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Open Science for Life Research


What’s Up Microbes?

AG-Nephele-side-by-side2There is no doubt that the little bugs that live inside our bodies and on our skin affect our health and well-being, even our state of mind, but what we want to know is, by studying them, can we prevent disease or even just a bad mood? And how can we monitor them on a daily basis? Will there be an app called “What’s up microbes?” that communicates with some new device that checks on those microbes and reports back what we should eat or if we should go see the doctor, or go for a run, or take it easy and relax to ensure we maintain a healthy microbial equilibrium?

A few months ago, I shipped my “gut microbiome” inside a narrow transparent tube via the US postal mail service to American Gut. My microbiome made the long trip from Miami to California stuck on a Q-tip. At the time, it seemed that the scientific research into this tiny new world of microbes had come a long way, but to my disappointment, I found out that there is still much to be learned. I found out that my microbiome had not survived the trip intact and had started to bloom, aka “grow new bacteria” during the trip.

In recent years, the microbiome has been featured prominently in the news as one of several paths to personalized medicine. Researchers from diverse fields such as psychology or nutrition or cancer, and many others, are trying to join the race to decipher it. There is great promise in its research, which is why the sector is receiving billions in funding, with major research initiatives in the US and worldwide. But as of today, the microbiome is still a mystery.

A 2014 article titled “20 Things you Didn’t Know About the Human Gut Microbiome” aptly describes the microbiome this way:

The microbiome is defined as all the bacteria, viruses, fungi, archaea, and eukaryotes that inhabit the human body. Collectively referred to as the “second human genome”, the gut microbiome in particular is now being considered a separate “organ” with distinct metabolic and immune activity. The two major areas of microbiota investigation include taxonomic diversity to identify “who” is there and functional metagenomics to figure out what they are doing. There are other human microbiome sites as well, including skin, oral, and vaginal, but the gut is the most popular and diverse neighborhood.

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In the News: Sugar Industry Manipulated Heart Studies To Shift Blame to Fat

Cross-posted in Quantified-Self

After reading this article we have to worry once again how much we really know about the food we eat and the information we can trust, when evidence keeps showing up that big industries only care about profits and blatantly disregard our health:

Sugar industry secretly paid for favorable Harvard research

The food industry’s greed is so out-of-control and unchecked, that they will bribe unethical scientists to report false health information to the public. In the US, public health is not a priority, profits are a priority. The food industry is entrenched in lobbying strongholds in the US congress and will not allow passage of any new laws and regulations that reduce their profits.

But there is hope for us. The internet is helping change this trend. Movements like Quantified Self will help us discover what really makes us feel good and stay healthy! We only need to get more people to use the Internet to get informed. And we need more people asking for affordable access to personalized health information, like genetics and routine tests, and access to affordable sensors that capture personal health and fitness data.

From Genotype to Phenotype: Things you can do with your 23andMe SNP data


Those of us who are curious about the hidden secrets encoded in our genes are excited about the new biomedical technologies that give us access to this genetic information. Our genes can tell a story about who we are. Only a “partial” story because we know that our environment and life style will add to the story. A well-established model of health is represented by this equation: Genome*Exposome=Phenome. The Exposome, is the collection of things we are exposed to, our life style and it has great influence on how we feel overall. Science tells us that we can prevent health problems if we are better informed about our “genetic” health risks, Genome and Genotype information, and adapt our life style to fit our genes. The Phenome and phenotypes are the observed outcomes of the interaction between Genome and Exposome, such as an observed disease, a symptom, a physical change such as weight loss or accelerated heart rate, or a mental state like depression or joy. Doctors, therapists and trainers have been measuring our different phenotypes, and have been monitoring our exposome whenever things go wrong, but they and we have little knowledge about our genetic predisposition for certain phenotypes.

And so, we want to know. At $199, or somewhat less with a discount coupon, the price tag for 23andMe genetic testing is only accessible to few. There are other options that are similarly expensive, among them deCODEme and FamilyTreeDNA offer similar genetic testing services.  Those prices are expected to drop as more genetic testing services compete against each other and as sequencing technologies become cheaper. When that happens, more people will benefit from understanding their genes and health risks.

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Fitness, Diet, Clinical, Genome, Microbiome Data, it is All Yours


There are ongoing efforts to merge your health data and have it in a central place. Other efforts involve transferring or exchanging your health data between hospitals and doctors and you look forward to not having to spend 20 minutes filling out the same paper form you filled out at another doctor’s office. Yes, that will happen, eventually. But should this central place that holds your data only serve your doctors or should the information it contains directly guide your life style and life choices? You have read that eventually, a smart computer will access your health data and make a faster, more accurate diagnosis or create a personalized treatment plan. You have read that such a system will make recommendations on your diet, your physical exercise regimen and even your social life and your career (work less, take time off). These recommendations will help you lead a happier, healthier and fuller life. It is already happening today, with apps like Fitbit and MyFitnessPal being pioneers in the field.

Today, doctors, clinics and hospitals have portions of your health data. It is spread across filing cabinets, devices, and the computers owned by these institutions. According to HIPPA regulations you can ask for that data but the data collected at a particular health provider belongs to him or her.  Now consider this: 23andme and similar institutions have your genetic data but they don’t have your doctors’ health data. uBiome has your microbiome data but nothing else. Your Fitbit or similar fitness tracker has your fitness data but they don’t have your genetic data or your medical health history. You have been recording your weight and consumed calories in applications like MyFitnessPal, but nobody but you has that data. Ultimately, you have the right to access and own all that data and share it as you seem fit.

