Paraprevotella: the cause of my atypical ME?

[Cheesus]

@jepps
I would suggest your friend starts low and goes slow with the methylation supps, as I have had a lot of inflammation even with Rich's protocol. I am not at all a fan of Freddd's approach and I have seen no evidence to suggest that his paradoxical folate deficiency theory is legitimate. I think there is also a serious concern of people dangerously fluctuating back and fort her between hypo- and hyperkalemia if taking too much folate. I think your friend will be much better off and safer with the gentle approach that we actually have a small degree of evidence for.

 

[jepps]

Thanks @Cheesus for your reply and for your suggestion, I will pass it to my friend (she´s not so well in speaking Englisch. I also not, but she´s less than I am).
I also believe, that higher dosages of methylation supps can trigger to much inflammation. Low and slow is more healthy.
I also began with tiny dosages of folate and MB12 and AdenosylB12, and worked up to standard daily dosages within 1 year. Despite this lower dosages I developped histamine issues, that I never had before.
Histamine issues are a lot better, since I started with the protocol for the gut.
My friend now is yet working on the gut. She cannot take any prebiotics, and she want`s to take certain dosages of prebiotics, until she will begin with tiny dosages of methylation supps.
The whole thing is a long lasting project, but there are improvements, and so it´s worth it.

 

[alicec]

I've finally got around to comparing gut changes with supplement changes to see if I can spot any obvious pattern.

The most I can say is that while I've been taking relatively high doses of methyl folate, both B12s and acetylcarnitine, firmicutes and bacteroidetes are closer together. When taking very small doses or none at all, there is more discrepancy - firmicutes much higher, bacteroidetes relatively low.

Of course this wasn't a controlled experiment with no other variables changing and the pattern could be coincidence.

 

[Cheesus]

I have had another stool test back and paraprevotella is now negligible (0.12%). The rest of the bacteria in my gut have also changed dramatically. My whole microbiome fluctuates so readily and to such a large extent that each test is completely unrecognisable from the last. Judging by these tests you would not know how ill I am, and you certainly could not pick me out as having CFS as Maureen Hansen did in her recent study.

I can only conclude that the cause of the foamy urine and possibly my ME is not a gut bacteria. I believe it is possibly a systemic infection, and I am pursuing more testing, including private shotgun metabolomics testing and potentially private sequencing with next generation technology to get to the bottom of it.

 

[alicec]

Judging by these tests you would not know how ill I am, and you certainly could not pick me out as having CFS as Maureen Hansen did in her recent study.

I know what you mean. My last uBiome test gave me a 97% wellness match! I couldn't recognise myself in Maureen Hansen's study either.

As I've mentioned previously, I have seen a lot of variability in my results too. I wouldn't go so far as to say each test is unrecognisable from the last. There does seem to be an underlying pattern, its just that every now and then these is a huge overgrowth of something which by next time has disappeared.

I am pursuing more testing, including private shotgun metabolomics testing and potentially private sequencing with next generation technology to get to the bottom of it.

Do let us know how you go.

 

[jepps]

I can only conclude that the cause of the foamy urine and possibly my ME is not a gut bacteria. I believe it is possibly a systemic infection, and I am pursuing more testing, including private shotgun metabolomics testing and potentially private sequencing with next generation technology to get to the bottom of it.

I also hope, that in future we receive an affordable test with the full profile of bacteria, viruses and fungi.
The Ubiometest tells only abour microbial relations within the microbiome, but nothing about the relation to viruses. Interesting would be tests, that show, if therapeutic inverventions reduce viruses, and increase bacteria.

Anyway, I see, that I have low actinos, that keep pathogens under control, and I hold on working on improving them.
Also I see, that viral infections change the microbiome immediate, and result in more dysbiosis.

Additionally, there are - as @alicec posts, some patterns, where I conclude to improvements. F.ex. a year ago: high proteos, no detectable akkermansia, this year: increasing proteos means increasing akkermansia. As akkermansia degrade LPS, LPS are better degraded than a year ago. So I assume, controlling the bacteria via tests tells us something about the whole microbes in the gut.

