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!

The People Who Get Their Own Gut Bacteria Fed Back to Them

Can you “bank” your microbiome?

Imagine what it would be like to have your gut bacteria stored away
somewhere, then fed back into you one day.

Sound crazy?

Well don’t get grossed out. It’s already happening.

Disease and serious illness are a sad part of life, affecting the healthiest
of us, often out of the blue.

Of course the human body has evolved a sophisticated immune system
which usually does an amazing job of battling pathogens.

The fact that it’s called a “system” should serve as a reminder that it’s not a
single entity, but a complex network of organs, tissues, and cells working
together to protect the body, and included in this setup is the microbiome, the
rich diversity of bacterial life that lives in and on the human body.

But sometimes even the most robust immune system may not be up to the job
of providing protection, and even supposedly helpful treatments can
themselves have unwanted side effects that a compromised immune
system can do little to battle.

Doctors are recognizing this and learning that patients’ recoveries can be
sped up if their microbiomes are somehow protected.

But how do you do this when an invasive treatment such as chemotherapy or
radiation tends to kill a patient’s healthy cells alongside their cancer cells?

Italian researchers, for example, found that children receiving treatment for
bone marrow or blood cancers such as multiple myeloma or leukemia
experienced an enormous influx of new bacterial species post–treatment, but
saw less than 10% of their original microbiota remain.

One way to protect the microbiome is both simple and effective, but sounds
decidedly yucky.

Just like “banking” a patient’s own blood before an operation, a patient’s gut
microbiome can be stored, then returned after treatment.

And it’s done via what might best be termed a “stool deposit”.

Basically a patient’s feces are mixed with saline solution in a special lab
blender called a “Stomacher”, then stored in a freezer at -70°C.

When it’s time to re-inoculate the patient, it can go back in either via a tube
down the nose, or up the other end during a colonoscopy or even as an
enema. Not exactly a pleasant thought, I know, but actually these procedures
are also used in fecal microbial transplants (FMT) which we’ll talk about in a
future Monday email.

Yup, you’ve got that one to look forward to.

Doctors at the world’s largest private cancer center, the Memorial Sloan
Kettering in Manhattan, use the procedure as part of bone marrow treatments,
calling it “autologous restoration of gastrointestinal flora” which while sounding
rather complex and clinical is maybe more patient-friendly than labelling it a
poop transplant. (“Autologous”, by the way, means cells or tissue obtained
from the same individual.)

Similarly, clinicians at North York General Hospital in Toronto bank patients’
stools in case they experience a hospital acquired infection such as C. diff.

Although fecal transplants can also be used effectively in this situation,
using a patient’s own poop spares them from exposure to bacterial species
that may be harmful. It also avoids the need for the time-consuming and expensive
testing necessary when fecal matter is transplanted from one person to another.

The procedure is currently fairly unusual, but perhaps it will become more

You see, hospital acquired infections are a giant problem.

At any given time in the USA, around one in 25 inpatients has an infection
related to hospital care
, leading to the loss of tens of thousands of lives every

Reacquiring your own stool admittedly sounds like a pretty rough procedure.

Not so nasty if it ends up saving your life, though.

Feeding My Curiosity – And My Microbes

humanWe’re delighted today to have a guest post from Alanna Collen, author of 10% Human: How Your Body’s Microbes Hold the Key to Health and Happiness.

In honor of this insightful book, we’re presenting a double offer today:
50% off uBiome gut kits from now until midnight tonight (August 14, 2015), if you use the discount code 10HUMAN50 at ubiome.com.

People who use this code will also be entered into a draw to win one of ten free 10% Human books! Thanks for the inspiration, Alanna. Take it away.

At the age of twenty-eight, I developed hay fever and eczema for the first time in my life.

The acne I had had as a teenager returned after years of absence. And I began to suffer from respiratory infections with the apparent immune naivety of a toddler. I had just finished a 14 month-long course of multiple oral antibiotics, intended to treat an infection I had picked up while working as a tropical biologist in Malaysia.

I visited my doctor. What could I do about the acne and the infections, I asked. His response?

Take antibiotics.

I protested – it seemed to me that it was antibiotics that had got me in this situation in the first place. “Impossible,” he said. “Only left-field alternative health types think that disrupting ‘friendly bacteria’ can cause health problems.”

