ORCID Profile
0000-0001-5603-5294
Current Organisation
Monash University
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Microbiology | Infectious Agents | Virology | Medical Molecular Engineering of Nucleic Acids and Proteins | Bioinformatics | Microbiology not elsewhere classified | Bacteriology
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Infectious Diseases | Expanding Knowledge in Technology |
Related Links
Publications
Screening for Lysogen Activity in Therapeutically Relevant Bacteriophages
Publisher: Bio-Protocol, LLC
Date: 2021
Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters
Publisher: Proceedings of the National Academy of Sciences
Date: 19-10-2015
Abstract: Bacteriophages (phages) are viruses that infect and kill bacteria. Being inanimate, phages rely on diffusion to search for bacterial prey. Here we demonstrate that a phage that adheres weakly to mucus exhibits subdiffusive motion, not normal diffusion, in mucosal surfaces. Supporting theory and experiments revealed that subdiffusive motion increases bacterial encounter rates for phages when bacterial concentration is low. To the best of our knowledge, no other predator has been shown to effectively use a subdiffusive search mechanism. Mucosal surfaces are vulnerable to infection. Mucus-adherent phages reduce bacterial infection of lifelike mucosal surfaces more effectively than nonadherent phages. These findings provide a basis for engineering adherent phages to manipulate mucosal surface microbiomes for protection from infection and other purposes.
Point of emission air filtration enhances protection of healthcare workers against skin contamination with virus aerosol
Publisher: Wiley
Date: 13-02-2022
DOI: 10.1111/RESP.14227
Abstract: See related Editorial
The sustainability characteristics of Michelin Green Star Restaurants
Publisher: Informa UK Limited
Date: 19-07-2023
Comparative metabolomics revealed key pathways associated with the synergistic killing of multidrug-resistant Klebsiella pneumoniae by a bacteriophage-polymyxin combination
Publisher: Elsevier BV
Date: 2022
Bacteriophage-resistant Acinetobacter baumannii are resensitized to antimicrobials
Publisher: Springer Science and Business Media LLC
Date: 11-01-2021
Phage Interaction with the Mammalian Immune System
Publisher: Springer International Publishing
Date: 2019
Engineering laminated paper for SARS-CoV-2 medical gowns
Publisher: Elsevier BV
Date: 04-2021
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
Publisher: Springer Science and Business Media LLC
Date: 24-07-2014
DOI: 10.1038/NCOMMS5498
A bacteriophages journey through the human body
Publisher: Wiley
Date: 30-08-2017
DOI: 10.1111/IMR.12565
Abstract: The human body is colonized by a erse collective of microorganisms, including bacteria, fungi, protozoa and viruses. The smallest entity of this microbial conglomerate are the bacterial viruses. Bacteriophages, or phages for short, exert significant selective pressure on their bacterial hosts, undoubtedly influencing the human microbiome and its impact on our health and well-being. Phages colonize all niches of the body, including the skin, oral cavity, lungs, gut, and urinary tract. As such our bodies are frequently and continuously exposed to erse collections of phages. Despite the prevalence of phages throughout our bodies, the extent of their interactions with human cells, organs, and immune system is still largely unknown. Phages physically interact with our mucosal surfaces, are capable of bypassing epithelial cell layers, disseminate throughout the body and may manipulate our immune system. Here, I establish the novel concept of an "intra-body phageome," which encompasses the collection of phages residing within the classically "sterile" regions of the body. This review will take a phage-centric view of the microbiota, human body, and immune system with the ultimate goal of inspiring a greater appreciation for both the indirect and direct interactions between bacteriophages and their mammalian hosts.
Bacteriophages targeting Acinetobacter baumannii capsule induce antimicrobial resensitization
Publisher: Cold Spring Harbor Laboratory
Date: 26-02-2020
DOI: 10.1101/2020.02.25.965590
Abstract: Carbapenem-resistant Acinetobacter baumannii is responsible for frequent, hard-to-treat and often fatal healthcare-associated infections. Phage therapy, the use of viruses that infect and kill bacteria, is an approach gaining significant clinical interest to combat antibiotic-resistant infections. However, a major limitation is that bacteria can develop resistance against phages. Here, we isolated phages with activity against a panel of A. baumannii strains and focused on clinical isolates AB900 and A9844 and their phages for detailed characterization. As expected, coincubation of the phages with their hosts in vitro resulted in the emergence of phage-resistant bacterial mutants. Genome sequence analysis revealed that phage-resistant mutants harbored loss-of-function mutations in genes from the K locus, responsible for the biosynthesis of the bacterial capsule. Using molecular biology techniques, phage adsorption assays, and quantitative evaluation of capsule production, we established that the bacterial capsule serves as the primary receptor for these phages. As a collateral phenotype of impaired capsule production, the phage-resistant strains could not form biofilms, became fully sensitized to the human complement system, showed increased susceptibility to beta-lactam antibiotics, and became vulnerable to additional phages. Finally, in a murine model of bacteremia, the phage-resistant A. baumannii demonstrated a diminished capacity to colonize blood and solid tissues. This study demonstrates that phages can be used not only for their lytic activity but, if combined with a posteriori knowledge of their receptors and the mechanism of bacterial resistance, for their potential synergy with other antimicrobial agents, thus providing even broader clinical options for phage therapy.
Evidence for bacteriophage activity causing community and performance changes in a phosphorus-removal activated sludge
Publisher: Oxford University Press (OUP)
Date: 30-09-2010
DOI: 10.1111/J.1574-6941.2010.00967.X
Abstract: Bacteria are known to play important roles in biogeochemical cycles and biotechnology processes, but little is known about the influence of bacteriophage on these processes. A major impediment to the study of host-bacteriophage interactions is that the bacteria and their bacteriophage are often not available in a pure culture. In this study, we detected an unexpected decline in the phosphorus-removal performance of a granular laboratory-scale wastewater treatment reactor. Investigations by FISH, transmission electron microscopy and proteomics led us to hypothesize that a bacteriophage infection of the uncultured Candidatus 'Accumulibacter phosphatis' was responsible for the decline in performance. Further experiments demonstrated that the addition of a putative bacteriophage-rich supernatant, obtained from the previous failed reactor to phosphorus-removal reactors, caused a decrease in the abundance of Accumulibacter in both granular and floccular activated sludges. This coincided with increases in bacteriophage-like particles and declining phosphorus-removal performance. The granular sludge did not recover after the attack, but the floccular sludge regained Accumulibacter numbers and phosphorus-removal performance. These findings suggest that bacteriophage may play a significant role in determining the structure and function of bacterial communities in activated sludges.
Missing a Phage: Unraveling Tripartite Symbioses within the Human Gut
Publisher: American Society for Microbiology
Date: 25-06-2019
DOI: 10.1128/MSYSTEMS.00105-19
Abstract: Tripartite symbioses between bacteriophages, the epithelial cell layers of the human gut, and bacterial symbionts may play an important and unrecognized role in the function of the gut microbiome. Traditionally, phages residing within the gut were considered to interact only with their bacterial hosts and thereby to facilitate indirect interactions with the epithelial cell layers, and yet a growing body of literature is demonstrating the surprising and erse ways in which phages directly interact with the eukaryotic cells, organs, and systems of the body.
