Articles

A systematic search for discriminating sites in the 16S ribosomal RNA gene

The 16S rRNA is by far the most common genomic marker used for prokaryotic classification, and has been used extensively in metagenomic studies over recent years. Along the 16S gene there are regions with more...

Authors: Hilde Vinje, Trygve Almøy, Kristian Hovde Liland and Lars Snipen

Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions

Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review...

Authors: Kerensa McElroy, Torsten Thomas and Fabio Luciani

Sialic acid utilization by Cronobacter sakazakii

The Cronobacter genus is composed of seven species, and can cause infections in all age groups. Of particular concern is C. sakazakii, as this species is strongly associated with severe and often fatal cases of n...

Authors: Susan Joseph, Sumyya Hariri, Naqash Masood and Stephen Forsythe

Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data

High throughput sequencing is now fast and cheap enough to be considered part of the toolbox for investigating bacteria, and there are thousands of bacterial genome sequences available for comparison in the pu...

Authors: David J Edwards and Kathryn E Holt

An efficient rRNA removal method for RNA sequencing in GC-rich bacteria

Next generation sequencing (NGS) technologies have revolutionized gene expression studies and functional genomics analysis. However, further improvement of RNA sequencing protocols is still desirable, in order...

Authors: Clelia Peano, Alessandro Pietrelli, Clarissa Consolandi, Elio Rossi, Luca Petiti, Letizia Tagliabue, Gianluca De Bellis and Paolo Landini

Bioinformatic identification of Mycobacterium tuberculosis proteins likely to target host cell mitochondria: virulence factors?

M. tuberculosis infection either induces or inhibits host cell death, depending on the bacterial strain and the cell microenvironment. There is evidence suggesting a role for mitochondria in these processes.

Authors: María Maximina Bertha Moreno-Altamirano, Iris Selene Paredes-González, Clara Espitia, Mauricio Santiago-Maldonado, Rogelio Hernández-Pando and Francisco Javier Sánchez-García

Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains)

The genus Mycobacterium comprises different species, among them the most contagious and infectious bacteria. The members of the complex Mycobacterium tuberculosis are the most virulent microorganisms that have ki...

Authors: Fathiah Zakham, Othmane Aouane, David Ussery, Abdelaziz Benjouad and Moulay Mustapha Ennaji

Analysis of evolutionary patterns of genes in Campylobacter jejuni and C. coli

The thermophilic Campylobacter jejuni and Campylobacter coli are considered weakly clonal populations where incongruences between genetic markers are assumed to be due to random horizontal transfer of genomic DNA...

Authors: Lars Snipen, Trudy M Wassenaar, Eric Altermann, Jonathan Olson, Sophia Kathariou, Karin Lagesen, Monica Takamiya, Susanne Knøchel, David W Ussery and Richard J Meinersmann

Bacterial phylogenetic tree construction based on genomic translation stop signals

The efficiencies of the stop codons TAA, TAG, and TGA in protein synthesis termination are not the same. These variations could allow many genes to be regulated. There are many similar nucleotide trimers found...

Authors: Lijing Xu, Jimmy Kuo, Jong-Kang Liu and Tit-Yee Wong

Growth comparison of several Escherichia coli strains exposed to various concentrations of lactoferrin using linear spline regression

We wanted to compare growth differences between 13 Escherichia coli strains exposed to various concentrations of the growth inhibitor lactoferrin in two different types of broth (Syncase and Luria-Bertani (LB)). ...

Authors: Camilla Sekse, Jon Bohlin, Eystein Skjerve and Gerd E Vegarud

Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction

Protein-protein interaction (PPI) networks (interactomes) of most organisms, except for some model organisms, are largely unknown. Experimental methods including high-throughput techniques are highly resource ...

Authors: Seshan Ananthasubramanian, Rahul Metri, Ankur Khetan, Aman Gupta, Adam Handen, Nagasuma Chandra and Madhavi Ganapathiraju

Metagenomics - a guide from sampling to data analysis

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for subst...

Authors: Torsten Thomas, Jack Gilbert and Folker Meyer

Linear normalised hash function for clustering gene sequences and identifying reference sequences from multiple sequence alignments

Comparative genomics has put additional demands on the assessment of similarity between sequences and their clustering as means for classification. However, defining the optimal number of clusters, cluster den...

