Changes in Gut and Plasma Microbiome following Exercise Challenge in ME/CFS

[M Paine]

It seems that the authors are dropping hints that they did see increases in read counts in blood post exercise. I wonder if they removed them during peer-review due to being an unreliable metric. Other metagenomic studies which have looked at microbial communities often do see that read count correlates to the abundance of taxa seen via other sampling methods.

Perhaps with those figures given as context, this paper would make a bit more sense, but without overall microbial population growth or decline as context, statements like this seem suggestive of something not demonstrated by the data:

"There was also a significant difference in clearance of specific bacterial phyla from blood following exercise with high levels of bacterial sequences maintained at 72 hours post-exercise in ME/CFS patients versus clearance in the controls."

Assuming that CFS patients maintain high levels of bacteria in the blood post exercise, the question becomes, why?

 

[adreno]

It seems almost universal from the reports I've seen that PWMEs deteriorate following ingestion of many pre- and probiotics. The Lactobacillus family of species (which are Firmicutes) are intolerable to just about everyone. It is almost uncanny how the effects of these resemble the symptoms of PEM after exercise. A few studies have also found overgrowth of these bacteria in PWMEs.

 

[Kati]

It seems that the authors are dropping hints that they did see increases in read counts in blood post exercise. I wonder if they removed them during peer-review due to being an unreliable metric. Other metagenomic studies which have looked at microbial communities often do see that read count correlates to the abundance of taxa seen via other sampling methods.

Perhaps with those figures given as context, this paper would make a bit more sense, but without overall microbial population growth or decline as context, statements like this seem suggestive of something not demonstrated by the data:

"There was also a significant difference in clearance of specific bacterial phyla from blood following exercise with high levels of bacterial sequences maintained at 72 hours post-exercise in ME/CFS patients versus clearance in the controls."

Assuming that CFS patients maintain high levels of bacteria in the blood post exercise, the question becomes, why?

Can you please explain what you mean by read counts? I am trying to understand. Thx.

 

[M Paine]

Sure, so in this paper, they took blood and stool samples, they then purified DNA from the samples and sequenced them, looking for bacterial DNA sequences. (This is a really simplified description)

In the case of bacteria, it's been found that looking for DNA sequences that encode for ribosomal RNA (rRNA) is one way to identify and classify bacteria. This is a highly conserved region of bacterial genomes (mutations occur infrequently) so when sequencing a large volume of DNA, researchers look for a particular DNA sequence belonging to a particular ribosomal subunit of rRNA affectionately called '16S'

For each 16S sequence identified, it's then classified into a bacterial phyla based on the makeup of the sequence. For a given sample of blood, there might be a lot of DNA (both eukaryotic host DNA and prokaryotic bacterial sequences, not to mention viral or archaea sequences). The absolute read count we are referring to is how many DNA sequences read out of that entire sample were were identified to be a 16S ribosomal subunit sequence belonging to a bacterial genome.

The relative read count refers to a percentage of how many of the 16S sequences each phyla accounted for out of the total absolute read count.

 

[A.B.]

It seems almost universal from the reports I've seen that PWMEs deteriorate following ingestion of many pre- and probiotics. The Lactobacillus family of species (which are Firmicutes) are intolerable to just about everyone. It is almost uncanny how the effects of these resemble the symptoms of PEM after exercise. A few studies have also found overgrowth of these bacteria in PWMEs.

A "water kefir" probiotic produced marked brain fog for me. It took a few weeks to get better, and then I had a bad relapse which I suspect could have been connected to this as well.

This study http://www.ncbi.nlm.nih.gov/pubmed/24004255 says

Culture-independent, high-throughput, sequencing-based analyses revealed that the bacterial fraction of each water kefir and grain was dominated by Zymomonas, an ethanol-producing bacterium, which has not previously been detected at such a scale. The other genera detected were representatives of the lactic acid bacteria and acetic acid bacteria. Our analysis of the fungal component established that it was comprised of the genera Dekkera, Hanseniaspora, Saccharomyces, Zygosaccharomyces, Torulaspora and Lachancea.

But the exact composition varies between different cultures.

