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 …

The bacterial epigenome

MA Sánchez-Romero, J Casadesús - Nature Reviews Microbiology, 2020 - nature.com
In all domains of life, genomes contain epigenetic information superimposed over the
nucleotide sequence. Epigenetic signals control DNA–protein interactions and can cause …

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

Q Liu, L Fang, G Yu, D Wang, CL Xiao… - Nature communications, 2019 - nature.com
DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine
(6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and …

Mapping DNA methylation with high-throughput nanopore sequencing

AC Rand, M Jain, JM Eizenga, A Musselman-Brown… - Nature …, 2017 - nature.com
DNA chemical modifications regulate genomic function. We present a framework for
mapping cytosine and adenosine methylation with the Oxford Nanopore Technologies …

Mechanisms of drug-induced tolerance in Mycobacterium tuberculosis

SN Goossens, SL Sampson… - Clinical microbiology …, 2020 - Am Soc Microbiol
Successful treatment of tuberculosis (TB) can be hampered by Mycobacterium tuberculosis
populations that are temporarily able to survive antibiotic pressure in the absence of drug …

Deciphering bacterial epigenomes using modern sequencing technologies

J Beaulaurier, EE Schadt, G Fang - Nature Reviews Genetics, 2019 - nature.com
Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine
and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of …

Pyruvate cycle increases aminoglycoside efficacy and provides respiratory energy in bacteria

Y Su, BO Peng, H Li, Z Cheng… - Proceedings of the …, 2018 - National Acad Sciences
The emergence and ongoing spread of multidrug-resistant bacteria puts humans and other
species at risk for potentially lethal infections. Thus, novel antibiotics or alternative …

A CRISPR–Cas9-based gene drive platform for genetic interaction analysis in Candida albicans

RS Shapiro, A Chavez, CBM Porter, M Hamblin… - Nature …, 2018 - nature.com
Candida albicans is the leading cause of fungal infections; yet, complex genetic interaction
analysis remains cumbersome in this diploid pathogen. Here, we developed a CRISPR …

Antibiotic resistance and epigenetics: more to it than meets the eye

D Ghosh, B Veeraraghavan, R Elangovan… - Antimicrobial agents …, 2020 - Am Soc Microbiol
The discovery of antibiotics in the last century is considered one of the most important
achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity …

Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis

PH Oliveira, JW Ribis, EM Garrett, D Trzilova… - Nature …, 2020 - nature.com
Clostridioides (formerly Clostridium) difficile is a leading cause of healthcare-associated
infections. Although considerable progress has been made in the understanding of its …