The surprising connection between you and a giant panda.

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The remarkable story behind just one of your microbiome’s thousands of bacterial species.

The singer-songwriter Prince has been through more than his fair share of stage names.

As you may have heard, he spent seven years wishing to be known as an unpronounceable squiggle.

But quite frankly Prince’s name changing is nothing compared to a species of bacteria called Enterobacter cloacae.

You see, since being described for the first time in 1890, it’s had no fewer than twelve names.

Yup, Enterobacter cloacae is the bacterium formerly known as Pseudomonas dissolvens.

Enterobacter cloacae (let’s call it E. cloacae for short, its ‘E’ not to be confused with Escherichia in E. coli) is a mean little microbe responsible for all sorts of infections, often acquired through contamination in hospitals, yet it’s actually found in small quantities in the guts of very many healthy individuals.

Perhaps you and me.

Mind you, I say that, but it depends on your sex. E. cloacae comes from an order of bacteria called Enterobacteriales which is 400% more abundant in women than it is in men.

An “order” is one of the levels in biological classification – we humans belong to the order “Primates”, so you can see that orders generally represent pretty wide groups.

The “entero” part of its name, by the way, comes from the Greek word “enteron”, meaning intestine, from which we also get enteritis and enterologist.

Cloacae is the plural of cloaca, and was used to name this particular bacterium thanks to its Latin meaning – “sewer” – because besides lurking in the human gut, E. cloacae is often found in aquatic environments such as water and sewage.

Under a powerful microscope you’d see that a single E. cloacae bacterium is rod-shaped (a bit like a long grain of rice) with a multitude of tiny whip-like appendages that enable it to propel itself.

Imagine a jellyfish with a long, thin body and you’d just about have it.

E. cloacae bacteria are tiny, but not ridiculously so. 225 of them placed end to end would make up the width of a human hair, and a single E. cloacae bacterium is roughly the size of one transistor on an Intel microchip, as of 2015. Moore’s Law being what it is, E. cloacae will almost certainly look like a giant in a few years time.

In addition to sewers and human guts, E. cloacae pops up in some other surprising places.

For instance in Hawaii it’s responsible for a perplexing problem in papaya horticulture that results in internal yellowing of the fruit.

Curiously it also has an industrial application where it’s used to biodegrade explosives such as TNT. Basically there’s a strain of E. cloacae that eats high explosives for breakfast.

And then of course there’s panda poop.

In 2012, a draft genome sequence of E. cloacae was published, and the bacteria used in the study were isolated from giant panda feces.

As a hospital-acquired infection, E. cloacae is a bit of a bully. Classed as an opportunistic pathogen, it preys particularly on the elderly and the young.

In recent years it has been responsible for serious multiple outbreaks of infection in neonatal intensive care units.

Last but not least, E. cloacae may also be associated with obesity.

When researchers in China took a strain of E. cloacae (B29) from the gut of a volunteer who weighed in at 385 pounds and transplanted it into germ-free mice, the rodents themselves then became obese compared to similar mice fed an identical diet, but without the E. cloacae.

Of course, E. cloacae is just one of as many as 1,000 species of bacteria which can be found in the human gut alone.

There could be ten times this many in the entire human microbiome.

I happened to have picked on E. cloacae today, but each of our body’s bacteria has its own story to tell.

Are we ready to listen?

Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth
uBiome

 

Further reading

10,000 Microbes Cornered in Map of Human Body

Cloacae

Enterobacter cloacae

Enterobacter cloacae

Enterobacteriaceae

Enterobacteriales

Human microbiota

Prince

Taxonomy browser (Enterobacter)

The Degradation of Nitrate Ester Explosives and TNT

The ISME Journal – An opportunistic pathogen

Natasha’s Story: Eating Disorders and the Microbiome

natasha

Hi, I’m Natasha.

One of the first things the doctor said to me when I was first diagnosed with an eating disorder was that by going down this path, I’m basically committing a very slow suicide. Calmly, she explained that as the eating disorder progresses, the brain will shrink and my cognitive functions will decline. The body will begin to reclaim muscle non-selectively to try and obtain the protein and other nutrients it’s not receiving through diet – potentially leading to problems and/or failure of the heart or other organs. The stomach will shrink, and the digestive system will atrophy, since it’s not being fed, and therefore can’t properly carry out its activities.

Through experience, I also learned that the idea of food becomes difficult to stomach, relationships decay, and life in general becomes very difficult to cope with.

These symptoms sound terrifying – and they are. For anyone else, this would be more than enough motivation to do anything that would allow them to recover as soon as possible. For the most part this means drastically increasing food intake. And who wouldn’t want an excuse to eat more? Or be encouraged to eat whatever they want and as much as they want so that they can get back to a healthy weight?

For someone with an eating disorder, the prospect of eating and putting on even a few hundred grams is more terrifying than all of these things.

