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.

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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

Moa

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

January 5-for-1 Sale!

Do you track how well your new year’s resolutions are working? Why not get a snapshot of your microbiome today, and see how it changes as you do. Here’s to the very best of health for you in 2016.

Starting right now, a 5-site microbiome testing kit is just $89 instead of the usual $399.

You can meet all the bacteria currently living in your gut, and also learn about your mouth, nose, skin, and genital microbiomes at the same time.

Offer valid until Sunday, 1/17 Monday, 1/18 at midnight, or while supplies last.

Use discount code 5FOR1JAN when you checkout at ubiome.com.

We appreciate you 🙂

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.

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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


References

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.

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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.

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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.

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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.

Cheers.

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

Alexandra Carmichael
Director of Product, Community, and Growth
uBiome


 

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

Purell

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