB. Mol Microbiol. 2012 Jun;84(5):874-91.
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Islands containing slowly hydrolyzable GTP analogs promote microtubule rescues
Tropini C, Roth EA, Zanic M, Gardner MK, Howard J. PLoS One. 2012;7(1):e30103.
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Megapixel digital PCR
Heyries KA, Tropini C, Vaninsberghe M, Doolin C, Petriv OI, Singhal A, Leung K, Hughesman CB, Hansen CL. Nat Methods. 2011 Jul 3;8(8):649-51.
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Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium
Chen YE, Tropini C, Jonas K, Tsokos CG, Huang KC, Laub MT. Proc Natl Acad Sci U S A. 2011 Jan 18;108(3):1052-7.
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Nonexponential kinetics of DNA escape from α-hemolysin nanopores
Wiggin M, Tropini C, Tabard-Cossa V, Jetha NN, Marziali A. Biophys J. 2008 Dec;95(11):5317-23.
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Multi-nanopore force spectroscopy for DNA analysis
Tropini C, Marziali A. Biophys J. 2007 Mar 1;92(5):1632-7.