What do your intestines have in common with a sewer pipe?


I’m not being funny but…

Did you ever stop to think about how much poop you produce in a year?

Unless you have too much time on your hands, probably not.

So let me tell you.

The average individual pops out about an ounce a day for each 12 pounds of body weight, so do the math and this suggests you flush away almost twice your own weight each year.

Now, to you that’s just waste matter, but to the uBiome labs it’s our bread-and-butter.

I know. An unpleasant metaphor, but I hope you get my point.

Fortunately we need only the smallest sample of your poop to analyze your microbiome.

Just a Q-tip’s worth collected from your used toilet paper in fact.

So you have our blessing to carry on happily flushing the rest away.

However, while our laboratory is content to test your microbiome using mere smears, other researchers are getting down and dirty with the more prodigious volumes you and I dispatch into the void each day.

A current project, appropriately called Underworlds, in Cambridge, Massachusetts, is experimenting with smart sewers that enable public health experts to study a city’s collective microbiome.

They can detect foodborne pathogens, enabling them to pick up localised outbreaks of food poisoning, and also look for biomarkers that flag up other diseases and health conditions.

The work is being done in conjunction with Kuwait, where officials are anxious to learn more about childhood obesity. More than a third of Kuwaiti children are obese.

But what does obesity have to do with sewage?

Surprisingly, quite a bit.

A remarkable University of Wisconsin-Milwaukee study earlier this year analyzed bacteria from sewage collected in 71 cities in 31 U.S. states, and could predict whether it had been gathered from a community categorized as either lean or obese with close to 90% accuracy.

Lean and obese individuals typically have differing intestinal bacterial profiles (more of this, less of that etc.) and the study showed that this same differential was also reflected down in the sewers.

Sewage sleuthing has been a thing for some time.

European studies have studied the stuff in sewers to monitor population-level trends in illicit drug-use, showing for example that cocaine and ecstasy are big at the weekends in major metropoles, while cannabis and methamphetamine use is pretty constant throughout the week.

Impressive, huh? There’s clearly a lot to be discovered by looking into effluent.

And a lot to be grateful for, too, when you consider the sewage systems of developed countries.

In fact readers of the British Medical Journal voted sanitation the greatest medical advance since 1840, comfortably beating antibiotics, anesthesia, widespread vaccinations, and even the discovery of DNA.

Although we don’t have time to go into how sewage is processed, I couldn’t leave you without brief mention of a project in India, in which the job is done by allowing sewage to sit in pools of duckweed and fish for five days.

Apparently it does the job brilliantly, but somewhat uncomfortably the whole operation is then funded by selling the fish.

I’m sure it’s just a coincidence that you can rearrange the letters of the particular species they use to spell something else altogether.


Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth


Further reading

Poop Health – Everything You Want to Know But Haven’t Asked

Sanitation rated the greatest medical advance in 150 years

Sewage Reflects the Microbiomes of Human Populations

Smart Sewer Project Will Reveal a City’s Microbiome

Smart Sewers Will Reveal What’s in Cambridge Citizens’ Guts

Spatial differences and temporal changes in illicit drug use

Sewage Treatment: All The Pooey Facts

Why variety is the spice of life – and the sign of a good gut


A healthy gut is a diverse gut.

You need good eyesight to work in the uBiome laboratory. Our research focus tends to be on the microscopically tiny.

Of course, we’re all about the trillions of bacterial cells that are hitching a ride in, and on, your body right now.

But let’s just for one minute exchange our microscope for a “macroscope” and consider overall biological diversity.

Our planet plays host to somewhere between 10 and 14 million species, or types, of life.

If this sounds like a unforgivably slapdash and imprecise estimate, it is.

You see we know precious little about so many of the other life forms which share our world.

In fact over 86% of our co-living species haven’t even been described yet.

And if we’re going to make an impression on this task, well we’d better get a move on.

Something like 99% of all the species that have ever lived on earth are already extinct. And some estimates suggest that literally dozens more are becoming extinct every single day.

Now this is pretty disturbing news.

In general, biodiversity is a good thing – an essential component of nature.

The less diverse our world becomes in terms of its life-forms, the poorer it becomes as an environment capable of supporting those life-forms.

One of which is us.

Okay, so now let’s return to the micro from the macro.

What do we know about the diversity of the microbiome?

Is it, in general, a good thing to have a wide variety of bacteria in your gut? Very probably, but it’s not exactly easy to separate cause from effect.

Healthy people do indeed tend to have a wider diversity of microbes in their guts, but it’s not obvious whether one causes the other.

