misleading – Jonathan Eisen's Lab

9 things PBS Newshour famously gets horrible wrong in story on fast food and microbiomes

Well, this is one of the worst microbiome news stories in a long time: Fast food kills gut bacteria that can keep you slim, book claims. So many things wrong with it I don’t even know where to go. Here are nine:

1. The original headline: “Fast food kills gut bacteria that can keep you slim, study finds”

Here is the Tweet

Fast food kills gut bacteria that can keep you slim, study finds http://t.co/3fPIhJTuAB | @newshour

— PBS (@PBS) May 11, 2015

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2. The correction:

is just completely lame and they should, as the New York Times does when it makes a correction, say what it used to say before they changed it

3. The sentence with the reference to Rob Knight is just bad reporting #1

Here is the quote:

Previous studies made similar findings: Professor Rob Knight of the University of Colorado Boulder, who collaborates with Spector, famously showed that transferring gut bacteria from obese humans to mice could make the rodents gain weight.

First of all – the paper they link to does include Rob Knight as a co-author, but the corresponding and senior author is Jeffrey Gordon and Rob is fourth to last (mind you I love Rob and his work, but in this case, saying this is something Rob showed without mentioning Gordon is just not right).

4 . The sentence with the reference to Rob Knight is just bad reporting #2

What the *$*$# does “famously showed” mean? Really. What does it mean?

5 . The sentence with the reference to Rob Knight is just bad reporting #3

The statement “Previous studies made similar findings” is just so incredibly misleading. It seems to be referring back to the previous sentences:

“What is emerging is that changes in our gut microbe community , or microbiome, are likely to be responsible for much of our obesity epidemic, and consequences like diabetes, cancer and heart disease,” he said. “It is clear that the more diverse your diet, the more diverse your microbes and the better your health at any age.”

This is just completely overblown. The more diverse your diet the better your health at any age? Oh #FFS that is just not based on any science. And the “likely responsible for” is silly too.

6 . The sentence with the reference to Rob Knight is just bad reporting #4

Why exactly tell us he is collaborating with Rob Knight? So some of Rob’s good work rubs off? I mean, Spector may do some fine work (and he has done some really good stuff). But casually mentioning he collaborates with Knight who famously showed something (when actually it was more Jeff Gordon’s work) which did not actually show what the article implies it showed. Aaaaaaaaaaarg.

7. Good news.

Spector’s book claims that the diversity of microbes in the human body has decreased almost a third over the last century. But there’s also good news: Foods like dark chocolate, garlic, coffee and Belgian beer may help increase gut microbes.

Really? Thinking about microbes MAY also increase gut microbes. And so might listening to NPR. Not something worth reporting here.

8. This sentence

This discovery suggested to his father that many cases of obesity may not simply be due to overeating.

That is right. Looking at his son’s poop and the microbes in it is the key to knowing that obesity might actually be fuc$*@#@ complex and not only caused by overeating. Oh, that and 100 years of epidemiology and research.

9. This sentence

“Once on the diet I rapidly lost 1,300 species of bacteria and my gut was dominated by a different group called bacteroidetes. The implication is that the McDonald’s diet killed 1,300 of my gut species,” he said.

Sorry but that is NOT the implication.

UPDATE 1: May 11, 2015. 8:00 PM

Thanks to a Tweet from Jennifer Gunter I changed the title of my post from ” 9 things horribly wrong with Newshour story on fast food and microbiomes” to “9 things PBS Newshour famously gets horrible wrong in story on fast food and microbiomes”

@PBS famously showed bad science reporting https://t.co/8VuGq5njWU

— Jennifer Gunter (@DrJenGunter) May 12, 2015

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Misleading microbial headline of the month: Bacteria in Brains Suggest Alzheimer’s-Gum Disease Link

Wow. Check out this story from Bloomberg: Bacteria in Brains Suggest Alzheimer’s-Gum Disease Link – Bloomberg. The title suggests that there is some connection between Alzheimer’s and Gum Disease. And so does the story. Plus check out these other stories:

All based on the same work. Sounds like a real connection was made in this new work showing a link between bad dental hygiene and Alzheimer’s, and also between the bacterium Porphyromonas gingivalis and Alzheimer’s. These would both be a big big deal. After all – tooth decay is something you can do something about. And if tooth decay causes Alzheimer’s – then – well – we could probably prevent Alzheimer’s.

Sounds awesome. Was going to go invest in companies that are working on this topic. Then I made a dreadful mistake. I decided to look at the paper that all of this is based on: Determining the Presence of Periodontopathic Virulence Factors in Short-Term Postmortem Alzheimer’s Disease Brain Tissue.

