Archive Science

Monday Micro – frozen poop pills! Siouxsie Wiles Oct 13


It’s still Monday so time for a very quick post about a paper just out in the Journal of the American Medical Association. I’ve blogged before about faecal transplants – giving a patient a dose of faeces from a healthy donor to resolve infection with the diarrhoea-causing bacteria Clostridium difficile.

One of the problems with faecal transplants is the way they are delivered – either by a tube through the nose and into the colon, or the more direct route of up the bum. Researchers at Massachusetts General Hospital in Boston have tried something a little more palatable. They took faecal material, blended it to make a suspension, removed all the particulate matter, added glycerol as a cryoprotectant and then froze it in small amounts inside of capsules that could withstand transit through the acidic environment of the stomach. If you are interested, apparently 48 grams of faecal matter makes 30 capsules.

Next the researchers gave the frozen poop capsules to 20 people with C. difficile infection. This involved patients fasting for 4 hours and then taking 15 capsules each day for 2 days. Nobody suffered any serious side effects and that 2 day course of frozen poop pills cured the diarrhoea of 14 of the 20 patients. Of the 6 people who didn’t respond, 4 of them got better after another course of the poop pills, giving an overall success rate of 90%. This is quite promising data, although the study was small and there was no placebo control group.

It will certainly make things easier if the poop needed for faecal transplants doesn’t need to be fresh, and people are definitely more likely to prefer popping pills to tubes up their noses!

Youngster et al. Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection. JAMA Preliminary Communication, October 11, 2014.

Monday Micro: glowing dog bones in Taranaki! Siouxsie Wiles Sep 29


glowing meat

From the Taranaki Daily News comes a story that is right up my street. Fiona Wallis gave her dog a bone and found it to be giving off an eerie blue light. What could it be? It’s most likely to be coming from bacteria so the questions people are likely to be asking are: what is it, is it dangerous, and how did it get on the dog bone?

What is it?

First off, its not radioactive! I think the light is most likely to be bioluminescence coming from a colony of glowing bacteria and there are many different species it could be. Almost all glowing bacteria live in water; there is only one well-documented species that lives on land. Of the species that live in water, the vast majority either live in or on fish and other creatures (like my favourite the Hawaiian bobtail squid). This will be the reason why you can sometimes see an eerie glow coming from fish if you’ve left it in the fridge for a few days.

The glowing bones in question had been packaged in salty water as one of its preservatives (also known as brine). This suggests to me that the bacteria is one that naturally lives in the sea, as they like high salt environments. An interesting feature of bioluminescence is that it is a chemical reaction that requires oxygen. This means that it won’t be possible to see light from the bones if they are in a sealed pack. But as soon as the package is opened and the bacteria get a whiff of oxygen…

I’ve made contact with the manager of the company that produced the product and he is getting samples to our lab so that we can isolate the bacteria and identify it, so watch this space.

Is it dangerous?

It’s highly unlikely. There are a couple of glowing bacterial species that produce toxins; the soil bacterium Photorhabdus luminescens produces toxins that kill insects, while some strains of Vibrio cholerae, the bacterium that causes cholera, glow. But it’s far more likely is that it is a harmless sea bacterium.

How did it get on the dog bone?

Once we know what the source of the glow is, we can start to figure out how it got on the dog bone. I know the company involved are working with their suppliers to find out exactly where everything came from. My guess would be that somewhere in the process, something has come into contact with either sea water or a product from the sea. Another case of watch this space.

UPDATE 29/09/14: Glowing bone has arrived!

This evening we received one of the glowing bones as well as an unopened packet from the same batch. The bone is indeed glowing (below is a picture from taken on our imaging machine) but it was the only one. None of the three bones in the unopened packet from the same batch number were glowing. We’ve swabbed both sets of bones and we’ll see whether any bacteria grow over the next few days.

photo 2

The threats of antibiotic resistant superbugs to New Zealand Siouxsie Wiles Sep 26

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In this week’s New Zealand Medical Journal is a paper by Deborah Williamson and Helen Heffernan on antimicrobial resistance in New Zealand (1). This comes hot on the heels of the WHO report which gave a global picture of antibiotic resistance (2), and highlights what the big challenges are for New Zealand.

