A phage by any other name would smell as sweet – The trials and tribulations of naming your phage

If you’ve ever wandered into the clearance section of your local bookstore I’m sure you’ll have seen at least one book about baby names. Titles like “100,000 Baby Names”, “Cool Names for Babies” and the “The Baby Name Wizard” offer parents with seemingly endless ideas and options for choosing the perfect name for their little bundle of joy. Parents can spend months trying to settle on the right name for their child, and who can blame them? After all, a person’s name can affect how they are treated and perceived, impacting their interpersonal relationships, self-perception, and even their career. 

Naming can be quite a stressful affair.Though I have never had a child of my own, I found myself in a similar situation only a few weeks back when I was trying to find a name to call my phage.


Let me explain: For the past semester I have been involved in the SEAPHAGES Phage Hunt at Massey University. Bacteriophages (or phages) are viruses that infect bacteria, hijacking their cellular functions and forcing the bacteria to manufacture more and more virus particles until they lyse the bacteria and break out – ready to start the cycle all over. It’s like a tiny microscopic version of Ridley Scott’s Alien.

As a part of the Phage Hunt Program we collected soil samples to try find phages that infect Mycobacterium smegmatis, a close relative of the tuberculosis bacteria. The hope is that perhaps these bacteriophages could be used to kill these bacteria and treat diseases.

The process was a great learning experience where we got find phage, purify the tiny microscopic viruses, and even extract and analyze their DNA. And the cherry on top: we get to name our very own phage! This was the part I looked forward to the most, what an honor!


Created by Digital Micrograph, Gatan Inc.

This is my phage Daegal. Isn’t he just ADORABLE?

Now perhaps I was just naive but I didn’t expect the very first step of the process, finding a phage to be so hard. Despite searching in very many samples (including those from areas where others had found phage), I found not a single phage. Weeks went by as my classmates found phage after phage, and I grew more and more envious. By the time I finally adopted a phage from one of my friends I was determined to keep it alive and give it the best name I could possibly find.


The only thing is, naming is harder than you’d think. Especially when you have to think of name no one else has thought of. Unlike a human child, the phages registered as part of our hunt – on the PhagesDB database – could not have the same name as another. If there was already a phage named Brittany, that name is completely out of bounds for your phage. This makes sense, as every species should have a distinct name in order to avoid confusion. Still it is awfully disappointing when your phage, who is clearly a Marcus, has to be named something else. As a result, I scoured PhagesDB to see what names were still available, and I was surprised by what I saw.



In the description of each phage, there is a section in which a hunter could explain why they named the phage what they did. As I curiously scrolled through the names, some of the explanations were surprisingly heartfelt. There was no shortage of phages named in honor of children, family, mentors and beloved pets. Names reflected the friendships forged between partner phage founders, honored significant events, and gave a curious insight into the phage hunters themselves. My favorite description was that of the phage “NoodleTree”: In the words of one of the phage discovers “I come to school to grow my noodle.” From a choice of name alone, you can get a snapshot of the friendship between phage hunters. You can read about this and many other great phages at PhagesDB.


This made me wonder, what makes a person name their phage what they do? And what does that say about them? In speaking with my classmates, they seemed to feel a sense of responsibility and privilege in choosing a name. My classmate Jo – who named her phage after a Grandmother who she never really got the chance to know as an adult – explained it in a way that seemed to resonate with how I felt. She said this might be our only ever chance to do something like this, name our very own species and leave our mark on the scientific world. We had worked so hard to get here, it would make sense that we would want to choose a name that was meaningful, carefully chosen, and would hopefully inspire in others the same interest in our phage that we had. Though I’m sure the phages couldn’t care less what we call them, what we call a phage often means a lot to us. And when you’re naming a creature you’ve never even seen with your bare eyes, it says a lot about you too.



Posted in Uncategorized | Leave a comment

The Viralcoaster: My highs and lows

Wow, we are at the end of a semester already!  I don’t know about the rest of my class, but I have been left wanting.  Despite all the time, effort and experience that has been packed into these last 14 weeks, all I want to do is keep coming into the lab and playing with my phage.

There’s something about this ‘choose your own adventure’ styled course that has gotten its hooks into me (or perhaps that’s just a wayward podovirus [1.]).  One of my absolute favourite parts of this journey has been designing or modifying my own experiments to characterise my phage, and I just don’t want to stop!

My hunt for phage began with a stubborn determination to shirk the easy route, the obvious choices.  For the first three weeks I was tramping through our beautiful (and muddy) native bush, picking my way across equine graveyards, and coming perilously close to falling into multiple lakes, all in the quest to conquer the challenge I set for myself – finding a phage somewhere other than a compost bin.  I should have paid more attention to the obvious facts: bacteria love compost, and phages love bacteria.

Eventually I caved, and I get a kind of sentimental warmth from knowing that my phage came from the location-that-shall-not-be-named of my darling mum, an avid gardener.  Not only did my search end somewhere symbolic of my mother, but the name I chose for my precious virus came from my father’s mother.  Both women are actually named Colleen, but my Nana was always known by her middle name, Dulcie.  We lost her when I was a teenager, and I think it’s nice that I’ve taken this opportunity to connect to her a little more in my adult life.  She wouldn’t have given a toss about bacteriophages, but she would have appreciated the thought.

nana photo

I know what you’re thinking: the resemblance is uncanny.


