Phages: Nature’s (very) tiny demolition teams

 

Okay, so as a result of me being the procrastinator that I am, everything that needs doing gets done in the mystical land of “tomorrow”. And so here we are, approximately eight months from the time our Phage Hunt at Massey University started (in July 2015)- and this is my very first blog post. It’s been on the “to-do” list for a while now, about eight months actually, and so we have already concluded our Phage-Hunting labs. The next step will be the genome annotation of the bacteriophages that were found by our class of 2015/2016, and this intriguing process will begin in about four weeks’ time.

To back-track a little bit, the existence of the wonderful world of bacteriophages was first brought to my attention in a Biology of Cells lecture at Massey University in 2014 which was given by Dr Heather Hendrickson. The idea of such tiny organisms in such a high abundance around the world was almost impossible to fathom at that point. And to be honest, it still is, even though I have seen the presence of phage while working in the lab and have even seen them “in real life” using an Electron Microscope.

For those people who haven’t come across Phages before, and for those people who need to refresh their memories because it’s been a while (erhm, me), here is a bit of an overview of the world of phages:

Diagram for Blog Post 1

As illustrated above, phages are a specific class of viruses and they infect only bacteria. To give you an idea about relative sizes, a bacterial cell can be anywhere between 1-5µm across, this is x10-6m which is incredibly tiny in relation to us. Phages then, being parasites of bacteria, are even smaller than this, about 100-200nm across, which is 0.1-0.2µm which is x10-9m. There is an interactive video here that might help put things into perspective, but do you understand now why I can’t always get my head around their existence? In terms of abundance, it is estimated that there is a total of about 1031 phages on Earth. That’s crazy right?

While the bacterial cells can be viewed under a microscope, bacteriophages are far too small for this. Instead, we observe the presence of bacteriophages by plating our chosen bacteria- in this case Mycobacterium smegmatis (the not-so-nasty cousin of the well-known Mycobacterium tuberculosis) which has been infected with phage. For those not so familiar with scientific processes, basically we use those stereotypical petri dishes along with a growth medium to cultivate the infected bacteria. The bacteriophages then make themselves known by producing ‘plaques’. These are holes, either perfectly clear or cloudy, in the so-called ‘bacterial lawn’ that we have grown. They are the spots where the phage has ‘eaten’ away the bacteria. The images below are an example of this, there are both clear and cloudy plaques produced by the spot tests. See how the spots are not all the same? This indicates that there is more than one type of phage present- cool huh?

Just as plaque morphology varies, so too does the morphology of the phage themselves. However, regardless of their morphology, the general structure (basic components) of the phage does not change. The image below gives you a closer look at these important features. And here is a rather dramatic animation of how the phages ‘eat’ the bacterial cells to form these plaques. Remember that what you see is happening on a MUCH larger scale since the individual bacteria are so small and there are MANY of them, hence the plaques are visible to the naked eye.

Phage Image 4

Image credit

After being bombarded with all of that information, I suppose the obvious question now is- why bother studying these tiny masters of demolition? Of what use could they be to us?

To answer these questions I think it might be a good idea to talk more about bacteria and bacterial infections. So, first things first- what are bacteria?

Well, bacteria are prokaryotes or single-celled organisms. They are very diverse and are found pretty much anywhere on Earth that you could possibly think of. As with bacteriophages, bacteria have varied morphology but have basic components that are common to all bacterial cells, and the image below illustrates these. Bacteria are able to grow at exponential rates, meaning that entire bacterial populations increase in numbers at a very rapid rate when they are in their preferred environment. This becomes a serious problem when certain bacteria infect plants, animals or people, and in many cases antibiotics (which kill off bacterial cells) have to be administered.

Phage 5

Diagram of a generic bacterial cell.

Image credit

As I mentioned earlier, we worked with Mycobacterium smegmatis in the lab, and this particular species is not pathogenic (disease-causing). However, it does belong to the genus Mycobacterium, which contains many known pathogens that are disease-causing in mammals, the most commonly known being Mycobacterium tuberculosis. M.tuberculosis is responsible for the deaths of millions of people around the world every year, and while these numbers have declined over recent years due to improved treatments and access to treatments, there is a constant threat of the TB bacterial cells developing a resistance to antibiotic treatments. (Click here to have a look at the WHO global tuberculosis report for 2015). Multidrug-resistant TB strains already exist and this is a cause for great concern, as it seems that new antibiotics are set to become a thing of the past (but more on this next time).

There is a solution to this problem though, and it’s called Phage Therapy. The basic idea is to use bacteriophages to treat bacterial infections, which would make perfect sense since their sole purpose is to find and ultimately destroy bacterial cells. It is a process that has been used at the Phage Therapy Centre in Georgia for the last 80 years, with varying degrees of success.

I intend to discuss this topic further in my next blog post, so keep an eye out for that in the next few days. But in the meantime, have a read of Sam’s story, a first-hand account of his experience with Phage Therapy- it’s very interesting indeed!

Until next time then,

Catherine 🙂

 

 

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4 Responses to Phages: Nature’s (very) tiny demolition teams

  1. Hey Catherine!

    Awesome blog post – thanks for summing up the course so far, great to have a bit of a refresher as it’s definitely been a while. A couple of the things caught my attention (in a positive way!) – one being when you showed us the photograph you took of your bacteriophage plaques post-spot test, what plaque did you end up choosing to progress forward with? As you mentioned “not all spots are the same” what made you decide to pick and purify the one you ended up choosing? Did anything about the plaque morphology jump out at you saying “pick meeee!” or was it just random?

    I’m also loving the phage video you attached, really puts it all into perspective! I remember Heather attached a link in one of her blogs http://htwins.net/scale2/ which is another cool little interactive diagram that shows phage all the way down at 10^-6m! As you say, it’s unbelievable how small they really are but how much of an important impact they can have in the biology world and beyond!

    Thanks again for a great read,
    Courtney 🙂

    • Hey Courtney,
      Thanks for your comment 🙂 Yeah, a refresher is always good to jog the memory!

      I ended up choosing spots 2 and 4, and eventually made the decision to go with just the phage from spot 2, which had a higher titre value. To be honest, the choice was mostly random- I wanted two with different morphologies to take forward and purify, but there wasn’t really a selection process per se. I guess maybe I have a subconscious preference for even numbers!

  2. drhhnz says:

    Hey Catherine! Great blog post. I just sent the link to your old pal Mrs. O’Sullivan at LBC for her class to check out before our PHAGE HUNT begins over there! I was interested in your venn diagram of phages in the world of viruses. I wonder what the real ratio of these is like? Have you seen any numbers for what the relative ratios of phages and viruses might be?

    Nice work!

    HH

  3. Hey Heather,

    Thank you! 🙂

    I hadn’t actually even given those ratios a thought when I drew the Venn diagram initially- I just used it to convey the message of where exactly phage fit in terms of our great big planet.
    But after some further investigation… I’ve found that while there are some estimates of the total virus abundance on Earth, there has yet to be an “educated” ball-park figure estimate made.

    Mostly, articles just quote “trillions” or “many billions” or in this specific post (http://phenomena.nationalgeographic.com/2013/02/20/an-infinity-of-viruses/), 10^31 where I think perhaps they misinterpreted the number of “phage” as the number of “viruses”.

    So in short, I guess the answer is no, I haven’t seen any concrete number to indicate what the relative ratios might be like… But I guess that is just reflective of the majority of ongoing microbial research, at the moment what we know is far less than what we don’t know, and so it is a field that is rapidly growing with vast potential for future research 🙂

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