Mike the Mad Biologist

Poop on the Potty
Shamelessly stolen from Dr. Isis

Yes, you read the title correctly. As I’ve mentioned before, I’m involved with the Human Microbiome Project, which examines how the microbes that live on and in us affect human health and disease. One of the things we do is look at human gut communities. In most cases, examining the bacteria growing on the side of gastrointestinal tract is…difficult. Think the Mother of All Protological Exams. So we use feces as a proxy of what lives in your gut. And since you were going just flush that stuff anyway, mind if we….

Well, you get the idea. Now you might think that collecting poop is straightforward. You would be wrong. We actually have to be quite rigorous about poop collection. For example, we don’t some stools sitting around at room temperature and in the presence of oxygen, which allows some bacteria to grow while others can’t (many will die in the presence of oxygen).

This becomes even more complicated, since there are 300 people being sampled. Most people don’t poop on command, and following them around with buckets isn’t really practical–not to mention, incredibly creepy. Fortunately, we have detailed instructions for our volunteers.

So here’s how to take an NIH-sanctioned study-acceptable poop:

Raise the toilet seat. Place the stool collection frame on the back of the toilet bowl. All four corners of the collection frame should be supported by the toilet bowl.

Place collection bowl in frame (if you don’t, it kinda defeats the purpose of the whole exercise):

Place toilet seat down (do people really crap without doing this?):

DON’T PEE IN THE BUCKET! (That’s actually in the instructions, although not put as elegantly). Not only will the urine alter the microbial community of your poop, but it’s really gross too. Thankfully, there’s an emergency backup container (poop collection is like the Apollo missions, but without rocketships. And with lots of poop).

Remove and seal tightly! Like so:

Place the container in a Ziploc bag–cuz it’s a bucket of shit:

Now we have to ship it–and we have to keep said poop cool, but not frozen (freezing can lyse cells). Using seven ice packs, completely surround the container with the packs, like so:

Then follow the shipping instructions.

Government-approved pooping!

All kidding aside, one of the key things the HMP will have accomplished–although it’s not very sexy science–is developing standard methods. Without this, we simply don’t know to what extent community differences are due to interesting biology versus methodological variability.

For this, and other methods, check out this website (the sample collection manual is available as a pdf here).

Ain’t science cool?

Comments

#1 Mike Lisieski
September 22, 2010

This is wonderful.

“Place the container in a Ziploc bag–cuz it’s a bucket of shit”

Somehow I doubt that made it into the instructions verbatim.
#2 mad the swine
September 22, 2010

[Limbaugh]

My God, look at all that time and effort and energy being wasted on studying shit. Literally, shit. Talk about government waste! They’re literally flushing your money away!

[/Limbaugh]
#3 Liz
September 22, 2010

What a great post! It’s a good example of the many details researchers need to think out carefully. And, of course, I *had* been wondering about how this sample collection happens.
#4 wazza
September 22, 2010

this isn’t so different from the standard for faeces samples for medical testing, except that a small sample is kept rather than the whole thing, and it’s a fridge rather than an ice pack…

…and I put an ice cream container down there rather than one of those fancy collector frames.
#5 AnyEdge
September 22, 2010

You know, I have never been happier that my sort of medical research doesn’t involve specimens of any sort whatsoever.
#6 Willy
September 22, 2010

Working at a DOE fuel reprocessing site in SE Idaho they did whole-body scans for radiation exposure but sometimes you got the “lunchbox”. It was a regular working-guy lunchbox but it had a jar for collecting your urine and a plastic tub (like the one pictured) for your poop. For the day all your eliminations and evacuations were to be collected and turned in to Health Physics for analysis.

Carrying the lunchbox was a cue for derisive comments from your colleagues. (I eventually got the lunchbox.)
#7 darwinsdog
September 22, 2010

And since you were going (to) just flush that stuff anyway..