After finally hitting the jackpot with plaque assays that I tend to compare to swiss cheese, I proceeded to isolate and process my phage samples ready for the next stage of our adventure.  I started off isolating two phages, before abandoning one to focus my attention on Dulcie.

plate photo for blog

From discovery…                                  to isolation…                                      to amplification


Once I had isolated my phage and achieved a high-titer lysate to work with, I proceeded to extract dear Dulcie’s DNA and take a look at it using restriction enzyme digests and gel electrophoresis.  I was pretty stoked with the concentration of DNA in my fourth and fifth rounds of extraction, in which I used a spun-down sample of my lysate.  Those concentrated samples yielded an average of 250 µg of DNA per mL, six times more concentrated than previous extractions.  I had more DNA than I knew what to do with!

My first attempt at gel electrophoresis didn’t go so well, with some degradation of the DNA occurring due to over-enthusiastic nucleases [2].  Use of EDTA solved that smudgy little problem, and the next gel I ran had me dancing on the spot when I saw the photo:

copy for blog Dulcie gel electrophoresis labelled

Dulcie’s DNA following restriction enzyme digest and gel electrophoresis


From there, life in phage lab has been all about figuring out which experiments I wanted to run to distinguish Dulcie from other phages, and waiting for the much-anticipated trip to view ‘her’ using transmission electron microscopy.  Memories of that visit will have me smiling for the rest of the year; not solely due to the experience, but also the recollection of four grown-ass independent young women reduced to squeals, ‘ooh’s ‘aah’s and ‘whoa’s with each image that popped up on the monitor.

Created by Digital Micrograph, Gatan Inc.

Can you blame us?  Lots of little Dulcies is pretty phagin’ cool!

In the remaining weeks of semester, I have been putting Dulcie through her paces.  We’ve been testing whether she can switch to the lysogenic cycle (still not sure on that one, our tests were inconclusive), how hot she likes her spa pool (apparently 50ºC is just the ticket), and also just how viral a virus she is.

We are just about to send our DNA samples away to be sequenced under the SEA-PHAGES program, so the next exciting chapter will be finding out what her genome looks like.  Until then, I’ll be spending my time gazing wistfully out the window and daydreaming about that one time, in phage lab…


[1]  Aksyuk, A. A., Bowman, V. D., Kaufmann, B., Fields, C., Klose, T., Holdaway, H. A., . . . Rossmann, M. G. (2012). Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry. Proceedings of the National Academy of Sciences, 109(35), 14001-14006.

[2]  Nishino, T., & Morikawa, K. (2002). Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors. Oncogene, 21(58), 9022-9032.


Posted in Uncategorized | Leave a comment

Super Bugs.

I was stumped as to what to write my blog about so I rang my sister who is studying medicine and asked her if she could give me any inspiration. We proceeded to chat about antibiotic resistance and discussed a news article from the weeks news. In this article, they talked about the bacterium MRSA which interested my sister as it is a bacterium in hospital that she regularly encounters. MRSA stands for Methicillin-resistant Staphylococcus aureus which is a strain of bacteria that is really difficult to treat in humans which she mentioned. The patients that are infected with this bacteria have to be screened and placed in a separate ward. The doctors and nurses working within these wards have to wear full safety gear to avoid contamination. To me, this seemed like extreme measures for a media exaggerated scare mongering superbug.

Following the talk with my sister I went on to do some research on common superbugs, namely MRSA. Antibiotic resistance is arguably the greatest threat to human health in the twenty first century. These bacteria have mutated and developed to become resistant to most or all antibiotics. Staphylococcus aureus the common original strain of the mrsa bacteria and is not always pathogenic.[1] It can be the cause of abscesses on the skin, skin infections, food poisoning and respiratory infections. This was first being treated in the 1940s with penicillin and 1950s it became more common. In 1961, we began using Methicillin to treat these resistant strains and within only a year of usage, resistant strains started to appear. These days MRSA is resistant to a large list of antibiotics including Vancomycin which is often considered a last line of defence. [2]

MRSA is carried by 30% of the population and is often found in areas such as under the armpits and around the groin.[2, 3] It only becomes a problem once it has penetrated into our skin. MRSA now contributes to more US deaths than HIV. 2] Resistant strains of bacteria is beginning to gain attention in the media.  The media label them superbugs and MRSA has appeared a number of times in the news this last month. There was a report that had findings from a study regarding hospitals screening for the bug.[4]

How does bacteria that causes a minor skin infection to start with become so scary. Media often refer to the superbugs as having developed or learnt to evade our bodies but infact it has evolved.[4] Bacteria can evolve quickly due to their short reproduction time and large population size. Despite the medias apparent scare mongering, antibiotic resistance is still a serious issue with around 700,000 dying worldwide due to this resistance. This number is only set to rise with an estimated 10 million fatalities annually by 2050. [5] Research and figures are scary but they highlight the importance of programs such as the one I’m involved. Phage hunt is a paper I take that aims to assist with the effort to find alternatives to antibiotics. Phage Hunt works to find bacteriophages that are able to destroy bacteria. Many strains of bacteria have become resistant to antibiotics and the bacteria that haven’t will soon become resistant with their rapid evolution.