So what are the antibiotic resistant superbugs that pose a risk to the health of New Zealanders?

According to the authors, there are four main superbugs we need to be watching:
1. Methicillin Resistant Staphylococcus aureus also known as MRSA
2. Extended-spectrum B lactamase (ESBL) producing Enterobacteriaceae, especially E. coli and Klebsiella pneumonia
3. Mycobacterium tuberculosis which causes the lung diseases tuberculosis (TB)
4. Neisseria gonorrhoeae which causes gonorrhoea

What are the key factors driving antibiotic resistance in New Zealand?

The authors highlight three main drivers which they believe are contributing to the problem:
1. The use and overuse of antibiotics in people and animals
2. Transmission of antibiotic resistant microbes in both the community and within healthcare facilities, including rest homes
3. Increasing globalisation – we are importing many of our antibiotic resistant superbugs from abroad

MRSA – a problem of our own making

Over the last few years there has been a huge increase in the number of skin and soft tissue infections caused by S. aureus in New Zealand. Alongside this, there has been a huge increase in prescriptions for a topical antibiotic called fusidic acid. As a consequence, one of the major clones of S. aureus now causing disease in New Zealand is an MRSA clone called AK3 which is resistant to fusidic acid (3).

Importation of resistant superbugs

Some of the superbugs of worry, notably extremely resistant strains of E. coli, K. pneumonia and M. tuberculosis are mainly being imported into New Zealand from countries like India, China and those in south-east Asia. This is going to be an area to watch, especially given the importance of countries like China for trade and tourism in New Zealand.

Gonorrhoea – the tip of the iceburg for sexually transmitted diseases

In New Zealand, sexually transmitted infections (with the exception of HIV) are not notifiable. This means that the data we have on these diseases is based on the voluntary provision of the numbers of diagnosed cases from laboratories and sexual health and family planning clinics. What’s crucial to this is that many people can have no symptoms, hiding the true burden of disease. Gonorrhoea is one of these. While most men will have symptoms when they have the disease, half of women can be asymptomatic. Importantly, untreated infection can lead to infertility in women.

In 2013 there were 3,334 cases of gonorrhoea in New Zealand (4). What is shocking is that 1,145 of these cases were in young people under the age of 19. In fact, there has been a 43% increase in the rate of gonorrhoea in 15–19 year old women between 2009 and 2013. Less than half of sexually active young people report using condoms (5) which goes some way to explaining why our rates are rising. If we end up with a completely untreatable strain of N. gonorrhoeae taking hold in New Zealand this could have a huge impact on our future fertility.

1. Williamson DA & Heffernan H (2014). The changing landscape of antibiotic resistance in New Zealand. New Zealand Medical Journal.
2. World Health Organisation (2014). Antimicrobial resistance: global report on surveillance 2014. ISBN: 978 92 4 156474 8.
3. Williamson DA et al (2014). High Usage of Topical Fusidic Acid and Rapid Clonal Expansion of Fusidic Acid-Resistant Staphylococcus aureus: A Cautionary Tale. Clin Infect Dis. pii: ciu658.
4. Sexually transmitted infections in New Zealand 2013. Institute of Environmental Science and Research Limited.
5. Clark TC et al (2013). Youth’12 Overview: The health and wellbeing of New Zealand secondary school students in 2012. Auckland, New Zealand: The University of Auckland.

Fighting antibiotic resistance: from Obama to TV3! Siouxsie Wiles Sep 25

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Ascomycetes“. Licensed under CC BY-SA 2.5 via Wikimedia Commons.

