Why There’s Little Straight-Talk About, Well, Using the Bathroom

A routine activity that’s built on euphemisms

There are people who claim they can tell your fortune through the reading of tea leaves, an art known as tasseography.

As for us, well, we guess you might say we can tell you a lot about yourself by reading your toilet paper.

You see, this is the method of collection we use to collect a gut microbiome sample for our DNA sequencing process. Continue reading “Why There’s Little Straight-Talk About, Well, Using the Bathroom”

Does Where You Live Affect the Type of Bacteria in Your Gut?

How your microbiome can be influenced by geography

Why don’t polar bears eat penguins?

I’m told it’s a conundrum that regularly pops up in lists of tricky interview questions, easily answered if you know your geography.

Of course polar bears live only in the Arctic, while penguins are only ever found down in Antarctica, safe from the jaws of hungry bears.


We take it for granted that different animal and vegetable species live in different parts of the world.

But what about bacteria?

Could where you live affect the trillions of microorganisms hitching a ride in and on your body?

Well yes, quite a bit actually, and what we know about the geographical diversity of the human microbiome makes for a fascinating story.

Actually perhaps I should begin by saying that scientists’ knowledge on this subject is relatively early-stage.

For example one of the biggest microbiome research projects in the world was the $173 million, five-year Human Microbiome Project.

While it unquestionably generated a huge amount of invaluable data, the project studied just 242 humans, almost all white Americans, 80% of whom came from two cities – Houston and St Louis, about 12 hours drive away from each other on a good day.

Not terribly diverse, then, in almost any way, but a fantastic start.

With a little digging, we can find some truly eye-opening microbiome studies involving more far-flung groups of our planet’s population.

Consider for example the remarkable 2008 research headed by a microbiologist at New York University which studied 12 hunter-gatherers from the Yanomami people in Venezuela, who’d never met anyone outside their own cultural group.

Scientists took advantage of an opportunity to gather stool samples from these incredible individuals when the Venezuelan government helpfully decided they needed to give them medicines and vaccines in case they inadvertently came across illegal miners who might introduce diseases to them.

The results of a painstaking study published after seven years of research showed that the Yanomami have the highest gut bacterial diversity ever reported in a human group – twice as high as the average American city-dweller.

Incredibly, some of their bacterial strains also had antibiotic-resistant genes despite them obviously never having taking antibiotics.

Another amazing piece of research was conducted in 2014, focused on 27 Hadza people from Tanzania in East Africa.

Although the Hadza are modern humans, their lifestyle is believed to closely resemble that of Palaeolithic tribes.

Like the Yanomami, the Hadza are also hunter-gatherers, and once again they showed substantially greater bacterial diversity than the average Houston or St Louis inhabitant, with microbiomes rich in bacteria that help to digest fibers.

Interestingly there was a substantial microbiome difference between the sexes.

When our own data science team compared the microbiota of men and women who have submitted samples to uBiome, we found them to be statistically similar.

In the case of the Hadza, however, the difference is thought to be correlated with their sexual division of labor.

Their women forage for tubers and plants, and spend a lot of time with their children, while the men travel widely hunting game and collecting honey.

Apparently both sexes tend to snack during the day, with the result that the women have higher concentrations of bacterial groups such as Treponema, helpful in processing fibers.

Finally, just in case I’ve led you to conclude that all the geographic microbiome studies involve remote tribespeople and hunter-gatherers, consider a fascinating 2010 study which showed that some Japanese individuals are able to extract otherwise inaccessible nutrients from seaweed (the average Japanese person eats 14 grams of it a day) by virtue of ingesting a type of marine bacteria which then transfers its genes to gut bacteria.

In 1940, American health food and weight loss expert Victor Lindler wrote the book “You Are What You Eat”, popularizing the phrase.

76 years later, perhaps it would also be fair to add,
“And You Are Where You Eat”.

Have a great week!


Further reading

Antibiotic resistance is ancient

First look at the microbes of modern hunter-gatherers

Gut bacteria give super seaweed-digestion power to Japanese

Gut microbiome of the Hadza hunter-gatherers

Human gut microbiome viewed across age and geography

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

Searching for a ‘healthy’ microbiome

Surprises emerge as more hunter-gatherer microbiomes come in

The microbiome of uncontacted Amerindians

Three nations divided by common gut bacteria

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

The Secrets of the 5,000 Year Old Microbiome

What scientists are learning from the bacterial DNA of ancient humans.

