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

What Happens to Your Microbiome If You Own a Dog?

How a canine companion can affect your bacteria.


Given that dogs are such popular pets, you may imagine that the origin of the word “dog” would be easy to pin down.

Not so.

Until the 14th century, man’s best friend was known in English as the hound, but somewhere along the line the name of just one canine subtype – dog (a kind of mastiff) – came to represent the entire species.

Nowadays, of course, plenty of households own dogs – in the U.S. the figure is somewhere around 40% – so what do we know about the effect of a canine companion on the microbiome of its human owner?

Quite a lot, it turns out.

For a start it’s probably not surprising to learn that bacteria from a dog’s fur and paws is easily transferred to the skin of humans living in the same space.

A 2013 study based at the University of Colorado showed that adults share more microbes with their own dogs than they do with dogs owned by other people.

Perhaps more unexpectedly, the same study showed that simply owning a dog has an impact on the sharing of microbes between one person and another living in the same place.

Cohabiting couples who owned dogs had more bacteria in common with each other than couples who didn’t have dogs.

The researchers concluded it was because couples with dogs had more ways to transfer microorganisms from one to the other.

One person strokes the dog, leaving their bacteria behind, then the other picks it up when they also pet the pet.

Humans have lived alongside dogs for a heck of a time.

It’s widely believed that dogs evolved from a group of wolves which came into contact with European hunter-gatherers somewhere between 18,000 and 32,000 years ago.

What are some of the health benefits of dog ownership?

Well there’s pretty good evidence that people who own dogs are happier, less-stressed, and even less likely to die of heart disease.

But could it be possible that dogs might even act as a source of healthy bacteria?

Could a dog in fact be a kind of probiotic?

Actually, two intriguing studies do seem to point in this direction.

UCSF scientists who conducted a study in 2013 suggested that living with a dog in infancy may lower a child’s risk of developing asthma and allergies, largely as a result of exposure to what they call “dog-associated house-dust”.

You’ll know all about that if you’re a dog-owner.

Or a cleaner.

The researchers’ hypothesis was that babies and small children need to be exposed to harmless bacteria in order to “train” their developing immune systems.

Just as fascinating, and perhaps already a candidate for one of the year’s most heart-warming ideas, is a current Arizona study that’s exploring whether dogs can directly improve the health of older people.

They’ve adopted unwanted dogs from the Humane Society, then given them to people over 50 who’ve either never owned a dog, or who haven’t had one for a while.

They’re then monitoring the physical and mental health of both owner and dog.

Their theory is that good bacteria from the dogs may be transferred to their new owners, along with other health-boosting benefits.

In fact, compared to humans, dogs have relatively simple gut microbiota.

Although they’re omnivores, they evolved as canines and unlike humans don’t rely on their gut bacteria to maintain their energy balance.

Dogs can, however, have pretty complex oral microbiomes.

Researchers in Cambridge, Massachusetts examined samples taken from the mouths of 50 dogs and found a total of 353 different types of bacteria.

80% of them didn’t even have pre-existing names.

Dogs and humans had very different oral bacteria, too.

Just 16.4% of the bacterial types they found in dogs were also found in humans.

Finally, although it’s a virus rather than a bacterium, one microorganism you definitely don’t want passed from dog to human is the rabies virus, fortunately becoming less and less of an issue these days.

This doesn’t stop dogs biting humans, though.

Statistics suggest that around one out of 50 people in the U.S. is bitten by a dog each year.

Thankfully not the same person.

Anyway, if you do have a (non-biting) dog, why not have a good dose of cuddling up with it today? Your microbiome may just thank you.

See if you have bacteria from your pet with a uBiome kit!

Further reading

Cohabiting family members share microbiota with one another 

Could man’s best friend be man’s best medicine

Dog germs may be good for you

Dogs and Human Health

Effect of prenatal indoor pet exposure on the trajectory of total IgE levels in early childhood

Where does the word “dog” come from

Gut microbiota of humans, dogs and cats

House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection

Humans Share Microbiomes With Their Dogs, Study Finds 

Man’s Best Germs – Does Your Dog Influence Your Health

Origin of Domestic Dogs

Pet Statistics

Swapping microbes with your dog

The Canine Oral Microbiome

Why a Man’s Nose Is Twice as Dirty as a Woman’s

The truth about the bacteria that live in your nose.

