Monday, April 30, 2018

No Microbiome Santa Claus we cannot magically convert correlative studies into causal ones. And scientists dishing out medical advice about vaping based on such bad science is ridiculous.

Aaarrrrrrrg.  That is how I feel right now.

Many microbiome studies involve examining the microbiome in various samples and asking and answering "Are there differences in the microbiome between my sample types?".  This is a standard correlative analysis used in all sorts of areas of science. and it can be quite useful in many cases.

However, in most cases it is not OK to take information from a correlative study and infer that the microbiome was "changed" due to some factor that differed between the samples.  Generally this would only be possible to do in some sort of controlled experimental manipulation experiment.  But so so so many people make such inferences and I am going to highlight an example that relates to a new study of vaping and the microbiome.

There is a new paper on this topic and an associated press release:
Basically the researchers compared microbiomes in three groups of people who had different behaviors (some non smokers, some smokers, some papers vapers).  Note - they did not study people before and after vaping or smoking.  They compared different people who differed in these behaviors but also differ in 100s to 1000s of other things like diet, gender, age, activity, housing, childhood, and more.

And when they did comparisons in relation to the main variables of non smoker, smoker, vaper, they found some differences in microbiomes and some similarities.  Small study.  But potentially interesting.

However, the PR significantly misrepresents what they did and found. Here are some examples of wording I have a problem with:

Press Release:
  • "Vapers and non-smokers have the same flourishing gut flora."
    • OK this has nothing to do with the point of my post but they do not in any way show "flourishing" flora.
  • "whilst smokers have significant changes to their microbiome".  
    • No.  They show differences.  Not changes
  • Significant changes were found in the gut bacteria of the smokers, with an increase in the Prevotella bacteria which is linked to an increased risk of colon cancer and colitis.
    • Again.  No.  They show differences.  They do not know if they are changes since they do not know what these people had before smoking. And thus they cannot show "increases" either.
  • There was also a decrease in the presence of Bacteroides in smokers, a beneficial bacteria or probiotic.
    • No - no decrease shown.  And for that matter - not all Bacteroides are beneficial or probiotic. 
  • More investigation is needed but to find that vaping is less-damaging than smoking on our gut bacteria adds to the incentive to change to e-cigarettes and for people to use them as a tool to quit smoking completely.
    • Jesus #(@(@.  No.  They did not show this. 
  • This revealed significant changes in the gut bacteria of the faecal samples.
    • Again, no. 

This is one of the more problematic press releases I have seen in a while.  Really disappointing.  However, much more surprising is that many of these word choice and inference issues are also in the paper.  Here are some examples of problems with the wording in the paper (not all cases - just examples).
  • Title: Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study
    • No - they do not study effects of smoke or vapor at all. They study differences in people who do these activities.
  • Abstract: In this pilot study, we sought to determine if ECs or tobacco smoking alter the oral and gut microbiota in comparison to non-smoking controls.
    • No.  They are not able to determine if these "alter" anything. 
  • Abstract: Tobacco smoking had a significant effect on the bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. 
    • Noooooooo.  They did not show this.  
  • Abstract: The Shannon diversity was also significantly reduced (P = 0.009) in fecal samples collected from tobacco smokers compared to controls
    • No. They showed it was lower.  Not reduced.  To use "reduced" requires that they know what it was before.  But they do not.
  • Abstract: From a microbial ecology perspective, the current pilot data demonstrate that the use of ECs may represent a safer alternative compared to tobacco smoking
    • Oh Jesus ($(## again.  No they do not have any data that supports this claim. 
  • Results: The Shannon diversity was significantly reduced in fecal samples collected from tobacco smokers compared to controls (P = 0.009), but the number of observed OTUs was comparable between all groups (Fig. 1A).
    • No. They showed it was lower.  Not reduced.  To use "reduced" requires that they know what it was before.  But they do not.
  • Results: showed tobacco smokers had significantly altered fecal bacterial profiles
    • Again.  Different.  Not altered.
  • Results: Prevotella had significantly increased relative abundance.
    • No
  • Results: Whereas Bacteroides showed significantly decreased relative abundance 
    • No
  • Discussion. We report, for the first time, that regular use of ECs does not measurably influence oral or gut bacterial communities
    • No they do not show this.  They show that people who use ECs do not have significant differences from those that do not. 
  • Discussion: Only the fecal microbiota was found to have specific genera significantly altered by exposure, with increased relative abundance of Prevotella, in accordance with existing data 
    • Again. No.  They do not show ANY alteration by exposure.  Just correlations. 
  • Discussion: Conversely, smoking tobacco cigarettes significantly decreased the relative abundance of Bacteroides compared to EC users and controls
    • Nope. 
  • Conclusions. In summary, we found that tobacco smoking significantly alters the bacterial profiles in feces, buccal, and saliva samples.
    • Nooooooooooooooooo. Nooooooo. No.
So - you might ask -- why does this matter?  This is just a little bit of a word choice issue right?  Wrong. The press release and the paper mislead as to what was found here.  