If you take a trip to New Zealand you should be grateful you won’t bump into a moa.

You see, the moa – a type of flightless bird – has been extinct for about 700 years, but meeting one would have been a pretty scary encounter.

Moas weighed more than 500 pounds and stood over 12 feet tall, which is one and a half times as big as that other celebrated Big Bird.


It was through examination of the fossilised remains of the moa, though, that researchers at the Australian Centre for Ancient DNA were able to estimate how long DNA is likely to last.

Apparently DNA has a half-life of 521 years (I know, pretty exact, right?) which suggests that under ideal conditions it would be 6.8 million years before the DNA bonds in a sample are all completely destroyed.

This can come in extraordinarily handy as it means that when scientists are let loose on ancient human specimens, they can do some amazing things with sequencing.

Take for example the fascinating case of the University of Copenhagen researchers who examined human bones from Europe and Asia, ranging in age from 3,000 to 5,000 years old.

When you look for human DNA in a sample, you start by retrieving all the DNA, most of which is actually not human, being made up of genetic information from microorganisms (that’s right, the microbiome).

But instead of just chucking out the non-human stuff, the Danish researchers decided to look instead at the bacterial DNA, among which, to their surprise, they found pathogens.

This led them to study the calcified plaque on human teeth up to 5,000 years old, from which they were able to extract the plague bacterium Yersinia pestis.

Historically, of course, the plague has been deadly.

It killed roughly a third of the European population during the 14th century’s Black Death.

Before that, the earliest known incidence of Yersinia pestis had been in the 6th century during the Plague of Justinian, a terrible pandemic that killed over 25 million people in the Eastern Roman Empire.

Suddenly, though, analysis of the ancient microbiome placed the presence of Yersinia pestis thousands of years earlier.

Prehistoric microbiomes have been in the news recently after scientists in Italy re-examined the 5,300-year-old mummified body of Ötzi the Iceman, originally accidentally discovered by a pair of hikers in the eastern Italian Alps.

Remarkably it was possible to sequence Ötzi’s gut bacteria, which were found to contain Helicobacter pylori, a bacterium which infects around half the population and occasionally causes stomach ulcers.

Now, the type of Helicobacter pylori carried by most present-day Europeans is a hybrid of two ancient strains.

One originated in Africa, the other in Eurasia, and it had previously been supposed that the hybridization occurred about 2,000 years ago.

But Ötzi’s stomach only contained the Eurasian strain, so once again it became necessary to revise hypotheses.

It’s now thought that the African strain was carried to Europe by the first farmers, who migrated from the Middle East starting around 8,000 years ago.

Scientists can extract historic microbial DNA from all kinds of sources.

As we’ve seen, the Italians used a mummified stomach. The Danes used teeth.

But a 2012 team from the University of Oklahoma used coprolites, which are essentially fossilised feces.

Now coprolites are a fascinating concept.

Depending on how regular you are, every day you pull the handle to dispatch your waste into the sewers, thinking little of it I’m sure.

But imagine just one of your “specimens” going on to be turned into stone, then poked and prodded by lab technicians thousands of years later.

3,400 years later in the case of the University of Oklahoma scientists, who were incredibly able to deduce that one of their pieces of petrified poop almost certainly came from a child.

It contained a bacterium generally only present when an infant has been breastfed.

Have a great week!

Further reading

Ancient Dentistry – Learning from DNA

Early Divergent Strains of Yersinia pestis in Eurasia

Fossilised Moa bones help scientists unravel the mystery of DNA 

How Long Does DNA Last?

In Ancient DNA, Evidence of Plague Much Earlier Than Previously 

Insights from Characterizing Extinct Human Gut Microbiomes

Institute for Mummies and the Iceman


Mystery of DNA decay unravelled

Ötzi the Iceman’s Stomach Bacteria Offers Clues on Human Migration

Prehistoric Man Had Much Healthier Teeth and Gums than Modern Humans

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

Tooth gives up oldest human DNA

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
1447785319910screensavescreenshot-ubiome.com 2015-11-17 10-34-27 (1)
screenshot-ubiome.com 2015-11-17 10-34-27 (2)

How to enter:

Submit your funny, cute, awesome bacteria cartoons to Zack: zfediay@ubiome.com


  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 zfediay@ubiome.com, but please be weary of his inbox. He gets cranky easily.

Why you’re speaking with your mouth full. Even when it’s empty.


