Metagenomics: DNA sequencing of environmental samples

SG Tringe, EM Rubin - Nature reviews genetics, 2005 - nature.com
Although genomics has classically focused on pure, easy-to-obtain samples, such as
microbes that grow readily in culture or large animals and plants, these organisms represent …

A bioinformatician's guide to metagenomics

V Kunin, A Copeland, A Lapidus… - Microbiology and …, 2008 - Am Soc Microbiol
As random shotgun metagenomic projects proliferate and become the dominant source of
publicly available sequence data, procedures for the best practices in their execution and …

Genome sequence of the bioplastic-producing “Knallgas” bacterium Ralstonia eutropha H16

A Pohlmann, WF Fricke, F Reinecke, B Kusian… - Nature …, 2006 - nature.com
The H2-oxidizing lithoautotrophic bacterium Ralstonia eutropha H16 is a metabolically
versatile organism capable of subsisting, in the absence of organic growth substrates, on H2 …

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

SY Gerdes, MD Scholle, JW Campbell… - Journal of …, 2003 - Am Soc Microbiol
Defining the gene products that play an essential role in an organism's functional repertoire
is vital to understanding the system level organization of living cells. We used a genetic …

The genome of the ammonia‐oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations

A Spang, A Poehlein, P Offre… - Environmental …, 2012 - Wiley Online Library
The cohort of the ammonia‐oxidizing archaea (AOA) of the phylum Thaumarchaeota is a
diverse, widespread and functionally important group of microorganisms in many …

The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode

J Foster, M Ganatra, I Kamal, J Ware, K Makarova… - PLoS …, 2005 - journals.plos.org
Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate
alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial …

The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) σ factor protein family

A Staroń, HJ Sofia, S Dietrich, LE Ulrich… - Molecular …, 2009 - Wiley Online Library
The ability of a bacterial cell to monitor and adaptively respond to its environment is crucial
for survival. After one‐and two‐component systems, extracytoplasmic function (ECF) σ …

The proteolytic system of lactic acid bacteria revisited: a genomic comparison

M Liu, JR Bayjanov, B Renckens, A Nauta, RJ Siezen - BMC genomics, 2010 - Springer
Background Lactic acid bacteria (LAB) are a group of gram-positive, lactic acid producing
Firmicutes. They have been extensively used in food fermentations, including the production …

Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes

DA Rodionov, AG Vitreschak, AA Mironov… - Journal of Biological …, 2003 - ASBMB
Using comparative analysis of genes, operons, and regulatory elements, we describe the
cobalamin (vitamin B 12) biosynthetic pathway in available prokaryotic genomes. Here we …

Structural variation in the glycan strands of bacterial peptidoglycan

W Vollmer - FEMS microbiology reviews, 2008 - academic.oup.com
The normal, unmodified glycan strands of bacterial peptidoglycan consist of alternating
residues of β-1, 4-linked N-acetylmuramic acid and N-acetylglucosamine. In many species …