Semi-Acquaintance Society in Rural Community-Based Tourism: Case Study of Moon Village, China
Publisher: MDPI AG
Date: 11-03-2023
DOI: 10.3390/SU15065000
Abstract: Tourism development provides a unique context for studying guanxi in acquaintance society in rural areas in China. Taking the case of Moon village from the perspective of guanxi, this study conducted a qualitative study to analyze the structural characteristics of the semi-acquaintance society in the tourism context. A buffer guanxi circle develops when strangers immerse themselves into an acquaintance-based society through social interaction, where affection and reasoning define the boundary, guanxi and the interests on which the social consensus is based, as well as the elite and collective actions vitalizing the community. These findings on how the semi-acquaintance society contributes to guanxi imply a co-governance structure for informal relations in governance in community-based rural tourism.
Editorial: The Application of Phages Against Infectious Diseases
Publisher: Frontiers Media SA
Date: 20-12-2021
Bacteriophage uptake by Eukaryotic cell layers represents a major sink for phages during therapy
Publisher: Cold Spring Harbor Laboratory
Date: 08-09-2020
DOI: 10.1101/2020.09.07.286716
Abstract: For over 100 years, bacteriophages have been known as viruses that infect bacteria. Yet it is becoming increasingly apparent that bacteriophages, or phages for short, have tropisms outside their bacterial hosts. During phage therapy, high doses of phages are directly administered and disseminated throughout the body, facilitating broad interactions with eukaryotic cells. Using live cell imaging across a range of cell lines we demonstrate that cell type plays a major role in phage internalisation and that smaller phages ( 100 nm) are internalised at higher rates. Uptake rates were validated under physiological shear stress conditions using a microfluidic device that mimics the shear stress to which endothelial cells are exposed to in the human body. Phages were found to rapidly adhere to eukaryotic cell layers, with adherent phages being subsequently internalised by macropinocytosis and functional phages accumulating and stably persisting intracellularly. Finally, we incorporate these results into an established pharmacokinetic model demonstrating the potential impact of phage accumulation by these cell layers, which represents a major sink for circulating phages in the body. Understanding these interactions will have important implications on innate immune responses, phage pharmacokinetics, and the efficacy of phage therapy.
The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None
Publisher: Frontiers Media SA
Date: 06-09-2019
Correction for Nguyen et al., “Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers”
Publisher: American Society for Microbiology
Date: 07-03-2018
Personal protective equipment does not sufficiently protect against virus aerosol unless combined with advanced air purification or ventilation techniques
Publisher: Cold Spring Harbor Laboratory
Date: 05-09-2021
DOI: 10.1101/2021.09.02.21263008
Abstract: Healthcare workers (HCWs) are at risk from nosocomial transmission of SARS-CoV-2 from virus laden aerosols. This study aimed to: 1) quantify the degree of protection from virus aerosol provided by different types of mask (surgical, N95, fit-tested N95) and personal protective equipment (PPE) 2) determine if the use of a portable HEPA filter can enhance the effectiveness of PPE 3) determine the effectiveness of a decontamination shower to remove virus aerosol contamination of a HCW. Virus aerosol exposure experiments were conducted using bacteriophage PhiX174 (10 8 copies/mL). A HCW wearing PPE (mask, gloves, gown, faceshield) was exposed to nebulised viruses for 40mins in a sealed clinical room. After exiting, the HCW doffed PPE. Virus exposure was quantified via skin swabs applied to the face and nostrils, forearms, neck, and forehead. Experiments were performed with and without the presence of a portable HEPA filter (set to 470m3/hr). Swabs quantified significant virus exposure under the surgical and N95 mask. Only the fit-tested N95 resulted in lower virus counts compared to no mask control (p=0.027). Nasal swabs demonstrated very high virus exposure, which was not mitigated by the surgical or N95 masks, although there was a trend for the fit-tested N95 mask to reduce virus counts (p=0.058). The addition of HEPA filtration substantially reduced virus counts from all swab sites, and to near zero levels when combined with a fit-tested N95 mask, gloves, gown and faces shield. Virus counts were substantially reduced to near zero levels following a shower. These data demonstrate that quantitatively fit tested N95 masks combined with a HEPA filter can offer protection against high virus aerosol loads at close range and for prolonged periods of time. Skin contamination from virus aerosol can be effectively by removed by showering. Epworth Hospital Capacity Building Research Grant ID: EH2020-654
Phage Cocktail Targeting STEC O157:H7 Has Comparable Efficacy and Superior Recovery Compared with Enrofloxacin in an Enteric Murine Model
Publisher: American Society for Microbiology
Date: 29-06-2022
DOI: 10.1128/SPECTRUM.00232-22
Abstract: With the increasing severity of antibiotic resistance and other adverse consequences, animal experiments and clinical trials investigating the use of phages for the control and prevention of enteric bacterial infections are growing. However, the effects of phages and antibiotics on organisms when treating intestinal infections have not been precisely studied.
Dynamic microbial response of sulfidogenic wastewater biofilm to nitrate
Publisher: Springer Science and Business Media LLC
Date: 25-05-2011
DOI: 10.1007/S00253-011-3330-3
Abstract: Nitrate is one of the chemicals often added to wastewater to control hydrogen sulfide production by sulfate-reducing bacteria (SRB). While the effect of nitrate in various SRB pure cultures is well documented, the effect observed in mixed microbial communities is not consistent. This study investigates the response of mixed SRB communities to nitrate, by examining the changes in activity and community composition of sulfidogenic wastewater biofilm over a 10-day period with 10 mmol L(-1) nitrate exposure. Biofilms were enriched in SRB belonging to the Desulfobacter, Desulfobulbus, Desulfomicrobium, and Desulfovibrio genera. Nitrate exposure decreased dsrB transcription within 4 h, and sulfate consumption within 10 days, but it did not fully eliminate sulfide production in the biofilms. The effect of nitrate on SRB was genus specific Desulfobacter and Desulfobulbus disappeared while Desulfovibrio and Desulfomicrobium persisted in the biofilms. Nitrate exposure also led to the rapid proliferation of nitrate-reducing bacteria within the biofilms, and increased the biofilm thickness. Nitrate consumption began within 2 h of nitrate exposure and gradually increased in rate over time. Transcription of the nitrate reductase napA, and the ersity of nitrate reductase genes narG and napA also increased concurrently. Our results demonstrate that some SRB, presumably those able to tolerate or detoxify nitrite, will persist in sulfidogenic wastewater biofilms despite continuous exposure to high levels of nitrate. Nitrate is therefore unlikely to provide lasting hydrogen sulfide suppression in wastewater biofilms harboring Desulfovibrio or Desulfomicrobium populations.
Introduction of the Bacteriophage Biology & Therapeutics SIG
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/MA19013
Host diversity slows bacteriophage adaptation by selecting generalists over specialists
Publisher: Springer Science and Business Media LLC
Date: 11-01-2021
DOI: 10.1038/S41559-020-01364-1
Abstract: Most viruses can infect multiple hosts, yet the selective mechanisms that maintain multi-host generalists over single-host specialists remain an open question. Here we propagate populations of the newly identified bacteriophage øJB01 in coculture with many host genotypes and find that while phage can adapt to infect any of the new hosts, increasing the number of hosts slows the rate of adaptation. We quantify trade-offs in the capacity for in idual phage to infect different hosts and find that phage from evolved populations with more hosts are more likely to be generalists. Sequencing of evolved phage reveals strong selection and the genetic basis of adaptation, supporting a model that shows how the addition of more potential hosts to a community can select for low-fitness generalists over high-fitness specialists. Our results show how evolution with multiple hosts alters the rate of viral adaptation and provides empirical support for an evolutionary mechanism that promotes generalists over specialists.
