[HTML][HTML] FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genome and metagenome assemblies

AI Garber, KH Nealson, A Okamoto… - Frontiers in …, 2020 - frontiersin.org
Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and
electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a …

Analysis of the global ocean sampling (GOS) project for trends in iron uptake by surface ocean microbes

E Toulza, A Tagliabue, S Blain, G Piganeau - PLoS One, 2012 - journals.plos.org
Microbial metagenomes are DNA samples of the most abundant, and therefore most
successful organisms at the sampling time and location for a given cell size range. The study …

NEAT: a domain duplicated in genes near the components of a putative Fe3+siderophore transporter from Gram-positive pathogenic bacteria

MA Andrade, FD Ciccarelli, C Perez-Iratxeta, P Bork - Genome biology, 2002 - Springer
Background Iron uptake from the host is essential for bacteria that infect animals. To find
potential targets for drugs active against pathogenic bacteria, we have searched all …

Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments

V Bonnefoy, DS Holmes - Environmental Microbiology, 2012 - Wiley Online Library
This minireview presents recent advances in our understanding of iron oxidation and
homeostasis in acidophilic Bacteria and Archaea. These processes influence the flux of …

Computational reconstruction of iron-and manganese-responsive transcriptional networks in α-proteobacteria

DA Rodionov, MS Gelfand, JD Todd… - PLoS computational …, 2006 - journals.plos.org
We used comparative genomics to investigate the distribution of conserved DNA-binding
motifs in the regulatory regions of genes involved in iron and manganese homeostasis in …

On the road to strain-resolved comparative metagenomics

N Segata - MSystems, 2018 - Am Soc Microbiol
Metagenomics has transformed microbiology, but its potential has not been fully expressed
yet. From computational methods for digging deeper into metagenomes to study designs for …

Iron transporters in marine prokaryotic genomes and metagenomes

BM Hopkinson, KA Barbeau - Environmental microbiology, 2012 - Wiley Online Library
In the pelagic environment, iron is a scarce but essential micronutrient. The iron acquisition
capabilities of selected marine bacteria have been investigated, but the recent proliferation …

Comparative genomic insights into ecophysiology of neutrophilic, microaerophilic iron oxidizing bacteria

S Kato, M Ohkuma, DH Powell, ST Krepski… - Frontiers in …, 2015 - frontiersin.org
Neutrophilic microaerophilic iron-oxidizing bacteria (FeOB) are thought to play a significant
role in cycling of carbon, iron and associated elements in both freshwater and marine iron …

Over 50,000 metagenomically assembled draft genomes for the human oral microbiome reveal new taxa

J Zhu, L Tian, P Chen, M Han, L Song… - Genomics …, 2022 - academic.oup.com
The oral cavity of each person is home to hundreds of bacterial species. While taxa for oral
diseases have been studied using culture-based characterization as well as amplicon …

Buried treasure: evolutionary perspectives on microbial iron piracy

MF Barber, NC Elde - Trends in Genetics, 2015 - cell.com
Host–pathogen interactions provide valuable systems for the study of evolutionary genetics
and natural selection. The sequestration of essential iron has emerged as a crucial innate …