Viome - trying to prove that my calling them "The Theranos of Microbiome Companies" was an understatement ...

A month or so I wrote the post below that I thought was an example of really bad misleading advertising.  And it is indeed.  But keep reading past the discussion of this ad, because today I got a much worse example.

Post I drafted a month ago but did not actually make public:

Uggh.  This is just such BS.  I saw a Viome ad on Facebook.

 

Here is the text:

DNA tests can tell you a lot about where you came from.
Your past. Your family history, and your ancestry.
But that doesn’t help you right now.
That doesn’t help you today.
DNA tests also told her what foods were best for, but the recommendations never changed, even as symptoms got worse.
Just like you, Kelly wanted to know how to make the most of her health.
DNA tests told Kelly what diseases she was more at risk for genetically,
but they don’t give her any actionable advice on how to lower that risk.
Frustrated with generic guidelines like “exercise more and eat healthy,” Kelly finally found Viome, and it made all the difference.
That’s because Viome didn’t test her DNA. Viome tested the RNA of the microbes that make up Kelly’s gut microbiome to tell her what her microbes were up to and how they were affecting her.
The same microbes that are responsible for making most of the neurotransmitters, nutrients, and other compounds her body needs to be healthy.
Just like Kelly’s microbes eat what Kelly eats, your microbes eat what you eat, and if they don’t get the right foods at the right time, they begin making compounds that contribute to chronic inflammation.
That means:
Poor sleep,
Bloating,
Weight gain (the bad kind),
And a significantly increased risk for all kinds of chronic diseases.
Once Kelly got her Viome results, she knew which foods she needed in her unique personalized diet to boost the good guys (and which foods to avoid!) to take action to improve her health.
You can do the same thing as Kelly using the Viome Gut Intelligence Test.
End the guesswork and take charge of your health.
Order your Viome Gut Intelligence Test today.

And today in #microbiomania (aka overselling the microbiome) - ridiculous claim from Raphael Kellman's book marketing group

Just got this email below.  It is from a marketing person promoting Raphael Kellman's new book.  And it has an absolutely dangerous, ridiculous claim in it.  They claim that if you have memory loss, or mood problems, these are not in your head at all - this is caused my problems in your microbiome. What absolutely bullshit.  Sure, the microbiome can impact the brain and mood.  But to go from that to claiming that all memory loss and mood issues are due to problems with the microbiome.  Dangerous.  Deceptive.  Scary.  Snake oil.

But yes, I would be happy to write about your book.  Right here.  Right now.

Here is the email

Hello!

We are excited to announce the publication of The Microbiome Breakthrough: Harness the Power of Your Gut Bacteria to Boost Your Mood and Heal Your Body by Raphael Kellman, M.D. This revolutionary guide by the author of The Microbiome Diet offers a medication-free, scientifically-based approach to healing depression, anxiety, and brain fog by focusing on your “whole brain” – the brain, the gut, the microbiome, and the thyroid. 

If you are one of the millions of people who feel that you have memory loss or an inability to maintain a balanced, happy mood, the problem is not “in your head,” it is in your microbiome (the trillions of health-promoting bacteria in your body) and your gut. In The Microbiome Breakthrough, you’ll learn about the latest cutting-edge science and discover the Whole Brain Protocol, a powerful four-week plan that advises you on what to eat and which supplements and probiotics to take, so that your brain functions at its best level. Along with delicious, health-supporting recipes, meal plans, and other tips and strategies, The Microbiome Breakthrough will help make your brain work better, enabling you to feel calm, energized, and clear headed without prescription medications.

We would love to partner with you to spread the word about this groundbreaking book from a pioneer in holistic and functional medicine. If you would like to review it on your blog or website, promote it on your social media or email newsletter, or host a giveaway, we would be more than happy to send you a copy.

I look forward to hearing from you!

Thank you,

NAME 

--

NAME 

Marketing Department

Da Capo Press | Lifelong Books | Seal Press

An Imprint of Perseus Books | A Hachette Book Group Company

53 State St., 9^th Fl. | Boston, MA 02109

Koalas, Chlamydia, Microbiomania, Katie Dahlhausen, John Oliver, Russell Crowe, and me.

I love Chlamydia.  Really I do.  It was in a paper analyzing two Chlamydial genomes that I first noticed a very strange pattern of genome evolution.



This in turn led to our discovery that large genome inversions in bacteria and archaea are most common when they are symmetric around the origin of replication.



