Tuesday, July 04, 2017

Human microbiome studies really are oversold, new study suggests #UCLA #Microbiomania

Blargh.  I saw this headline and I was suckered in.  I thought there might actually be something novel behind it:: Human emotions really are affected by gut bacteria, new study suggests - ScienceAlert But no - despite the headline, this is just about a paper that showed correlation between microbiome community patterns and various behavioral traits. Not a shred of cause vs effect tested.  And yet despite that this is just a correlative study, the article just completely overstates the implications
"But it's clear that there's something going on between the organisms in our gut and the thoughts and feelings we experience, and the sooner we delve into this, the sooner we'll comprehend just how emotionally powerful our 'second brain' really is."
No no no no no and no.  They do not show ANY connection between our thoughts and our microbiome.  They just report a correlation.  It could be that people with different thought patterns eat differently.  Or people with different thought patterns exercise differently.  Or $(#($(#@@ just abo9ut anything. Alas, many other stories about this work also make false inferences. See the Huffington Post for example: Your Gut Bacteria Really Do Affect Your Emotions 
"A new study looked at how ‘microbiota’ bacteria in the human gut influences our emotional responses, as the evidence suggests there is a direct correlation between the two."
 Again, no no no no and no.  They do not study how microbiota influence emotional responses.

And how about the Daily Mail: Gut feelings are real: Some people have stomach bacteria that makes them more anxious and stressed, study shows. What a horribly misleading, inaccurate headline.

So one might ask - where could these news sources have gotten the idea that this was more than a correlative study?  Hmm.  I wonder.  Maybe we should look for any press releases from UCLA?  So I googled the lead authors name and found this:

Research suggests association between gut bacteria and emotion published on June 29 from UCLA.  And this PR does not start well.  The first sentence is simply wrong at best.  Misleading and deceptive I think:
Researchers have identified gut microbiota that interact with brain regions associated with mood and behavior.
No no no no no and no.  There is no evidence that these gut microbiota interact with brain regions in any way.  Later in the article there is a bit of a caveat -
Researchers do not yet know whether bacteria in the gut influence the development of the brain and its activity when unpleasant emotional content is encountered, or if existing differences in the brain influence the type of bacteria that reside in the gut.
But it is too little too late.  And it is not actually accurate either.  There are other possibilities - like there is a third factor that affects both the microbiome and the brain but where the brain and microbiome don't impact each other.  What could that factor be? Oh I don't know - how about something called the immune system?  It is just bad science to report that this has to be the gut affecting the brain or the brain affecting the gut.

And for this I am giving out a coveted "Overselling the Microbiome Award" to UCLA and their Press Office.

I have also rewritten the original headline that caught my attention.

There.  I feel better already.  Must be my microbiome.

Monday, July 03, 2017

A time capsule from my father's youth - the secrets of a 62 year old Bar Mitzvah book on his 75th birthday

Today, July 3, 2017, is my father - Howard Jay Eisen's birthday.  He would have been 75 today.  I am sure we would have had a grand celebration of some kind.  I will make a toast in his honor tonight.

Sadly, he is no longer alive.  He passed away in 1987, when I was a freshman in college.  It was a painful ending of his life.  I have written about this.  As has my brother Michael.  As have some other people here and there. If you want to know more about that, well, here are some links to read.

But that is not what I want to write about today.  The pain of his suicide will be with me forever I am sure.  But I want to focus on his life.  And that I know remarkably little about.  So it was with great interest that a few years ago his sister Arleen came to visit us in California.  And as part of this visit she gave me my father's Bar Mitzvah Book.  

I glanced at it and then it sat in a box for a while.  I have never been religious and did not have a Bar Mitzvah myself.  So it seemed foreign to me.  

