The core human microbiome: does it exist and how can we find it? A critical review of the concept
The core microbiome, which refers to a set of consistent microbial features across
populations, is of major interest in microbiome research and has been addressed by …
populations, is of major interest in microbiome research and has been addressed by …
Metagenomic approaches to analyze antimicrobial resistance: an overview
Antimicrobial resistance is a major global public health problem, which develops when
pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic …
pathogens acquire antimicrobial resistance genes (ARGs), primarily through genetic …
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets
Background Long-read shotgun metagenomic sequencing is gaining in popularity and offers
many advantages over short-read sequencing. The higher information content in long reads …
many advantages over short-read sequencing. The higher information content in long reads …
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools
In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic
classification of reads by comparison to a database of previously taxonomically classified …
classification of reads by comparison to a database of previously taxonomically classified …
Landfill microbiome harbour plastic degrading genes: A metagenomic study of solid waste dumping site of Gujarat, India
Globally, environmental pollution by plastic waste has become a severe ecological and
social problem worldwide. The present study aimed to analyse the bacterial community …
social problem worldwide. The present study aimed to analyse the bacterial community …
Deep learning of a bacterial and archaeal universal language of life enables transfer learning and illuminates microbial dark matter
A Hoarfrost, A Aptekmann, G Farfañuk… - Nature …, 2022 - nature.com
The majority of microbial genomes have yet to be cultured, and most proteins identified in
microbial genomes or environmental sequences cannot be functionally annotated. As a …
microbial genomes or environmental sequences cannot be functionally annotated. As a …
Statistical and machine learning techniques in human microbiome studies: contemporary challenges and solutions
The human microbiome has emerged as a central research topic in human biology and
biomedicine. Current microbiome studies generate high-throughput omics data across …
biomedicine. Current microbiome studies generate high-throughput omics data across …
Complex marine microbial communities partition metabolism of scarce resources over the diel cycle
Complex assemblages of microbes in the surface ocean are responsible for approximately
half of global carbon fixation. The persistence of high taxonomic diversity despite …
half of global carbon fixation. The persistence of high taxonomic diversity despite …
Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories
Background and aims Birth mode and other early life factors affect a newborn's microbial
colonization with potential long-term health effects. Individual variations in early life gut …
colonization with potential long-term health effects. Individual variations in early life gut …
metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data
H Zafeiropoulos, M Beracochea, S Ninidakis… - …, 2023 - academic.oup.com
Abstract Background Genomic Observatories (GOs) are sites of long-term scientific study
that undertake regular assessments of the genomic biodiversity. The European Marine …
that undertake regular assessments of the genomic biodiversity. The European Marine …