Water Res
October 2023
State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
Granular sludge combined n-DAMO and Anammox (n-D/A) is an energy-efficient biotechnique for the simultaneous removal of nitrogen and dissolved methane from wastewater. However, the lack of knowledge so far about the metabolic interactions between n-DAMO and Anammox in response to operation condition in granular sludge restrains the development of this biotechnology. To address this gap, three independent membrane granular sludge reactors (MGSRs) were designed to carry out the granule-based n-D/A process under different conditions.
View Article and Find Full Text PDFBMC Res Notes
August 2023
Microba Life Sciences, Queensland, Brisbane, Australia.
Objectives: In order to provide a better insight into the functional capacity of the human gut microbiome, we isolated a novel bacterium, "Candidatus Intestinicoccus colisanans" gen. nov. sp.
View Article and Find Full Text PDFMicrob Genom
August 2023
The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland, 4072, Australia.
Sci Rep
August 2023
Flinders University, Bedford Park, SA, Australia.
Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations.
View Article and Find Full Text PDFNat Biotechnol
May 2024
Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA.
Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.
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October 2023
Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
Structure probing combined with next-generation sequencing (NGS) has provided novel insights into RNA structure-function relationships. To date, such studies have focused largely on bacteria and eukaryotes, with little attention given to the third domain of life, archaea. Furthermore, functional RNAs have not been extensively studied in archaea, leaving open questions about RNA structure and function within this domain of life.
View Article and Find Full Text PDFMicrob Genom
July 2023
University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, QLD 4557, Australia.
FEMS Microbiol Lett
January 2023
The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics,, St Lucia QLD 4072, Brisbane, Australia.
The Genome Taxonomy Database (GTDB) is a taxonomic framework that defines prokaryotic taxa as monophyletic groups in concatenated protein reference trees according to systematic criteria. This has resulted in a substantial number of changes to existing classifications (https://gtdb.ecogenomic.
View Article and Find Full Text PDFGenome Biol Evol
July 2023
Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary.
Environ Res
October 2023
Australian Centre for Water and Environmental Biotechnology (formerly AWMC), The University of Queensland, St. Lucia, QLD, 4072, Australia; School of Chemical Engineering, The University of Queensland, St Lucia, QLD, 4072, Australia. Electronic address:
Biofilms of P. aeruginosa are known to be resilient forms of survival of this opportunistic pathogen, both within the host and in natural or engineered environments. This study investigated the role of phages in the disruption and inactivation of clinical P.
View Article and Find Full Text PDFFront Chem
June 2023
School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
β-Lactams are the most widely employed antibiotics in clinical settings due to their broad efficacy and low toxicity. However, since their first use in the 1940s, resistance to β-lactams has proliferated to the point where multi-drug resistant organisms are now one of the greatest threats to global human health. Many bacteria use β-lactamases to inactivate this class of antibiotics via hydrolysis.
View Article and Find Full Text PDFSci Total Environ
October 2023
State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
Thermophilic microorganisms mediated significant element cycles and material conversion in the early Earth as well as mediating current thermal environments. Over the past few years, versatile microbial communities that drive the nitrogen cycle have been identified in thermal environments. Understanding the microbial-mediated nitrogen cycling processes in these thermal environments has important implications for the cultivation and application of thermal environment microorganisms as well as for exploring the global nitrogen cycle.
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June 2023
MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China.
Recent discoveries of methyl-coenzyme M reductase-encoding genes () in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs.
View Article and Find Full Text PDFBioorg Med Chem Lett
August 2023
School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; Australian Centre for Ecogenomics, The University of Queensland, St. Lucia, QLD 4072, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia; Sustainable Minerals Institute, The University of Queensland, St. Lucia, QLD 4072, Australia. Electronic address:
Metallo-β-lactamases (MBLs) are a group of Zn(II)-dependent enzymes that pose a major threat to global health. They are linked to an increasing number of multi-drug resistant bacterial pathogens, but no clinically useful inhibitor is yet available. Since β-lactam antibiotics, which are inactivated by MBLs, constitute ∼65% of all antibiotics used to treat infections, the search for clinically relevant MBL inhibitors is urgent.
View Article and Find Full Text PDFISME Commun
June 2023
Australian Institute of Marine Science, Townsville, Queensland, Australia.
Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis.
View Article and Find Full Text PDFEnviron Sci Technol
July 2023
Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Pokfulam, 99077 Hong Kong, China.
Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.
View Article and Find Full Text PDFMicrob Genom
June 2023
The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland, 4072, Australia.
is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. is currently the only axenic representative of its class, the , according to the Genome Taxonomy Database. However, substantial additional diversity has been revealed in this lineage through culture-independent exploration of anoxic habitats.
View Article and Find Full Text PDFSci Total Environ
September 2023
School of Earth & Environmental Sciences, The University of Queensland, St. Lucia 4072, Australia.
The primary solid waste product of surface coal mining is overburden (also known as spoil), the material that is moved to access the underlying coal seams. Once removed, this material is generally stored in large (>100 m in height) piles until it is re-contoured in preparation for post-mining rehabilitation, often remaining there for decades. Under ideal conditions, these new landforms would have at least 30 cm veneer of topsoil applied as a growth medium for plants.
View Article and Find Full Text PDFVet Microbiol
August 2023
Murdoch University, Centre for Animal Production and Health, Perth, Western Australia 6150, Australia. Electronic address:
Chlamydia pecorum is a veterinary pathogen associated with abortions and perinatal mortality in sheep. Recent studies investigating foetal and perinatal lamb mortality in sheep from Australia and New Zealand identified C. pecorum clonal sequence type (ST)23 strains in aborted and stillborn lambs.
View Article and Find Full Text PDFBMC Bioinformatics
May 2023
University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.
Background: Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration.
Results: GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes.
Microbiol Spectr
June 2023
Australian Infectious Disease Research Centre, Faculty of Science, The University of Queensland, Brisbane, Australia.
To investigate an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) sequence type 78 (ST78) in a large tertiary Australian hospital. A collection of 63 VREfm ST78 isolates, identified during a routine genomic surveillance program, were subjected to genomic epidemiological analysis based on whole-genome sequencing (WGS) data. The population structure was reconstructed using phylogenetic analysis, and a collection of publicly available VREfm ST78 genomes were used to provide global context.
View Article and Find Full Text PDFISME J
August 2023
Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.
Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
May 2023
The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, Queensland, Australia.
Appendix 9, Section E of the International Code of Nomenclature of Prokaryotes provides guidelines on how to form adjectival specific and subspecific epithets that reflect the geographical location where the organism was found or studied. It does not mention ways of naming genera after geographical locations. We here propose emendation of Appendix 9 with the recommendations on how to form such names.
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May 2023
Department of Integrative Biology, University of South Florida, Tampa, FL, United States.
J Appl Microbiol
May 2023
The University of Queensland, School of Agriculture and Food Sciences, Brisbane QLD 4072, Australia.
Aims: Sub-therapeutic use of antibiotics as a growth promoter in animal diets has either been banned or voluntarily withdrawn from use in many countries to help curb the emergence of antibiotic-resistant pathogens. Probiotics may be an alternative to antibiotics as a growth promoter. We investigated the effects of a novel probiotic strain, Bacillus amyloliquefaciens H57 (H57) on the performance and microbiome-associated metabolic potential.
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