A microbiome scientist working at a tech startup in Silicon Valley, Sam Westreich provides insights into science and technology, exploring the strangest areas of biology, science, and biotechnology.
It's a silly question, but a new study shows why it’s important for our health
Despite what you may have learned in elementary school, we all poop — men, women, and especially children. (I’ve changed plenty of baby diapers; so much poop.)
But here’s a question that you probably have not pondered: is the poop inside your body the same as the stuff that comes out?
This might seem like a stupid question, but let me reframe it in more scientific terms, and perhaps you’ll see why it’s important to ask:
We commonly collect fecal samples and use those as a method to determine whether a patient is healthy or if they may have a disease or condition of concern. However, do fecal samples (collected after the patient has defecated) properly represent the composition of feces from inside the individual’s colon? Or are we getting skewed results?
The gut microbiome — the rich and diverse collection of bacteria inside the intestinal tract — is an area of great interest and seems to be correlated with a wide range of health and disease outcomes. The microbiome seems to play at least some role in keeping us healthy, and an unbalanced microbiome appears to at least be correlated with certain bowel diseases, like irritable bowel syndrome, inflammatory bowel disease, or Crohn’s disease.
If we’re going to continue studying the gut microbiome, we need to collect accurate data on which species are present, and what they’re doing.
But if we wait until feces have left the body, are we waiting too long to get a good picture of the bacteria present?
A paper recently published by researchers at the University of Aberdeen, in the U.K., aims to answer this question.
Why we care about examining the gut microbiome
I’m a microbiome scientist by study, meaning that I did my PhD research examining diverse groups of bacteria. Specifically, I focused my studies on the human gut microbiome, which is the collection of many different types of bacteria that live in unstable, uneasy semi-harmonious partnerships inside our small and large intestine.
Feel free to check out the above article to get more information on microbiomes in general. Focusing specifically on the bacteria living in our intestinal tract, we already know about some direct benefits of their presence:
We’ve also found that there’s some degree of a link between our microbiome and our wider health:
There’s a long list of associations between the details of the blend of bacteria living in our intestine, and our own health. But we still need to do more work to determine whether this is a case of causation, or just spurious correlation. (Is the gut microbiome responsible for causing weight gain or a chronic disease? Or is the gut microbiome simply changing because it’s influenced by the disease?)
How do we look at the gut microbiome?
Most of the time, when we want to examine the gut microbiomes of humans, we go with the collection of fecal samples.
When you go to the bathroom, you pass out waste — but a good fraction of that waste is actually just a mass of bacteria. By some estimates, bacteria make up anywhere from 30% to 55% of the mass of what you pass! (Estimates vary depending on whether you look at dry weight, or wet weight, of the feces.)
Researchers can take a fecal sample and use DNA extraction and high-throughput sequencing to look at which bacteria are present. Each species of bacterium has its own, unique DNA sequence. Instead of trying to identify the bacteria by growing them out on culture plates, we can simply pull out all the DNA, put it all into a sequencer, and turn it all into digital data. We can then use computers to match each piece of DNA back to the species from which it originated.
This approach works well… assuming, of course, that a fecal sample is comparable to what’s happening inside the patient’s body.
(We really want this to be the case! It’s far easier to convince participants in a study to collect a sample of their poop than it is to perform an invasive swabbing or extraction from inside their colon.)
So this is what the University of Aberdeen researchers set out to test in their recent paper, “Comparison of microbial signatures between paired faecal and rectal biopsy samples from healthy volunteers using next-generation sequencing and culturomics”.
What did researchers find about the bacteria inside vs. outside your body?
Feel free to check out the full paper (it’s open access, so no fee is required to read it!), but I’ll summarize their findings.
The researchers collected samples in a few different ways:
The inner walls of your large intestine are coated in layers of mucus, which help keep things flowing smoothly and also shield the walls of your intestine from direct contact with the bacteria and inner contents. Some bacteria burrow deeply into this mucus, but most only attach lightly, and are commonly shed along with the poop. This is why the researchers separated the biopsy tissue from the wash liquid.
Overall, the bacterial composition seemed pretty similar when looking at the fecal aliquots, the homogenized feces, and the biopsy wash. Only the biopsy tissue itself showed a significantly different bacterial profile.
Put together, these results paint a picture of two different groups of bacteria inside your gut:
This is good news for all of our previous studies, which have relied on the approach of collecting fecal samples after they’ve left the body! Those fecal samples likely did a pretty good job of including all the bacteria that are present in the lumen.
It does suggest, however, that a fecal sample probably isn’t going to capture all the activity that might be happening in the mucosa, that thick, protective layer of mucus that shields our intestinal wall cells from direct contact with bacteria. This area, and the microbes burrowed into it, may be yet another complex system that we’ll need more time and data to understand.
Any limitations to this research?
There is one big limitation that I want to call out: the type of microbe identification used by these researchers.
They used an approach called 16S rRNA sequencing, which is often referred to as “barcoding”. It uses one particular DNA sequence, present in all bacteria but with differences between taxonomic groups, to identify which bacteria are present.
16S rRNA sequencing is cheap and easy, and it requires a lot less total digital data. But it’s not exact; it can’t tell us exactly which species of bacteria are present, only their general families. It’s like knowing that a mall has two Chinese restaurants, three Italian restaurants, and five American restaurants — but you can’t get the fine-grained detail of the menus, so you don’t know what exact food is served at each place.
I’d love to see a similar experiment but with more fine-grained sequencing, to get more specifics on how each individual species of bacteria compares in the different samples.
In summary: fecal samples do represent the bacteria floating loose in the intestine
It turns out that a question that seems stupid and obvious at first glance ends up being quite important! “Is your poop the same inside your body as once it’s left your body?” Seems silly, but is very relevant and important to answer from a science perspective.
However, we need to recognize that bacteria in our intestine aren’t all mixed evenly. Some are floating freely in the innermost, open area (the intestinal lumen), while others are burrowed snugly into the thick mucus layer that coats the edges of the intestinal walls (the intestinal mucosa). Those burrowed-in bacteria hold on too snugly to be shed in our poop, so they won’t show up in analyses of fecal samples.
If all of this seems complex, well, you’re right — it is! Study of the gut microbiome is still ongoing work, and it’s going to take plenty more research to unravel all the ways that this complex organ impacts our overall health.
Think about it when you next visit the bathroom: you’re not just passing waste, but all sorts of info on your health, based on the bacteria in your poo!
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A microbiome scientist working at a tech startup in Silicon Valley, Sam Westreich provides insights into science and technology, exploring the strangest areas of biology, science, and biotechnology.
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