Microbial Phylomon- Salmonella enterica

To get everyone in the mood for #microtwjc tonight, I give you the microbial phylomon card for Salmonella enterica.

Previous Microbial phylomon posts can be found below:
http://defectivebrain.fieldofscience.com/2011/08/more-microbial-phylomon.html
http://defectivebrain.fieldofscience.com/2011/09/even-more-microbial-phylomon.html
http://defectivebrain.fieldofscience.com/2011/12/when-phylomon-fall-from-sky.html
http://defectivebrain.fieldofscience.com/2011/08/microbial-phylomon.html
http://defectivebrain.fieldofscience.com/2011/10/microbial-phylomon-it-came-from-beneath.html
http://defectivebrain.fieldofscience.com/2011/08/microbial-phylomon-and-friends.html

#Microtwjc A Salmonella of Doubt ?

The microbiology twitter journal club beckons, and it is now time to wade through the latest paper, on Salmonella, and how to spot different subtypes of this bacteria. This allows us to get a look at the recent evolutionary history of the bacteria, and to track new subtypes as they arise. In the past, the ways these new subtypes were tracked and analysed through serotyping. 

#microtwjc Do Electric Guts Dream of Android Burgers ? part 2

In part 1 of this post, I briefly described the key piece of equipment used in this study- the TIM2 machine, designed to model the large intestine.

Do Electric Guts Dream of Android Burgers? Part 1 #microtwjc

The next paper for #microtwjc raises some interesting questions about what effects probiotics have on the gut. If you want to study the gut, and the bacteria within it, there are a number of little problems. For instance, many of the bacteria in the gut are anaerobes, and will shrivel up the moment they get exposed to air. It is thought that the distribution of different bacteria varies throughout the gut, so just taking faecal samples won't cut it. 
So what can you do? There are animal models, where you can try and sample the bacteria in different areas of the intestine after dissection, or perhaps use techniques like bioluminescence to look at bacteria directly within the digestive tract. I remember hearing someone pitch a project to use magnetic resonance spectroscopy (using some fancy MRI technology) to analyse bacterial metabolites within the guts of human volunteers.
There is another way that researchers can try and work out what's happening in the gut. Through the creation of an artificial gut.
Consider for a second that in simple terms, your gut is basically a fancy bioreactor. It is a vessel in which enzymes, bile and bacteria all get mixed together to help you digest your food. So what if we tried to create this system artificially, and what would reveal about digestion
 Minekus et al (published in 1999) developed the system, where they essentially created an artificial model of the large intestine, which over the last ten years has been developed to the one seen in the week 6 #microtwjc paper.
So how does this machine replicate the way that the Large Intestine works ?

• Peristalsis- Your gut moves food around through squeezing it's walls and pushing the food along. The inside of this machine has a series of flexible walled tubes, which have water pumped along the outside of them. The pumping of the water passing through the system causes periodic compressions to be transferred through the system, mirroring the peristaltic movement seen in actual human guts.
• Temperature: The water passing through the gut is heated to body temperature, which is 37 °C.
• Bile: Bile performs a number of functions, such as introducing a number of salts which act to emulsify fats. Another function it performs is neutralising gut acid, and keeping the pH of the large intestine stable. To ensure that the pH of the electric version of this system is stable,  pH sensors were present to control the infusion of sodium hydroxide, preventing it from getting too acidic.
• Absorption: The main function of the gut is to absorb nutrients, such as short chain fatty acids. To replicate this, fibre membranes placed at strategic points along the machine allow for small molecules to pass through them. These are hooked up to pumps an pressure sensors to ensure that the pressure within the system remains constant. 
•  Metabolites: In the human large intestine, partially digested food comes in from the small intestine. To replicate the present of this food, metabolites are added into this system, and because of the way the absorption works (via osmosis) the action of that system also acts to keep the metabolite levels within the gut fairly constant.
• Anaerobic- It is generally thought that the human gut is mostly colonised by anaerobic bacteria*. So air was prevented from entering the system by flushing it with gaseous nitrogen.

This is the basis for the TIM2 system. Now, anyone can easily see that it isn't a perfect model for the gut. With any model, physical or computational, there are limitations. What you get is based off of your assumptions when creating it, and if you forget those, then you can be lead badly astray.
So the question is is it useful?

The only way to determine this is to validate the model.
In the initial paper, they found that the system absorbed short chain fatty acids, and maintained pH fairly well with "standard" fermenter flora and allowed them to survive in the system.
Also "Three successive experiments were carried out using fecal inocula from three diff€erent methane-excreting volunteers". They did not mention whether these people were chosen on the basis of their methane excretion. They looked at how well the faecal flora survived in the large intestine.
So from this first paper, they showed that this model of the gut could keep bacteria from the human gut alive, and that this system could absorb short chain fatty acids.


