Paraprevotella: the cause of my atypical ME?

[Cheesus]

I am a man, 25, suffering from extremely severe, atypical CFS/ME with objective abnormalities. My illness was triggered three years ago when herbal antimicrobials caused me to crash from prodromal CFS/ME into serious illness. Strangely, the antimicrobials caused very foamy urine. The foam declined but did not disappear after discontinuing the antimicrobials. Testing is consistently negative for proteinuria (excess protein is the only known cause of foamy urine). Probiotics cause dramatic fluctuations in this symptom, which is sometimes seen on Lyme and Candida forums.

A year after onset I discovered a liver enzyme (ALT) was elevated. All known causes are ruled out. After a period when the foamy urine was considerably elevated, my ALT went from ~100 to 330 (reference range 0-40). The foam declined and my ALT fell back to ~100.

Because antimicrobials triggered the idiopathic foamy urine, I hypothesised that the cause of my atypical CFS/ME and elevated ALT is a novel bacterial toxin that is visible as foam in my urine. As probiotics can influence this symptom, I surmised the bacteria is in my gut. To investigate, I had my gut microbiome profiled as part of the British Gut Project at Kings College London.

According to my report, the Gram-negative genus paraprevotella comprises 0.5% of total bacteria in the average gut. In my gut, paraprevotella comprises 12.5% of total bacteria. Very little is known about paraprevotella and it produces a number of "unknown fatty acids."

In addition to this unusual overgrowth was a marked lack of diversity. Two genera, bacteroides and paraprevotella, account for ~70% of total bacteria. Furthermore my PCR did not detect any lactobacilli, bifidobacteria, escherichia, butyrivibrio, veillonella, streptococcus, peptococcus or even prevotella. There are possibly other genera absent that I am not familiar with. The test is sensitive to genera accounting for >0.01%. My gut is radically different to both patients and controls in existing research on the gut microbiome in CFS/ME.

I have no GI symptoms at all.

My plan is to have a Fecal Microbial Transplant at the Taymount Clinic, but I am not nearly well enough at the minute. I am seeing some green shoots of improvement 2 months into a methylation protocol after 18 months of no change.

What do you all think?

ETA: If you want to a full profile of the bacteria in your gut, you can get a 10% discount at uBiome with this link: http://ubiome.refr.cc/T3B95SK

 

[Deltrus]

Maybe you can try VSL#3 which is the strongest probiotic on the market. The satchels contain 450 billion bacteria, and I've heard a few good things about it.

Very interesting post, I'd like to learn what my own gut microbiome is like.

 

[alicec]

What do you all think?

You sound like a definite candidate for FMT. That is a seriously disturbed gut microbiota!

It is hard to imagine diet, pre and probiotics being sufficient to turn that around. Something more drastic is needed to break the pattern. I hope the clinic you plan to go to is supportive - you have serious problems. Congratulations on working out what you have.

Bacteroides is usually the single most prevalent genus in the gut, on average around 20%, but 57.5% is way too high. It has filled the gap left by your collapsed Firmicutes phylum.

The absent genera you list are all pretty minor (apart from Prevotella is some people, but this tends to have an inverse relationship with Bacteroides, so in your case it is not surprising that it is absent). Yes Bifodiobacterium is known to be important, but is still on average only a bit over 1%. The much vaunted Lactobacillus is an extremely minor gut constituent, as is Eschericia, despite what traditional culture-based gut tests would have us believe.

Far more worrying is the loss of the normally dominant Firmicutes phylum, sometimes up to 70% total, though in Western guts, usually a bit lower than this. Dominant genera are clearly much diminished in your gut - these would include star butyrate producers such as Faecalibacterium, av 10%, Roseburia, av 4.7%, to name just a couple of the most abundant, plus other members of the phylum which play different roles - eg Blautia, av 8%, Ruminococcus, av 6%, and on through the many other less numerous members.

Do keep us posted on your progress. I have some knowledge of the microbiome so I would be happy to help if I can.

 

[alicec]

I'd like to learn what my own gut microbiome is like

It's easy to order a test either through uBiome or American Gut (or British offshoot, depending on where you live).

Mind you knowing what the results mean is not so easy!

 

[Cheesus]

Maybe you can try VSL#3 which is the strongest probiotic on the market. The satchels contain 450 billion bacteria, and I've heard a few good things about it.

Very interesting post, I'd like to learn what my own gut microbiome is like.

I tried VSL3, but it made me feel worse, and as methylation is helping, I didn't want to overcomplicate things right now. However it is waiting in the fridge for me.

If you want a 10% discount with uBiome, here is the link: http://ubiome.refr.cc/T3B95SK

 

[Cheesus]

You sound like a definite candidate for FMT. That is a seriously disturbed gut microbiota!

It is hard to imagine diet, pre and probiotics being sufficient to turn that around. Something more drastic is needed to break the pattern. I hope the clinic you plan to go to is supportive - you have serious problems. Congratulations on working out what you have.

Bacteroides is usually the single most prevalent genus in the gut, on average around 20%, but 57.5% is way too high. It has filled the gap left by your collapsed Firmicutes phylum.