I wish you good luck for your next tests and for new insights

 

[PDXhausted]

@Cheesus are you still getting on ok with the LDN?

I got my ubiome results back, and nothing really stuck out in terms of anything looking pathogenic or like an overgrowth.. The biggest issue was probably just a lack of lactobacillus and bifidobacterium, probably from antibiotics I've taken. And that is despite pretty significant SIBO symptoms, food intolerances and an obvious infection on my tongue.

I too am pursuing the idea of systemic infection for various suspicious symptoms. Hope you're able to find something that helps!

 

[Cheesus]

Yeah the LDN is doing great. It's the first thing I've ever used that obviously actually helps. I'm improving rapidly and would be doing even better if I could pace myself even a little bit! Haha.

The foamy urine increased massively when I started it. I presume this would be because the immune system is killing something that is releasing it, which is what I have suspected the foamy urine to be from the outset. Obviously I have no way of knowing it that is true. I am in the process of doing shotgun metabolomics on the foamy urine with a company in Germany. They are doing the analysis and everything for me (not cheap) so I really hope I will get some solid answers in the not too distant future.

 

[Cheesus]

The biggest issue was probably just a lack of lactobacillus and bifidobacterium, probably from antibiotics I've taken.

And I also had a serious lack of bifidobacteria and lactobacilli - which is especially strange because this test was done after a month of drinking kefir and taking VSL - but that doesn't really seem to matter when you have a broad diversity of genera more generally. I'm not sure why uBiome focus on those taxa so much in their overview. Maybe because they are the big names in probiotics? It's not clear that they are particularly significant for your health.

 

[Cheesus]

I haven't updated this thread recently, but I have had some new developments.

First, I had more testing from another lab back at the end of May. This time I was using looking for microbes in other fluids/sites in addition to the gut. The purpose was to find any pathogens that could be making me sick.

I have written about this testing in another thread, so I won't go into it much here. However one interesting outcome was that it identified paraprevotella yet again as having a significant abundance in my gut (15%). This time it identified not only the genus, but also the species as paraprevotella clara gen (there are only two species within the genus).

I have now had 5 different tests from 3 different labs employing 2 different sampling methodologies. Of those 5 tests, only 1 showed no significant overgrowth of paraprevotella. The first and last test are about 18 months distant, and both showed a significant overgrowth. So, at this point I am fairly confident that this is a chronic state.

Second, I have another very interesting data point. I may have mentioned previously (I am not sure) that I am in contact with another person that had this very strange symptom of foamy urine. In my case it was triggered by a herbal antimicrobial (which also triggered my ME), in his case it was triggered by the antibiotic azithromycin. This person does not have ME. Instead they describes a condition that sounds very much like RA, but which has not been diagnosed as such.

This person also tested their gut with the American Gut Project. Not only did they have an overgrowth of paraprevotella, but it actually accounted for almost 50% of the total bacteria in their gut!

I am no statistician, but for us both to share this very strange symptom triggered by antimicrobials AND have an excessive levels of paraprevotella seems unlikely to be a coincidence. The question of causality is another matter, but it has certainly reinvigorated my pursuit of the gut microbiome as a treatment objective.

Do you have any thoughts on this, @alicec?

 

[pamojja]

If I may ask, what was the herbal antibiotic which caused the foamy urine? And at what doses?

 

[Cheesus]

If I may ask, what was the herbal antibiotic which caused the foamy urine? And at what doses?

Oil of oregano. I can't remember the dose but I was using up to 6 tablets a day on the recommendations of the functional medicine doctor.

 

[alicec]

I am no statistician, but for us both to share this very strange symptom triggered by antimicrobials AND have an excessive levels of paraprevotella seems unlikely to be a coincidence. The question of causality is another matter, but it has certainly reinvigorated my pursuit of the gut microbiome as a treatment objective.

Do you have any thoughts on this, @alicec?

I agree, it certainly seems more than coincidence.

It's impossible to know if the overgrowth is cause or effect but trying to get it under control and observing the effects seems like the only way to proceed.