Last week President Obama signed an Executive Order aimed at combating antibiotic resistant superbugs. The order establishes a task force and a Presidential Advisory Committee which will look at how the US can implement a national strategy to deal with antibiotic resistance. The order covers areas such as surveillance, antibiotic use (now being called antibiotic stewardship) as well as promoting new and next generation antibiotics and diagnostics.

Speaking of which, Massey University’s Dr Heather Hendrickson and myself featured in a recent TV3 3rd Degree episode on antibiotic resistance in New Zealand, showcasing the work that we are doing in our labs. You can watch our clip from the episode here.

In my lab we are starting to collaborate with researchers at Landcare Research to screen the thousands of species of New Zealand and Pacific fungi that have never been mined for new antibiotics. We are currently writing lots of grants to try to get some money to support this work but if you’d like to help get started and are a New Zealand-based user of Facebook then please consider voting for our project for the People’s Choice Award for an AMP scholarship. And tell all your friends!

Monday Micro – artificial sweeteners & a dose of bad science Siouxsie Wiles Sep 22

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Sugarcubes” by PallboOwn work. Licensed under Public domain via Wikimedia Commons.

There has been quite a bit of coverage of a recent Nature paper reporting a link between artificial sweeteners and high blood glucose levels (1) – an important finding if true, as high blood glucose levels are a step towards insulin resistance and type 2 diabetes. The study was carried out mostly in mice and was found to be mediated by the gut microbes. The paper isn’t open access so you’ll need $32 to read it if you don’t have a subscription to Nature.

The authors report that consumption of artificial sweeteners changes the microbes present in the gut of mice (and 4 out of 7 healthy human volunteers), with some microbes becoming more abundant and others less so or disappearing altogether, and that this is correlated with a rise in blood glucose levels. The effect disappears when mice are treated with antibiotics. The effect can also be transferred to animals who haven’t been fed artificial sweeteners by giving those animals a faecal transplant from animals with the altered gut microbiome.

The researchers first tested the effect of giving groups of mice access to drinking water spiked with three different artificial sweeteners currently used by people: saccharin (marketed as ‘Sweet’N Low’ in the USA), sucralose (marketed as ‘Splenda’) and aspartame (marketed as ‘NutraSweet’ and ‘Canderel’). The results of the blood glucose tests in mice are shown in Figure 1b of their paper, reproduced below. Despite not being widely used as an artificial sweetener in processed food and drinks anymore, saccharin was the sweetener the researchers chose to do the rest of their studies with, including feeding it to their 7 healthy volunteers.

So why did the researchers choose saccharin for their studies?

Let’s take a closer look at Figure 1b. It’s a graph that shows the area under curve of the data for the blood glucose tests for the mice. The higher the value, the higher or more prolonged the blood glucose levels. Each individual symbol is the value for an individual animal.


The first three groups of animals are the controls – the first were fed plain water (black circles), the second sucrose (black triangles) and the third glucose (black squares). The sucrose and glucose groups are an attempt to control for the sweet taste of the water containing artificial sweetener. The next three groups (blue) are the animals that have been fed the artificial sweeteners: saccharin (blue circles), sucralose (blue squares) and aspartame (blue triangles). The red and grey groups have been fed different antibiotics to knock down their gut microbes in addition to being either control animals or having had the artificial sweeteners.

What is immediately obvious to me is that there are about 4-5 animals in the saccharin and sucralose groups who have very high area under curve values – they look quite different from the rest of the animals in their groups. I think we can call these outliers. That doesn’t mean the effect isn’t real – just that they might not be quite representative of the rest of their cohort. When looking at the data for the rest of the animals, and for the aspartame group, there is quite a lot of overlap between the control groups and the groups fed the artificial sweeteners. I’d love to have access to this data to reanalyse it because I’m surprised the groups are significantly different from the controls, especially for aspartame. But this does explain why they chose saccharin – it showed the biggest difference when compared to the controls.

So could something else be going on with the saccharin group?

