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

Our Microbiomes Also Sleep

You might imagine that the quantity and diversity of the microorganisms making up any one individual’s microbiome are reasonably fixed and unchanging. However, our microbiomes may be more volatile than we believe.

mic2 (1)

Scientists in Israel have proposed a mechanism through which the composition and functionality of our microbiota are regulated throughout the day to achieve a state of metabolic homeostasis synchronized with the body’s own circadian cycle (Thaiss et al, 2014). Homeostasis is the process of the body maintaining a condition of balance or equilibrium within itself, even when experiencing external changes. A simple example of homeostasis is our ability to maintain an internal temperature of around 98.6 degrees Fahrenheit, whatever outside temperature. Metabolic homeostasis within the microbiome represents its ability to maintain balance in the chemical processes necessary for the maintenance of life occurring within its cells and organisms.

A mechanism of this nature may explain previous reports of the microbiome’s tendency to quickly adapt to changing circumstances, such as a new diet (David et al, 2013).

A circadian rhythm is any biological process that displays a self-driven oscillation of about 24 hours. Circadian rhythms can generally be affected by external circumstances, and have been widely observed in plants, animals, fungi, and cyanobacteria (a large group of bacteria which obtain their energy through photosynthesis).

Of course plants also photosynthesize, and in the same way that they do so during daylight hours and take in oxygen at night, the human body is programmed to perform certain functions best at particular times of day.

Before the advent of electric light in the home, people woke as the sun rose and went to bed when it set. There were no external factors affecting their circadian clocks. However, once homes were lit with electricity people could continue to go about their lives after dusk, ignoring their circadian rhythm in favor of more work or leisure time. This led to questions being asked about the effects such a lifestyle might have on individuals’ health. For example, studies have indicated that sleeping for less than eight hours a day could lead to weight gain, or be related to mental health problems such as depression. There are even suggestions that too little sleep may raise the risk of developing cancer (Shanmugam et al, 2013).

As we begin to better understand the human microbiome, and how the microorganisms living within us affect our health, it is logical to ask what happens to them if we change our schedules.

The Israeli study mentioned above shows that the gut bacteria living in both humans and mice exhibit diurnal oscillations, not only in functionality but also in composition, and that these 24-hour cycles are governed by the feeding rhythm of the host. The study also concludes that misalignments in the circadian cycle can result in metabolic imbalance and dysbiosis (a lack of bacterial balance), and that these may in turn have relevance in the diagnosis of modern human diseases.

In order to study how it affects the microbiome, the scientists induced jet lag in mice, noting that it changed the composition and functionality of the microbiome, suggesting that chronic jet lag can cause significant disruption to the microbiome’s balance and composition. This is principally the result of significant changes in the host’s feeding rhythms.

The learning is clear. Next time you consider cramming for an exam, working late, or partying until dawn, think about the effect it could have on your microbiome and how this will in turn affect you.

Written by Catalina & Daniel of the Data Science Team


1. Thaiss et al (2014). Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis

2. David et al (2013). Diet rapidly and reproducibly alters the human gut microbiome

3. Shanmugam et al (2013). Disruption of circadian rhythm increases the risk of cancer, metabolic syndrome and cardiovascular disease

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

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.

Experimenting with a Gut Cleanse – By Richard Sprague

Guest post by Richard Sprague

Your gut microbiome changes constantly in response to everything from diet to exercise, so when looking at multiple uBiome test results side-by-side it can be complicated to figure out what caused a particular change. What if you could radically alter your microbiome with a cleanse and just track that, along with precisely what you eat afterwards? What could you learn?

I recently tried exactly that, using a colon cleanse – the kind you do before a colonoscopy screening. By flushing most of the bacteria from my system and carefully watching them grow back with side-by-side uBiome tests, I learned a few things that might interest you as well:

My gut microbiome recovers pretty quickly. Unlike antibiotics, which are known to cause long-term (and possibly permanent) changes, losing bacteria this way seems only to affect the total numbers, but they sprout right back just like a haircut. In two weeks I was as good as new.

This is an overall view of how my gut biome changed:


Amounts and ratios changed, but not the specific organisms. Of course I lost a bunch of bacteria – that was the point – but surprisingly I didn’t seem to gain anything really new, even after an aggressive attempt at re-seeding. I didn’t gain or lose a single phyla. Other than amounts and ratios, I had to dig down to the Class level of the biological hierarchy to find anything that was permanently lost, and even at the very fine-grained Genus level, only two taxa that had been regularly present beforehand were now extinct. (Holdemania and Methanomassiliicoccus).

There is more change when you look at this functional view, but even then watch how quickly it bounces back:


A couple of weird ones, at small amounts, made a brief appearance. I was especially intrigued by five new taxa that showed up just once, the day after the cleanse, and then disappeared. Maybe I found some that ordinarily get lost in the noise of the microbiome and only show up when the rest of the forest has been cleared. These are some hardy guys and I’m glad I know their names and can watch for them again: Abiotrophia, Bacillus, Catonella, Christensenella, Parvimonas.

It’s pretty hard to make a significant change. These days a little googling will find plenty of web sites, books, diets, and supplements that claim to “fix” or “change” your microbiome. I’m a healthy, reasonably fit adult, so maybe I didn’t try as hard as somebody might with a specific health problem, but I thought simply popping probiotics and eating a variety of new and fermented foods would have a big effect. Nope. There are exceptions – my past experience with sleep hacking demonstrated conclusively to me that I can temporarily change my bifidobacterium levels for example – but those examples are harder to find than I had hoped.

Here’s another important ratio that microbiologists have found useful to see how the gut biome changes:

See much change? Me neither. There’s a short spike during the cleanse, but then it just pops back to normal.

Follow me on Twitter, or check my personal web site for more details of my experiment, and please let me know if you did or are thinking of something similar!


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