Your Microbes, Your Health: Products of Your Age, Lifestyle, and More


Our bodies are home to trillions of microorganisms that play a critical role in digestion, the synthesis of vitamins, and our immune function. But, how much are we able to harness our microbiome to take control of our health?

In a previous post, we discussed how nature, nurture, and plain old chance can influence your microbiome. This week, we dive deeper into the science that suggests how these factors can impact your microbiome, and in turn, your overall wellness.

For starters, our station in the circle of life is revealing.

Upon birth, we are immediately exposed to outside elements. For instance, our delivery method (vaginal versus cesarean section) and whether we feed on breast milk or formula help to shape our emerging microbial fingerprint.

Studies suggest that the exposure — or lack thereof — to microorganisms in our early years could contribute to predispositions toward allergies and asthma, among other conditions. Certain babies are more at risk for these conditions when they possess low levels of common bacteria such as BifidobacteriumAkkermansia, and Faecalibacterium and a relatively increased presence of fungi (Candida and Rhodotorula).

At just three years of age, our microbiome stabilizes and roughly resembles the profile of an adult.

Illness and the use of antibiotics can temporarily alter your microbiome, often resulting in decreased diversity of microbial species. Antibiotics are modern miracles in fighting bacterial infections — but since they indiscriminately kill good bacteria along with bad bacteria, they can impact the fragile microbiome. Overuse of antibiotics, especially after repeated administration in a relatively short amount of time, has been associated with intestinal dysbiosis — an umbrella classification that can describe a range of symptoms such as gas, bloating, constipation, and diarrhea, among others.

The aftermath from these experiences can linger for years, but in time, your microbiome usually adjusts back to its baseline state.

As we reach old age, our microbiome decreases in diversity, making our immune system more vulnerable. Low microbial diversity has also been correlated with frailty. Studies show that the elderly experience lower levels of Bifidobacterium, which has anti-inflammatory properties that can help curb disease.

But age is only one variable that governs our microbial landscape.

Location, lifestyle, and genetics also impact your microbiome and wellbeing.

Where one lives — whether it be rural or metropolitan, industrialized or developing — shapes our microbial ecosystem. One study evaluated the gut microbiomes of rural Malawians, indigenous people of Venezuela, and U.S. city dwellers, and found that more pronounced differences existed among the group of U.S. urban residents as compared to the Malawians and natives of Venezuela.

Culture also impacts our microbiome and predisposition toward certain illnesses. For example, a Western diet — typically consisting of low fiber, high sugar, animal-based protein, and processed food — tends to give rise to a predominance of Bacteroides over Prevotella. This diet can be a risk factor for some chronic diseases, including irritable bowel disease (IBD).

Conversely, other communities with high plant fiber diets exhibit vastly different microbiome profiles than their Western counterparts. One such group, Tanzanian hunter-gatherers known as the Hazda, possess an abundance of Prevotella and nearly no Bifidobacterium, among other differences. Notably, autoimmune diseases are virtually nonexistent among these tribe members.

While no one particular healthy microbial profile exists, microbial diversity is known to promote wellness by protecting against foreign pathogens, increasing our natural line of defense. Research indicates that demographic variables including body mass index (BMI), race, and sex are significantly associated with microbial diversity.

Scientists are continuing to explore how social and environmental factors influence the microbiome. What’s more, researchers across multiple disciplines are investigating how these elements contribute to the unique health profiles — and needs — of various populations, whether they’re grouped by sex, age, race, geography, etc. uBiome has engaged in various research collaborations to help bridge this knowledge gap.

As our understanding deepens, we’ll all be more empowered to optimize our health, and our microbes.


Interview with Dr. Vincent Pedre, author of Happy Gut


We are excited to welcome Dr. Vincent Pedre to the uBiome Doctor’s Corner blog. Dr. Pedre is a top Functional Medicine specialist, and the acclaimed author of Happy Gut.

Enjoy this interview with him to learn how you might be able to incorporate microbiome health and wellness into your own practice!

How did you first get involved in the microbiome field?

At an early age, I was always interested in biology. In fact, I became a member of the Biology Club in my high school to have more time to explore the world of bacteria and parasites through the microscope. During that time, I was subjected to multiple rounds of antibiotics, due to the best intentions of my pediatricians to treat recurrent episodes of sinusitis and bronchitis. My gut microbiome was decimated by antibiotics like Cipro, and as a result I developed leaky gut syndrome and multiple food sensitivities. During the quest to heal my gut from the ravages of years of misguided health interventions and an inflammatory diet, I discovered Functional Medicine. That was the first time I heard about that hidden world inside us, the microbiome, which has since influenced everything I do as a clinical health practitioner.