Bacteriophage adaptation to a mammalian mucosa reveals a trans–domain evolutionary axis
Publisher: Cold Spring Harbor Laboratory
Date: 11-05-2021
DOI: 10.1101/2021.05.11.443681
Abstract: The majority of viruses within the human gut are obligate bacterial viruses known as bacteriophages (phages) 1 . Their bacteriotropism underscores the study of phage ecology in the gut, where they sustain top–down control 2—4 and co–evolve 5 with gut bacterial communities. Traditionally, these were investigated empirically via in vitro experimental evolution 6—8 and more recently, in vivo models were adopted to account for gut niche effects 4,9 . Here, we probed beyond conventional phage–bacteria co–evolution to investigate the potential evolutionary interactions between phages and the mammalian ″host″. To capture the role of the mammalian host, we recapitulated a life–like mammalian gut mucosa using in vitro lab–on–a–chip devices (to wit, the gut–on–a–chip) and showed that the mucosal environment supports stable phage–bacteria co–existence. Next, we experimentally evolved phage populations within the gut–on–a–chip devices and discovered that phages adapt by de novo mutations and genetic recombination. We found that a single mutation in the phage capsid protein Hoc — known to facilitate phage adherence to mucus 10 — caused altered phage binding to fucosylated mucin glycans. We demonstrated that the altered glycan–binding phenotype provided the evolved mutant phage a competitive fitness advantage over their ancestral wildtype phage in the gut–on–a–chip mucosal environment. Collectively, our findings revealed that phages — in addition to their evolutionary relationship with bacteria — are also able to engage in evolution with the mammalian host.
Rethinking phage-bacteria-eukaryotic relationships and their influence on human health
Publisher: Elsevier BV
Date: 05-2021
Phage research in ‘organ-on-chip’ devices
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/MA19006
Abstract: The use of ‘organ-on-chip' devices in microbiology research presents enormous opportunities for fundamental and translational research1–4. Yet these approaches have not been widely embraced by the microbiology field. This is particularly evident with bacteriophage (phage) research applications. Traditionally phage research has been an early adopter of experimental techniques and approaches5, having catalysed research in biotechnology, environmental biology, sequencing, and synthetic biology. Here we discuss some of the opportunities that organ-on-chip devices present to both phage and microbiology research, and provide a ‘how to' guide for researchers interested in utilising this approach.
Phages to shape the gut microbiota?
Publisher: Elsevier BV
Date: 04-2021
Innate and acquired bacteriophage-mediated immunity
Publisher: Informa UK Limited
Date: 11-07-2013
DOI: 10.4161/BACT.25857
Phage on Tap: A Quick and Efficient Protocol for the Preparation of Bacteriophage Laboratory Stocks
Publisher: Springer New York
Date: 2018
DOI: 10.1007/978-1-4939-8682-8_4
Abstract: A major limitation with traditional phage preparations is the variability in titer, salts, and bacterial contaminants between successive propagations. Here, we introduce the Phage On Tap (PoT) protocol for the quick and efficient preparation of homogenous bacteriophage (phage) stocks. This method produces homogenous, laboratory-scale, high titer (up to 10
Expanding our view of genomic diversity in C andidatus A ccumulibacter clades
Publisher: Wiley
Date: 27-08-2014
Abstract: Enhanced biological phosphorus removal (EBPR) is an important industrial wastewater treatment process mediated by polyphosphate-accumulating organisms (PAOs). Members of the genus Candidatus Accumulibacter are one of the most extensively studied PAO as they are commonly enriched in lab-scale EBPR reactors. Members of different Accumulibacter clades are often enriched through changes in reactor process conditions however, the two currently sequenced Accumulibacter genomes show extensive metabolic similarity. Here, we expand our understanding of Accumulibacter genomic ersity through recovery of eight population genomes using deep metagenomics, including seven from phylogenetic clades with no previously sequenced representative. Comparative genomic analysis revealed a core of shared genes involved primarily in carbon and phosphorus metabolism however, each Accumulibacter genome also encoded a substantial number of unique genes (> 700 genes). A major difference between the Accumulibacter clades was the type of nitrate reductase encoded and the capacity to perform subsequent steps in denitrification. The Accumulibacter clade IIF genomes also contained acetaldehyde dehydrogenase that may allow ethanol to be used as carbon source. These differences in metabolism between Accumulibacter genomes provide a molecular basis for niche differentiation observed in lab-scale reactors and may offer new opportunities for process optimization.
Pharmacokinetics/pharmacodynamics of antipseudomonal bacteriophage therapy in rats: a proof-of-concept study
Publisher: Elsevier BV
Date: 09-2020
DOI: 10.1016/J.CMI.2020.04.039
Abstract: Pan-drug-resistant (PDR) Pseudomonas aeruginosa is one of the three top-priority pathogens identified by the WHO, and bacteriophages have been investigated as an alternative therapy. However, knowledge on the pharmacokinetics harmacodynamics (PK/PD) of phage therapy is sparse, limiting its clinical applications. This study aimed to evaluate the PK/PD of the antipseudomonal phage øPEV20 in vivo following intravenous administration. Healthy Sprague-Dawley rats were given øPEV20 as a single intravenous bolus of ~6, 9 and 11-log A three-compartment model with non-linear clearance described the exposure of øPEV20 in blood. Model evaluation indicated that the model was robust and parameter estimates were accurate. The median (standard error) values of model-predicted PK parameters for V We developed a robust PK model to describe the disposition of phages in healthy rats. This model may have significant potential in facilitating future preclinical and clinical PK/PD investigations.
Further limitations of phylogenetic group-specific probes used for detection of bacteria in environmental samples
Publisher: Springer Science and Business Media LLC
Date: 04-2010
Impact of bacteria motility in the encounter rates with bacteriophage in mucus
Publisher: Springer Science and Business Media LLC
Date: 11-11-2019
DOI: 10.1038/S41598-019-52794-2
Abstract: Bacteriophages—or phages—are viruses that infect bacteria and are present in large concentrations in the mucosa that cover the internal organs of animals. Immunoglobulin (Ig) domains on the phage surface interact with mucin molecules, and this has been attributed to an increase in the encounter rates of phage with bacteria in mucus. However, the physical mechanism behind this phenomenon remains unclear. A continuous time random walk (CTRW) model simulating the diffusion due to mucin-T4 phage interactions was developed and calibrated to empirical data. A Langevin stochastic method for Escherichia coli ( E. coli ) run-and-tumble motility was combined with the phage CTRW model to describe phage-bacteria encounter rates in mucus for different mucus concentrations. Contrary to previous theoretical analyses, the emergent subdiffusion of T4 in mucus did not enhance the encounter rate of T4 against bacteria. Instead, for static E. coli, the diffusive T4 mutant lacking Ig domains outperformed the subdiffusive T4 wild type. E. coli ’s motility dominated the encounter rates with both phage types in mucus. It is proposed, that the local fluid-flow generated by E. coli ’s motility combined with T4 interacting with mucins may be the mechanism for increasing the encounter rates between the T4 phage and E. coli bacteria.