But then, when Arleen passed away relatively suddenly, I felt really disconnected form my father's history.  And so one day I opened the book and leafed through it more carefully. And I became a bit obsessed with it.  The book had dozens of pictures from the event.  And cards and telegrams congratulating my father.  And all sorts of notes and notations of various kinds.  I barely recognized any of the people.  Of course, this was from 1955 so that is not that surprising.  But part of this is that I have never been that close to my father's family.  I always got along with them, but just never saw them that often before my father died and even less afterwards.  So the key to me was - how could I figure out just what was in the book. And more importantly to me, could I figure out who was at this event.  This was one of the only tangible things I had to hold about my father's childhood.  I did not know too many stories.  I did not have many artifacts of any kind.  And here was this major major event.  And I literally had the book about it.  

So today I am here to tell you, I have digs into this book.  And stunningly, it not only told me about one event, it told me about my family.  A lot.  It did this because I was able to figure out who most of the people were at the Bar Mitzvah - and most of them were family.  In addition, I have used some family tree databases such as Ancestry and My Heritage to track down information about these people and have been able to use this one book to basically figure out, I think quite accurately, many generations of my father's family tree.

Friday, June 30, 2017

Thank you Gizmodo and Ryan Mandelbaum for anti-poop-doping story

Thank you Gizmodo and Ryan F. Mandelbaum for this: Athlete Poop Won't Improve Your Athletic Performance.  I like this in particular
“A bunch of elite cyclists have a microbiome that looks like this,” the way Petersen describes, fecal transplant expert and professor Elizabeth Hohmann from Massachusetts General Hospital told Gizmodo. “So what? Is that because of the foods they eat?” After all, it could be the lifestyle that makes their microbiome look the way it does, not the microbiome that makes them better performers. “There are associations, but not causal. The idea that [microorganisms like] Methanobrevibacter smithii or Prevotella will make you a better performer is ridiculous.”
and this
And the fact that Petersen felt better after a fecal transplant is an anecdote that could simply be the placebo effect in action.

and this
There’s always the chance that poop doping could be harmful, too. “There’s the risk of transmission of infections agents for sure,”
and more definitely worth a read.

Wednesday, June 28, 2017

More awful reporting on the "poop doping" claimed by Dr. Lauren Peterson


Been trying to stamp out the awful reporting on the poop doping claims of Dr. Lauren Peterson.  See

But the crap keeps flowing.  Here is the last - in the NY Post: Poop transplants are the final frontier in athletic doping | New York Post

Here are some quotes from the story and my comments about them.

  • "The treatment helped her battle Lyme Disease, however, there was a downside."
    • No evidence exists that this treatment helped her battle Lyme disease.
  • "“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,”"
    • This is reported with no caveats when there should be plenty.  This is almost certainly a incorrect interpretation by her.
  • "What’s worse, during graduate school Petersen had her digestive system tested and discovered that she was full of gram-negative pathogens. Common strains of the pathogens include E.coli and Salmonella."
    • Almost certainly this is also a misinterpretation.  Most tests such as those by American Gut which she claimed to have done would not have been able to say if she had pathogenic versions of these bugs.
  • The results were astounding
    • This implies cause and effect which has not been shown.
  • It turns out that Petersen probably would not have been doing as well if she’d gotten a couch potato’s poop. 
    • No evidence for this exists.
  • she already knows that it plays a critical part of muscle recovery.
    • I am deeply skeptical of this claim. 
  • Besides creating flatulence, decreasing the amount of hydrogen in our gut increases the amount of calories that are extracted from food, a study published in PLos One suggests.
    • It is really great that they link to a paper thus trying to show there is evidence for a claim.  Alas, the paper does not show what is claimed here.  This paper is just about comparing abundance of different microbes in obese, anorexic and control patients.  So to say they "suggest" that this papers shows this methanogen is involved in increasing the amount of calories extracted from food is misleading.  The authors hypothesize that sure.  So in one sense they "suggest" this but the way this is written implies they actually studied that, when they did not.