What are you most excited about with the microbiome?

The microbiome is this uncharted territory that for years has been influencing our health; however, it is only within the last decade that research has elucidated the many critical roles the gut microbiome plays in overall health, including production of neurotransmitters, insulin sensitivity, weight management, mental health, learning, and long-term memory. I’m excited to see where this frontier takes us as we learn more about the role of the microbiome in our health.

What do you think are the best questions to ask patients to get a sense of their health habits/diet?

In order to get a good sense of patients’ health habits and diet, I like to ask them the following question: “Walk me through a typical day in your life (what do you eat).” I have found this gives me more accurate information than asking them broad questions, like “Do you eat meat?” or “Are you vegetarian?” The details are really important. For example, if they drink coffee, do they drink it black or with milk, cream or nut milk? Do they put sugar in their coffee?  If so, what type? All these details are important when considering the potential effects on their gut microbiome.

What dietary advice do you most often give patients?

In general, people don’t eat enough vegetables and fiber. And non-digestible fibers are the key to a healthy gut microbiome. So I am constantly reminding people to include more vegetables in their diet. But also, to not be monochromatic in their choices. We tend to get comfortable eating within a certain range of foods, but in order to get all the nutrients and antioxidants our bodies need, we need to branch out and incorporate all the colors in the rainbow in our diets. The exception to this rule are people with markedly reduced gut function and dysbiosis (an imbalance between good and bad bugs in the gut, favoring an over-predominance of the “bad” guys). Such people lack the digestive power to break down these foods due to a damaged gut lining and paucity of probiotic bacteria to help with digestion. In these patients, I go slow, keeping within the bounds of the foods they tolerate, and vegetables are cooked (not raw) until they heal enough to started tolerating raw vegetables.

Do you have any personal habits that you have cultivated to improve the health of your own microbiome?

I incorporate fermented vegetables into my diet regularly. And I eat a variety of prebiotic-rich foods (like scallions, garlic, asparagus, dark leafy greens like dandelion greens) as well. These foods help feed and build a strong, favorable gut microbiome. I follow a plant-rich, gluten-free modified paleo diet, meaning I eat more plants than animal protein, with plenty of healthy fats. I allow dairy in the form of cheese and cultured kefir seasonally in the summer when I don’t have to worry about allergies or viruses. And I modify it by allowing some grains (like brown rice) and beans, which help improve the diversity of the gut microbiome. This is the individualized plan that works best for me after years of experimentation.

What has recently surprised you in the microbiome and functional nutrition field?

When it comes to the microbiome and functional nutrition, the level of individuality that needs to be applied to each person’s diet is extraordinary. There really is no one size that fits all. Learning how to apply individuality to the diet  can be quite challenging. And knowing how to walk yourself or a patient through this challenging process is the key to overcoming many chronic health issues. That’s why, when I was asked by mindbodygreen to become one of the course instructors in their upcoming Advanced Functional Nutrition Training, I couldn’t turn it down. There is so much to share about how to tailor a diet for optimal individual results. I am excited to be part of a world-class team of doctors and nutritionists that have put together a robust, self-paced online course. For more details click here.

Where do you hope microbiome work will be in 10 years?

Within 10 years, I would love to be able to look towards microbiome testing as part of the standard of care for patients with a variety of gut-related issues (including allergies, asthma, skin rashes, and autoimmune diseases like Hashimoto’s, multiple sclerosis, and rheumatoid arthritis). I hope our ability to utilize microbiome information in a more detailed and individualized way to treat patients will have evolved even more, allowing us to choose appropriate probiotics based on testing results.

What is your biggest concern with microbiome testing?

My biggest concern with microbiome testing is that there are still a lot of unknown variables. The testing is limited by what you are looking at. So far, we have been focusing on bacteria, and sometimes limited strains of fungi. However, the microbiome is much broader than that, including the possibility of multiple species of fungi which may have made their home in the gut of individuals, along with the viome — a whole uncharted territory of viruses that live in the gut as well.

What do you think are the top three ways to improve the health of one’s microbiome?

The top three ways to improve the health of one’s microbiome are:

  1. Eat prebiotic-rich foods.
  2. Consume fermented foods and beverages.
  3. Take a probiotic supplement.

What is your favorite microbiome-friendly food?