Bacteriophage adhering to mucus provide a non–host-derived immunity
Publisher: Proceedings of the National Academy of Sciences
Date: 20-05-2013
Abstract: Mucosal surfaces are a main entry point for pathogens and the principal sites of defense against infection. Both bacteria and phage are associated with this mucus. Here we show that phage-to-bacteria ratios were increased, relative to the adjacent environment, on all mucosal surfaces s led, ranging from cnidarians to humans. In vitro studies of tissue culture cells with and without surface mucus demonstrated that this increase in phage abundance is mucus dependent and protects the underlying epithelium from bacterial infection. Enrichment of phage in mucus occurs via binding interactions between mucin glycoproteins and Ig-like protein domains exposed on phage capsids. In particular, phage Ig-like domains bind variable glycan residues that coat the mucin glycoprotein component of mucus. Metagenomic analysis found these Ig-like proteins present in the phages s led from many environments, particularly from locations adjacent to mucosal surfaces. Based on these observations, we present the bacteriophage adherence to mucus model that provides a ubiquitous, but non–host-derived, immunity applicable to mucosal surfaces. The model suggests that metazoan mucosal surfaces and phage coevolve to maintain phage adherence. This benefits the metazoan host by limiting mucosal bacteria, and benefits the phage through more frequent interactions with bacterial hosts. The relationships shown here suggest a symbiotic relationship between phage and metazoan hosts that provides a previously unrecognized antimicrobial defense that actively protects mucosal surfaces.
A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients
Publisher: Frontiers Media SA
Date: 18-02-2015
Pandemic pharmaceutical dosing effects on wastewater treatment: no adaptation of activated sludge bacteria to degrade the antiviral drug Oseltamivir (Tamiflu®) and loss of nutrient removal performance
Publisher: Oxford University Press (OUP)
Date: 06-12-2010
DOI: 10.1111/J.1574-6968.2010.02163.X
Abstract: The 2009-2010 influenza pandemic saw many people treated with antivirals and antibiotics. High proportions of both classes of drugs are excreted and enter wastewater treatment plants (WWTPs) in biologically active forms. To date, there has been no study into the potential for influenza pandemic-scale pharmaceutical use to disrupt WWTP function. Furthermore, there is currently little indication as to whether WWTP microbial consortia can degrade antiviral neuraminidase inhibitors when exposed to pandemic-scale doses. In this study, we exposed an aerobic granular sludge sequencing batch reactor, operated for enhanced biological phosphorus removal (EBPR), to a simulated influenza-pandemic dosing of antibiotics and antivirals for 8 weeks. We monitored the removal of the active form of Tamiflu(®), oseltamivir carboxylate (OC), bacterial community structure, granule structure and changes in EBPR and nitrification performance. There was little removal of OC by sludge and no evidence that the activated sludge community adapted to degrade OC. There was evidence of changes to the bacterial community structure and disruption to EBPR and nitrification during and after high-OC dosing. This work highlights the potential for the antiviral contamination of receiving waters and indicates the risk of destabilizing WWTP microbial consortia as a result of high concentrations of bioactive pharmaceuticals during an influenza pandemic.
Temporal stability and genetic diversity of 48-year old T-series phages
Publisher: Cold Spring Harbor Laboratory
Date: 25-09-2020
DOI: 10.1101/2020.09.24.312751
Abstract: T-series phages have been model organisms for molecular biology since the 1940s. Given that these phages have been stocked, distributed, and propagated for decades across the globe, there exists the potential for genetic drift to accumulate between stocks over time. Here we compared the temporal stability and genetic relatedness of laboratory-maintained phage stocks with a T-series collection from 1972. Only the T-even phages produced viable virions. We obtained complete genomes of these T-even phages, along with two contemporary T4 stocks. Performing comparative genomics, we found 12 and 16 nucleotide variations, respectively, in the genomes of T2 and T6 whereas there were ~172 nucleotide variations between T4-sublines when compared with NCBI RefSeq genome. To account for the possibility of artefacts in the NCBI RefSeq, we used the 1972 T4 stock as a reference and compared genetic and phenotypic variations between T4-sublines. Genomic analysis predicted nucleotide variations in genes associated with DNA metabolism and structural proteins. We did not however, observe any differences in growth characteristics or host range between the T4-sublines. Our study highlights the potential for genetic drift between in idually maintained T-series phage stocks, yet after 48-years, this has not resulted in phenotypic alternations in these important model organisms. T-series bacteriophages have been used throughout the world for various molecular biology researches, which were critical for establishing the fundamentals of molecular biology – from the structure of DNA to advanced gene-editing tools. These model bacteriophages help keep research data consistent and comparable between laboratories. However, we observed genetic variability when compared contemporary sublines of T4-phages to a 48-year old stock of T4. This may have effects in the comparability of results obtained using T4 phage. Here, we highlighted the genomic differences between T4 sublines and examined phenotypic differences in phage replication parameters. We observed limited genomic changes but no phenotypic variations between T4 sublines. Our research highlights the possibility of genetic drift in model bacteriophages.
A metabolic perspective into antimicrobial tolerance and resistance
Publisher: Elsevier BV
Date: 03-2022
Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection
Publisher: American Society for Microbiology
Date: 10-2017
DOI: 10.1128/AAC.00954-17
Abstract: Widespread antibiotic use in clinical medicine and the livestock industry has contributed to the global spread of multidrug-resistant (MDR) bacterial pathogens, including Acinetobacter baumannii . We report on a method used to produce a personalized bacteriophage-based therapeutic treatment for a 68-year-old diabetic patient with necrotizing pancreatitis complicated by an MDR A. baumannii infection. Despite multiple antibiotic courses and efforts at percutaneous drainage of a pancreatic pseudocyst, the patient deteriorated over a 4-month period. In the absence of effective antibiotics, two laboratories identified nine different bacteriophages with lytic activity for an A. baumannii isolate from the patient. Administration of these bacteriophages intravenously and percutaneously into the abscess cavities was associated with reversal of the patient's downward clinical trajectory, clearance of the A. baumannii infection, and a return to health. The outcome of this case suggests that the methods described here for the production of bacteriophage therapeutics could be applied to similar cases and that more concerted efforts to investigate the use of therapeutic bacteriophages for MDR bacterial infections are warranted.
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Publisher: Cold Spring Harbor Laboratory
Date: 26-01-2019
DOI: 10.1101/527796
Abstract: Microbiomes are vast communities of microbes and viruses that populate all natural ecosystems. Viruses have been considered the most variable component of microbiomes, as supported by virome surveys and ex les of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared to other environments. Here we investigate the origin, evolution, and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboratory, we obtained DNA sequences of crAssphage from over one-third of the world's countries, and showed that its phylogeography is locally clustered within countries, cities, and in iduals. We also found colinear crAssphage-like genomes in both Old-World and New-World primates, challenging genomic mosaicism and suggesting that the association of crAssphage with primates may be millions of years old. We conclude that crAssphage is a benign globetrotter virus that may have co-evolved with the human lineage and an integral part of the normal human gut virome.
Bacteriophages
Publisher: CSIRO Publishing
Date: 2019
DOI: 10.1071/MA19002
Abstract: In order to avoid a return to the pre-antibiotic era, alternative treatments to combat microbial diseases are urgently needed. In this context, bacteriophages, which have been used effectively in distant parts of the world during the cold war era, are now gaining significant interest in the West. This special issue of the Microbiology Australia thus focusses on bacteriophages with contributions from Australia and from the members of the Expert round table on acceptance and re-implementation of bacteriophage therapy.
