Fecal metagenomic profiles in subgroups of patients with ME/CFS

[Murph]

Lighten up. It's a legitimate question and the first question that any funding panel member would ask. In fact they shouldn't/wouldn't need to as a funding application would state a working hypothesis (that ME/CFS will be found to be 'associated' with changes to the microbiome and that association is theoretically/clinically relevant because ....etc.

I expect they will state this in the full paper - I was hoping someone had an idea what their working hypothesis was.

One broad hypothesis is that CFS features an immune disturbance driven by a leaky gut. The leaky gut can be caused by a change in gut microbiota changing the permeability of the gut wall. The transit of microbes and signalling molecules into the blood stream can cause immune responses.

You seem to want to know if this is a cause or an effect. Porque non los dos? We draw a lot of one dimensional logical chains in trying to describe CFS in ways our brains can grasp. The reality is likely to be cycles interlinking with cycles, including vicious cycles that perpetuate the disease.

This is exploratory research. Identifying the features of the disease is the first step to understanding it, which is the first step to solving it.

Perhaps one day by changing our gut microbiome we can throw a spanner into a vicious cycle?

EDIT: got to the discussion section and here it is in their own words: "An altered microbiome is postulated to lead to increased gut permeability (“leaky gut”) and intestinal inflammation with gastrointestinal symptoms. Increased translocation of lipopolysaccharides (LPS) from gram-negative bacteria leads to autoantibody production, disruption of tight junctions, and both local gastrointestinal and systemic inflammation [12, 32, 33]."

 

[lansbergen]

Perhaps one day by changing our gut microbiome we can throw a spanner into a vicious cycle?

Or help the immune system to eliminate the agent starting it all so the microbiome can go back to normal.

 

[Tuha]

Or help the immune system to eliminate the agent starting it all so the microbiome can go back to normal.

But if an agent disturbed the microbiome is it still there and does that agent still make problems? Or that agent already diappeared and the problem is the microbiome?
Still so many questions.

 

[Murph]

Important and probably quite disappointing negative finding buried in the paper: Cytokines did not distinguish patients from controls

Immune profiling (Additional file 1: Table S4A) was performed to test for alterations in the ME/CFS and IBS subgroups. No significant findings were obtained after adjusting for multiple comparisons of all 61 cytokines. However, prior to adjustment, TNF-α was increased in the ME/CFS cases compared to the controls (Additional file 1: Table S4B) and plasma levels of leptin, CSF-2, CXCL-8, and TNF-α were higher in the ME/CFS + IBS patients than the controls (Additional file 1: Table S4B). The ME/CFS patients without IBS had a pre-adjustment trend toward increased TNF-α compared to controls.


Unsupervised hierarchical clustering was used to visualize the variation in plasma cytokine levels between the total ME/CFS, ME/CFS + IBS, ME/CFS without IBS, and controls. Although the clusters did distinguish a range of cytokine profiles in individuals (ranging from high to low cytokine profiles), there was no distinct clustering observed between disease groups (Additional file 2: Figure S2).


A predictive logistic regression model restricted solely to immune data showed little accuracy in distinguishing between the ME/CFS diagnostic groups and controls (total ME/CFS, ME/CFS + IBS, or ME/CFS without IBS vs. controls; data not shown).

 

[A.B.]

Another intimidatingly complex paper by Lipkin and Horning .

I wonder how the difference in atrazine degradation should be interpreted? Atrazine is a herbicide and suspected endocrine disruptor. Does this mean that these patients are significantly more exposed to atrazine?

Altered bacterial metabolic pathways define ME/CFS and ME/CFS subgroup with IBS co-morbidity. Histogram of the log-transformed LDA scores computed with LEfSe for bacterial metabolic pathways found to be differentially abundant between ME/CFS groups and controls. Positive LDA score indicates enrichment of pathways in a ME/CFS, b ME/CFS + IBS, and c ME/CFS without IBS vs. controls. Negative LDA indicates enrichment of pathways in control subjects (reduced in ME/CFS groups). The LDA score indicates the effect size and ranking of each superpathway. An alpha value of 0.05 for the Kruskal-Wallis test and a log-transformed LDA score of 2.0 were used as thresholds for significance in LEfSe analyses. Asterisks next to pathways indicate significant differences were also found for a given pathway based on nonparametric Mann-Whitney U test with Benjamini-Hochberg correction (adjusted p < 0.2)

 

[Murph]

The findings below could inform attempts to transform the microbiome. Perhaps some antibiotics target some of these bugs. Or perhaps some are available as probiotics. Where the gut bugs can't be cultured and therefore can't be turned into probiotics, sufferers could perhaps seek an FMT donor rich in these species and taxa.