I was far from a ‘left-field, alternative health type’ – I had a PhD in evolutionary biology and no particular interest in unconventional therapies and pseudo-scientific theories. But despite his discouragement, my evolutionary outlook on the world made me think. If we had evolved with our friendly bacteria for millennia, wasn’t it quite a stretch of the imagination to assume that disrupting our inner ecosystem might not harm our own bodies?

Delving into the scientific literature that afternoon, I discovered that a whole new world of microbiological research had opened up in the past decade. Our microbes, it seemed, were connected not only to hay fever and acne, but a huge range of illnesses, from autoimmune diseases to mental health conditions, and even obesity.

What’s more, these illnesses were on the rise, having been quite rare just 60 years ago.

Over the coming weeks and months, my interest in, and knowledge of, microbiome science deepened, expanding from a personal quest to understand my own health problems into a broader curiosity about how microbes contributed to the health and happiness of all of us.

I learned about the role of microbes in weight gain, allergic disorders, autoimmune diseases and mental health conditions. I read about the impact of antibiotics on the microbiota of both children and adults. I discovered the amazing potential of faecal microbiota transplants to restore people to health after C. diff infections had brought them close to death. And I realized the role that diet had to play in shaping a beneficial community of microbes in the gut.

Soon, I had pulled together a story of this fascinating new science that led to me being commissioned to write a popular science book on the microbiota. Now published, the result of my efforts is 10% Human: How your body’s microbes hold the key to health and happiness.

So what of my own microbes, I wondered as I wrote?

Would it be possible to detect the impact of my months and years of antibiotics in the make-up of my own inner ecosystem? And could I improve the community I harbored by putting what I had learned about diet into practice?

Eager to begin my own ‘n=1’ experiment, I sent a stool sample to uBiome after eating my normal omnivorous diet, including the sugar, meat, cheese and alcohol that I regularly consumed. I then embarked on two weeks of vegetarian living, cutting out meat and simple sugars, and increasing my intake of dietary fiber.

I ate more legumes, grains, beans and peas, and bigger portions of vegetables, and a few more fermented foods than usual. At the end of my fortnight of high-fibre eating, I sent a second sample to uBiome and waited to see if I had encouraged any of the beneficial species I’d been writing about.

One species in particular had captured my attention. A team of Belgian researchers, led by Professor Patrice Cani, had discovered that a member of the phylum Verrucomicrobia, known as Akkermansia muciniphila, seemed to be found in greater numbers in lean people compared without overweight and obese people.

In mice, Cani’s team showed that Akkermansia encouraged the cells of the gut lining to produce a thick mucus layer, and helped to prevent a bacterial compound from crossing into the blood stream, where it provoked the inflammation that went along with weight gain. Not only did it shore up the gut lining, but Akkermansia numbers were easily boosted – by eating fiber.

Sure enough, when I received my results from uBiome following my dietary intervention, one species stood out to me. Before my dietary shift I had had no detectable Akkermansia.

In just two weeks of eating more fiber, I had at least 100 times more of this intriguing bacterium occupying my gut.

Whether it can noticeably improve my health remains to be seen, but I know I’ll be doing my best to keep it – and other species that benefit from fiber – as a prominent member of my much cherished microbiota.

What’s Really In Your Poop?

The lowdown on the brown.

Does it seem like life dumps a load of poop into your mailbox at times?

Here at uBiome, this is literally the case. And I have to tell you we couldn’t be happier.

Much to our delight the postal service brings us stacks of fresh stool samples every morning (along with material swabbed from four other sites on people’s bodies – mouth, ears, nose and genitals).


Oh yes. We love your poop. It’s so wonderfully rich in information about the microbiome, unlocked when we analyze it using DNA sequencing technology to reveal the make up of the three to six pounds of bacteria you carry in and on your body.

But what exactly is poop? Since so much (excuse the expression) ‘passes’ through our lab, you might not be too surprised that we know a thing or two about its ingredients.

First and foremost, feces contains a boatload of water. About 75% to be exact.

Put that aside, however, and things get more interesting.

About 50 to 80% of the remainder is bacteria, both living and dead. This is the stuff we’re focused on.

On top of that there’s protein, undigested food residue (more on this in a minute), waste material from food, cell membranes, fats, salts and material released from your intestines and liver (e.g. mucus).

If you’re anything like the average person you’ll produce around half your own body weight in feces every year.

That’s a lot.

Fortunately we require the tiniest proportion of this when you send in a gut microbiome test sample to us. It’s also far less yucky than you might imagine: simply swab your used toilet paper to collect just enough to turn the tip of the cotton swab brown.