In our lab we work with Mycobacterium Smegmatis which is similar to mycobacterium tuberculosis. I began to wonder if bacteriophages had had any success in the case of MRSA. I do not have to look far to find heaps of positive research that demonstrated using bacteriophage to successfully kill MRSA. One example was a student from Brigham Young University who had a keen interest in MRSA after his father had lost his leg due to the bacterial infection. The student was using a methods that was similar to the the ones we were using in our lab and  he was able to find six unique bacteriophages that could kill off MRSA cells and his research is continuing to find more.[2]

Other studies even incorporated phages with traditional antibiotics. [6] Continuing research in this field has exciting prospects with making a real difference in the fight against antibiotic resistance and bacterium superbugs.




  1. Staphylococcus aureus.
  2. New method to treat antibiotic resistant MRSA: Bacteriophages. Science daily, 2015.
  3. ChB, D.A.S.M., Methicillin-resistant Staphylococcus aureus. 2015.
  4. Superbug, super-fast evolution. 2008.
  5. Rise of the Superbugs: How is Biotech Fighting Antibiotic Resistance? 2017.
  6. Sandeep Kaur, K.H., and Sanjay Chhibber, Methicillin-Resistant Staphylococcus aureus Phage Plaque Size

Enhancement Using Sublethal Concentrations of Antibiotics. American Society for Microbiology 2012. 78(23).


Posted in Uncategorized | Leave a comment

The Search for Mahuika

Tēnā koutou katoa.  Ngā mihi nui anō ki a koutou, ki ngā manuhiri o taku pae tukutuku.

Welcome everyone, again to my blog.

In this post I will be sharing with you some of the mahi – work, that I have been doing through Massey University, as well as intorudce you to my phage friend, Mahuika.

What did we learn last time we explored Te Ao o ngā Huakita me ngā Huaketo – The world of Bacteria and Viruses?

  1. Our health and enviornment can be affected by bacteria in good and bad ways
  2. Antibiotic resistance occurs, when BAD BUGS are immune to antibiotics
  3. Bacteriophages are viruses, that infect and kill bacteria

As we learned last time, bacteriophages are EVERYWHERE and they are very useful in treating bacterial infections.  This is an area that many scientists and medical professionals are reyling on, to provide an alternative to antibiotics.

To find an alternative, we must find or HUNT for new bacteriophages. They must possess the ability to infect and kill the types of bacteria that are infecting us.  This is why I joined the course at Massey University called The Phage Hunt.

In this course, a group of young, ambitious scientists joined forces in the lab; to discover, purify and sequence, undiscovered bacteriophages.

Photo on 6-2-17 at 12.09 PM #2 2 (1)

The Phage Whanau

How do you hunt for viruses that infect bacteria?

We look in places where there is a lot of bacteria!  For example taepu – soil.

My hunt began by collecting soil samples from my backyard, the beach and compost bins.  I  found a number of phages in the University compost bin!

How do you know that you have found a phage?

You add a phage sample to a plate (like the one pictured), that contains bacteria cells. Leave them over night and they form small clearings, called plaques.  These plaques are areas when the phage has infected the bacteria and killed them, leaving a clear spot on the plate.


Plaques on bacterial plate 

As seen in the picture, there are different sized plaques that have different morphologies (characteristics, i.e. cloudy or clear).  This means that there are different bacteriophages present.  From this plate I managed to purify three different phages.  Two of these phages were whangai – adopted out to other class mates, and I kept one to work on further.

The Phage Hunt course allows you use an Electron Microscope to get images of your phage and you get to name your phage.

So, I present to you, Mahuika.

Screen Shot 2017-06-02 at 9.38.04 PM

My phage, Mahuika

Mahuika is about 315 nanometers long.  That is 0.00035 of a millimeter.

He tino iti – very small!

The capsid contains the phage DNA.  The tail fibers allow the phage to recognize and attach to their host bacteria.  The tail allows the phage DNA to infect the host bacteria.  Mahuika’s sister phages that were adopted out are named Mooo and Naira.

Click here to have a look at the Phage Data Base

Why did I name my phage Mahuika?

Mahuika is the Māori Goddess of Fire.  She is the wife of Auahitūroa and the teina – younger sister of Hine-nui-o-te-pō.  Some of you will have heard about the Goddess of Fire from the pukapuka – story, about how Māui brought fire to the world; or maybe I should say tricked Mahuika and stole her fire!

Mahuika and Maui

Mahuika is not impressed by Māui (1)

*Tsk tsk tsk*

Here is a short version of the story.  Māui was curious about where fire came from.  So one night, he put out all the fires in the pa – village.  In the morning his mother Taranga, sent Māui to the ends of the earth to find Mahuika in the maunga – mountain of fire where she dwelled.

When Māui arrived he asked Mahuika for her fire to take back to the tāngata – people of the world.  She gave him one of her nails which contained the fire.  Māui left with the fire but thought to himself, what would happen if Mahuika didn’t have any fire left?  Where would she get more fire from?  So Māui threw the nail into a near by stream and  then returned to Mauhika’s maunga-mountain.