Sunday, June 25, 2017

Wrap up of recent posts of relevance on microBEnet

I have been doing a lot of blogging at microBEnet and don't always do a good job of cross posting or even posting here to let people know of the cross talk / related posts.

So I am trying to do that briefly now.  Here are some posts from the last few months on microBEnet that may be of interest, These are posts from March through today.

Wednesday, June 21, 2017

Irresponsible reporting on "poop doping" from the Washington Post

UPDATE 1 - see below - the author updated her article including some of my critiques.
UPDATE 2 - also see Embryette Hyde's post about using (or not using) the American Gut data to inform lifestyle changes
UPDATE 3. June 25. - Boing Boing picked up the story.  Without major caveats.  I posted a comment there pointing to my blog and answered one other comment but then was not aware the discussion was going on much more there until a Tweet today.  Some interesting discussions there and also some strange things.  Some criticisms of me (some reasonable .. some a bit much).
UPDATE 4. June 26. Nicholas Starapoli at the Genetic Literacy Project critiques the stories on poop doping. Poop doping: No, elite athletes can’t improve performance by optimizing gut bacteria
UPDATE 5. Also see Beth Skwarecki Sex, Poop, and Champagne Are Great, But Their Health Benefits Are Overrated

Went on a bit of a Twitter tirade last night. See more below

The Washington Post story, by Marissa Payne, requires a log in but the article is now in other papers that are free online including the Denver Post here.

It is just really bad reporting because the claims of one scientist are presented as facts without any scrutiny and these claims need lots of scrutiny.

Recently this story was covered in Bicycling Magazine and I gave them an "overselling the microbiome" award for their reporting on it.  I guess I am pretty surprised that the Washington Post doubled down on some of the claims.

Here is some commentary on just some of what is wrong with the Post article.

"Peterson, herself a pro endurance mountain biker, has discovered that the most elite athletes in the sport have a certain microbiome living in their intestines that allow them to perform better"
No evidence has been presented anywhere that these microbes "allow them to perform better".  At best, there may be evidence that elite athletes in this case have different microbes.   That as far as I know has not been presented for the case here.  Seems possible.  But this of course does not mean that those microbes they have allow for better performance.  There could be dozens of reasons why such athletes have differences in their micro biomes (e.g., diet, exercise, interactions all effect the microbiome).
Peterson didn’t decide on the fecal transplant solely to enhance her performance during her mountain bike races, but to cure a host of symptoms that have affected her since she was a child and contracted Lyme disease.
Seriously?  This basically is implying that she did a self fecal transplant that enhanced her performance and cured her Lyme disease.  She is an N of 1.  She did a fecal transplant and then some of her self assessed health changed.  What about, say, the placebo effect?  Or, how about - 100 other things changed in her life before and after the fecal transplant which could have affected her.  Or maybe the antibiotics she claimed to have taken before the transplant did something?  Ridiculous to make any claims about her self fecal transplant having any known impact.

Then there is this
“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,” she told Bicycling.
This is a pretty stunning claim. She had no microbes that help break down food before this?  And she also had been infected by microbes from the lab where she worked?  I don't buy either of these claims.

And what about
“I just did it at home,” she said of the February 2014 procedure. “It’s not fun, but it’s pretty basic.”
Referring to home fecal transplants.  I mean, I am all for people doing really whatever they want at home.  But they should do it with their eyes as wide open as their other parts.  And that requires the full poop on fecal transplants.  They have real and potential risks (e.g., see this).  One can get pathogens from them.  The transplant itself could have negative effects.  And if one assumes the microbiome has major effects, then one might get other unwanted traits from the donor too.  It is dangerous to promote self fecal transplants without discussing any of the possible risks.

Overall, I find this reporting by the Post to be dangerous.  And no the one caveat in the article below is not enough
Peterson said it’s too early to make any concrete conclusions about how the microbiome affects performance, but she’s convinced there’s enough evidence to suggest it does make a difference.
How about instead of "she is not convinced" saying "There is no evidence for any of her claims and this is snake oil".  That would be more accurate.

