Looking back on iVoM: Six webinars covering all aspects of viruses of microbes

Issue 126 | May 14, 2021
22 min read
Capsid and Tail

Winner of the VoM Abstract Book Image Contest, by Carlos Omar Lomelí Ortega

This week, we’ve got highlights and recordings for the six “iVoM” webinars we co-hosted with the VoM/ISVM team from Sept 2020 to March 2021! These webinars included talks by 18 expert speakers and brought together more than 1000 unique virus-of-microbe enthusiasts!

What’s New

Adaptive Phage Therapeutics (APT), a clinical-stage US biotech company, just closed a $40.75 million Series B investment round led by Deerfield Management Company (and also including Mayo Clinic). This will enable APT to accelerate clinical development of their PhageBank™ phage therapies.

Biotech newsFunding newsPhage Therapy

Technophage, a Portuguese clinical-stage biopharma company, announced today that the US FDA has granted Fast Track designation to TP-102, the company’s first phage cocktail, for the treatment of infected diabetic foot ulcers caused by three different bacteria (Pseudomonas aeruginosa, Staphylococcus aureus and/or Acinetobacter baumannii).

Biotech newsPhage Therapy

Bridget Watson (University of Exeter) and colleagues published a new review in Cell Host & Microbe on coevolution between bacterial CRISPR-Cas systems and their phages. They discuss when and why CRISPR-Cas immunity against phages evolves, and how this selects for the evolution of immune evasion by phages.

CRISPRPhage defense systemsReview

Adam Wahida (Technical University of Munich) and colleagues published a new minireview on phage-bacteria-eukaryotic relationships and their influence on human health.

Phage-Eukaryote interactionsReview

Lorenz Leitner (Balgrist University Hospital, University of Zürich) and colleagues published a new paper in Spinal Cord on the potential role of phages in prolonging life after spinal cord injury.

PerspectiveSpinal cord injuryPhage Therapy

Latest Jobs

Post Doc
Hany Anany (University of Guelph and Agriculture and Agri-Food Canada) has a postdoc position available starting July to study Campylobacter and Salmonella phages (for host interaction and biocontrol applications). Only open to Canadian Citizens at this time.
Technician
Texas A&M Agrilife Research is hiring a Technician II to work on phage-related (and plant/greenhouse-related) experiments.
Post Doc
Steven Wilhelm (University of Tennessee) is seeking a postdoc to join their team and study giant viruses that infect algae.
Research AssociateScientist
Felix Biotech (a clinical stage US phage therapy-focused biotech company) is hiring scientists, research associates, & associate scientists.
Technician
Adaptive Phage Therapeutics is hiring a Banking Manufacturing Technician to work within the BioBanking Department and may also have the opportunity to work across other manufacturing departments.

Community Board

Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

Thanks so much to everyone who attended PHAVES #16 this week! Here’s the recording!

Dr. Greg Canfield and Dr. Laura Damioli from the CU Anschutz and CU Denver gave a fantastic joint talk entitled: Freedom from antibiotic purgatory?: Salvage phage therapy for cure of spinal hardware infection.

Watch this and other past PHAVES recordings on the Phage Directory YouTube channel here.

Virtual EventRecording

PHAVES #17 will be May 18, 5pm CEST (Paris time). Quentin Lamy-Besnier, a PhD student in the Debarbieux lab at the Institut Pasteur in Paris will present their team’s newly launched Viral Host Range Database, an online tool for recording, analyzing and disseminating virus-host interactions.

Come learn from Quentin how to use this much-needed new tool for the phage community! Small group networking to follow.

Register for this talk and others in the PHAVES series at https://seminars.phage.directory!

Virtual Event

Has anyone in the community used/heard of an automated system that does plaque identification, picking, and subculturing? Please email [email protected] with suggestions/links — thanks!

Seeking tool

My name is Gábor Apjok, a PhD student from the Biological Research Centre of Szeged, Hungary. Recently, our hospitals in Hungary have detected multidrug resistant Acinetobacter baumannii, which we have started to collect. We are familiar with isolating phages from the environment, however, we have failed to do so in case of Acinetobacter phages. We investigated hospital sewage from various sources, river sediment, soil, to no avail. Next, we will check samples directly from patients (e.g. fecal samples, swabs etc.), however it takes time to get permission to handle samples of the sort. Because of the above reasons, we thought it would be best to seek help from the phage community. We are seeking Acinetobacter phages (and their cognate hosts to maintain phages) and would appreciate any help you can provide. Please contact me at: [email protected].

