As you may know, we’re launching a peer-reviewed publication platform for the phage community. We want to improve the publishing experience for authors and reviewers, and we’d love to hear from you!
Vorrapon Chaikeeratisak and colleagues at UC San Diego, the group that discovered that certain Pseudomonas phages replicate their DNA inside a phage-encoded nucleus-like structure, have now published that the capsids of these phages traffic along phage-encoded, “treadmilling” tubulin filaments. The “nucleus” rotates as a result of this treadmilling action, which distributes capsids for efficient DNA packaging. Paper | News article | Youtube video | Apply for a job in this lab!
A new paper by Saima Aslam and colleagues at the Center for Innovative Phage Applications and Therapeutics (IPATH) at UC San Diego reports their early clinical experience with phage therapy in lung transplant recipients.
Intralytix announced that it will be collaborating with the Eliava Foundation and Ferring Pharmaceuticals to develop new phage-based drugs to improve reproductive medicine and women’s health through modulation of the vaginal microbiome.
ContraFect has received a $7.2 Million grant from the US Army Medical Research and Development Command to advance their engineered phage lysin candidate CF-296 for Staphylococcus aureus infections.
Md. Shamim Ahasan and colleagues at James Cook University in Queensland, Australia have published a study comparing phage therapy to antibiotics in treating gut dysbiosis in endangered green turtles. They found that phages (isolated from sewage on turtle gut strains) reduced the targeted Acinetobacter, but did not otherwise significantly alter the microbiota. Antibiotics also reduced Acinetobacter load, but also led to microbiome disruption. Paper | Press release
Postdoctoral positions are immediately available in the laboratories of Dr. Elizabeth Villa and Dr. Joe Pogliano in the Department of Biology at the University of California San Diego. We are seeking highly-motivated, energetic and passionate individuals to join our collaborative team to study Pseudomonas phage that replicate using a nucleus-like structure. The project focuses on using a combination of cryo-electron microscopy, fluorescence microscopy, CRISPR/Cas gene editing tools, proteomics, and RNA seq to identify and study the structure and function of every essential protein encoded by these unique phage. The “phage nucleus” is a new field of biology that is incredibly rich with a high potential for making novel discoveries. The applicant should have a Ph.D., M.D., or equivalent title in biology and have a demonstrated record of productivity.
[If you enjoyed the paper on phage “treadmilling” we highlighted above, here’s a chance to work with the group who made that discovery!]
The Hub for Biotechnology in the Built Environment (HBBE) is a £8M initiative between Northumbria and Newcastle Universities. HBBE will develop biotechnologies to create a new generation of buildings which are responsive to their environment, grown using engineered living materials, metabolise their own waste, and modulate their microbiome to benefit human health.
We are now seeking to appoint a highly committed, motivated and creative scientist to join the research team under ‘Microbial Environments’ theme. The research will see development of techniques to sense, predict and then modulate bacterial communities using bacteriophages in a built environment setting. The post is a fixed term for 36 months. The successful candidate will work closely with computational biologists, microbial ecologists, architects, material scientists and civil engineers.
CARB-X, a Boston University Global Partnership, has an exciting opportunity for a talented individual to join our core team at Boston University in the role of Director of Research & Development. CARB-X is a new organization located at the BU School of Law, focused on accelerating the pre-clinical development of drugs, vaccines and diagnostics to address antibiotic resistance. The Director of R&D is a new senior role on the leadership team of CARB- X. The Director of R&D will take responsibility for the planning, review, awarding and monitoring of novel R&D projects addressing the antimicrobial resistance issue on a global basis.
I am Ibtihadj Souda, a PhD student at the University of Constantine 1 in Algeria working on isolation and characterization of new bacteriophages from wastewater in the Sahara Desert of Algeria (North Africa). Recently, I have been offered a fully funded scholarship from our university (to cover travel and accommodation), so I have an opportunity to spend a one-month internship at a laboratory to do molecular characterisation of the phages we have isolated. I would like to observe my phages by transmission electron microscopy and perform genome sequencing. The location of the lab can be anywhere, and the timing of the visit can be anytime from June-Dec 2019, but I need to submit an invitation letter by June 30, so I need to find a host lab as soon as possible. Please email me at [email protected] and we can discuss details! Thank you!
I am seeking samples of T4 and T7 phage for research. Please email me at [email protected] if you can help. Thank you!