Hello, and a very warm welcome to our first email of 2016! I hope you’re healthy and enjoyed some festive time.

It’s a time of year in the northern hemisphere when many will suffer from head colds, so my commiserations if this includes you right now.


But it does at least provide an ideal opportunity for us to check out a fascinating aspect of your bacterial ecosystem that frequently gets overlooked: your nasal microbiome, one of six sites you can explore with a uBiome test.

Compared to their subterranean cousins downstairs in the gut, the microorganisms of the nasal cavity have been relatively unstudied, which is surprising because they’re potentially important for a host of diseases such as sinusitis, allergies and staph infection.

Speaking of “staph”, it’s crucial to know just what species and strain you’re talking about, for virtually all of us carry members of the Staphylococcaceae family (a bit of a mouthful, or should I say, noseful) up our schnozzes.

Some are harmless while others are frankly pretty unpleasant.

Researchers at the University of Michigan found some types of staph – especially Staphylococcus aureus – in the nasal cavities of all their study participants, but never once found it in oral cavities.

Of course your nose and mouth are both connected to your throat, which is why you’re able to swallow mucus, and boy do you do that in prodigious quantities.

Sorry to report this, but a healthy adult swallows over a litre of mucus every day, much more than enough to fill a bathtub every year.

Some of us (but not all, and more of that in a minute) think of nasal mucus as nasty stuff but it’s actually incredibly useful, acting as a kind of lubricant and moistener, protecting all the bodily tubes it coats.

Snot also acts a bit like flypaper, trapping dust and bacteria before they get into the body.

Moreover it contains antibodies that can help your body recognize invading viruses and bacteria, and enzymes which kill these unwanted guests.

While the great majority of us host Staphylococcus aureus up our noses or on our skin, the one place you really, really don’t want it is in your bloodstream.

Its initials form the last two letters of a scary acronym – MRSA.

Methicillin Resistant Staphylococcus Aureus is a highly dangerous infection which can be acquired in healthcare facilities, particularly if careless and unhygienic insertion of a needle causes a particular strain of skin-borne Staphylococcus aureus to be passed into the blood.

MRSA is a bacteria that is resistant to many antibiotics, sometimes known as “golden staph” because of its distinctive yellow pus.

I know, pretty nasty, right?

Changing the subject to something (slightly) less gross…

You may be interested to know that men’s noses are substantially more bacteria-ridden than women’s.

A 2015 study led by researchers at Johns Hopkins School of Medicine discovered that women had about half as many bacteria in their noses as men did.

The same research, which examined both identical and fraternal twins, found that host genetics played no significant role in nasal microbiota composition, but it did contribute to the density of bacteria in the nose.

So while you don’t inherit the types of bacteria which live in your nose, you do inherit the amount that’s in there.

Finally I know I said you may imagine most people find the whole nasal mucus thing pretty unpleasant, but according to British author Stefan Gates, it could in fact be only a slim majority.

You see, in his 2006 book “Gastronaut”, he explained that 44% of the people he questioned owned up to having eaten and enjoyed their own boogers as adults, a practice which even has its own scientific name – mucophagy.

I was going to say that perhaps we shouldn’t knock it till we’ve tried it.

But like I said, whether you like it or not, you’re already downing a bucketful of the green stuff every week.

Anyway, as long as we’re drinking, let me raise a glass of something a little more sparkly in your direction in order to wish you a very Happy New Year!

Further reading

Anterior nares specimen collection

Eating mucus

Golden staph – the deadly bug that wreaks havoc in hospitals

Methicillin resistant Staphylococcus aureus (MRSA) in the community

Mucus (snot, phlegm) color, function, coughing, and more

Nasal bacteria may be predictor of skin infections

Staphylococcus aureus and the ecology of the nasal microbiome

Stefan Gates

The nasal cavity microbiota of healthy adults

Understanding the nasal microbiome

What Will A Holiday Drink Do To Your Microbiome?

