As we’ve observed before, your mouth probably contains as many different bacterial species as there are animal species in the National Zoo in Washington, D.C. (about 300).
But your oral cavity is a mere minnow in bacterial diversity compared to your gut, where somewhere between 500 and 1,000 different types of bacteria hang out.
Now, with such variety and, dare I say it, imprecision (500 to 1,000 seems like a wide range to me), you really can’t blame scientists for trying to introduce some structure and classification into the microbiome.
It’s what we humans do, after all.
We classify things to help us stay organised.
Safeway and Home Depot both sell stuff, but it’s different stuff, so we call one a supermarket and the other a home improvement store, and we know where to go when we want to buy dinner, and where to go when we want to paint the kitchen.
In fact, as experts at UCSD point out, our prehistoric ancestors stayed alive to some extent because their rudimentary classification systems enabled them to know which plants and animals were safe, and which weren’t.
Of course, scientists love a good taxonomy, a systematic structure of groups and categories, and the king of taxonomies has to be Swedish scientist Carl von Linnaeus’s “Systema Naturae” published in 1735, which labels, groups and classifies every living thing.
We have him to thank for being able to identify ourselves as Homo sapiens (from the genus “Homo”, and the species “sapiens”), for instance.
So back to the microbiome, and it would clearly be helpful if there was some broad overarching way to categorize our overall gut microbiomes.
Indeed, for a while in 2011 it looked as though this might indeed be possible.
A study led by Peer Bork from the European Molecular Biology Laboratory in Germany suggested the existence of three very specific overall bacterial profiles which he called “enterotypes”.
Bork et al proposed that these might operate something rather like blood types, not dictated by age, gender, body weight or nationality/race.
Type 1, he said, was typical of those who eat a typical Western diet with plenty of protein and animal fats, and was dominated by high levels of Bacteroides.
Type 2 had few Bacteroides but plenty of Prevotella, which would be true of someone consuming more carbohydrates, especially fibre.
Type 3, meanwhile, was notable for high levels of Ruminococcus, a genus that sits in the Firmicutes division.
This all seemed convenient. Tidy even.
But then more science happened.
And along came a much more ambitious 2012 study, with 663 participants as opposed to 2011’s rather modest 22.
It showed that the boundaries between the enterotypes were fuzzier than the earlier work had suggested.
The new research also added the genus Methanobrevibacter to Type 3.
Sadly, to some extent, once the walls had started to crumble, they then came tumbling down.
Don’t you just hate it when that happens?
In fact an even bigger study in 2012 (with 1,200 participants) concluded that the idea of enterotypes really didn’t stack up at all, and that our microbial communities actually exist on a continuum, albeit one with a preponderance of Bacteroides or Prevotella at the ends (where most people’s microbiota sit).
Will the jury is out, to be honest.
Some say the whole enterotypes thing doesn’t hold water, but then others (like the authors of a 2014 Korean paper) suggest that those in their study definitely fell into one of two groups.
Hmm. More work needed probably.
But there’s no denying the value of a robust taxonomy which, as Wikipedia thoughtfully reminds us, is not to be confused with taxidermy.
But come on though, has a Wikipedian seriously ever *tried* to stuff a bacterium?
Have a great week!
Director of Product, Community, and Growth uBiome
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After around 22 months stuck in the womb, you might forgive an infant elephant feeling a little peckish post-delivery.
Mmmm, a nice comforting slurp of mother’s milk perhaps?
Well, no, actually.
In fact an elephant calf’s welcome-to-the-world meal is more likely to consist of a great big scoop of mom’s poop.
You see elephants, along with hippos, koalas and pandas, are born with sterile intestines, and the only way for them to digest vegetation is by getting a bellyful of bacteria, which they do by being fed their mother’s feces, the polite term for which is coprophagia.
As ever, nature is way ahead of us.
Transplanting feces from one creature to another turns out to be an extraordinarily powerful way to restore microbial balance, and it’s precisely what is achieved through a process called fecal microbiota transplantation (FMT), when healthy bacteria from a donor are introduced into the colon of someone who is diseased.
Not to put too fine a point on it, it’s a poop transplant.
And although that probably sounds gross, FMT achieves astonishing results in the treatment of C. difficile, a gut disease affecting almost half a million Americans a year, killing around 15,000.
The usual treatment for C. difficile is with antibiotics, but about one in five patients don’t respond to them.
Remarkably, though, randomized controlled trials of FMT have proved 85% to 90% effective.
If that weren’t enough, it’s not only gut diseases which respond to FMT.
Ongoing research is investigating its use in conditions as varied as autoimmune disorders, obesity, diabetes, Crohn’s disease, multiple sclerosis, and Parkinson’s disease.
The first description of FMT was published in 1958 when a team of Colorado surgeons successfully used it to treat four critically ill patients.
But even these surgeons were beaten to the post by the 16th century Chinese physician Li Shizhen who treated abdominal diseases with brews of fresh, dried, or fermented stool he wisely labelled as “yellow soup” and “golden syrup”.
Clearly a marketing man ahead of his time.