After a while, the process of eating becomes not only psychologically uncomfortable, but also physically painful, frequently leading to bloating, gas, constipation, and sometimes nausea.

A few months after I was diagnosed, I was due to start university at the age of 16. What was already to be a huge transition was made more difficult, as I was undergoing treatment. I began to blog about my experiences, more as a way of helping myself cope with it all, and to explain to those around me what it was like – since it was often confronting for them. I soon found that people started to approach me, and tell me that they were experiencing similar things. What scared me here was the state of their wellbeing, and how common it was. I certainly didn’t wish what I was feeling on anyone else.

At this stage, I was also developing an interest in molecular and microbiology, and by my second semester I had transferred to another university to pursue this. It wasn’t until my second year that I got to take my first microbiology course. While I was excited about everything I was going to learn, I never expected it to be more than an academic interest. I was lucky enough to have an incredible lecturer that pushed us to work hard and develop problem solving skills – and while normally I’d be overwhelmed by this, my increasing love of microbiology made me more determined to get through it. With this determination came the small but powerful push to try to get better, and the confidence to do things I was too afraid to do otherwise. While I still haven’t put on the weight, it at least encouraged me to eat enough to function at the level required – which was a big step.

This wasn’t the only benefit though. Because I was so keen to learn about microbiology, I started reading everything I could about it, and trying to stay up to date with new developments. Just over a year ago, the word “microbiome” started to pop up everywhere, and all of the sudden people were learning that the bacteria on, around, and in our bodies play a much larger role than previously thought. Studies into how it (particularly the microbiome of the gut) affects mood, depression, obesity, immunity, and many other aspects of health were being conducted. This led me to start asking about the effects of eating disorders on the microbiome, how this in turn affected the body, and how it could possibly lead to something that could help people suffering from eating disorders.

Recently, uBiome announced that they are collaborating with Dr. Cynthia M. Bulik at the University of North Carolina Centre of Excellence for Eating Disorders to attempt to answer some of these questions.

The gut microbiome has been shown to have significant impacts on the functioning of digestion, the immune system, and many other functions of the body. An imbalance of the microbiome can contribute to many diseases, and can allow selection for bacteria such as C. difficile – a bacterium commonly found in the gut which in high numbers is associated with ulcerative colitis. Bacteria deprived of nutrients can also begin to eat into the gut lining, and cause inflammation and problems in the gut – decreasing the ability to digest food properly and absorb nutrients.

This makes people with eating disorders particularly susceptible, since their food intake is insufficient to sustain their microbiome (not to mention themselves). Lack of nutrients taken in would drastically decrease both the diversity and abundance of microbes in the gut – sometimes permanently – and as described above, this can have serious consequences.

Studies into the role the gut microbiome plays in eating disorders and vice versa are therefore incredibly important and may lead to discoveries about what influences the development of eating disorders, likelihood of relapse, and insights into how to make the re-feeding process more comfortable. While it’s only early, and will likely take several studies to fully understand the relationship between eating disorders and the gut microbiome, this is a significant first step in the process, and one which will hopefully lead to new ways of helping to treat, or even cure them.

Bacterial Functions, Diversity Score, And A Hallowe’en Treat

What are your bacteria actually doing in there?

We’re proud to announce some exciting new additions to the uBiome website:

1. Bacterial functions. How well do your bacteria process caffeine compared to other people? What do your carbohydrate and fat metabolism capacities look like? We’ve added 106 bacterial functions for you to explore in your gut microbiome data, and we’re giving everyone this new feature for free.

Login at http://app.ubiome.com and let us know what you think!

2. Diversity score. Is your gut microbiome more or less diverse than all other samples in the uBiome dataset? The chart below shows my actual data. In the gut, bacterial diversity is generally positive, so I guess I’m in good shape, diversity-wise.

And finally, we’d like to wish you and your bacteria a very happy Hallowe’en! All uBiome kits are 50% off until midnight on the 31st, so be sure to claim your treat, whether you dress up yourself, or just your bacteria do. (And it’s actually 100 trillion trick-or-treaters, thanks to a sharp reader for noticing!)

Hope you enjoy the new features. We’d love to hear your feedback.
Bugs and hisses,
Alexandra

Why you’re speaking with your mouth full. Even when it’s empty.

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The wild world of your oral microbiome

The National Zoo in Washington, D.C. is home to roughly 300 different species of animals. And just so you know, right now your mouth probably houses about the same number of species of bacteria.

Yup, at any one time, there’s a whole zoo’s worth of tiny microbes – between 200 and 300 species – in your mouth, merrily mingling with each other and their host.

That’s you.

But that’s literally only half the story, because the experts who run the Human Oral Microbiome Database estimate there are actually a total of about 700 different bacterial species that can inhabit humans’ mouths, and their records are being updated almost every day as more and more is learned about these miniature critters.