The point I would like to make about this model system is that yes, it does have limitations. It is not a perfect representation of the human gut.  Even though we can't extrapolate findings with this equipment directly into humans, we can still put this machine to good use. It can be use to grow bacteria with different nutrients, and furthermore elucidate some of the more complex relationships between them within the human large intestine. 
It is with that in mind that I shall look at the actual #microtwjc paper in part 2 of this post.


  Minekus, M., Smeets-Peeters, M., Bernalier, A., Marol-Bonnin, S., Havenaar, R., Marteau, P., Alric, M., Fonty, G. & Huis in't Veld, J.H.J. (1999). A computer-controlled system to simulate conditions of the large intestine with peristaltic mixing, water absorption and absorption of fermentation products, Applied Microbiology and Biotechnology, 53 (1) 114. DOI: 10.1007/s002530051622

Part 2 is up here

* I should point out right now that I am not entirely certain whether the mammalian gut is entirely an anaerobic environment. For instance, I pointed out a study using bioluminescence to study bacteria as they invaded the gut. The bioluminescence reaction shown there requires oxygen to be present in order to function. So this indicates strongly that there is oxygen in the mammalian gut, but again, this conflicts with what is known about most of the microbiota present, which tend to shrivel and die at the mere mention of that element.

Cower Before Pretzlcoatlus !

The long neck of the Quetzlcoatlus always looked really odd to me, until I realised that all of the fossil conformations looked completely off.And when I zoomed in to the pictures of quetzlcoatlus fossils, I noticed that all of the structures were strangely square, almost like pixels. I propose that these are salt crystals ! Taking this new evidence into account,  I suggest an entirely new reconstruction for this beast. Ladies and Gentlemen, I present Pretzlcoatlus !

No, I'm not just overinterpreting every blemish on the paleontological images just to support my theory. I have verified it with tracing paper and crayon. And I need your support to get this new creature recognised by the paleontological community.
Ignore the unsavoury musings that can be found at tetrapod zoology http://blogs.scientificamerican.com/tetrapod-zoology/2012/07/03/world-must-ignore-reptileevolution-com/
And the distasteful take found in Laelaps http://www.wired.com/wiredscience/2012/07/pterosaurs-done-wrong/
And you should almost certainly disregard the  "lacking in snacky-goodness" views of the paleo king
http://paleoking.blogspot.co.uk/2011/05/strange-journey-of-david-peters.html

Hail Pretzlcoatlus !

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#microtwjc- What's living in your bathroom.. Weeee

And so dawns another week of the microbiology twitter journal club. This week we're discuss public toilets. WEEEEEEE!

Because the greatest concern when anyone goes to the restroom is the bacteria. Yes, you can't see them, but you know they're there.... watching...waiting...plotting.

But who are these mysterious bacteria? Can the 6 layers of two-ply really protect you as you sit straining atop your cushioned throne? This paper probably won't answer that.

This paper was an attempt to work out the identities of the bacteria in the restrooms, and where they come from.

Science, It's a meritocratic thing?

#sciencegirlthing meme confused me, because when I started at university, there was a 60:40 girl boy ratio on my science course. There seem to be plenty of girls going into science courses, but where do they go? This got me thinking about something that I wanted to blog about a while ago, but was too angry to do anything other than mash the keyboard with my own face.

In my early days working in the lab, I had the fortune to work with an amazing post doc. This post doc always knew what they were doing. Some days, they would be the first one in the lab, and last one out. Not because anyone told them to, not because they felt it gave them an air of arrogant superiority, but because the experiments demanded it. Through an extraordinary level of organisation, they managed to do a huge amount of work with very little time. It was an acknowledged fact in our lab that this post doc was some sort of superhero. Seeing that level of dedication, organisation and productivity affected me a lot, and I still am attempting to emulate their example.

So hearing that she wanted to get out of science sent my head spinning.

After which I was directed to look at the academics in higher positions. Most of them were men. It doesn't take a genius to see that something was going on.

There is a phrase that I've heard bandied about a number of places,  "Too smart for science". Occasionally a lab will be blessed with an amazing student who, despite being excellent at science decides that they'll be better off doing another career, because the job opportunities are so small. And they do well, because they are smart enough to excel at anything they do. But it is still a loss for science.

So when you present such a person with a game so stacked against them, is it any surprise when they cash their chips and go elsewhere ? Why go through the sacrifice and hard work of a career in science when there is very likely no pay off at the end of it. 

So seeing someone who had played such a key inspiration for me, decide that science wasn't the best use for her talents, was devastating. Hence the face/keyboard/laptop chewing implied earlier. Because I had my main preconceptions of science shattered.

 I realised that no matter how good I am as a scientist, some arbitrary crap that I have no control over can prevent me from pursuing a career. Actually we don't always have the best people solving our scientific problems because the system is tipped against a lot of them. This is a career where the smartest people don't get to the top, they get out. 

Can we really claim science is a meritocracy when we are haemorrhaging some of our best talent ?