Alcohol, Bacteria, Christmas. A Festive ABC.

With the holidays a few days away, perhaps you’ll join me in a small glass of eggnog, traditionally souped-up with a shot of rum.


Early American settlers, by the way, drank their rum from carved wooden mugs called noggins, which may be how the egg-and-rum mixture got its name.

Now I’m sure you won’t be surprised to learn that alcohol consumption goes up during the winter holidays, with figures suggesting Americans drink 28% more than their monthly average in December.

But while an alcoholic drink or two may sometimes help the party go with a swing, what effect does it have on your microbiome?

Let’s begin our brief investigation with an Old Wives’ Tale which suggests that drinking alcohol with a meal prevents food poisoning.

After all, alcohol is widely used for its antibacterial qualities.

For instance, it forms a significant part of hand sanitizers like Purell, which claims to “kill 99.99% of the most common germs that may cause illness in as little as 15 seconds”.

Wow, if ethyl alcohol can do that to your hands, could it do the same for your gastrointestinal tract?

Surprisingly, the answer could be yes.

According to a 2002 study in the journal Epidemiology, Spanish health officials investigated an outbreak of salmonella among people who’d eaten contaminated potato salad and tuna at a banquet. They found that sickness levels were lowest in those who’d consumed large amounts of beer, wine or spirits.

Bottoms up, then.

Let’s raise our glasses to the Spanish, as we have them to thank for another intriguing alcohol and bacteria study.

Research in 2012 suggested that people who drank two glasses of dry red wine a day (the researchers served Merlot) had higher levels of beneficial bacteria like Enterococcus, Prevotella, Bacteroides and Bifidobacterium.

But while the wine seemed to help, other participants drank gin, which brought no bacterial benefits, leading the scientists to conclude that it was the red wine’s polyphenols and resveratrol (a bacteria-busting phenol found in the skins of grapes) that did the trick, rather than its alcoholic content.

Of course moderation is crucial.

People who become alcohol-dependent often end up with severely affected microbiomes.

In fact, alcoholism can lead to a nasty condition called leaky gut, where bacterial metabolites pass through the GI tract into the bloodstream.

And trust me, you don’t want a leaky gut.

But perhaps alcohol only damages the microbiome if it’s misused over a long period?

Surely one party can’t do much harm?

Think again.

Researchers at the University of Massachusetts Medical School recruited 25 healthy individuals for a binge-drinking session, during which participants were instructed to knock back 2 mL of vodka for each kg of body weight (between four and five shots for an average person).

Blood samples, tested for bacterial DNA, showed a disturbing 50% increase an hour after drinking.

Levels were still significantly higher 24 hours after the party, er, experiment.

Finally, before we leave the fascinating world of the holidays and the microbiome, a friendly reminder that this time of year can be a vicious one for foodborne bacterial infections including Salmonella, Staphylococcus aureus and Listeria monocytogenes, so please do your very best to keep your kitchen surfaces well-wiped, ensure all food is properly cooked, and wash those hands – perhaps even resorting to the hand sanitizer.

Mind you, whatever you do, don’t be tempted to down a slug of Purell.

Apparently the manufacturers of sanitizers purposely add a bitter taste to their products to make them unpleasant to drink.

So I’d stick to the Merlot, Cabernet Sauvignon, or Syrah if I were you.


Wishing you and your loved ones the happiest of holidays!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth


Further reading

Acute Binge Drinking Increases Serum Endotoxin and Bacteria

Alcohol – Balancing Risks and Benefits 

Alcohol Facts and Statistics 

Alcohol Research – Current Reviews

Alcoholism and the microbiome

An Egg and a Grog in a Noggin

Christmas Drinking

Christmas Food Safety

Comparative Study of Microbial-Derived Phenolic Metabolites

Drinking Alcohol With a Meal Prevents Food Poisoning

History of Eggnog

Host-Microbiome Interactions in Alcoholic Liver Disease

Influence of red wine polyphenols and ethanol on the gut microbiome

Intestinal permeability and gut-bacterial dysbiosis

Misuse Ingestion


The Protective Effect of Alcoholic Beverages on the Occurrence of a Salmonella Food-Borne Outbreak

How To Make Sauerkraut, The Perfect Christmas Gift For Your Gut

Oh Little Town of Bacterium

Just ten days to Christmas Eve, a night on which Polish families celebrate “Wigilia” (vigil) with a meatless supper of 12 courses, one for each month of the year.