The wild world of your oral microbiome

The National Zoo in Washington, D.C. is home to roughly 300 different species of animals. And just so you know, right now your mouth probably houses about the same number of species of bacteria.

Yup, at any one time, there’s a whole zoo’s worth of tiny microbes – between 200 and 300 species – in your mouth, merrily mingling with each other and their host.

That’s you.

But that’s literally only half the story, because the experts who run the Human Oral Microbiome Database estimate there are actually a total of about 700 different bacterial species that can inhabit humans’ mouths, and their records are being updated almost every day as more and more is learned about these miniature critters.

There’s still a way to go. Right now only about half of them even have names.

But we humans have been aware of microbes for a few hundred years. In fact the first person on record to see oral bacteria was Antonie Van Leeuwenhoek, a citizen scientist if ever there was one.

Despite having no scientific education or training, he built over 500 “microscopes” and went on to make some extraordinary discoveries with them.

Actually his devices were just hand-ground magnifying lenses rather than compound microscopes like the ones used in today’s laboratories, but they were exceptionally powerful, enabling him to magnify specimens over 200 times.

Among the samples he chose to observe in 1683 were scrapings removed from the mouths of two old men who had never cleaned their teeth.

Never. In their whole lives.

Apparently unfazed by such grossness, according to a letter Van Leeuwenhoek wrote to the Royal Society in London, when he examined the gentlemens’ plaque he observed “an unbelievably great company of animalcules … in such enormous numbers that all the water [saliva] … seemed to be alive.”

How very lovely.

What he called animalcules (little animals), we now know as bacteria, but in fact over 250 years later in 1929 the zoologist Charles Atwood Kofoid was still writing about “animal parasites of the mouth and their relation to dental disease”.

Speaking of disease, we may tend to think of bacteria as being bad for health, but in fact there’s quite a bit of evidence that at least some of the species found in the mouth are good for us, keeping pathogenic microbes at bay by stopping them sticking to different oral surfaces.

So while cleaning your teeth is important, overdoing it with antibacterial mouthwashes may be a bad thing, removing the good microbes with the bad.

That’s no excuse for skipping good dental hygiene, though, as many adults do. In fact half of Americans don’t floss daily, and one in five don’t brush twice a day.

Maybe this is why 10% of American adults between 50 and 64 have no teeth left.

If you imagined that the mouth contained one homogenous microbial ecosystem, think again.

Certain species live on the tongue, others opt for the roof of the mouth or inside the cheeks.

Some like to hang out on the teeth, others on the gums.

Then there are those that specialize in living on dental fillings or false teeth, and, incredibly, there are even microbes which prefer the tonsils.

Of course bad dental hygiene allows the wrong kinds of bacteria to multiply, leading to halitosis, gum disease, tooth loss, and heart disease.

Curiously, researchers at Luzhou Medical College in China even observed erectile dysfunction when they deliberately induced gum disease in their experiment’s participants.

This was with rats, mind you, but perhaps it should serve as an extra reminder to human males too.

Don’t forget to brush your teeth before bed.

Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth


Further reading

Antonie van Leeuwenhoek

Charles Atwood Kofoid

Effect of Periodontitis on Erectile Function

HOMD – Human Oral Microbiome Database

Meet Our Animals – National Zoo

Mining the Mouth’s Many Microbes

Oral Health – The Mouth-Body Connection

The Oral Microbiota – Living with a Permanent Guest

Tooth Loss in Adults

What Happens When You Don’t Brush Your Teeth


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

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!

Announcing the uBiome Smoking Study on the Oral Microbiome


uBiome Seeks Citizen Scientists to Explore Smoking’s Effect on Mouth Bacteriasmokingstudy

uBiome, the leading microbial genomics company, seeks smokers, ex-smokers, and non-smokers to take part in a free ground-breaking study investigating the effects of tobacco smoking on the mouth’s microbial make-up.


San Francisco, California – July 15th, 2015 – Although tobacco use in the United States is in slow decline, almost one in five adults is a smoker. While a great deal has been learned over the past fifty years about smoking’s serious health implications, it has only recently become feasible to investigate its impact on the oral microbiome. Biotech startup uBiome is giving smokers, ex-smokers, and non-smokers the chance to contribute to important research while also receiving their individual data showing the bacterial composition of their own mouth. Study participants will get a free at-home, mail-in mouth testing kit. They will also learn how their microbiome compares to those of other smokers, non-smokers, and ex-smokers.