Naw, not me. The flush toilet is something I’ve given up using. Still have two of them, and my wife uses them but not me. I pee outdoors and poop into a five gallon plastic bucket that sets under a wooden frame with a toilet seat on top. I wipe with brown paper towels ‘cuz I don’t want chlorine bleached paper going into the compost. Once everything’s come out okay I cover the poop with a layer of leaf litter, straw, peat moss or other organic stuff then close the bucket lid. Once the bucket’s full I dig down into a working compost bin, dump and bury it. When the compost is finished the poop is gone but much of the nutrients remain. There’s no smell, if the poop’s kept covered. Human feces is just too valuable of a resource to waste. Wish I had access to 300 people’s poop. I hope that you’re composting the collected samples once you’ve done your thing with them.
#8 Paul
September 22, 2010

@ Limbaugh.

No, it’s not a waste of money. These are things we need to know for health reasons.

My job is centered around poop, both animal and human. But, I don’t deal with it until after it’s been collected from a treatment system. My responsibility is to ensure that we can grow crops with poop. To be honest, poop is cleaner than a lot of the other materials I deal with, such as wastes from meat packing and rendering plants.
#9 Paul
September 22, 2010

@ darwinsdog

Go to a local wastewater treatment plant and they’ll probably give you as “poop” as you want. They’ll probably send it to a landfill anyway. If they have drying beds, you can shovel it yourself.
#10 Julie
September 22, 2010

I was involved with the Orlistat study many years ago and had to give these very instructions to my patients. Orlistat blocks intestinal uptake of fat, so it is lost in the stool, sometimes with the side effect of, wait for it…anal leakage! Yay!

So we gave out these hats, gave out the coolers and ice packs and had our patients collect their stools.

But it gets better. We had to ship it to Norway. Yes, I shipped 800 pounds of human poop to Norway. I’m assuming that I put enough dry ice in the container because I never got a complaint from the other side.

Science is WONDERFUL!!
#11 DuckPhup
September 22, 2010

Oh, good. Perhaps… with your expertise in approved and sanctioned pooping methodology… you may be able to shed some light upon a historical/biblical/scatological puzzle, having potentially HUGE theological and metaphysical implications.

Throughout the Holy Bible… along with all the contradictions, lies, fantasy, misperceptions of reality, and such… there are places that seem to be unfinished. Some bits seem like they WOULD make sense, if only there were a couple more lines. So, were those couple of sense-making lines removed?… or were they never there, in the first place? In either case… why was it fiddled-with?

From Deuteronomy…

23:12 And thou shalt have a paddle upon thy weapon; and it shall be, when thou wilt ease thyself abroad, thou shalt dig therewith,

23:13 and shalt turn back and cover that which cometh from thee: For the LORD thy God walketh in the midst of thy camp…

Well, that last bit comes across as sort of a lame explanation, doesn’t it? “[...] For the LORD thy God walketh in the midst of thy camp…?”

That’s IT?

That’s ALL?

That doesn’t make much sense at all… UNLESS there was something removed, or left out. Something like this, perhaps…

23:13(a) … and skulketh amongst thee unseen in the wee hours, like unto a freakin’ Peepin’ Thomas;

23:13(b) and verily, it honketh Him off mightily when He trompeth upon a steaming pile of thine poop, and it squisheth up warmly and fragrantly betwixt His toeses.

Left as-is, the verse raises more questions than it answers…

* The verse suggests that, at the very least, The Lord is afflicted with poor night-vision. Doesn’t that seem like a rather lame limitation, for an all-powerful supernatural super-being?

* IF The Lord is omniscient, doesn’t he already KNOW where all the vagrant piles of shit are deposited? He should be able to avoid them blindfolded.

* IF The Lord REALLY IS concerned about encountering stray turds during His late-night skulk-a-thons, does that not raise questions about the nature of His ‘being’? He is reputed to be a ‘spirit’… but one would think that a spirit would not be affected by human excrement. Or, perhaps we are to assume that He did His creeping-around in HUMAN form; but that suggests that it was Jesus who was doing the midnight wandering… but considering that Deuteronomy is OLD Testament stuff, THAT creates an uncomfortable anachronism.