Diversified repertoire of phage defenses inKlebsiella pneumoniae: Bi-directional steering effects impacting antibiotic susceptibility
Publisher: Cold Spring Harbor Laboratory
Date: 15-11-2022
Bacteriophage uptake by mammalian cell layers represents a potential sink that may impact phage therapy
Publisher: Elsevier BV
Date: 04-2021
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
Publisher: Springer Science and Business Media LLC
Date: 08-07-2201
Precision Engineers: Bacteriophages Modulate the Gut Microbiome and Metabolome
Publisher: Elsevier BV
Date: 06-2019
DOI: 10.1016/J.CHOM.2019.05.010
Abstract: The precise and rational manipulation of the gut microbiome may enable new therapies for gut health and disease. In this issue of Cell Host & Microbe, Hsu et al. (2019) reveal that bacteriophage predation reduces target bacteria and results in cascading interactions that alter non-target species and the gut metabolome.
Bacteriophage transcytosis provides a mechanism to cross epithelial cell layers
Publisher: American Society for Microbiology
Date: 29-12-2017
Abstract: Bacterial viruses are among the most numerous biological entities within the human body. These viruses are found within regions of the body that have conventionally been considered sterile, including the blood, lymph, and organs. However, the primary mechanism that bacterial viruses use to bypass epithelial cell layers and access the body remains unknown. Here, we used in vitro studies to demonstrate the rapid and directional transcytosis of erse bacteriophages across confluent cell layers originating from the gut, lung, liver, kidney, and brain. Bacteriophage transcytosis across cell layers had a significant preferential directionality for apical-to-basolateral transport, with approximately 0.1% of total bacteriophages applied being transcytosed over a 2-h period. Bacteriophages were capable of crossing the epithelial cell layer within 10 min with transport not significantly affected by the presence of bacterial endotoxins. Microscopy and cellular assays revealed that bacteriophages accessed both the vesicular and cytosolic compartments of the eukaryotic cell, with phage transcytosis suggested to traffic through the Golgi apparatus via the endomembrane system. Extrapolating from these results, we estimated that 31 billion bacteriophage particles are transcytosed across the epithelial cell layers of the gut into the average human body each day. The transcytosis of bacteriophages is a natural and ubiquitous process that provides a mechanistic explanation for the occurrence of phages within the body. IMPORTANCE Bacteriophages (phages) are viruses that infect bacteria. They cannot infect eukaryotic cells but can penetrate epithelial cell layers and spread throughout sterile regions of our bodies, including the blood, lymph, organs, and even the brain. Yet how phages cross these eukaryotic cell layers and gain access to the body remains unknown. In this work, epithelial cells were observed to take up and transport phages across the cell, releasing active phages on the opposite cell surface. Based on these results, we posit that the human body is continually absorbing phages from the gut and transporting them throughout the cell structure and subsequently the body. These results reveal that phages interact directly with the cells and organs of our bodies, likely contributing to human health and immunity.
Protocols for studying bacteriophage interactions with in vitro epithelial cell layers
Publisher: Elsevier BV
Date: 09-2021
Component Parts of Bacteriophage Virions Accurately Defined by a Machine-Learning Approach Built on Evolutionary Features
Publisher: American Society for Microbiology
Date: 29-06-2021
DOI: 10.1128/MSYSTEMS.00242-21
Abstract: In response to the global problem of antimicrobial resistance, there are moves to use bacteriophages (phages) as therapeutic agents. Selecting which phages will be effective therapeutics relies on interpreting features contributing to shelf-life and applicability to diagnosed infections.
Rapid assessment of changes in phage bioactivity using dynamic light scattering
Publisher: Cold Spring Harbor Laboratory
Date: 02-07-2023
DOI: 10.1101/2023.07.02.547396
Abstract: Extensive efforts are underway to develop bacteriophages as therapies against antibiotic-resistant bacteria. However, these efforts are confounded by the instability of phage preparations and a lack of suitable tools to assess active phage concentrations over time. Here, we use Dynamic Light Scattering (DLS) to measure changes in phage physical state in response to environmental factors and time, finding that phages tend to decay and form aggregates and that the degree of aggregation can be used to predict phage bioactivity. We then use DLS to optimize phage storage conditions for phages from human clinical trials, predict bioactivity in 50-year-old archival stocks, and evaluate phage s les for use in a phage therapy/wound infection model. We also provide a web-application (Phage-ELF) to facilitate DLS studies of phages. We conclude that DLS provides a rapid, convenient, and non-destructive tool for quality control of phage preparations in academic and commercial settings. Phages are promising for use in treating antibiotic-resistant infections, but their decay over time in refrigerated storage and higher temperatures has been a difficult barrier to overcome. This is in part because there are no suitable methods to monitor phage activity over time, especially in clinical settings. Here, we show that Dynamic Light Scattering (DLS) can be used to measure the physical state of phage preparations, which provides accurate and precise information on their lytic function – the key parameter underlying clinical efficacy. This study reveals a “structure-function” relationship for lytic phages and establishes DLS as a method to optimize the storage, handling, and clinical use of phages.
Viable virus aerosol propagation by positive airway pressure circuit leak and mitigation with a ventilated patient hood
Publisher: European Respiratory Society (ERS)
Date: 10-12-2020
DOI: 10.1183/13993003.03666-2020
Abstract: Nosocomial transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a major feature of the COVID-19 pandemic. Evidence suggests patients can auto-emit aerosols containing viable viruses these aerosols could be further propagated when patients undergo certain treatments, including continuous positive airway pressure (PAP) therapy. Our aim was to assess 1) the degree of viable virus propagated from PAP circuit mask leak and 2) the efficacy of a ventilated plastic canopy to mitigate virus propagation. Bacteriophage phiX174 (10 8 copies·mL −1 ) was nebulised into a custom PAP circuit. Mask leak was systematically varied at the mask interface. Plates containing Escherichia coli host quantified viable virus ( via plaque forming unit) settling on surfaces around the room. The efficacy of a low-cost ventilated headboard created from a tarpaulin hood and a high-efficiency particulate air (HEPA) filter was tested. Mask leak was associated with virus contamination in a dose-dependent manner (χ 2 =58.24, df=4, p .001). Moderate mask leak (≥21 L·min −1 ) was associated with virus counts equivalent to using PAP with a vented mask. The highest frequency of viruses was detected on surfaces m away however, viable viruses were recorded up to 3.86 m from the source. A plastic hood with HEPA filtration significantly reduced viable viruses on all plates. HEPA exchange rates ≥170 m 3 ·h −1 eradicated all evidence of virus contamination. Mask leak from PAP may be a major source of environmental contamination and nosocomial spread of infectious respiratory diseases. Subclinical mask leak levels should be treated as an infectious risk. Low-cost patient hoods with HEPA filtration are an effective countermeasure.