Mahuika giving her fire to Māui (2)

Maui then lied to Mahuika and said that he accidently dropped the first nail and needed another.  She gave him another one, but Māui also threw that one away.  Māui continued this nonsense, until Mahuika only had a few nails left.  When she realized what Māui was doing, she became very angry!  She threw one of her nails at Māui and a wild fire exploded around him!

Māui fled from the mountain, into the forest.  The wild fire followed him and hit the Mahoe tree, the Tōtara, the Patete, the Pukatea, and the Kaikōmako trees.  Unlike Māui, the trees knew that Mahuika’s fire was a great gift, and so they grasp onto the fire.  When Māui returned to the pa – village, he brought with him dry wood from the trees to show the villagers how to start a fire by rubbing together the wood.

That is the pukapuka – story, of how Māui brought fire to the world.  This is one of my favorite stories of Māui’s adventures.



Although, this story doesn’t exactly relate to bacteria and viruses , I once read an account of an old koro (elderly man) exclaiming “E hika! Ko Mahuika koe!” (Oh my! You are Mahuika!) when he was shown a radio for the first time.  I do not think he meant that the radio was the Goddess of fire, or that it was going to burst into flames, rather it surprised and intrigued him.  This is how I felt about by phage!  Surprised and intrigued by the complexity of such a simple biological particle.

In addition, Māui’s curiosity is the same kind of curiosity that I feel when I think about Te Ao o ngā Huakita me ngā Huaketo.   Albert Einstein once said “I have no special talents; I am only passionately curious.” For me being a scientist simply means being curious enough and bold enough, to ask questions.

Māui’s curiosity lead him to Mahuika, just as my curiosity lead me to my phage.  This is why I named my phage after the Goddess of fire.  However, I do intend to treat my Mahuika better than Māui treated his.

Nō reira – therefore

Until next time whanau, think about what intrigues you?

Are you curious enough, like Māui or like me, to search for your Mahuika?

Ngā mihi ki a koutou – thank you all.

Ka kite anō,

Anezka Hoskin



  1. Mahuika and Maui. Retrieved from https://sugarskulldragon.tumblr.com/post/156147644096/making-a-disney-reference-with-other-disney
  2. Amber Stotts (2007). Maui and Mahuika.  Retrieved from https://www.amberstottsart.com
Posted in Uncategorized | Leave a comment

Fenn the Phage

As I mentioned in my last blog, at the beginning of this semester I found a phage that infects the bacterium Mycobacterium smegmatis. My journey with my phage, who I’ve named Fern, has been interesting and filled with many unexpected twists and turns.

Everything began back in March when we were collecting environmental samples. I collected a LOT of environmental samples, a grand total of… 40 samples. I was told compost bins are a good place to find them, so to compost bins I went… mine, my friend’s, my friend’s Grandma’s. Nothing. I continued trying in the garden, ponds and streams. Still my plates were free of plaques. Eventually, from a sample from the soil from on top of our old garage door that had been lying in the vegetable patch, I found a plaque, and not just one, I found 3 differently shaped plaques! The picture below shows this very plate with some plaques that have been circled. A plaque is a circular clearing that forms on plates due to a phage infecting the bacteria on the plate. If you’re interested in more information about how phages form plaques on plates click here [1].


Photo of direct isolation plate

Unfortunately, a few labs later I was back to only one phage (the other two did not survive the phage buffer).

The plaques of the surviving phage seemed to have quite a range of different morphologies. Some were completely clear, while others had cloudy rings around the outside and some were small, some medium and some large, as you can see in the photo below. Plaques of one phage tend to have plaques with the same morphologies so I was cautious that I may have had multiple phages. However, multiple morphologies continued to be the case even after purification so I assumed that I had purified my phage.

10-3 serial dilutions 2 24:3

Photo from phage purification showing different plaque morphologies

A few weeks later we were extracting the DNA of our phage. I was very lucky and miraculously I only had to do it once. I was so surprised that something actually worked the first time as this was not my experience of phage lab so far. Some of this DNA will be sent off to the University of Pittsburgh to be sequenced!

One of my favourite parts about this journey was when I got to see my phage! Phages are way, way, way too small to see with the human eye. Fern has a head of about 62 nm and a tail of about 137nm. That’s 0.000137 mm! To see that small, we need an electron microscope. We went to the electron microscope at Auckland University and saw our phages. This is what Fern looks like…


Fern the phage from the electron microscope

As you can see from these pictures the phage has a head and a tail. The head is covered by a capsid (a protein shell) and contains the DNA [2]. The tail is the part that attaches to the bacterium, pierces the bacterium then passes the phage DNA into the bacterium [3].

Near the end of the semester I was ready to explore more characteristics of my phage and I decided that burst size would be interesting. The burst size is the number of phages produced when a bacterium is infected by a phage. If you want to find out more about burst size click here [4]. I was modifying a protocol for a different type of bacteria using a lysate with a different concentration of phage so there was some guessing and trial and error involved. The first time I tried this experiment the concentration of my phage lysate was way too high and I couldn’t see anything. When I tried again I got the concentration right. However, I did not do the experiment for long enough.