It’s a meal that often features sauerkraut, a delicious and healthy fermented foodstuff that’s actually dead-easy to brew up at home.

The good news?

If you make a batch now it ought to be ready for your own Christmas celebrations, a perfect present for your about-to-be overwhelmed microbiome.

The even better news?

There’s a recipe below.

But first, a soupçon of sauerkraut history and biology (yup, it’s loaded with yummy bacteria).

Sauerkraut is German for sour cabbage, so it’s not surprising that many think of it as a German invention.

In fact laborers building the Great Wall of China 2,000 years ago commonly ate shredded cabbage fermented in rice wine, and the Roman writer Cato the Elder wrote of preserving cabbage with salt in his book de Agri Cultura in around 160 BC.

It was the use of salt rather than wine which caught on, which is how the sauerkraut which accompanied Captain James Cook’s crews on their voyages in the 18th century was made.

Their fermented cabbage made for great maritime rations as it needed no refrigeration and helped prevent scurvy.

Sauerkraut popped up in the history books again in World War I when American manufacturers worried that the slightest whiff of an affiliation to Germany would be catastrophic for sales, so for the duration of the war they slyly renamed it Liberty Cabbage.

Sauerkraut is formed in a three-part lactic acid fermentation, each stage involving bacteria.

First the anaerobic (oxygen-hating) bacteria Klebsiella and Enterobacter begin creating an acidic environment which favors subsequent fermentation.

Then, when conditions have become more acidic, Leuconostoc take over.

Finally, Lactobacillus get to work fermenting any remaining sugar.

Now although this may sound complicated, all you have to do in fact is sit around while nature does its work.

And the delicious results are great for your gut. Sauerkraut is loaded with vitamins C, B, and K.

It’s low in calories, high in magnesium and calcium, and a great source of dietary fiber.

What’s more, the homemade kind, if uncooked, contains live Lactobacillus – probiotics which tend to improve digestion and promote the growth of healthy gut flora.

Sounds good, doesn’t it?

Here’s a quick summary sauerkraut recipe, courtesy of The Kitchn (please see below for a link to their comprehensive instructions).


One medium-sized cabbage (about 3 pounds)
1.5 tablespoons salt


One large glass jar – e.g. a two-quart (about 2 litre) Mason jar
One small jar that fits in the mouth of the larger one – e.g. a jelly (jam) jar
Clean marbles, stones or other weights to go in the small jar


1. Discard the cabbage’s outer leaves, then slice it into very thin shreds.

2. Place the cabbage in a mixing bowl and sprinkle it with the salt, working salt and cabbage together with your (clean, please) hands for between 5 and 10 minutes.

3. Pack the cabbage into the jar as tightly as possible, making sure the cabbage is submerged under the brine your handiwork with the salt will have produced.

4. Weigh down the cabbage and its brine using the smaller jar full of marbles/stones.

5. Cover the jar with a cloth, secured with twine or a rubber band.

6. Over the next 24 hours, press down the cabbage with the smaller jar from time time.

7. Ferment the cabbage for 3 to 10 days at cool room temperature (65°F to 75°F) avoiding direct sunlight. You may see bubbles in the cabbage, or foam or white scum on the top. This is fine. They’re simply signs that fermentation is taking place. Scoop off the scum if you like.

8. Start tasting after three days. When it seems good to you, remove the weight, screw on the top, and refrigerate. You can store sauerkraut for several months.

That’s it. You’ve made your own sauerkraut.

Many of us will subject our tummies to an almighty onslaught over the holidays.