Poop is generally brown, by the way, largely because of a pigment called bilirubin produced when your red blood cells break down.

And speaking of toilet paper, although it might seem as if you’re forever buying the stuff, this relatively minor inconvenience has to be better than living in Ancient Rome.

In those days you’d have wiped yourself with a communal sponge rinsed in a bucket of water or vinegar after use. Nice.

Oh yes, one last thing about that undigested food residue in your poop. (It’s okay, just about everyone has it, as some food is simply indigestible.)

The outside of corn kernels is a perfect example. While you’ll probably have no trouble processing the insides, the hulls are made of cellulose so they generally pass through your body intact.

Examine your poop after eating yellow corn, therefore, and you’ll likely spot what looks like intact kernels – actually just the “skins”.

In fact they can provide a neat way to time how long your body takes to digest food.

Like we said, your poop can tell you an enormous amount. All you have to do is listen.

Or at least send a little of it our way.

Have a great week!

Alexandra 🙂

Alexandra Carmichael
Director of Community, Product, and Growth

Tracking Poop, Gut Parasites, and Antibiotic Effects

At the recent Quantified Self conference in San Francisco, self-experimenter Mark Moschel talked about his unfortunate encounter with a parasite-filled bowl of ceviche in the streets of Ecuador. But in true QS fashion, Mark turned it into an opportunity to learn about his body. He took several uBiome tests, and shares what he learned in the video below. Thanks Mark!

Resistance: A Film About Antibiotics

Are we at war with the bacteria that live in and on our bodies, or do we need their help? A new documentary film called Resistance looks at that question.

With touching personal stories, insightful expert comments, and fun snippets of old-style public service announcements, filmmaker Michael Graziano helps us to see that using antibiotics to kill our bacterial inhabitants should be a practice used incredibly sparingly.

Here’s a preview of the film below, and my favorite quote from it. Check it out!

“Our challenge is not to defeat them; our challenge is to learn to live in balance with them.” – Resistance


Acne and the Microbiome: Christi Investigates

Christine Preston is back to share more microbiome research insights with us. Thanks Christi!

Hi again, everyone!

This week I’ve been battling some nasty skin flare-ups, and it occurred to me that I didn’t really know what types of bacteria cause or contribute to acne.

There is a multi-billion dollar industry trying to sell washes, creams, medications, and makeup to the acne-prone masses(1). I figured there must be some fascinating research about the relationship between my skin microbiome and the zits currently erupting on it.

Screen Shot 2015-03-22 at 3.53.20 PM

It turns out that there is a LOT of research on acne, and at least one bacteria, Propionibacterium acnes, is involved. However P. acnes is one of those bacteria that is always found on human skin, regardless of how flawless or pimply your skin looks.

P. acnes is an unusual bug. It happens to be the only bacteria that can live in our skin follicle glands (the places where zits are made), consuming the oily sebum made there. Researchers think acne has a LOT to do with how much sebum is produced in our follicles -which is related to diet, genetics, and hormones-, and how our individual immune systems react to the P. acnes growing in our skin follicles(2).

In other words, those bacteria-laden, pus-filled pimples you *absolutely never* pop may have a lot more to do with your parents (Thanks Dad!), and your diet (quesadillas are awesome!), than the bacteria that hangs out in them. And here I was hoping for a quick solution that didn’t involve my quesadillas! Intriguingly, it turns out there are some fascinating differences in the skin microbiomes of acne-prone and non-prone people.

One group looked at the bacteria species in skin follicles of acne and non-acne prone people(3). Overall, P. acnes was the dominant species found in everyone’s follicles. However, in non-acne skin it was the only species found. Acne-prone skin was different. A lot of the acne-prone people had multiple bacterial species hanging out at low frequencies in their follicles! The actual bacteria species varied, but a lot of the acne-prone people had small levels of Staphylococcus epidermidis in their follicles, with Corynebacterium tuberculostearicum Actinobacterium, Staphylococcus hominis hominis. Anaerococcus, and Pripionibacterium granulosum all found in at least one acne prone person.

Another group from UCLA looked very closely at the genetics of P. acnes in the skin of acne-prone and non-prone people(4). They found that the overall level of P. acnes on the skin of the two groups was comparable, however the strains (the subspecies groupings) were different. Acne-prone skin had different P. acnes strain compositions than the non-prone skin. This demonstrates genetic differences in the P. acnes that grown on acne-prone versus non-prone skin.