Granule formation mechanisms within an aerobic wastewater system for phosphorus removal
Publisher: American Society for Microbiology
Date: 15-11-2010
DOI: 10.1128/AEM.00864-10
Abstract: Granular sludge is a novel alternative for the treatment of wastewater and offers numerous operational and economic advantages over conventional floccular-sludge systems. The majority of research on granular sludge has focused on optimization of engineering aspects relating to reactor operation with little emphasis on the fundamental microbiology. In this study, we hypothesize two novel mechanisms for granule formation as observed in three laboratory scale sequencing batch reactors operating for biological phosphorus removal and treating two different types of wastewater. During the initial stages of granulation, two distinct granule types (white and yellow) were distinguished within the mixed microbial population. White granules appeared as compact, smooth, dense aggregates dominated by 97.5% “ Candidatus Accumulibacter phosphatis,” and yellow granules appeared as loose, rough, irregular aggregates with a mixed microbial population of 12.3% “ Candidatus Accumulibacter phosphatis” and 57.9% “ Candidatus Competibacter phosphatis,” among other bacteria. Microscopy showed white granules as homogeneous microbial aggregates and yellow granules as segregated, microcolony-like aggregates, with phylogenetic analysis suggesting that the granule types are likely not a result of strain-associated differences. The microbial community composition and arrangement suggest different formation mechanisms occur for each granule type. White granules are hypothesized to form by outgrowth from a single microcolony into a granule dominated by one bacterial type, while yellow granules are hypothesized to form via multiple microcolony aggregation into a microcolony-segregated granule with a mixed microbial population. Further understanding and application of these mechanisms and the associated microbial ecology may provide conceptual information benefiting start-up procedures for full-scale granular-sludge reactors.
Phage Therapy in the Postantibiotic Era
Publisher: American Society for Microbiology
Date: 20-03-2019
DOI: 10.1128/CMR.00066-18
Abstract: Antibiotic resistance is arguably the biggest current threat to global health. An increasing number of infections are becoming harder or almost impossible to treat, carrying high morbidity, mortality, and financial cost.
Mammalian cells internalize bacteriophages and utilize them as a food source to enhance cellular growth and survival
Publisher: Cold Spring Harbor Laboratory
Date: 11-03-2023
DOI: 10.1101/2023.03.10.532157
Abstract: There is a growing appreciation that the direct interaction between bacteriophages and the mammalian host can facilitate erse and unexplored symbioses. Yet the impact these bacteriophages may have on mammalian cellular and immunological processes is poorly understood. Here we applied highly purified phage T4, free from bacterial by-products and endotoxins to mammalian cells and analyzed the cellular responses using luciferase reporter and antibody microarray assays. Phage preparations were applied in vitro to either A549 lung epithelial cells, MDCK-I kidney cells, or primary mouse bone marrow derived macrophages with the phage-free supernatant serving as a comparative control. Highly purified T4 phages were rapidly internalized by mammalian cells and accumulated within macropinosomes but did not activate the inflammatory DNA response TLR9 or cGAS-STING pathways. Following eight hours of incubation with T4 phage, whole cell lysates were analyzed via antibody microarray that detected expression and phosphorylation levels of human signaling proteins. T4 phage internalization led to the activation of AKT-dependent pathways, resulting in an increase in cell metabolism, survival, and actin reorganization, the last being critical for macropinocytosis and potentially regulating a positive feedback loop to drive further phage internalization. T4 phages additionally down-regulated CDK1 and its downstream effectors, leading to an inhibition of cell cycle progression and an increase in cellular growth through a prolonged G1 phase. These interactions demonstrate that highly purified T4 phages do not activate DNA-mediated inflammatory pathways but do trigger protein phosphorylation cascades that promote cellular growth and survival. We conclude that mammalian cells are internalizing bacteriophages as a food source to promote cellular growth and metabolism.
Phage-antibiotic combination is a superior treatment against Acinetobacter baumannii in a preclinical study
Publisher: Elsevier BV
Date: 06-2022
Viruses and the origin of microbiome selection and immunity
Publisher: Springer Science and Business Media LLC
Date: 16-12-2016
Mammalian cells internalize bacteriophages and use them as a resource to enhance cellular growth and survival
Publisher: Public Library of Science (PLoS)
Date: 26-10-2023
Is Gen Z really that different? Environmental attitudes, travel behaviours and sustainability practices of international tourists to Canterbury, New Zealand
Publisher: Informa UK Limited
Date: 12-10-2022
Efficacy of a patient isolation hood in reducing exposure to airborne infectious virus in a simulated healthcare setting
Publisher: Cold Spring Harbor Laboratory
Date: 29-07-2022
DOI: 10.1101/2022.07.24.22277784
Abstract: Healthcare workers treating patients with SARS-CoV-2 are at risk of infection from patient-emitted virus-laden aerosols. We quantified the reduction of airborne infectious virus in a simulated hospital room when a ventilated patient isolation (McMonty) hood was in use. We nebulised 10 9 plaque forming units (PFU) of bacteriophage PhiX174 virus into a 35.1m 3 room with a hood active or inactive. The airborne concentration of infectious virus was measured by BioSpot-VIVAS and settle plates using plaque assay quantification on the bacterial host Escherichia coli C . The particle number concentration (PNC) was monitored continuously using an optical particle sizer. Median airborne viral concentration in the room reached 1.41 × 10 5 PFU.m -3 with the hood inactive. Using the active hood as source containment reduced infectious virus concentration by 374-fold in air s les. This was associated with a 109-fold reduction in total airborne particle number escape rate. The deposition of infectious virus on the surface of settle plates was reduced by 87-fold. The isolation hood significantly reduced airborne infectious virus exposure in a simulated hospital room. Our findings support the use of the hood to limit exposure of healthcare workers to airborne virus in clinical environments. COVID-19 patients exhale aerosol particles which can potentially carry infectious viruses into the hospital environment, putting healthcare workers at risk of infection. This risk can be reduced by proper use of personal protective equipment (PPE) to protect workers from virus exposure. More effective strategies, however, aim to provide source control, reducing the amount of virus-contaminated air that is exhaled into the hospital room. The McMonty isolation hood has been developed to trap and decontaminate the air around an infected patient. We tested the efficacy of the hood using a live virus model to mimic a COVID-19 patient in a hospital room. Using the McMonty hood reduced the amount of exhaled air particles in the room by over 109-times. In our tests, people working in the room were exposed to 374-times less infectious virus in the air, and room surfaces were 87-times less contaminated. Our study supports using devices like the McMonty hood in combination with PPE to keep healthcare workers safe from virus exposure at work.
The gut virome in two indigenous populations from Malaysia
Publisher: Springer Science and Business Media LLC
Date: 03-02-2022
DOI: 10.1038/S41598-022-05656-3
Abstract: The human gut contains a complex microbiota dominated by bacteriophages but also containing other viruses and bacteria and fungi. There are a growing number of techniques for the extraction, sequencing, and analysis of the virome but currently no standardized protocols. This study established an effective workflow for virome analysis to investigate the virome of stool s les from two understudied ethnic groups from Malaysia: the Jakun and Jehai Orang Asli. By using the virome extraction and analysis workflow with the Oxford Nanopore Technology, long-read sequencing successfully captured close to full-length viral genomes. The virome composition of the two indigenous Malaysian communities were remarkably different from those found in other parts of the world. Additionally, plant viruses found in the viromes of these in iduals were attributed to traditional food-seeking methods. This study establishes a human gut virome workflow and extends insights into the healthy human gut virome, laying the groundwork for comparative studies.