This may be my favorite paper from my entire career and I owe it all to Chlamydia.

Plus, there are all sorts of jokes one can make with the Giant Microbe Chlamydias like

Ironic I know but putting Chlamydia near my special place makes it awkward to go #ucdmicroboome pic.twitter.com/DR8eEJdDOA

— Jonathan Eisen (@phylogenomics) October 27, 2017

and

It reminds me of when we all kept giving each other chlamydia with @phylogenomics 's 'Gut Check' game at #scifoo :D who doesn't love a free set of crabs lol! https://t.co/ltuxAbKFFC

— Carin Anne Bondar (@carinbondar) February 14, 2018

Retraction of paper on "Gut Makeover Diet" and the microbiome retracted for fundamental flaws including that it did not in any way look at the microbiome #overselling #hype #microbiomania

Made a Twitter moment that people may be interested in about a Buzzfeed article by Stephanie Lee on retraction of a deeply flawed paper supposedly connecting the Gut Makeover Diet to the microbiome and to beneficial health effects.

 See below

  "Gut Makeover" paper retracted for fundamental flaws #microbiome

Offensive overselling of the #microbiome in breast cancer from the Cleveland Clinic

This is just sickening to me.

I saw a news story that smelled funny:  Breast cancer: Bacterial deficiency linked with onset. And I went and found the scientific paper and then the press release from the Cleveland Clinic that the news story seemed based on.  And, well, the press release turns out to be ridiculous.

The paper showed something somewhat interesting but very limited.  Here is the abstract with key parts bolded and underlined by me

It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients with and without cancer, and none have investigated distant body-site microbiomes outside of the gut. We hypothesize that cancerous breast tissue is associated with a microbiomic profile distinct from that of benign breast tissue, and that microbiomes of more distant sites, the oral cavity and urinary tract, will reflect dysbiosis as well. Fifty-seven women with invasive breast cancer undergoing mastectomy and 21 healthy women undergoing cosmetic breast surgery were enrolled. The bacterial 16S rRNA gene was amplified from urine, oral rinse and surgically collected breast tissue, sequenced, and processed through a QIIME-based bioinformatics pipeline. Cancer patient breast tissue microbiomes clustered significantly differently from non-cancer patients (p=0.03), largely driven by decreased relative abundance of Methylobacterium in cancer patients (median 0.10 vs. 0.24, p=0.03). There were no significant differences in oral rinse samples. Differences in urinary microbiomes were largely explained by menopausal status, with peri/postmenopausal women showing decreased levels of Lactobacillus. Independent of menopausal status, however, cancer patients had increased levels of gram-positive organisms including Corynebacterium (p<0.01), Staphylococcus (p=0.02), Actinomyces (p<0.01), and Propionibacteriaceae (p<0.01). Our observations suggest that the local breast microbiota differ in patients with and without breast cancer. Cancer patient urinary microbiomes were characterized by increased levels of gram-positive organisms in this study, but need to be further studied in larger cohorts.

That is it.  Barely significant finding of some clustering of the microbiomes of breast cancer patients versus those of patients without breast cancer.  And yet, this turned in the press release into cancer causing bacteria that they will be fighting with nanotechnology.  Seriously.

The press release title and subtitle is semi OK:

Cleveland Clinic Researchers Find Link Between Bacterial Imbalances and Breast Cancer. Study compares bacterial composition in healthy vs. cancerous breast tissue

But it goes way way way downhill from there.  Here are the parts with problems

•  In our wildest dreams, we hope we can use microbiomics right before breast cancer forms and then prevent cancer with probiotics or antibiotics
• Sure, in my wildest dreams I would cure cancer too.  
• In addition to the Methylobacterium finding, the team discovered that cancer patients’ urine samples had increased levels of gram-positive bacteria, including Staphylococcus and Actinomyces. Further studies are needed to determine the role these organisms may play in breast cancer.
• Umm.  No. Further studies are needed to see if these organisms play ANY role of any kind in breast cancer.
• Co-senior author Stephen Grobymer, M.D., said, “If we can target specific pro-cancer bacteria, we may be able to make the environment less hospitable to cancer and enhance existing treatments. Larger studies are needed but this work is a solid first step in better understanding the significant role of bacterial imbalances in breast cancer.
• Noooooooooooooooooooooooooooo.  You have not shown anywhere that there are "pro cancer" bacteria and this quote clearly implies that you have. 
• The study provides proof-of-principle evidence to support further research into the creation and utilization of loaded submicroscopic particles (nanoparticles), targeting these pro-cancer bacteria. 
• What?  This study does not provide ANY proof of principle of this sort.  You have not shown there are any pro-cancer bacteria.  This is ridiculous and offensive.  

