Using the little things to tackle the big things: Can we use phages to impact climate change?

Issue 82 | July 3, 2020
11 min read
Capsid and Tail

Can phages be used to target bacteria in the rumen microbiome to reduce methane emissions and maybe save the world? (Images under Creative Commons from PixaBay).

This week, Jess Friedersdorff of Aberystwyth University in Wales tells us about her fascinating research into phages of the rumen microbiome.

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Urgent July 3, 2020

Urgent need for Staphylococcus epidermidis phages for a patient

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We are urgently seeking Staphylococcus epidermidis phages for a patient in the USA.

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What’s New

Eligo Bioscience was awarded funding from CARB-X to develop CRISPR-based phage therapeutics (up to $1.82 million now, and up to $7.05 million if project milestones are met). This is the first CRISPR-based phage project CARB-X has funded.

Biotech newsFunding news

The Academy of Finland has granted 10 million Euro for research into COVID-related projects, and part of that will fund phage work! Researchers at the University of Jyväskylä and University of Helsinki in Finland were awarded funding for a project on treating severe COVID-19 associated secondary bacterial infections with phage therapy under the Declaration of Helsinki.

COVIDGrant funding newsPhage Therapy

Hugo Oliveira (University of Minho, Portugal) and colleagues published a new paper in Applied and Environmental Microbiology showing that a phage tailspike with EPS-depolymerase activity, encoded by a phage belonging to a new genus within the Autographivirinae, makes Providencia stuartii (a nosocomial pathogen) susceptible to serum-mediated killing.

AMRAntibiotic resistancePhage TherapyResearch paper

Marta Lourenço (Institut Pasteur) and colleagues published a new paper in Cell Host and Microbe on how spatial heterogeneity in the gut limits phage predation and supports phage-host coexistence.

GutPhage ecologyResearch paper

Andrew Hryckowian and Eric Martens have written a nice article on the backstory behind their recent paper on how capsular polysaccharides influence phage interactions with the gut symbiont Bacterioides thetaiotaomicron. Behind-the-paper | Nature Microbiology article.

GutPhage-host interactionsResearch paper

Josef Prazak (Bern University Hospital, Switzerland) and colleagues published a new paper in Critical Care Medicine showing that prophylactically administering nebulized phages to rats with experimental ventilator-associated pneumonia reduced MRSA burden in lungs and improved rat survival.

AMRAntibiotic resistancePhage TherapyResearch paper

Bartłomiej Grygorcewicz (Pomeranian Medical University in Szczecin, Poland) and colleagues published a new paper in Microbial Drug Resistance showing that Acinetobacter baumannii phages could reduce biofilm biomass in a human urine model, and that some of the antibiotics commonly used in UTI treatment act synergistically with phage cocktails.

AMRAntibiotic resistanceBiofilmsBiotechPhage TherapyResearch paperUrogenital tract

Heather Hendrickson’s lab at Massey University in New Zealand is working on finding phages for honeybee pathogens. Here’s a nice video update from Heather, which also features Danielle Kok, a PhD student isolating the phages for this project.

Phage TherapyPhages for beesProject update

TAILOR, a non-profit initiative in Houston, Texas that provides therapeutic phages as a service, has a new website! Read more about TAILOR here!

Phage TherapyService center

Latest Jobs

Heather Allison (University of Liverpool) and Chloe James (University of Salford) are hiring two postdocs, one at Liverpool and one at Salford, for a joint project entitled “Prophage host interactions: pulling back the curtains on Pseudomonas puppet masters”.
Armata Pharmaceuticals, a phage therapy biotech company in Los Angeles, is hiring for several positions.

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!

IBRC Webinar July 9: Prof. Yves Briers

International Bacteriophage Research Consortium

International Bacteriophage Research Consortium (IBRC), created by Open Health Systems Laboratory (OHSL), USA and Acharya Narendra Dev College (ANDC), University of Delhi, India is organizing an online lecture by Prof. Yves Briers from Ghent University, Belgium on “From discovery to high-throughput engineering of phage lysins targeting Gram-negative bacteria”. Recently, Yves Briers and team have developed a brilliantly conceptualized high-throughput discovery platform ‘VersaTile’ an iterative approach to design, build, and screen engineered lysins. Yves Briers will be joining us from Ghent, Belgium on 9 July (Wednesday) at 5.00 pm Indian Standard Time (IST)/ 1.30 pm Central European Summer Time (CEST). We look forward to your participation. For registration, please click: https://bit.ly/3dWKrD4

LysinsVirtual Event

PHAVES is back on Tuesday with Dr. Elyse Stachler!

Phage Directory

Our virtual event series, PHAVES, continues this coming Tuesday, July 7 at 11:00 AM Eastern (GMT-4) / 5:00 PM Zurich (GMT+2). Dr. Elyse Stachler, postdoc at Eawag in Switzerland, will share her research into combining phages with disinfectants. After that, we’ll host a set of small-group breakout rooms so everyone can meet a few new faces in the phage field. Register here: https://seminars.phage.directory/

Phage DirectoryVirtual Event

Seeking research & networking opportunities

Abiola Olaitan

I am excited about moving to Canada and seeking research opportunities (academia or industry) in phage therapy in Canada. I am an early-career researcher with robust experience in bacterial antibiotic resistance and host-pathogen interactions. I plan to transition into phage therapy research at the interphase of microbial antibiotic resistance and virulence. I am currently seeking networking and research opportunities in academic or industrial institutions in Canada. Email: [email protected]

Seeking collaboratorSeeking opportunities

Seeking labs that have cultured soil viruses

Gary Trubl

Hey virus people! I would like to get a list of labs that have cultured soil viruses. If you are one or know one can you add to the list? Only the lab name & website are required. This resource would really help the community. RT — @gtrubl on Twitter

Soil viruses

Watch: All About Phage Therapy Episode 7

Vitalis Phage Therapy

In case you missed it, Pranav Johri of Vitalis Phage Therapy interviewed Jean-Paul Pirnay of the Queen Astrid Military Hospital in Belgium today on All About Phage Therapy. Watch the recording here!