UPDATE June 21 2:54 PM

Marissa Payne updated her story with some comments from me

See https://twitter.com/MarissaPayne/status/877631691883298816

Because the text has been changed in the Washington Post story I am posting the text here from the Denver Post version in case it gets updated too, so people can see the original.

To be a professional cyclist, one must have guts, microbiologist Lauren Peterson says, and she doesn’t just mean that in the metaphorical sense. Peterson, herself a pro endurance mountain biker, has discovered that the most elite athletes in the sport have a certain microbiome living in their intestines that allow them to perform better, and if you don’t have it, well, there may soon be a way to get it.

“Call it poop doping if you must,” Peterson told Bicycling magazine last week about her research.

Peterson, a research scientist at the Jackson Laboratory for Genomic Medicine in Farmington, Connecticut, heads up an initiative called the Athlete Microbiome Project, in which she compares stool samples of elite cyclists to amateur bikers. Her findings strikingly shine a light on a handful of microorganisms that apparently separate the guts of elite athletes from average people.

The most important, perhaps, is Prevotella. Not typically found in American and European gut microbiomes, Prevotella is thought to play a role in enhancing muscle recovery.

“In my sampling, only half of cyclists have Prevotella, but top racers always have it,” she told Bicycling. “It’s not even in 10 percent of non-athletes.”

Peterson reports she hosts Prevotella in her own gut – but not naturally. In fact, she might be the first case of “poop doping,” thanks to a fecal transplant she administered herself three years ago. Her donor? Another elite athlete.

Peterson didn’t decide on the fecal transplant solely to enhance her performance during her mountain bike races, but to cure a host of symptoms that have affected her since she was a child and contracted Lyme disease.

“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,” she told Bicycling.

But, she continued, “I couldn’t find a doctor who could help me” since in the United States, fecal transplants are only performed to treat serious cases of Clostridium difficile, a disease that causes chronic diarrhea. And so Peterson went rogue.

Peterson detailed her decision to perform the “risky” procedure on herself on the podcast “Nourish Balance Thrive” last year. She admitted to thinking it was a “bad idea” at first because if not done with proper screenings of both parties, it could worsen a person’s problems. But through chance, she came across a donor, an elite long-distance racer, who had his microbiome mapped and screened after a case of food poisoning, which showed he was otherwise healthy. So Peterson took antibiotics to wipe out her own gut bacteria and essentially performed a reverse enema.

“I just did it at home,” she said of the February 2014 procedure. “It’s not fun, but it’s pretty basic.”

Within a month, Peterson said, she began feeling better than she’d felt in years.

“I had more energy than I knew what to do with,” she told the same podcast last year. “Like everything just changed.”

More importantly for her life’s work, however, her own success with the fecal transplant gave her the idea to start the Athlete Microbiome Project, for which she rounded up 35 of her cycling friends, according to the Scientist magazine, to kick off her research.

Along with Prevotella, Peterson said she also identified another possibly performance-enhancing microbe called Methanobrevibacter archaea, which Peterson found to be more prevalent in the samples from elite athletes. This bacteria’s function is also opaque, however, Peterson told the Scientist, “it allows your entire gut microbiome to work more efficiently” by more effectively breaking down complex carbohydrates in the gut.

Peterson said it’s too early to make any concrete conclusions about how the microbiome affects performance, but she’s convinced there’s enough evidence to suggest it does make a difference.

“What we’re learning is going to change a lot for cyclists as well as the rest of the population,” Petersen told Bicycling magazine. “If you get tested and you’re missing something, maybe in three years you’ll be able to get it through a pill instead of a fecal transplant. We’ve got data that no one has ever seen before, and we’re learning a lot. And I think I can say with confidence that bacterial doping . . . is coming soon.”