Francesco Asnicar
A5023870348- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Diet and metabolism studies
- Clostridium difficile and Clostridium perfringens research
- Metabolomics and Mass Spectrometry Studies
- Nutritional Studies and Diet
- Nutrition, Genetics, and Disease
- Cancer Immunotherapy and Biomarkers
- Gene expression and cancer classification
- Bacterial Identification and Susceptibility Testing
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Bacteriophages and microbial interactions
- Gene Regulatory Network Analysis
- Antimicrobial Resistance in Staphylococcus
- Pancreatic and Hepatic Oncology Research
- Mycobacterium research and diagnosis
- Plant Virus Research Studies
- Diphtheria, Corynebacterium, and Tetanus
- Cancer, Stress, Anesthesia, and Immune Response
- Dietary Effects on Health
- Immunotherapy and Immune Responses
- Immune responses and vaccinations
University of Trento
2016-2025
European Institute of Oncology
2023
Eli Lilly (Singapore)
2023
University of Milan
2023
Daiichi Sankyo (Germany)
2023
Daiichi-Sankyo (South Korea)
2023
Merck (Germany)
2023
Bayer (United States)
2023
Amgen (United States)
2023
Istituti di Ricovero e Cura a Carattere Scientifico
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...
The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization very large-scale microbial community paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations genomes metagenomes. This includes phylogenies spanning up to thousands taxa, annotated metadata ranging from abundances physiology or host environmental phenotypes. has been...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
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...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during months. Links between configuration infant health are being shown, but a comprehensive strain-level assessment microbes vertically transmitted from mother is still missing. We collected fecal breast milk samples multiple mother-infant pairs year applied shotgun metagenomic sequencing followed by computational profiling. observed that several specific strains, including those...
Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes explored the genetic population structure of P. copri. encompasses four distinct clades (>10% inter-clade divergence) propose constitute complex, all were confirmed by isolate sequencing. These are nearly ubiquitous co-present in non-Westernized populations. Genomic analysis showed...
Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution individual genes. Here we build a reference phylogeny 10,575 evenly-sampled bacterial and archaeal genomes, based on comprehensive set 381 markers, using multiple strategies. Our trees indicate remarkably closer proximity between Archaea Bacteria than previous estimates that were limited to fewer "core" genes, such as ribosomal proteins. The...
Abstract The composition of the gut microbiome has been associated with clinical responses to immune checkpoint inhibitor (ICI) treatment, but there is limited consensus on specific characteristics linked benefits ICIs. We performed shotgun metagenomic sequencing stool samples collected before ICI initiation from five observational cohorts recruiting ICI-naive patients advanced cutaneous melanoma ( n = 165). Integrating dataset 147 previously published studies, we found that a relevant,...
Abstract The human microbiome is an integral component of the body and a co-determinant several health conditions 1,2 . However, extent to which interpersonal relations shape individual genetic makeup its transmission within across populations remains largely unknown 3,4 Here, capitalizing on more than 9,700 metagenomes computational strain-level profiling, we detected extensive bacterial strain sharing individuals (more 10 million instances) with distinct mother-to-infant, intra-household...
Limited experimental evidence bridges nutrition and cancer immunosurveillance. Here, we show that ketogenic diet (KD) - or its principal ketone body, 3-hydroxybutyrate (3HB), most specifically in intermittent scheduling induced T cell-dependent tumor growth retardation of aggressive models. In conditions which anti-PD-1 alone combination with anti-CTLA-4 failed to reduce mice receiving a standard diet, KD, oral supplementation 3HB reestablished therapeutic responses. Supplementation KD...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.