There’s still a way to go. Right now only about half of them even have names.

But we humans have been aware of microbes for a few hundred years. In fact the first person on record to see oral bacteria was Antonie Van Leeuwenhoek, a citizen scientist if ever there was one.

Despite having no scientific education or training, he built over 500 “microscopes” and went on to make some extraordinary discoveries with them.

Actually his devices were just hand-ground magnifying lenses rather than compound microscopes like the ones used in today’s laboratories, but they were exceptionally powerful, enabling him to magnify specimens over 200 times.

Among the samples he chose to observe in 1683 were scrapings removed from the mouths of two old men who had never cleaned their teeth.

Never. In their whole lives.

Apparently unfazed by such grossness, according to a letter Van Leeuwenhoek wrote to the Royal Society in London, when he examined the gentlemens’ plaque he observed “an unbelievably great company of animalcules … in such enormous numbers that all the water [saliva] … seemed to be alive.”

How very lovely.

What he called animalcules (little animals), we now know as bacteria, but in fact over 250 years later in 1929 the zoologist Charles Atwood Kofoid was still writing about “animal parasites of the mouth and their relation to dental disease”.

Speaking of disease, we may tend to think of bacteria as being bad for health, but in fact there’s quite a bit of evidence that at least some of the species found in the mouth are good for us, keeping pathogenic microbes at bay by stopping them sticking to different oral surfaces.

So while cleaning your teeth is important, overdoing it with antibacterial mouthwashes may be a bad thing, removing the good microbes with the bad.

That’s no excuse for skipping good dental hygiene, though, as many adults do. In fact half of Americans don’t floss daily, and one in five don’t brush twice a day.

Maybe this is why 10% of American adults between 50 and 64 have no teeth left.

If you imagined that the mouth contained one homogenous microbial ecosystem, think again.

Certain species live on the tongue, others opt for the roof of the mouth or inside the cheeks.

Some like to hang out on the teeth, others on the gums.

Then there are those that specialize in living on dental fillings or false teeth, and, incredibly, there are even microbes which prefer the tonsils.

Of course bad dental hygiene allows the wrong kinds of bacteria to multiply, leading to halitosis, gum disease, tooth loss, and heart disease.

Curiously, researchers at Luzhou Medical College in China even observed erectile dysfunction when they deliberately induced gum disease in their experiment’s participants.

This was with rats, mind you, but perhaps it should serve as an extra reminder to human males too.

Don’t forget to brush your teeth before bed.

Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth
uBiome


 

Further reading

Antonie van Leeuwenhoek

Charles Atwood Kofoid

Effect of Periodontitis on Erectile Function

HOMD – Human Oral Microbiome Database

Meet Our Animals – National Zoo

Mining the Mouth’s Many Microbes

Oral Health – The Mouth-Body Connection

The Oral Microbiota – Living with a Permanent Guest

Tooth Loss in Adults

What Happens When You Don’t Brush Your Teeth

 

Employee Profile – Orli Kadoch

Meet Orli Kadoch, Research and Collaborations Lead:

 

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Name?

Orli Kadoch

 

How did you find out about uBiome?

I was watching the Exponential Medicine Panel on live stream and saw Jessica’s talk about uBiome and the future of citizen science.  I hadn’t heard much about uBiome previously, but I instantly identified with her message and the direction of the company.  I did a bit more research and it sounded as though this company aligned perfectly with my career goals.

 

What do you love about working for uBiome?

uBiome gives you the opportunity for exponential growth, and I’m not just talking about bacteria! I’m someone who excels when given new experiences and the ability to learn, and I have been able to truly utilize all of my science and business skills as well as my entrepreneurial drive to forge partnerships, come up with new ideas, and rub elbows with the best and the brightest in the industry. The co-founders are incredible mentors who really emphasize a positive career trajectory. They see the bigger picture and will go the extra mile to help you get there!

 

What did you do before working at uBiome?

I’ve had a largely scientific and medical background, focusing on neurobiology at UC Davis and then conducting research in thoracic oncology at UCSF. I’ve also worked in medical clinics and hospitals, in oncology, plastic surgery, and pediatrics.  

 

What did you want to be when you grew up?

I wanted to be a neurosurgeon until my junior year of college. I still have tremendous respect for the field, but I was better suited for an environment where I could engage with the world on a larger scale. Now I work with surgeons to create partnerships and studies, so I’m happy to still be involved in the field to some degree. My hope is that I can help advance the fields of medicine and science.  

 

What tips do you have for someone who wants to follow in your footsteps?