For more, check out (and add to) this Twitter thread!
If you’re attending ASM Microbe, we’re looking for a phage researcher to write a guest post for Capsid & Tail about insights/impressions from the conference! Email [email protected] if you’re interested, and we’ll send you more info! Looking for a draft to be written by mid-July.
Aquaculture (growing/farming fish for food) is the fastest growing food industry globally. According to the Food and Agriculture Organization (FAO), it has been recording positive annual growth rates since the early 60s (Figure 1). It achieved a new record in 2016 when global fish production through aquaculture reached ~10 kg fish supply per capita, for the first time higher than the supply from capture fisheries (the term for wild fisheries, ie. fish and shellfish captured by fisherman). Today, fish account for 16.6 % of animal protein supply and 6.5 % of total protein for human consumption, and fish has been the major source of animal protein in developing countries of Asia and Africa. Aquaculture is thus an important food-producing sector that contributes high quality protein to support the world’s growing population.
Figure 1. The total amount of wild fish captured by fishing activities (capture fisheries) and the total amount of cultured fish and shellfish produced by aquaculture, in millions of tonnes globally. [Figure from The state of world fisheries and aquaculture, FAO report 2018]
As in any other animal production industry, diseases are a significant setback for aquaculture. According to a World Bank report from 2014, diseases in aquaculture account for productivity losses of approximately 6 billion USD annually. Since bacteria are major disease agents, excessive administration of antibiotics has been the most commonly applied strategy, especially in countries where legislatory framework on environmental issues is looser.
Taking the case of Vibrio pathogens as an example (eg. V. anguillarum, V. harveyi, V. splendidus, V. alginolyticus, V. parahaemolyticus): they have been named as the “scourge” of marine fish and shellfish. They are the causative agents of a fatal disease known as vibriosis (Figure 2). Vibrios often use live feeds as vehicles to infiltrate the marine hatchery systems, eventually leading to massive mortalities at very early stages of the process (Figure 3).
Figure 2. Massive mortalities caused by vibriosis in different developmental stages. a,b) cultured European seabass, Dicentrarchus labrax, c) cultured European seabass, Dicentrarchus labrax juveniles and d) cultured gilthead sea bream, Sparus aurata larvae in the hatchery. [Figure from Kalatzis et al., 2018]
Figure 3. Facilities for live feed production from a commercial fish farm unit. a) Artemia salina in culture tanks with vigorous aeration, where the naturally present presumptive Vibrio load is regularly estimated between 10^7 and 10^8 cells per mL; b) Brachionus plicatilis culture tanks, where the naturally present presumptive Vibrio load is regularly between 10^2 and 10^8 cells per mL. [Figure from Kalatzis et al., 2018]
Antibiotics that are applied in aquaculture (eg. oxytetracycline, florfenicol, tetracycline, flumequine, oxolinic acid, sulphadiazine/trimethroprim) are not different from those intended for human use. Hence, use of antibiotics in aquaculture raises serious concerns about the development of antimicrobial resistance (AMR), but also about antibiotic dispersal and dissemination among humans. In addition, antibiotics in aquaculture are administered through feed, and since sick fish have decreased appetites, a large fraction of the antibiotics end up in the environment. Here they can remain for years, leading to the disturbance of the natural microbiota in the water column and in the sediment.
Vaccination can be efficient in disease prevention in aquaculture, however there is a limited number of commercially available vaccines that address only a few of the bacterial diseases affecting fish in aquaculture. Further, vaccines cannot be used efficiently for disease control during the larval and fry (juvenile) stages of cultured fish, since their immune system is still in its infancy, and other cultured animals such as shellfish and crustaceans lack an adaptive immune system.
Phage therapy represents a promising alternative to antibiotics when it comes to bacterial disease control in aquaculture (Figure 4). The aquatic environment is one of the most common sources for isolation of phages against pathogens.
Figure 4. Major advantages of bacteriophage application in the battle against AMR.
The use of phages against pathogenic bacteria in aquaculture was first introduced experimentally in Japan against Lactococcus garvieae in 1999, and it has since been a topic of great interest for the aquaculture-related scientific community. Over the last 20 years, there have been numerous publications describing novel lytic phages that may be applied against bacterial diseases in aquaculture, none of them showing any side effects and all generally increasing survival of the phage-treated cultured organisms.