PS: my d-lactate was about 2x the upper limit of the reference range.

 

[anciendaze]

It seems that the authors are dropping hints that they did see increases in read counts in blood post exercise. I wonder if they removed them during peer-review due to being an unreliable metric. Other metagenomic studies which have looked at microbial communities often do see that read count correlates to the abundance of taxa seen via other sampling methods.

Perhaps with those figures given as context, this paper would make a bit more sense, but without overall microbial population growth or decline as context, statements like this seem suggestive of something not demonstrated by the data:

"There was also a significant difference in clearance of specific bacterial phyla from blood following exercise with high levels of bacterial sequences maintained at 72 hours post-exercise in ME/CFS patients versus clearance in the controls."

Assuming that CFS patients maintain high levels of bacteria in the blood post exercise, the question becomes, why?

I think it is important to distinguish here between evidence of bacterial components, including nucleic acids, reaching the blood and actual living bacteria causing sepsis. If we had sepsis this would become a progressive disease. We have to be careful to avoid claiming this is progressive, and having data judged by criteria appropriate for such. It is chronic or episodic, with episodes triggered by exercise.

I am also tantalized by that comment on clearance. In addition to exercise I reported long ago that I was "wiped out" for three days following a glucose tolerance test or a high carbohydrate meal which produced a feeling like a hangover. (My blood sugar remained low.) This characteristic time is typical for intestinal transit. How you impair clearance is yet another question.

If bacterial translocation is taking place, we can expect some kind of specific immune response to those bacterial species. The exact nature of the response would depend on populations of gut flora and the mechanism of translocation. It need not be identical in different patients.

I've tried and failed to come up with means of changing those relative proportions without having material from the gut, though not necessarily complete bacteria, cross mucous membranes. Perhaps I just lack imagination.

 

[M Paine]

Yes, good point, my question was worded poorly.

"Assuming that CFS patients maintain high levels of bacteria in the blood post exercise, the question becomes, why?"

Should be

"Assuming that CFS patients maintain high levels of bacterial components in the blood post exercise, the question becomes, why?"

If we had actual translocation of living bacteria, surely we would see evidence of pathogenic E.coli strains causing some serious problems for people?

 

[lansbergen]

If we had actual translocation of living bacteria, surely we would see evidence of pathogenic E.coli strains causing some serious problems for people?

I would think so.

 

[Kati]

We know that HIV patients also have gut issues. My wish would be that HIV patients get compared with ME patients. Surely it would provide insight, no? let's compare gulf war illness patients while we're there. Lyme. Sepsis survivors. Crohn's.

 

[M Paine]

This translocation topic got me thinking, would translocation of live bacteria from the intestinal tract into blood cause sepsis?

This paper came up and mentions a couple of interesting points:

Translocation of gut flora and its role in sepsis. Vaishnavi C

"Bacterial translocation may be a normal phenomenon occurring on frequent basis in healthy individuals without any deleterious consequences"

I'm... Surprised, a little confused...

 

[MeSci]

I am also tantalized by that comment on clearance. In addition to exercise I reported long ago that I was "wiped out" for three days following a glucose tolerance test or a high carbohydrate meal which produced a feeling like a hangover. (My blood sugar remained low.) This characteristic time is typical for intestinal transit. How you impair clearance is yet another question.

If you felt as though you had a hangover and your blood glucose remained low, could that be because the sugar was being rapidly converted to ethanol (alcohol) by gut microorganisms?

 

[A.B.]

We know that HIV patients also have gut issues. My wish would be that HIV patients get compared with ME patients. Surely it would provide insight, no? let's compare gulf war illness patients while we're there. Lyme. Sepsis survivors. Crohn's.

Hopefully the funding to do this sort of research will be made available.

 

[Kati]

Hopefully the funding to do this sort of research will be made available.

Some 32 millions $ was awarded to Dr Lipkin to study microbiome, either this year or last year. But none of that was earmarked for ME.

 

[anciendaze]

If you felt as though you had a hangover and your blood glucose remained low, could that be because the sugar was being rapidly converted to ethanol (alcohol) by gut microorganisms?

