Ian T. Paulsen
A5069669892- Microbial Community Ecology and Physiology
- Antibiotic Resistance in Bacteria
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Microbial Metabolic Engineering and Bioproduction
- Bacteriophages and microbial interactions
- Plant-Microbe Interactions and Immunity
- Bacterial biofilms and quorum sensing
- RNA and protein synthesis mechanisms
- Vibrio bacteria research studies
- Protist diversity and phylogeny
- Drug Transport and Resistance Mechanisms
- Legume Nitrogen Fixing Symbiosis
- Plant Pathogenic Bacteria Studies
- Fungal and yeast genetics research
- Biofuel production and bioconversion
- Algal biology and biofuel production
- Gene Regulatory Network Analysis
- Antimicrobial Resistance in Staphylococcus
- Enzyme Structure and Function
- Trace Elements in Health
- Coal Properties and Utilization
- Methane Hydrates and Related Phenomena
- Gut microbiota and health
- Metal Extraction and Bioleaching
Macquarie University
2016-2025
ARC Centre of Excellence in Synthetic Biology
2019-2025
Australian Genome Research Facility
2011-2025
Australian Research Council
2018-2024
Joint Genome Institute
2009-2021
University of Technology Sydney
2020
IE University
2020
Western Sydney University
2015
J. Craig Venter Institute
2002-2014
Australian Wine Research Institute
2011
We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs nonredundant sequence was generated, annotated, analyzed elucidate gene content, diversity, relative abundance organisms within these environmental samples. These data are estimated derive at least 1800 genomic species based relatedness, including 148 previously unknown...
Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It model system for studying chloroplast-based photosynthesis, as well the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited common ancestor animals, but lost in plants. We sequenced ∼120-megabase nuclear genome performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated...
Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report high-quality draft sequence N. genome. The approximately 40-megabase genome encodes about 10,000 protein-coding genes--more than twice as many fission yeast Schizosaccharomyces pombe only 25% fewer fruitfly Drosophila melanogaster. Analysis gene set yields insights into unexpected aspects biology including identification genes potentially associated with...
The 2,160,837–base pair genome sequence of an isolate Streptococcus pneumoniae , a Gram-positive pathogen that causes pneumonia, bacteremia, meningitis, and otitis media, contains 2236 predicted coding regions; these, 1440 (64%) were assigned biological role. Approximately 5% the is composed insertion sequences may contribute to rearrangements through uptake foreign DNA. Extracellular enzyme systems for metabolism polysaccharides hexosamines provide substantial source carbon nitrogen S. also...
Summary Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as biosafety host for the cloning of foreign genes. The also considerable potential biotechnological applications. Sequence analysis 6.18 Mb genome strain KT2440 reveals diverse transport and metabolic systems. Although there high level conservation with pathogenic Pseudomonad aeruginosa (85% predicted coding regions are shared), key virulence factors including exotoxin A type III...
We present a draft sequence of the genome Aedes aegypti, primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times size malaria Anopheles gambiae. Nearly 50% Ae. aegypti consists transposable elements. These contribute to factor 4 6 increase in average gene length sizes intergenic regions relative An. gambiae Drosophila melanogaster. Nonetheless, chromosomal synteny generally maintained among all three insects, although conservation...
ABSTRACT Staphylococcus aureus is an opportunistic pathogen and the major causative agent of numerous hospital- community-acquired infections. epidermidis has emerged as a infections often associated with implanted medical devices. We have sequenced ∼2.8-Mb genome S. COL, early methicillin-resistant isolate, ∼2.6-Mb RP62a, biofilm isolate. Comparative analysis these other staphylococcal genomes was used to explore evolution virulence resistance between two species. The are syntenic...
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members Proteobacteria, Cyanobacteria, and Fungi. appear to be versatile heterotrophs. Genomic culture indicate use carbon sources that span simple sugars more complex substrates such hemicellulose, cellulose, chitin. encode low-specificity major facilitator superfamily transporters high-affinity ABC for sugars, suggesting...
The complete genome sequence of Enterococcus faecalis V583, a vancomycin-resistant clinical isolate, revealed that more than quarter the consists probable mobile or foreign DNA. One predicted elements is previously unknown vanB vancomycin-resistance conjugative transposon. Three plasmids were identified, including two pheromone-sensing plasmids, one encoding undescribed pheromone inhibitor. apparent propensity for incorporation probably contributed to rapid acquisition and dissemination drug...
The complete sequence of the 1,267,782 bp genome Wolbachia pipientis wMel, an obligate intracellular bacteria Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety invertebrate species, great interest due to their diverse interactions with different hosts, range from many forms reproductive parasitism mutualistic symbioses. Analysis wMel genome, particular phylogenomic comparisons other bacteria, revealed insights into biology and evolution general. For...
We report the complete genome sequence of model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on and Arabidopsis thaliana . The (6.5 megabases) contains a circular chromosome two plasmids, collectively encode 5,763 ORFs. identified 298 established putative virulence genes, including several clusters genes encoding 31 confirmed 19 predicted type III secretion system effector proteins. Many were members paralogous families also proximal to mobile...
Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities, conferred in part by multicomponent, branched electron transport systems. Here we report the sequencing S. genome, which consists a 4,969,803–base pair circular chromosome with 4,758 predicted protein-encoding open reading frames (CDS) and 161,613–base plasmid 173 CDSs. We identified first lambda-like phage, providing potential tool further genome engineering....
The human malaria parasite Plasmodium vivax is responsible for 25–40% of the ∼515 million annual cases worldwide. Although seldom fatal, elicits severe and incapacitating clinical symptoms often causes relapses months after a primary infection has cleared. Despite its importance as major pathogen, P. little studied because it cannot be propagated continuously in laboratory except non-human primates. We sequenced genome to shed light on distinctive biological features, means drive development...
The 5.67-megabase genome of the plant pathogen Agrobacterium tumefaciens C58 consists a circular chromosome, linear and two plasmids. Extensive orthology nucleotide colinearity between genomes A. symbiont Sinorhizobium meliloti suggest recent evolutionary divergence. Their similarities include metabolic, transport, regulatory systems that promote survival in highly competitive rhizosphere; differences are apparent their structure virulence gene complement. Availability sequence will...
We describe the genome sequence of protist Trichomonas vaginalis , a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds ∼160-megabase genome, reflecting recent massive expansion genetic material. This expansion, in conjunction with shaping metabolic pathways that likely transpired through lateral gene transfer from bacteria, amplification specific families implicated pathogenesis phagocytosis host proteins may exemplify adaptations parasite...
The EcoCyc database ( http://EcoCyc.org/ ) is a comprehensive source of information on the biology prototypical model organism Escherichia coli K12. mission for to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways molecular interactions in E.coli . Through ongoing manual curation, extensive such as summary comments, regulatory information, literature citations evidence types has been extracted from 8862 publications added Version 8.5...
Pathway Tools is a production-quality software environment for creating type of model-organism database called Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding genes, proteins, metabolic network and regulatory an organism. This article provides overview capabilities. The performs multiple computational inferences including prediction pathways, pathway hole fillers operons. It enables interactive editing PGDBs by DB curators. supports web publishing...