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 …

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 …

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 …

Towards the biogeography of prokaryotic genes

LP Coelho, R Alves, ÁR Del Río, PN Myers… - Nature, 2022 - nature.com
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 …

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

C Duvallet, SM Gibbons, T Gurry, RA Irizarry… - Nature …, 2017 - nature.com
Hundreds of clinical studies have demonstrated associations between the human
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 …

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 …

The healthy human microbiome

J Lloyd-Price, G Abu-Ali, C Huttenhower - Genome medicine, 2016 - Springer
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 …

A review of the global ecology, genomics, and biogeography of the toxic cyanobacterium, Microcystis spp.

MJ Harke, MM Steffen, CJ Gobler, TG Otten… - Harmful algae, 2016 - Elsevier
This review summarizes the present state of knowledge regarding the toxic, bloom-forming
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 …