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

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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

Reference:
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.

What Kiwis die of – Part III: Changes with age Siouxsie Wiles Feb 15

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Over the last month we have been looking at the data on the primary causes of death recorded by the Ministry of Health for the 29,204 people who died in New Zealand in 2009. First we looked at what people thought they would die of, and then we looked at differences in the causes of death recorded for men and women. Accompanying each post was a gorgeous infographic by Mike Dickison.

This week we decided to look at how causes of death differ with age. We’ll start with a table of the total numbers of people who died in each age bracket:

I was interested to see that the number of people who died under the age of 80 was really similar to the number of people over 80 (14,371 under 80 versus 14,833). Striking also to see the greater numbers of males dying than females for all age brackets, except the over 80′s.

To show how some of the causes change with age, Mike has chosen to represent as little line graphs:

No surprises for dementia and Alzheimer’s, with the graphs skewed towards the upper age brackets. And probably no surprises that the deaths from traffic accidents peaks for people in their the 20′s. But I’m blown away by the data on assaults. I would never have expected there to be such a huge peak for children, similar to the number of people assaulted in their 30′s. Shocking.

To see if people’s perceptions tallied up with reality, again we took to social media and asked people what they thought was the major cause of death for different ages*. So what did the Kiwis we surveyed think? Results are summarised in the slideshare presentation below.



People were pretty much spot on with the major cause of death for children under five being accidents. But interestingly, while of our survey respondents were right thinking traffic accidents were the major cause of death for people on their 20′s, the number of people committing suicide is almost the same (98 versus 95). For people in their 30′s the major cause of death is cancer, but less than 20% of our survey participants picked this option. More popular choices were accidental death and transport accidents (with about 30% of the votes each). For people in their 40′s, cancer is again the biggest killer, by quite a margin. But again only 20% of our respondents picked this option. The most popular choice was circulatory diseases (heart attacks and strokes). I wonder if this misperception around cancer means those in their 30′s and 40′s are more less likely to miss early warning signs.

* We used Twitter, Facebook, and email to entice over 100 people to fill out our survey using the SurveyMonkey website. Like all online surveys, ours should not be considered representative of the population of New Zealand, but rather of people on social media who were happy to fill out our survey.

This post is the second in a series inspired by the Guardian newspaper’s infographic ‘What we die of’ and is a collaboration between myself, chief number cruncher Dr Paul Gardner and data visualisation extraordinaire Dr Mike Dickison. Dr Paul Gardner (@ppgardne) is a Royal Society of NZ Rutherford Discovery Fellow and Senior Lecturer in Bioinformatics at the University of Canterbury’s School of Biological Sciences. He gets very excited about RNA. Dr Mike Dickison (@adzebill) is a freelance information designer with a PhD on the evolution of giant flightless birds. He quite likes ukuleles too. Dr Siouxsie Wiles (@SiouxsieW) is a Health Research Council of NZ Hercus Fellow at the University of Auckland’s Faculty of Medical & Health Sciences. She is rather keen on nasty bacteria and anything that glows in the dark.

What Kiwis die of – Part II: The battle of the sexes Siouxsie Wiles Jan 31

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Two weeks ago, we asked Kiwis what they thought they would die of, and compared their responses to the primary causes of death recorded by the Ministry of Health for the 29,204 people who died in New Zealand in 2009. Mike Dickison produced a beautiful infographic* of the causes that were responsible for more than 1% of those deaths. Obviously this data reflects what was recorded on the death certificate which may not always be the immediate cause of death. In fact, there was some discussion afterwards about the reality of ‘old age’ being an unacceptable cause of death here!

This week we decided to take a look at differences for causes of death recorded for men and women. Mike has worked his magic again and produced the infographic below. This time the little coffins each represent 25 people.

Its striking that more men die of prostate cancer than women die of ovarian, and twice as many men than women die from cancer of the bladder and kidney. But lots more women die of cerebrovascular diseases, that is strokes and brain haemorrhages, and dementia. To see if people’s perceptions tallied up with reality, we took to social media and asked people whether they thought there were any differences between what men and women died of**. So what did the Kiwis we surveyed think? Results are summarised in the slideshare presentation below.



The first striking thing to come from our survey participants is that the majority thought that more men die than women, and that more men die of diabetes, cerebrovascular diseases, traffic accidents and suicide. But not skin cancer. In actual fact, the numbers of men and women who died in 2009 was very similar, 14,615 men and 14,589 women. As you can see from the infographic, more men died in traffic accidents and diabetes, or committed suicide. But our respondents were way off with cerebrovascular diseases. And with the fact that skin cancer killed more men than women. The other question we asked related to breast cancer deaths in men. 8.2% of our respondents thought that men couldn’t get breast cancer. In fact, in New Zealand in 2009, 1 in 100 breast cancer deaths were in men.

As several people pointed out with our first infographic, these differences between perception and reality could be dangerous if they mean resources are diverted away from where they are really needed.

*Head on over to Mike’s Pictures of Numbers blog to see how the infographic came about and for a downloadable version.

** We used Twitter, Facebook, and email to entice over 100 people to fill out our survey using the SurveyMonkey website. Like all online surveys, ours should not be considered representative of the population of New Zealand, but rather of people on social media who were happy to fill out our survey.

