A5078785577- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Wastewater Treatment and Nitrogen Removal
- Atmospheric and Environmental Gas Dynamics
- Microbial metabolism and enzyme function
- Protist diversity and phylogeny
- Bacteriophages and microbial interactions
- Metabolomics and Mass Spectrometry Studies
- Anaerobic Digestion and Biogas Production
- Molecular Biology Techniques and Applications
- Microbial Fuel Cells and Bioremediation
- Gut microbiota and health
- Mycobacterium research and diagnosis
- Diet and metabolism studies
- Cancer Research and Treatments
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Cell Image Analysis Techniques
- Immunotherapy and Immune Responses
- Advanced biosensing and bioanalysis techniques
- Genetics, Bioinformatics, and Biomedical Research
- Algorithms and Data Compression
- Cutaneous Melanoma Detection and Management
- Biomedical Text Mining and Ontologies
California Institute of Technology
2015-2022
The University of Queensland
2011-2015
Donovan H. Parks1, Michael Imelfort1, Connor T. Skennerton1, Philip Hugenholtz1,2 and Gene W. Tyson1,3 1Australian Centre for Ecogenomics, School of Chemistry Molecular Biosciences, The University Queensland, St. Lucia, QLD 4072, Australia; 2Institute Bioscience, 3Advanced Water Management Centre, Australia Corresponding authors: d.parks{at}uq.edu.au, g.tyson{at}uq.edu.au
<ns3:p>The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. provides implementations of probabilistic k-mer counting data structure, compressible De Bruijn graph representation, partitioning, and digital normalization. implemented in C++ Python, under the BSD license at <ns3:ext-link xmlns:ns4="http://www.w3.org/1999/xlink" ext-link-type="uri"...
Molecular surveys of aphotic habitats have indicated the presence major uncultured lineages phylogenetically classified as members Cyanobacteria. One these has recently been proposed a nonphotosynthetic sister phylum to Cyanobacteria, Melainabacteria, based on recovery population genomes from human gut and groundwater samples. Here, we expand phylogenomic representation Melainabacteria through sequencing six diverse bioreactor samples supporting inference that this lineage is...
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods substantial reductions sequencing costs. While this increasing breadth draft is providing key information regarding the evolutionary functional diversity microbial life, it become impractical to finish all available reference genomes. Making robust biological inferences requires accurate estimates their completeness contamination. Current for assessing...
Clustered regularly interspaced short palindromic repeats (CRISPR) constitute a bacterial and archaeal adaptive immune system that protect against bacteriophage (phage). Analysis of CRISPR loci reveals the history phage infections provides direct link between their hosts. All current tools for identification have been developed to analyse completed genomes are not well suited analysis metagenomic data sets, where difficult assemble owing repetitive structure population heterogeneity. Here,...
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods substantial reductions sequencing costs. While this increasing breadth draft is providing key information regarding the evolutionary functional diversity microbial life, it become impractical to finish all available reference genomes. Making robust biological inferences requires accurate estimates their completeness contamination. Current for assessing...
Summary Enhanced biological phosphorus removal ( EBPR ) is an important industrial wastewater treatment process mediated by polyphosphate‐accumulating organisms PAOs ). Members of the genus C andidatus A ccumulibacter are one most extensively studied PAO as they commonly enriched in lab‐scale reactors. different clades often through changes reactor conditions; however, two currently sequenced genomes show extensive metabolic similarity. Here, we expand our understanding genomic diversity...
ABSTRACT The anaerobic oxidation of methane by methanotrophic (ANME) archaea in syntrophic partnership with deltaproteobacterial sulfate-reducing bacteria (SRB) is the primary mechanism for removal ocean sediments. their syntrophy has been subject much research as traditional intermediate compounds, such hydrogen and formate, failed to decouple partners. Recent findings have indicated potential extracellular electron transfer from ANME SRB, though it unclear how electrons are integrated into...
Abstract Background An increasing body of evidence implicates the resident gut microbiota as playing a critical role in type 2 diabetes (T2D) pathogenesis. We previously reported significant improvement postprandial glucose control human participants with T2D following 12-week administration 5-strain novel probiotic formulation (‘WBF-011’) double-blind, randomized, placebo controlled setting (NCT03893422). While clinical endpoints were encouraging, additional exploratory measurements needed...
Biofilms are ubiquitous in nature, forming diverse adherent microbial communities that perform a plethora of functions. Here we operated two laboratory-scale sequencing batch reactors enriched with Candidatus Accumulibacter phosphatis (Accumulibacter) performing enhanced biological phosphorus removal. Reactors formed distinct biofilms, one floccular biofilm, consisting small, loose, aggregates, and granular larger, dense, spherical aggregates. Using metagenomic metaproteomic methods,...
The relationship between phage and their microbial hosts is difficult to elucidate in complex natural ecosystems. Engineered systems performing enhanced biological phosphorus removal (EBPR), offer stable, lower complexity communities for studying phage-host interactions. Here, metagenomic data from an EBPR reactor dominated by Candidatus Accumulibacter phosphatis (CAP), led the recovery of three complete six partial genomes. Heat-stable nucleoid structuring (H-NS) protein, a global...
Sulfate is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process carried out by a syntrophic consortium methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that still poorly understood. It was previously hypothesized ANME alone could couple to dissimilatory reduction, but genetic biochemical basis this proposal has not been identified. Using comparative genomic phylogenetic analyses,...
Hydrothermal vents are an important contributor to marine biogeochemistry, producing large volumes of reduced fluids, gasses, and metals housing unique, productive microbial animal communities fueled by chemosynthesis. Methane is a common constituent hydrothermal vent fluid frequently consumed at sites methanotrophic bacteria that serve control escape this greenhouse gas into the atmosphere. Despite their ecological geochemical importance, little known about ecophysiology uncultured...
Marine methane seep habitats represent an important control on the global flux of methane. Nucleotide-based meta-omics studies outline community-wide metabolic potential, but expression patterns environmentally relevant proteins are poorly characterized. Proteomic stable isotope probing (proteomic SIP) provides additional information by characterizing phylogenetically specific, functionally activity in mixed microbial communities, offering enhanced detection through system-wide product...
Molecular surveys of aphotic habitats have indicated the presence major uncultured lineages phylogenetically classified as members Cyanobacteria. One these has recently been proposed a non-photosynthetic sister phylum to Cyanobacteria, Melainabacteria, based on recovery standard draft population genomes from human gut and groundwater samples. Here, we expand phylogenomic representation Melainabacteria through sequencing six diverse bioreactor samples supporting inference that this lineage is...
Abstract The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring syntrophic partnership between methanotrophic (ANME) archaea and reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota , none which have been isolated in pure culture. Here we reconstruct 28 genomes from environmental metagenomes flow sorted consortia. Together with reanalysis previously published datasets, these...
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods substantial reductions sequencing costs. While this increasing breadth draft is providing key information regarding the evolutionary functional diversity microbial life, it become impractical to finish all available reference genomes. Making robust biological inferences requires accurate estimates their completeness contamination. Current for assessing...
The Biopython Project is a long-running distributed collaborative effort, supported by the Open Bioinformatics Foundation, which develops freely available Python library for biological computation.We present here details of latest release - version 1.66. New features include: extended Bio.KEGG and Bio.Graphics modules to support drawing KEGG pathways with transparency; “abi” Bio.SeqIO parser decode almost all documented fields used ABIF instruments; QCPSuperimposer module using Quaternion...