Among all ME/CFS cases, the increased relative abundances of R. gnavus, C. bacterium, C. bolteae, and C. asparagiforme were associated with better vitality, health change, and motivation scores. Decreased relative abundances of F. prausnitzii and C. catus were associated with worse emotional wellbeing scores, while decreased abundances of R. inulinivorans and D. formicigenerans were associated with improved motivation scores.


In the ME/CFS + IBS cases, decreased relative abundance of unclassified Alistipes, D. longicatena, and R. inulinivorans were associated with improved vitality, health change, and fatigue scores. Decreased relative abundance of C. comes and Faecalibacterium species were associated with worse fatigue scores and worse pain scores, respectively.


In ME/CFS without IBS cases, the increased relative abundance of P. capillosus was associated with worse vitality, emotional wellbeing, health changes and motivation scores. The relative abundances of D. formicigenerans and C. scindens were associated with improved motivation scores, similar to patterns observed in total ME/CFS.

 

[AndyPR]

Blog on the study from the MDP team - http://microbediscovery.org/2017/04...eria-in-mecfs-may-influence-disease-severity/

 

[Marky90]

Thanks for sharing Murph, that`s important to know!

While i appreciate this recent research on the gut, and any finding is important, my gut (pun intended), says we should be looking elsewhere. Having said that, when we know as little as we do about possible mechanisms, we ought to be really open minded. It was pointed out above that humans tend to look for pieces of the puzzle, but what`s the right way to go about when you don`t know what the puzzle is?! A lot of medical breakthroughs come about when looking for something else, it`s a bit like the tendency to end up in a relationship when your not looking for love.

Also, after what Murph shared.. And this is just a general comment.. It seems to me to be somewhat of a trend with ME/CFS-research that very little is able to be replicated. Which of voursecan be due to all sorts of reasons.. methodological.. bias tendencies etc. Therefore it strikes me as important to perhaps aim to replicate before building research on unreplicated findings. Reason being that there is in fact a danger in narrowing down on hypothesizes, if the hypothesis is on shaky ground. Unfortunately, in that scenario, the group of researchers have to wait for it to be independently replicated ideally, and that`s too slow as well..

I understand some of this is "political" also, a group of researchers cant just go out and say "our research shows jack all" in a underfunded disease like this.

Again, this is not directly related to this paper, but just some thoughts i have after Murphs comment.

 

[Marky90]

The findings below could inform attempts to transform the microbiome. Perhaps some antibiotics target some of these bugs. Or perhaps some are available as probiotics. Where the gut bugs can't be cultured and therefore can't be turned into probiotics, sufferers could perhaps seek an FMT donor rich in these species and taxa.

Among all ME/CFS cases, the increased relative abundances of R. gnavus, C. bacterium, C. bolteae, and C. asparagiforme were associated with better vitality, health change, and motivation scores. Decreased relative abundances of F. prausnitzii and C. catus were associated with worse emotional wellbeing scores, while decreased abundances of R. inulinivorans and D. formicigenerans were associated with improved motivation scores.


In the ME/CFS + IBS cases, decreased relative abundance of unclassified Alistipes, D. longicatena, and R. inulinivorans were associated with improved vitality, health change, and fatigue scores. Decreased relative abundance of C. comes and Faecalibacterium species were associated with worse fatigue scores and worse pain scores, respectively.


In ME/CFS without IBS cases, the increased relative abundance of P. capillosus was associated with worse vitality, emotional wellbeing, health changes and motivation scores. The relative abundances of D. formicigenerans and C. scindens were associated with improved motivation scores, similar to patterns observed in total ME/CFS.

My guess would be that those score differences are in fact superficial, maybe not statistically, but we know from experience that that doesn't necessarily matter depending on the underlying methodology. Not saying anything has been done wrong, but ME/CFS is not a very suitable disease to measure functioning based on questionnaires solely. Patients have often been sick so long that they could report that they feel healthy, even if they are currently on disability! It is all relative, and the mind plays tricks. So, when you are looking for something to come up, findings like this could very well be random. But it is a long time since i studied statistics, so maybe someone like @Simon could refresh me on the chances for that in this particular case. I just remember that the p-values dont always paint the full picture

 

[arewenearlythereyet]

One thing to note is that we don't really have too much information about what "normal" looks like yet. There is still a long way to go to work out inter dependencies and synergism's between species.