I think a few new-hires have probably heard me say this, but for someone in the startup environment, I’d advise them to “just say yes.” As I mentioned, we’re given such a wonderful opportunity at uBiome to grow and try new things.   A lot of these things will be out of your comfort zone, but saying “yes” means that you have the chance to learn and grow in order to meet those challenges. Looking back, I remember many times where saying “yes” completely changed my role at uBiome for the better.  

 

What is something most people don’t know about you?

For the most part, I like to keep my feet on the ground, so many would be surprised to know that I went skydiving a couple years ago! It was a fantastic experience and one that I am happy to be able to cross off my “bucket list.” Would I do it again?  Probably not–I’m happy I got away unscathed the first time and don’t want to push my luck!

 

What do you like to do outside work?

Jump out of planes!  Just kidding…

We live in a beautiful city, so on most weekends you can find me exploring new scenic trails on a long hike with friends or sipping a delicious mint mojito from Philz (admittedly, I’m a bit addicted)! I also love spending time with my family, seeing movies, and meeting new people. I don’t count this as work, but it is also important to me to keep up to date on relevant scientific articles and the latest in biotech news. 

 

What do your intestines have in common with a sewer pipe?

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I’m not being funny but…

Did you ever stop to think about how much poop you produce in a year?

Unless you have too much time on your hands, probably not.

So let me tell you.

The average individual pops out about an ounce a day for each 12 pounds of body weight, so do the math and this suggests you flush away almost twice your own weight each year.

Now, to you that’s just waste matter, but to the uBiome labs it’s our bread-and-butter.

I know. An unpleasant metaphor, but I hope you get my point.

Fortunately we need only the smallest sample of your poop to analyze your microbiome.

Just a Q-tip’s worth collected from your used toilet paper in fact.

So you have our blessing to carry on happily flushing the rest away.

However, while our laboratory is content to test your microbiome using mere smears, other researchers are getting down and dirty with the more prodigious volumes you and I dispatch into the void each day.

A current project, appropriately called Underworlds, in Cambridge, Massachusetts, is experimenting with smart sewers that enable public health experts to study a city’s collective microbiome.

They can detect foodborne pathogens, enabling them to pick up localised outbreaks of food poisoning, and also look for biomarkers that flag up other diseases and health conditions.

The work is being done in conjunction with Kuwait, where officials are anxious to learn more about childhood obesity. More than a third of Kuwaiti children are obese.

But what does obesity have to do with sewage?

Surprisingly, quite a bit.

A remarkable University of Wisconsin-Milwaukee study earlier this year analyzed bacteria from sewage collected in 71 cities in 31 U.S. states, and could predict whether it had been gathered from a community categorized as either lean or obese with close to 90% accuracy.

Lean and obese individuals typically have differing intestinal bacterial profiles (more of this, less of that etc.) and the study showed that this same differential was also reflected down in the sewers.

Sewage sleuthing has been a thing for some time.

European studies have studied the stuff in sewers to monitor population-level trends in illicit drug-use, showing for example that cocaine and ecstasy are big at the weekends in major metropoles, while cannabis and methamphetamine use is pretty constant throughout the week.

Impressive, huh? There’s clearly a lot to be discovered by looking into effluent.

And a lot to be grateful for, too, when you consider the sewage systems of developed countries.

In fact readers of the British Medical Journal voted sanitation the greatest medical advance since 1840, comfortably beating antibiotics, anesthesia, widespread vaccinations, and even the discovery of DNA.

Although we don’t have time to go into how sewage is processed, I couldn’t leave you without brief mention of a project in India, in which the job is done by allowing sewage to sit in pools of duckweed and fish for five days.

Apparently it does the job brilliantly, but somewhat uncomfortably the whole operation is then funded by selling the fish.

I’m sure it’s just a coincidence that you can rearrange the letters of the particular species they use to spell something else altogether.

Carp.

Have a great week!
Alexandra 🙂

Alexandra Carmichael
Director of Product, Community, and Growth
uBiome

 

Further reading

Poop Health – Everything You Want to Know But Haven’t Asked

Sanitation rated the greatest medical advance in 150 years

Sewage Reflects the Microbiomes of Human Populations

Smart Sewer Project Will Reveal a City’s Microbiome

Smart Sewers Will Reveal What’s in Cambridge Citizens’ Guts

Spatial differences and temporal changes in illicit drug use

Sewage Treatment: All The Pooey Facts

Jessica Richman, Co-founder/CEO of uBiome Will Answer Your Questions

Have a question for Jessica Richman?

jessica-richman-AMA

Here’s your chance to ask her anything!

Jessica will be doing a reddit AMA (Ask Me Anything) tomorrow, 10/16 from 10-11am PT. This is your chance to ask her about uBiome, citizen science, the microbiome, bacteria, or anything at all.

If you are unfamiliar with reddit, HERE is a guide that will help prepare you for her upcoming AMA. We will be emailing and posting the link to the AMA when it is live, tomorrow.

Looking forward!