Viable virus aerosol propagation by PAP circuit leak and mitigation with a ventilated patient hood – a model for improving health care worker safety in the COVID-19 pandemic
Publisher: Cold Spring Harbor Laboratory
Date: 05-09-2020
DOI: 10.1101/2020.09.04.20187922
Abstract: Nosocomial transmission of SARS-CoV-2 has been a major cause of morbidity and mortality in the COVID-19 pandemic. Emerging evidence suggests patients auto-emit aerosols containing viable respiratory viruses. These aerosols could be further propagated when patients undergo certain treatments including continuous positive airway pressure (PAP) therapy. This study aimed to assess the degree of viable virus propagated from mask leak in a PAP circuit and the mitigation of virus propagation by an air filter combined with a plastic canopy. Bacteriophage PhiX174 (10 8 copies/mL) was nebulised into a custom PAP circuit within a non-vented clinical room. Mask leak was systematically varied to allow 0, 7, 21, 28 and 42 L/min at the mask interface. Plates containing Escherichia coli host assessed the degree of viable virus (via plaque forming unit) settling on surfaces around the room. In order to contain virus spread, the efficacy of a simple, low-cost ventilated headboard, created from a plastic tarpaulin hood and a high efficiency particulate air (HEPA) filter was tested. Increasing mask leak was associated with virus contamination in a dose response manner (χ 2 = 58.24, df = 4, p 0.001). Clinically relevant levels of leak (≥21 L/min) were associated with virus counts equivalent to using PAP with a standard vented mask. The highest frequency of viruses was detected on surfaces 1m from the leak source, however, viable viruses were recorded on all plates (up to 3.86m from source). A plastic hood with HEPA filtration significantly reduced viable viruses on all plates. HEPA exchange rates of 170 and 470m 3 /hr eradicated all evidence of virus contamination. Mask leak from PAP circuits may be a major source of environmental contamination and nosocomial spread of infectious respiratory diseases. Subclinical levels of leak should be treated as an infectious risk. Cheap and low-cost patient hoods with HEPA filtration are an effective countermeasure. National Health and Medical Research Council of Australia (1139745). Nosocomial spread of SARS-CoV-2 results in increased infection rates among healthcare workers compared to the general population. Those workers involved in the delivery of non-invasive ventilation are at higher risk based on evidence from previous SARS outbreaks. However, little is known about virus aerosol spread and environmental contamination from respiratory interventions like non-invasive ventilation, which is one of few life-saving treatments for COVID-19 patients. We therefore searched through PubMed with no language restrictions from inception to August 21, 2020 using the search terms ([NIV] or [non-invasive ventilation] or [noninvasive ventilation] or [CPAP] or [continuous positive airways pressure] or [PAP] or [positive airways pressure]) and ([aerosol spread] or [aerosol dispersion] or [aerosol generation]). The search returned 130 publications of which 28 related to the generation or spread of aerosols. Of the 28 related papers, 17 were consensus or opinion papers, 4 were reviews and 7 were original research papers. All previous studies investigating aerosol propagation with respiratory interventions utilised particle sizers or smoke visualisation techniques. These methodological limitations mean that particles are counted or visualised close to the aerosol source and reveal little about wider aerosol spread. Furthermore, they ignore the inherent biological aspects of viral aerosol dispersion in that the aerosol needs to contain viable virus in order to be infectious. It has not been directly established that clinical respiratory interventions are capable of propagating viable virus aerosol and no attempt has been made to systematically quantify the degree of environmental contamination from viable virus aerosol escaping from non-invasive ventilation circuits. There are no current studies informing us as to the effectiveness of air filtration interventions at mitigating environmental contamination with viable virus aerosol escaping from non-invasive ventilation circuits. Our study quantifies the degree of viable virus aerosol spread from clinically relevant levels of noninvasive ventilator circuit mask leak, and demonstrates a risk mitigation strategy using a hood and air-purifier at completely eliminating viable virus aerosol environmental contamination. We developed a viable virus aerosol model utilising bacteriophage PhiX174 which is similar in size to SARS-CoV-2 and is harmless to humans. Through nebulising a solution of PhiX174 into a custom ventilation circuit with controllable mask leak settings, we were able to demonstrate that increasing circuit leak was associated with environmental virus contamination in a dose response manner (p 0.001). Even sub-clinically apparent levels of circuit leak ( 7L/min) were associated with detectable virus propagation up to 3.86 metres from the leak source. Deployment of a hood and air-purifier setup as described by the United States Centres for Disease Control and Prevention, completely eliminated environmental virus contamination from viral aerosol dispersion. Non-invasive ventilator circuit mask leak can propagate live virus containing aerosol and can lead to extensive environmental contamination up to 3.86 metres from the leak source, even at levels of leak that would be difficult to detect clinically. This raises important safety considerations for open wards delivering non-invasive ventilatory support and could explain the noted increased risk of nosocomial SARS infections in healthcare workers delivering non-invasive ventilation treatment. Point of emission air filtration with simple hood and air-purifier completely eliminates environmental contamination with viable virus and could be readily deployed to protect health care workers in the COVID-19 pandemic.
Phage on tap–a quick and efficient protocol for the preparation of bacteriophage laboratory stocks
Publisher: PeerJ
Date: 26-07-2016
DOI: 10.7717/PEERJ.2261
Abstract: A major limitation with traditional phage preparations is the variability in titer, salts, and bacterial contaminants between successive propagations. Here we introduce the Phage On Tap (PoT) protocol for the quick and efficient preparation of homogenous bacteriophage (phage) stocks. This method produces homogenous, laboratory-scale, high titer (up to 10 10–11 PFU·ml −1 ), endotoxin reduced phage banks that can be used to eliminate the variability between phage propagations and improve the molecular characterizations of phage. The method consists of five major parts, including phage propagation, phage clean up by 0.22 μm filtering and chloroform treatment, phage concentration by ultrafiltration, endotoxin removal, and the preparation and storage of phage banks for continuous laboratory use. From a starting liquid lysate of 100 mL, the PoT protocol generated a clean, homogenous, laboratory phage bank with a phage recovery efficiency of 85% within just two days. In contrast, the traditional method took upwards of five days to produce a high titer, but lower volume phage stock with a recovery efficiency of only 4%. Phage banks can be further purified for the removal of bacterial endotoxins, reducing endotoxin concentrations by over 3,000-fold while maintaining phage titer. The PoT protocol focused on T-like phages, but is broadly applicable to a variety of phages that can be propagated to sufficient titer, producing homogenous, high titer phage banks that are applicable for molecular and cellular assays.
Bacteriophages evolve enhanced persistence to a mucosal surface
Publisher: Proceedings of the National Academy of Sciences
Date: 29-06-2022
Abstract: The majority of viruses within the gut are obligate bacterial viruses known as bacteriophages (phages). Their bacteriotropism underscores the study of phage ecology in the gut, where they modulate and coevolve with gut bacterial communities. Traditionally, these ecological and evolutionary questions were investigated empirically via in vitro experimental evolution and, more recently, in vivo models were adopted to account for physiologically relevant conditions of the gut. Here, we probed beyond conventional phage–bacteria coevolution to investigate potential tripartite evolutionary interactions between phages, their bacterial hosts, and the mammalian gut mucosa. To capture the role of the mammalian gut, we recapitulated a life-like gut mucosal layer using in vitro lab-on-a-chip devices (to wit, the gut-on-a-chip) and showed that the mucosal environment supports stable phage–bacteria coexistence. Next, we experimentally coevolved lytic phage populations within the gut-on-a-chip devices alongside their bacterial hosts. We found that while phages adapt to the mucosal environment via de novo mutations, genetic recombination was the key evolutionary force in driving mutational fitness. A single mutation in the phage capsid protein Hoc—known to facilitate phage adherence to mucus—caused altered phage binding to fucosylated mucin glycans. We demonstrated that the altered glycan-binding phenotype provided the evolved mutant phage a competitive fitness advantage over its ancestral wild-type phage in the gut-on-a-chip mucosal environment. Collectively, our findings revealed that phages—in addition to their evolutionary relationship with bacteria—are able to evolve in response to a mammalian-derived mucosal environment.