No wonder the news stories imply that this study is about preventing breast cancer.  The press release from the Cleveland Clinic is deceptive.  It makes claims about the work that are irresponsible, misleading, and potentially dangerous. The Cleveland Clinic should be ashamed.

And thus the Cleveland Clinic is the winner of this edition of the Overselling the Microbiome Award.


UPDATE 10/16/17

And so the deceptive PR from Cleveland Clinic is now leading to claims of "Antibiotics May Prevent Breast Cancer" See

Deceptive PR from @ClevelandClinic https://t.co/b9IDgeRsfK on breast cancer-microbiome leads to stuff like this: https://t.co/jqBNMMzChL 1/n pic.twitter.com/u9LxdujnVm

— Jonathan Eisen (@phylogenomics) October 16, 2017

In this "news" article, based on PR from @ClevelandClinic there is a statement that "antibiotics may prevent breast cancer" 2/n pic.twitter.com/yP8AcSuexn

— Jonathan Eisen (@phylogenomics) October 16, 2017

Straight line from misleading PR of @ClevelandClinic "targeting these pro-cancer bacteria" to "antibiotics may prevent breast cancer" 3/n

— Jonathan Eisen (@phylogenomics) October 16, 2017

Today in misleading, dangerous, overselling of the microbiome - UNC on babies and cognitive development

Uggh. Was pointed to this on Twitter:

In baby's dirty diapers, the clues to baby's brain development | EurekAlert! Science News

@phylogenomics https://t.co/whMlHNlk6d

— Dylan Mackay (@DylanMacKayPhD) July 22, 2017

And I read the PR and made a quick Twitter response but decided to fill that in here a bit.

Some ridiculous overselling of the #microbiome in that press release #microbiomania pic.twitter.com/zGElsVCOoV

— Jonathan Eisen (@phylogenomics) July 22, 2017

Basically the study being discussed found a correlation between the microbiome in babies poop and their cognitive development. There are 100s of possible causes for such a correlation. But the press release misleading went on about how their work suggests they maybe able to somehow intervene to guide development by manipulating the microbiome. Ridiculous.

Here are some problematic quotes

• "In baby's dirty diapers, the clues to baby's brain development"
• Not really any clues providing in this work towards brain development. They have an interesting observation. It is unclear if it provides any insight into brain development.
• Findings from the UNC School of Medicine shed light on the surprising role of bacteria in how our brains develop during the first years of life
• No no no no no and no. They do not show ANY role of bacteria in how brains develop.
• Our work suggests that an 'optimal' microbiome for cognitive and psychiatric outcomes may be different than an 'optimal' microbiome for other outcomes."
• Oh #FFS. They do not show in any way what is or is not an "optimal" micro biome. They have a $*(#($# correlation. That is it.
• Though the findings are preliminary, they suggest that early intervention may hold the key to optimizing cognitive development.
• Well sure if you use the term "may" generously here they may hold such a key. But if you want to use it generously then these results may also suggest that UNC may be a dangerous place to bring babies because some of them may get a defective microbiome there which may lead them to have cognitive problems. You see, the findings in this work actually do not really suggest anything about early intervention at this point. Ridiculous to even suggest it.
• One was that when measuring the microbiome at age one, we already see the emergence of adult-like gut microbiome communities -- which means that the ideal time for intervention would be before age 1."
• No not really. Even if intervention was actually indicated here (which again, it is not) this does not mean that the time to intervene can be determined by looking at where they get an "adult" like micro biome. Because they have no mechanism here. It could be something in the baby and adult microbiome that is doing this (again, assuming there is a causal connection which there is not one shred of evidence for).

And then this is the worst.

"Big picture: these results suggest you may be able to guide the development of the microbiome to optimize cognitive development or reduce the risk for disorders like autism which can include problems with cognition and language," said Knickmeyer. "How you guide that development is an open question because we have to understand what the individual's microbiome is and how to shift it. And this is something the scientific community is just beginning to work on."