Plate from burst size experiment showing the two morphologies: small and large

Although I was unsuccessful in establishing the burst size I discovered something very interesting … I had two distinct plaque morphologies. Could there still be two phages? There were two distinct morphologies: small and large. So, did I ever purify my phage properly?

My first reaction was that there must be two phages. To try to figure this out I picked all the different plaques morphologies (large, small and cloudy or clear) and plated them separately. The new plates all showed small plaques, all with similar morphologies. This lead me to believe it was only one phage and why this was happening was still a mystery.

Next I thought maybe it had something to do with the age of the bacteria culture as this had only started happening later when the bacteria were older. However, after plating with both old and new bacteria I saw no difference, so it wasn’t this. Further confusing me, this time there were no small plaques. There could be so many reasons why this is happening… rapid mutations, the time at which the phage infects the bacterium and I’m sure many more things of which I’m unaware, but currently it’s still a mystery.

This course has shown me firsthand how in the real world everything doesn’t fit into the categories and rules we often try to make in science. It’s a lot more complicated than that. Currently no one knows why my phage is making two different morphologies sometimes and that’s amazing. It really reminds me of how much we don’t know and how much there is to still discover.


[1] Microbial Genetics (2002). Phage Plaques. Retrieved from: http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/phage/plaques.html

[2] Orlova, E. V. (2009). How viruses infect bacteria? The EMBO Journal28(7), 797–798. http://doi.org/10.1038/emboj.2009.71

[3] Ecole Polytechnique Fédérale de Lausanne. (2016). How viruses infect bacteria: A tale of a tail. ScienceDaily. Retrieved from http://www.sciencedaily.com/releases/2016/05/160518133816.htm

[4] S. T. Abedon. (n.d) Burst Size. Retrieved from: http://www.archaealviruses.org/terms/burst_size.html

Posted in Uncategorized | Tagged , , , | Leave a comment

The adventures of a budding scientist and her so-called bacteriophage.

Welcome back.

My relationship with phage lab is one of much uncertainty. One thing I am certain of is that it is testing my usual calm and positive attitude towards life. Science is very much like that and if I want to continue my work in the field of science I shall just try and get used to it. It can be frustrating and tedious and challenging.  Phages and success in phage lab seems to avoid me at me at all cost. If you have read my last blog, you will know that I haven’t had much luck with phage lab but after I had gathered a lysate from my phage I hoped my luck would change.



Bacteria Gifts

DNA extraction is the next step of phage lab and possibly the most tedious, closely rivaling direct isolation. DNA is a molecule that carries our genetic code and in order to find out more about the phage I had finally we had to extract the phage’s DNA. DNA provides all of the information you could ever want from an organism. A protocol similar to what we followed can be found here. [1]

Luck continued to evade me and for some unexplained reason I could not find my phages DNA to save my life. I had to repeat the DNA extraction protocol 6 times in order to find enough DNA to move on to the next step. The first reading I got was so low that there wasn’t even any point in keeping the sample. The process takes around an hour of continuous work and so it wasn’t the easiest protocol to follow but by the end of this stage I had all but memorised it. The next time I got another low reading and I was thinking ‘oh no, here we go again’. I thought I had gotten passed the unluckiness that plagued me but alas it had reared its ugly head again. I ended up having to spin my lysate (the liquid that contained my bacteriophages) so that the phages concentrated at the bottom in order to get a greater concentration of the bacteria. Thankfully the next time I did DNA extraction I got a much larger concentration of DNA but I still had to end up doing it three more times.

I had gotten to the stage where I had almost had enough DNA to take to the next step and then suddenly a whole tube of DNA appeared one day in lab. I had labelled the tube as being DNA but I had no record of it in my log book nor did I know where the heck it had come from. If this DNA sample was actually DNA then I would have more than enough DNA to take to the next step and wouldn’t have to go through another round of extraction which had become mind-numbing at this point. I ran the DNA on a gel which would tell me whether or not I had DNA. An in-depth explanation of this step can be found here.[2] Somehow my sample that had come out of nowhere was DNA and good DNA at that.


This is “Mooo”.

We got to see our phages through an Electron Microscope which was awesome as its really hard to see any progress when working in lab because you can’t see your phage and so to see it in real life was rewarding. The Electron Microscope we used cost over half a million dollars and so I was almost too scared to touch it, knowing how clumsy I am.

I tend to be a person who doesn’t follow the recipe book exactly while cooking and so there may be too much of one thing and not enough of the over. This doesn’t really matter when it comes to cooking but when it comes to science it is a bit of a problem. Following a protocol exactly how it is lined out in the book is really important because accuracy is key to success in science. I struggled with this precision which lead to many mishaps and mistakes made. It would seem that maybe science wouldn’t be the thing for me due to my clumsy nature and inability to precisely follow a protocol. Things are not always as they seem and I’m here to show you that even clumsy people can eventually make fabulous scientists.

The next step of phage lab now is to sequence the DNA of our bacteriophage. I have named my phage “Mooo” which is fitting as its appearance is short and stubby, kind of like its founder! Science requires one to be persistent and to just keep going and that is exactly what we had to do. It challenges you in a way that can make you question your sanity and even though it may not seem like it, everything will turn out okay in the end. It’s a fickle business but getting through the lab work and being able to see what we achieved in the end makes it all worth it.

