A5016809205- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Gut microbiota and health
- Polar Research and Ecology
- Bacteriophages and microbial interactions
- Gene expression and cancer classification
- Clostridium difficile and Clostridium perfringens research
- Cancer Genomics and Diagnostics
- Protist diversity and phylogeny
- Antibiotic Resistance in Bacteria
- Genomics and Chromatin Dynamics
- Pancreatic and Hepatic Oncology Research
- Bioinformatics and Genomic Networks
- Molecular Biology Techniques and Applications
- Probiotics and Fermented Foods
- Ion channel regulation and function
- Chromosomal and Genetic Variations
- Evolution and Genetic Dynamics
- Marine and coastal ecosystems
- Mycobacterium research and diagnosis
- Methane Hydrates and Related Phenomena
- Distributed and Parallel Computing Systems
- Computational Physics and Python Applications
- Scientific Computing and Data Management
- Machine Learning in Healthcare
University of Technology Sydney
2016-2024
Agricultural Institute
2020
New South Wales Department of Primary Industries
2020
UNSW Sydney
2001-2014
The Critical Assessment of Metagenome Interpretation (CAMI) community initiative presents results from its first challenge, a rigorous benchmarking software for metagenome assembly, binning and taxonomic profiling. Methods profiling are key to interpreting data, but lack consensus about complicates performance assessment. challenge has engaged the global developer benchmark their programs on highly complex realistic data sets, generated ∼700 newly sequenced microorganisms ∼600 novel viruses...
Many marine bacteria have evolved to grow optimally at either high (copiotrophic) or low (oligotrophic) nutrient concentrations, enabling different species colonize distinct trophic habitats in the oceans. Here, we compare genome sequences of two bacteria, Photobacterium angustum S14 and Sphingopyxis alaskensis RB2256, that serve as useful model organisms for copiotrophic oligotrophic modes life specifically relate genomic features strategy these define their molecular mechanisms adaptation....
Viruses are abundant ubiquitous members of microbial communities and in the marine environment affect population structure nutrient cycling by infecting lysing primary producers. Antarctic lakes microbially dominated ecosystems supporting truncated food webs which viruses exert a major influence on loop. Here we report discovery virophage (relative recently described Sputnik virophage) that preys phycodnaviruses infect prasinophytes (phototrophic algae). By performing metaproteogenomic...
Heterotrophic marine bacteria play key roles in remineralizing organic matter generated from primary production. However, far more is known about which groups are dominant than the cellular processes they perform order to become dominant. In Southern Ocean, eukaryotic phytoplankton producers. this study we used metagenomics and metaproteomics determine how bacterial archaeal plankton processed bloom material. We examined microbial community composition 14 metagenomes found that relative...
Article17 July 2012Open Access Global biogeography of SAR11 marine bacteria Mark V Brown School Biotechnology and Biomolecular Sciences, The University New South Wales, Sydney, Australia Evolution Ecology Research Centre, Search for more papers by this author Federico M Lauro Matthew Z DeMaere Les Muir CSIRO Marine Atmospheric Research, Castray Esplanade, Hobart, Tasmania, David Wilkins Torsten Thomas Centre Bio-Innovation, Martin J Riddle Australian Antarctic Division, Channel Highway,...
Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation underlying biological systems, but also differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, effectively assess performance metagenomic analysis software, a wide range benchmark required.We describe CAMISIM community simulator. The software can model different abundance profiles, multi-sample time series, differential studies, includes...
Most proteins adopt a well defined three-dimensional structure; however, it is increasingly recognized that some can exist with at least two stable conformations. Recently, class of intracellular chloride ion channel (CLICs) has been shown to in both soluble and integral membrane forms. The structure the form CLIC1 typical glutathione S-transferase superfamily protein but contains glutaredoxin-like active site. In this study we show on oxidation undergoes reversible transition from monomeric...
