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The Human Virome: Viral Metagenomics, Relations with Human Diseases, and Therapeutic Applications
Viruses, 2022 The human body is colonized by a wide range of microorganisms. The field of viromics has expanded since the first reports on the detection of viruses via metagenomic sequencing in 2002. With the continued development of reference materials and databases,
Geng-Hao Bai +3 more
semanticscholar +1 more source
Bracken: estimating species abundance in metagenomics data
bioRxiv, 2016 We describe a new, highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomy labels assigned by ...
Jennifer Lu +3 more
semanticscholar +1 more source
Genome binning of viral entities from bulk metagenomics data
Nature Communications, 2021 Despite the accelerating number of uncultivated virus sequences discovered in metagenomics and their apparent importance for health and disease, the human gut virome and its interactions with bacteria in the gastrointestinal tract are not well understood.
Joachim Johansen +10 more
semanticscholar +1 more source
PLoS ONE, 2014 Next generation sequencing technologies led to the discovery of numerous new microbe species in diverse environmental samples. Some of the new species contain genes never encountered before. Some of these genes encode proteins with novel functions, and some of these genes encode proteins that perform some well-known function in a novel way.
Szalkai, Balázs +4 more
openaire +5 more sources
DNA structure at the plasmid origin-of-transfer indicates its potential transfer range
Scientific Reports, 2018 Horizontal gene transfer via plasmid conjugation enables antimicrobial resistance (AMR) to spread among bacteria and is a major health concern. The range of potential transfer hosts of a particular conjugative plasmid is characterised by its mobility ...
Jan Zrimec, Aleš Lapanje
doaj +1 more source
BMC Genomics, 2023 Background While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes ...
Sophie A. Simon +5 more
doaj +1 more source
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
Science, 2016 “Normal” for the gut microbiota For the benefit of future clinical studies, it is critical to establish what constitutes a “normal” gut microbiome, if it exists at all. Through fecal samples and questionnaires, Falony et al.
A. Zhernakova +30 more
semanticscholar +1 more source
Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens
Microorganisms, 2021 Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegetables, with a corresponding increase in economic losses caused by the introduction of transboundary plant pathogens.
E. Piombo +5 more
semanticscholar +1 more source
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
Nature Communications, 2019 Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome
R. Hendriksen +32 more
semanticscholar +1 more source
Methods for comparative metagenomics [PDF]
BMC Bioinformatics, 2009 Metagenomics is a rapidly growing field of research that aims at studying uncultured organisms to understand the true diversity of microbes, their functions, cooperation and evolution, in environments such as soil, water, ancient remains of animals, or the digestive system of animals and humans.
Daniel H. Huson +4 more
openaire +3 more sources