One of the things the researchers did was put the animals in ‘metabolic cages’. This allows the researchers to monitor the food and drink intake of the animals as well as how active they are. In their paper the authors state:

“Metabolic profiling of normal-chow or HFD-fed mice in metabolic cages, including liquids and chow consumption, oxygen consumption, walking distance and energy expenditure, showed similar measures between NAS- and control-drinking mice (Extended Data Fig. 3 and 4.)”

Let’s have a look at Extended Data Fig. 3, shall we?

extended fig

“Similar measures”? It looks to me like the saccharin group (and glucose group) drank more and ate less than the other groups. The saccharin group also looked like they expended more energy. Hmmmm. I think ‘similar measures’ is stretching the truth a little.

I’d love to know what the reviewers said about this paper. There’s far too much cherry-picking in it for my liking.

1. Suez J, et al (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature doi:10.1038/nature13793

Monday Micro – from cat poo to kai moana! Siouxsie Wiles Sep 15


Hector's Dolphins at Porpoise Bay 1999 a cropped

Last week I attended a symposium hosted by Massey University’s Infectious Diseases Research Centre (IDReC). There were many fascinating talks but one that caught my attention was by Dr Wendi Roe, a veterinary pathologist, about her work on Hector’s dolphins.

Hector’s dolphins are an endangered species living off the coast of New Zealand. [A 2010/2011 survey found only 55 adults remaining. - Edit 17/9/14 oops, that's Maui's dolphins. There are about 6000 Hector's dolphins...] Dr Roe has been looking at causes of death in Hector’s dolphins and her results were surprising; 7 of the 28 she examined had evidence of extensive infection with the parasite Toxoplasma gondii (1).

If you need reminding, T. gondii is the parasite that makes mice lose their fear of cats, and has been associated with the development of schizophrenia, depression and suicide in people (2).

So how on earth are dolphins getting toxoplasmosis?! Dr Roe speculated that the parasite may be getting into the marine environment after being shed in cat poo. She is now wanting to do a study to see if the parasite can be found in filter feeders like mussels and from her pilot data it looks like the answer is yes. This isn’t the first evidence of marine animals being exposed to T. gondii – a survey of sea otters in California found that 42% had antibodies to T. gondii.

1. Roe WD, Howe L, Baker EJ, Burrows L, Hunter SA (2013). An atypical genotype of Toxoplasma gondii as a cause of mortality in Hector’s dolphins (Cephalorhynchus hectori). Vet Parasitol. 192(1-3):67-74. (doi: 10.1016/j.vetpar.2012.11.001)
2. Henriquez SA, Brett R, Alexander J, Pratt J, Roberts CW (2009). Neuropsychiatric Disease and Toxoplasma gondii Infection. Neuroimmunomodulation 16:122–133 (DOI: 10.1159/000180267)

Monday Micro – the microbiome of death! Siouxsie Wiles Sep 01



With microbiome analysis being all the rage at the moment, it was only a matter of time before someone decided to profile the microbes present in human cadavers. Which is what Ismail Can and colleagues have just published in the Journal of Microbiological Methods (alas, it’ll cost you almost $40 to read their article if you don’t have a subscription).

The researchers wanted to know what happens to our microbiome – the microbes that live in and on us, and outnumber our own cells by 10 to 1 – after we die. What happens to the human body after death is pretty well documented. When the heart stops pumping, the lack of oxygen causes our cells to become hypoxic which triggers the release of enzymes which in turn cause our cells to lyse. This cell lysis releases nutrients into the surrounding tissues, allowing any microbes present to feast and multiply. The lack of oxygen also causes the microbes to shift from aerobic to anaerobic fermentation resulting in the build-up and release of gases, including hydrogen sulphide and methane.

Ismail and colleagues collected samples from the blood, brain, heart, liver and spleen of 11 corpses with known times of death, ranging from 20 hours to 10 days. The organs they chose are ones which would not have any microbes present in a normal healthy person. They then isolated and amplified microbial DNA from the samples and sent them off to be sequenced, to find out which microbes were present.

