That time when I accidentally made genitalia glow in the dark

This post is written by Dr Faraz Alam, formerly a London-based member of the Bioluminescent Superbugs Lab and describes one of the figures in a PLOS One paper from his PhD studies.

There are moments in science that you can never really prepare for. There are times when you go into an experiment with expectations that get upended completely. This is the story of one of those moments.

I was studying a bacterium named Streptococcus pyogenes, a very versatile pathogen that can cause sore throats and skin diseases, and can infect wounds. S. pyogenes is also the only bacterium that has been documented to spread through farting (1,2)! But you may recognise it by its most extreme manifestation – necrotizing fasciitis, the flesh-eating disease. The aim of my PhD was to make glowing S. pyogenes so we could track it during an infection.

The experiment I was setting out to do on this particular day was to directly compare the amount of light produced during a nasal infection with the numbers of bacteria present. That way, I could build a curve that I could use to estimate the numbers of bacteria within the nose based on the light they produce. At least, that was the point of the experiment, but as is often the case in science, things don’t always go according to plan. It was a Monday morning, and I’d been working through the weekend to get this experiment finished, when something weird happened. Something that I hadn’t expected, and could barely explain. The nose of the mouse was glowing, as I had expected because that was where the bacteria were supposed to be causing an infection. But another signal was detected in the mouse’s ….*ahem*

An unexpected glow!

An unexpected glow!

The photo pretty much tells the whole story. The mouse did most of the work, I merely took the pictures. The following exchange occurred after I e-mailed this image to Siouxsie.

email exchange

Regrettably the “self-stimulating” mouse hypothesis had a very short shelf life. If that was the only thing that was going on, then wouldn’t all of the mice have glowing vagina’s? I should point out that mice naturally groom themselves, and eat their own faeces, which means that all of the mice should have been able to transfer the bacteria in their nose to their genitals. But some mice were more susceptible than others, and my current hypothesis is that it is to do with the specific stage of their menstrual cycle that actually makes it a very hospitable place for bacteria.

The mouse vaginal tract is believed to actually use bacteria as the first line of defense, primarily a bacterium named Lactobacillus. At certain points of the menstrual cycle, it is believed that the oestrogen causes the vagina to produce sugars which the Lactobacillus can feed on. This is meant to boost its population, and help it defend against infections from nastier bacteria. However, other bacteria can take advantage of this system if given the opportunity. In this case, I suspect that the bioluminescent S. pyogenes has snuck in and begun to colonise this area.

The reason why it happens so rarely is because of something called the Lee-Boot effect. Mice tend to use pheromones to determine whether to start their menstrual cycle. The most well documented example of this is the Whitten effect, where mice can synchronise their cycles when they have regular exposure to the scent of male mice. There was a failed attempt to extrapolate this behaviour into humans known as the McClintock effect that has actually been disproven because humans don’t produce pheromones, nor has it been proven that humans have a functioning pheromone sensing organ (called a vomeronasal organ) to detect them.

Mice on the other hand have a number of different responses to pheromones. When female mice are housed together with no males present, they can produce pheromones that suppress the menstrual cycle. This kind of suppression is known as the Lee-Boot effect. Considering that the mice in these experiments were all female, it is likely that they all are exposed to the Lee-Boot effect. This is my best guess as to why only a relatively few mice in each cage had glowing genitalia during the course of an experiment.

You won’t see this speculation in an actual paper, because as nice an idea as it is, I didn’t have comprehensive evidence to back it up. I did a few follow up experiments messing with mouse pheromones and hormones, but I could never reliably predict when this kind of colonisation could occur, nor could I reliably trigger it. I was fully prepared for it to live out the rest of its days in the junk drawer. Everything changed when my paper went to be reviewed. I had submitted a paper to PLOS One showing off how these bugs can be used to show whether a vaccine is working or not (3). The reviewer wanted us to show exactly why bioluminescence was such a big deal. Suddenly, the true value of this data revealed itself.