However, learning from “macro” biodiversity would seem to suggest the wisdom of covering your bases by welcoming in as many species of healthy bacteria as possible.

Modern life can play havoc with our guts.

If we look to the hunter-gatherer Yanomami people in the Venezuelan rainforest, some of whom have lived without contact with the rest of the world for thousands of years, we find that they have the most diverse populations of gut microbes ever seen.

They eat a high-fiber diet, and have also never been exposed to antibiotics.

I think we may also safely assume that they don’t make great use of anti-bacterial soaps and cleansers.

And here’s another thing.

Researchers at the University of Oklahoma in Norman have found a clever way of studying the microbiomes of our ancestors.

They’ve collected fecal samples direct from the intestines of mummified humans around North and South America, then subjected them to a similar kind of DNA analysis that we use at uBiome.

Interestingly, ancient feces between 1,400 and 3,000 years old had much more in common bacterially with children in rural Africa than with modern Americans.

It is estimated that a human gut can contain between 500 and 1,000 different bacterial species.

You might argue that this is a relatively small number compared to the species on earth, so perhaps “working on” your microbiome’s diversity may not be an entirely impossible task.

Some simple tips, then?

It can help to eat fermented foods like sauerkraut, kimchi and kombucha.

Consuming fiber-rich foodstuff such as beans (a prebiotic) will give your new healthy bacteria something tasty to munch on.

Avoid meat from animals which have been dosed with antibiotics (often used as a growth agent).

And last but not least don’t overdo it with the antibacterial hand cleanser.

In short, treat your gut with the same kind of respect we should all be paying to the rainforest, and you won’t go too far wrong.



Further reading

Antibiotics are wonder drugs no more

Antibiotics may make you fat


I had the bacteria in my gut analysed.

Is super-diverse Amazon microbiome something to strive for?

Microbiome Monday – How Do We Build Our Microbiomes

Our Modern Lifestyle May Be Destroying Microbiome Diversity

The Extinction Crisis

The Scientists Who Want to Fix America’s Guts

Why Flatulence Is Simply A Sign Your Bacteria Are Doing Their Job

air-160492_1280Farting. There, I said it.

Here at uBiome we often refer to the microbiome as the bacteria that live in and on your body, but according to a paper co-authored just last month by James Meadow, a former University of Oregon researcher, we really ought to add a third microbial environment to this – the space around the body.

You see, according to Meadow each of us is surrounded by a personal “cloud” of bacteria, at least some of which is generated in the form of flatulence.

And when you fart, your emissions contain a cocktail of different gases accompanied by a liberal side-order of gut bacteria.

Whatʼs more, a good deal of the flatus itself (the scientific word for a fart) is the result of fermentation in your gut, and the work of its bacteria.

The average individual passes wind between 8 and 20 times a day, generating a volume of something like half a liter every 24 hours.

Out of (admittedly rather random) interest it would therefore take about three years for the average person to inflate a camping air mattress with their gastrointestinal gas.

No wonder they sell those little hand pumps.

Although we tend to think of farts as smelly, in fact 99% of their volume is non-odorous, made up of oxygen and nitrogen we swallow, plus carbon dioxide, hydrogen and methane produced by our gut bacteria.

By the way, methane has no odor and, whatʼs more, not everyoneʼs flatus contains it. As a matter of fact itʼs only found in around half the population, so not everybody can pull off the old dorm “fart-lighting” trick.

Even if they wanted to.

The pungent smell of flatus comes from volatile sulfur compounds, including hydrogen sulfide, which make up just 1% of its volume.

Now while you and I probably do our best to avoid other peopleʼs farts, in China there are professional flatus smellers who can allegedly diagnose illness and tell you where it is in the body, simply by taking a sniff.

Actually these experts are not the only ones to actively seek out peopleʼs gas.

According to a recent study at the University of Exeter in the UK, smelling farts could even be good for you.

Apparently a sniff or two of hydrogen sulfide can help to preserve your mitochondria (part of the cell structure of important microorganisms in your body).

Todayʼs brief wander through the world of farts would be incomplete without brief acknowledgement of a phenomenon called High Altitude Flatus Expulsion.


Quite simply, it describes many peopleʼs increased need to pass wind on flights – not because of the airline food – but because of the reduced air pressure outside our bodies.

Thank goodness for efficient aeronautic ventilation, I say.

Finally, it would be remiss of me not to at least tip my hat to a 19th-century entertainer at the Moulin Rouge in Paris who used the stage-name La Pétomane, which loosely translates to “The Fartomaniac”.