Hmm .. that is weird. The paper does not seem to have anything in it really closely tied to all the claims in the news stories. Here is the Abstract:

The aim of this study was to establish a link between periodontal disease and Alzheimer’s disease (AD) with a view to identifying the major periodontal disease bacteria (Treponema denticola, Tannerella forsythia, and Porphyromonas gingivalis) and/or bacterial components in brain tissue from 12 h postmortem delay. Our request matched 10 AD cases for tissue from Brains for Dementia Research alongside 10 non-AD age-related controls with similar or greater postmortem interval. We exposed SVGp12, an astrocyte cell line, to culture supernatant containing lipopolysaccharide (LPS) from the putative periodontal bacteria P. gingivalis. The challenged SVGp12 cells and cryosections from AD and control brains were immunolabeled and immunoblotted using a battery of antibodies including the anti-P. gingivalis-specific monoclonal antibody. Immunofluorescence labeling demonstrated the SVGp12 cell line was able to adsorb LPS from culture supernatant on its surface membrane; similar labeling was observed in four out of 10 AD cases. Immunoblotting demonstrated bands corresponding to LPS from P. gingivalis in the SVGp12 cell lysate and in the same four AD brain specimens which were positive when screened by immunofluorescence. All controls remained negative throughout while the same four cases were consistently positive for P. gingivalis LPS (p = 0.029). This study confirms that LPS from periodontal bacteria can access the AD brain during life as labeling in the corresponding controls, with equivalent/longer postmortem interval, was absent. Demonstration of a known chronic oral-pathogen-related virulence factor reaching the human brains suggests an inflammatory role in the existing AD pathology.

Alas, even via UC Davis Libraries I do not have access to the full article. So my inferences will have to be based on the abstract (note to authors, if you want people to judge your full papers not just your abstracts, well, it would be good to have your paper be available). From what I can tell – what they showed in this paper is that antibodies that are known to find to lipopolysaccharide (LPS) from P. gingivalis showed positive binding to brain material from a few patients who had Alzheimer’s and did not show binding to brain material from controls. So let’s ask and try to answer a few questions about this:

Does LPS from a specific organism in the brain mean that the organism was in the brain: I don’t think so – LPS could move around?
Does binding by the antibody they used mean that there is LPS from P. gingivalis there? Definitely no – there could be cross reactivity with other LPSs or even other molecules?
Did they do any more specific tests (e.g., DNA)? Doesn’t seem like it.

But let us just assume that they really did detect P. gingivalis in the brains of Alzheimer’s patients. Would this mean PG causes Alzheimer’s? Obviously it does not mean that. Let us even assume (ridiculously) that PG causes Alzheimer’s. Would this mean the periodontal disease leads to Alzheimer’s? No – PG could come into brains in other ways.

I could go on and on. There are so so so so so so so many jumps that are needed to go from the limited results presented in this paper to getting anywhere near supporting a hypothesis that periodontal disease causes Alzheimer’s that it makes we want to scream. The news reporting here is awful. The scientists involved seem to be overhyping their work to extremes with risky, dangerous possible consequences (e.g., – oh – so you have Alzheimer’s – it’s your fault for not taking care of your teeth … we need more money for dental care to prevent Alzheimer’s; everyone should take prophylactic antibiotics to prevent Alzheimer’s and so on).

Crosspost from http://microbe.net: A very misleading “bacteria in buildings” advertisement presented as “news”

Am crossposting this from http://microbe.net where I posted it earlier. See original post here: A very misleading “bacteria in buildings” advertisement presented as “news”

Wow this “story” (which is really an ad) is just so incredibly bad I do not know what to say: Dangerous Bacteria Isolated in Healthcare HVAC Evaporator Coils. I do not even know where to begin with criticism so I will just go step by step through some of the advertisement.

1. Title: Dangerous Bacteria Isolated in Healthcare HVAC Evaporator Coils

There is no evidence that the bacteria being looked at here are dangerous.

2. First sentence ”A recent study suggests that doctors may want to monitor the environmental condition of their air conditioners evaporator coil before surgery to help prevent the spread of bacterial infections”

No evidence is presented anywhere that monitoring AC coils has any even remote potential value here.

3. Second sentence: Dr. Rajiv Sahay, Laboratory Director at Environmental Diagnostics Laboratory (EDLab) and his colleagues sampled evaporator coils in healthcare air handling systems and isolated Pseudomonas aeruginosa a known noscocomial pathogen.

Well, Pseudomonas aeruginosa is indeed a known pathogen. However, there is no evidence presented that all the things they detect are indeed pathogenic/virulent. In fact, later in the article they report their results as being for “Pseudomonas sp” which suggests that their typing was very broad. It is very possible that many of the cells they detected are not pathogenic.

4. Ignore the middle part. It is just saying that Pseudomonas aeruginosa can be nasty in compromised patients.

5. They then go on to discuss their study more “In the study, over 560,000 colony forming units (CFU)/gram of Pseudomonas sp were isolated from deep within the evaporator coil system.”

What study? No data is presented. No methods. No results. Nothing.

6. They then say “Potential aerosolization of these micro-organisms from the infested coil is immense due to a discharge of air stream with 6 miles/hours (commonly observed) across the evaporator coils”

Not so sure about that. Would have been much better to study ACTUAL aerosolization.

7. Then we find out that they person who conducted the study Dr. Rajiv Sahay is also the one selling the cleaning service to clean your air coils. That does not instill confidence in me.

So a person selling HVAC cleaning reports unpublished results that they claim suggest if you do not clean your HVACs in hospitals you put all your patients at risk. I am on board with the need to study microbes in hospitals more. I am on board with the potential risks of microbes in AC systems. I am not on board with not presenting data, and with getting the science wrong.