That glowing vagina was a demonstration of how versatile Streptococcus pyogenes is as a pathogen. It showed how bacteria can travel between different organs of the body, and turn up in the least likely places (3). Even if I couldn’t comprehensively explain how these genitals came to glow, the fact that they were glowing was important enough in its own right. You may laugh at the glowing vagina, but it is powerful demonstration of how diseases can take unexpected turns, and glowing bacteria can show us what happens when they do.

1. Schaffner W, Lefkowitz LB Jr, Goodman JS, & Koenig MG (1969). Hospital outbreak of infections with group a streptococci traced to an asymptomatic anal carrier. The New England journal of medicine, 280 (22), 1224-5 PMID: 4889553
2. McKee WM, Di Caprio JM, Roberts CE Jr, & Sherris JC (1966). Anal carriage as the probable source of a streptococcal epidemic. Lancet, 2 (7471), 1007-9 PMID: 4162660
3. Alam FM, Bateman C, Turner CE, Wiles S, Sriskandan S (2013) Non-Invasive Monitoring of Streptococcus pyogenes Vaccine Efficacy Using Biophotonic Imaging. PLoS ONE 8(11): e82123. doi:10.1371/journal.pone.0082123

Siouxsie wins NZ Prime Minister’s Science Media Communication Prize

Last week Siouxsie was awarded the Prime Minister’s 2013 Science Media Communication Prize which comes with $50,000 to spend on science communication. Radio NZ recorded the prize-giving so you can hear her acceptance speech here (about 9 minutes in) and her getting excited about what she will spend the money on here.

Safe to say, she couldn’t have done it without the support and tolerance of her wonderful friends, family and lab members!

Siouxsie with the Prime Minister John Key   (Photo by Mark Tantrum [])

Siouxsie with the Prime Minister John Key
(Photo by Mark Tantrum [])

Art (& Science!) in the Dark

This weekend, Western Park in Auckland was transformed with the installation of 40 works of art. And a little bit of science….

Our little installation, Living Light, a collaboration between myself and artist Rebecca Klee, was powered by glowing bacteria.


Art In The Dark
Picture above was taken by Peter Jennings

Inside our little tent hung a circle of twelve 3D printed squid (you can catch a small glimpse of a squid being printed here or even print your own), each filled with approximately 250 billion glowing bacteria. This reliance on a living organism to bring our installation to life caused me just a little stress – I was so worried the cultures might not grow or glow properly and all we would have was a tent full of (very beautiful) squid that no one could see. But fortunately the little critters (over a trillion of them…) behaved as expected and were glowing beautifully by the time people started to arrive. And arrive they did. In fact, they even spontaneously formed an orderly queue and waited patiently to get inside our tent!

It was so exciting to see our installation come together after so much planning and hard work. It was also brilliant to see people reacting so positively to it. It makes all the hard work worthwhile! Rebecca and I are very keen to show Living Light again so, when the dust has settled, we will look into how and where we could do that. We are also keen to collaborate again so I’m sure we will be putting in an application for Art in the Dark next year.

I’d like to extend a huge thanks to everyone who has been involved in this project. It may have said Rebecca Klee and Siouxsie Wiles on the signage, but Living Light wouldn’t have happened without the hard work put in by Danny of Vivenda (who designed and printed the squid) and Benedict and Jimmy from my lab (who prepared all the media and kept the bacterial cultures ticking over). It also wouldn’t have been possible without the generous financial support of the Faculty of Medical and Health Sciences at the Univesity of Auckland (thanks to Tim Greene and Katie Elliot) and the Maurice Wilkins Centre for Molecular Biodiscovery. And finally I would like to thank my family for their tolerance of the time this project has taken me away from them, and for putting up with all the bacteria growing in our kitchen!

Here’s just a little sample….This is what 10 trillion bacteria look like!


Glowing squid come ashore in Auckland!

