The human gut microbiome is a complex, diverse and dynamic ecosystem important to health. Primarily, we study it using multi-omics techniques, especially metagenomics. From it, we obtain DNA reads which give us information about the identity and relative proportions of all forms of life inhabiting our gastrointestinal tracts.
About
Structural and Functional Genomics
The human gut microbiome is a complex, diverse and dynamic ecosystem important to health. Primarily, we study it using multi-omics techniques, especially metagenomics. From it, we obtain DNA reads which give us information about the identity and relative proportions of all forms of life inhabiting our gastrointestinal tracts. The dominating view of the microbiome is based on taxonomy (identity) of bacteria and archaea. Similarly, the vast majority of studies to-date focused on a cross-sectional aspect of the microbiome, for example, what differentiates healthy population from the sick in different diseases related to the microbiome. The microbiome health relationships are far-reaching and important – from disorders closely related to the gastrointestinal tract, such as inflammatory bowel disease, to more complex relationships in cancer, mental health, type-1 diabetes, and more.
Our work involves method development to predict the function and dynamics of the human microbiome. We use protein structures, functions, and interactions of microbes and microbial proteins to build a structural and functional genomics view of microbiome composition and dynamics. We analyse microbial data to understand how the changes in the microbiome impact human health. Thus, we want to move beyond the population-level studies to personalized solutions.
Long-term, we want to develop a multi-scale understanding of the microbiome, from genes, through structures, to functions, and therapies.
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The tool for exploring the landscape of proteins
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The impact of maternal microbial transfer on the infant gut microbiome after cesarean delivery: a systematic review
Authors: Jurgiel Jan, Gromowski Tomasz, Król Joanna, Bomba-Opoń Dorota, Kościółek Tomasz, Wielgoś Mirosław
Journal article in: American Journal of Obstetrics & Gynecology
read the publicationSynthetic deformylated α-helical PSMα3 as a selective inhibitor of human amyloid aggregation
Authors: Aleksandra Kalitnik, Alicja W. Wojciechowska, Jakub W. Wojciechowski, Oliwia Polańska, Przemysław Sareło, Monika Szefczyk & Małgorzata Kotulska
Journal article in: Scientific Reports Published by: Springer
read the publicationGut microbiome and blood biomarkers reveal differential responses to aerobic and anaerobic exercise in collegiate men of diverse training backgrounds
Authors: Kinga Humińska-Lisowska, Monika Michałowska-Sawczyn, Tomasz Kosciolek, Paweł P. Łabaj, Andrzej Kochanowicz, Jan Mieszkowski, Patrizia Proia, Paweł Cięszczyk, Kinga Zielińska
Journal article in: Scientific Reports Published by: Springer
read the publicationExplainable Artificial Intelligence for Bioactivity Prediction: Unveiling the Challenges with Curated CDK2/CDK4/CDK6 Breast Cancer Dataset
Authors: Adam Sułek, Jakub Klimczak, Jakub Jończyk, Tomasz Kosciolek, Tomasz Danel, Barbara Pucelik
Conference manuscript: 25th International Conference on Computational Science
read the publicationExperimental methods for studying amyloid cross-interactions
Authors: Aleksandra Kalitnik, Anna Lassota, Oliwia Polańska, Marlena Gąsior-Głogowska, Monika Szefczyk, Agnieszka Barbach, Jarosław Chilimoniuk, Izabela Jęśkowiak-Kossakowska, Alicja W. Wojciechowska, Jakub W. Wojciechowski, Natalia Szulc, Małgorzata Kotulska, Michał Burdukiewicz
Journal article: Protein Science Published by: Wiley
