A5035489365- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Climate change and permafrost
- Medical Imaging Techniques and Applications
- Radiomics and Machine Learning in Medical Imaging
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Peatlands and Wetlands Ecology
- Protist diversity and phylogeny
- Genetics, Bioinformatics, and Biomedical Research
- Atmospheric and Environmental Gas Dynamics
- Gene expression and cancer classification
- Geology and Paleoclimatology Research
- Molecular Biology Techniques and Applications
- Marine Bivalve and Aquaculture Studies
- Polar Research and Ecology
- Marine Sponges and Natural Products
- Cryospheric studies and observations
- Malaria Research and Control
- Environmental DNA in Biodiversity Studies
- Machine Learning in Bioinformatics
- Biosensors and Analytical Detection
- Wastewater Treatment and Nitrogen Removal
- Algorithms and Data Compression
Translational Research Institute
2021-2025
Queensland University of Technology
2020-2025
The Ohio State University
2023
The University of Queensland
2012-2022
ETH Zurich
2016
The University of Melbourne
2009-2015
Walter and Eliza Hall Institute of Medical Research
2011-2012
Kenya Medical Research Institute
2012
Sainsbury Laboratory
2012
KU Leuven
2012
Abstract Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances sequencing throughput and computational techniques that allow for cultivation-independent recovery genomes from metagenomes. Here, we report reconstruction 7,903 bacterial archaeal >1,500 public All are estimated to be ≥50% complete nearly half ≥90% with ≤5% contamination. These increase genome trees >30% provide first...
Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence Amphimedon queenslandica, a demosponge Great Barrier Reef, and show it is remarkably similar to animal genomes in content, structure organization. Comparative analysis enabled by sequencing sponge reveals genomic events linked origin early evolution animals, including appearance, expansion diversification pan-metazoan transcription factor,...
Methanogenesis is the primary biogenic source of methane in atmosphere and a key contributor to climate change. The long-standing dogma that methanogenesis originated within Euryarchaeota was recently challenged by discovery putative methane-metabolizing genes members Bathyarchaeota, suggesting may be more phylogenetically widespread than currently appreciated. Here, we present divergent methyl-coenzyme M reductase population genomes recovered from anoxic environments with high flux belong...
This work is part of a 10-year project to examine thawing permafrost peatlands and the first virome-particle-based approach characterize viruses in these systems. method yielded >2-fold-more viral populations (vOTUs) per gigabase metagenome than vOTUs derived from bulk-soil metagenomes same site (J. B. Emerson, S. Roux, J. R. Brum, Bolduc, et al., Nat Microbiol 3:870–880, 2018, https://doi.org/10.1038/s41564-018-0190-y ). We compared ecology recovered along thaw gradient found (i) habitat...
Metagenomic binning methods that leverage differential population abundances in microbial communities (differential coverage) are emerging as a complementary approach to conventional composition-based binning. Here we introduce GroopM, an automated tool primarily uses coverage obtain high fidelity genomes from related metagenomes. We demonstrate the effectiveness of GroopM using synthetic and real-world metagenomes, show produces results comparable with more time consuming, labor-intensive methods.
Abstract Comparing newly obtained and previously known nucleotide amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but challenging to use on new data sets. We combined user-centric design philosophy with sustainable software development approaches create Sequenceserver, running visually inspecting results interpretation. Sequenceserver uses simple algorithms prevent potential analysis errors provides flexible text-based visual...
Advances in DNA sequencing and bioinformatics have dramatically increased the rate of recovery microbial genomes from metagenomic data. Assessing quality metagenome-assembled (MAGs) is a critical step prior to downstream analysis. Here, we present CheckM2, an improved method predicting completeness contamination MAGs using machine learning. We demonstrate effectiveness CheckM2 on synthetic experimental data, show that it outperforms original version CheckM MAG quality. substantially faster...
Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in global carbon cycle. However, our understanding their origin, evolution, and ecological functions remains poorly constrained. Here, we present largest dataset Bathyarchaeia metagenome assembled genome to date reclassify into eight order-level units corresponding former subgroup system. Highly diversified versatile metabolisms were found among different orders, particularly atypical C1 metabolic pathways,...
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....
The capacity to biomineralize is closely linked the rapid expansion of animal life during early Cambrian, with many skeletonized phyla first appearing in fossil record at this time. appearance disparate molluscan forms period leaves open possibility that shells evolved independently and parallel least some groups. To test proposition gain insight into evolution structural genes contribute shell fabrication, we compared expressed nacre (mother-of-pearl) forming cells mantle bivalve Pinctada...
The post-genomic era of malaria research provided unprecedented insights into the biology Plasmodium parasites. Due to large evolutionary distance model eukaryotes, however, we lack a profound understanding many processes in biology. One example is cell nucleus, which controls parasite genome development- and cycle-specific manner through mostly unknown mechanisms. To study this important organelle detail, conducted an integrative analysis P. falciparum nuclear proteome.We combined high...
Large-scale metagenomic datasets enable the recovery of hundreds population genomes from environmental samples. However, these do not typically represent full diversity complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view by examining each read independently, but traditional pairwise comparison over-classify taxonomy and scale poorly with increasing metagenome database sizes. Here we introduce GraftM, tool that uses gene specific packages rapidly...
Abstract The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly early emergence various clades their role in life’s evolution debated. Here, we reconstructed analysed genomes an uncharacterized archaeal phylum ( Candidatus Undinarchaeota), revealing that its members have and, while being able to conserve energy through fermentation, likely depend on partner for acquisition certain...
The fate of carbon sequestered in permafrost is a key concern for future global warming as this large stock rapidly becoming net methane source due to widespread thaw. Methane release from moderated by methanotrophs, which oxidise 20-60% before emission the atmosphere. Despite importance methanotrophs cycling, these microorganisms are under-characterised and have not been studied across natural thaw gradient. Here, we examine methanotroph communities active layer gradient Stordalen Mire...
An uncultured non-photosynthetic basal lineage of the Cyanobacteria, Melainabacteria, was recently characterised by metagenomic analyses aphotic environmental samples. However, a predatory bacterium, Vampirovibrio chlorellavorus, originally described in 1972 appears to be first cultured representative Melainabacteria based on 16S rRNA sequence recovered from lyophilised co-culture organism. Here, we sequenced genome V. chlorellavorus directly 36 year-old material that could not resuscitated...
High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes microscale analysis ecosystems and exploration low biomass samples. Current methods amplifying environmental DNA bypass this introduce considerable bias into metagenomic profiles. Here we describe validate a simple modification Illumina Nextera XT library preparation kit which allows creation shotgun from sub-nanogram amounts Community composition...
The methyl-coenzyme M reductase (MCR) complex is a key enzyme in archaeal methane generation and has recently been proposed to also be involved the oxidation of short-chain hydrocarbons including methane, butane, potentially propane. number clades encoding MCR continues grow, suggesting that this was inherited from an ancient ancestor, or undergone extensive horizontal gene transfer. Expanding representation MCR-encoding lineages through metagenomic approaches will help resolve evolutionary...