Posts Tagged microbiology

What’s the collective noun for a group of scientists?! Siouxsie Wiles Aug 22

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Next week over 1000 scientists are descending on Queenstown, New Zealand, for the annual Queenstown Research Week and Queenstown Molecular Biology (QMB) Meetings. This year there are 12 meetings on topics ranging from enzyme engineering and epigenetics to neuroscience and personalised medicine.

This year, Dr Deborah Williamson, Prof Greg Cook and I have organised a joint QMB and Webster Centre for Infectious Diseases Satellite meeting on translational medical microbiology. Our two day meeting will cover molecular microbiology, host-pathogen interactions and disease modelling, and we have a great line-up of international and local speakers. I’m also pleased to announce that we have a 50:50 gender split for our speakers, something I was passionate about achieving.

Our plenary talks are being given by Associate Professor Bill Hanage from the Harvard School of Public Health, Associate Professor Tim Stinear from the University of Melbourne and Dr Nico Petty from the iThree Institute at the University of Technology, Sydney.

I’m really excited to have been part of organising this meeting, which brings together scientists and clinicians from all over New Zealand with an interest in infectious diseases. Translational medical microbiology is a research area of great need in New Zealand – our rates of infectious diseases are bucking international trends, increasing by 50% over the last two decades. Added to that, our high rates of sexually transmitted diseases are a ticking infertility time bomb.

It is sad then that what is arguably one of the most important health challenges facing our country has been left out of the upcoming National Science Challenges. Something we can ask Minister Steven Joyce about when he opens the main QMB meeting!

To follow along with our satellite and all the other meetings going on during Queenstown Research Week, we will be live tweeting using the hashtag #QRW13.

*And if you are wondering what the collective noun for a group of scientists is then check out this fabulous storify from Twitter last year – #sciencecollectivenouns. It’s hilarious. I quite like ‘hyper-proliferation of oncologists’. Being a microbiologist I was also quite taken with ‘a colony of microbiologists’

Monday Micro Siouxsie Wiles Dec 03

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Welcome back to Monday Micro. Last week’s Monday was lacking in microbiology factoids as I was at the New Zealand Microbiology Society‘s annual meeting*. This year it was at the University of Otago in Dunedin. Highlights for me were keynotes by Rob Knight (microbiomes and Next Gen Sequencing), Eric Ruben (TB) and Steven Wilhelm (cyanobacterial blooms). Tweets of some of the talks are here.

Highlights for me:

Finding that lots of people flush public toilets with their feet, that cyanobacteria are a bad food source “like ordering pizza and only eating the box”** and that “we are all accidents of history”***.

Moving on, Round 3 of the SciFund Challenge is in full swing so if you fancy supporting some microbiology projects Amy Truitt wants so study butterflies and their sexually transmitted diseases, Will Helenbrook is studying the effects of infectious diseases on Mantled howler monkeys and Andy MacDonald is working on Lyme disease.

* The slides for my talk (Fireflies and superbugs: when science and nature collide) are up on slideshare. I started my talk with my Meet the Lampyridae animation….

** Steven Wilhelm
*** Unknown kilted MC of conference dinner :)

Monday Micro Siouxsie Wiles Nov 19


“Would you chop your vegetables on your toilet seat? I think pretty much all of us would say No. But maybe we should think again.”

So writes the BBC’s Charlotte Pritchard in her article Is the toilet seat really the dirtiest place in the home?. According to Prof Charles Gerba* of the University of Arizona, it most certainly is not. With the average toilet seat harbouring around 50 bacteria per square inch, much more dangerous is the humble kitchen cloth with a million bacteria per square inch. If you want to see just where all the microbes in your home are likely to be lurking, check out this fabulous infographic on the Hygiene Council’s website. And in case you thought you were safe at work, a recent paper by Gerba and colleagues published in PLOS One (open access, yay!) sampled 90 randomly chosen offices in three different office buildings in New York, San Francisco and Tucson [1]. Their findings?

- Surfaces in men’s offices were consistently more contaminated than those from women’s offices
- Chairs and phones were the most contaminated of the surfaces tested
- Offices in San Francisco tended to be less contaminated than those in New York or Tucson

Another recent paper (again PLOS One and hence open access, yay!) explored the microbes present in another environment of significance to us [2]. As the authors put it:

“The belly button is one of the habitats closest to us, and yet it remains relatively unexplored.”

Until now! Robert Dunn has been getting people to send him swabs of their belly buttons in his ‘Belly Button Biodiversity’ citizen science project. The upshot? The richness of bacterial life in human belly buttons compares to that of the biodiversity found in rainforests! One participant, who admitted having not showered or bathed for several years, was home to several ‘extremophile’ bacteria not previously reported to live on human skin.