Authors: Manal Helal, Fanrong Kong, Sharon CA Chen, Fei Zhou, Dominic E Dwyer, John Potter and Vitali Sintchenko

Use of the University of Minnesota Biocatalysis/Biodegradation Database for study of microbial degradation

Microorganisms are ubiquitous on earth and have diverse metabolic transformative capabilities important for environmental biodegradation of chemicals that helps maintain ecosystem and human health. Microbial b...

Authors: Lynda BM Ellis and Lawrence P Wackett

Stringent response of Escherichia coli: revisiting the bibliome using literature mining

Understanding the mechanisms responsible for cellular responses depends on the systematic collection and analysis of information on the main biological concepts involved. Indeed, the identification of biologic...

Authors: Sónia Carneiro, Anália Lourenço, Eugénio C Ferreira and Isabel Rocha

PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences

Periodic spacing of short adenine or thymine runs phased with DNA helical period of ~10.5 bp is associated with intrinsic DNA curvature and deformability, which play important roles in DNA-protein interactions...

Authors: Jan Mrázek, Tejas Chaudhari and Aryabrata Basu

Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157

Although the crocodilepox virus (CRV) is currently unclassified, phylogenetic analyses suggest that its closest known relatives are molluscum contagiosum virus (MCV) and the avipox viruses. The CRV genome is a...

Authors: Nicole S Little, Taylor Quon and Chris Upton

Natural genetic engineering: intelligence & design in evolution?

There are many things that I like about James Shapiro's new book "Evolution: A View from the 21st Century" (FT Press Science, 2011). He begins the book by saying that it is the creation of novelty, and not sel...

Authors: David W Ussery

Translational web robots for pathogen genome analysis

Authors: Vitali Sintchenko and Enrico W Coiera

Quantifying the effect of environment stability on the transcription factor repertoire of marine microbes

DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content o...

Authors: Ivaylo Kostadinov, Renzo Kottmann, Alban Ramette, Jost Waldmann, Pier Luigi Buttigieg and Frank Oliver Glöckner

The zinc-ribbon domain of Helicobacter pylori HP0958: requirement for RpoN accumulation and possible roles of homologs in other bacteria

Helicobacter pylori HP0958 protein (FlgZ) prevents the rapid turnover of RpoN (σ⁵⁴), a transcription factor required for expression of several flagellar genes in H. pylori. FlgZ possesses a zinc-ribbon domain (DU...

Authors: Lara E Pereira, Jennifer Tsang, Jan Mrázek and Timothy R Hoover

Where the bugs are: analyzing distributions of bacterial phyla by descriptor keyword search in the nucleotide database

The associations between bacteria and environment underlie their preferential interactions with given physical or chemical conditions. Microbial ecology aims at extracting conserved patterns of occurrence of b...

Authors: Andrea Squartini

Large-scale experimental studies show unexpected amino acid effects on protein expression and solubility in vivo in E. coli

The biochemical and physical factors controlling protein expression level and solubility in vivo remain incompletely characterized. To gain insight into the primary sequence features influencing these outcomes, w...

Authors: W Nicholson Price II, Samuel K Handelman, John K Everett, Saichiu N Tong, Ana Bracic, Jon D Luff, Victor Naumov, Thomas Acton, Philip Manor, Rong Xiao, Burkhard Rost, Gaetano T Montelione and John F Hunt

The Regulatory Network of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an important bacterial model due to its metabolic and pathogenic abilities, which allow it to interact and colonize a wide range of hosts, including plants and animals. In this work we c...

Authors: Edgardo Galán-Vásquez, Beatriz Luna and Agustino Martínez-Antonio

Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset

The world's oceans are home to a diverse array of microbial life whose metabolic activity helps to drive the earth's biogeochemical cycles. Metagenomic analysis has revolutionized our access to these communiti...

Authors: Peter E Larsen, Frank R Collart, Dawn Field, Folker Meyer, Kevin P Keegan, Christopher S Henry, John McGrath, John Quinn and Jack A Gilbert

Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments

Base-By-Base is a Java-based multiple sequence alignment editor. It is capable of working with protein and DNA molecules, but many of its unique features relate to the manipulation of the genomes of large DNA ...

Authors: William Hillary, Song-Han Lin and Chris Upton

The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist

Scientific discovery is incremental. The Merriam-Webster definition of 'Scientific Method' is "principles and procedures for the systematic pursuit of knowledge involving the recognition and formulation of a p...

Authors: Jack A Gilbert, Ronald O'Dor, Nicholas King and Timothy M Vogel

Welcome to Microbial Informatics and Experimentation

Authors: Michael J Wise and Barry L Wanner