A5080556560- Legume Nitrogen Fixing Symbiosis
- Plant nutrient uptake and metabolism
- Nematode management and characterization studies
- Microplastics and Plastic Pollution
- Genomics and Phylogenetic Studies
- Pharmaceutical and Antibiotic Environmental Impacts
- Pancreatic function and diabetes
- Animal Genetics and Reproduction
- Agronomic Practices and Intercropping Systems
- Metabolism, Diabetes, and Cancer
- Microbial Community Ecology and Physiology
- Climate change and permafrost
- Historical and Archaeological Studies
- Botany and Plant Ecology Studies
- Lichen and fungal ecology
- Gut microbiota and health
- Genetics, Bioinformatics, and Biomedical Research
- Insect symbiosis and bacterial influences
- Polar Research and Ecology
- Muscle metabolism and nutrition
- Agriculture Sustainability and Environmental Impact
- Metabolomics and Mass Spectrometry Studies
- Diet and metabolism studies
- Zoonotic diseases and public health
Queensland University of Technology
2021-2025
Translational Research Institute
2024
University of Oxford
2020-2024
The University of Queensland
2014-2022
Agriculture and Food
2013-2014
ARC Centre of Excellence for Plant Success in Nature and Agriculture
2014
Determining the taxonomy and relative abundance of microorganisms in metagenomic data is a foundational problem microbial ecology. To address limitations existing approaches, we developed ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. SingleM accurately profiles complex communities known species, only tool that detects species without genomic representation, even those representing novel phyla. Given SingleM’s computational efficiency,...
Genome-centric analysis of metagenomic samples is a powerful method for understanding the function microbial communities. Calculating read coverage central part analysis, enabling differential binning recovery genomes and estimation community composition. Coverage determined by processing alignments to reference sequences either contigs or genomes. Per-reference typically calculated in an ad-hoc manner, with each software package providing its own implementation specific definition coverage....
Significance Rhizobia are soil-dwelling bacteria that form symbioses with legumes and provide biologically useable nitrogen as ammonium for the host plant. High-throughput DNA sequencing has led to a rapid expansion in publication of complete genomes numerous rhizobia, but analysis gene function increasingly lags discovery. Mariner-based transposon insertion allowed us characterize fitness contribution bacterial genes determine those functionally important Rhizobium– legume symbiosis at...
Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene (also known as styrofoam), is among the most commonly produced plastics worldwide recalcitrant to microbial degradation. In this study, we assessed changes in gut microbiome of superworms (Zophobas morio) reared on bran, or under starvation conditions over a 3 weeks period. Superworms all diets were able complete life cycle pupae imago,...
Microbiome responses to warming may amplify or ameliorate terrestrial carbon loss and thus are a critical unknown in predicting climate outcomes. We quantified microbial response over seven years thawing permafrost peatland, using large-scale multi-omics data. integrated analyses of organisms (via taxonomy), functions metabolic pathways proteins), community organization network structure ecological assembly) deeply characterize mechanisms. This revealed unexpected comprehensive microbiome...
Microbiomes shape ecosystems through functional profiles influenced by gene gains and losses. While culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate flux, quantitative field data remains scarce. Here we leverage large-scale soil meta-omic to develop apply analytics for studying MGEs. In our model permafrost-thaw ecosystem, Stordalen Mire, identify ~2.1 million MGE recombinases across 89 microbial phyla assess ecological distributions, functions impacted,...
Liver glycogen, a highly branched polymer of glucose, is important for maintaining blood-glucose homeostasis. It was recently shown that db/db mice, model Type 2 diabetes, are unable to form the large composite glycogen α particles present in normal, healthy mice. In this study, structure mouse-liver over diurnal cycle characterized using size exclusion chromatography and transmission electron microscopy. Glycogen found be formed as smaller β particles, then only assembled into with broad...
Motility and chemotaxis are crucial processes for soil bacteria plant-microbe interactions. This applies to the symbiotic bacterium Rhizobium leguminosarum, where motility is driven by flagella rotation controlled two systems, Che1 Che2. The cluster particularly important in free-living prior establishment of symbiosis, with a che1 mutant delayed nodulation reduced competitiveness. Che2 system alters bacteroid development nodule maturation. In this work, we also identified 27 putative...
Recovery of microbial genomes from metagenomic datasets has provided genomic representation for hundreds thousands species diverse biomes. However, low abundance microorganisms are often missed due to insufficient coverage. Here we present Bin Chicken, an algorithm which substantially improves genome recovery through automated, targeted selection metagenomes coassembly based on shared marker gene sequences derived raw reads. Marker that divergent known reference can be further prioritised,...
Bacterial persistence in the rhizosphere and colonization of root niches are critical for establishment many beneficial plant-bacteria interactions including those between Rhizobium leguminosarum its host legumes. Despite this, most studies on R. have focused symbiotic lifestyle as an endosymbiont nodules. Here, we use random barcode transposon sequencing to assay gene contributions during competitive growth various plant species. This facilitated identification 189 genes commonly required...
Summary The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes natural and human associated environments. Recent large-scale metagenome surveys record variety of microbial life oceans 1 , wastewater 2 gut 3,4 earth 5,6 with compilations encompassing thousands public datasets 7–13 . So far, microbiome studies either miss functional information or consistency sample processing, although they may cover locations, these are missing...
ABSTRACT Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene also known as styrofoam, is among the most commonly produced plastics worldwide recalcitrant to microbial degradation. In this study, we assessed changes in gut microbiome of superworms ( Zophobas morio ) reared on bran, polystyrene, or under starvation conditions over a three weeks’ time period. Superworms all diets were able...
Abstract By analyzing successive lifestyle stages of a model Rhizobium -legume symbiosis using mariner-based transposon insertion sequencing (INSeq), we have defined the genes required for rhizosphere growth, root colonization, bacterial infection, N 2 -fixing bacteroids and release from legume (pea) nodules. While only 27 are annotated as nif fix in leguminosarum , show 603 genetic regions (593 genes, 5 tRNAs RNA features) competitive ability to nodulate pea . Of these, 146 common growth...