Ahh, as a microbiome-friendly food, we need to turn to the fermented veggies. So many ways to do this at home are popping up. For example, KrautSource® is one company that is changing the game by offering innovative kitchenware to simplify making fermented foods.

What advice do you have for doctors who want to get more involved? What have been your go-to resources to learn more about this area?

For anyone who wants to get involved, you have to start with the basics. Learning to use functional foods as medicine is the key to long-term health. Luckily, mindbodygreen is launching a new course for the busy professional, stay-at-home mom, or health practitioner who wants to deepen their knowledge of functional food nutrition to help themselves and others live a healthier life. The Advanced Functional Nutrition Training starts November 1 but registration ends on October 26. This is a first-of-its-kind opportunity to learn from the best of the best (including Dr. Mark Hyman, Dr. Frank Lipman, Dr. Joel Kahn and myself) on a variety of topics ranging from how to stock your kitchen and follow an elimination diet, to special diets for different conditions, including gut health, inflammation, autoimmune disease, and detoxification. The best resource includes curated information from top health practitioners who  have taken the time to weed through the confusion, making the latest information easy to understand and apply. That’s what this course is all about.

How do you stay up to date on the latest medical research?

I stay abreast of the latest medical research by: 1) using Google keyword notifications, 2) reading the Science Times, 3) following people who post interesting topics/research papers on social media, and 4) going to continuing education conferences, like the Human Microbiome Congress, to stay cognizant of the latest bench-side research from the scientists who are doing it.

Who are your mentors in medicine?

My early mentors before I entered medical school were Dr. Deepak Chopra and Dr. Andrew Weil. Their books (respectively), “Quantum Healing” and “Spontaneous Healing,” shaped the type of doctor I knew I wanted to become. Their words  influenced me to become the out-of-the-box practitioner that I am. My mentors in functional medicine have been Dr. Leo Galland, Dr. Mark Hyman, Dr. Frank Lipman, and the great instructors at the Institute for Functional Medicine. What I admire about all of these doctors is they were not afraid to challenge our ingrained knowledge and point to another way we can view health and healing.

What is your favorite microbe?

My favorite microbes by far are the bifidobacteria. B. infantis is critical for the development of the early microbiome in children. But more importantly, bifidobacteria are involved in a feeding chain that results in the production of the SCFA (short-chain fatty acid) butyrate, which is critical for the health of the colon as well as an epigenetic regulator of learning and memory. This is one of the best examples of the gut-brain axis.

Check out Dr. Pedre and his book Happy Gut, or learn more from him at his upcoming MindBodyGreen course: Advanced Functional Nutrition Training.


Peace, Love, and Gut Bacteria


How hippie food became mainstream.

“The Hippies Have Won.” That was the conclusion of a New York Times article on April 4th, which suggested that “just as yoga and meditation have gone mainstream, so have ideas and products surrounding health, wellness and eating that play like a flashback to the early 1970s.”

The nicely-observed piece supported its claims in part by explaining that fermented foods such as kombucha and kimchi are no longer fringe-fads, but are now considered by many to promote good gut health, supporting the development of a healthy microbiome.

Well, right on.

In fact, the NYT says that kombucha, for example, has gone from being “something your art teacher might have made in her basement [to where] the company GT’s Kombucha brews more than a million bottles annually and sells many of them at Walmart and Safeway.”

Fermented foods, as well as being undeniably tasty, tend to be rich in bacteria – particularly those strains that might be classified as probiotics, which, in general, are a good thing when they arrive in your gut.

But has the world of fermented food been entirely taken over by corporate giants?

Thankfully not.

While we’re definitely grateful that big business is banging the drum for these healthy diet additions, getting them into the hands (and mouths) of a wider market, it’s comforting to report that a great deal of grass-roots fermentation is still going on, and, indeed, there’s been something of a revival in this area.

Our attention was drawn to a new edition of the 2003 classic “Wild Fermentation,” written by a man named Sandor Katz, who describes himself as a “fermentation fetishist.”

Whatever tickles your pickle, one might say.

Sandor, who’s so into fermentation that he’s known and loved by many as Sandorkraut, has been described by food author and activist Michael Pollan as showing you “why an act as practical as making your own sauerkraut represents nothing less than a way of engaging with the world.”

There’s a delightful short documentary film on the NYT website, showing Sandor making sauerkraut in a satisfyingly “earthy” way.

A charming, messy kitchen.

Plenty of bare-handed squishing of shredded cabbage.

Repurposed old jars.

And splendidly-aged fermentation crocks in stone-walled basements.