This post is the second in a series inspired by the Guardian newspaper’s infographic ‘What we die of’ and is a collaboration between myself, chief number cruncher Dr Paul Gardner and data visualisation extraordinaire Dr Mike Dickison. Dr Paul Gardner (@ppgardne) is a Royal Society of NZ Rutherford Discovery Fellow and Senior Lecturer in Bioinformatics at the University of Canterbury’s School of Biological Sciences. He gets very excited about RNA. Dr Mike Dickison (@adzebill) is a freelance information designer with a PhD on the evolution of giant flightless birds. He quite likes ukuleles too. Dr Siouxsie Wiles (@SiouxsieW) is a Health Research Council of NZ Hercus Fellow at the University of Auckland’s Faculty of Medical & Health Sciences. She is rather keen on nasty bacteria and anything that glows in the dark.

What do Kiwis die of? Siouxsie Wiles Jan 18

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I have never really understood why some people are desperate for immortality. Like those crazy millionaires who have their heads frozen in liquid nitrogen. I am not afraid of dying, but I would like to die painlessly and without much fuss, and preferably with all my faculties intact*. But what am I likely to die of? We looked at figures recorded by the Ministry of Health of the primary causes of death for the 29,204 people who died in New Zealand in 2009. For simplicity, we have only looked at the causes that were responsible for more than 1% of those deaths and have summarised them in the infographic** below. It is important to bear in mind though, that the figures cover what was recorded on the death certificate which may not always be the immediate cause of death. For example, many of those who are recorded as having died of Alzheimer’s disease are more likely to have died of pneumonia or a urinary tract infection.

To see if people’s perceptions tallied up with reality, we took to social media and asked people what they thought were the biggest killers and what they were likely to die of***. So what did the Kiwis we surveyed think? Firstly, and unsurprisingly, that many would like to thought they would die of ‘old age’. Sadly this is not recognised as a cause of death by the Ministry of Health! It was also interesting how discomforting many people found the survey, with a number of people telling us that they did not want to think about how they might die, or skipping that question entirely. But many people did take the time to think about it, so how did their perceptions match the Ministry’s statistics?

31% of those surveyed thought they would die of conditions like angina, heart attacks, strokes and high blood pressure, which are classed as ‘circulatory diseases’. And they are probably right, because in 2009 circulatory diseases were New Zealand’s biggest killer, responsible for 35.5% of deaths (10,372 people).

71.8% of our survey participants underestimated the number of cancer deaths in New Zealand, although 22% of them thought that cancer would be the cause of their demise. In fact, cancer is the second largest killer, responsible for 29.1% of deaths (8,500 people) in 2009. Interestingly, 66% of those surveyed did not know that cancers of the digestive system are the most frequent cause of cancer deaths in New Zealand, though they recognised lung cancer is one of the biggest killers.

In 2009, traffic accidents and suicides were both responsible for more deaths in New Zealand than skin cancer (melanoma). Yet 48% of our survey participants perceived melanoma as the greater risk. Perhaps this shows how successful the ‘slip, slap, slop’ message has been.

Despite respiratory diseases being the third biggest killer of Kiwis, they were largely unrecognised by our survey participants with only 2.1% listing it as what they may die of.

It was very sad to see that 10 of the people we surveyed listed suicide as their cause of death, giving suicide a higher representation in our survey population than in real life. Could social media be a good forum for offering support to those struggling with thoughts of harming themselves.


Over the next few months we will be delving into the stats more closely, so if there is something you would like us to examine then please get in touch.

[Edited 18/01/2013 to correct a sentence]

*Then I would like to be buried in a shroud or biodegradable casket and return my vast store of nutrients back to the land. If space is an issue, then I quite like the idea of being cremated and popped into one of Spanish designer Martin Azua’s Bios Urns which are made from coconut shell, compacted peat and cellulose and contain the seed of a tree.

**Head on over to Mike’s Pictures of Numbers blog to see how the infographic came about and for a downloadable version.

*** We used Twitter, Facebook, SciBlogs and email to entice over 360 people to fill out our survey using the SurveyMonkey website. The full results are available on Shareshare. Like all online surveys, ours should not be considered representative of the population of New Zealand, but rather of people on social media who were happy to fill out our survey.

This post was inspired by the Guardian newspaper’s infographic ‘What we die of’ and is a collaboration between myself, chief number cruncher Dr Paul Gardner and data visualisation extraordinaire Dr Mike Dickison. Dr Paul Gardner (@ppgardne) is a Royal Society of NZ Rutherford Discovery Fellow and Senior Lecturer in Bioinformatics at the University of Canterbury’s School of Biological Sciences. He gets very excited about RNA. Dr Mike Dickison (@adzebill) is a freelance information designer with a PhD on the evolution of giant flightless birds. He quite likes ukuleles too. Dr Siouxsie Wiles (@SiouxsieW) is a Health Research Council of NZ Hercus Fellow at the University of Auckland’s Faculty of Medical & Health Sciences. She is rather keen on nasty bacteria and anything that glows in the dark.

What do you think Kiwis die of? Siouxsie Wiles Jan 15

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The inhabitants of NZ, that is, rather than our feathered and flightless friends!

I’m trying to find out what people think those living in New Zealand die from. Will you tell me what you think? Please fill out this short survey and ask your friends and family to do the same.

All will be revealed at the end of the week. Thanks!

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