What the living #$*@(#(@? Now they are suggesting that their results say you may be able to optimize cognitive development and reduce the risk of autism. All from a simple correlation for which they have no clue whether there is any mechanistic connection. Offensive. Dangerous. Ridiculous. Sad.

Kudos to Bicycling Magazine for pedaling so so so much overselling of the microbiome

Well ... this was not a fun read.

There is an article in Bicycling Magazine by Berne Broudy and it is pretty painful to read.  The article is ​Is Poop Doping the Next Big Thing? | Bicycling.

And the answer should be "We have no $(*#()$()@#)@#  idea if this is a good idea". But instead the answer was hype, overselling, and some bad microbiology reporting.

Here are some parts I am not a fan of.

The results showed she was populated by 96% gram-negative pathogens so toxic that if they got into her blood stream they could kill her. “I had no microbes to help me break down food, and I had picked up bugs in the lab where I was working because my system was so weak and susceptible.”

I doubt much off this.  I don't think the American Gut project can say anything about pathogens nor do I think they do say this.  My guess is this is a misinterpretation by the scientist here or more likely the reporter.  Also I doubt the American Gut data could be used to say anything about picking up bugs in the lab.

She observed that Prevotella, a microorganism she received in her own transplant, is common amongst elite racers. “The more a person trains, the more likely they are to have Prevotella,” says Petersen. “In my sampling, only half of cyclists have Prevotella, but top racers always have it... it’s not even in 10% of non-athletes.”
She is currently extracting Prevotella to understand what it is, and how to boost its abundance naturally or through a probiotic pill for athletes or aspiring athletes. What she already knows: Prevotella synthesize branch chain amino acids critical for muscle recovery.

This too has some dubious parts.  Especially going from a correlation (althetes vs. Prevotella) to "how to boost its abundance."  How about first showing that is has any effect?

Archeon are ancient microorganisms that have managed to survive for millions of years in hostile habitats like sulfur springs and deep in the ocean. They also live in the human digestive system, where they have specialized functions. Like Prevotella, Elite cyclists often have M. smithii, but it’s less common in amateur racers. That’s significant because M. smithii also appears to be a performance-enhancing microbe.

Well - no modern organisms are ancient, first of all.  And no Archaea have not managed to survive for millions of years - they live and die and their lineages evolve.  As far as I know, nobody has shown this organism is performance enhancing - I could not find anything in the literature about this.  It is a nice model.  But many models are nice and then are wrong.

And then there is this

As for actual poop doping…. fecal transplants are available, but not in the U.S. “If you have the money for the procedure, you can go to a clinic in the UK or the Bahamas,” says Petersen. “But you can’t choose your donor, and it’s a risky procedure. As with any transplant, your immune system could reject what you get. It’s not something you should take lightly. I did a lot of research, and I took a risk for sure.”

Umm - she is a single case study and there is no evidence I know of that her transplant let to any improvement in performance.  Dangerous claims right here.  Fecal transplants indeed have real risks.  Encouraging people to use them for doping is dangerous.

And thus Bicycling Magazine is a recipient of the Overselling the Microbiome Award.

Overselling the microbiome award: Marie Claire for its "article" on Mother Dirt

Wow.  And not in a good way.  Marie Claire has bough in to the Mother Dirt sales pitch wholesale.  Here are some quotes form an article by Roxanne Adamiyatt published today in Marie Claire (see Probiotic Mist - Cleansing Body Mist)

"Like Febreze for your body, Mother Dirt's AO + Mist is a live probiotic spray that restores essential bacteria to our microbiomes. How? In short, the ammonia-oxidizing bacteria works to consume sweat on your body and turn it into a beneficial byproduct your skin can use."

Ugh.  No that is just not true.  This is what the people from Mother Dirt may claim.  But I have yet to see any evidence for this.

And then there is

"For example, if you were to use this formula on your face, the "good" bacteria in the mist would consume the ammonia (which raises pH) and restore balance to the skin i.e. it would become less sensitive, dry, or oily. And it's not just your face and body that can benefit from a reset spritz. You can use it in your hair too."

Ugh again.

And then the president of Mother Dirt is quoted

According to Jasmina Aganovic, president of Mother Dirt, it can help you go longer between washes. "The bacteria converts your sweat into byproducts your skin can use and with that, you're restoring a microorganism that once naturally existed on the scalp," she explains.

And there is more

You can also use AO+ as a quick post-workout fix as the good bacteria will consume the ammonia and urea in your sweat, AKA food for body odor. 