The documentary directors even found a great old country song named “Sauerkraut” for the soundtrack.

The tune, incidentally, was sung back in 1926 by country music pioneer Riley Puckett, best known for being the first country artist to yodel in his performances.

What’s not to like about a yodelling country singer with a song about fermented cabbage?

Actually, he was probably on controversial ground, since sauerkraut had been renamed Victory Cabbage as a marketing move during World War I (1914-18) because of the word sauerkraut’s associations with Germany.

By 1926, however, it was clearly safe to go back to how things had been pre-war.

Sandor Katz explains that wild fermentation refers to the reliance on naturally-occurring bacteria and yeast to ferment food.

He points out that humans didn’t really discover fermentation, as it was already occurring in the wild.

We just found ways to harness this natural process.

So, fruit already has yeast on its surface, which enables the fermentation process to take place, as it does in the wild – much to the delight of certain species of tropical bats.

And cabbage leaves provide a home for bacteria that, in anaerobic conditions, produce carbon dioxide and lactic acid, the latter being what kickstarts fermentation.

Sandor grew up in New York City, but moved to rural Tennessee after a life-changing diagnosis of AIDS.

He’d originally been a “policy wonk,” so moving to an off-the-grid rural community was indeed a significant life change.

His new focus has led to him teaching hundreds of food workshops in the US and all over the world, and he now runs a fermentation school at Walnut Ridge, a restored 1820s log cabin in Liberty, Tennessee.

What do we know about the scientific basis of probiotics, though?

It’s often suggested that the microorganisms concerned may not actually reach the gut intact, and, of course, it’s their presence in the lower gut, in particular, that is believed to be beneficial.

Well, in an article published in The American Journal of Clinical Nutrition, Dr Anatoly Bezkorovainy, an assistant professor in the biochemistry department at Rush Medical College, reported that estimates suggest that 20-40% of selected strains of probiotics make it through the stomach into the gut.

Their main obstacles are gastric acidity and the action of bile salts.

Interestingly, however, Dr Bezkorovainy went on to report that there’s little evidence that probiotic bacteria adhere to the mucosal walls in the intestine, so they tend to pass through you, like sh**s in the night.

This seems to support the notion that the benefits of fermented food don’t really result from a “fix-it-and-forget-it” action.

Instead, it appears to be important to consume it on a regular basis.

Finally, returning to Riley Puckett, although he erroneously sang about vinegar being part of the sauerkraut-making process, when, in fact, the dear old cabbage just needs the addition of salt for it to make its own acid, it seemed apt to end on his words from 90 years ago, clearly not only a time when you could write a hit song about cabbage, but also a time of lower prices:

If you will only listen to who I speak about,
I ain’t no voice to tell you how to make that sauerkraut,
It’s made out of vinegar, so everyone suppose,
And of that little flower, they call that cabbage rose.

Oh sauerkraut is bully, I told you it was high,
I think I ought to know for why,
I eat him all the time.

Then it’s sauerkraut, then it’s sauerkraut,
Priced good you know, because you love it so.
Then it’s sauerkraut, then it’s sauerkraut,
Only five cents, one pint.


Salmon Sperm and Bee Venom in Your Eye?


Excuse us, you have something in your eye: bacteria.

Pop quiz. Which part of your body is just about the same size now as it was on the day you were born?

In fact, you’re almost certainly making use of it right now.

Yup, an eyeball remains around one inch in diameter from the minute we’re born until the day we die, and it’s why the small head of an infant can make us believe that babies have big eyes. It’s actually a matter of scale.

Unless you’re reading this via some kind of whizzy text-to-speech gizmo, you’re now using your eyes, and reading our words through a thin biofilm that contains bacteria. That could explain the fuzziness.

Welcome to your ocular microbiome.

Until pretty recently, it was widely believed that, unless they were infected, our eyes were bacteria-free. But studies now show that a healthy eye does indeed contain its own ecosystem of microorganisms that remain in place despite tears and the approximately twelve times a minute that we blink.

It was in 2009 that scientist Valery Shestopalov, from the Bascom Palmer Eye Institute at the University of Miami, founded the Ocular Microbiome Project, an initiative that now has twelve collaborators in five universities.

Dr. Shestopalov’s early work showed that the surfaces of what he termed the “exposed mucosal epithelium” in the eye are densely populated with microorganisms.

In the eye, the mucosal epithelium is the wet membrane that forms the surface of the eye, and the insides of the eyelids.