Seeking collaboratorSeeking phages

Looking back on iVoM: Six webinars covering all aspects of viruses of microbes

Profile Image
Researcher
University of Minho
Skills

Biotechnology, Molecular Biology, Phage Therapy, Teaching

Ivone is a researcher at the Centre of Biological Engineering. Her current research is focused in the development of phage-based tools for the diagnostic and treatment of neurodegenerative diseases. For that, she uses Phage Display technology as well as genetic and chemical manipulation of the M13 bacteriophage.

Phage Hosts
Profile Image
Postdoctoral Researcher
University of Minho
CEB - Centre of Biological Engineering, Braga, Portugal
Twitter @MeloLDR
Skills

Bioinformatics, Biotechnology, Teaching, Phage isolation, Phage-host interactions, Molecular Biology, Phage Therapy

I am a postdoctoral reaercher interested in understand phage-host interactions in order to develop better phages against staphylococcal biofilms. I am currently coordenating a project about Helicobacter pylori phages and prophages.

This week, we bring you the highlight reel and recordings for the six “iVoM” webinars co-hosted by the VoM 2020 team, ISVM and Phage Directory from Sept 2020 to March 2021. These webinars included talks by 18 expert speakers and brought together more than 1000 unique virus-of-microbe enthusiasts! Thanks to everyone who attended, presented, sponsored and helped organize!

Highlights of iVoM #1: Ecology and evolution of microbial viruses

This session was chaired by Corina Brussaard and Debbie Lindell who introduced the three invited speakers and managed the Q&A session. The session can be visualized at: https://www.youtube.com/watch?v=qoUv5eFvbs4.

Spread of viruses: Global, Regional and Local distributions of crAssphage by Rob Edwards

  • The main question of this talk was how the crAssphage is spreading globally, regionally and locally and the differences between them.
  • The phylogeny of several thousand genomes was built and data suggests a strong country specific signal. A study in Poland, suggested that there is a strong regional signal which can led researchers to predict from which city that crAssphage comes (Edwards et al., Nature Microbiology, 2019).
  • Sampling from San Diego region suggested a temporal signal rather than a geographic signal.

This was a very interesting talk about how phages are spreading. This results as a result of a complex interaction between phage, bacteria and human. The factors that drive both temporal and geographical variation is the next questions to be pursued.

Diversity in marine algal virus host relationships and their effect on phytoplankton community structure by Ruth-Anne Sandaa

  • The main question of this talk was if virus-host data can be used to predict what is happening in the ocean environment.
  • Latent period, environmental decay, host range, virulence, infectivity and mode of transmission are key traits in algal virus-host relationships. Data suggests that all fitness traits come with a biological trade-off (Sandaa et al., submitted).
  • Acute infections are characterized by viruses with narrow host range and short latent period and higher infectivity and virulence, which leads to a higher diversity within virus-host pairs. On persistent infections, the opposite happens and this is always present on the oceans.

This talk opened new horizons on the impact of different virus-host interactions and their ecological roles.

The story of CrAssphage so far by Colin Hill

  • The goal of this work was to study the diversity of crAss phages and culture them for the first time (Shkoporov et al., Nature Communications, 2018).
  • 239 crAss-like phage genomes were analyzed and an ICTV proposal was performed where crAss viruses are an order of phages containing up to 78 genera (Guerin et al., Cell & Host Microbe, 2018). Despite the genomic differences between them, crAss phages were already detected 5 thousand years ago.
  • In some individuals, crAss phages can represent 95% of the faecal virome and although with different magnitudes, these viruses were detected in every individual in all time points tested (Shkoporov et al., Cell & Host Microbe, 2018).

This very interesting talk showed that all 4 isolated crAss-phages have Bacteroides sp. as host and opened a set of different studies that are currently being performed at the lab scale.

