New uBiome Women’s Health Study: Understanding the Vaginal Microbiome

Women’s Health Study

uBiome is launching a ground-breaking study investigating how the vaginal microbiome changes over the course of the menstrual cycle, and during different phases of life.

If you are a cisgender female and are currently NOT pregnant or menopausal/peri-menopausal:

  • Join the uBiome woman’s health study for a detailed analysis of your vaginal microbiome
  • Get a FREE uBiome kit (first 500 only) using coupon code: WOMENSHEALTH15
  • Help discover how the vaginal microbiome is affected by monthly cycles

Results from the study will be used to advance research, and findings will be shared with the public. Please join us today.

Wishing you a wonderful day!

P.S. The link to sign up for this study and get your free vaginal microbiome kit is

What Type of Microbiome Do You Have? Spoiler Alert: We Probably Can’t Tell

The start-stop world of microbiota classification

cupcakes-525518_640As 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).

Since then?

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!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth


Further reading

Binomial nomenclature


Gut Bacteria Divide People Into 3 Types, Scientists Report

Enterotypes of the human gut microbiome

Diet, Gut Enterotypes and Health: Is There a Link?

PLOS Computational Biology – A Guide to Enterotypes

Stability of Gut Enterotypes in Korean Monozygotic Twins

What is Life

Black Friday Sale: 5-for-1 Microbiome Kits

Happy Black Friday! (or should we say Brown Friday?)

In the spirit of giving thanks for how wonderful our uBiome community is (including you!), we’re offering you our last sale of the season.

Now you can meet all the bacteria currently living in your gut, and also learn about your mouth, nose, skin, and genital microbiomes at the same time.

Starting right now, a 5-site microbiome testing kit is just $89 instead of the usual $399.

Offer valid until Friday at midnight, or while supplies last.

Use discount code 5FOR1BF when you checkout at

We wish you a joyous Thanksgiving filled with delicious treats.

Your friends at uBiome

Want to Learn How to Heal Your Gut?

The Microbiome Solution Workshop
January 30th, 2016 8am – 6pm
The Grand Hyatt, Washington DC


Learn from the Experts – Heal Your Gut, Restore Your Health!

Use Coupon code: UBMBSW for a 20% discount!

*The Microbiome Solution Workshop is not associated with or sponsored by uBiome 
The Microbiome Solution Workshop is designed for those suffering from an imbalanced microbiome, for healthcare professionals, and for individuals eager to learn more about microbial health. The workshop will offer an extensive and personalized education on the microbiome – what it is, how it is disrupted, and how to restore it.


All participants will receive The Microbiome Solution Kit (a robust probiotic, plant fiber, zinc, glutamine, and curcumin), 2 uBiome Gut Kits, a personalized microbial analysis, access to The Microbiome Solution online community, deep discounts on nutrition coaching packages, and more! To find out more and register, please visit:


We are limiting workshop attendance in order to maintain a high level of personalized attention for all participants. Don’t miss out on this incredible opportunity to learn about your microbiome and gain the skills needed to achieve balanced, healthy gut flora.
*The Microbiome Solution Workshop is not associated with or sponsored by uBiomeInline image 1
Inline image 1

The icky but remarkably effective world of fecal transplants

University of Minnesota post doctorate fellow Matt Hamilton displays a sample of fecal bacteria at the St. Paul, Minn. campus Nov. 14, 2012. The fecal matter is donated and used to treat patients with Clostridium difficile, an intestinal disease that is caused when a person's gut flora is eliminated by antibiotics.
University of Minnesota post doctorate fellow Matt Hamilton displays a sample of fecal bacteria at the St. Paul, Minn. campus Nov. 14, 2012. The fecal matter is donated and used to treat patients with Clostridium difficile, an intestinal disease that is caused when a person’s gut flora is eliminated by antibiotics.

One person’s poop is another person’s soup

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.

No sir.

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!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth


Further reading


Faecal transplant eases symptoms of Parkinson’s – New Scientist

FDA struggles to regulate fecal transplants – CBS News

Fecal bacteriotherapy

Fecal Microbiota Transplantation – Indications, Methods, Evidence

Fecal Transplant At Home – DIY Instructions – The Power of Poop

Fecal Transplantation (Bacteriotherapy) – Johns Hopkins Division

Fecal transplantation – Health at Iowa

Fecal Transplants Made (Somewhat) More Palatable – The New York Times

FMT Capsule G3 — OpenBiome

Gestation period

Information and Facts About Elephant Babies

The Fecal Transplant Foundation

The Power of Poop

Therapeutic Poop – Hope for Cure of Childhood Diarrhea

Toothbrush Fecal Matter – MythBusters – Discovery

Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis

Bacteria Cartoon Contest


Are you an artist, a designer, a sketcher, or just have a ballpoint pen laying around?cultured bacteria

Introducing the uBiome Bacteria Cartoon Contest

Grand Prize: $399 value                  Second Prize: $199 Value                Third Prize: $89 Value 2015-11-17 10-34-27 (1) 2015-11-17 10-34-27 (2)

How to enter:

Submit your funny, cute, awesome bacteria cartoons to Zack:


  1. Must be your own, original work of “art”. You can use any means (digital, good ‘ol fashion pen and paper, etc.)
  2. Submission deadline is 11/24 by midnight. Winners will be chosen the next day and posted on this blog.
  3. Points will be given for:
    1. Comedy (did it make us laugh)
    2. Originality (have we never seen something like it before)
    3. Visually appealing (is it pretty like a butterfly?)
    4. Digital Formatting (was it scanned into your computer? Please don’t just take a photo of your cartoon, unless you are a master photographer.)
  4. Have fun!

Any questions can be emailed to, but please be weary of his inbox. He gets cranky easily.

On The Menu Today: Prehistoric Poop and Jerusalem Artichokes


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”.

Fossilized feces.

Petrified poop.

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.

Which is, indeed, a bunch.

Have a great week!

Further reading

Fiber and Prebiotics: Mechanisms and Health Benefits

John Harvey Kellogg