And finally, in more serious news, doctors are celebrating the development of a vaccine against one of the commonest causes of meningitis, meningococcal group B disease, known as MenB. The European Medicines Agency have apparently just given the vaccine, Bexsero, a ‘positive opinion’ and now have 60-90 days to decide whether to grant a licence.

1. Hewitt KM, Gerba CP, Maxwell SL, Kelley ST (2012) Office Space Bacterial Abundance and Diversity in Three Metropolitan Areas. PLoS ONE 7(5): e37849. doi:10.1371/journal.pone.0037849
2. Hulcr J, Latimer AM, Henley JB, Rountree NR, Fierer N, et al. (2012) A Jungle in There: Bacteria in Belly Buttons are Highly Diverse, but Predictable. PLoS ONE 7(11): e47712. doi:10.1371/journal.pone.0047712

*As an amusing aside, Prof Gerba lists his appearance in numerous** Who’s Who publications. This is presumably to impress, but these publications have apparently been referred to by Tucker Carlson as the “The Hall of Lame”. His argument: the selection process is neither rigorous nor meaningful, people can self nominate and thousands of people not particularly notable are included. The publisher seems to make money by selling tat (sorry, ‘personalised keepsakes’) to those who want to celebrate the ‘achievement’ of being listed. Carlson claims the publisher also makes money selling details of those included to direct mail marketers.

**Who’s Who in Technology Today, 1984, 1986, 1989; International Who’s Who in American Education, 1992-1993, 1995, 1996-1997;Who’s Who in the West, 1987-present; Who’s Who in Emerging Leaders in America, 1989-1990, 1991-1992; Who’s Who in the World, 1989-1995-present; American Men & Women of Science, 1992-1993, 1996-1997-present; Who’s Who in Science and Engineering, 1992-1993, 1996-1997; Who’s Who in America, 1994 – present; Who’s Who in Medicine and Healthcare, 1997-1998-present.

Citizen science…. Siouxsie Wiles Aug 26

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For the last few weeks I’ve been going into a local primary school to do some microbiology with a group of 6-7 year old kids. The first week I took a load of different petri dishes and a huge bag of swabs along. After a quick chat with the kids about good and bad microbes, we set about swabbing. First up was fingers before and, by far the highlight of the day, after picking their noses. We also swabbed the toilets and soil. I wasn’t sure how long the swabbing would keep them occupied so I took in some glowing bacteria which I had used to write letters of the alphabet. I got the kid to sit in a circle and spell out some words and then threw a big black blanket over their heads. The squeals of delight as they saw the glowing words made my day.

A few days ago, I took their (very smelly!) plates back and we had a look at all the bacteria and fungi that had grown. Every child swore they wouldn’t be picking their nose again, having seen what was living there :) They also took lots of pictures of their petri dishes and have told me they are going to make a presentation so they can tell the rest of the school about bacteria.

For those who would like to get more involved in such citizen science, @scicheer has started a really fantastic website called scistarter which allows you to find science projects the general public can get involved in. What are you waiting for?!

SciFund Challenge – Day 1! Siouxsie Wiles May 03


What a start to round 2 of the SciFund Challenge. Over 18,000 dollars raised for science so far!

How about the stats for my project Evolution In Action? The last 24ish hours have seen 15 contributors donating $840 to support my research — that puts me at a third of the way to my target!

A special thanks go to the brilliant Daniel Hurley for being my first supporter.

Other contributors today were:

Susan and Craig Shearer
Ben and Olivia Albert
Jin Koo Niersbach
Steven Galbraith
Elf Eldridge
Alan Huett
Nathan Hayward
Riccardo Guidi
Jimmy Dalton
Tina Arora
Maire Litchfield
Diana & Michael
Sarah Johnson

Thanks also to Ed Yong (@edyong209) writer of the excellent Not Exactly Rocket Science for tweeting and everyone who has posted my #SciFund link to Facebook or shared on Google+.

30 more days to go!

An introduction Siouxsie Wiles Nov 09


I thought I would use my first post to introduce myself and explain the reason(s) for infectious thoughts. I am a research scientist with a background in medical and environmental microbiology. I’ll come back to what I do and what I’m interested in a bit later. As well as microorganisms, I am also obsessed with bioluminescence (the production of light by living organisms – think glow worms and fireflies).  I feel immensely privileged to have made a career out of combining these two passions, as in a nutshell, I make bacteria glow in the dark for a living. After many years working in the UK, I was recently awarded a Hercus Fellowship from the Health Research Council (HRC) of New Zealand and relocated to the University of Auckland (UoA). It goes without saying that the views I will be expressing are my own and in no way represent the views of the UoA or the HRC!