Highlights of iVoM #2: Virus structures and function

This session was chaired by Deborah M. Hinton and Paulo Tavares who introduced the three invited speakers and managed the Q&A session. The session can be visualized at: https://www.youtube.com/watch?v=6u_sPy7zeRo.

Structure and function of central spike proteins by Petr Leiman

  • This talk described how contractile tail system works on phages and what happens to the tailspike after interaction with the host.
  • There are three types of central spike complexes with a huge diversity of gene organization (Browning et al., Structure, 2012). Moreover, the diversity of the structure of different tip proteins was described.
  • Many tail tips are related or have evolved from the apex domains of spikes.

This stimulating talk described the diversity of the structure and function of central spike complex components which can justify different phage-bacteria interactions.

Giant Viral Infection Mechanisms: Dropping acid makes you see stars by Kristin N. Parent

  • The main goal of this talk was to explain the stability of giant viruses.
  • Giant viruses were isolated from a wide range of environments and were cultured in lab by infecting amoeba.
  • A technique named “Bubblegrams” using cryo-EM was performed to identify the stargate structure on giant virus capsids (Schrad et al., Cell, 2020). Despite their great stability, capsids were affected by pH and temperature variations.

This exciting talk showed that stargate opening mechanisms seem to be universal to giant viruses.

Phage capsids turned into versatile nanocarriers by Pascale Boulanger

  • This talk described the versatility of using phage capsids as nanocarriers.
  • The cryo-EM structure of four different forms of phage T5 capsid has been solved and results showed that expanded capsid has the same geometry as the virion capsid (Huet et al., PNAS, 2020).
  • A system of a quasi-irreversible capsid protein decoration was developed. The decoration was modified using a modified protein.

This important talk showed that T5 capsids are tunable display nanoparticles and empty capsids can be good nanocarriers for vaccine development.

Highlights of iVoM #3: Virus-host interaction: overcoming cell barriers

This session was chaired by Madalena Pimentel and Ry Young who introduced the three invited speakers and managed the Q&A session. The session can be visualized at: https://www.youtube.com/watch?v=WYl1qgdxiG4.

Sweet and sour: how cell surface glycosylation affects phage sensitivity and virulence by Martin J. Loessner

  • This talk described the gains and losses of phage-resistant bacteria Listeria monocytogenes.
  • Different L. monocytogenes serovars are characterized by different types of wall-teichoic acids (Shen et al., JBC, 2017). Phage affects glycosylation patterns on teichoic acids, which occur by single point mutations (Eugster et al., Molecular Microbiology, 2015).
  • Bacteriophage resistant variants occur on teichoic acids. These mutants lost virulence and the lost the ability to internalize mammalian cells (Sumrall et al., PLoS Pathogens, 2019).

This talk provided a very important take-home message, in which after being challenged with phages, bacteria can become avirulent. Moreover, the concept of reprogramming the host range of phages by genetic manipulation was introduced (Dunne et al., Cell Reports, 2019).

License to lyse: factors impacting endolysin lytic action on Gram-positive bacteria by Carlos São-José

  • This talk described the factors impacting Gram-positive endolysins action.
  • As it happens during phage infection in which holins affect proton-motive force (PMF), conditions promoting dissipation of membranes potential increase endolysin activity, when added externally (Fernandes et al., Molecular Microbiology, 2016).
  • To simulate the creation of this PMF lost, antimicrobial peptides (AMP) were used. In S. aureus, endolysin and AMP demonstrated a synergistic effect. Moreover, it was showed that AMPs increase endolysin binding to staphylococcal cells.

This talk was important to inform researchers why some endolysins are not so active in in vitro conditions. Moreover, the importance of internal in-frame translation start site on endolysin domain multimerization opened now horizons on endolysins research.

Bacterial tolerance to phages by Sigal Ben-Yehuda

  • This talk reported the kinetics of phage plaque formation and bacterial tolerance response of neighbor non-infected cells.
  • The plaque development by two lytic phages infecting Bacillus subtilis host using high-resolution confocal microscopy. After an increasing on the plaque size, it was observed an unexpected shrinking after eight hours.
  • Data revealed that plaque spread is restricted by the activation of a transient phage tolerance response in non-infected bacteria in response to lysis of their neighbors, which happens as a consequence of cell surface alterations that limit phage adsorption.