You might then say "so what - what does it matter?".  Well, it does matter because when you make these types of misleading statements they might get picked up by the press or the public.  Like in the examples below:

Let's check out those bullet points:
  • This puts them at higher risk of colon cancer, colitis, Crohn's disease and obesity
  • E-cig users have similar microbiomes to those without the notoriously bad habit
  • Scientists today labelled the study an 'incentive' for smokers to switch to vaping
  • This is the first study to compare the microbiome between vapers and smokers
Wow.  This study provides incentive for people to switch from smoking to vaping.  Sorry - but the F@#$*)@#) it does.  Ridiculous.

And it shows that this puts people who smoke at higher risk of colon cancer, colitis, Crohn's and obesity.  The #(!@)($!@)( it does.

Just wait.  I am sure more news stories will come out with inaccurate information.  Sometimes that is the fault of reporters.  But in many cases, such as this one, the fault lies COMPLETELY with the scientists who use misleading statements in the papers and in the press releases.  Really sad and shameful.


And look.  What a surprise.  The pro- vaping community has picked up the bogus claims and is using them to say vaping is not bad for you.

UPDATE 2 - Another story saying vaping is not bad for your microbiome

UPDATE 3- - even more stuff on vaping and now it is not just not bad for you - it is good for you

UPDATE 4 - and the BS spawned by this misleading paper continues

Check out

There it is stated
As more facts are discovered about vaping and how it affects the human body, new research has emerged showing that using e-cigarettes is highly beneficial to the gut microbiome — microorganisms that live in the intestines and are essential for living a healthy life. As long as these tiny creatures are themselves healthy, that is.

UPDATE 5: 9/25/2018 - Paper has been "corrected"

The paper has been corrected. See

After publication, it was pointed out to the authors that some of the language implied causality. In order to avoid potential misinterpretation, they have edited the language by replacing “increased” with “higher”, replacing “decreased/reduced” with “lower”, replacing “changed/altered” with “different”, and removing the phrase “the effect(s) of” throughout the introduction, results, discussion, and conclusion. 
They have also removed “From a microbial ecology perspective, this study supports the perception that electronic cigarettes represent a safer alternative to tobacco smoking” from the conclusion in order to avoid language that might be considered as providing medical advice. Similar language was also removed from the abstract’s discussion section. 
In the discussion, the authors oversimplified a sentence relating to some species of Bacteroides considered probiotic and to avoid misrepresentation they have also added “though some [Bacteroides] are considered opportunistic human pathogens”. 
The authors confirm that none of these changes affect the overall reported associations or the conclusions of the work.
This is a good step.  But of course it does not fix the misleading press that came with their deceptive and  dangerous claims.  And it does not fix all of the issues with the paper.

1 comment:

  1. And then there is the fact that they used the word "flora". Aaarrrgggghhhhh


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