Thanks to an extraordinary ability to inhale through his back passage (yup, really) Joseph Pujol (his real name) could produce the sound of cannon fire and thunderstorms from his rear end.

Apparently he also played “O Sole Mio” on an ocarina powered by a rubber tube inserted where the sun donʼt shine, and could blow out a candle from several yards away.

Of course flatulence is the, um, butt of many a good joke.

But the simple truth is that itʼs generally a good indicator of a healthy gut. When your gut bacteria are doing their work, the inevitable side-effect is gastrointestinal gas.

So put that in your ocarina and play it.

Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth

Further reading

15 Explosive Facts About Farts


Flatulence expert defines ʻnormalʼ output rate

Help Wanted: Professional Fart-Smeller

Humans differ in their personal microbial cloud

Le Pétomane

Study: Smelling farts may be good for your health

Your Body Is Surrounded by Clouds of Skin and Fart Bacteria

Why Your Microbiome is Older Than You Are.

Now we know. A baby’s microbiome starts developing in the womb.

You probably wonʼt remember this, but the very first poop you popped out as a baby was pretty extraordinary.

So extraordinary, in fact, that it even had a name.


A babyʼs first bowel movement consists of stuff that was already in the gut before the first meal.

And Meconium is like no other stool youʼll ever pass.

Itʼs kind of dark olive-green with a tarry, viscous consistency, barely any smell, and made up of stuff you ingested when you were in the womb, including skin cells and “lanugo” – that thin downy hair often found on an infantʼs body.

Delightful, right?

But thatʼs not all meconium is made up of.

Researchers at the University of Florida discovered in 2010 that new-born babiesʼ meconium contains a diversity of bacteria, and that came as something of a shock.

You see, back in 1900 a French pediatrician called Henry Tissier had confidently declared that unborn babies were bacteria–free.

So according to popular myth, a baby was effectively sterile until the moment of birth.

Now to be fair to Tissier, he also isolated and named a bacterium called Bifidus that went on to play an important part in the world of probiotics, but thereʼs no doubt that he caused over 100 years of microbial misunderstandings with his sterile baby theory.

However, while itʼs certainly true that babies are born with a certain amount of bacteria, most of their microbiome builds up over time, with the first few minutes of life being especially important.

If a baby is delivered vaginally, she receives a dose of bacteria from her mother as she passes through the birth canal, getting covered in a microbial film that includes species which will help her digest her first meal.

But what happens if she enters the world as a result of a Cesarean section?

Well then her first dose of bacteria is likely to come from her motherʼs skin rather than her vagina, an observation supported by a Swedish study which showed that babies born via C-section have gut bacteria which show significantly less resemblance to their mothers compared to those delivered vaginally.

Some parents restore the balance after C-sections by “inoculating” their babies with a vaginal swab: incubating a piece of gauze in the vagina for an hour prior to delivery, then wiping it over the mouth, face, and body of the infant after delivery, in a process sometimes called “seeding”.

Quite a wake-up call.

A babyʼs microbiome continues developing after birth, resembling that of an adult by the age of three.

In fact babies pick up microbes from every single person and thing they touch, which in general is A Good Thing.

Humans tend to do best when they play host to a diverse microbial community.

A University of Idaho study found that there are even important bacteria in breast milk, meaning that the guts of babies given formula differ from those fed on breast milk.

All in all thereʼs no doubt about it.

Your bacteria play a vital part in your health, and always have.

Ever since you passed that rather outlandish first poop.

Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Community, Product, and Growth

Further reading

Your Changing Microbiome

Nurturing A Babyʼs Microbiome, Before And After Birth

The Maternal Microbiome

Maturation of the Infant Microbiome

Human Microbiome May Be Seeded Before Birth

The infant gut microbiome: New studies on its origins and how it’s knocked out of balance

The Human Microbiome, Diet, and Health: Workshop Summary

How to seed your baby with a healthy microbiome to last a lifetime

Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health

Microbirth: Why ‘Seeding Baby’s Microbiome’ Needs to Be on Every Birth Plan

Intestinal Microbial Ecology in Premature Infants Assessed Using Non-Culture Based Techniques

Characterization of the Diversity and Temporal Stability of Bacterial Communities in Human Milk

Why You’re Probably Not Eating Enough Fiber, and Why It Should Bother You.

Fail to feed your bacteria properly and they’ll start eating you.

I donʼt want to frighten you, but right now there are around 100 trillion bacteria chomping away in your gut.

Itʼs a hungry job being a microbe.

Thereʼs something like three pounds of bacteria lining your intestinal tract,
probably made up of about 500 different species.

