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Hardly a day goes by without a research study or article published talking sh*t—or more precisely, talking about the gut microbiome. When it comes to cutting-edge innovations in medicine, all signs point to the microbiome. Maybe we should have listened to Hippocrates: “All disease begins in the gut.”
Your microbiome is mostly located in your gut and contains trillions of little guys and gals called microbes. If you want to optimize your health, biohack your body, make progress against chronic disease, or know which foods are right for you—almost all of this information can be found in your microbiome.
My company, Viome, offers technology to measure your microscopic organisms and their behavior at a molecular level. Think of it as the Instagram of your inner world. A snapshot of what’s happening inside your body. New research about the microbiome is changing our understanding of who we are as humans and how the human body functions.
It turns out the microbiome may be mission control for your body and mind. Your healthy microbiome is part best friend, part power converter, part engine, and part pharmacist. At Viome, we’re working to analyze these microbial functions and recommend a list of personalized food and supplements to keep these internal complex machines in a finely tuned balance.
We now have more information than ever before about what your microbiome is doing, and it’s going to help you and the rest of the world do a whole lot better. The new insights emerging from microbiome research are changing our perception of what keeps us healthy and what makes us sick. This new understanding of the microbiome activities may put an end to conflicting food advice and make fad diets a thing of the past.
What are these new insights showing us? The information is nothing short of mind-blowing. The value of your poop just got an upgrade.
Here are some of the amazing things we’ve learned from our work at Viome.
1. Was Popeye wrong? Why “health food” isn’t necessarily healthy.
Each week there is a new fad diet released, discussed, and followed. The newest “research” shows that this is now the superfood to eat for everyone. But, too often, the fad diet is just a regurgitation of what worked for one person and shouldn’t be followed by everyone else.
For example, we’ve been told to eat our greens and that greens and nuts are “anti-inflammatory,” but this is actually not always true. Spinach, bran, rhubarb, beets, nuts, and nut butters all contain oxalate. We now know that oxalate-containing food can be harmful, unless you have the microbes present that can metabolize it into a non-harmful substance.
30% of Viome customers do not have the microbes to metabolize oxalates properly. In other words, “healthy foods” like spinach are actually not healthy for these people.
Looks like not everyone should follow Popeye’s food plan.
2. Aren’t foods containing “antioxidants” always good for everyone?
Just like oxalates, polyphenols in foods are usually considered very healthy, but unless you have microbes that utilize specific polyphenols, you may not get full benefit from them. One example is a substance found in these foods called ellagic acid. We can detect if your microbiome is metabolizing ellagic acid and converting it into urolithin A. It is only the urolithin A that has anti-inflammatory and antioxidant effects. Without the microbes to do this conversion you will not benefit from the ellagic acid in foods.
Examples: Walnuts, raspberries, pomegranate, blackberries, pecans, and cranberries all contain ellagic acid.
We have analyzed tens of thousands of people, and only about 50% of the people actually benefit from eating more foods containing ellagic acid.
3. You’re probably eating too much protein (and it may be causing inflammation).
When you think high-protein diet, you think paleo, keto, and high-performance diets.
Protein is considered good for you. It helps build muscle and provide energy—but if you eat too much, it can cause inflammation and decrease longevity.
We can analyze the activity of your microbiome to determine if you are eating too much protein that feeds protein-fermenting bacteria like Alistipes putredinis and Tannerella forsythia, and if these organisms are producing harmful substances such as ammonia, hydrogen sulfide, p-cresol, or putrescine. These substances can damage your gut lining and lead to things like leaky gut.
4. Something’s fishy. Are “healthy foods” causing heart disease?
Choline in certain foods can get converted by bacteria into a substance called trimethylamine (TMA) that is associated with heart disease when it gets absorbed into your body and converted to TMAO. However, TMA conversion doesn’t happen in individuals without these types of bacteria in their microbiome.
We can see the TMA production pathways and many of the gammaproteobacteria that do this conversion.
What foods contain choline? Liver, salmon, chickpeas, split peas, eggs, navy beans, peanuts, and many others.
Before you decide to go full-on pescatarian or paleo, you may want to check if your microbiome is producing TMA with that salmon or steak.
5. Hold up, Iron Man. We can see inflammation from too much iron.
Minerals like iron in your food can, in certain inflammatory microbial environments, promote growth of pathogens like Esherichia, Shigella, and Salmonella.
Maybe it wasn’t just that raw chicken that gave you food poisoning, but your toxic microbiome that made you sick.
On the other hand, when you don’t have enough iron, you could become anemic leading to weakness and shortness of breath.
So, just like Iron Man, it’s about finding your balance so that you can fly.
6. Are you anxious or stressed? Your poop will tell you.
Our gut and brain are connected via the vagus nerve. A large majority of neurotransmitters are either produced or consumed by our microbiome. In fact, some 90% of all serotonin (a feel-good neurotransmitter) is produced by your gut microbiome and not by your brain.
