Performance and application of 16S rRNA gene cycle sequencing for routine identification of bacteria in the clinical microbiology laboratory

DL Church, L Cerutti, A Gürtler, T Griener… - Clinical microbiology …, 2020 - Am Soc Microbiol
This review provides a state-of-the-art description of the performance of Sanger cycle
sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical …

Within-host evolution of bacterial pathogens

X Didelot, AS Walker, TE Peto, DW Crook… - Nature Reviews …, 2016 - nature.com
Whole-genome sequencing has opened the way for investigating the dynamics and
genomic evolution of bacterial pathogens during the colonization and infection of humans …

[HTML][HTML] Open-access bacterial population genomics: BIGSdb software, the PubMLST. org website and their applications

KA Jolley, JE Bray, MCJ Maiden - Wellcome open research, 2018 - ncbi.nlm.nih.gov
The PubMLST. org website hosts a collection of open-access, curated databases that
integrate population sequence data with provenance and phenotype information for over …

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

M Inouye, H Dashnow, LA Raven, MB Schultz… - Genome medicine, 2014 - Springer
Rapid molecular typing of bacterial pathogens is critical for public health epidemiology,
surveillance and infection control, yet routine use of whole genome sequencing (WGS) for …

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

CS Chin, DH Alexander, P Marks, AA Klammer… - Nature …, 2013 - nature.com
We present a hierarchical genome-assembly process (HGAP) for high-quality de novo
microbial genome assemblies using only a single, long-insert shotgun DNA library in …

A proposed genus boundary for the prokaryotes based on genomic insights

QL Qin, BB Xie, XY Zhang, XL Chen… - Journal of …, 2014 - Am Soc Microbiol
Genomic information has already been applied to prokaryotic species definition and
classification. However, the contribution of the genome sequence to prokaryotic genus …

The complex microbiota of raw milk

L Quigley, O O'Sullivan, C Stanton… - FEMS microbiology …, 2013 - academic.oup.com
Here, we review what is known about the microorganisms present in raw milk, including milk
from cows, sheep, goats and humans. Milk, due to its high nutritional content, can support a …

MLST revisited: the gene-by-gene approach to bacterial genomics

MCJ Maiden, MJJ Van Rensburg, JE Bray… - Nature Reviews …, 2013 - nature.com
Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based
method for identifying clonal relationships among bacteria. Today, in the whole-genome era …

Carbon dot-based platform for simultaneous bacterial distinguishment and antibacterial applications

J Yang, X Zhang, YH Ma, G Gao, X Chen… - … applied materials & …, 2016 - ACS Publications
In this work, we prepared quaternized carbon dots (CDs) with simultaneous antibacterial
and bacterial differentiation capabilities using a simple carboxyl–amine reaction between …

Beneficial microbes affect endogenous mechanisms controlling root development

EH Verbon, LM Liberman - Trends in plant science, 2016 - cell.com
Plants have incredible developmental plasticity, enabling them to respond to a wide range of
environmental conditions. Among these conditions is the presence of plant growth …