A5082240217- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Clostridium difficile and Clostridium perfringens research
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Epigenetics and DNA Methylation
- Microbial infections and disease research
- Microbial Community Ecology and Physiology
- Antibiotic Resistance in Bacteria
- Yersinia bacterium, plague, ectoparasites research
- Plant Virus Research Studies
- Parasites and Host Interactions
- Mycobacterium research and diagnosis
- Neonatal and Maternal Infections
- Bacterial Identification and Susceptibility Testing
- biodegradable polymer synthesis and properties
- Streptococcal Infections and Treatments
- Legume Nitrogen Fixing Symbiosis
- Microplastics and Plastic Pollution
- Antimicrobial Resistance in Staphylococcus
- vaccines and immunoinformatics approaches
- Metabolomics and Mass Spectrometry Studies
- Bacillus and Francisella bacterial research
- Dermatology and Skin Diseases
- Milk Quality and Mastitis in Dairy Cows
University of Cambridge
2022-2025
Universidade Nova de Lisboa
2024
European Bioinformatics Institute
2018-2023
Wellcome Sanger Institute
2018-2023
Wellcome Trust
2021-2022
European Molecular Biology Laboratory
2020
Institut Pasteur
1993-2019
Centre National de la Recherche Scientifique
2015-2019
CNR de la Résistance aux Antibiotiques
2016-2019
Sorbonne Université
2015-2019
The composition of the human gut microbiota is linked to health and disease, but knowledge individual microbial species needed decipher their biological roles. Despite extensive culturing sequencing efforts, complete bacterial repertoire remains undefined. Here we identify 1,952 uncultured candidate by reconstructing 92,143 metagenome-assembled genomes from 11,850 microbiomes. These substantially expand known collective microbiota, with a 281% increase in phylogenetic diversity. Although...
Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant from 4,644 prokaryotes. These encode >170 million protein sequences, which we collated in Protein (UHGP) catalog. The UHGP more than doubles number proteins comparison to those Integrated Gene Catalog. More 70% UHGG species lack cultured...
Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced isolates, representing 273 species (105 novel species) from 31 families found in human gastrointestinal microbiota. The HBC increases number genomes derived microbiota by 37%....
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over past 2 years, (formerly EBI Metagenomics) has more than doubled number publicly available analysed datasets held within resource. Recently, an updated approach been unveiled (version 5.0), replacing previous single pipeline with multiple pipelines tailored...
Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence human gut remains largely unknown. Here, we introduce Gut Phage Database, a collection ∼142,000 non-redundant genomes (>10 kb) obtained mining dataset 28,060 globally distributed metagenomes 2,898 reference cultured bacteria. Host assignment revealed is highest Firmicutes phyla ∼36% clusters (VCs) are not...
Abstract Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, dependency most methods on reference genomes, which are currently unavailable for a substantial fraction species, introduces estimation biases. We present an updated functionally extended tool based universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling profiling...
The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report analysis of 1,167 nonredundant genomes (608 high-quality genomes) recovered from gastrointestinal tract, sampled across 24 countries and rural urban populations. We identified previously undescribed taxa including 3 genera, 15 species 52 strains. Based on distinct genomic features, justify split Methanobrevibacter smithii clade into two separate...
Human health and disease have increasingly been shown to be impacted by the gut microbiota, mouse models are essential for investigating these effects. However, compositions of human microbiotas distinct, limiting translation microbiota research between hosts. To address this, we constructed Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository 26,640 high-quality microbiota-derived bacterial genomes. This catalog enables species-level analyses mapping functions interest identifying...
Early-life human gut microbiome is a pivotal driver of homeostasis and infant health. However, the viral component (known as "virome") remains mostly unexplored. Here, we establish Early-Life Gut Virome (ELGV), catalog 160,478 non-redundant DNA RNA sequences from 8130 virus-like particles (VLPs) enriched or bulk metagenomes in first three years life. By clustering, 82,141 species are identified, 68.3% which absent existing databases built mainly adults, 64 8 based on VLPs-enriched...