Who wouldn't want to see a load of 3D printed squid filled with glowing bacteria?!

Who wouldn’t want to see a load of 3D printed squid filled with glowing bacteria?!

This week, the Bioluminescent Superbugs Lab is taking part in the annual Art in the Dark festival, which sees Auckland’s Western Park transformed into a place of wonder and delight from Thursday the 7th to Saturday the 9th of November.

For the last few months, Siouxsie has been collaborating with artist Rebecca Klee to bring glowing bacteria to Art in the Dark. They have been blogging about the process here. After much discussion of the best way to show off bioluminescence to as many as 40,000 people over 3 nights in an inner city park, Siouxsie and Rebecca settled on displaying glowing bacteria inside 3D printed squid. Rebecca met Danny Dillon of Vivenda who set about designing and printing the squid. Back in the lab it was all hands on deck, with everyone pitching in to make media and figuring out when the bacteria glow their brightest and in which liquid broth.

A big thanks to the Maurice Wilkins Centre for Molecular Biodiscovery and the Faculty of Medical & Health Sciences at the University of Auckland for funding this project.

Why glowing squid?

Rebecca got in touch with Siouxsie after seeing her short animation about the Hawaiian bobtail squid and its bioluminescent invisibility cloak on You Tube. The animation was produced with the support of a public engagement grant from the UK Society for Applied Microbiology, to engage the services of graphic artist Luke Harris and his team.

What didn’t fit into 3 minutes…

The Hawaiian bobtail squid, Euprymna scolopes, is just 3 cm in length and lives in the shallow moonlit waters off Hawaii. It spends its days sleeping buried in the sand, emerging at night in search of food. It has a very cunning trick to hide its shadow from fish looking for a meal, or from creatures like shrimp that it feeds on. It houses a colony of glowing bacteria (Vibrio fischeri) in a special organ on its underside. These bioluminescent bacteria shine their light down so that to any creatures looking up, the squid just looks like the moon. What is even more clever is that the squid uses its ink sac to match the intensity of moonlight hitting its back, dimming the light from the glowing bacteria as needed. This is important not just for cloudy nights but as the squid moves through different depths of water.

Baby squid are born without V. fischeri or a light organ. Instead they just have a small opening in their mantle (the bulbous bit of their body) that is bathed by sea water. What is incredible is that only V. fischeri can colonise this opening – once they do, the squid cells start to change and the light organ forms. The ability to glow is crucial though – scientists have made versions of V. fischeri which can’t glow and they aren’t able to colonise either.

Adult squid have an ingenious way of ensuring that there is plenty of V. fischeri floating around in the water to colonise baby squid. Each morning, before they settle down in the sand to sleep for the day, they expel 99.9% of the bacteria from their light organ into the sea. This serves another purpose too, ensuring the bacteria left behind in their light organ are constantly growing and have plenty of nutrients. Bacteria that run out of nutrients start to shut down to save energy. Producing light takes quite a bit of energy and the last thing the squid wants is a mantle full of lazy dim bacteria!

When scientists first identified V. fischeri and grew it in the lab they noticed something quite interesting. The bacteria only switch on their light when they have reached a critical population size. This makes perfect sense. There is no point going to all the trouble of making light if it isn’t bright enough to be seen. Each bacterium produces a chemical, called the autoinducer, that diffuses out of the bacterial cell. The more bacteria there are, the more autoinducer is produced. If those bacteria are growing in a confined space like a flask, or the light organ of the squid, the autoinducer will accumulate. Once it reaches a critical concentration, the autoinducer triggers the bacteria to switch on the genes for producing light*. This phenomenon is called quorum sensing.

Scientists then used the bioluminescence reaction to see if other species of bacteria produce autoinducers. Surprise, surprise, it turns out that lots of different bacteria use quorum sensing to signal to each other that they are in the right numbers or environment to do something, which is not worth doing otherwise. From the bacterial form of sex, to swimming, to switching on the genes needed to cause disease in plants, animals and humans. Now we just have to find a way of exploiting this to our advantage!