When you have a toxic microbiome that’s producing a large amount of toxins like hydrogen sulfide, the lining of your gut starts to deteriorate into what’s known as leaky gut. Think of leaky gut as your gut not having healthy borders or boundaries. And when this happens, all kinds of disease can emerge. When the barrier of the gut breaks down, it starts a chain reaction causing low-grade chronic inflammation—which has been identified as a potential source of depression and higher levels of anxiety, in addition to many other chronic diseases.
We’re not saying you shouldn’t meditate, but if you want to get the most out of your meditation and really reduce your stress levels, make sure you are eating the right food that promotes a healthy microbiome.
7. Your microbiome is better than Red Bull.
If you want more energy, get your microbiome back into balance.
No you don’t need three pots of coffee to keep you going, you just need a balanced microbiome.
Your microbiome is responsible for calorie extraction, or creating energy, through pathways such as the Tricarboxylic acid cycle. Our bodies depend on the energy that our microbiome produces.
How much energy we get from our food is dependent on how efficient our microbiome is at converting the food into energy. High-performing microbiomes are excellent at converting food into energy. This is great when you are an athlete and need the extra energy, but if you don’t use up the energy it may be the source of some of those unwanted pounds.
If the microbes can’t or won’t metabolize the glucose (sugar) that you eat, it will be stored as fat. If the microbes are extracting too many calories from your food or producing lipopolysaccharides (LPS) and causing metabolic endotoxemia leading to activation of toll-like receptors and insulin resistance you may end up storing what you eat as fat.
Think of your microbiome as Doc Brown’s car from the future—it can take pretty much anything and turn it into fuel if it’s strong and resilient enough.
8. We can see your joint pain in your poop.
Got joint pain? Your microbiome can tell you why.
Lipopolysaccharide (LPS) is a key pro-inflammatory molecule made by some of your microbes. If your microbes are making too much LPS, it can wreak havoc on your immune system by putting it into overdrive. When your immune system goes on the warpath there is often collateral damage to your joints and other body parts.
Perhaps balancing your microbiome is a better solution than reaching for the glucosamine. Think of your microbiome as the top general of your immune army. It puts your immune system through basic training and determines when it goes to war.
Ideally, your immune system wins the quick battle and gets some rest, but sometimes if your microbiome keeps it on constant high alert it becomes a long, drawn-out war resulting in chronic inflammation and chronic diseases.
Are you really “getting older” or is your microbiome just making you “feel” older because it keeps giving warnings to your immune system ultimately leading to chronic pain?
Before you throw in the towel on your favorite activities, check your microbiome. And, if you have anything with “itis” in it, it’s possible that when you balance your microbiome the inflammation from your “itis” will be reduced.
9. Your gut is doing the talking for your mouth.
When you have low stomach acid, your mouth bacteria makes it down to your GI tract.
Stomach acid is there to protect you from the bacteria in your mouth and the parasites and fungi that are in your food. If you don’t have enough of it, the bacteria in your mouth will invade your gut. This invasion is associated with and a risk factor for autoimmune disease and inflammation in the gut.
We are learning that low stomach acid is perhaps one of the major causes of chronic disease. This stomach acid is essential to kill mouth bacteria and help us digest our food.
What kinds of things cause low stomach acid? Stress and antacids like Nexium, Zantac, and Prilosec.
10. Carbs can be protein precursors.
Rejoice! Perhaps carbs aren’t as bad as we thought (as long as your microbiome is up to the task). We can see if some of the starches you eat can be made into amino acids by the microbiome.
Our microbiome makes 20% of our branched-chain amino acids (BCAAs) for us, and it will adapt to make these vital BCAAs for us in almost any way it can.
Essentially, your microbiome is hooking up carbons and hydrogens into different formulations of BCAAs, depending on what you feed it. The microbiome is excellent at adapting and pivoting based on the food you feed it and the environment that it’s in.
So, good news: Carbs are protein precursors, as long as you have the right microbiome.
Stop Talking Sh*t Now
Your microbiome is a world class entrepreneur that can take low-grade sources of food and turn them into valuable and useable energy.
You have a best friend and confidant within you that is working wonders to make sure you have energy and that all of your needs are met.
And, just like a best friend, if you take great care of your microbiome, it will take great care of you.
Given the research emerging daily about the microbiome and its importance on your quality of life, prioritizing the health of your microbiome is essential.
When you have a healthy microbiome, you’ll have a healthy life.
It’s now clear that some of the greatest insights for your health will come from your poop.
It’s time to stop talking sh*t and get your sh*t together. Your life may depend on it.
Viome can help you identify what your microbiome is actually doing. The combination of Viome’s metatranscriptomic technology and cutting-edge artificial intelligence is paving a brand new path forward for microbiome health.