These days there are three main ways to introduce donor fecal matter into a patient.
To put it bluntly, it can go down a tube inserted in the mouth, up the other end via a pipe popped into the colon, or (very new) swallowed in the form of a novel type of capsule, although you’d need to knock back thirty of these to get a single dose, along with a hefty price-tag of over $600.
If this seems steep, however, it’s worth knowing that donor stool needs to be rigorously and expensively screened before transplantation, since the risk of introducing new disease that could make things worse is actually pretty significant.
Clinicians (and the FDA) suggest that donor and patient should be known to one another, or at least to the treating physician. Even so, donors should be scrupulously blood- and stool-tested.
OpenBiome, a Massachusetts-based nonprofit, operates the USA’s first public stool bank. But they don’t take just any old poop.
In fact only 3% of prospective donors make it through their screening.
OpenBiome supplies clinicians with frozen ready-to-administer stool samples, mainly for use in treating C. difficile.
Unfortunately, despite its effectiveness – especially for treating C. difficile – FMT is still seen by some clinicians as a controversial alternative, meaning that some patients find it hard to get referred.
So a few literally take matters into their own hands, performing DIY transplants at home.
Although we can’t possibly recommend it, comprehensive instructions are available online, but I do warn you that they’re not for the squeamish, involving kitchen blenders, enema kits, and copious volumes of personal lubricant.
By the way, I love that these directions recommend using a cheap blender, presumably on the grounds that you’re not going to want to use it to whip up a banana smoothie after it’s had number twos in it.
Someone else’s number twos at that.
Seriously, it probably really isn’t wise to consider the DIY route.
Mind you, if you share a bathroom with someone at home, sorry, but you’re probably already ingesting their feces.
The popular TV show Mythbusters proved that toothbrushes kept for a month in the vicinity of a toilet got regularly bathed in an aerosol of tiny contaminated water droplets whenever it was flushed, a microbiologist confirming that the brushes’ bristles did indeed harbor fecal matter.
Not enough for a transplant, perhaps, but still hard to swallow.
Have a great week!
Director of Product, Community, and Growth uBiome
One reason our ancestors may have eaten more healthily than we do.
Nope. There’s no way around this.
In writing about dietary fiber, once again I’ve inevitably got to talk about, um, number twos.
In doing so, though, I follow in illustrious footsteps.
In fact, way back in 430 BC the celebrated ancient Greek physician Hippocrates was writing about the laxative effects of coarse wheat in comparison with refined wheat.
It seems he was an early fan of roughage.
A couple of millennia later, John Harvey Kellogg, physician, co-inventor of corn flakes, and the holder of some pretty extreme views about sexual abstinence (don’t ask) published widely on the virtues of bran.
He claimed consuming it increased stool weight, eased bowel movements, and prevented disease.
Bran, by the way, is the outer hard layer of any cereal grain, so Hippocrates’ coarse wheat would certainly have contained a modicum of bran.
Of course neither of these gentlemen knew of dietary fiber’s role in feeding the bacteria that we now know reside in our guts, as well as in and on our bodies.
It was only in the mid-1990s that dietary fiber was classified as a prebiotic.
“Biotic” comes from the Greek word “bios”, meaning life, by the way, which when you stop to think about it makes the literal meaning of antibiotic rather unfriendly.
Anyway, prebiotic means “before life”, referring to bacteria, and specifically prebiotics are “nondigestible food ingredients that beneficially affect the host by selectively stimulating the growth and/or activity of bacteria in the colon, thus improving host health.”
Yup, in more ways than one, that’s a bit of a mouthful.
The important thing to understand is that dietary fiber is important. But most of us get far too little.
Although the recommended daily amount of fiber in the US is 25 grams, Americans typically only consume half this amount (about 15 grams a day).
Broadly you’ll boost your fiber intake by adding whole grains, vegetables, fruits, and legumes to your diet.
However prebiotics don’t all deliver equally.
By broad consensus, about 6 grams of your daily fiber consumption should come from prebiotics, and to get this you could eat just 9.3 grams (0.33 oz) of raw chicory root, or 19 grams (0.67 oz) of raw Jerusalem artichoke.
At the opposite end of the scale, your 6 grams of prebiotics could come from a whopping 600 grams (1.3 lbs) of raw banana.
That’s roughly five whole bananas.
Chicory root’s prodigious prebiotic performance is principally due to the presence of inulin.
Inulins are naturally-occurring polysaccharides (long-chain carbohydrate molecules) that are used by some plants as a way of storing energy.
There’s nothing new about consuming inulin, though, as we know that at least some of our prehistoric ancestors got more than their fair share.
What evidence is there for this?
Well, archaeologists working in the northern Chihuahuan Desert have found well-preserved coprolites in caves.
Literally, “dung stones”.
And analysis of these little beauties suggests that a typical male hunter-gatherer got around 135 grams of inulin a day, mainly from desert plants rich in the substance.
Good thing they didn’t have to rely on bananas, of course.
To get 135 grams of inulin they’d have needed to eat around 110 bananas a day.