Things can only improve from here, surely.

See y’all in the next instalment of this scientific adventure.



  1. Gill, J.J., Gill: Phage Genomic DNA extraction 2015.
  2. Addgene, Agarose Gel Electrophoresis.


Posted in Uncategorized | Leave a comment

The Beauty of Science

When I hear that “scientists are working on a new weight loss treatment”, or “scientists have found that that bacteriophages can help fight the war against antibiotic resistance”, I don’t really think twice about what goes into these research projects. It’s only once I started doing my own inquiry-based lab work that I started to understand some tunnels seemed like they had no light at the end, and how much blood, sweat, and tears accompany the satisfaction of progressing in science.


I took part in the SEA PHAGES program, an international university course that allows you to discover viruses that kill bacteria in some dirt that you collect, purify them and name them, then rip the DNA out and send it through enzymes that chops it up into little pieces so you can examine your “phage”.

Sounds reasonably simple, right?

Well, I collected eight samples, and found no phage at all. Nudda. It demotivated me to keep going, but I would’ve failed the course if I didn’t collect more.

Wrong mind set, I know.

The next soil sample had amazing results: the phage had eaten all of the bacteria I had fed it! I was pretty stoked. But, after I started purifying and pulling the DNA out of my little phage (I called it “Mushball”, after my nickname), problem after problem occurred. When I added enzymes to cut the DNA, my DNA was gone.

That’s when the opportunity arose. I repeated the whole process, changing up little things in the hope that I got something. I ended up repeating it at least seven times, with the last time was the best result I could’ve got! I was ecstatic. So much frustration and perseverance had finally paid off, and the light at the end of the dark tunnel shone bright for me.

Science takes many turns that you would never have expected, and no matter how many repetitions you do, or how closely you follow the protocol to a “T”, you can never avoid a sigh of disappointment, a cry in the bathroom, or a broken piece of equipment you just threw at a wall. You begin to accept this, which makes it so much more exciting!

Who wants to discover something that does exactly what you expect it to?

“We learn wisdom from failure much more than from success; we often discover what will do, by finding out what will not do; and probably he who never made a mistake, never made a discovery.”

Samuel Smiles

That’s the beauty of science.


Posted in Uncategorized | 1 Comment

Seek and you shall NOT find.

Bacteriophages are viruses that infect bacteria. They are highly abundant and were discovered around 100 years ago but there unrealised potential is only being discovered now. In the future, bacteriophages may have the possibility to advance health care and medicine, especially when it comes to the antibiotic resistance crisis. This is why they are of immense interest to the scientific community as they could revolutionise modern medicine. Antibiotic resistance is becoming a huge problem in the modern world as illnesses and infections cannot always be cured by antibiotics now. Phage therapy is an alternative to using antibiotics and could be used to save millions of lives. In the United States alone, more than 23000 people die every year due to antibiotic resistance.[1]  If you want to find out more about phage therapy, you can do so here.[2]

Bacteriophages are the most abundant organism [3] on the planet and so there are potentially millions of bacteriophages in a compost bin and yet they all evade me. Taking environmental samples to find bacteriophages is the first step to phage hunt. This shouldn’t have been that hard considering that there are trillions of bacteriophages in a garden let alone around the world. I thought that this would’ve been the easiest step but I was so wrong. It was so much harder than I thought as I took 27 soil samples from locations around the North Shore and didn’t find a single bacteriophage. I collected the samples in batches of 10, each round taking about an hour to finish. I looked in compost bins and gardens and worm farms and streams and paddocks hoping to find these elusive phages. I started to think that we had been told wrong as these things that we were searching for were mean to be in such high abundance that it should’ve been easy to find them. By the end of it I was sick of collecting samples in plastic tubes only to find out after the first round of processing and plating that I hadn’t found anything. Links to some of the protocols we followed can be found here and here. The second link is similar, but not identical, to a protocol that we followed.[4, 5]

I was considered the unluckiest phage hunter in our lab by our supervisors, sampling for a solid three weeks with no phages found after first round processing. Some of my co phage hunters were lucky enough to find phages in their first round of samples and yet they remained in hiding for me. The graphs show the number of environmental samples taken before people found or adopted a phage. The positive graph shows those who found phages and the negative, obviously, shows those who were unsuccessful at finding phages. There didn’t really seem to be any relationship between finding a phage and the number of samples taken. It seemed to come down to a bit of luck and looking in the right places.

Negative phagepositive phage

The phages we were looking for were ones that infected the bacteria Mycobacterium Smegmatis. If the phages infect Smegmatis then they also have the potential to infect Mycobacterium Tuberculosis. M.T is a close relative to M.Smeg and so there is the hope that our experiments and research could lead to finding a phage that could be used in fighting Tuberculosis. It could potentially save the lives of millions of people and help improve modern medicine and move past the overuse of antibiotics. With antibiotic resistance becoming an ever increasing problem in our world, this kind of research can possibly contribute to the ongoing scientific research of bacteriophages. The diversity and abundance of bacteriophages is immense and so there is still so much to learn about them and the possibilities they can bring.