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Earth’s oceans are having a rough go of it these days. On top of being the repository for millions of tons of plastic waste, global warming is affecting the oceans and upsetting marine ecosystems in potentially irreversible ways.
Coral bleaching, for example, occurs when warming water temperatures or other stress factors cause coral to cast off the algae that live on them. The coral goes from lush and colorful to white and bare, and sometimes dies off altogether. This has a ripple effect on the surrounding ecosystem.
Warmer water temperatures have also prompted many species of fish to move closer to the north or south poles, disrupting fisheries and altering undersea environments.
To keep these issues in check or, better yet, try to address and improve them, it’s crucial for scientists to monitor what’s going on in the water. A paper released last week by a team from MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) unveiled a new tool for studying marine life: a biomimetic soft robotic fish, dubbed SoFi, that can swim with, observe, and interact with real fish.
SoFi isn’t the first robotic fish to hit the water, but it is the most advanced robot of its kind. Here’s what sets it apart.
It swims in three dimensions
Up until now, most robotic fish could only swim forward at a given water depth, advancing at a steady speed. SoFi blows older models out of the water. It’s equipped with side fins called dive planes, which move to adjust its angle and allow it to turn, dive downward, or head closer to the surface. Its density and thus its buoyancy can also be adjusted by compressing or decompressing air in an inner compartment.
“To our knowledge, this is the first robotic fish that can swim untethered in three dimensions for extended periods of time,” said CSAIL PhD candidate Robert Katzschmann, lead author of the study. “We are excited about the possibility of being able to use a system like this to get closer to marine life than humans can get on their own.”
The team took SoFi to the Rainbow Reef in Fiji to test out its swimming skills, and the robo fish didn’t disappoint—it was able to swim at depths of over 50 feet for 40 continuous minutes. What keeps it swimming? A lithium polymer battery just like the one that powers our smartphones.
It’s remote-controlled… by Super Nintendo
SoFi has sensors to help it see what’s around it, but it doesn’t have a mind of its own yet. Rather, it’s controlled by a nearby scuba-diving human, who can send it commands related to speed, diving, and turning. The best part? The commands come from an actual repurposed (and waterproofed) Super Nintendo controller. What’s not to love?
Image Credit: MIT CSAIL
Previous robotic fish built by this team had to be tethered to a boat, so the fact that SoFi can swim independently is a pretty big deal. Communication between the fish and the diver was most successful when the two were less than 10 meters apart.
It looks real, sort of
SoFi’s side fins are a bit stiff, and its camera may not pass for natural—but otherwise, it looks a lot like a real fish. This is mostly thanks to the way its tail moves; a motor pumps water between two chambers in the tail, and as one chamber fills, the tail bends towards that side, then towards the other side as water is pumped into the other chamber. The result is a motion that closely mimics the way fish swim. Not only that, the hydraulic system can change the water flow to get different tail movements that let SoFi swim at varying speeds; its average speed is around half a body length (21.7 centimeters) per second.
Besides looking neat, it’s important SoFi look lifelike so it can blend in with marine life and not scare real fish away, so it can get close to them and observe them.
“A robot like this can help explore the reef more closely than current robots, both because it can get closer more safely for the reef and because it can be better accepted by the marine species.” said Cecilia Laschi, a biorobotics professor at the Sant’Anna School of Advanced Studies in Pisa, Italy.
Just keep swimming
It sounds like this fish is nothing short of a regular Nemo. But its creators aren’t quite finished yet.
They’d like SoFi to be able to swim faster, so they’ll work on improving the robo fish’s pump system and streamlining its body and tail design. They also plan to tweak SoFi’s camera to help it follow real fish.
“We view SoFi as a first step toward developing almost an underwater observatory of sorts,” said CSAIL director Daniela Rus. “It has the potential to be a new type of tool for ocean exploration and to open up new avenues for uncovering the mysteries of marine life.”
The CSAIL team plans to make a whole school of SoFis to help biologists learn more about how marine life is reacting to environmental changes.
Image Credit: MIT CSAIL Continue reading
In the myth about the Tower of Babel, people conspired to build a city and tower that would reach heaven. Their creator observed, “And now nothing will be restrained from them, which they have imagined to do.” According to the myth, God thwarted this effort by creating diverse languages so that they could no longer collaborate.
In our modern times, we’re experiencing a state of unprecedented connectivity thanks to technology. However, we’re still living under the shadow of the Tower of Babel. Language remains a barrier in business and marketing. Even though technological devices can quickly and easily connect, humans from different parts of the world often can’t.
Translation agencies step in, making presentations, contracts, outsourcing instructions, and advertisements comprehensible to all intended recipients. Some agencies also offer “localization” expertise. For instance, if a company is marketing in Quebec, the advertisements need to be in Québécois French, not European French. Risk-averse companies may be reluctant to invest in these translations. Consequently, these ventures haven’t achieved full market penetration.