read the publicationLarge protein databases reveal structural complementarity and functional locality
Authors: Paweł Szczerbiak, Lukasz M Szydlowski, Witold Wydmański, P Douglas Renfrew, Julia Koehler Leman, Tomasz Kosciolek
Journal article: Nature Communications Published by: Springer Nature
read the publicationEsmTemp – Transfer Learning Approach for Predicting Protein Thermostability
Authors: Adam Sułek, Jakub Jończyk, Patryk Orzechowski, Ahmed Abdeen Hamed, Marek Wodziński
Conference manuscript: Computational Science – ICCS 2024
read the publicationTargeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome
Authors: Stefanie Duller, Simone Vrbancic, Łukasz Szydłowski, Alexander Mahnert,
Marcus Blohs, Michael Predl, Christina Kumpitsch, Verena Zrim, Christoph Högenauer, Tomasz Kosciolek, Ruth A. Schmitz, Anna Eberhard, Melanie Dragovan, Laura Schmidberger, Tamara Zurabischvili, Viktoria Weinberger, Adrian Mathias Moser, Dagmar Kolb, Dominique Pernitsch, Rokhsareh Mohammadzadeh, Torben Kühnast, Thomas Rattei, Christine Moissl-Eichinger
Journal article: Nature Communications Published by: Springer Nature
read the publicationSARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx
Authors: Cameron Martino, Benjamin P. Kellman, Daniel R. Sandoval, Thomas Mandel Clausen, Robert Cooper, Alhosna Benjdia, Feryel Soualmia, Alex E. Clark, Aaron F. Garretson, Clarisse A. Marotz, Se Jin Song, Stephen Wandro, Livia S. Zaramela, Rodolfo A. Salido, QiyunZhu, Erick Armingol, Yoshiki Vázquez-Baeza, Daniel McDonald, James T. Sorrentino, Bryn Taylor, Pedro Belda-Ferre, Promi Das, Farhana Ali, Chenguang Liang, Yujie Zhang, Luca Schifanella, Alice Covizzi, Alessia Lai, Agostino Riva, Christopher Basting, Courtney AnnBroedlow, Aki S. Havulinna, Pekka Jousilahti, Mehrbod Estaki, Tomasz Kosciolek, Rayus Kuplicki, Teresa A. Victor, Martin P. Paulus, Kristen E. Savage, Jennifer L. Benbow, Emma S. Spielfogel, Cheryl A. M. Anderson, Maria Elena Martinez, James V. Lacey, Jr, Shi Huang, Niina Haiminen, Laxmi Parida, Ho-Cheol Kim, Jack A. Gilbert, Daniel A. Sweeney, Sarah M. Allard, Austin D. Swafford, Susan Cheng, MichaelInoyue, Teemu Niiranen, Mohit Jain, Veikko Salomaa, Karsten Zengler, Nichole R. Klatt, Jeff Hasty, Olivier Berteau, Aaron F. Carlin, Jeffrey D. Esko, Nathan E. Lewis, Rob Knight
Journal article: mBio Published by: ASM
Effects of data transformation and model selection on feature importance in microbiome classification data
Authors: Zuzanna Karwowska, Oliver Aasmets, Estonian Biobank research team, Tomasz Kosciolek, Elin Org
Journal article: Microbiome Published by: Springer Nature
read the publicationTranscriptomic profiling of “brain-eating amoeba” Naegleria fowleri infection in mice: the host and the protozoa perspectives
Authors: Vincent Guerlais, Nina Allouch, E. Ashley Moseman, Alicja W. Wojciechowska, Jakub W. Wojciechowski, Isabel Marcelino
Journal article: Frontiers in Cellular and Infection Microbiology Published by: Frontiers
Refining antimicrobial photodynamic therapy: effect of charge distribution and central metal ion in fluorinated porphyrins on effective control of planktonic and biofilm bacterial forms
Authors:Barbara Pucelik, Agata Barzowska, Adam Sułek, Mateusz Werłos, Janusz M. Dąbrowski
Journal article: Photochemical & Photobiological Sciences Published by: Springer Nature
read the publicationAdaptation to space conditions of novel bacterial species isolated from the International Space Station revealed by functional gene annotations and comparative genome analysis
Authors: Lukasz M. Szydlowski, Alper A. Bulbul, Anna C. Simpson, Deniz E. Kaya, Nitin K. Singh, Ugur O. Sezerman, Paweł P. Łabaj, Tomasz Kosciolek, Kasthuri J. Venkateswaran
Journal article: Microbiome Published by: Springer Nature
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