A5031917371- Gut microbiota and health
- Probiotics and Fermented Foods
- Genomics and Phylogenetic Studies
- Clostridium difficile and Clostridium perfringens research
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Dermatology and Skin Diseases
- Immune responses and vaccinations
- Epigenetics and DNA Methylation
- Oral microbiology and periodontitis research
- Psoriasis: Treatment and Pathogenesis
- Bacteriophages and microbial interactions
- Food Security and Health in Diverse Populations
- Mental Health and Patient Involvement
- HIV, Drug Use, Sexual Risk
- Dental Health and Care Utilization
- Colorectal Cancer Screening and Detection
- Salivary Gland Disorders and Functions
- Nail Diseases and Treatments
- Cancer, Lipids, and Metabolism
- Oral Health Pathology and Treatment
- Diet and metabolism studies
- Plant Pathogens and Fungal Diseases
- Bioinformatics and Genomic Networks
- Enterobacteriaceae and Cronobacter Research
Yale University
2021-2024
University of Trento
2017-2023
University of New Haven
2023
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances methods for biological profiling via shotgun metagenomics. Opportunities improvement continue accelerate, with greater access multi-omics, reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set integrated, improved taxonomic, strain-level, functional, phylogenetic metagenomes newly developed build on largest sequences now...
The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% high quality) spanning body sites, ages, countries, lifestyles. recapitulated 4,930 species-level genome bins (SGBs), 77% without public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% well-assembled samples), expand underrepresented...
Abstract Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper obtaining metagenome-assembled (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands must thus be efficiently scalable sensitive from closely related strains divergent phyla. We present PhyloPhlAn 3.0, accurate, rapid, easy-to-use method for large-scale microbial genome characterization phylogenetic analysis multiple levels...
Abstract Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms most metagenomes. Here we present MetaPhlAn 4, which integrates information metagenome assemblies and isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference metagenome-assembled genomes, define unique marker genes 26,970 species-level genome bins, 4,992 them taxonomically unidentified...
Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative Critical Assessment Metagenome Interpretation (CAMI). The CAMI II challenge engaged community to assess methods on realistic complex datasets with long- short-read sequences, created computationally from around 1,700 new known genomes, as well 600 plasmids viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due...
Psoriasis is an immune-mediated inflammatory skin disease that has been associated with cutaneous microbial dysbiosis by culture-dependent investigations and rRNA community profiling. We applied, for the first time, high-resolution shotgun metagenomics to characterise microbiome of psoriatic unaffected from 28 individuals. demonstrate ear sites have a decreased diversity psoriasis increase in Staphylococcus, but overall microbiomes display few discriminative features at species level. Finer...
Abstract The influence of unicellular eukaryotic microorganisms on human gut health and disease is still largely unexplored. Blastocystis spp. commonly colonize the gut, but its clinical significance ecological role are currently unsettled. We have developed a high-sensitivity bioinformatic pipeline to detect subtypes (STs) from shotgun metagenomics, applied it 12 large data sets, comprising 1689 subjects different geographic origin, status lifestyle. confirmed extended previous observations...
Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide better understanding of the human microbiome. Comparative metagenomic analysis non-human primate (NHP) microbiomes offers promising approach study this symbiosis. Very few species been in NHP due their poor representation available cataloged diversity, thus limiting potential such comparative approaches.We reconstruct over 1000 previously...
Abstract Metagenomic assembly enables novel organism discovery from microbial communities, but most metagenomes it can only capture few abundant organisms. Here, we present a method - MetaPhlAn 4 to integrate information both metagenome assemblies and isolate genomes for improved more comprehensive metagenomic taxonomic profiling. From curated collection of 1.01M prokaryotic reference metagenome-assembled genomes, defined unique marker genes 26,970 species-level genome bins, 4,992 them...
Abstract Culture-independent analyses of microbial communities have advanced dramatically in the last decade, particularly due to advances methods for biological profiling via shotgun metagenomics. Opportunities improvement continue accelerate, with greater access multi-omics, reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set integrated, improved taxonomic, strain-level, functional, phylogenetic metagenomes newly developed build on largest...
When humans assemble into face-to-face social networks, they create an extended environment that permits exposure to the microbiome of others, thereby shaping composition and diversity at individual population levels1–6. Here we use comprehensive network mapping detailed sequencing data in 1,787 adults within 18 isolated villages Honduras7 investigate relationship between structure gut composition. Using both species-level strain-level data, show microbial sharing occurs many types, notably...
The gut microbiome is integral to human health, yet research data date has emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,889 individuals from rural Honduras, providing the most comprehensive dataset Central America. We identify a distinct microbial composition enriched in Prevotella species, with 861 previously unreported bacterial species. Functional profiling reveals unique carbohydrate metabolism adaptations consistent high-fiber...
We present curatedMetagenomicData, a Bioconductor and command-line interface to thousands of metagenomic profiles from the Human Microbiome Project other publicly available datasets, ExperimentHub, platform for convenient cloud-based distribution data R desktop. The resource provides standardized per-participant metadata linked bacterial, fungal, archaeal, viral taxonomic abundances, as well quantitative metabolic functional profiles. datasets can be immediately analyzed in or software with...
Psoriasis is a systemic immune-mediated disease primarily manifesting as skin redness and inflammation. Balneotherapy proved to be successful non-pharmacological option reduce the areas affected by disease, but specific mechanisms underlying this effect have not been elucidated yet. Here we test hypothesis that of thermal treatments on psoriatic lesions could partially mediated changes in resident microbial population, i.e., microbiome. In study, enrolled patients with psoriasis monitored...
Despite a growing interest in the gut microbiome of non-industrialized countries, data linking deeply sequenced microbiomes from such settings to diverse host phenotypes and situational factors remain uncommon. Using metagenomic community-based cohort 1,871 people 19 isolated villages Mesoamerican highlands western Honduras, we report associations between bacterial species human factors. Among them, socioeconomic account for 51.44% total associations. Meta-analysis species-level profiles...