Around a dozen bacterial genera dominate the eye’s conjunctiva, which is the white of the eye (the “sclera”) and the eyelids.

Interestingly, on the corneal surface (the transparent part of your eye, which covers your iris and pupil) there’s likely to be a slightly different microbial community, although again with about twelve predominant genera.

You see? Even when you’re healthy, there’s a barn load of bacteria in your eye.

But what happens when you get an infection, though?

Well, the two most common eye infections are styes and conjunctivitis (sometimes called “pink eye”).

Styes are those pesky little bumps that can form on the eyelid, generally the result of skin bacteria getting into the hair follicle of an eyelash.

Conjunctivitis can indeed be caused by bacteria, but it’s also possible that a virus or allergy could be the culprit.

Other causes can be substances that cause irritation, contact lens products, eye-drops, or eye ointments.

More on contact lenses in a moment, but first some intriguing findings about infections of the cornea, which are known as keratitis (the eye is a complicated space when it comes to naming infections).

Research has shown that during keratitis, bacterial diversity on the cornea actually reduces rather than increases, and these changes typically occur before eye infections are diagnosed, making it possible that monitoring of the ocular microbiome might form some kind of future diagnostic tool.

But what of contact lenses, then?

The US Food and Drug Administration (FDA) reports that around 30 million Americans wear them, so does this affect the bacteria in their eyes?

Yes indeedy.

A study at New York University School of Medicine (NYU) compared the ocular microbiomes of lens-wearers with those of non-wearers, and found considerable differences.

In fact, contact lens wearers tend to have an ocular microbiome which is more like their skin microbiome.

It’s tempting to jump to the conclusion that this is simply because contact lens wearers are frequently poking their fingers into their eyes (an idea many non-wearers probably flinch at), but although the NYU researchers acknowledge that this could indeed be the reason, they say it’s actually too early to be sure.

It is, however, a good time to remind all lens-wearers of the importance of thorough hand-washing before dealing with contacts.

Dr. Shestopalov’s team sequenced bacteria from contact lenses used for one day, finding relatively little diversity on their surfaces, as well as further evidence that contact lens wearers have an ocular microbiome that differs from those who don’t wear contacts.

Wearing lenses can, in and of itself, be a cause of eye problems, and estimates suggest that anywhere between 7% and 25% of contact lens wearers experience irritation and redness.

Actually, some researchers hypothesize that contact lenses make it easier for pathogens to colonize the eye by giving bacteria something to adhere to.

However, if this gives you a lightbulb moment, and makes you think about inventing an antimicrobial contact lens – well, sorry to tell you this – someone else got there first.

A medical microbiologist at the University of New South Wales in Australia is heading a team of scientists who are developing antimicrobial contact lenses by coating them with a synthetic peptide called melimine.

That’s melimine with an “i,” rather than Melamine with an “a.”

One’s an antimicrobial agent, while the other is, well, the stuff that unbreakable tableware is made from, and you wouldn’t want picnic plates in your eyes.

Although, when you read the following, you may well think the same about melimine (with an i.)

You see, melimine is a combination of two other substances – protomine, and milletin – hence its portmanteau name.

And somewhat unbelievably, protomine was originally isolated from salmon sperm, while mellitin is the principal active component of bee venom.

Quite honestly, two stranger substances to place in your eye are difficult to imagine.

Despite the thoroughly odd provenance of this antimicrobial agent, early tests on humans by the Australian scientists suggest that the melimine-coated contacts are as safe as regular lenses, and seem to be effective as an antimicrobial against two major pathogens – Pseudonymous aeruginosa and Staphylococcus aureus.

What do you get if you cross salmon sperm and bee venom?

There’s probably one heck of a good one-liner answer to that (and we’d love to hear your suggestions) but the real truth is that it’s antimicrobial contact lenses.


Microbes in the Mansion: US Presidents and their Bacteria


The often surprising truth about presidential-bacterial connections.

With so much media coverage of presidential matters over the past year, and particularly with last week’s inauguration of the 45th President of the United States, you might think every possible presidential angle has been covered.

This, though, would be seriously underestimating your good friends here at uBiome.

For it is with considerable pleasure this week that we bring you a collection of presidential bacteria stories over a time period beginning with the first president, and ending with the 44th.

Let’s start with number nine, William Henry Harrison, who has entered the record books for at least two significant achievements.

The first was delivering the longest inaugural address in history, speaking for an hour and 45 minutes in a DC snowstorm, without an overcoat, gloves, or scarf.

The second (perhaps not entirely disconnected)?