* What if this is actually informing us that the ‘supernatural’ aspect of a being IS susceptible or vulnerable to human activities? The ‘metaphysical’(***) implications of THAT would be incalculable! NO WONDER they boogered around with the text!

(***) Metaphysics: “The blind leading the stupid into the unknown, on a quest for the unfathomable.” ~ DuckPhup (my personal definition)
#12 stripey_cat
September 22, 2010

Now my take on the Deut. quotes was that it would be really good to have something about not crapping “in the midst of thy camp” – I suspect more people were injured tripping over patches of newly-dug soil than would have been attacked by bandits or predators creeping off into some bushes.
#13 Onkel Bob
September 22, 2010

Could be worse – You could need to use the Wag Bag. As a climber, I know these things these things are de rigueur on many mountains.
#14 Art
September 22, 2010

I would have thought there would be some effort to exclude air. Perhaps a squirt of CO2 before sealing the container. Or pooping into a bag and then vacuum packing.

Composting poop is pretty easy. First step is to exclude urine. Without urine the feces surface dry and are much less smelly. Covered with leaf litter, sawdust or peat moss it doesn’t smell much at all.
#15 Calli Arcale
September 22, 2010

That was delightful. Thank you for sharing.

poop collection is like the Apollo missions, but without rocketships. And with lots of poop

Cue space-geek mode….

Poop collection is a major problem in space. During the Apollo missions, it was a lot like the procedures listed above, only without all the glamor and comfort. Step one: eat low-residue food to reduce the need to poop. Step two: hold it as long as you possibly can. Step three: when you are left with no other alternative, tape a bag to your butt and do your thing, in a space roughly the size of a closet, in front of two your closest professional colleagues. Step four: carefully remove the bag from your butt, because “floater” has a whole new meaning in this context, seal it away, and live with the fact that you’ll be sharing this tiny space with several of those bags for the next week or so*. Yay!

* Unless you landed on the Moon. Then you get to chuck it out the door before blastoff. Ah, the elegance, majesty, and grandeur of spaceflight!
#16 wazza
September 23, 2010

darwinsdog: be careful, studies have shown that plant viruses can survive the human digestive tract, making it not so good for your tomatoes.
#17 KAT
September 24, 2010

Mike- this is totally awesome. What about the representativeness of the sampling popluation to the larger population in question?
#18 sumomax
March 27, 2011

Not a lot of simple snoring gıdermke deve fırms ugrasıoyr yapomak it so easy to eee what you olurmu yapıyorse iu
I do not understand why why why desne had come on why do not oomuyor
#19 plumbing
May 15, 2011

What a strange blog. You deliver a poop to the government for it’s approval? But the funny is, you seal the poop tightly!
#20 plumbing
May 25, 2011

Thanks for the insights,Good thing that you include the proper procedure so that we comply with the standards given by the government.
#21 Dennis
March 18, 2012

Looks good. Very clean and proper method. I found -by the way- another interesting solution on the internet. http://www.fecotainer.eu
#22 Borf Bundafute, M.D.
April 3, 2012

I have long felt that poop has been unfairly stigmatized. A bowel movement can be a highly spiritual experience. During my dark times, when I was addicted to crystal meth, touring the world opening for George strait, my only solace came while sitting on the toilet, squeezing a solid nugget or two into the bowl. George made me save my stool. He would demand it from me. After every movement, he would be there, with a net and a ziploc baggie. I used to think he was keeping them to create a sculpture of me, as a gift. I later discovered he was testing my poop for drugs. I was fired, but I will never blame poop. Sweet, aromatic poop…luckily, I was able to fall back on my phd, and I am now surrounded by stool samples all day. I sometimes take my work home with me. I am a copropheliac.