Antibiotic‐resistant bacteria of the genus Pandoraea , frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown.…
Abstract Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a major health risk and a serious worldwide issue. MAFLD typically arises from aberrant lipid metabolism, insulin resistance, oxidative stress, and inflammation. However, subjacent causes are multifactorial. The gut has…
Abstract Background The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial signatures of NAFLD has been a great challenge, mainly due to its co-occurrence…
Abstract Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer-related deaths worldwide. Although the risk of developing CRC increases with age, approximately 10% of newly diagnosed cases occur in individuals under the age of 50. Significant changes…
Non-alcoholic fatty liver disease (NAFLD) is the most prevalent form of liver disease worldwide and is linked to various chronic conditions. This dissertation investigates the role of gut microbiota in NAFLD using bioinformatics techniques, including metagenomics and metabolomics. A prospective study…
The microbes that live in the gut, also known as the gut microbiota, play an important role in the well-being of the host. In the last years, the development of metagenomics and metabolomics have helped to better understand the vital role of the gut microbiome in human health and disease, however, the…
Background: Aspergillus fumigatus is a major fungal pathogen that causes severe problems due to its increasing resistance to many therapeutic agents. Fludioxonil is a compound that triggers a lethal activation of the fungal-specific High Osmolarity Glycerol pathway. Its pronounced antifungal activity…
Simple Summary Atopic dermatitis (AD) is a skin disease associated with changes in the gut microbiome early in life. We conducted a comprehensive study to investigate the gut microbiome of Thai children with AD compared to their healthy counterparts. Our study involved both longitudinal analysis, starting…
Background A growing body of evidence suggests that the gut microbiota is strongly linked to general human health. Microbiome-directed interventions, such as diet and exercise, are acknowledged as a viable and achievable strategy for preventing disorders and improving human health. However, due to the…
Aspergillus fumigatus , an opportunistic human pathogen, frequently infects the lungs of people with cystic fibrosis and is one of the most common causes of infectious-disease death in immunocompromised patients. Here, we construct 252 strain-specific, genome-scale metabolic models of this important…
Candida species overgrowth in the human gut is considered a prerequisite for invasive candidiasis, but our understanding of gut bacteria promoting or restricting this overgrowth is still limited. By integrating cross-sectional mycobiome and shotgun metagenomics data from the stool of 75 male and female…
The application of bacterial strains as a groundbreaking, natural method to combat metabolic diseases is rapidly expanding. However, previous screenings have overlooked their relevance in human metabolic diseases like Non-alcoholic Fatty Liver Disease (NAFLD). Given NAFLD's global prevalence and the…
Depression is highly prevalent (6% 1-year prevalence) and is the second leading cause of disability worldwide. Available treatment options for depression are far from optimal, with response rates only around 50%. This is most likely related to a heterogeneous clinical presentation of major depression…
The fungal kingdom is omnipresent in a multitude of ecosystems across the earth's biosphere. In this dissertation, the fungal abundance was analyzed in a broad-scale way to determine general and specific patterns. Starting with a case study of the human gut and simulations modeling the metabolic…
The 1980s were very prolific years not only for music, but also for molecular biology and genetics, with the first publications on the microbiome and ancient DNA. Several technical revolutions later, the field of ancient metagenomics is now progressing full steam ahead, at a never seen before pace. While…
Humans represent a complex ecosystem colonized not only by our cells but trillions of other microbes such as bacteria, archaea, fungi, and viruses. This microbiome gains increasing interest due to its involvement in human health and disease. While we live in symbiosis with most of these travellers, dysbiosis…
The main thematic area of the present thesis is the development and application of bioinformatics pipelines, namely whole-genome sequence (WGS) analysis and transcriptome profile analysis. These pipelines were applied to study the fungal pathogen Aspergillus fumigatus (Manuscripts I, III, and IV) and…
In an ever-growing worldwide population, human infectious diseases are an increasingly serious problem for public health. In particular, more than a million deaths and millions of infectious disease cases per year caused by fungal pathogens have been reported globally in recent years. Hence, more investments…
Candida albicans is a leading cause of life-threatening hospital-acquired infections and can lead to Candidemia with sepsis-like symptoms and high mortality rates. We reconstructed a genome-scale C. albicans metabolic model to investigate bacterial-fungal metabolic interactions in the gut as determinants…