What the researchers wanted to know was whether there would be a specific pattern and timing for when particular classes of microbes turn up in the different organs after death. If this happens, then it may be that the microbes could be used to indicate how much time has passed since the person died. The authors coined a new phrase for the microbiome of cadavers, the thanatomicrobiome. In Greek mythology, Thanatos is the god of death.

So will we soon be hearing talk of thanatomicrobiomes on CSI? Probably not. The results did show some difference between the bacteria present and the age of the corpse, with the organs of the newest corpses having bacteria such Streptococcus, Lactobacillus and Escherichia coli present (these are bacteria able to mop up any oxygen left in the tissues after death), and the organs of older corpses more likely to contain bacteria that live in the absence of oxygen, like species of Clostridium. But there was a lot of variation between the corpses, and no pattern to which microbes where found in a particular organ. Looks like those CSI teams may have to stick to using insect larvae to date their cadavers for now.

H/T to Kent Atkinson for suggesting this paper for a Monday Micro post

Can I, Javan GT, Pozhitkov AE, Noble PA (2014). Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans. J Microbiol Methods. 106C:1-7. doi: 10.1016/j.mimet.2014.07.026.

Monday Micro – 200 million light years of viruses?! Siouxsie Wiles Aug 05

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Polio EM PHIL 1875 lores” by CDC/ Dr. Fred Murphy, Sylvia Whitfield – This media comes from the Centers for Disease Control and Prevention‘s Public Health Image Library (PHIL), with identification number #1875..

Over the weekend I got an email from broadcaster Graeme Hill telling me about an amazing statement he had heard about the number of viruses on the planet and if it could be true. The statement came from a 2010 BBC Horizon documentary about viruses which you can hear here: Viruses

“Viruses are the most abundant life form on Earth. If you laid all the viruses on the planet end to end, they’d form a line 200 million light years long.”

“Can this possibly be true?” Graeme asked.

Let’s take a look and see how the BBC came up with that astonishing factoid.

The figure seems to be based on the following equation:

10^31 viruses on Earth x 200 nm = 2 x 10^24 metres = 200 million light years

The estimate of 10^31 viruses on Earth appears quite a bit in the literature and seems to trace back to this paper (1) which bases it on the estimate for the number of bacteria on Earth from this paper (2). The logic behind this is that the vast majority of viruses that exist are likely to be preying on bacteria (so-called bacteriophages). So if that number is true, it doesn’t account for any of the other viruses on the planet.

The estimate of 200 nm for the average size of a virus is also a ‘guestimate’. Most viruses that have been discovered have a diameter that ranges from 20 and 300 nm, although the filamentous viruses that make up the Filoviridae family (of which Ebola is a member) can be up to 1400 nm in length. I would use 20 nm for the size estimate to be on the conservative size, but that would still put it at 20 million light year’s worth of viruses!

So instead of using estimates, is there any actual data out there quantifying viruses?

Wommack and colleagues looked at the abundance of viruses in Chesapeake Bay, an estuary of the coast of the USA (3). They collected water samples and visualised the viruses present by transmission electron microscopy after ultracentrifugation. Virus counts ranged between 2.6 x 10^6 and 1.4 x 10^8 viruses per ml of water, with a mean of 2.5 x 10^7 viruses per ml. Estimates for the amount of water in Chesapeake Bay put it at 18 trillion gallons which is 68 trillion litres. This means that, if we use the mean value from Wommack’s study and an average size of 20 nm, in Chesapeake Bay alone there are one twenty-fifth (0.004) of a light year’s length of viruses! Another study, this time along a transect in the western Gulf of Mexico found a similar value for the number of viruses present – from 10^7 to 10^8 per ml (4).

So if we take a value of 10^7 viruses per ml of seawater and multiply this by the estimate for the amount of water in the Earth’s oceans (about 10^21 litres) we get the equivalent of almost 3 million light year’s worth of 20 nm sized viruses. Just in the oceans. Looks like Horizon’s claim may actually be pretty close to the mark!


