A5024396962- Gut microbiota and health
- Diet and metabolism studies
- Probiotics and Fermented Foods
- Coffee research and impacts
- Salmonella and Campylobacter epidemiology
- Cocoa and Sweet Potato Agronomy
- Plant Virus Research Studies
- Identification and Quantification in Food
- Listeria monocytogenes in Food Safety
- Genomics and Phylogenetic Studies
- Vibrio bacteria research studies
- Nutritional Studies and Diet
- Polyamine Metabolism and Applications
- Child Nutrition and Water Access
- Microbial Metabolites in Food Biotechnology
- Viral gastroenteritis research and epidemiology
- Insect-Plant Interactions and Control
- Clinical Nutrition and Gastroenterology
- Clostridium difficile and Clostridium perfringens research
- Metabolomics and Mass Spectrometry Studies
- Gene expression and cancer classification
- CRISPR and Genetic Engineering
- Bacteriophages and microbial interactions
- Plant Disease Resistance and Genetics
- Insect and Pesticide Research
Nestlé (Switzerland)
2016-2024
École Polytechnique Fédérale de Lausanne
2018-2022
University of Geneva
2022
Gut microbes influence their hosts in many ways, particular by modulating the impact of diet. These effects have been studied most extensively humans and mice. In this work, we used whole genome metagenomics to investigate relationship between gut metagenomes dogs, humans, mice, pigs. We present a dog microbiome gene catalog containing 1,247,405 genes (based on 129 total 1.9 terabasepairs sequencing data). Based taxonomic abundance profiling, show that is closer human than either pigs or To...
Abstract Coffea arabica , an allotetraploid hybrid of eugenioides and canephora is the source approximately 60% coffee products worldwide, its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies a di-haploid C. accession modern representatives diploid progenitors, . The three species exhibit largely conserved genome structures between parents descendant subgenomes, with no obvious global subgenome dominance. find evidence for founding...
Salmonella is one of the most common causes food-borne diseases worldwide. While molecular subtyping by Whole Genome Sequencing (WGS) increasingly used for outbreak and source tracking investigations, serotyping remains as a first-line characterization isolates. Traditional phenotypic method logistically challenging, it requires use more than 150 specific antisera well trained personnel to interpret results. Consequently, not routine majority laboratories. Several rapid methods targeting O H...
Summary Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. is an allotetraploid (2 n = 4 x 44) originating from a hybridization event of two diploid eugenioides 2 22). Interestingly, these progenitor harbour greater level genetic variability source genes to broaden narrow Arabica base. Here, we describe development, evaluation use single‐nucleotide polymorphism ( SNP ) array for coffee trees. A total...
Whole genome sequencing (WGS), using high throughput technology, reveals the complete sequence of bacterial in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its discriminatory power. In food industry, tracking beneficial support contamination investigations. Despite increased use, no standards or guidelines are available today use and/or trace-back Here we present validation our (end-to-end) workflow Listeria...
Abstract Caffeine is the most consumed alkaloid stimulant in world. It synthesized through activity of three known N -methyltransferase proteins. Here we are reporting on 422-Mb chromosome-level assembly Coffea humblotiana genome, a wild and endangered, naturally caffeine-free, species from Comoro archipelago. We predicted 32,874 genes anchored 88.7% sequence onto 11 chromosomes. Comparative analyses with African Robusta coffee genome ( C. canephora ) revealed an extensive conservation,...
The assessment of population vulnerability under climate change is crucial for planning conservation as well ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that mainly distributed the lowland rainforests tropical Africa. Also known Robusta, commercial value constitutes a significant revenue many human populations countries. Comparing ecological and genomic vulnerabilities within species' range can provide valuable insights about habitat loss adaptive...
We report streptococcal dysbiosis in acute diarrhoea irrespective of aetiology. Compared with 20 healthy local controls, 71 Bangladeshi children hospitalized (AD) viral, mixed viral/bacterial, bacterial and unknown aetiology showed a significantly decreased diversity loss pathways characteristic for the distal colon microbiome (mannan degradation, methylerythritol phosphate thiamin biosynthesis), an increased proportion faecal streptococci belonging to Streptococcus bovis salivarius species...
Centromeric regions of plants are generally composed large array satellites from a specific lineage Gypsy LTR-retrotransposons, called Retrotransposons. Repeated sequences interact with H3 histone, playing crucial function on kinetochore formation. To study the structure and composition centromeric in genus Coffea, we annotated classified Retrotransposons allotetraploid C. arabica genome its two diploid ancestors: Coffea canephora eugenioides. Ten distinct CRC (Centromeric Coffea) families...
Malnutrition predisposes to diarrhea and adversely affects the nutritional status creating a vicious cycle.1Guerrant R.L. et al.Malnutrition as an enteric infectious disease with long-term effects on child development.Nutr Rev. 2008; 66: 487-505Crossref PubMed Scopus (341) Google Scholar The role of gut microbiome in malnutrition is active research area.2Blanton L.V. al.Childhood undernutrition, microbiota, microbiota-directed therapeutics.Science. 2016; 352: aad9359Crossref (137) Parenteral...
Abstract Coffea arabica , an allotetraploid hybrid of C. eugenioides and canephora is the source approximately 60% coffee products worldwide, its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies a di-haploid accession modern representatives diploid progenitors, . The three species exhibit largely conserved genome structures between parents descendant subgenomes, with no obvious global subgenome dominance. find evidence for founding...
In 2013, during a routine laboratory analysis performed on food samples, one finished product from European factory was tested positive for Salmonella Hadar. At the same period, environmental isolate in serotyped Prior to this event, proficiency testing involving sample spiked with NCTC 9877 The concomitance of Hadar detection led suspicion cross-contamination between used and found by laboratory. Since classical phenotypic serotyping method is able attribute serotype isolates common...
WGS is used to define if isolates are "in" or "out" of an outbreak and/or microbial root cause investigation. No threshold genetic differences fixed and the conclusions on similarity between mainly based knowledge generated from previous investigations reported mutation rates. Mutation rates in Salmonella when exposed food processing conditions lacking. Thus, this study, ability heat dry stress changes two serotypes frequently isolated low moisture foods was investigated. S. enterica...
Lactobacillus fermentum NCC2970 (CNCM I-5068) is a lactic acid bacterium originating from the Nestle Culture Collection. Here, we disclose its full 1.9-Gb genome sequence comprising one chromosome with no plasmid.