Unfortunately neither of these studies shows that bacteria differences cause acne, or suggest quick fixes for the acne-prone. I’m very glad this research is being done, and I’m excited to see more results from further studies! In the meantime I’m running a completely uncontrolled study on whether yoga and broccoli help clear up my skin.

(1) http://www.bloomberg.com/apps/news?pid=conewsstory&tkr=COPN:SW&sid=aK0MBQHKoXhs

(2) http://www.ncbi.nlm.nih.gov/pubmed/22189793

(3) http://www.ncbi.nlm.nih.gov/pubmed/18716234

(4) http://www.ncbi.nlm.nih.gov/pubmed/23337890

Baby Microbiomes: Christi Investigates

Let’s give a warm welcome to Christine Preston, a post-doc from UC Berkeley who is now part of the uBiome family. She’s here to help us better understand the current state of research on the microbiome. Thanks Christi!

Hello to the uBiome community!ChristiPreston

When Alexandra asked me if I wanted to do a blog post I jumped to say yes. While I am a scientist, I don’t really know much about microbiology, so I figured I could use this space to share some of the cool research I’m learning about.

And trust me; there is LOTS of amazing knowledge out there about our microbiomes!

Earlier this week I realized I didn’t know much about the beginnings of the human microbiome, so in the spirit of fresh starts I decided to start there. It didn’t surprise me to learn that infants and adults have different microbiomes, however HOW babies get their microbiome, and how infant microbiomes changes during the first few years of life is fascinating. I’ve linked to some articles below that I found especially exciting.

The first thing I learned is that newborn infants probably do not have much of a microbiome before they are born. In fact, a baby’s microbiome is ‘seeded’ by their mother during birth, and researchers can actually tell the difference between babies that are born vaginally and babies that are born by a caesarian section based on their microbiome (1)!

Babies that are born vaginally have microbiomes comparable to their mother’s vagina, with high levels of Lactobacillus and Prevotella bacteria. Babies born by C-section have microbiomes with high levels of the bacteria that hang out on their mother’s skin; specifically Staphylococcus, Corynebacterium and Propionibacterium bacteria. Other groups have looked at whether birth method has a long term-effect on the bacteria in the microbiome of the infants, and find differences in the microbiomes of babies born by C-section versus vaginal births for months (2) or possibly years (3) after birth.

Another major area of research is how the infant microbiome changes as babies grow. There is TONS of research on this, however one study I found especially intriguing was a report that looked at how bacteria species in the gut of a single baby changed over the first 2½ years of his life (4).

This group found that as the baby aged, the bacterial diversity in his gut increased — diversity being generally a good thing in the gut. They also found that some major life changes for the baby affected the bacteria species in his gut, with big changes in bacteria species occurring when the baby was sick, started on solid food, and given antibiotics.

Shortly after the baby was started on solid foods like peas, his gut levels of Bacteroidetes increased. Bacteroidetes are involved in breaking down plant food. The researchers also estimated that a baby’s gut microbiome starts to look like that of an adult around 3 years old.

Stay tuned for more microbiome investigations as I dig and learn more. See you soon!


(1) http://www.ncbi.nlm.nih.gov/pubmed/20566857

(2) http://www.ncbi.nlm.nih.gov/pubmed/16380405

(3) http://www.ncbi.nlm.nih.gov/pubmed/15306608

(4) http://www.ncbi.nlm.nih.gov/pubmed/20668239


My Microbiome Experience from Start to Results

Thanks to Dr. Brooke Anderson-White for this guest post today!

Everyday I'm Samplin'

For the past couple of years my Twitter feed, Facebook wall, and blog have been overrun with all things microbiome; however, until a couple months ago, I had yet to contribute my own microbial ecosystem to the growing dataset. While at uBiome, I joined the movement and quantified my own microbiome with their five site kit. My experience was not completely authentic since I missed out on the excitement of receiving the sleek, black kit in the mail and I gained the excitement of processing my own samples, but I still want to share and promote some citizen science at the end.

uBiome Kit

 In the beginning…

Usually your sequencing adventure begins with ordering your kit online, but I sped up the process by bringing one home with me. When I opened the kit, the instruction card greeted me and directed me to register my kit online. Easy enough. With registration complete, I was ready to get started sampling. Not as easy. To get the most accurate representation of your microbiome, sampling should be done after about eight hours without microbial ecology disruption. This includes showering, brushing your teeth, kissing, swimming in a chlorinated pool, etc.

uBiome the Whole Kit and Caboodle

As my friends will attest, I would gladly use sampling as an excuse to delay a shower, but I sleep less than eight hours a night and leave no extra time in my morning routine, so avoiding everything for eight hours is tough. I decided to stay up a little later than usual and do everything at once; except for the fecal sample, that would come in its own time (though we runners do have our tricks).