Phage TherapyVirtual Event

Using the little things to tackle the big things: Can we use phages to impact climate change?

Profile Image
PhD Research Scholar
Aberystwyth University
Skills

Bioinformatics, Molecular Biology, Teaching, Phage isolation

Finishing up my thesis, looking for the next step. Hoping to apply for funding to continue researching the goldmine that is the rumen microbiome. The phage population is thought to be rich and diverse, yet we know relatively little compared to other microbes in the rumen microbiome. So many questions, so little time!

As someone embarking on a career in research and academia, I, like many other scientists, endeavour to carve a path I can follow and be passionate about. I have chosen the not-so-luxurious and rather foul-smelling rumen microbiome as the topic of interest. With this piece, I introduce this topic, list some of the questions that need answering, and hopefully convince you that, actually, the idea of using phages to help climate change might not be so far-fetched as it seems.

What is the rumen microbiome and why study it?

The rumen is the first chamber of the stomach system found in ruminants such as cows, sheep, goats etc. It is essentially a large anaerobic fermentation sack, home to a wide variety of microbes, including bacteria, archaea, fungi, protozoa and, of course, phages (and some other viruses). The microbiome is integral to the animal host, breaking down the fibrous grassy food to produce nutrients and energy. This is a complex process and has many variables, but ultimately ends with the fermentation processes producing CO2 and H2 which need to be dealt with.

This is where the archaea come in — methanogens are a hydrogen sink, taking these gasses and producing methane, which is eructed (burped) from the animal. Methane, as we all know, is a green house gas contributing to global warming. Whilst the archaea are therefore important, other bacteria, not so much.

Remember how I said that there are many variables? Well, the rumen isn’t exactly efficient, and depending on what you feed the animals, effects can be seen in not just methane production, but other wastes, such as nitrogen loss in the form of ammonia and urea, removed in the urine and polluting the fields they stand in. So, now you can see why studying the microbes and their functions might be important, especially taking into account the importance of ruminants in the future of the ever increasing human population.

What has been done before?

There has been ample research into looking for ways to control the microbiome to tackle methane emissions and efficiency, including feeding plant extracts, oils, antibiotics and many more. Phage therapy is one that always seems to be an aside, an “oh, by the way, this would be cool” addition to review papers. Yet, no one has really tried it, and there is very little in the way of publications on this. But this isn’t the only way that ruminants + phages = profit.

At this point, it’s possible to split research on ‘ruminants and phages’ into three parts:

  • Phages as a part of the rumen microbiome.
  • Using phages to treat or prevent pathogens in ruminants.
  • The prospects of phage use in the dairy and livestock industry.

Phages as part of the rumen microbiome

This review paper pretty much sums up all the rumen virome research done to date. Generally, more work is needed here, and there are still lots of questions to answer (I go on to list some below).

Phages to prevent pathogens

It seems like most ‘ruminants and phages’ research that doesn’t focus on the virome looks at phage therapy for E. coli O157:H7. Known to cause bad gastrointestinal infections (probably an understatement) and even death in ruminants, it is also problematic for us humans. This is often seen reviewed together with phages in the livestock industry, but there was some fascinating research in 2003 that used the artificial rumen system to test their phages.

Phages in the dairy and livestock industry

This review paper nicely sums up the points in the dairy processes where phages could be or are being used. Probably more research is done in this area than is published, as a fair bit may well be hidden behind patents because of commercial aspects.

Conclusions

I want to study phages in the rumen, with the ultimate aim of using them to target bacterial species that make CO2 and/or H2 (which are used to make methane) and those that use up nutrients that are otherwise good for the animal.

As a starting point, I can look into phages + livestock pathogens, and phages + dairy.

Which questions still need answering?

I am more interested in the microbiome part; understanding the role of phages, and using them to manipulate the microbiome to have wider effects. There are many things that we need to answer before we can start chucking phages into cow tummies.

  1. Phages have to be lytic, so which ones do we use? Do we have their genomes (probably important, right?)?

  2. Which bacteria do we target? What functions do they have? Have we looked at their genomes?

  3. What happens if we add phages into the rumen? How many? Do they ever meet their target?

  4. Does the amount of CO2 and H2 decrease? Does methane decrease? Is this more efficient/is there less waste?

Plea for help

Has this triggered that lightbulb in your mind? Are you dusting off some info from an article you read and stored in the back of your mind? Or just have a bunch more questions? Please get in touch, I’d be intrigued to build this idea!

Papers linked in text:

My rumen phage publication can be found here:

The Isolation and Genome Sequencing of Five Novel Bacteriophages from the Rumen Active Against Butyrivibrio fibrisolvens


Rohit Kongari helped us produce this week’s article by helping us source and write the What’s New section. Thanks Rohit!!

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Email [email protected].


July 4, 2020
Update: we added the message about IBRC’s upcoming webinar with Yves Briers to the Community section; this post was mistakenly left out of the version sent out July 3.

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