The best bet is to look at this as a very complex ecology that is out of balance rather than bugs we need to find and kill.

We may be able to have an influence on this, but the level of complexity makes me think it would be an easier task to reset our metabolism and let the microflora re-find its balance. Logic suggests that it is easier to influence the host rather than the multitude of species that live on\in it?

 

[Helen]

Also Frémont et.al., including KDM, investigated the mikrobiome in a group of ME/CFS patients living in Belgium and Norway . This study was published 2013. KDM regularly investigates and treats overgrowth of well-known pathogenic bacterias in the microbiome in his patients (I´m one of them). I would assume that he will publish more in the future.

http://www.sciencedirect.com/science/article/pii/S1075996413000929

 

[AndyPR]

Just to add to the discussion, Maureen Hanson recently did an overview of the microbiome, including thoughts on potential treatments, in this article, http://www.biochemist.org/bio/03902/0010/039020010.pdf. A thread exists already on PR for the article, http://forums.phoenixrising.me/inde...icrobiome-in-myalgic-encephalomyelitis.50747/

 

[ChrisD]

My two cents; I see the Microbiome as the Automatic Quartz in a self-winding watch (If you will). With regular dietary and environmental behaviour, it maintains a balance and continues to provide energy to the mechanism (The body) via normal and adequate synthesis of Vitamins, Minerals, Neurotransmitters etc. UNTIL a stress/viral event (Imagine the watch taking a bash or being dropped - to which the quartz works intermittently or skips a beat), at this moment a variety of imbalances are caused with bacteria that is initially pathogenic either disappearing or appearing with more prevalence and causing even more imbalance. It seems to me that unless we intervene with antibiotics/probiotics, then the balance will not be restored (Chronic) and as certain bacteria overgrow - symptoms of neuro-inflammation increase. That's my understanding, perhaps not the best analogy.

ANYWAY, who has had the opportunity to compare their UBIOME of DD Stool Tests to the findings of the study? Mine correlate with the findings, particularly Faecalibacterium, Roseburia, Coprococcus, Clostridium, Ruminococcus, alistipes

It makes even more sense to me now that when I use probiotics like Kefir, Colostrum, Bravo Yogurt in large amounts, that I have a temporary remission of symptoms but they must not be making impactful changes to the microbiome i.e. probiotics like lactobacilli are not colonising the gut :thumbdown:

 

[lansbergen]

But if an agent disturbed the microbiome is it still there and does that agent still make problems? Or that agent already diappeared and the problem is the microbiome?
Still so many questions.

Good question.

Looking at how my improvemeny went, considering what was already known 50 years ago in veterinary medecine, reading the literatire of the infection I suspect and finding something about a recent discovered early immune response in the gut I am pretty sure when the agent level can be lowered enough, the cell machinery can deal with it good enough to let the reactive oxigen response go down.

 

[caledonia]

Interesting there are a few cases of patients using lots of probiotics and herbs to change their gut who are now recovered or doing very well.
Ken Lassesen being one of them https://cfsremission.com/probiotics/

Ken Lassesen found out he had a blood coagulation defect and blood thinners made him well.

 

[adreno]

We may be able to have an influence on this, but the level of complexity makes me think it would be an easier task to reset our metabolism and let the microflora re-find its balance.

Blast away the current microbiome and follow up with FMT.

 

[AdamS]

Xifaxin seemed to help this person somewhat.

 

[Marco]

EDIT: got to the discussion section and here it is in their own words: "An altered microbiome is postulated to lead to increased gut permeability (“leaky gut”) and intestinal inflammation with gastrointestinal symptoms. Increased translocation of lipopolysaccharides (LPS) from gram-negative bacteria leads to autoantibody production, disruption of tight junctions, and both local gastrointestinal and systemic inflammation [12, 32, 33]."

OK - Thanks for that - they have a working hypothesis assuming a causal relationship and not just a non-directional association.

Which brings me back to my original question :

is there any evidence that the gut microbiota directly and unamiguously cause any disease?

 

[Marco]

Important and probably quite disappointing negative finding buried in the paper: Cytokines did not distinguish patients from controls

Which does rather contradict a hypothesis based on bacterial translocation causing systemic inflammation as an ongoing driver of ME/CFS symptoms.

 

[lansbergen]

is there any evidence that the gut microbiota directly and unamiguously cause any disease?

Weaned piglets E-coli can kill whole litters.