A5053250175- Gut microbiota and health
- Colorectal Cancer Screening and Detection
- Diet and metabolism studies
- Clostridium difficile and Clostridium perfringens research
- Metabolomics and Mass Spectrometry Studies
- Genetic factors in colorectal cancer
- Probiotics and Fermented Foods
- Dietary Effects on Health
- Cancer Research and Treatments
- Genomics and Phylogenetic Studies
- Machine Learning in Healthcare
- Antibiotic Resistance in Bacteria
- Microscopic Colitis
- Oral microbiology and periodontitis research
- Microbial Community Ecology and Physiology
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Simulation Techniques and Applications
- Statistical Methods and Inference
- Bacteriophages and microbial interactions
- Herbal Medicine Research Studies
- Cancer, Lipids, and Metabolism
- Pancreatic and Hepatic Oncology Research
- Colorectal Cancer Treatments and Studies
- Gastrointestinal motility and disorders
Stanford University
2024-2025
European Molecular Biology Laboratory
2018-2024
RWTH Aachen University
2016-2023
European Bioinformatics Institute
2019-2023
European Molecular Biology Laboratory
2022-2023
Heidelberg University
2016-2022
European Molecular Biology Organization
2020
Joint Research Centre
2016
McGill University
2015
The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to intestine considered a rare aberrant event, and hallmark disease. By studying salivary fecal microbial strain populations 310 in 470 individuals from five countries, we found that transmission to, subsequent colonization of, large microbes common extensive among healthy individuals. We evidence for vast majority be transferable, with increased levels colorectal cancer rheumatoid arthritis...
Abstract The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software scarce, overoptimistic evaluation limited cross-study generalization are prevailing issues. To address these, we developed SIAMCAT, a versatile R toolbox ML-based comparative metagenomics. We demonstrate its capabilities in meta-analysis of fecal metagenomic studies (10,803 samples). When naively transferred across studies, ML...
Recent evidence suggests a role for the microbiome in pancreatic ductal adenocarcinoma (PDAC) aetiology and progression.To explore faecal salivary microbiota as potential diagnostic biomarkers.We applied shotgun metagenomic 16S rRNA amplicon sequencing to samples from Spanish case-control study (n=136), including 57 cases, 50 controls, 29 patients with chronic pancreatitis discovery phase, German (n=76), validation phase.Faecal classifiers performed much better than saliva-based identified...
Factor analysis is a widely used method for dimensionality reduction in genome biology, with applications from personalized health to single-cell biology. Existing factor models assume independence of the observed samples, an assumption that fails spatio-temporal profiling studies. Here we present MEFISTO, flexible and versatile toolbox modeling high-dimensional data when spatial or temporal dependencies between samples are known. MEFISTO maintains established benefits multimodal data, but...
Population studies provide insights into the interplay between gut microbiome and geographical, lifestyle, genetic environmental factors. However, low- middle-income countries, in which approximately 84% of world's population lives1, are not equitably represented large-scale research2-4. Here we present AWI-Gen 2 Microbiome Project, a cross-sectional study sampling 1,801 women from Burkina Faso, Ghana, Kenya South Africa. By engaging with communities that range rural horticultural to...
Abstract Background Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms biological samples. Available methods using shotgun metagenomic data generally depend on deposition sequenced taxonomically annotated genomes, usually from cultures isolated strains, reference databases (reference genomes). However, majority have not been cultured yet. Thus, substantial fraction microbial community members remains...
The gut microbiota has been suggested to play a significant role in the development of overweight and obesity. However, effects calorie restriction on obese adults, especially over longer durations, are largely unexplored.Here, we longitudinally analyzed intermittent (ICR) operationalized as 5:2 diet versus continuous (CCR) fecal 147 or adults 50-week parallel-arm randomized controlled trial, HELENA Trial. primary outcome trial was differential ICR CCR gene expression subcutaneous adipose...
Abstract Background Extraintestinal symptoms are common in inflammatory bowel diseases (IBD) and include depression fatigue. These highly prevalent especially active disease, potentially due to inflammation-mediated changes the microbiota-gut-brain axis. The aim of this study was investigate associations between structural functional microbiota characteristics severity fatigue depressive patients with IBD. Methods We included clinical data 62 prospectively enrolled IBD an disease state....
Abstract Background Colorectal cancer (CRC) is a complex multifactorial disease. Increasing evidence suggests that the microbiome involved in different stages of CRC initiation and progression. Beyond specific pro-oncogenic mechanisms found pathogens, metagenomic studies indicate existence signature, where particular bacterial taxa are enriched metagenomes patients. Here, we investigate to what extent abundance can be explained by growth advantage resulting from presence metabolites tumor...
Abstract The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software scarce overoptimistic evaluation limited cross-study generalization are prevailing issues. To address these, we developed SIAMCAT, a versatile R toolbox ML-based comparative metagenomics. We demonstrate its capabilities in meta-analysis of fecal metagenomic studies (10,803 samples). When naively transferred across studies, ML...
Bacterial populations that originate from a single bacterium are not strictly clonal. Often, they contain subgroups with distinct phenotypes. Bacteria can generate heterogeneity through phase variation: preprogrammed, reversible mechanism alters gene expression levels across population. One well studied type of variation involves enzyme-mediated inversion specific intergenic regions genomic DNA. Frequently, these DNA inversions flip the orientation promoters, turning ON or OFF adjacent...
Abstract Background The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This due mainly the current technical analytical strategy limitations characterise tumour-associated bacteria. Methods Here, we propose an approach detect bacterial signals in human RNA sequencing data associate them with clinical of tumours. method was tested on public datasets from...
Abstract Population studies are crucial in understanding the complex interplay between gut microbiome and geographical, lifestyle, genetic, environmental factors. However, populations from low- middle-income countries, which represent ∼84% of world population, have been excluded large-scale research. Here, we present AWI-Gen 2 Microbiome Project, a cross-sectional study sampling 1,803 women Burkina Faso, Ghana, Kenya, South Africa. By intensively engaging with communities that range rural...
Abstract The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to intestine considered a rare aberrant event, and hallmark disease. By studying salivary fecal microbial strain populations 310 in 470 individuals from five countries, we found that transmission to, subsequent colonization of, large microbes common extensive among healthy individuals. We evidence for vast majority be transferable, with increased levels colorectal cancer rheumatoid...
Abstract Background Multiple sclerosis (MS) is a major health problem, leading to significant disability and patient suffering. Although chronic activation of the immune system hallmark disease, its pathogenesis poorly understood, while current treatments only ameliorate disease may produce severe side effects. Methods Here, we applied network-based modeling approach based on phosphoproteomic data uncover differential in signaling wiring between healthy donors, untreated patients, those...