I say probably, because everyoneʼs different. Although you and I share around 99.5% of the same DNA,
our microbiomes almost certainly vary widely, one of the reasons itʼs so fascinating to explore yours
with a uBiome test.

The thing is, a lot of your bacteria keep you healthy – theyʼre helping you digest
food and synthesize vitamins, for instance.

Doesnʼt it therefore make sense, in return, to keep them healthy too?

One way to do that is to ensure theyʼre properly fed, and hereʼs where things
get interesting and actually pretty serious.

You see, a prime source of bacterial nutrition comes from fiber, but most
peopleʼs diets are vastly underrepresented in this respect.

An average individual in the West gets roughly 15 grams of fiber a day, which
is nowhere near enough. In fact, The Institute of Medicine recommends
women should get 25 grams per day, while men should consume 38 grams.

Does this matter much?

Well, yes.

Actually it matters enough for the U.S. governmentʼs dietary guidelines to label
dietary fiber as a “nutrient of concern”. A public health issue, no less.

Itʼs long been accepted that having enough fiber in your diet can contribute to
a feeling of fullness (so you know when to stop eating) and what
gastroenterologists politely call “healthy laxation” (regularity in the bowel
movement department).

More seriously, a low fiber diet may also be associated with the risk of
developing various conditions, including heart disease, diabetes, diverticular
disease, and constipation.

But now studies are showing that failing to provide enough fiber to the gutʼs
bacteria may lead to them feeding on the gut itself.

Researchers at the University of Michigan Medical School found that when
mice were placed on a fiber-free diet, their microbes began to eat away at the
gutʼs protective mucus lining, potentially triggering inflammation and disease.

So fiberʼs important.

How easy is it to get enough, then?

Well since most of us are only getting around half as much as we should,
clearly not very. Eating a salad every night, for instance, would only provide
two or three grams of fiber.

Dieticians say itʼs best to get fiber as part of your regular diet, but supplements
can help.

In a small study at the University of Illinois at Urbana Champaign, adults ate a
fiber-enriched snack bar containing 21 grams of fiber once a day for three

The good news?

Their gut bacteria composition shifted from a profile similar to that found in
obese individuals to one which was more like the microbial make-up of lean

The bad news?

The minute the experiment was over, participantsʼ microbiomes returned to the
way theyʼd been before the experiment began.

So to keep your gut healthy, itʼs vital to eat a high fiber diet every day.
Whole grains, legumes, vegetables, and fruits. Raspberries, bran, split peas, artichokes.
Whatever roughage you like.

Your bacteria will thank you for it.

Split peas for dinner tonight, anyone?

Have a great week!

Further reading
Fiber-Famished Gut Microbes Linked to Poor Health

Shift in gut bacteria observed in fiber supplement study may offer good news for weight loss

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial

Think Globally, Act Locally: Regulated Deployment of Polysaccharide Degradation Abilities by our Symbiotic Gut Bacteria


Are Your Gut Bacteria Getting You Down? 3 Remarkable Mood-Microbiome Studies.

Could mood disorders have a bacterial origin?

Those microbes of yours perform some truly extraordinary feats.

Right now, for example, several pounds of bacteria in your gut are helping you digest food and process vitamins. Thanks guys.

But that’s just the tip of the iceberg.

You see, many researchers suggest that alongside plenty of other aspects of health, your microbiome has a profound effect on the way your mind works.

Low levels of certain species of bacteria in your gut could be associated with depression or anxiety. There could even be a connection between the microbiome and autism.

Maybe we shouldn’t be quite so surprised about the gut-brain connection though.

Consider neurons, for example. Your brain has around 100 billion of them, but I wonder if you knew that your alimentary canal, that 27-meter tube winding its way from your mouth to your rear end (yup, it’s a long way down), has another 100 million or so neurons embedded in its walls.

That’s right, the idea of a ‘gut feeling’ contains more than a grain of truth.

And those neurotransmitters, the chemicals which can play a big part in emotion: 50% of your dopamine and 95% of your serotonin isn’t in your brain. It’s in your gut.

Back to bacteria, though. Let me tell you very briefly about three quite remarkable studies.

In 2011 a team of Irish and Canadian scientists found that mice which were dosed with Lactobacillus rhamnosus (a bacterium found in probiotic yogurt) and then dropped into a tank of water from which there was no escape, took longer to give up in despair than a control group that didn’t have the bacteria.

In fact the L. rhamnosus mice behaved in the same chilled-out, relaxed way that mice given antidepressants like Zoloft and Prozac did.

Because they tend to respond to stimuli in similar ways to humans, mice are frequently used in laboratory experiments. When you learn something from mice there’s a pretty good chance you’ll find the same thing in humans.