Mycobacterium Smegmatis is said to be found in places with lots of nutrients / water sources which is why I looked in places that had an abundance of one and or the other. I collected all of my samples from places like this and hence my confusion and frustration when I didn’t find any!

Due to my inability to find phages, I had come to the end of a month of searching with no success. I was lucky enough to adopt a phage from my friend. She had managed to find three in one sample. Things were going great and by week six I was up to making a high titre lysate of my tiny little phage. A link to what protocol we followed can be found here. [6]  I was beginning to think that I might have gotten a handle on phage lab but as always I managed to lose the phage I had adopted. I had nicknamed my phage “Moppet” as it formed small plaques. My phage was not surviving in phage buffer so I had to go and adopt another phage from one of my other amazing co phage hunters. This meant that I had to redo the webbed plating and making a high titre lysate processes. It may have taken a long time to get to this stage but I got there in the end and had found a bacteriophage.

Hunting for bacteriophages is a tricky business but once you find a phage that you have spent tedious amounts of time finding and purifying and amplifying it all becomes worth it. While my hunt for phages didn’t result in finding my own phages, I was still able to come out with a phage that will hopefully see me through to the end and you can’t say I didn’t try.

Stay tuned for the next instalment.


  1. Antibiotic Resistance Threats in the United States, 2013.
  2. What is Phage Thearpy.
  3. Martha RJ Clokie, A.D.M., Andrey V Letarov, and Shaun Heaphy, Phages in nature. Bacteriophage, 2011 Jan-Feb.
  4. Biosciences, B., Plaque Assay
  5. Trevor Cross, C.S., Dylan Chudoff, LIbby Graves, Haley Broomell, Katrina Terry, Jennifer Farina, Alexandra Correa, David Shade, and David Dunbar An Optimized Enrichment Technique for the Isolation of Arthrobacter Bacteriophage Species from Soil Sample Isolates.
  6. Phagesdb, Manufacturing a high titre lysate.


Posted in Uncategorized | Leave a comment

Antibiotic resistance and what we can do about it

Something that has really struck me this year is learning about antibiotic resistance. It is such a widespread issue that affects every single one of us.

So, let’s start at the beginning…

What are antibiotics?


Antibiotics are widely used in the western world and most of us will have used antibiotics at some point in our lives. Antibiotics are great for many reasons, they are both convenient and effective. They prevent and treat bacterial infections by killing bacteria and can be taken in 5-7 day courses [1]. Before the times where antibiotics were widely used, people could die from something as small as a cut getting a bacterial infection. So, if they’re so easy to use and great at their job then what’s the problem?

What is antibiotic resistance?

Antibiotic resistance is the growing problem of bacteria becoming resistant to antibiotics. This happens because bacteria generally have a fast generation time, meaning the time it takes to asexually reproduce another generation is a short amount of time. Due to the fast generation time and large amount of offspring, mutations happen often. Sometimes the mutations may make the bacteria resistant to the antibiotics and therefore they will survive and continue to reproduce making a whole lot of antibiotic resistant bacteria. These bacteria then can’t be killed by such antibiotics.

This is a massive problem because antibiotics are vital in treating infectious diseases such as tuberculosis, pneumonia and blood poisoning [1]. We need antibiotics.

Antibiotic resistance is a widespread problem affecting us all but what can we do about it?

The overuse and misuse of antibiotics


Antibiotic Costume“, Beatrice the Biologist (2014)

One of the reasons antibiotic resistance is on the rise is the overuse of antibiotics. Antibiotics kill bacteria and therefore should only be used to treat bacterial infections. In 2015 the World Health Organisation estimated that in half of antibiotic prescriptions the conditions are caused by viruses [2]. They do not cure viruses such as colds and the flu [3]. When people go to the doctor they often expect antibiotics even when they don’t need them. This is a problem because it exposes bacteria to antibiotics and therefore more bacteria become resistant.

There are things we can all do to prevent this such as not requesting or taking antibiotics when you do not need them, for example for a virus [2, 3]. Also make sure you finish the full course of antibiotics as otherwise some bacteria may survive and return.

Antibiotics in Agriculture

Antibiotics are commonly used in agriculture. They have many uses such as treating, controlling and preventing diseases [4]. They may also be used to promote animal growth [4]. There has been some evidence that antibiotic use in agriculture can impact antibiotic resistance in humans [4]. The use in animal growth is not necessary to the health of the animal and therefore is not necessary and may be contributing to antibiotic resistance. It is important for avoiding antibiotic resistance that we stop this from happening.

In New Zealand, so far there has been no evidence that in-feed antibiotics cause antibiotic resistance in humans [5]. However, there has not been much research. The Ministry for Primary Industries has said that most antibiotics in New Zealand agriculture can only be used to treat an individual showing symptoms or an individual in a group with others showing symptoms [5]. However, this ruling does not cover all the antibiotics and there is little information on exactly what is being done. We should be able to find out this information as it impacts us all. We should advocate for a decrease in the use of antibiotics in agriculture in New Zealand and across the world, especially as antibiotic resistance continues to increase.