This very interesting talk clarified the molecular response occurring during phage plaque formation on non-infected neighbor bacteria and provided to the audience an important take-home message “The night plaques are different from the morning plaques”.

Highlights of iVoM #4: Virus-host interaction: molecular mechanisms

This session was chaired by Karen Maxwell and Julia Frunzke who introduced the three invited speakers and managed the Q&A session. The session can be visualized at: https://www.youtube.com/watch?v=e8hSuZR5caA.

New immune systems in bacteria by Rotem Sorek

  • This talk reported a systematic way to find new defense systems. An example was the new defense systems found in defense islands in bacterial genomes (Doron et al., Science, 2018).
  • They have focused on Viperin - an effector viral gene in the human immune system which homologs appear in bacterial defense islands.
  • It was observed that bacterial viperins produce a family of new antiviral molecules and that eukaryotic viperins originated from bacterial ones (Bernheim et al., Nature, 2020).

This was a very interesting talk describing recent discoveries on new mechanisms by which bacteria encode anti-viral small molecules to defend themselves against phages.

The regulation and activity of Class 1 CRISPR-Cas systems by Peter Fineran

  • This talk discussed multiple regulatory networks controlling CRISPR-Cas immunity to understand how bacteria control the adaptive immune system. The CRISPR-Cas in Serratia sp. ATCC39006 was studied and they used a non-biased genome-wide approach (Smith et al., in press).
  • Rcs (regulator of capsule synthesis)-membrane stress response regulates type III cas expression and Rcs pathway activation increases plasmid acquisition controlling type I expression and interference.
  • Moreover, Rcs activation inhibits spacer acquisition and enhances plasmid retention, and Rcs stress response inversely controls surface and CRISPR-Cas adaptive immunity to discriminate plasmids and phages.

This was a very interesting talk who provided insights on how CRISPR-Cas systems are regulated in bacteria and the observation that the Rcs pathway confers cell-surface phage immunity.

Molecular hijacking of Pseudomonas by Rob Lavigne

  • This talk focused on phage-encoded mechanisms in bacteria able to modify replication, transcription and (post)translational modifications within the cell.
  • The expression of the Pseudomonas phage LUZ24 ORFANs revealed Igy – a Pseudomonas-specific toxic peptide (Wagemans et al. Frontiers in Microbiology, 2015).
  • Igy induces and elongated cell morphology, indicative of replication/cell wall inhibition. Deletion of Igy do not retain the toxicity towards P. aeruginosa, and Gyrase B (an important antibacterial target in Pseudomonas) was identified as an interaction partner, confirming that Igy is a novel inhibitor of the Pseudomonas DNA gyrase peptide (De Smet et al., Cell Reports, under review).

This was a talk of utmost importance about the use of phage-encoded mechanisms that modify important genetic processes within the cell, which can be exploited in the future for antibacterial design strategies and biotechnological applications.

Highlights of iVoM #5: Agro-food, veterinary and environmental biotechnology applications

This session was chaired by Mathias Middelboe and Lone Brøndsted who introduced the three invited speakers and managed the Q&A session. The session can be visualized at: https://www.youtube.com/watch?v=kH7x_M09yp4.

Engineered phages for environmental monitoring by Sam R. Nugen

  • This talk described the genetic engineering of phages to contain reporter enzymes and allow for covalent and oriented conjugation on magnetic nanoparticles.
  • The phages were used to detect E. coli in drinking water by inserting a luminescent gene into the genome of the T4 phage.
  • This methodology provided, and compared, favorably to current testing methods.

This was a very interesting talk about the use of phages as biosensors to report for the presence of E. coli in drinking water, which can be used to detect other bacteria.

Phage therapy in Apiculture — prospects by Ana Oliveira

  • This talk focused on the possibility of using phages to control American Foulbrood (AFB) disease, orally administered to adult bees, by characterizing phage safety, biodistribution and activity in hive conditions.
  • Given orally to bees, phages could effectively reach young larvae, but with loss of activity. Phage treatment caused the rise of phage-insensitive strains inside larvae (Ribeiro et al., Scientific Reports, 2019).
  • This can be a promising strategy to fight AFB if protection of phages from hive-derived conditions and phage engineering to remove integration genes, are considered.