Point of emission air filtration enhances protection of health care workers against skin contamination with virus aerosol
Publisher: Cold Spring Harbor Laboratory
Date: 18-08-2021
DOI: 10.1101/2021.08.15.21261997
Abstract: Rationale: We recently demonstrated that a patient hood with a high efficiency particulate air filter eliminates virus aerosol contamination when very large quantities of bacteriophage virus are aerosolised into a clinical room. While this containment method is relatively low cost, it is unclear whether similar efficacy can be achieved with lower cost/commercial grade air purifiers, or if such an approach protects healthcare workers against virus aerosol contamination. Method: A total of 109 (10 ml of 108) PhiX174 bacteriophages was nebulized into a sealed clinical room. Surface contamination was detected by settle plates left uncovered during exposure. A healthcare worker remained in the room, personal exposure was determined by skin swabs after exiting the room, following doffing of personal protective equipment (PPE). Four skin areas were swabbed: forearms/hands, neck, forehead, under N95 mask. Three conditions were tested, 1) hood with hospital grade air purifier (IQ Air Health Pro 250), 2) hood with commercial air purifier (Philips 1000i), and 3) control (no hood/air-purification). Findings: The control condition demonstrated extensive environmental and limited skin contamination underneath PPE, which was highest under an N95 mask. The commercial air purifier and hood provided environmental control of virus aerosol and almost zero skin contamination. In comparison, the hospital grade purifier provided complete environmental and skin contamination protection, despite a lower clean air filtration rate (240m3/hr vs 270m3/hr). Virus counts on plates and swabs were significantly lower for both air purifiers and across neck, forehead, and under the N95. There were no statistically significant differences in detected virus counts between air purifiers. Conclusion: This cheap and scalable method may be an effective way to reduce the spread of COVID-19 in hospitals by enhancing the effectiveness of PPE worn by health care workers who care for COVID-19 patients and who are exposed to virus aerosol.
High Temperatures and Tourism: Enlightenment from China
Publisher: MDPI AG
Date: 17-08-2023
DOI: 10.20944/PREPRINTS202308.1181.V1
Abstract: Climate and its fluctuations have wide-ranging impacts on the tourism industry. High temperatures, as a typical meteorological and climatic factor, influence tourists& #039 travel intentions and spatial behavior. This study conducted a descriptive analysis and market trend analysis of Chinese tourism during periods of high temperatures, revealing several key findings. Firstly, tourists seeking respite from summer heat exhibit a preference for short-distance trips and resource-rich destinations. Secondly, heat-escape tourism products undergo changes over time, gradually shifting towards mountainous areas and waterfront locations. Furthermore, taking Shanghai Disneyland as a case study demonstrates that the holiday system holds greater significance than temperature constraints. Despite experiencing a significant decline in the quality of their tourist experience in high-temperature environments, long-distance travelers are not deterred from choosing pre-booked tourism products by sudden bouts of hot weather.
Temporal Stability and Genetic Diversity of 48-Year-Old T-Series Phages
Publisher: American Society for Microbiology
Date: 23-02-2021
DOI: 10.1128/MSYSTEMS.00990-20
Abstract: T-series bacteriophages have been used throughout the world for various molecular biology researches, which were critical for establishing the fundamentals of molecular biology, from the structure of DNA to advanced gene-editing tools. These model bacteriophages help keep research data consistent and comparable between laboratories.
Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm
Publisher: Wiley
Date: 21-10-2016
Abstract: Biofilms are ubiquitous in nature, forming erse 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 two distinct biofilms, one floccular biofilm, consisting of small, loose, microbial aggregates, and one granular biofilm, forming larger, dense, spherical aggregates. Using metagenomic and metaproteomic methods, we investigated the proteomic differences between these two biofilm communities, identifying a total of 2022 unique proteins. To understand biofilm differences, we compared protein abundances that were statistically enriched in both biofilm states. Floccular biofilms were enriched with pathogenic secretion systems suggesting a highly competitive microbial community. Comparatively, granular biofilms revealed a high-stress environment with evidence of nutrient starvation, phage predation pressure, and increased extracellular polymeric substance and cell lysis. Granular biofilms were enriched in outer membrane transport proteins to scavenge the extracellular milieu for amino acids and other metabolites, likely released through cell lysis, to supplement metabolic pathways. This study provides the first detailed proteomic comparison between Accumulibacter-enriched floccular and granular biofilm communities, proposes a conceptual model for the granule biofilm, and offers novel insights into granule biofilm formation and stability.
Temperate gut phages are prevalent, diverse, and predominantly inactive
Publisher: Cold Spring Harbor Laboratory
Date: 18-08-2023
DOI: 10.1101/2023.08.17.553642
Abstract: Large-scale metagenomic and data mining efforts have uncovered an expansive ersity of bacteriophages (phages) within the human gut 1–3 . These insights include broader phage populational dynamics such as temporal stability 4 , interin idual uniqueness 5,6 and potential associations to specific disease states 7,8 . However, the functional understanding of phage-host interactions and their impacts within this complex ecosystem have been limited due to a lack of cultured isolates for experimental validation. Here we characterise 125 active prophages originating from 252 erse human gut bacterial isolates using seven different induction conditions to substantially expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 17% of computationally predicted prophages were induced with common induction agents and these exhibited distinct gene patterns compared to non-induced predictions. Active Bacteroidota prophages were among the most prevalent members of the gut virome, with extensive use of ersity generating retroelements and exhibiting broad host ranges. Moreover, active polylysogeny was present in 52% of studied gut lysogens and led to coordinated prophage induction across erse conditions. This study represents a substantial expansion of experimentally validated gut prophages, providing key insights into their ersity and genetics, including a genetic pathway for prophage domestication and demonstration that differential induction was complex and influenced by ergent prophage integration sites. More broadly, it highlights the importance of experimental validation alongside genomic based computational prediction to enable further functional understanding of these commensal viruses within the human gut.
Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System
Publisher: MDPI AG
Date: 25-12-2018
DOI: 10.3390/V11010010
Abstract: The human body is host to large numbers of bacteriophages (phages)–a erse group of bacterial viruses that infect bacteria. Phage were previously regarded as bystanders that only impacted immunity indirectly via effects on the mammalian microbiome. However, it has become clear that phages also impact immunity directly, in ways that are typically anti-inflammatory. Phages can modulate innate immunity via phagocytosis and cytokine responses, but also impact adaptive immunity via effects on antibody production and effector polarization. Phages may thereby have profound effects on the outcome of bacterial infections by modulating the immune response. In this review we highlight the erse ways in which phages interact with human cells. We present a computational model for predicting these complex and dynamic interactions. These models predict that the phageome may play important roles in shaping mammalian-bacterial interactions.
Unlocking the next generation of phage therapy: the key is in the receptors
Publisher: Elsevier BV
Date: 04-2021
Related Organisations
Related Funding Activities
Discovery Projects - Grant ID: DP210103296
Start Date: 03-2021
End Date: 03-2025
Amount: $536,190.00
Funder: Australian Research Council
View Funded ActivityDiscovery Early Career Researcher Award - Grant ID: DE170100525
Start Date: 2017
End Date: 12-2019
Amount: $372,000.00
Funder: Australian Research Council
View Funded Activity