And

So whether it's balancing your skin, helping you prolong a blowout, or functioning as a deodorant, AO+ is working overtime to keep your hygiene in check...even if you're not. So we can't imagine something more useful to have on hand for summer.

I normally would not go the next step but I think it may be needed here - is it time to ask if Marie Claire is getting any money from Mother Dirt for this advertisement?

And for presenting the spray from Mother Dirt as proven to do things without presenting any evidence, I am giving Marie Claire a coveted Overselling the Microbiome Award.

----------------
Update: 5/1/2017 8:50 PM

But wait.  A little search of the Maria Claire web site pulled up another advertisement for Mother Dirt that is pretending to be an actual article:

Is Bacteria the Secret to Healthy Skin? by Renee Saleh in 2016.

In this article, the author basically reports on PR from Mother Dirt as though it is factual.  For example consider this:

Take acne, for example. Aganovic, who has a degree in chemical and biological engineering from MIT, has studied the presence of ammonia-oxidizing bacteria (a key component of the Mother Dirt product line) in both Western and aboriginal communities. She found that there were almost no acne cases in the aboriginal communities of Paraguay and New Guinea. These communities also shared the universal presence ammonia-oxidizing bacteria in skin cultures. In Western communities, however, acne occurs in 80 percent of adolescents, and there is less than a one percent occurrence of detectable ammonia-oxidizing bacteria on the skin. The absence of this type of bacteria in the West can be traced to the ingredients found in common household soaps and cleansers—and the decrease in time we spend in the great outdoors.

I mean.  It is a nice story.  But what is the evidence for this? None as far as I can tell.  I searched Google Scholar for papers by Aganovic on acne or aboriginal communities and found nothing.  Again, I am left wondering if Mother Dirt has paid Marie Claire for this advertising.

Today in Overselling the #microbiome: Lick-hiker's guide to Inner Strength

Well, thanks, I think to Christie Aschwanden https://christieaschwanden.com for pointing me to this.

Valio unveils Lick-hiker’s Guide to Inner Strength with travel presenter Ian Wright - hasan & partners




Valio - Gefilus Trailer from hasan & partners on Vimeo.

From the Press Release

International travel presenter Ian Wright is on a mission to seek out and lick the dirtiest locations in Europe for The Lick-hiker’s Guide to Inner Strength, a campaign that promotes the virtues of Gefilus, a good bacteria product range by dairy giant, Valio.

Simultaneously almost certainly over-promoting the benefits of this one probiotic and also the risks of licking things all over the globe.

Our 25-minute documentary sees Wright’s tongue come into contact with places that harbour bad bacteria - all in the name of testing immunity, gut health, and science. These include a metro station, public toilet, telephone, kindergarten, river, €10 note, bronze statue and Tottenham Hotspur FC.

Did they really have to pick on Tottenham?

Valio commissioned hasan & partners to demonstrate the power of Gefilus, which contains the friendly Lactobacillus rhamnosus GG and vitamins. Lactobacillus rhamnosus GG is the world’s most researched lactic acid bacterium and its qualities have since been scrutinized in more than 800 scientific studies globally.

Umm - just because there are 800 papers does not mean it is necessarily good for you. I mean, published papers is a good thing. But there are also 1000s of papers on anthrax and smallpox ...

Armed with bottles of good bacteria and a luminometer to count germs, the two-week tongue tour of Europe tests Wright’s taste buds and nerve to the limit. Viewers will find out if he survived the ordeal without contracting any stomach bugs and where in the world is the location with the worst bacterial score.

OK - well then. A luminometer will reveal everything you need to know about a sample of microbes. We should just use them for every microbial study everywhere (nothing against luminometers per se, but they really are not what is needed here).

Jussi Lindholm, COO of hasan & partners, comments: "Good bacteria in Gefilus products has been carefully studied and people believe in it. But seeing is believing, so the documentary is both educational and fun, designed to physically draw attention to the link between the gut, our inner strength, and our wellbeing. World traveller Ian Wright has experienced many challenges and Gefilus was probably the weirdest."

OK. Doesn't actually seem that weird. Just oversold ...