The problem with that idea is that I do not have the low threshold for drunkeness you find in people with such intestinal flora. Some do exist, for example in Japan.

Long ago, I learned that nothing stopped me from drinking myself into a condition where the next day I would be worried I might live. It is hard to get me high.

I'm more inclined to blame flu-like symptoms on disturbances in mucosa similar to those that take place with influenza. We tend to see "stomach" flu and respiratory flu as two different diseases, but both involve viral infections of mucous membranes. Exactly how much the symptoms depend on the virus itself, and how much on normal flora on those mucosa invading surrounding tissues, or on immune response to either the virus or bactera, are good questions.

 

[MeSci]

The problem with that idea is that I do not have the low threshold for drunkeness you find in people with such intestinal flora. Some do exist, for example in Japan.

Long ago, I learned that nothing stopped me from drinking myself into a condition where the next day I would be worried I might live. It is hard to get me high.

I'm more inclined to blame flu-like symptoms on disturbances in mucosa similar to those that take place with influenza. We tend to see "stomach" flu and respiratory flu as two different diseases, but both involve viral infections of mucous membranes. Exactly how much the symptoms depend on the virus itself, and how much on normal flora on those mucosa invading surrounding tissues, or on immune response to either the virus or bactera, are good questions.

My brain isn't quite awake yet, but I thought that the greater susceptibility of Oriental people to intoxication and flushing from alcohol was due not so much to an increased tendency to create it from sugar in the gut with particular microorganisms as to an impaired ability to break it down (in the liver?) with endogenous enzymes.

 

[anciendaze]

My brain isn't quite awake yet, but I thought that the greater susceptibility of Oriental people to intoxication and flushing from alcohol was due not so much to an increased tendency to create it from sugar in the gut with particular microorganisms as to an impaired ability to break it down (in the liver?) with endogenous enzymes.

There are definite differences in intestinal flora. I never had the ability to digest the seaweed in oriental diets. To me it was like cellophane. This is however all anecdotal stuff. I'd like to stay closer to the topic.

Added: Hope I can clarify something without leading us far off topic. This is a memory of very old news from a time when everything was not indexed by search engines. My memory is definitely not reliable for such tasks, so perhaps someone else will have another reference. What I recall is from a news story about a Japanese man charged with drunk driving who claimed he had not consumed any alcohol. There were two measures of alcohol, in blood and breath. Eventually doctors were able to demonstrate that he really could have significant detectable blood alcohol levels without consuming anything remotely alcoholic. As a result this was considered a medical rather than a criminal problem. (Wish I knew how it was treated.)

Note that this was not a case of a low threshold for drunkenness when ingesting alcohol. He had to be manufacturing the chemical entirely inside his own body.

 

[msf]

Could this be one of the metabolites Lipkin has found? He didn´t say they were human metabolites, did he?

Bacterial translocation occurs through the transcellular and the paracellular pathways and can be measured both directly by culture of mesenteric lymph nodes and indirectly by using labeled bacteria, peripheral blood culture, detection of microbial DNA or endotoxin and urinary excretion of non-metabolisable sugars.

(From the article posted above by M Paine).

 

[msf]

This paper seems interesting, particularly the bit about diseases other than sepsis where bacteria may be present in the blood: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4487407/

 

[MeSci]

This paper seems interesting, particularly the bit about diseases other than sepsis where bacteria may be present in the blood: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4487407/

Wow - what a huge paper (especially the reference list)! Looks fascinating, but I don't have the time or brainpower to read it thoroughly. What do you think of this paper, @Jonathan Edwards?

 

[Jonathan Edwards]

Wow - what a huge paper (especially the reference list)! Looks fascinating, but I don't have the time or brainpower to read it thoroughly. What do you think of this paper, @Jonathan Edwards?

An awful lot of technical stuff confirming what we have known since I was a student - that there are a few live bacteria in blood much of the time. But not much on whether this matters. I am not impressed by the comment about RA in the discussion. The diurnal variation in RA is because joints stiffen up with rest. It happens agin after lunch if you lie down. Sounds a bit like empire building to me!