So why would glowing bacteria be useful? Well, for a start, we could see them coming! Actually, that is closer to the truth than you might expect. Tagging bacteria with the genes for bioluminescence allows us to use light as a surrogate for actually physically counting the numbers of bacteria present in a sample, which is what you do after plating samples onto selective agar. Instead we can use a luminometer or charged coupled device (CCD) camera to give us a measure of light intensity (relative light units [RLU]). One of the first things we have to do is determine the relationship between light and bacterial numbers, but once this is done we can get a pretty good idea of how many bacteria are present using the RLUs. This can be especially useful if the bacteria take many weeks to grow on an agar plate, like Mycobacterium tuberculosis (the agent of TB) does. The other neat thing about luminescence is that only living organisms will glow so it can be an easy way to tell if something is dead or alive. This feature formed the crux of my PhD research which involved generating bacterial biosensors to monitor the toxicity of industrial effluents from a wastewater treatment plant. The more toxic the industrial effluent, the less the bacterial sensors glow. While it wasn’t great for the company, or indeed, the river into which the treated wastewater is discharged, during my studies the treatment plant failed and it was fantastic to find that my sensors would have been able to predict the failure. Shame though that they are genetically modified organisms and therefore highly unlikely to ever be used for real-time monitoring.

While I enjoyed my PhD studies, I came to realise I was more interested in bacteria that cause human disease so for my post-doctoral research I moved back to medical microbiology, the subject of my undergraduate degree. And this is where bioluminescent bacteria come in really handy. I am not ashamed to say that I am one of those scientists who work with mice. Providing they are used appropriately, animals are still very important in medical research. As someone interested in infectious bacteria, many aspects of the interactions between microorganisms and their hosts just cannot be replicated in a cell line. But we don’t use mice for everything; alternatives include worms and insect larvae. But when we do have to use mice, having bioluminescent bacteria is a bonus. If you haven’t tried this simple experiment before, give it a go: hold a torch up against your hand and you will see a beautiful red light coming out the other side. This is because light can travel through flesh. Not all wavelengths can get through though, hence why the white light ends up coming out red. We are fortunate that there are now sensitive CCD cameras available that can detect even very dim signals coming through flesh. This allows us to visualise where our bacteria are from inside an animal, a technique known as biophotonic imaging (BPI). Usually the animals are anaesthetised, but they can be imaged while awake too. Biophotonic imaging means we can use a lot less animals in experiments; instead of needing separate groups to take organs for plating onto agar plates at different time points, we can follow the bioluminescence from each animal and watch the bacterial numbers and locations change over time. In this way, we can often stop an experiment before the mice start to show any symptoms of disease, saving them from unnecessary suffering. My research is currently focused on using BPI to investigate three particularly nasty bacteria: Staphylococcus aureus (the hospital superbug MRSA), Streptococcus pyogenes (the flesh-eating bug) and M. tuberculosis.

So why blog? There are two reasons really. The first is to try to convey the wonder and admiration I have for microorganisms by writing about recent publications I have found interesting. However, the second reason is perhaps more important, in the grand scheme of things. Twice a day I have to walk past the Christian Science Reading Room (and no, I’m not going to change my route…). These misguided souls go on the teachings of Mary Baker Eddy (1821-1910) who wrote Science and Health with Key to the Scriptures, first copyrighted in 1875 and still in print today. These guys deserve a post all their own, but what really got my blood boiling was this sign in the window. Contagion: a spiritual responseNow Baker Eddy could perhaps be excused. Robert Koch, one of the founding fathers of microbiology, first isolated Bacillus anthracis (the agent of anthrax) two years after Baker Eddy’s first edition, in 1877, with the isolation of M. tuberculosis following in 1882 and Vibrio cholerae (the agent of cholera) in 1883. He was awarded a Nobel Prize in 1905. But what is the excuse of other editions?! As a microbiologist I am obviously a proponent of the germ theory of disease and believe vaccination to be one of the wonders of medicine.

Recently I read Trick or Treatment, by Simon Singh and Edzard Ernst, reviewing the evidence for the effectiveness of complementary and alternative medicine. Despite no evidence for the success of these treatments, they are widely used. In the final chapter, the authors list some reasons why this might be. Surprisingly, scientists are on their list. Singh and Ernst argue that alternative health practitioners are highly vocal and many of their claims go unchallenged. They believe scientists have a responsibility to make their voices heard too. I found Singh and Ernst’s call to arms inspirational. Instead of cursing under my breath at Baker Eddy’s disciples twice a day (amongst many other things…) I should be more vocal. SciBlogs seems a great forum for such an endeavour!

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