Deanna Pepin
Doctor of Philosophy in Microbiology and Immunology (PhD)
Research Topic
Impact of osmotic perturbations on the gut microbiota
Carolina Tropini
Assistant Professor
Research Classification
Research Interests
Bacteria
Bacteriophages
Bioengineering
Bioinformatics
Biological and Biochemical Mechanisms
Biophysics
Gut microbiota
Inflammatory bowel disease
Relevant Thesis-Based Degree Programs
Affiliations to Research Centres, Institutes & Clusters
Research Options
I am available and interested in collaborations (e.g. clusters, grants).
I am interested in and conduct interdisciplinary research.
Research Methodology
Imaging
Gnotobiotic mouse models
bioinformatics
Computational modeling
Recruitment
Master's students
Doctoral students
Postdoctoral Fellows
Any time / year round
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Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.
Differential response of probiotics in perturbed pH and osmolality are correlated with genomic feature abundance (2022)
Probiotics have been identified as potential therapeutic vessels for numerous intestinal conditions, but we do not yet understand their ability to colonize a host, particularly one whose gut environment has been affected by disease. Physical factors are key in determining the ability of bacteria to survive and colonize within the gut and need to be investigated in the context of probiotic therapy. This project aims to characterize the strain-specific adaptability of commercially available probiotic strains to disease-relevant physical parameters – pH and osmolality. Different strains of lactic acid producing bacteria and Bifidobacterium spp. were isolated from ten commercially available probiotics and assessed for their growth in various pH and osmolality conditions and for their ability to impact their surrounding abiotic environment. We found that probiotic strains from the same phyla exhibit differential growth responses to high osmolality and low pH conditions, and we performed comparative genomic analysis to identify candidate genes involved in probiotic stress response. This study highlights the impact of biophysical parameters on commensal bacteria survival and helps to inform characteristics that are important for probiotic strains to establish sufficient viability in the dynamic gastrointestinal environment and will ultimately facilitate the development of other microbiota-based therapies.
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Publications
- A bacterial record collection (2022)
Cell Host & Microbe, - The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut (2022)
mBio, 13 (2) - Cause or effect? The spatial organization of pathogens and the gut microbiota in disease (2021)
Microbes and Infection, 23 (6-7), 104815 - Erratum: The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome (Proceedings of the National Academy of Sciences of the United States of America (2021) 118 (e2010217118) DOI: 10.1073/pnas.2010217118) (2021)
Proceedings of the National Academy of Sciences of the United States of America, 118 (11) - How the Physical Environment Shapes the Microbiota (2021)
mSystems, 6 (4) - The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome (2021)
Proceedings of the National Academy of Sciences of the United States of America, 118 (6) - Visualization of Gut Microbiota-host Interactions via Fluorescence In Situ Hybridization, Lectin Staining, and Imaging (2021)
Journal of visualized experiments : JoVE, (173) - A single-cell transcriptomic atlas characterizes ageing tissues in the mouse (2020)
Nature, 583 (7817), 590-595 - Ageing hallmarks exhibit organ-specific temporal signatures (2020)
Nature, 583 (7817), 596-602 - Bacterial species singled out from a diverse crowd (2020)
Nature, 588 (7839), 591-592 - Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation (2020)
Cell Host and Microbe, 27 (4), 659-670.e5 - Erratum: Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs (Cell Host & Microbe (2019) 26(5) (650–665.e4), (S1931312819305359), (10.1016/j.chom.2019.10.011)) (2020)
Cell Host and Microbe, 28 (4), 628 - Molecular hallmarks of heterochronic parabiosis at single cell resolution (2020)
bioRxiv, - A single cell transcriptomic atlas characterizes aging tissues in the mouse (2019)
bioRxiv, - Recovery of the gut microbiota after antibiotics depends on host diet and environmental reservoirs (2019)
- Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs (2019)
Cell Host and Microbe, 26 (5), 650-665.e4 - Mechanical Perturbations to the Gut Microbiota (2018)
Biophysical Journal, 114 (3), 329a - Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris (2018)
Nature, 562 (7727), 367-372 - Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota (2018)
Cell, 173 (7), 1742-1754.e17 - Deep Phenotypic Mapping of Bacterial Cytoskeletal Mutants Reveals Physiological Robustness to Cell Size (2017)
Current Biology, 27 (22), 3419-3429.e4 - Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials (2017)
ACS Central Science, 3 (12), 1294-1303 - Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library (2017)
BMC Biology, 15 (1) - The Gut Microbiome: Connecting Spatial Organization to Function (2017)
Cell Host and Microbe, 21 (4), 433-442 - High-throughput, highly sensitive analyses of bacterial morphogenesis using ultra performance liquid chromatography (2015)
Journal of Biological Chemistry, 290 (52), 31090-31100 - Your gut microbiome, deconstructed (2015)
Nature Biotechnology, 33 (12), 1238-1240 - A dynamically assembled cell wall synthesis machinery buffers cell growth (2014)
Proceedings of the National Academy of Sciences of the United States of America, 111 (12), 4554-4559 - Principles of Bacterial Cell-Size Determination Revealed by Cell-Wall Synthesis Perturbations (2014)
Cell Reports, 9 (4), 1520-1527 - Interplay between the Localization and Kinetics of Phosphorylation in Flagellar Pole Development of the Bacterium Caulobacter crescentus (2012)
PLoS Computational Biology, 8 (8) - Islands containing slowly hydrolyzable GTP analogs promote microtubule rescues (2012)
PLoS ONE, 7 (1) - Measuring the stiffness of bacterial cells from growth rates in hydrogels of tunable elasticity (2012)
Molecular Microbiology, 84 (5), 874-891 - Physical constraints on the establishment of intracellular spatial gradients in bacteria (2012)
BMC Biophysics, 5 (1), 17 - Megapixel digital PCR (2011)
15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011, 1 (8), 302-304 - Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium (2011)
Proceedings of the National Academy of Sciences of the United States of America, 108 (3), 1052-1057 - Trade-Off Between Localization and Expression Levels in Flagellar Pole Development of the Bacterium Caulobacter Crescentus (2010)
Biophysical Journal, 98 (3), 236a - Nonexponential kinetics of DNA escape from α-hemolysin nanopores (2008)
Biophysical Journal, 95 (11), 5317-5323 - Multi-nanopore force spectroscopy for DNA analysis (2007)
Biophysical Journal, 92 (5), 1632-1637 - Real-time control of nanopore wall potential for single-molecule analyses (2007)
Proceedings of the 11th International Conference on Miniaturized Systems for Chemistry and Life Sciences, uTAS 2007, , 1592-1594
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