Phage therapy has been applied in various growth stages of cultured animals such as shrimps, lobsters, sea cucumbers, salmon, turbot, cod with promising results on pathogen control and survival of the cultured organisms. No side effects such as toxicity or stimulation of the immune system (antibody production) have been recorded. The situation in aquaculture is similar whenever phage therapy has been applied against other bacterial pathogens such as species of the genus Flavobacterium, Edwardsiella, Aeromonas, Pseudomonas, Yersinia etc., with numerous publications available in the literature.
Injection and immersion are common methods of administration, however, production of phage-coated fish pellets is considered to be the most efficient because it ensures the constant presence of high titer phages in the system via a daily feeding routine. In semi-closed systems like marine hatcheries where the renewal of the water is limited, deployment of antibiotics would disturb the natural microbiota. The reduction of potentially pathogenic bacteria populations that enter such fragile systems could be significantly reduced if phage-based disinfection of live feeds is embraced as part of the daily aquaculture management routine.
It is worth mentioning that the British company Fixed Phage has been quite successful when it comes to phage binding on different substrates, and its products can be customized according to each particular case.
A current EU-funded research project, BONUS Flavophage, led by Prof. Mathias Middelboe at the University of Copenhagen explores the possibility of using phage-coated feed to control Flavobacterium pathogens in rainbow trout aquaculture, where there are strong restrictions to the use of antibiotics and increasing concerns about AMR.
After intense sampling at 28 different fish farms (Finland, Sweden, Denmark, Poland, Germany, Latvia and Russia), a collection of 47 phages infecting Flavobacterium psychrophilum, 63 phages infecting Flavobacterium columnare, 119 F. psychrophilum isolates and 133 F. columnare isolates has been established. The objective of the project is to improve the sustainability, food safety, and productivity of aquaculture in the Baltic Sea region by developing environmentally-balanced phage-based strategies to control important Flavobacterium pathogens.
Very recently, ACD Pharmaceuticals launched its first phage-based product, CuSTuS®, which can be used for effective biocontrol of Yersinia ruckeri; it has so far been quite successful in Norwegian aquaculture. Proteon Pharmaceuticals has launched BAFADOR®, a phage cocktail that claims to target Pseudomonas and Aeromonas infections while stimulating the immune system of fish. Apart from these cases, there are no other phage-based products for aquaculture today in the EU.
Aquatic Biologicals is paving the way to sustainable disease prevention and biological control in aquaculture. It is the first marine biotechnology company in Greece and the first EU company that offers a full package of disease surveillance, management, control and prevention in aquaculture.
All aquaculture-related bacterial pathogens are present in the water, so the best way to avoid an outbreak is to keep their populations low. This reduces the likelihood that pathogens will take advantage of the cultured animals and the potential stressors that may occur under aquaculture conditions.
In line with The 2030 Agenda for Sustainable Development, which was shaped by the United Nations, the scope of Aquatic Biologicals encompasses four main sustainable development goals (SDGs):
Aquatic Biologicals is working toward these goals via three lines of action:
Overall, it is expected that the increasing focus on developing alternatives to antibiotics for disease control in aquaculture, including phage-based products, will reduce the use of antibiotics in this industry and contribute to developing a high-technology sector of sustainable, profitable farming with healthy and high quality animals.
Kalatzis, P.G., Castillo, D., Katharios, P. and Middelboe, M. (2018) Bacteriophage Interactions with Marine Pathogenic Vibrios: Implications for Phage Therapy. Antibiotics 7(1). pii: E15. doi: 10.3390/antibiotics7010015.
Kalatzis, P.G., Bastias, R., Kokkari, C., Katharios, P. (2016) Isolation and characterization of two lytic bacteriophages, φSt2 and φGrn1; Phage therapy application for biological control of Vibrio alginolyticus in aquaculture live feeds. PLoS ONE 11(3): e0151101. doi: 10.1371/journal.pone.0151101
For every issue of Capsid & Tail, we are committed to getting our facts straight, but we’re not experts in the information we’re bringing to you. If you feel that we’ve missed an important viewpoint, or if you have something to add, please reach out to us by emailing [email protected]. We’d love to hear from you, and we’d be happy to revisit topics we’ve covered (ideally with added information and viewpoints from community members like you!).
Lastly, please reach out if you’re interested in writing for us, or have suggestions for future issues!