Abstract Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play role in modulating infection resistance. Here we uncover global ecological patterns linked to colonization and abundance by leveraging large-scale dataset 12,238 public metagenomes spanning 45 countries. Machine learning analyses identified robust microbiome signature associated with...
Abstract Background Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring composition complex microbial ecosystems. Quantitative Insights Into Microbial Ecology (QIIME) and mothur have most widely used taxonomic analysis tools this purpose, with MAPseq QIIME 2 being two recently released alternatives. However, no independent direct comparison between these four main performed. Here, we compared default classifiers MAPseq, mothur, QIIME, using...
Abstract Background The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies been largely focused on pathogenic species. In this study, we expanded analyses lineages that inhabit various environments using a collection 840 genomes. Results Several were discovered inhabiting the human gut, ground water, bioreactors hypersaline lake spanning Haloplasmatales Mycoplasmatales orders. A phylogenomics analysis...
Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present Early-Life Gut Genomes (ELGG) catalog with 32,277 representing 2172 species from 6122 fecal metagenomes collected children under 3 years old spanning delivery mode, gestational age, feeding pattern, geography. The ELGG substantially expanded phylogenetic diversity by...
Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe first functional PET-active enzymes from Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, identified several PETase candidates Flavobacteriaceae Porphyromonadaceae. Among them, two promiscuous cold-active esterases derived Aequorivita sp. (PET27) Kaistella jeonii (PET30) showed depolymerizing activity on...
An increasingly common output arising from the analysis of shotgun metagenomic datasets is generation metagenome-assembled genomes (MAGs), with tens thousands MAGs now described in literature. However, discovery and comparison these MAG collections hampered by lack uniformity their generation, annotation storage. To address this, we have developed MGnify Genomes, a growing collection biome-specific non-redundant microbial genome catalogues generated using publicly available isolate genomes....
Abstract Background Human-to-human transmission of symbiotic, anaerobic bacteria is a fundamental evolutionary adaptation essential for membership the human gut microbiota. However, despite its importance, genomic and biological adaptations underpinning symbiont remain poorly understood. The Firmicutes are dominant phylum within intestinal microbiota that capable producing resistant endospores maintain viability environment germinate intestine to facilitate transmission. impact host on...
The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations sparked widespread interest in developing computational strategies that support comprehensive characterisation based sequencing data. Here we introduce VIRify, a new pipeline designed to provide user-friendly accurate functional taxonomic communities. VIRify identifies contigs prophages from metagenomic assemblies annotates them using...
Group B Streptococcus (GBS) is a host-generalist species, most notably causing disease in humans and cattle. However, the differential adaptation of GBS to its two main hosts, risk animal human infection remain poorly understood. Despite improvements control measures across Europe, still one causative agents bovine mastitis Portugal. Here, by whole-genome analysis 150 isolates we discovered that single CC61 clone spreading throughout Portuguese herds since at least early 1990s, having...
In spite of growing evidence supporting the occurrence complex interactions between Schistosoma and gut bacteria in mice humans, no data is yet available on whether worm-mediated changes microbiota composition are dependent baseline microbial profile vertebrate host. addition, impact such susceptibility to, pathophysiology of, schistosomiasis remains largely unexplored. this study, colonized with populations from a human donor (HMA mice), as well microbiota-wild type (WT) animals, were...
Automatic annotation of protein function is routinely applied to newly sequenced genomes. While this provides a fine-grained view an organism's functional repertoire, proteins, more commonly in coordinated manner, such as pathways or multimeric complexes. Genome Properties (GPs) define entities series steps, originally described by either TIGRFAMs Pfam entries. To increase the scope coverage, we have migrated GPs companion resource utilizing InterPro Having introduced GPs-specific versioned...
SUMMARY Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and prevalence human gut remains largely unknown. Here, we introduce Gut Phage Database (GPD), a collection ∼142,000 non-redundant genomes (>10 kb) obtained mining dataset 28,060 globally distributed metagenomes 2,898 reference cultured bacteria. Host assignment revealed is highest Firmicutes phyla ∼36% clusters...