I think Paraprevotella would be susceptible to Rifaximin, it would certainly be worth investigating. If you can't find a friendly doctor who would prescribe it you can always buy it from an online pharmacy.

It could be worth trying a few rounds of this to see if it makes any difference to how you feel. You could do before and after gut tests, and of course lots of pre and probiotics in between doses.

Given your bad experience with oil of oregano you may be reluctant to try this, in which case the FMT option you canvassed originally might come back into focus. Usually with these there is intensive antibiotic treatment prior to the transplant.

I don't know what else to suggest I'm afraid.

 

[Cheesus]

Thank you, @alicec. I appreciate your thoughts. Rifaximin is an option I have considered, but you're right that I am nervous about it given my history. I am also nervous about causing other problems, because as of right now I at least do not experience gastrointestinal complaints.

I am currently in the beginning phase of helminth therapy. I am hoping that will lead to significant enough improvements to be able to get to the clinic for an FMT. Helminths also modulate the gut microbiome with some evidence suggesting they decrease the abundance of bacteroidetes, so perhaps that will help. Unfortunately I did not test immediately before starting.

Anyway, thanks again for your thoughts. I will update this thread with any major developments.

 

[alicec]

I am currently in the beginning phase of helminth therapy.

Great - have read interesting things about that. It's a bit of a drastic way to modulate the gut and affect the host immune response and of course a black box, but some people have had dramatic improvements from it.

I'll look forward to a report about it.

 

[Jesse2233]

good luck @Cheesus!

 

[SB_1108]

Just wanted to chime in and say that I also have an overgrowth of Prevotella and/or Bacteroides. I've tried every herbal and prescription antibiotic and they have all made it worse. The initial culprit of the worsening was caused berberine but other antibiotics like Rifaximin have only magnified the problem. I'm currently trying mild hyperbaric oxygen therapy because Bacteroides are Obligate anaerobes and are poisoned by oxygen. Dr Sarah Myhill has a page about this where she says that bile salts might help: http://www.drmyhill.co.uk/wiki/Ferm..._CFS#Bacteroides_including_Prevotella_species

There does not appear to be an antibiotic that Prevotella is sensitive to, but apparently it can be reduced by taking bile salts. These are also available on prescription as Ursodeoxycholic acid and I would suggest 150mg with meals, perhaps more! I am currently trying rifaxamin 400mgs tds for 14 days (perhaps longer) to tackle upper fermenting gut by anaerobes. The idea here is to use a dose of rifaxamin sufficient to kill the billions of bacteria in the upper gut but not the trillions in the lower gut. Initially this must be done with a protein fat only diet (no carbs or vegetable fibre).

 

[SB_1108]

I wonder if this product is worth a try...
http://www.jarrow.com/product/284/Bile_Acid_Factors

 

[Cheesus]

Hi @SB_1108,

I don't think any one supplement is going to help at this stage unfortunately. The list of things I have tried is painfully long and expensive. Really I think I just need an FMT. I've tried so many things that I feel like I am trying to treat C. Difficile!

There is a clinic in the UK that does FMTs. I don't know if that might be available to you?

Interestingly, what I have is actually not a prevotella species. Paraprevotella is an entirely different genus to prevotella. They have a 94% genetic overlap, which sounds like a hell of a lot, but when you consider that humans and chimpanzees share something like 96% of their genes it becomes apparent that you're dealing with something that has quite different traits.

 

[SB_1108]

I definitely agree with you @Cheesus - no one supplement will fix this ridiculous disaster in my gut. The bile salts are just a supplement I'm considering ordering to see if it alleviates any of my issues since Dr Myhill recommends it.

I have tried approximately 50 FMTs without much success. You can see more about my experience here: http://forums.phoenixrising.me/index.php?threads/fecal-transplant-diyers.28574/
That's not to say it wouldn't work for someone else, we are each different and what works for one person doesn't work for someone else.

You are right about the paraprevotella differentiation from prevotella. They are both from the Prevotellacae family and the bacteroides genus so I still think the HBOT might be a potential solution.
https://www.datapunk.net/substrata/display.pl?171552