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 …

Xanthomonas diversity, virulence and plant–pathogen interactions

S Timilsina, N Potnis, EA Newberry… - Nature Reviews …, 2020‏ - nature.com
Xanthomonas spp. encompass a wide range of plant pathogens that use numerous
virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine …

Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study

JP Pirnay, S Djebara, G Steurs, J Griselain… - Nature …, 2024‏ - nature.com
In contrast to the many reports of successful real-world cases of personalized bacteriophage
therapy (BT), randomized controlled trials of non-personalized bacteriophage products have …

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4

A Blanco-Míguez, F Beghini, F Cumbo, LJ McIver… - Nature …, 2023‏ - nature.com
Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …

Pharokka: a fast scalable bacteriophage annotation tool

G Bouras, R Nepal, G Houtak, AJ Psaltis… - …, 2023‏ - academic.oup.com
In recent years, there has been an increasing interest in bacteriophages, which has led to
growing numbers of bacteriophage genomic sequences becoming available. Consequently …

A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome

CN Vassallo, CR Doering, ML Littlehale… - Nature …, 2022‏ - nature.com
The ancient, ongoing coevolutionary battle between bacteria and their viruses,
bacteriophages, has given rise to sophisticated immune systems including restriction …

Enterococci enhance Clostridioides difficile pathogenesis

AB Smith, ML Jenior, O Keenan, JL Hart, J Specker… - Nature, 2022‏ - nature.com
Enteric pathogens are exposed to a dynamic polymicrobial environment in the
gastrointestinal tract. This microbial community has been shown to be important during …

A roadmap for genome-based phage taxonomy

D Turner, AM Kropinski, EM Adriaenssens - Viruses, 2021‏ - mdpi.com
Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago.
Genome sequencing has put pressure on the classification system and recent years have …

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

T Yang, R Liu, Y Luo, S Hu, D Wang, C Wang… - Nature …, 2022‏ - nature.com
Complete and accurate reference genomes and annotations provide fundamental resources
for functional genomics and crop breeding. Here we report a de novo assembly and …

A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

B Ma, C Lu, Y Wang, J Yu, K Zhao, R Xue… - Nature …, 2023‏ - nature.com
Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter,
presenting an untapped reservoir of microbial biodiversity and genetic resources, but has …