You can hear Siouxsie chatting about the squid and quorum sensing on Radio New Zealand’s Nine to Noon programme with Kathryn Ryan here (13’12”)

*For those who really want to know, the autoinducer is the product of the luxI gene. When it reaches a critical concentration, it interacts with the product of the luxR gene, and together this complex binds to a region of DNA upstream of the genes under their control called the lux box which then triggers their transcription.

Our experiment in open science begins!


In early 2012 I came across the SciFund Challenge started by two ecologists from the US National Center for Ecological Analysis and Synthesis in California, Dr. Jai Ranganathan and Dr. Jarrett Byrnes. With a passion for communicating science to the public, and spurred on by budget cuts, Jai and Jarrett wanted to see if the crowdfunding model successfully used by artists and musicians could be applied to support science.

Rather than relying on one wealthy benefactor for full funding, crowdfunding seeks small contributions from lots of people to get projects off the ground. Using the popular crowdfunding site RocketHub as a platform, the SciFund Challenge has run three rounds, with scientists raising money for projects as diverse as parasitic plants, flying foxes, Amazonian crabs, domesticating algae, duck erections, Roman slaves, zombie fish and undersea kelp forests.

I took part in Round 2 of the SciFund Challenge in May 2012, to support a fledgling project in the lab that had been something myself and an old colleague of mine, Bill Hanage (now an Associate Professor at Harvard) had talked about doing for years. I have tried to get this project fully funded several times through traditional grants but, despite excellent feedback from overseas reviewers, have had no luck. Fortunately I was given a little seed money from the Maurice Wilkins Centre for Molecular Biodiscovery, one of New Zealand’s Centres of Research Excellence, to get the project started. Through the SciFund Challenge, 79 people from all over the world, half of them strangers to me, donated about US$4500 to help this project along. In this funding environment, every little helps!

So what is the project? It is based on the fact that bacteria are masters at adapting to their environment, rearranging their genetic material or gaining new genes from their surroundings. This has allowed them to colonise pretty much every conceivable environment, from boiling hot geysers to human beings. While many are harmless or pretty beneficial, plenty have evolved to cause us serious harm. In fact, bacterial adaptation is how we get antibiotic resistance and new diseases emerging. So what I want to know is, how do bacteria evolve to cause disease?

We are studying the evolution of a bacterium called Citrobacter rodentium which infects mice using the same ‘modus operandi’ as food poisoning strains of E. coli do in humans. They go in one end… and come out the other! And because mice like to eat poo (more technically known as coprophagia) they easily spread C. rodentium to each other. We have spent this year allowing the bacterium to spread from mouse to mouse to mouse to mouse to… you get the picture, each time freezing bacteria that are shed in the poo. We now have a freezer full of ‘evolved’ bacteria that we are itching to analyse. What changes might have happened? And if they have, will they have made the bacterium more or less infectious?

As this project has already made its web debut, it seemed a perfect candidate for an experiment of another sort – the Bioluminescent Superbugs Lab’s first open science project. We have created an online lab book and Hannah, who is working on the project for her PhD, will be publishing her lab notes in real time, for all to see.  Working with such a limited budget, it doesn’t make sense to do this project as normal – beavering away in the lab for years and then having reviewers turn around saying “you should have done x,y & z”. Instead we are hoping to engage others in the field to help guide our experiments in real time. If we should be doing things differently, we need to know now!

So feel free to drop by and see how we are getting on from time to time. Even better, if it looks like we are barking up the wrong tree, tell us!

Our new website

The Bioluminescent Superbugs Lab at the University of Auckland has a new website. We’re happy to have a place where we can share our research as well as more information about all the people who work in the lab. We’re especially pleased to have created an Open Lab Book, a place where lab members can keep notes on their experiments and protocols, and make them public when the work is done.