Harrison was the first president to die in office – exactly one month after being sworn in – which for 150 years was widely claimed to be because of pneumonia he developed after standing in the cold for so long.

However, thanks to some excellent detective work by two researchers – Jane McHugh and Philip Mackowiak – it’s now believed that President Harrison died of enteric fever (also known as paratyphoid fever) brought on by gastroenteritis, a bacterial infection.

What’s more, the recent research uncovered the fact that two other presidents of that era, James Knox Polk and Zachary Taylor, are also believed to have died from gastrointestinal infections.

And the thinking is that this sickness came about through unsanitary conditions.

Very possibly, there may have been no hand-wash in the White House.

Actually, in the 1840s, Washington DC’s systems for the disposal of what was then euphemistically termed “night soil” were, to say the least, primitive.

Not to put too fine a point on it, barrels of fecal sludge were hauled through the streets of Washington DC at government expense, and dumped in a depository where the sludge stagnated and formed a marsh.

Unfortunately, this was just seven blocks from the White House water supply, and it was therefore probably no surprise that these three presidents became, well, ex-presidents.

As a matter of fact, bacteria probably also played a part in the demise of the very first president, George Washington.

His life was plagued by numerous serious diseases, mostly of a viral nature, but his death in 1799 at the age of 67 may have been partly the result of epiglottitis, a throat infection that can be caused by the Haemophilus influenzae bacterium, following a serious cold Washington developed.

Yet another presidential death associated with bacteria was the sad case of William McKinley, who was shot by an assassin at the 1901 Pan-American Exposition in Buffalo, New York.

Two bullets were fired into McKinley’s body, but only one was retrieved.

A projectile in his stomach was elusive, so a hastily-gathered surgical team, led by a gynecologist, stitched up the President with the ammo still inside him.

One of his aides, concerned about this laissez-faire surgical attitude got in touch with Thomas Edison, requesting that the inventor lend them an x-ray machine, which was delivered but never used.

Soon after, McKinley died – not from the bullet itself, but from septic shock caused by a bacterial infection which led to the development of gangrene along the pathway taken by the bullet.

A bacterial infection also took the life, not of Calvin Coolidge himself, but his son, Calvin Coolidge Jr.

Tragically, Coolidge Jr. developed a simple blister on his toe while playing lawn tennis on the White House grounds.

Unfortunately, the blister became infected with the very common Staphylococcus aureus, which most of us carry on the surface of our skin, but in the case of President Coolidge’s son, led to his rapid demise.

It’s sobering to note that, although a simple course of antibiotics would have almost certainly prevented this death in 1924, this occurred just four years before Alexander Fleming discovered penicillin, the first true antibiotic.

And it’s kind of ironic that less than a century later, the 44th President, Barack Obama, issued an Executive Order in 2014 seeking to combat antibiotic-resistant bacteria, a phenomenon that has been largely brought about by the overuse of antibiotics, with the Center for Disease and Prevention estimating that antibiotic-resistant bacteria cause 23,000 deaths annually in the US.

George W. Bush made one of two presidential addresses relating to bacteria in November 2011 after the US had experienced a series of deadly anthrax attacks just a week after 9/11. Anthrax is a bacterium that was first identified in 1875 by the German scientist Robert Koch.

The other microbe-related presidential speech was made by Bill Clinton in 1996 after a team of US meteorite hunters said they’d identified bacteria from Mars in a meteorite they’d discovered in Antarctica.

Unfortunately, their claims were subsequently rejected by the wider scientific community, but not before President Clinton had suggested that the find was “one of the most stunning insights into our universe that science has ever uncovered.”

Or not.

We end our exploration of presidential bacteria with, once again, the outgoing president who, just last year, announced the National Microbiome Initiative, that is now fostering the integrated study of microbiomes across all manner of different ecosystems, and which we at uBiome are of course happy to support with our Microbiome Impact Grants.

As for bacterial connections with our latest president, well, we’ll simply have to wait.


Extreme Dieting, and Meeces Who Eat Feces


Also: why it’s good to be cautious about study-based news stories.

As we noted last week, at this time of year, millions of Americans put themselves on diets, so it’s no big surprise to find books like Travis Stork’s The Lose Your Belly Diet, doing well on the New York Times Best Sellers list.

It’s also no surprise to see the media picking up on our fascination with losing weight, and part of this most recent onslaught of interest has come about through an intriguing paper published just last week in the journal Cell Host & Microbe.

