19 Jul 2018

What’s in that monkey poop? (and how do we find out?)

[Audio file for this blog post from SoundCloud, Coming soon]

One small part of our project this year is collecting poop samples from a few of the crested macaque mothers (and control poop samples from other females) to check out their health. We want to see the total number of parasites per sample and the types of parasites per sample, which we can identify to the genus level. Now I’ve never done parasite analysis before, but Andre Pasetha (my PhD student counterpart) is an expert, so I’ve come to IPB in Bogor for one week for Andre to show me how it’s done.

Step One: Collect your monkey poop. With a small stick, scoop the end of the poop into the tube. There are different methods of preserving the poop, depending on how you want to analyse the parasites. Since we’re only counting them and identifying to genus, we can preserve them in formalin, but if you want them to survive so you can grow a culture, you need a different way of storing them.

All of our Sulawesi crested macaque poop sample tubes ready for analysis.

Step Two: Top up the tube with formalin and shake it up to homogenise it a bit. I missed this part of the process, but Andre said you need to stir it around with a stick as well as shaking, to make sure everything breaks apart.

Step Three: Pour 3ml of your now liquid poop sample into another new tube. Pour through a filter, or pour slowly enough that you don’t get any seeds into the new tube.

Pouring part of the sample into a new tube.

Step Four: Add 2ml of ethyl acetate to the 3ml of poop. This is going to help separate out the parts that we want went we shake up the tube. First shake the tube manually and then go find some shaking machines!

Using a pipette to add ethyl acetate to the sample.

Step Five: Hold the tube against this fancy shaking machine, a.k.a. the "Vortex Genie", to do a better job of shaking up the sample.

Agitating the sample with the Vortex Genie 2

Step Six: CENTRIFUGE!! Put the tube (or multiple tubes if you’ve been preparing them all at the same time) into the centrifuge for 3 minutes. This should be long enough for the sample to separate and look a little like the picture below.

Putting the sample tube into the centrifuge.

Two sample tubes after the centrifuge.
Step Seven: With a pipette, take the liquid near the bottom of the tube and squeeze a drop onto your microscope slide. Cover the drop with a coverslip, and you’re ready to look for poop critters!

Andre pipettes a drop of the sample onto a microscope slide.

Step Eight: MICROSCOPE TIME! Put the slide under the microscope and look for little parasites and protozoa lurking in your monkey poop. We have a couple of different microscopes here – the standard microscope that most people recognise from biology class, and another microscope that’s hooked up to a computer through “OptiScope” - a camera and software that projects the image from the microscope onto the computer screen. 

Andre looking through the microscope
That oval just left of centre is a Barantidium coli!

Today, I was just learning how to get to this point in the process. Next, Andre will be looking through all of these slides to count and identify the parasites. I asked him how he keeps track of all the parasites, and he said that he’s actually going to be using microscopes in another lab where he'll set up the microscope slide and coverslip with a grid so that he can count the number of poop critters in each grid square. In today’s samples we found Balantidium coli – commonly found in macaque poop. It's been fun learning a new technique that's such a departure from my normal research, and I’ll keep you posted on Twitter if we find anything super weird and exciting!

Looking for parasites on a computer screen through the OptiScope.

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