This was a very nice talk with application on apiculture, and with promising results to use phages to tackle AFB disease, promoting the wellbeing of the hive and decreasing the economic losses of this activity.

Encapsulation of bacteriophages for targeted delivery and controlled release by Danish Malik

  • This talk covered some encapsulation approaches that can be used for bacteriophages, including spray drying, microfluidic and membrane emulsification methods.
  • Using a Salmonella phage they concluded that spay drying is a scalable manufacturing unit operation for production of encapsulated phages in dry powder forms.
  • Moreover, they observed that pH responsive microcapsules allow delivery of fragile biotherapeutic cargo overcoming pH and enzymatic stresses in the gut and may be used for targeted delivery and controlled release to demonstrate efficacy of novel therapeutics.

This was a very interesting talk showing nice results on phage encapsulation for phages protection from environmental and processing stresses, namely exposure to gastric acidity and enzymatic activity. Targeted delivery and controlled release of high tires of phages may significantly improve phage treatment outcomes.

Highlights of iVoM #6: Biotechnology applications in health care

This session was chaired by Jeremy Barr and Joana Azeredo who introduced the three invited speakers and managed the Q&A session. The session can be visualized at: https://www.youtube.com/watch?v=F0SLQzTxVns&t=10s.

Phages (in)action in the gut by Laurent Debarbieux

  • The main question of this talk was how the population of bacteria and phages interact with each other in the gut of mammals.
  • It was observed in conventional mice that a phage adaptation occurs (De Sordi et al., Cell Host & Microbes, 2017), i.e. gut microbiota offers opportunities for phage adaptation.
  • To control the composition of the gut microbiota, they used gnotobiotic mice (axenic mice + defined microbes), in particular the OMM12 model, observing that phages are less abundant in the mucosal parts of the gut (Lourenço et al., Cell Host & Microbes, 2020).

This was a very interesting talk about phage-bacteria interactions in the gut, and how this knowledge can help understanding these dynamics in relation to human health.

A study that went wrong — phage engineering and phage pharmacokinetics by Krystyna Dabrowska

  • This talk described the engineering of phages in order to increase their circulation time in vivo, similar to long-circulating phages - a phenotype related to phages survival (Merril et al., PNAS, 1996).
  • They used targeting phages to the infection site by phage display using engineered T4 variants (Gorski et al., Future Microbiology, 2015), which demonstrated short-circulating phenotype, mainly due to the phage neutralization by the serum complement.
  • It is known that long-circulating phages expose particular amino acids on their surfaces and the exposure of lysine or arginine helps the phage to escape the immune response (Sokoloff et al., Molecular Therapy, 2000 and Vitiello et al., Virus Research, 2005).

This was an important talk to alert that phage engineering can affect phage pharmacokinetics, once it can destroy optimized biochemical properties of a phage particle making the phage more vulnerable to the immune system. Moreover, possibly phages pharmacokinetics can be designed by designing aminoacidic composition of capsids.

Phage therapy experience in France in the field of Bone and Joint infection by Tristan Ferry

  • The goal of the work described in this talk was the promotion of innovative treatments for bone and joint infections (BJI), by obtaining purified lytic phages against bacteria.
  • Personalized phage therapy is a potential adjunct treatment for patients with complex BJI due to pandrug-resistant bacteria.
  • Phage therapy has the potential to keep the function in patients with severe relapsing prosthetic joint infection (Ferry et al., Frontiers in Medicine, 2020).

This talk gives us the important message that having a multidisciplinary approach with international academic collaborations and interactions with national health authority and industry, are essential to go ahead and develop phage therapy in a close future.

Concluding remarks

We hope that you have enjoyed this recap. We would like to thank all the participants and their feedback. It was a great pleasure for us to organize the webinars and bring VoM community together again.

We would also like to invite you all to attend the VoM2022 Conference, in July 2022, to meet us personally in Portugal, and enjoy the beautiful city of Guimarães. More information is available at https://vom2020.org/, @VoM2020, @AzeredoLab or contact us at [email protected].

The iVoM organizing committee


Thanks to Atif Khan for help finding and summarizing this week’s phage jobs posts!

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