How to take part in the study: http://ubiome.com/smoking

The microbiome consists of the bacteria living in and on the human body, making up between three and six pounds of an individual’s overall weight. Bacteria can be both helpful and harmful. They play a crucial role in digesting food and synthesizing vitamins. However, they also contribute to serious issues such as autoimmune disorders, diabetes, heart conditions, bowel conditions, and skin conditions. The bacteria which make up the human microbiome are distributed across many different parts of the body – in the gut, ears, nose, genitals or mouth, for instance. The mouth alone can be home to around 1,000 different bacterial species.

Oral bacteria can cause tooth decay and gum disease, with figures showing that nearly 42 percent of periodontitis (gum disease) in the United States is attributable to tobacco smoking. There may be other links between smoking and the microbiome. For example a recent study by University Hospital Zurich suggested that the gut microbiomes of ex-smokers differ from those of smokers in a way which might partly account for the weight-gain often seen when people stop smoking. Potential weight-gain is a frequently cited reason for smokers refusing to give up, so understanding more about the interrelationship between bacteria, smoking, and weight change would be invaluable.

Jessica Richman, co-founder and CEO of uBiome, says the tobacco smoking study has significant potential. “Despite the known health risks, about 42 million Americans smoke. One way or another we’re all affected by smoking. Everyone either knows a smoker or is one themselves. We need to know more than we do, so this crucial study will shine a light on some of the unknowns. What difference does it make to the oral microbiome, for instance, if someone took up smoking as a teenager rather than coming to it later in life?”

Almost eighteen of every 100 U.S. adults aged 18 years or older currently smoke cigarettes. Although smoking rates in the U.S. have halved since 1964, the rate of decline has slowed. Smoking dropped from nearly 21 of every 100 adults  in 2005 to nearly 18 of every 100 adults in 2013. Cigarette smoking is the leading cause of preventable disease and death in the United States, accounting for more than 480,000 deaths every year, or 1 in 5 of all deaths.

Dr. Zachary Apte, CTO and co-founder of uBiome, says the oral microbiome samples from smokers, ex-smokers and non-smokers will be scrutinized in the company’s state of the art laboratory. “Just ten years ago it would have cost millions of dollars to analyze just one single person’s microbiome. Our sequencing service, based on research from the NIH Human Microbiome Project, can now do it for $89. For the first time, this makes large-scale research like uBiome’s new smoking study possible.”

uBiome’s mission is to use big data to understand the human microbiome by giving consumers the power to learn about their bodies, perform experiments, and see how current research studies apply to them. uBiome was launched in 2012 by UCSF scientists and Stanford and Cambridge technologists after a crowd-funding campaign raised over $350,000 from citizen scientists, roughly triple the initial goal. uBiome is now funded by Andreesen Horowitz, Y Combinator, and other leading angel investors.

Those interested in participating in the uBiome tobacco smoking study and getting a free mouth microbiome kit can find details here: http://ubiome.com/smoking


Alexandra Carmichael

3 Reasons to Love Your Bacteria!

Since it’s the season of love, I thought we should give a little love to all the hard-working and under-appreciated beings we share life with.

Our beautiful bacteria.

Now I’m not suggesting we write love letters to our E. coli or send flowers to our lactobacillus, although some of your gut bacteria might appreciate if you snatched a few mouthfuls of sweet chocolate. But feeling gratitude for these tiny yet influential beings is definitely justified.

Why? Read on.

1. For one thing, there are so many more of them on and inside of us than many people know. It’s been estimated in the past few years that there are trillions of microorganisms in the human body, about ten times more than the number of human cells. They’re much tinier than most human cells, so they only weigh a couple of pounds. But they still outnumber us 10 to 1 (not to mention that there are probably more than 10,000 different species of them in your body right now!)

2. And they’re powerful too. Research has found that changing the bacterial balance in the gut can trigger mice to be braver, or more anxious, or stronger against disease, or more susceptible to it. Human studies have yet to be done, but it looks like your microbiome could affect your mood, health, and well-being in ways we’re only just beginning to understand.

3. Your bacteria need you, but you need them too. Even though you can’t see them, they’re helping you digest your food, absorb nutrients, grow, fight disease, reduce inflammation, and more. And if they’re not taken care of, they might even play a role in chronic disease.

So let’s give a big loving hug to all the little helpers we didn’t even know we had.






http://www.youtube.com/watch?v=4BZME8H7-KU (PBS Digital Studios)