The population genetics of pathogenic Escherichia coli
E Denamur, O Clermont, S Bonacorsi… - Nature Reviews …, 2021 - nature.com
Escherichia coli is a commensal of the vertebrate gut that is increasingly involved in various
intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes …
intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes …
Examining horizontal gene transfer in microbial communities
IL Brito - Nature Reviews Microbiology, 2021 - nature.com
Bacteria acquire novel DNA through horizontal gene transfer (HGT), a process that enables
an organism to rapidly adapt to changing environmental conditions, provides a competitive …
an organism to rapidly adapt to changing environmental conditions, provides a competitive …
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences
K Kieft, Z Zhou, K Anantharaman - Microbiome, 2020 - Springer
Background Viruses are central to microbial community structure in all environments. The
ability to generate large metagenomic assemblies of mixed microbial and viral sequences …
ability to generate large metagenomic assemblies of mixed microbial and viral sequences …
Towards the biogeography of prokaryotic genes
Microbial genes encode the majority of the functional repertoire of life on earth. However,
despite increasing efforts in metagenomic sequencing of various habitats,–, little is known …
despite increasing efforts in metagenomic sequencing of various habitats,–, little is known …
Meta-analysis of gut microbiome studies identifies disease-specific and shared responses
Hundreds of clinical studies have demonstrated associations between the human
microbiome and disease, yet fundamental questions remain on how we can generalize this …
microbiome and disease, yet fundamental questions remain on how we can generalize this …
Genomics and pathotypes of the many faces of Escherichia coli
J Geurtsen, M de Been, E Weerdenburg… - FEMS microbiology …, 2022 - academic.oup.com
Escherichia coli is the most researched microbial organism in the world. Its varied impact on
human health, consisting of commensalism, gastrointestinal disease, or extraintestinal …
human health, consisting of commensalism, gastrointestinal disease, or extraintestinal …
Pan-genomics in the human genome era
RM Sherman, SL Salzberg - Nature Reviews Genetics, 2020 - nature.com
Since the early days of the genome era, the scientific community has relied on a single
'reference'genome for each species, which is used as the basis for a wide range of genetic …
'reference'genome for each species, which is used as the basis for a wide range of genetic …
The healthy human microbiome
Humans are virtually identical in their genetic makeup, yet the small differences in our DNA
give rise to tremendous phenotypic diversity across the human population. By contrast, the …
give rise to tremendous phenotypic diversity across the human population. By contrast, the …
A review of the global ecology, genomics, and biogeography of the toxic cyanobacterium, Microcystis spp.
This review summarizes the present state of knowledge regarding the toxic, bloom-forming
cyanobacterium, Microcystis, with a specific focus on its geographic distribution, toxins …
cyanobacterium, Microcystis, with a specific focus on its geographic distribution, toxins …
Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens
L Pritchard, RH Glover, S Humphris… - Analytical …, 2016 - pubs.rsc.org
Soft rot Enterobacteriaceae (SRE) are bacterial plant pathogens that cause blackleg, wilt
and soft rot diseases on a broad range of important crop and ornamental plants worldwide …
and soft rot diseases on a broad range of important crop and ornamental plants worldwide …