The instructions on how to sample are both on the card and on-line but I found the Vimeo video demonstrating skin sampling far more fun and informative. Swabbing was easy aside from the issue of working in the small spaces of the nostril and mouth (I definitely got a tap of skin and teeth in the samples, respectively). The extra swab was appreciated to take a second tooth-biome free mouth sample.

Creepy nostril sampling

When I ask my friends about their experience with swabbing, they unanimously complain about the nostril. Yeah, swabbing inside your nose is creepy, in a “send chills up your spin way,” but it isn’t painful. It just feels wrong.

No one ever mentions the fecal sample. It reflects our actual comfort with poop. If we are as bothered by poop as we assume we all are, diapers would never get changed and there wouldn’t be 14 “poop tracker” apps in the iTunes app store.

Usually the samples would be mailed back in the padded envelope provided, but I skipped USPS and brought them right back to the uBiome lab.


Once in the lab, the samples are entered into the system and the processing begins. A DNews video gives you a behind the scenes look at this part of the uBiome experience. Once again, I deviated from the typical experience, and processed my own samples.

Processing my uBiome samples

As your samples make their way through the sequencing pipeline, you receive encouraging email updates to track your precious microbes. Eventually, you get the email you’ve been waiting for and your data are ready.

In the end.

Upon entering the data delivery site, my suspicions were confirmed: my microbiome falls outside the norm. I have far more Firmicutes and far fewer Bacteroidetes than the average Western population (and maybe would fit in better with the Hadza). This is most likely the result of my high fiber diet of fruits and vegetables. According to the Mayo Clinic, a woman needs about 25 grams of fiber per day, but Americans average 15 grams. I average 35-40 grams per day. My Firmicutes are well fed.

In addition to comparisons to the overall data set, there are other options on the uBiome site to play with your data, as well as phyla descriptions, but what I really want to know is how to apply this information. Unfortunately, this is where I hit a wall. Much of the research linking specific bacteria to conditions, like obesity, is based on correlative data and the findings from one study to another are often contradictory.

uBiome gut sequencing results

The young field of microbiomics isn’t ready to prescribe behaviors or lifestyle changes based on sequencing results now, but it will be. We can all contribute to this progress by acting as citizen scientists. If you start a new probiotic, decide to go Paleo, or start Couch to 5K, take the opportunity to advance microbiomics and sequence yourself before and after. uBiome is not the only option for sequencing your microbiome, but I would suggest that you pick one service and stick with it to ensure all results are comparable. Sequencing results can vary based on the methods used to generate the data. (Yes, this is problematic and groups are working to create a solution.)

In the meantime, I’ll stick with my fiber and exercise and quietly keep quantifying myself until science catches up and tells me how to live better through bacteria.

Meet your Friendly Neighborhood Mouth Biome

Guess what? Living cozily inside your mouth right now are about 700 species of microbes.

They happily reside on your teeth, gums, tongue, the insides of your cheeks, the roof and floor of your mouth, even your tonsils. Some of them protect your health, and some of them are associated with cavities, gum disease, and infections like tonsilitis.

Would you like to meet your neighbors? At a high (phylum) level, their names are:

corcobphoto_creditriekenFirmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes, and Fusobacteria (most prevalent), and Euryarchaeota, Chlamydia, Chloroflexi, SR1, Synergistetes, Tenericutes, and TM7 (less prevalent).

These are kind of like names of major ethnic groups, and you can drill down all the way to the level of individual first names like S. pyogenes.

What’s important for a healthy mouth seems to be having the right diversity and balance of the bacteria in your mouth, and scientists are still working on modeling how all the different species interact with each other.

Stay tuned for breaking research about the oral microbiome in the months and years to come – imagine finding out the bacterial balance in people with lots of cavities, compared to people that have never had a cavity at all! And if you’d like to be part of it and help speed up discoveries, feel free to join our gut plus mouth study.

Guess what else? When you kiss someone, you’re passing millions of bacteria back and forth. Which, while fascinating, might not be quite the best thing to say to your Valentine in a moment of passion this weekend.