A5024748536- Gut microbiota and health
- Bacterial Identification and Susceptibility Testing
- SARS-CoV-2 detection and testing
- Clostridium difficile and Clostridium perfringens research
- Cystic Fibrosis Research Advances
- Nutritional Studies and Diet
- Meta-analysis and systematic reviews
- Diet and metabolism studies
- Probiotics and Fermented Foods
- Viral Infections and Immunology Research
- Urinary Tract Infections Management
- Nutrition, Health and Food Behavior
- COVID-19 Clinical Research Studies
- Gene expression and cancer classification
- Clinical practice guidelines implementation
- COVID-19 diagnosis using AI
- Genetics, Bioinformatics, and Biomedical Research
- SARS-CoV-2 and COVID-19 Research
- Infant Nutrition and Health
- Oral microbiology and periodontitis research
- Respiratory viral infections research
- Molecular Biology Techniques and Applications
- Nosocomial Infections in ICU
- Pediatric health and respiratory diseases
- Clinical Laboratory Practices and Quality Control
University of Lausanne
2017-2025
University Hospital of Lausanne
2020
Czech Academy of Sciences, Institute of Microbiology
2020
Summary: To enable flexible, scalable, and reproducible microbiota profiling, we have developed zAMP, an open-source bioinformatics pipeline for the analysis of amplicon sequence data, such as 16S rRNA gene bacteria archaea or ITS fungi. zAMP is complemented by two modules, one to process databases optimize taxonomy assignment, second benchmark primers, classifier performances. Coupled with zAMPExplorer, interactive R Shiny application that provides intuitive interface quality control,...
Trimethylamine-N-oxide (TMAO) can be produced by the gut microbiota from dietary substrates and is associated with cardiovascular disease. While dairy products contain TMAO precursors, effect of fermented on metabolism remains unclear. We used plasma urine samples collected for two randomised cross-over studies to evaluate effects consumption metabolism. In Study 1, thirteen healthy young men tested a yogurt an acidified milk during postprandial tests two-week daily intervention. 2, ten...
The gut and lung microbiomes play crucial roles in host defense mayserve as predictive markersfor clinical outcomes critically ill patients. Despite this, the simultaneous dynamics of during critical illness remain unclear. This study aims to assess longitudinal changes microbiota among mechanically ventilated ICU patients with without infection identify microbial features outcomes, including development ventilator associated pneumonia (VAP). In this prospective observational study, we...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms. Several evidences suggest that the intestine critical site of immune cell development, gut microbiota could therefore play key role in lung response. We designed monocentric longitudinal observational study to describe profile COVID-19 patients and compare it pre-existing cohort ventilated non-COVID-19...
Given the importance of microbiology results on patient care, high quality standards are expected. Internal assurance (IQA) could mitigate limitations internal control, competency assessment and external assurance, adding a longitudinal insight, including pre- post-analytical steps. Here, we implemented an IQA program in our clinical facilities with blind resubmission routine samples during 22 months. One-hundred-and-twenty-one out 123 (98.4%) serological analyses 112 122 (91.8%) molecular...
Abstract Since the beginning of COVID-19 pandemic, important health and regulatory decisions relied on SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in number RT-PCR, with up to 1,007 tests per day. To maintain turnaround time support patient management public authorities’ decisions, we moved from case-by-case validation RT-PCR an automated immediate transmission results clinicians. high quality track possible...
The contribution of intracellular and fastidious bacteria in Cystic fibrosis (CF) pulmonary exacerbations, progressive lung function decline remains unknown. This project aimed to explore their impact on bacterial microbiota diversity over time CF children.Sixty-one children enrolled the MUCOVIB multicentre prospective cohort provided 746 samples, mostly nasopharyngeal swabs, throat swabs sputa which were analysed using culture, specific real-time qPCRs 16S rRNA amplicon...
Introduction There is compositional overlap between the maternal intestinal microbiome, breast milk microbiome and infant oral microbiome. Antibiotics cause profound changes in However, effect of intrapartum early-life antibiotics on whether effects are only short term or persist long remain uncertain. Methods analyses In this prospective cohort study, we will use metagenomic sequencing to determine: (1) composition milk, including development persistence antibiotic resistance; (2) exposure...
Since the beginning of COVID-19 pandemic, important health and regulatory decisions relied on SARS-CoV-2 reverse transcription polymerase chain reaction (RT-PCR) results. Our diagnostic laboratory faced a rapid increase in number RT-PCR. To maintain turnaround time, we moved from case-by-case validation RT-PCR results to an automated immediate transmission clinicians. A quality-monitoring tool based homemade algorithm coded R was developed, preserve high quality track aberrant We present...
The gut microbiota adapts to age-related changes in host physiology but is also affected by environmental stimuli, like diet. As a source of both pre- and probiotics, dairy fermented foods modulate the composition, which makes them interesting food groups use for investigation interactions between diet ageing. Here we present effects excluding products limiting consumption 19 days on composition circulating metabolites 28 healthy, young (YA) older (OA) adult men. intervention microbial...
Various bacterial and viral assemblages composing Cystic Fibrosis (CF) lung microbiota contribute to long-term function decline over time. Yet, the impact of individual microorganisms on pulmonary functions remains uncertain in children with CF.As part 'Mucoviscidosis, respiratory VIruses, intracellular Bacteria fastidious organisms'' project, CF were longitudinally followed a Swiss multicentric study. Respiratory samples included mainly throat swabs sputa for culture 16S rRNA metagenomics...
Background: Sputum is the sample to monitor lower respiratory tract microbiota in cystic fibrosis (CF), but young patients often cannot expectorate. We hypothesized that throat swabs could reflect airway colonization and assessed concordance of bacterial community composition between paired sputum swab samples from children with CF. Methods: The prospective longitudinal multicenter MUCOVIB cohort included 379 61 CF children. Using V3-V4 16S rRNA amplicon metagenomics, we compared diversity...