Here is the full documentary

Microbiomania and Fecal Transplants

Had a bit of a Tweet scream about people promoting fecal transplants to cure all sorts of ailments. Yes fecal transplants are amazing, for C. diff infections.  And yes, they are worth testing for other ailments connected to microbes and inflammation.  But worth testing is very different than "they should be used for X".  So I posted a bit about this.  Here is a Storify summary of some of the discussion

Also see this discussion on Facebook

CureZone pushing Fecal Transplants for Parkinson's, Schizophrenia ,MS, Lupus, Depression and more http://www.curezone.org/cleanse/enema/fecal_transplantation.asp #Microbiomania

Posted by Jonathan Eisen on Wednesday, December 30, 2015

Some history of hype regarding the human genome project and genomics

Just taking some notes here - relates to a discussion going on online.  Would love pointers to other references relating to hype and the human genome project (including references that think it was not overhyped).  I note - see some of my previous posts about this issue including: Human genome project oversold? sure but lets not undersell basic science and various Overselling Genomics awards. 

Here are some things I have found:

White House press conference on announcing completetion of the human genome

Genome science will have a real impact on all our lives -- and even more, on the lives of our children. It will revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases. In coming years, doctors increasingly will be able to cure diseases like Alzheimer's, Parkinson's, diabetes and cancer by attacking their genetic roots. In fact, it is now conceivable that our children's children will know the term cancer only as a constellation of stars.

Collins et al. New Goals for the U.S. Human Genome Project: 1998–2003

The Human Genome Project (HGP) is fulfilling its promise as the single most important project in biology and the biomedical sciences— one that will permanently change biology and medicine.

Human Genome -The Biggest Sellout in Human History

The Human Genome Project: Hype meets reality

NOVA: Nature vs. Nurture Revisited

After a decade of hype surrounding the Human Genome Project, punctuated at regular intervals by gaudy headlines proclaiming the discovery of genes for killer diseases and complex traits, this unexpected result led some journalists to a stunning conclusion. The seesaw struggle between our genes (nature) and the environment (nurture) had swung sharply in favor of nurture.

The human genome project, 10 years in: Did they oversell the revolution? in the Globa and Mail by Paul Taylor referring to: "Deflating the Genomic Bubble"

Also see Genomic Medicine: Too Great Expectations? by PP O Rourke

Also Has the Genomic Revolution Failed?

And Human genome 10th anniversary. Waiting for the revolution.

Science communication in transition: genomics hype, public engagement, education and commercialization pressures.

The Medical Revolution in Slate.

A Decade Later, Genetic Map Yields Few New Cures in the New York Times.

In announcing on June 26, 2000, that the first draft of the human genome had been achieved, Mr. Clinton said it would “revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases.” 

At a news conference, Francis Collins, then the director of the genome agency at the National Institutes of Health, said that genetic diagnosis of diseases would be accomplished in 10 years and that treatments would start to roll out perhaps five years after that.

Bursting the genomics bubble - Nature 2010

Has decoding the genome lived up to hype? BBC - 2010

The ethics of expectations: biobanks and the promise of personalised medicine.

NNB report: Ten years later, Harvard assesses the genome map where regarding Eric Lander:

At the same time, , he said genomic research has “gone so much faster than I would have imagined.” He cited " an explosion of work that will culminate, I think in the next five years, in a pretty comprehensive list of all the target that lead to different kinds of cancers and give us a kind of roadmap for finding the Achilles heel of cancers for therapeutics and diagnostics."

while at the same time he blamed the press for the hype

From Great 15-Year Project To Decipher Genes Stirs Opposition in the Times June 1990

'Our project is something that we can do now, and it's something that we should do now,'' said Dr. James D. Watson, a Nobel laureate who heads the National Center for Human Genome Research at the National Institutes of Health. ''It's essentially immoral not to get it done as fast as possible.''

• Note the article has many complaining about the hype in the genome project even then ..

From SCIENTIST AT WORK: Francis S. Collins; Unlocking the Secrets of the Genome

And, Dr. Collins adds, there is nothing more important in science and medicine than the project he heads

Dr. Collins predicts that within 10 years everyone will have the opportunity to find out his or her own genetic risks, to know if cancer or heart attacks or diabetes or Alzheimer's disease, for example, lies in the future. 