1. Angly et al (2005). PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics. 6:41. doi: 10.1186/1471-2105-6-41.
2. Whitman et al (1998). Prokaryotes: The unseen majority. Proc Natl Acad Sci USA. 95:6578–6583. doi: 10.1073/pnas.95.12.6578.
3. Wommack et al (1992). Distribution of viruses in the Chesapeake Bay. Appl Environ Microbiol. 58(9):2965-70.
4. Hennes & Suttle (1995). Direct counts of viruses in natural waters and laboratory cultures by epifluorescence microscopy. Limnology & Oceanography 40:1050-1055.

You can listen to my chat with Graeme about this on RadioLive here (about 13 minutes in) but better yet watch the full episode of Horizon on YouTube:

YouTube Preview Image

Ebola outbreak – updates and links Siouxsie Wiles Aug 03


As the Ebola outbreak worsens, the WHO has announced a US$100 million response plan to help bring the outbreak under control by scaling up control measures and helping neighbouring at-risk countries prepare for any cases.

According to the latest WHO update, between 24 and 27 July, a total of 122 new cases of Ebola and 57 deaths were reported from Guinea, Liberia, Nigeria, and Sierra Leone. This brings the number of cases up to 1323 with 729 deaths. Sadly, it would seem that healthcare workers are still becoming infected, with reports that Sierra Leone’s top Ebola doctor has died.

Ian Mackay is charting all the data from the WHO’s Ebola updates while the UK’s Channel 4 have made a clicable map of the outbreak here.

A scary development has been the death of a man in Nigeria – he arrived in Lagos by air via Lomé, Togo, and Accra, Ghana. The man was symptomatic when he arrived in Nigeria which means he would have been infectious at least on his last flight. Officials are now trying to trace all he may have come into contact with on his travels. According to the report, 59 contacts (15 from among the airport staff and 44 from the hospital) have been identified so far.

The fact the man was American, of Liberian decent, and due to return to his family in Minnesota has now put the Ebola outbreak firmly on the radar of the US press. There are also now reports that two infected US aid workers are going to be evacuated from Liberia for treatment in Atlanta.

There is a good article here looking at how easily infectious diseases spread on planes. The answer from simulations seems to be ‘not very’, suggesting only those in the few rows around the infected person are at risk. As Ebola is spread through bodily secretions, this would also mean the potential for transmission by touching surfaces also touched by someone infectious.

And finally, Daniel Bausch and Lara Schwarz speculate on why Guinea and why now in a paper just published in the open access journal PLOS Neglected Tropical Diseases. In an nutshell, it’s likely to be due to the movement of bats and poverty driving people further into remote areas looking for resources to survive. Add to that porous borders and impoverished and neglected healthcare systems and you get an outbreak of this magnitude.

The academic publishing scam – how much research funding are we losing to journal subscriptions? Siouxsie Wiles Aug 01


Currently doing the rounds on twitter is this on the massive profits made by academic publishers:


If you are in Australia or New Zealand and want to know how much is spent just on purchasing subscriptions to academic journals then there is a very handy tool on the Council of Australian University Librarians website.

In 2013 New Zealand’s universities spent $51,135,180 on journal subscriptions.

That’s just our universities, so doesn’t include our CRI’s or independent research institutes. $51,135,180 to access work funded by the tax payer published in pay-walled journals that rely on unpaid labour by university academics for peer review and editorial duties.


To put that figure in perspective, the only funder of investigator-led blue-skies research in New Zealand, the Marsden Fund, awarded $59,000,000 in funding in 2013 – enough to fund 109 projects for 3 years.

In other words, we spend almost as much on buying access to research as we spend on blue-skies research.

I vote we scrap the subscriptions and use the money to double the Marsden Fund, giving each project an allocation to publish their results open access. Makes sense to me!

Hat/tip to Alex Holcombe (@ceptional) and Fabiana Kubke (@Kubke).

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