The least you can do?

Give your gut the gift of a scrumptious serving of brassica–based bacteria.

Have a great week!

Further reading

From The Kitchn: How To Make Homemade Sauerkraut in a Mason Jar

German Food Guide & Directory

Homemade sauerkraut recipe

Homemade Sauerkraut Recipe

How to make sauerkraut

Polish Christmas Recipes


The History of Sauerkraut


Sharing Our Microbiome

Your microbiome can be shaped by the environment you live in, the food you eat, your genes, and even your age. We know this. But can the people and, perhaps, pets you live with also influence the microorganisms that colonize your body?

Some studies suggest they can, and what’s more you may also change the microbial makeup of the places you frequent, leaving traces of your microbiome behind you.

In order to find out how the microbiomes of people and the places they live in differ from one another, researchers studied the microbial composition of six homes and the people and animals who lived in them. They found more similarities between people, their pets, and their homes than they did between people from different homes (Song et al., 2013).

The research also showed that different residences can have significantly different bacterial profiles. According to the study, although bacteria within homes can vary considerably from room to room, the most substantial similarities occur between the kitchen, front door knob, and bedroom floor. Likewise, the hands and feet of any home’s occupants have the greatest tendency to share the same bacteria.

The same study showed that when a family moves home, their new residence soon has a bacterial composition similar to their old one’s. Along similar lines, the research found that hotel rooms soon acquire their occupants’ bacteria, with a room’s surfaces showing traces of its guest’s microorganisms within 24 hours.

Another study explored the ways in which having children and pets in a household affects its microbiome (Lax et al., 2014). The research showed that the presence of either can lead to a home’s occupants sharing more unique bacteria from their individual guts and skin.

The authors proposed that this could be because of an increase in the number of shared sources of unique microbes. For example, one member of the household might transfer their bacteria to the dog’s bowl as they filled it, then this would be picked up by another person as they performed the same duty later.

sharing microbiome

The study also showed that dog owners from different families can share microbes which are not shared between people without dogs. The finding reinforces the idea that who we live with, in both human or animal terms, can shape the bacteria which colonize our bodies.

Some researchers suggest that the tendency for individuals to share their microbiomes in such ways may be caused by each of us having a microbial “aura” – a cloud of bacteria which hangs in the air around our bodies wherever we go (Meadow et al., 2015).

Indeed this has led some scientists to propose that it should be possible to identify an individual person from their microbiome alone, then to go on to develop an algorithm capable of matching someone to a specific gut microbiome using metagenomic markers (Franzosa et al, 2014). In fact they were able to identify individuals with an accuracy rate of 80%. However these researchers were unable to identify certain individuals over time, which they proposed was caused by people changing their habits in ways which affected their microbiome.

Written by Catalina and Daniel of the uBiome data science team


1. Cohabiting family members share microbiota with one another and with their dogs.
Se Jin Song, Christian Lauber, Elizabeth K Costello, Catherine A Lozupone, Gregory Humphrey, Donna Berg-Lyons, J Gregory Caporaso, Dan Knights, Jose C Clemente, Sara Nakielny, Jeffrey I Gordon, Noah Fierer, Rob Knight.

2. Longitudinal analysis of microbial interaction between humans and the indoor environment.
Simon Lax, Daniel P. Smith, Jarrad Hampton-Marcell, Sarah M. Owens, Kim M. Handley, Nicole M. Scott, Sean M. Gibbons, Peter Larsen, Benjamin D. Shogan, Sophie Weiss, Jessica L. Metcalf, Luke K. Ursell, Yoshiki Vázquez-Baeza, Will Van Treuren, Nur A. Hasan, Molly K. Gibson, Rita Colwell, Gautam Dantas, Rob Knight, Jack A. Gilbert.

3. Identifying personal microbiomes using metagenomic codes.
Eric A. Franzosa, Katherine Huang, James F. Meadow, Dirk Gevers, Katherine P. Lemon, Brendan J. M. Bohannan, and Curtis Huttenhower.

