51 hasil untuk "Francesco Asnicar"
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Artikel Jurnal Teks lengkap
Compact graphical representation of phylogenetic data and metadata with GraPhlAn
The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that…
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Profiling microbial strains in urban environments using metagenomic sequencing data
Abstract Background The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially…
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Genomic and metagenomic insights into the microbial community of a thermal spring
Abstract Background Water springs provide important ecosystem services including drinking water supply, recreation, and balneotherapy, but their microbial communities remain largely unknown. In this study, we characterized the spring water microbiome of Comano Terme (Italy) at four sampling points…
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Population-level impacts of antibiotic usage on the human gut microbiome
Here, the authors study the population-level impact of antimicrobial resistance genes (ARGs). By analyzing 8972 metagenomes and 3,096 gut microbiomes from healthy individuals not taking antibiotics, they demonstrate significant correlations between both the total ARG abundance and diversity and per…
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Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome
ABSTRACT Resistant starch (RS) can confer benefits for the gut microbiome and host cardiometabolic health. However, different types of resistant starch can differentially affect gut microbiome composition and functional capacity, especially given interindividual variability in responses, thus…
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Discovering Causal Relationships in Grapevine Expression Data to Expand Gene Networks. A Case Study: Four Networks Related to Climate Change
In recent years the scientific community has been heavily engaged in studying the grapevine response to climate change. Final goal is the identification of key genetic traits to be used in grapevine breeding and the setting of agronomic practices to improve climatic resilience. The increasing…
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Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling
ABSTRACT The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically…
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High dietary inflammatory index associates with inflammatory proteins in plasma
Abstract Background and aim Unhealthy dietary habits and highly caloric foods induce metabolic alterations and promote the development of the inflammatory consequences of obesity, insulin resistance, diabetes and cardiovascular diseases. Describing an inflammatory effect of diet is difficult to…
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Artikel Jurnal
Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species
Abstract Background Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes…
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Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data
Cas9 proteins require a target-adjacent sequence, the PAM, in order to cleave DNA. Here the authors develop a pipeline to accurately predict PAM sequences in order to facilitate the identification of Cas9s targeting specific sequences, including mutations.
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Protease-serpin-microbiome interactions in inflammatory bowel disease: toward integrated biomarkers of gut health
Proteolytic imbalance involving host and microbial serine proteases and their inhibitors (serpins) contributes to intestinal barrier disruption and chronic inflammation in inflammatory bowel disease (IBD). However, the interplay among these components remains insufficiently characterized. Here, we…
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Artikel Jurnal
Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis
Psoriasis: investigating microbial diversity Analysing microbial populations on the skin provides an insight into the diversity of microbes associated with psoriasis. Nicola Segata and colleagues at the University of Trento, Italy, used genetic analysis to compare the microbial populations on…
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Whole-genome epidemiology, characterisation, and phylogenetic reconstruction of Staphylococcus aureus strains in a paediatric hospital
Abstract Background Staphylococcus aureus is an opportunistic pathogen and a leading cause of nosocomial infections. It can acquire resistance to all the antibiotics that entered the clinics to date, and the World Health Organization defined it as a high-priority pathogen for research and…
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Diet and gut microbial associations in irritable bowel syndrome according to disease subtype
ABSTRACTThe role of diet and the gut microbiome in the etiopathogenesis of irritable bowel syndrome (IBS) is not fully understood. Therefore, we investigated the interplay between dietary risk factors and gut microbiota in IBS subtypes using a food frequency questionnaire and stool metagenome data…
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Characterization of antimicrobial resistant Empedobacter from fresh meat and meat preparations
Empedobacter has been identified as an opportunistic pathogen that frequently exhibits resistance to multiple antibiotics, including some of those known as of last-resort. This study describes the phenotypic and genotypic characterization of carbapenem-resistant Empedobacter isolates obtained from…
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Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seedingResearch in context
Summary: Background: Neuroblastoma is the most frequent extracranial solid tumour in children, accounting for ∼15% of deaths due to cancer in childhood. The most common clinical presentation are abdominal tumours. An altered gut microbiome composition has been linked to multiple cancer types, and…
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Artikel Jurnal Teks lengkap
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Microbial genomes are available at an ever-increasing pace, as cultivation and sequencing become cheaper and obtaining metagenome-assembled genomes (MAGs) becomes more effective. Phylogenetic placement methods to contextualize hundreds of thousands of genomes must thus be efficiently scalable and…
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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial…
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Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity
Abstract Background Vitamin A is essential for physiological processes like vision and immunity. Vitamin A’s effect on gut microbiome composition, which affects absorption and metabolism of other vitamins, is still unknown. Here we examined the relationship between gut metagenome composition and…