A5086888363- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Clostridium difficile and Clostridium perfringens research
- Metabolomics and Mass Spectrometry Studies
- Breastfeeding Practices and Influences
- Nutritional Studies and Diet
- Bioinformatics and Genomic Networks
- Food Security and Health in Diverse Populations
- Dental Health and Care Utilization
- Pancreatic and Hepatic Oncology Research
- Adolescent and Pediatric Healthcare
- Pediatric health and respiratory diseases
- Gallbladder and Bile Duct Disorders
- Pediatric Hepatobiliary Diseases and Treatments
University of Trento
2020-2024
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...
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 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...
Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess role both parents induced we analyzed two longitudinal metagenomic datasets (health early life microbiota [HELMi]: N = 74 infants, 398 samples, SECFLOR: 7 35 samples) with who received fecal transplantation (FMT). We found that father...
The composition and maturation of the early-life microbiota are modulated by a number perinatal factors, whose interplay in relation to microbial vertical transmission remains inadequately elucidated. Using recent strain-tracking methodologies, we analyzed mother-to-infant two different birth environments: hospital-born (vaginal/cesarean) home-born (vaginal) infants their mothers. While delivery mode primarily explains initial compositional differences, place impacts timing-being early...
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...