However, another study – at UCLA – involved 25 human subjects.

For four weeks, twelve people ate a cup of commercially-available probiotic yogurt twice a day, while the remainder were given a non-probiotic dairy product.

Before and after the four weeks, all were given fMRI brain scans during which they were shown images of human faces expressing emotions such as anger or fear.

The brain scans showed the people in the control group were more affected by these emotional triggers than the probiotic yogurt eaters, who by comparison were calmer and less stressed.

Returning to mice, a third study – at the California Institute of Technology – focused on a microbe called Bacteroides fragilis, an absence of which is often observed in the guts of people with autism.

By transplanting B. fragilis from human donors into the guts of mice with symptoms similar to autism, they found the rodents exhibited less anxiety-like behavior, interacted more with other mice, and also behaved less repetitively.

Radical stuff.

This mood-microbiome connection is pretty new and revolutionary, and it’s an area that seems ripe for self-experimentation:
1) Measure and track your mood for a while
2) Have your microbiome tested
3) Introduce new species of bacteria (by eating them)
4) Explore how this has affected your mood via your tracking, and your microbiome via a second test.

Such a promising area. You see, in any given year almost 10% of U.S. adults experience mood disorders. Many are prescribed medication.

What if bacteria could really offer an alternative to pharmaceuticals?

Have a great week!

Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth

Some further great reading:

Can the Bacteria in Your Gut Explain Your Mood?

When Gut Bacteria Changes Brain Function

Consumption of Fermented Milk Product With Probiotic Modulates Brain Activity

Think Twice: How the Gut’s “Second Brain” Influences Mood and Well-Being

17 Surprising Facts About Your Body’s Bacteria

Nothing personal, but your microbiome is a truly curious thing.

Gotta love those bacteria of yours. After all, right now many of them are doing a remarkable job of keeping your body in good shape.

We love them too of course, and every day our labs run genetic sequencing on unimaginable numbers of the little critters.

Not surprisingly our scientists know a thing or two about the bacteria in your body, some of it pretty extraordinary, so I figured a choice selection of facts would be a fun way to start your week.

1. A study of belly button bacteria found 1,458 different species. One person’s navel contained bacteria that had previously only ever been seen in soil from Japan. Curiously, this individual had never been to Japan.

2. A Dutch study showed that a ten second intimate kiss between two people results in the exchange of 80 million bacteria.

3. Japanese scientists discovered a new species of bacteria that can live in hairspray.

4. Partly because of oral bacteria, human bites are considered one of the most dangerous animal bites in the world. Around 1% of emergency department visits in the U.S. are associated with mammalian bites (not all are human of course).

5. If all the bacteria in and on your body was carefully scooped up, it would weigh three to five pounds and fill a large soup can.

6. Even when you clean your teeth thoroughly there will still be between 1,000 and 100,000 bacteria remaining on each tooth.

7. Certain kinds of bacteria help with digestion. Mice specially bred to have bacteria-free guts ate 41 percent more calories than mice whose intestines contained the usual microbes.

8. The average human body contains 100 trillion microbial cells, if each cell was represented by a dollar bill, the resulting stack of money would reach from the earth to the moon and back 14 times.

9. There are around 20 billion bacteria in your mouth alone (almost three times the number of people in the world). Some reproduce every five hours.

10. Bacteria are classified into three main shapes. Spheres (cocci), rods (bacilli) and spirals/corkscrews (spirilla/spirochaetes).

11. The average person swallows a litre of their own saliva every day, containing 100 billion bacteria.

12. Sweat has no smell but it combines with bacteria on the body to produce body odor.

13. One kilogram of the bacterium C. botulinum could, if properly distributed, kill the entire human population.

14. Babies are born with absolutely no bacteria in their bodies. They get their first dose as they pass through their mother’s birth canal.

15. Some bacteria move fast: speeds of 50 to 60 times their own length in a second have been observed. That’s the equivalent of a 6 foot human running at over 200 miles per hour, more than three times the speed of a cheetah.

16. To prove his hypothesis that stomach ulcers are caused by bacteria rather than stress, Australian scientist Barry Marshall swallowed a beaker of Heliobacter pylori. He did get a peptic ulcer. And the Nobel Prize in Medicine.

17. The gonorrhea bacterium is the strongest organism on earth. It can pull with a force equal to 100,000 times its body weight, the equivalent of a human dragging 10 million kilos. That’s the weight of 22 fully-laden Boeing 747s.

Like I said, you’ve got to love bacteria.

Have a great week!