From READING THE BOOK OF LIFE: THE DOCTOR'S WORLD; Genomic Chief Has High Hopes, and Great Fears, for Genetic Testing June 2000 in the NY Times

The story goes through some predictions Francis Collins made for the future in a talk.  These included:

• BY 2010, the genome will help identify people at highest risk of particular diseases, so monitoring efforts can focus on them.
• In cancer, genetic tests will identify those at highest risk for lung cancer from smoking. Genetic tests for colon cancer will narrow colonoscopy screening to people who need it most. A genetic test for prostate cancer could lead to more precise use of the prostate specific antigen, or P.S.A., test by identifying those men in whom the cancer is most likely to progress fastest. Additional genetic tests would guide treatment of breast and ovarian cancer.
• Three or four genetic tests will help predict an individual's risk for developing coronary artery disease, thus helping to determine when to start drugs and other measures to reduce need for bypass operations.
• Tests predicting a high risk for diabetes should help encourage susceptible individuals to exercise and control their weight. Those at higher risk might start taking drugs before they develop symptoms.
• BY 2020, doctors will rely on individual genetic variations in prescribing new and old drugs and choosing the dose. Pharmaceutical companies will take a second look at some drugs that were never marketed, or were taken off the market, because some people who took them suffered adverse reactions. It will take many years to develop such drugs and tests.
• Cancer doctors will use drugs that precisely target a tumor's molecular fingerprint. One such gene-based designer drug, Herceptin, is already marketed for treating advanced breast cancer.
• The genome project holds promise for the mental health field. ''One of the greatest benefits of genomic medicine will be to unravel some biological contributions to major mental illnesses like schizophrenia and manic depressive disease'' and produce new therapies, Dr. Collins said.

Rediscovering some critical terms of use in microbial discussions: #microbiomania and #microbophobia

Earlier this week I was trying to come up with a short term to use when referring to the "Overselling of the Microbiome" and related hype. And I came up with one I really really like: microbiomania. The term just captures the essence of hype about microbiomes to me I guess.

So - of course - the first thing to do was to see if anyone else used this term.  And the number one thing I looked at was domain names.  Nope.  Microbiomania.Com and Microbiomania.Org are now mine.  And then I started to search the interwebs. And surprsingly there was not much (in English at least).  But some links showed up to books in Google Books with passages from > 100 years ago.  And this is when the digging got to be fun.  Here are some of the things I found.

1. A section from "The Medical Era"

When copying this section of the search results I discovered Google Books has an embed tool for Google Books though not sure how well it works: here is a try




Anyway - the text of this section of the book reads:

The Paris correspondent of the Chicago Tribune in a recent letter says We hear very little now of microbist or anti microbist theories Dr Koch's so called discovery is regarded with skepticism though not refuted The truth is his assertions are generally held to be not proven Dr Peters the favorite pupil of the great surgeon Dr Trousseau denounces what he calls microbiomania as a social danger and declares that the micro bians doctrine is vain sterile and objectionable in every way as both needlessly alarming and wrongly reassuring 

So I guess there were some folks who did not like the Koch and his silly theories about germs.

2. The Eclectic Medical Journal Volume 48

Please make it stop - overselling the microbiome award for rugby, exercise, microbiome stories

Update added 11/2/14 - for all my posts on Overselling the Microbiome go here. 

Well, I think today's lesson is, many people, including many scientists and science reporters, just do not get that there is a difference between correlation and causation.  I know - this is like beating a dead horse since many write about this issue.  But it just needs to be called out every time until it stops.  And today's fun comes from stories and the original research articles about how exercise supposedly alters the gut microbiome.

I was pointed to this just a few minutes ago on Twitter:

Seems like more appropriate title would b "rugby players have different diets" http://t.co/nzNsnHCYtA @phylogenomics

— Bernat Olle (@bernatolle) June 10, 2014

In this Tweet Bernat Olle points to a "news" story in Medpage Today: Exercise Boosts Gut Microbiome Diversity by Kristina Fiore.   Well, so of course I started digging around.  And, not surprisingly, the study that this is based on shows absolutely no causal connection between exercise and the gut microbiome.  The study is in the journal "Gut": Exercise and associated dietary extremes impact on gut microbial diversity.  And here is what they did:

• They selected subjects - 40 "elite" rugby players.
• They identified healthy male "controls" with similar age and size and from similar place. 
• Then they collected faecal and blood samples from participants and did surveys about their nutrition and clinical data.
• Among many measurements, they did 16S sequencing from the fecal samples
• Then they did some bioinformatics and found differences between the rugby players and the controls in many features including microbiomes.

And amazingly, from this they report, in their abstract

The results provide evidence for a beneficial impact of exercise on gut microbiota diversity but also indicate that the relationship is complex and is related to accompanying dietary extremes.