The Laboratory of Cellular Genomics investigates the functional, metabolic, and immunological aspects of gastrointestinal health. We combine experimental and computational approaches to uncover the molecular mechanisms underlying chronic intestinal and liver diseases. Our research focuses on understanding how the gut microbiota shapes cellular states and intercellular communication during disease development and progression. 

Research Areas 

Gut-liver axis
We investigate the bidirectional interactions between the liver and the intestine, with particular emphasis on the resident gut microbiota. Our research focuses on the gut–liver axis as a central regulatory interface integrating host metabolism, immune responses, and microbial communities in chronic liver diseases, particularly metabolic dysfunction-associated steatotic liver disease (MASLD).
By integrating metagenomics, metabolomics, proteomics, and single-cell transcriptomics in patient cohorts and experimental models, we identify microbiota-derived biomarkers and molecular pathways driving disease initiation and progression. 

Microbiota-derived metabolites
We study how microbiota-derived metabolites regulate host physiology.
To uncover the molecular mechanisms governing host–microbiota interactions, we combine multi-omics with high-throughput screening in cell lines and primary cells. This approach enables systematic assessment of how microbial metabolites influence cellular functions and signaling pathways. 

Gastrointestinal Diseases
Our research addresses the mechanisms underlying chronic inflammatory disorders of the gastrointestinal tract, including chronic liver diseases.
We also investigate acute liver failure caused by poisoning with the death cap mushroom (Amanita phalloides). Our findings indicate that the gut microbiota may exacerbate liver injury, likely through immune activation associated with increased intestinal permeability.
Current studies integrate transcriptomics, immune profiling, and patient-derived samples to characterize toxin-induced RNA degradation and identify vulnerable cell populations. In parallel, we are developing biological and computational strategies to neutralize α-amanitin. 

Research Methods 

Multi-omics 

We develop and apply sequencing-based and omics technologies to comprehensively characterize host cellular phenotypes and microbial communities. Our approaches include metagenomics, metabolomics, proteomics, and single-cell transcriptomics.
Integrating these complementary datasets enables multidimensional characterization of biological processes in health and disease. 

High-Throughput Screening 

We employ high-throughput in vitro screening using cell lines and primary cells to identify mechanisms underlying host–microbiota interactions. 

These platforms allow us to systematically evaluate the effects of microbiota-derived metabolites on cellular functions and prioritize candidate mechanisms for experimental validation. 

Bioinformatics 

We develop and apply advanced bioinformatics methods to generate predictive models and biological hypotheses from multi-omics datasets, followed by experimental validation.
Following the concept of “data parasitism,” we systematically integrate and reanalyze underutilized public datasets to generate new biological insights. 

Scientific Impact 

Our laboratory investigates the genomic, metabolic, and immunological determinants of gastrointestinal health.
We study the molecular mechanisms underlying chronic intestinal and liver diseases, with particular emphasis on cellular phenotypes, disease-associated niches, and host–microbiota interactions.
We are establishing a new research direction focused on microbiome-based diagnostic biomarkers for MASLD. As part of a project funded by the Polish Medical Research Agency (ABM), the laboratory is conducting a study involving 400 participants to investigate liver health, gut microbiota composition, and the development of novel diagnostic approaches. 

Future Directions 

Our long-term goal is to understand host–microbiota interactions and translate this knowledge into improved prevention and treatment strategies for gastrointestinal diseases.
Over the coming years, our priorities include discovering microbiome-derived diagnostic biomarkers for MASLD and elucidating the molecular mechanisms governing host–microbiota interactions in this disease using high-throughput screening platforms and integrated multi-omics approaches.
We anticipate that these studies will provide the foundation for developing next-generation prebiotics, probiotics, and postbiotics capable of improving clinical outcomes. 

Collaborations 

• Prof. Samuel Nobs, Institute for Research in Biomedicine (IRB), Switzerland 
• Prof. Michał Grąt and Dr Łukasz Masior, Medical University of Warsaw, Poland 

Selected Current Funding 

• National Science Centre (NCN), OPUS LAP (2026–2030)
  Discovering the Diversity and its Drivers of Novel Lung Dendritic Cell Subsets in Asthma 
  In collaboration with Prof. Samuel Nobs (IRB Bellinzona)
  PLN 2,958,122 (awarded to IIMCB) 
  
  
• National Science Centre (NCN), OPUS (2024–2029) 
  Finding Molecular Mechanisms Behind the Activation of Stellate Cells 
  PLN 4,191,920 
  
  
• EMBO Installation Grant (2024–2028) 
  Role of Microbiota in Progression of Liver Disease 
   EUR 250,000 
  
  
• National Science Centre (NCN), SONATA (2023–2026) 
  The Role of the Gut–Liver Axis in Amanita Species Mushroom Poisoning 
  PLN 2,544,840
  
  
• Medical Research Agency (ABM) (2025–2026)
  Identification of Biomarkers of Metabolic Dysfunction-Associated Steatotic Liver Disease 
  PLN 5,244,375 

Visit the laboratory website for more details: olab.com.pl