Global markets are waiting, but AI-powered language translation isn’t ready yet, despite recent advancements in natural language processing and sentiment analysis. AI still has difficulties processing requests in one language, without the additional complications of translation. In November 2016, Google added a neural network to its translation tool. However, some of its translations are still socially and grammatically odd. I spoke to technologists and a language professor to find out why.
“To Google’s credit, they made a pretty massive improvement that appeared almost overnight. You know, I don’t use it as much. I will say this. Language is hard,” said Michael Housman, chief data science officer at RapportBoost.AI and faculty member of Singularity University.
He explained that the ideal scenario for machine learning and artificial intelligence is something with fixed rules and a clear-cut measure of success or failure. He named chess as an obvious example, and noted machines were able to beat the best human Go player. This happened faster than anyone anticipated because of the game’s very clear rules and limited set of moves.
Housman elaborated, “Language is almost the opposite of that. There aren’t as clearly-cut and defined rules. The conversation can go in an infinite number of different directions. And then of course, you need labeled data. You need to tell the machine to do it right or wrong.”
Housman noted that it’s inherently difficult to assign these informative labels. “Two translators won’t even agree on whether it was translated properly or not,” he said. “Language is kind of the wild west, in terms of data.”
Google’s technology is now able to consider the entirety of a sentence, as opposed to merely translating individual words. Still, the glitches linger. I asked Dr. Jorge Majfud, Associate Professor of Spanish, Latin American Literature, and International Studies at Jacksonville University, to explain why consistently accurate language translation has thus far eluded AI.
He replied, “The problem is that considering the ‘entire’ sentence is still not enough. The same way the meaning of a word depends on the rest of the sentence (more in English than in Spanish), the meaning of a sentence depends on the rest of the paragraph and the rest of the text, as the meaning of a text depends on a larger context called culture, speaker intentions, etc.”
He noted that sarcasm and irony only make sense within this widened context. Similarly, idioms can be problematic for automated translations.
“Google translation is a good tool if you use it as a tool, that is, not to substitute human learning or understanding,” he said, before offering examples of mistranslations that could occur.
“Months ago, I went to buy a drill at Home Depot and I read a sign under a machine: ‘Saw machine.’ Right below it, the Spanish translation: ‘La máquina vió,’ which means, ‘The machine did see it.’ Saw, not as a noun but as a verb in the preterit form,” he explained.
Dr. Majfud warned, “We should be aware of the fragility of their ‘interpretation.’ Because to translate is basically to interpret, not just an idea but a feeling. Human feelings and ideas that only humans can understand—and sometimes not even we, humans, understand other humans.”
He noted that cultures, gender, and even age can pose barriers to this understanding and also contended that an over-reliance on technology is leading to our cultural and political decline. Dr. Majfud mentioned that Argentinean writer Julio Cortázar used to refer to dictionaries as “cemeteries.” He suggested that automatic translators could be called “zombies.”
Erik Cambria is an academic AI researcher and assistant professor at Nanyang Technological University in Singapore. He mostly focuses on natural language processing, which is at the core of AI-powered language translation. Like Dr. Majfud, he sees the complexity and associated risks. “There are so many things that we unconsciously do when we read a piece of text,” he told me. Reading comprehension requires multiple interrelated tasks, which haven’t been accounted for in past attempts to automate translation.
Cambria continued, “The biggest issue with machine translation today is that we tend to go from the syntactic form of a sentence in the input language to the syntactic form of that sentence in the target language. That’s not what we humans do. We first decode the meaning of the sentence in the input language and then we encode that meaning into the target language.”
Additionally, there are cultural risks involved with these translations. Dr. Ramesh Srinivasan, Director of UCLA’s Digital Cultures Lab, said that new technological tools sometimes reflect underlying biases.
“There tend to be two parameters that shape how we design ‘intelligent systems.’ One is the values and you might say biases of those that create the systems. And the second is the world if you will that they learn from,” he told me. “If you build AI systems that reflect the biases of their creators and of the world more largely, you get some, occasionally, spectacular failures.”
Dr. Srinivasan said translation tools should be transparent about their capabilities and limitations. He said, “You know, the idea that a single system can take languages that I believe are very diverse semantically and syntactically from one another and claim to unite them or universalize them, or essentially make them sort of a singular entity, it’s a misnomer, right?”
Mary Cochran, co-founder of Launching Labs Marketing, sees the commercial upside. She mentioned that listings in online marketplaces such as Amazon could potentially be auto-translated and optimized for buyers in other countries.
She said, “I believe that we’re just at the tip of the iceberg, so to speak, with what AI can do with marketing. And with better translation, and more globalization around the world, AI can’t help but lead to exploding markets.”
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