4. Humans differ in their personal microbial cloud.
James F. Meadow, Adam E. Altrichter, Ashley C. Bateman, Jason Stenson, GZ Brown, Jessica L. Green, Brendan J.M. Bohannan.

Why Bacteria Could Soon Be Playing a Leading Role in Crime Busting

Solving crimes with bacterial evidence

It was 121 years ago today. December 7, 1894.


Sir Arthur Conan Doyle, the Scottish physician best known for writing fictional stories about the detective Sherlock Holmes, was spending his final day in New York before heading home to London after a U.S. trip.

If only he’d known then what we know now, because in Sherlock Holmes, Conan Doyle created a forensics expert ahead of his time.

Long before such procedures became commonplace in criminal investigation, Holmes used fingerprints, hair analysis, and blood tests to solve crimes.

Had he been alive today, though, he’d almost certainly have installed a DNA sequencer upstairs at 221B Baker Street.

Not just for its potential in comparing human DNA samples collected from suspects with biological material left at crime scenes, but also because there’s now great potential in using the sequencing of human bacteria for “CSI” purposes.

You see, much like a fingerprint, your microbiome could uniquely identify you.

For example, researchers at Harvard University found that stool samples were particularly reliable.

Apparently your poop has a signature all of its own.

In fact, when the study examined gut bacteria re-taken from participants a year after they’d first “donated”, researchers were able to identify individuals with 86% accuracy.

Everywhere you go, you leave microscopic traces of your bacteria, and you also gather microscopic traces of others.

Dr Josiah Zayner, currently a research fellow at NASA, suggests that banks and convenience stores could purposefully plant rare (but presumably harmless) species of bacteria on their floors which would then get picked up on the soles of criminals’ shoes, allowing investigators to prove that they, or at least their Nikes, had visited at some stage.

What about skin bacteria?

Well, it turns out that a great place to find this is on people’s cellphones, and in a world where more people own mobile phones than have access to working toilets, this could come in handy.

Could your bacteria be used to link your phone to you?

Pretty certainly, according to a University of Chicago researcher who has been able to differentiate between two people with 97% accuracy using only swabs taken from their phones.

Your body’s microbiome contains trillions of bacterial cells and weighs between three and six pounds.

But what happens to the microbiome after death?

The forensics world is extremely interested in this question, and only last year began referring to the “death microbiome” as the thanatomicrobiome (thanatos being the Greek word for death).

It refers to the process in which legions of your own gut bacteria take over your internal organs once you’re deceased.

In a healthy individual the brain, liver, spleen, and heart are free of microorganisms – your immune system keeps them in check.

But after death these bacteria spread, and it turns out that this migration can be used as a pretty accurate measure of the post-mortem interval: a duration which enables investigators to estimate time of death.

A team from Alabama State University (ASU) is working with the Freeman Ranch Body Farm in Texas to understand this better.

The Body Farm houses 150 donated cadavers which are used to study bodily decay. An additional 200 living people have pre-registered as donors.

The ASU team are particularly interested in grave soil, which they say teems with an immense amount of bacterial life after the death of a human.

Applying just the kind of next-generation metagenomic sequencing that we use here at uBiome, they’re developing tests that will enable PMI (post-morten interval) to be estimated with unprecedented accuracy.

All in all, it seems human bacteria is playing an ever-increasing part in the world of crime detection.

But that may not have surprised Sherlock Holmes.

As he might have said to his long-suffering assistant:
“Alimentary, my dear Watson, alimentary.”

Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth


Further reading

Deputy UN chief calls for urgent action to tackle global sanitation crisis

Distinctive thanatomicrobiome signatures found in the blood

Identifying personal microbiomes using metagenomic codes

In Forensics, Microbiome May Become Next Fingerprint

Introducing the Thanatomicrobiome

Paging ‘CSI’- Microbiome analysis may be the new fingerprint

Personal microbiomes shown to contain unique ‘fingerprints’

The Death Microbiome Could Inform Forensic Science And Medicine

The Dirty World of Body Farm Microbes

The Future of Microbiome Forensics

Microbial communities associated with human decomposition and their potential use as postmortem clocks

Your death microbiome could catch your killer

How People Influence Their Microbiomes

The human microbiome begins forming at birth then steadily evolves during an individual’s lifetime. Different areas of the body have their own individual microbial profiles. A child’s microbiome reaches a stable configuration at around 2-3 years of age, with its species and strain composition generally maintained throughout the individual’s life. However, although there tends to be relative stability within individuals, the composition of any one person’s microbiome is likely to differ substantially from any other’s. Genetics may play a part in the microbiome’s development, since a study of monozygotic twins showed that twins’ microbiomes resemble each other to a significantly greater degree than those of pairs of unrelated individuals.

The host and his or her microbiome influence one another, and in this short article we’ll look at three ways in which the host affects the microbiome:

1.  Reductions in NOD-like receptors increase presence of commensal bacteria

Human tissue cells have the ability to sense molecules which may threaten infection. They do so through pattern recognition receptors expressed in a cell’s cytosol (intra-cellular fluid), known as nucleotide-binding oligomerization domain receptors, in short NOD-like receptors (NLRs). NLRs play an essential role in controlling the intestine’s commensal bacteria, so an NLR deficiency can cause an increasing abundance of normally helpful microbes, resulting in a disequilibrium and a reduced capacity to eliminate newly colonizing bacteria. This is because NLRs regulate the bactericidal (bacteria destroying) ability of antimicrobial peptides secreted by the ileal crypt (a kind of ‘pocket’ in the wall of the small intestine) affecting microbiota composition and abundance. Several studies suggest that mutations of a type of NOD called NOD2, a protein coding gene associated with Crohn’s disease and Inflammatory bowel disease, can affect the interaction between host and microbiome through changes in antimicrobial activity.

2.  Immunomodulation leads to microbiome change

Microorganisms involved in inflammatory disease are capable of modulating the immune system’s response to their presence, allowing them to either establish or consolidate an infection. Either as a result of this process (known as immunomodulation) or through immunodeficiency, the composition of the microbiome can change, reciprocally influencing the disease process. Many examples of this are known, including graft-versus-host disease (a condition occurring when donor bone marrow or stem cells attack the recipient), problems in kidney transplantation, hepatitis, cirrhosis, psoriasis, Inflammatory bowel disease, and arthritis. Furthermore immunosuppressive drugs, used to prevent a recipient’s body from rejecting a transplant, generally affect the microbiome-immune system balance.

3.  Changing gene expression correlates with microbial diversity

Variations in a host’s gene expression have been found to correlate with changes in taxa distribution (microbial diversity) in the host’s microbiome. For example, differences in the expression of the lactase enzyme had a resultant impact on the abundance of Bifidobacteria in the gastrointestinal tract, probably since some bacterial strains appear to prefer lactose to glucose. In another case, enrichment of genes involved in the leptin-signaling pathway correlated with changes in the microbiota found in the nose, oral cavity, and skin. Leptin is a hormone which is among the best known markers for obesity, and the associated microbiome changes involved, for example, changing levels of: Veillonella (found in the anterior nares, the external part of the nostrils); Lachnospiraceae, and Haemophilus (located in the attached keratinized gingiva, part of the gum); Clostridium (in the right antecubital fossa, the part of the arm inside the elbow); Bacteroides (behind the ear); and Propionibacterium (in subgingival plaque, dental plaque formed under the gums).


Host genetic variation impacts microbiome composition across human body sites.
Ran Blekhman, Julia K. Goodrich, Katherine Huang, Qi Sun, Robert Bukowski, Jordana T. Bell, Timothy D. Spector, Alon Keinan, Ruth E. Ley, Dirk Gevers, and Andrew G. Clark.

Metagenomic cross-talk: the regulatory interplay between immunogenomics and the microbiome.
Maayan Levy, Christoph A. Thaiss, and Eran Elinav.

Host genetic architecture and the landscape of microbiome composition: humans weigh in.
Andrew K Benson.

Written and researched by: Francisco & Daniel of the Data Science Team

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