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The Market for Easy, Quick Blood-Testing is Ready Even if Theranos is Not

Theranos test menu

The take-home lesson from the Theranos fiasco is that unlike the emergence of other technologies that many did not see coming, the market for easy DIY tests exists, is huge and is waiting. Take over-the-counter pregnancy tests, they are popular and have become the norm, because women trust that most of the time they work reliably and accurately. What we can also learn from the Theranos controversy is that even when the market is ready, there is a need to wait when a new technology is not ripe or to be more exact, when it is flawed and the errors have greater consequences. When a computer or smartphone fails to turn on, it is an annoyance, but it is not comparable to getting a false result on a medical test. A false positive, as an erroneous positive test is called in statistics, can lead to worrying, spending time and money on doctor visits, and on more tests. Technologies that involve medical diagnosis and test kits need to be evaluated thoroughly even if the market, the public and investors clamor to get it now.

According to Theranos Yelp reviews, which seem legitimate because they involve complaints, it is clear what customers were looking for: “I can’t imagine going back to the way it was before when everything had to go through a doctor’s office for a lab order” and “very easy draws, and super fast results –  through an app no less”, and avoiding the wait at medical diagnostic offices. Together with the millions in funding that Theranos got, it shows that it is only a matter of time before the flood gates of self-measurement and personal health data collection and storage open wide. When that happens, medicine as we know it today will change. This leads us to consider the reasons that propelled Theranos to become the darling of biotech investments and the reasons that blindsided Walgreens into closing a rushed deal with a company they did not vet.

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Poverty Does Not Always Translate Into A Shorter Life

NYT Interactive Map

NYT Interactive Map

In a well-researched study by Chetty et al. published Monday in The Journal of the American Medical Association and discussed in this excellent article by the New York Times, a new pattern emerges that reveals the discrepancy in life expectancy between poor and rich. What the researchers discovered is that geography is a larger factor than wealth.

As the NYT article states:

The research, in the works for nearly three years and based on a vast trove of records on earnings and deaths, is the most detailed analysis to date of a pattern first identified at least a couple of centuries ago, that more money translates into a longer life.

It could be as simple as this: Wealth buys higher-quality medical care, which allows people to live into old age. But a long line of evidence, including the new work, suggests it’s less obvious than it might seem. The affluent seem to live in healthier ways. They exercise more, smoke less, feel less stress and are less likely to be obese

There is a trove of information in the article worth discussing but the most intriguing line-of-thought involves understanding the cause and effect of geography and life expectancy. As the study states, higher-quality medical care is not the determining factor.

The new paper, in fact, finds little correlation between a region’s Medicare spending rate or the proportion of the population with health insurance and how long its poor citizens live.

One aspect the study and the NYT article did not consider is how access to information and knowledge through technologies such as smartphones and the Internet correlates with longevity.

I would like to propose a hypothesis: That longevity correlates with access to information. It is possible that in those cities and areas of the country where the poor live longer, they also have more access to modern technologies that allow them to inquire about matters of health-care and wellbeing.

It is worth noting that the study is the result of a collaboration between several academic, private and governmental organizations: the Department of Economics, Stanford University, Department of Economics, Massachusetts Institute of Technology, McKinsey and Company, Department of Economics, Harvard University, and the Office of Tax Analysis, US Treasury, Washington, DC.


What’s New with the Microbiome Quality Control Project?

In 2013 two services, American Gut and µBiome (pronounced you-biome), launched through the crowdfunding website Indiegogo to sequence the human microbiome of anyone interested in doing so. In 2014, an intrepid blogger, decided to donate her used toilet paper to science. What she found out is that the results of the two services were almost complete opposites in regard to the proportion of certain bacteria that can say a lot about diet and health.

She wrote:

It turns out that I’m not the only one to notice problems with the companies’ fecal microbiome analysis. One blogger found differences between the microbes taken from two different parts of the same, uh, sample.

So what could have gone wrong with my microbiome? Perhaps the samples weren’t collected right. According to American Gut’s sampling instructions, too much brown stuff can interfere with the methods the scientists use to break open bacteria and pull out the DNA inside. Too little and they might not get an answer at all. I thought I had used Goldilocks-like precision, and that one — or maybe both — of the sequencing services must be wrong.

Another possibility: corrections to the data may differ between companies. Another blogger, who is a bioinformatician, got different results than American Gut reported to him when he used his own software to analyze the raw data. It turns out that some bacteria grow while in the mail and can take over the sample, so American Gut corrects the reports it sends to participants to account for that overgrowth.

In the end, I thought I’d go right to the experts for the straight poop. I approached Jessica Richman, one of the cofounders of µBiome, and Rob Knight, one of the leaders in the microbiome field. His lab group runs the American Gut project as part of their quest to learn how diet, lifestyle, geography and other variables influence the microbiome.

She mentioned that the Microbiome Quality Control (MBQC) project would bring some consistency to the field and that was in 2014. Almost 1.5 years later, in December 2015, the microbiome quality control project published a paper on “Baseline study design and future directions” reporting on the first MBQC baseline study project and workshop. Clear cut protocols that guarantee trustworthy results are being designed but still not fully implemented:

There was a consensus across the MBQC participating groups that although microbiome measurements face substantial challenges, this baseline project was very successful and represented impressive progress towards the overall goal of establishing practical guidelines for reproducibility within labs over time and across the field.

We expect that for those of us who waited long enough to sequence our microbiome, we will benefit from all the research that was conducted into establishing those quality control guidelines that make microbiome studies reproducible and reliable. That is why I sent my Q-Tips to American Gut last week! Now I am waiting for the results.


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