A5049254580- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Protist diversity and phylogeny
- Bacteriophages and microbial interactions
- Probiotics and Fermented Foods
- Methane Hydrates and Related Phenomena
- Marine Biology and Ecology Research
- Microplastics and Plastic Pollution
- Microbial Natural Products and Biosynthesis
- Environmental DNA in Biodiversity Studies
- Gut microbiota and health
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Amino Acid Enzymes and Metabolism
- Microbial Metabolic Engineering and Bioproduction
- Marine and coastal ecosystems
- Marine Sponges and Natural Products
- Pharmaceutical and Antibiotic Environmental Impacts
- Coral and Marine Ecosystems Studies
- Biosensors and Analytical Detection
- Diabetes Treatment and Management
- Insect symbiosis and bacterial influences
- Bacterial Genetics and Biotechnology
- Paleontology and Stratigraphy of Fossils
- Ammonia Synthesis and Nitrogen Reduction
The University of Queensland
2016-2025
Universität Innsbruck
2024-2025
Ecogenomics (Japan)
2020
Wellcome Centre for Mitochondrial Research
2018
University of Newcastle Australia
2018
Newcastle University
2018
ETH Zurich
2016
Joint Genome Institute
2011-2015
Lawrence Berkeley National Laboratory
2014
Washington State University
2008-2009
Genome sequencing enhances our understanding of the biological world by providing blueprints for evolutionary and functional diversity that shapes biosphere. However, microbial genomes are currently available limited phylogenetic breadth, owing to historical inability cultivate most microorganisms in laboratory. We apply single-cell genomics target sequence 201 uncultivated archaeal bacterial cells from nine diverse habitats belonging 29 major mostly uncharted branches tree life, so-called...
We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of Minimum Information about Any (x) Sequence (MIxS). The a Single Amplified Genome (MISAG) Metagenome-Assembled (MIMAG), including, but not limited to, assembly quality, estimates completeness contamination. These can be used in combination with other GSC checklists, including (MIGS), Metagenomic (MIMS), Marker Gene (MIMARKS). Community-wide...
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...
Abstract The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy for prokaryotic genomes sourced from the NCBI Assembly database. GTDB R06-RS202 spans 254 090 bacterial 4316 archaeal genomes, 270% increase since introduction of in November, 2017. These are organized into 45 555 2339 species clusters which is 200% integration June, 2019. Here, we explore diversity perspective highlight importance...
Cultivated bacteria such as actinomycetes are a highly useful source of biomedically important natural products. However, 'talented' producers represent only minute fraction the entire, mostly uncultivated, prokaryotic diversity. The uncultured majority is generally perceived large, untapped resource new drug candidates, but so far it unknown whether taxa containing talented indeed exist. Here we report single-cell- and metagenomics-based discovery producers. Two phylotypes candidate genus...
The Epsilonproteobacteria is the fifth validly described class of phylum Proteobacteria, known primarily for clinical relevance and chemolithotrophy in various terrestrial marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded protein marker analysis become more common, phylogenetic placement this has less certain. A number recent analyses bacterial tree life using both concatenated failed to recover as monophyletic with all other classes...
Abstract Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of has been limited by a lack cultured representatives and few sequenced genomes. Here, we conducted comparative phylogenomic analysis 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution ecology. Based on rank-normalised genome phylogeny, propose that is an order-level lineage for which name Candidatus...
Single cell genomics is a powerful and increasingly popular tool for studying the genetic make-up of uncultured microbes. A key challenge successful single sequencing analysis removal exogenous DNA from whole genome amplification reagents. We found that UV irradiation multiple displacement (MDA) reagents, including Phi29 polymerase random hexamer primers, effectively eliminates contaminating DNA. The methodology quick, simple, highly effective, thus significantly improving cells.
The canonical genetic code is assumed to be deeply conserved across all domains of life with very few exceptions. By scanning 5.6 trillion base pairs metagenomic data for stop codon reassignment events, we detected recoding in a substantial fraction the >1700 environmental samples examined. We observed extensive opal and amber reassignments bacteriophages bacteria. Our indicate that can infect hosts different demonstrate phage-host antagonism based on differences. abundance diversity codes...
Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code Nomenclature Prokaryotes. The recent practice proposing names for higher taxa without designation lower ranks nomenclature types one most important inconsistencies that needs to be addressed avoid nomenclatural instability. requires up rank class derived from type genus name, a proposal pending formalise this requirement phylum. Designation crucial providing priority ensures their uniqueness...
Abstract Microbial communities drive biogeochemical cycles through networks of metabolite exchange that are structured along energetic gradients. As energy yields become limiting, these favor co-metabolic interactions to maximize disequilibria. Here we apply single-cell genomics, metagenomics, and metatranscriptomics study bacterial populations the abundant “microbial dark matter” phylum Marinimicrobia defined We show evolutionary diversification major clades appears be closely related...
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 "Latescibacteria" (formerly WS3), member of the Fibrobacteres–Chlorobi–Bacteroidetes (FCB) superphylum, represents a ubiquitous candidate phylum found in terrestrial, aquatic, and marine ecosystems. Recently, single-cell amplified genomes (SAGs) representing were obtained from anoxic monimolimnion layers Sakinaw Lake (British Columbia, Canada), sediments coastal lagoon (Etoliko lagoon, Western Greece). Here, we present detailed in-silico analysis four SAGs to gain some insights on their...
Abstract Taxonomy is a fundamental organizing principle of biology, which ideally should be based on evolutionary relationships. Microbial taxonomy has been greatly restricted by the inability to obtain most microorganisms in pure culture and, lesser degree, historical use phenotypic properties as basis for classification. However, we are now at point obtaining genome sequences broadly representative microbial diversity using culture-independent techniques, provide opportunity develop...