Alternatives to antibiotics – phages


Virus Nope“, Beatrice the Biologist (2015)

A phage (bacteriophage) is a virus that infects bacteria. So, like bacteria they can be used to treat and prevent bacterial infections. To kill bacteria, they enter the bacterial cell then replicate to make a large amount of copies then burst the cell by releasing all the copies.

Phage therapy is the use of phages to kill specific bacteria in our bodies and is an alternative to antibiotics. This can be done by people taking cocktails containing the phage that will target the host bacterium we wish to kill [6]. This was done and is still practiced in some places in Russia and Eastern Europe. However, it is relatively new in the western world.

An example of a potential use is in the disease Tuberculosis (TB). It is in the top 10 causes of death in the world, having caused 1.8 million deaths in 2015 and infecting around a third of the population with latent TB [7]. The overuse of antibiotics has accelerated the evolution of Mycobacterium tuberculosis becoming antibiotic resistant [8]. If we could find a phage that could infect this bacterium we could have a potential cure for TB.

This year we have been finding phages that can infect the bacterium Mycobacterium smegmatis. This is similar to the TB bacterium and therefore there is potential that some phages may be able to infect both. Hence, we could be contributing to potentially finding a phage that could infect TB and we are definitely adding to the scientific pool of data about phages which will help us discover more about this very important field in the future. In my next blog post I’ll be discussing this journey and the phage that I found.


  1. World Health Organisation Antibiotic Resistance. 2016; Available from: http://www.who.int/mediacentre/factsheets/antibiotic-resistance/en/.
  2. World Health Organisation How to stop antibiotic resistance? Here’s a WHO prescription. 2015; Available from: http://www.who.int/mediacentre/commentaries/stop-antibiotic-resistance/en/.
  3. Antibiotic Resistance. Available from: http://www.health.govt.nz/your-health/conditions-and-treatments/treatments-and-surgery/medications/antibiotic-resistance.
  4. Timothy F. Landers, R., CNP,, et al., A Review of Antibiotic Use in Food Animals: Perspective, Policy, and Potential. Public Health Reports, 2012. 127.
  5. Industries, M.f.P. Antibiotics and resistance. 2017; Available from: https://www.mpi.govt.nz/food-safety/whats-in-our-food/chemicals-and-food/agricultural-compounds-and-residues/antibiotics-and-resistance/.
  6. Benjamin K Chan, S.T.A.C.L.-C., Phage cocktails and the future of phage therapy. Future Microbiology, 2013. 8(6): p. 769–783.
  1. World Health Organisation Tuberculosis. 2017; Available from: http://www.who.int/mediacentre/factsheets/fs104/en/.
  2. Nguyen, L., Antibiotic resistance mechanisms in M. tuberculosis: an update. Arch Toxicol, 2016. 90(7): p. 1585-604.
  3. http://www.beatricebiologist.com/
Posted in Uncategorized | Tagged , , , | 3 Comments

What you Might Find in Your Garden

Stephen Fry: where would be the best place to discover an entirely new species?

Alan Davies: the Amazon rainforest (klaxon)

No as Stephen Fry pointed out the Amazon rainforest is not the best place to discover a new species. That honour belongs to your own garden (anyone’s garden that is).  The diversity of life in an ordinary suburban garden is such that  Jennifer Owen in 1971 did a study of the insects in her garden in Leicester and found 533 different species of wasps 15 of which had never been recorded in Britain before and 4 of which were completely new to science.

Wasps though are just multicellular life.  To give you an idea of how unknown bacteria and other unicellular life forms are 2 Norwegian scientists Jostein Goksoyr and Vigdis Torsvik  took a gram of soil from a forest near their lab in Bergen examined it very thoroughly and found 4-5 thousand new species of bacteria then they proceeded to do the same with a sample from a coastal area a few km away and found 4-5 thousand different species of bacteria.

However participants in the SEA phages programme search for something else altogether the even smaller viruses infecting these bacteria.  A virus is a strange entity in essence a piece of DNA surrounded by a protein which can attach to  a cell and “reprogram” it to produce more viruses. It is so small that even with most microscopes you won’t be able to see one. The  Scale of the Universe website can give you an idea just how small you should check it out it has a lot of interesting things.  What I might find just as interesting is whether a virus is actually alive…  that discussion can wait for another blog though.

Even if a virus is not alive you may be surprised to learn that it can be very useful and not just for terrorists intending on making an epidemic like you might see in an action movie. Phage therapy is the practise of treating a bacterial infection with a bacteriophage (virus) that will infect the bacteria. It may be another surprise to know that bacteria can themselves get sick (I don’t think I ever even considered the idea before reading about it) but it does happen.

In any case phage therapy has been suggested as a way of treating bacterial infections especially those that have become immune to antibiotics. In fact this form of treatment has already been used in parts of Eastern Europe since the 1940s. Several universities include a course discovering and studying bacteriophages. Massey University, Albany campus is one of these. The phages discovered by their class this year may one day provide a preventative treatment for tuberculosis or leprosy ( although the later is thought of as a thing of the past it still does exist).Image result for searching for a new species

Most of these are found in the gardens of scientists and other equally mundane locations. So if you don’t think there is anything interesting in your garden then I think maybe you should look harder.


Posted in Uncategorized | Leave a comment