A5058290191- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Chronic Myeloid Leukemia Treatments
- Diet and metabolism studies
- Metabolomics and Mass Spectrometry Studies
- Microscopic Colitis
- Forensic and Genetic Research
- Gastrointestinal motility and disorders
- Epigenetics and DNA Methylation
- Chronic Lymphocytic Leukemia Research
- Herbal Medicine Research Studies
- Pancreatic and Hepatic Oncology Research
- Forensic Entomology and Diptera Studies
- Genomics and Phylogenetic Studies
- Colorectal Cancer Screening and Detection
- Pediatric health and respiratory diseases
- Mycobacterium research and diagnosis
- Liver Disease Diagnosis and Treatment
- Blood groups and transfusion
- Animal Genetics and Reproduction
- Molecular Biology Techniques and Applications
- Neonatal Respiratory Health Research
- Viral Infectious Diseases and Gene Expression in Insects
- Mast cells and histamine
- Phytochemicals and Antioxidant Activities
European Molecular Biology Laboratory
2014-2024
European Molecular Biology Laboratory
2017-2018
University of Osijek
2013
Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing samples identify taxonomic markers that distinguished CRC patients from tumor-free controls a study population 156 participants. Accuracy detection was similar standard occult blood test (FOBT) when both approaches were combined, sensitivity improved >...
Fecal microbiota transplantation (FMT) has shown efficacy in treating recurrent Clostridium difficile infection and is increasingly being applied to other gastrointestinal disorders, yet the fate of native introduced microbial strains remains largely unknown. To quantify extent donor colonization, we monitored strain populations fecal samples from a recent FMT study on metabolic syndrome patients using single-nucleotide variants metagenomes. We found extensive coexistence recipient strains,...
Accumulating evidence indicates that the gut microbiota affects colorectal cancer development, but previous studies have varied in population, technical methods, and associations with cancer. Understanding these variations is needed for comparisons potential pooling across studies. Therefore, we performed whole-genome shotgun sequencing on fecal samples from 52 pre-treatment cases matched controls Washington, DC. We compared findings a previously published 16S rRNA study to...
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...
Fecal microbiota transplantation (FMT) is a therapeutic intervention for inflammatory diseases of the gastrointestinal tract, but its clinical mode action and subsequent microbiome dynamics remain poorly understood. Here we analyzed metagenomes from 316 FMTs, sampled pre post intervention, treatment ten different disease indications. We quantified strain-level 1,089 microbial species, complemented by 47,548 newly constructed metagenome-assembled genomes. Donor strain colonization recipient...
The composition of the healthy human adult gut microbiome is relatively stable over prolonged periods, and representatives most highly abundant prevalent species have been cultured described. However, microbial abundances can change on perturbations, such as antibiotics intake, enabling identification characterisation otherwise low species.Analysing time-series data, we used shotgun metagenomics to create strain level taxonomic functional profiles. Community dynamics were modelled...
The microbiota in individual habitats differ both relative composition and absolute abundance. While sequencing approaches determine the abundances of taxa genes, they do not provide information on their abundances. Here, we developed a machine-learning approach to predict fecal microbial loads (microbial cells per gram) solely from abundance data. Applying our prediction model large-scale metagenomic dataset (n = 34,539), demonstrated that load is major determinant gut microbiome variation...
With the technological advances of last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given inherent sample complexity, there exists a need for methods which preserve much information possible about biological system at time sampling. Here, we analyzed samples preserved and stored different methods, applying metagenomics well metaproteomics. Our results demonstrate that preservation storage have significant effect on...
Changes in the gut microbiota are increasingly recognised to be involved many diseases. This ecosystem is known shaped by factors, including climate, geography, host nutrition, lifestyle and medication. Thus, knowledge of varying populations with different habits important for a better understanding microbiome.We therefore conducted metagenomic analysis intestinal from Kazakh donors, recruiting 84 subjects, male female healthy subjects metabolic syndrome (MetS) patients aged 25-75 years,...
The marine annelid
Through high-throughput next-generation sequencing of promoters solute carrier and ATP-binding cassette genes, which encode drug transporters, we aimed to identify SNPs associated with the response imatinib administered for first-line treatment patients chronic myeloid leukemia. In silico analysis using publicly available databases was done select SLC ABC genes their sequencing. were identified Fisher's exact probability tests subjected linkage disequilibrium analyses regulatory loci...
Abstract Multi‐omics analyses are used in microbiome studies to understand molecular changes microbial communities exposed different conditions. However, it is not always clear how much each omics data type contributes our understanding and whether they concordant with other. Here, we map the response of a synthetic community 32 human gut bacteria three non‐antibiotic drugs by using five layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics metabolomics). We find...
Abstract Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. , particular infection (CDI) cases, remains poorly characterised. To investigate gut microbiome CDI patients, we analysed 534 metagenomes from 10 publicly available study populations. We then tracked on a global scale, screening 42,900 253 public studies. Among cohorts, detected only 30% of stool samples patients. However, found that multiple...
Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. , particular infection (CDI) cases, remains poorly characterised. To investigate gut microbiome CDI patients, we analysed 534 metagenomes from 10 publicly available study populations. We then tracked on a global scale, screening 42,900 253 public studies. Among cohorts, detected only 30% of stool samples patients. However, found that multiple other...
Abstract Faecal microbiota transplantation (FMT) is an efficacious therapeutic intervention, but its clinical mode of action and underlying microbiome dynamics remain poorly understood. Here, we analysed the metagenomes associated with 142 FMTs, in a time series-based meta-study across five disease indications. We quantified strain-level 1,089 microbial species based on their pangenome, complemented 47,548 newly constructed metagenome-assembled genomes. Using subsets procedural-, host-...
Clostridioides difficile is an urgent threat in hospital-acquired infections world-wide, yet the microbial composition associated with C. , particular infection (CDI) cases, remains poorly characterised. To investigate gut microbiome CDI patients, we analysed 534 metagenomes from 10 publicly available study populations. We then tracked on a global scale, screening 42,900 253 public studies. Among cohorts, detected only 30% of stool samples patients. However, found that multiple other...