In case you don’t have a subscription, and since we’re pretty certain you won’t find a copy in your local supermarket checkout line, we thought it might be interesting to report on it, investigating in a little more depth than you may find in other sources.

As ever, once you start looking under the hood of a paper, there’s some fascinating learning (as well as a few caveats) to be had along the way.

The headline finding of the research is that there appears to be evidence that switching from a typical unrestricted American diet to a more healthy calorie-restricted plant-based diet may not get an immediate response from your body.

In “pop” terms, going on a profoundly different diet may not deliver instant results.

Let’s begin by checking on the provenance of the study, and this one’s good. In fact, they don’t get much better.

It was led by Jeffrey Gordon of Washington University School of Medicine.

Professor Gordon runs the distinguished Gordon Lab in Washington and has been responsible for some of the research community’s most important work on human gut microbial communities. He also played a pivotal role in the foundation of the Human Microbiome Project.

So how did Professor Gordon’s team go about this new investigation?

Well, they began by inoculating gnotobiotic mice (animals that had been bred to be “germ-free”) with fecal matter sampled from two different groups of humans.

The first group were individuals consuming what might be considered a standard American diet, typically defined as one that’s low in vegetables, fruits, poultry, seafood, and whole grains but high in carbohydrates, saturated fats, red meats, sugar, and processed food.

You know, all the things that are bad for you and none of those that are good for you.

The second group of participants were eating the aforementioned “healthy, calorie-restricted, plant-based diet,” and stay tuned for more about them in a minute: it gets interesting.

Once the mice were dosed with one of two types of human fecal matter, which we’ll term “American” or “calorie-restricted,” the two groups were again subdivided, and placed on either a simulated American or calorie-restricted diet.

Mice with a microbiome they’d inherited from calorie-restricted humans responded strongly to both types of diet.

Mice with an American microbiome, however, responded only partially to being fed the calorie-restricted diet.

Their American microbiome appeared to prevent the calorie-restricted diet having much of an effect.

But wait, who were the individuals who supplied the calorie-restricted fecal samples?

Well, we said it gets interesting, and in fact they were all members of an intriguing organization known as the Calorie Restriction Society, founded in 1994.

Members of the society take the view (and these are their words, not necessarily ours) that the only valid life extension method that has any proven scientific backing behind it is calorie restriction – the consumption of a diet with adequate quantities of all essential nutrients, except that the energy content of the diet (its caloric intake) is safely reduced by as much as 10-40% below the amount of energy (calories) that the body would tend to naturally desire.

In fact, the group members who participated in this study habitually consumed nearly 50% fewer calories than their American diet counterparts.

Somewhat extreme, you may agree.

But while it makes a ton of sense for researchers to investigate such clearly defined individuals, perhaps it’s less reasonable for the mainstream media to then extrapolate this to suggest that individuals modifying their diet – a little – won’t see results?

Actually, the second stage of the research was also deeply interesting.

When mice with the American microbiome were co-housed with calorie-restricted animals, the former gradually acquired some of the bacteria from the latter.

In fact, the researchers went on to argue that we need to think of our microbial communities not as isolated islands, but as part of an archipelago where bacteria can move from island to island.

However, lest you imagine that humans might therefore lose weight simply by hanging out with lean individuals – through some kind of airborne bacterial osmosis – the researchers noted that the mice in the experiment were actually, uh, coprophagic.


Yup, they were poop-eaters.

We’ve not seen any mainstream media coverage of the study mention this, but it’s a good demonstration of the care that’s required when taking perfectly legitimate, completely sound research, and jumping to sometimes unlikely conclusions.

Our thinking?

If you want to lose weight this New Year, following Michael Pollan’s simple rule “Eat food. Not too much. Mostly plants.” may make sense for many, and, in fact, one conclusion we can pretty safely take away from this recent research is that the increased microbial diversity of the calorie-restricted individuals seems at least partly based on their higher consumption of fruit and vegetables.

Probably best steer clear of the whole coprophagia thing, though.

Unless you’re a mouse.


Losing Weight is Most Popular New Year’s Resolution – Could Probiotics Help?


Spoiler Alert: Maybe, maybe not.

Right now, like many, you may be reflecting on the rapidly receding holiday season, ruing that you ate more, and were less physically active, than usual.

Perhaps you’ve even needed to loosen your belt a notch or two.

Don’t worry, you aren’t the only one.

In fact, a 2012 survey reported that weight loss was the number one New Year’s resolution for Americans (for 21% of those who set goals).