CLIC1 (NCC27) is a member of the highly conserved class chloride ion channels that exists in both soluble and integral membrane forms. Purified can integrate into synthetic lipid bilayers forming channel with similar properties to those observed <i>in vivo</i>. The structure form has been determined at 1.4-Å resolution. protein monomeric structurally homologous glutathione<i>S</i>-transferase superfamily, it redox-active site resembling glutaredoxin. complex glutathione shows occupies site,...
Significance Horizontal gene exchange across species boundaries is considered infrequent relative to vertical inheritance that maintains coherence. However, haloarchaea living in hypersaline environments take a more relaxed approach exchange. Here we demonstrate Deep Lake, Antarctica, DNA between distinct genera, not just species, with some of the being long (up 35 kb) and virtually 100% conserved. With extremely low cell division rates cold (e.g., six generations per year), remarkable...
Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim resolve individual genomes from metagenomes, so-called metagenome-assembled (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is function community complexity, target abundance, sequencing depth. We describe an unsupervised method that exploits hierarchical nature Hi-C interaction rates MAGs using single point. validate directly compare...
Summary We performed a metagenomic survey (6.6 Gbp of 454 sequence data) S outhern O cean ( SO ) microorganisms during the austral summer 2007–2008, examining genomic signatures communities across latitudinal transect from Hobart (44° to M ertz G lacier, A ntarctica (67° ). Operational taxonomic units OTUs SAR 11 and 116 clades cyanobacterial genera P rochlorococcus ynechococcus were strongly overrepresented north olar F ront PF Conversely, ammaproteobacterial ulfur xidizer‐ EOSA ‐1 GSO‐EOSA...
Bacteria are key contributors to microalgae resource acquisition, competitive performance, and functional diversity, but their potential metabolic interactions with coral microalgal endosymbionts (Symbiodiniaceae) have been largely overlooked. Here, we show that altering the bacterial composition of two widespread Symbiodiniaceae species, during free-living stage, results in a significant shift cellular metabolism. Indeed, abundance monosaccharides phytohormone indole-3-acetic acid (IAA)...
Abstract In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets evaluation metrics complicates proper performance assessment. The Critical Assessment Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on unprecedented complexity realism. Benchmark metagenomes were...
The genomes of halophilic archaea (haloarchaea) often comprise multiple replicons. Genomic variation in haloarchaea has been linked to viral infection pressure and, the case Antarctic communities, can be caused by intergenera gene exchange. To expand understanding genome and biogeography haloarchaea, here we assessed genomic between two strains Halorubrum lacusprofundi that were isolated from hypersaline lakes different regions (Vestfold Hills Rauer Islands). assess haloarchaeal populations,...
BackgroundChromosome conformation capture (3C) and Hi-C DNA sequencing methods have rapidly advanced our understanding of the spatial organization genomes metagenomes. Many variants these protocols been developed, each with their own strengths. Currently there is no systematic means for simulating sequence data from this family protocols, potentially hindering advancement algorithms to exploit new datatype.
We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, animals, fresh produce and environmental niches. Furthermore, E. within frequently drug resistant increasingly reported human animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny determine repertoire antimicrobial-resistance genes, virulence-associated genes...
Enterobacter hormaechei is an important emerging pathogen and a key member of the highly diverse cloacae complex. E. strains can persist spread in nosocomial environments, often exhibit resistance to multiple clinically antibiotics. However, genomic regions that harbour determinants are typically repetitive impossible resolve with standard short-read sequencing technologies.Here we used both short- long-read methods sequence genome multidrug-resistant hospital isolate (C15117), which...
IncHI2 ST3 plasmids are known carriers of multiple antimicrobial resistance genes. Complete plasmid sequences from drug resistant Escherichia coli circulating in Australian swine is however limited. Here we sequenced two related plasmids, pSDE-SvHI2 and pSDC-F2_12BHI2, phylogenetically unrelated multiple-drug strains SvETEC (CC23:O157:H19) F2_12B (ST93:O7:H4) geographically disparate pig production operations New South Wales, Australia. Unicycler was used to co-assemble short read (Illumina)...