Other popular focuses were on improving finances (14%), exercising (14%), and getting a new job (10%).

Dr. John Norcross, Distinguished Professor of Psychology at the University of Scranton, PA, estimates that between 40 and 50% of Americans make New Year’s resolutions, but his research suggests we’re not always successful at keeping them.

Dr. Norcross wrote the popular book Changeology, so he knows a thing or two about the psychology of behavior change.

In fact, he says, around a quarter of people make it no further than one measly week into the year before their resolve crumbles, and over a half have fallen off the wagon six months on.

Now, the food you ate toward the end of 2016 has probably had an impact on your microbiome, but is there any evidence that making deliberate changes to the bacterial composition of your gut can help you lose weight?

Well, perhaps – but as ever, it’s a very qualified perhaps.

Let’s look at one particular piece of research in detail, containing cautiously good news for women (sorry, guys). And along the way, we’ll also shine a light on the peculiar world of the patenting of bacteria.

This particular study was conducted by scientists from Laval University in Québec, Canada, alongside researchers from Nestlé in Switzerland (bet they had good chocolate in their meetings), and was published in the British Journal of Nutrition in December 2013.

Essentially, it explored the impact of swallowing a probiotic supplement – in capsule form – on obese men and women over a 24-week period.

The study was a double-blind, placebo-controlled, randomised trial. Half of the 125 participants received a probiotic, while the other half were administered an inert placebo, all in identical capsules.

During the first twelve weeks of the trial, participants were placed on personalized diet plans, which involved them consuming 500 calories per day less than they would need for weight maintenance.

This was followed by twelve weeks on a strict weight-maintenance diet.

So, what happened?

Well, as we hinted earlier, women in the study appeared to benefit from the probiotic supplement.

Those in the placebo group lost an average of 5.7 pounds in the first twelve weeks, but those receiving the probiotic experienced a greater average weight loss of 9.7 pounds.

What’s more, though, the probiotic recipients continued to lose weight after they stopped getting the supplement and were back on their weight maintenance diet. They ended up with an average loss of 11.5 pounds. Those on the placebo lost no further weight during the second half of the study.

But what about the men?

Disappointingly, those in the placebo group actually lost more weight than the participants who received the probiotic supplement during the first twelve weeks.

And by the end of 24 weeks, both groups of men had lost about the same – around 12.5 pounds.

Professor Angelo Tremblay, the study’s leader, said they didn’t know why the probiotics had no effect on men, but hypothesized that it may have been a question of dosage – or perhaps the study period was too short.

Even the study’s positive results on females have been questioned by some experts, who pointed out that the experiment was carried out on a very specific type of woman (e.g. none were pregnant, smoked cigarettes, had drug or alcohol problems, or took vitamins or supplements of any kind).

However, given such possible limitations, what was in those probiotic capsules?

They each contained 10 mg of a powdered version of a strain of Lactobacillus rhamnosus, known as Lactobacillus rhamnosus CGMCC1.3724, which provided 162 million colony-forming units.

This powder was accompanied by 300 mg of a mix of oligofructose and inulin (both dietary fibers/prebiotics) designed to help the active probiotic make it through the stomach’s acidity and into the gut.

Curiously, this particular strain of bacteria has since been patented by Nestlé.

In general, bacteria occur naturally, so they cannot be protected by patents, but in 1980, the US Supreme Court ruled that microorganisms created in the laboratory by genetic manipulation could indeed be patented.

This ruling followed an eight-year legal battle that began in 1972 after a microbiologist at General Electric created an oil-eating bacterium in the laboratory, and it allowed Nestlé to follow the now widely-adopted practice of obtaining a patent for a bacterial strain.

If you’re wondering about the “CGMCC1.3724,” it’s all to do with the Chinese General Microbiological Culture Collection (CGMCC), which is based in Beijing and acts as a kind of Library of Congress repository for those who wish to patent microorganisms.

The “1.3724” is simply the strain number, a label for a particular entry in the CGMCC catalog.

While this may be way more information than you’ll ever need, it fascinated us.

Nestlé refers to its bespoke strain as LPR, and uses it in certain yogurt products sold in European markets.

Professor Tremblay, however, believes that the probiotics found in dairy products in North America could have a similar effect to the Nestlé strain. (Don’t tell the company’s patent attorneys.)

Diet or not, good luck with your own New Year’s resolutions.

We’ve made one, too.

We’ll be doing our level best to keep you informed and, we hope, entertained with our weekly newsletters.

See you next time, and thank goodness for elasticated waists.