The absent genera you list are all pretty minor (apart from Prevotella is some people, but this tends to have an inverse relationship with Bacteroides, so in your case it is not surprising that it is absent). Yes Bifodiobacterium is known to be important, but is still on average only a bit over 1%. The much vaunted Lactobacillus is an extremely minor gut constituent, as is Eschericia, despite what traditional culture-based gut tests would have us believe.

Far more worrying is the loss of the normally dominant Firmicutes phylum, sometimes up to 70% total, though in Western guts, usually a bit lower than this. Dominant genera are clearly much diminished in your gut - these would include star butyrate producers such as Faecalibacterium, av 10%, Roseburia, av 4.7%, to name just a couple of the most abundant, plus other members of the phylum which play different roles - eg Blautia, av 8%, Ruminococcus, av 6%, and on through the many other less numerous members.

Do keep us posted on your progress. I have some knowledge of the microbiome so I would be happy to help if I can.

Thank you very much for this response. It was very helpful. The whole bacteriodetes phylum accounts for 80% of my biome. I do not have the information in front of me regarding the other genera you mentioned. However from memory they were much lower than the figures you have given here. Thank you for your offer of help. I will be in touch in time with specific details to see if I can get your opinion.

 

[PDXhausted]

This is really interesting-- I have a somewhat similar situation.

For me, I had mild/moderate ME/CFS symptoms. I developed an infection after a cyst rupture and took a long course of amoxicillin. After developing dysbiosis from the amoxicillin, my ME/CFS symptoms became severe.

I too developed elevated liver enzymes, as well as elevated ammonia and triglycerides for no other apparent reason. I don't have foamy urine but my urine turned very dark since the amoxicillin. I've also had foamy saliva and drooling when taking phosphatidylcholine.

I had a stool test done from Doctor's Data and it came back mostly normal, but some elevated "commensal bacteria" like staph, strep, and a few unusual strains of clostridium. My stool pH was low at 5.9.

My other counts were:
4+ Bacteroides fragilis
4+ Bifidobacterium
1+ E. coli
3+ Lactobacillus
NG Enterococcus

I felt much better when taking activated charcoal. My liver enzymes went back down, my brain and my muscles felt clearer. Unfortunately I ended up developing SIBO while on the charcoal so had to stop taking it. A combination Rifaximin and oregano oil was helpful with the SIBO but did not help the ME/CFS symptoms. And now after 2 rounds of Rifaximin, I now get some kind of brain swelling and severe light sensitivity from it. It supposedly only stays in the gut so I have to think this must have to do with something inside my gut.

Anyway, this is somewhat different than your case, but I'll be really interested to see how you do with FMT. Please keep us updated. I think I'm going to try and do uBiome to see what comes up.

 

[Cheesus]

This is really interesting-- I have a somewhat similar situation.

For me, I had mild/moderate ME/CFS symptoms. I developed an infection after a cyst rupture and took a long course of amoxicillin. After developing dysbiosis from the amoxicillin, my ME/CFS symptoms became severe.

I too developed elevated liver enzymes, as well as elevated ammonia and triglycerides for no other apparent reason. I don't have foamy urine but my urine turned very dark since the amoxicillin. I've also had foamy saliva and drooling when taking phosphatidylcholine.

I had a stool test done from Doctor's Data and it came back mostly normal, but some elevated "commensal bacteria" like staph, strep, and a few unusual strains of clostridium. My stool pH was low at 5.9.

My other counts were:
4+ Bacteroides fragilis
4+ Bifidobacterium
1+ E. coli
3+ Lactobacillus
NG Enterococcus

I felt much better when taking activated charcoal. My liver enzymes went back down, my brain and my muscles felt clearer. Unfortunately I ended up developing SIBO while on the charcoal so had to stop taking it. A combination Rifaximin and oregano oil was helpful with the SIBO but did not help the ME/CFS symptoms. And now after 2 rounds of Rifaximin, I now get some kind of brain swelling and severe light sensitivity from it. It supposedly only stays in the gut so I have to think this must have to do with something inside my gut.

Anyway, this is somewhat different than your case, but I'll be really interested to see how you do with FMT. Please keep us updated. I think I'm going to try and do uBiome to see what comes up.

Thank you for your response. The gut microbiome is emerging as a significant etiology for a subset of patients in the literature. To my knowledge the test from Doctor's Data is a culture, so will only have looked at aerobic bacteria. uBiome is much better option. Use the link above for a 10% discount.

 

[jepps]

According to my report, the Gram-negative genus paraprevotella comprises 0.5% of total bacteria in the average gut. In my gut, paraprevotella comprises 12.5% of total bacteria. Very little is known about paraprevotella and it produces a number of "unknown fatty acids."

@Cheesus according to this study high paraprevotella correlates with spondylitis:

file:///C:/Users/EVA/Downloads/Microbiome%20call%20document.pdf

Prevotella produces indole (a key stone in tryptophan metabolism). Indole is well known, that it can cause rheumatoid arthritis.

Clostridium (member of the firmicutes) and some member of the actinos degrade indole. To build up firmicutes and actinos could help you, if you were vulnerable to arthritis.

Ankylosing spondylitis (AS) is an inflammatory condition that affects the joints in the spine. AS is part of a group of conditions known as spondyloarthritis; this group shares many of the same symptoms. The HLA-B27 allele has been linked to AS with approximately 90% of AS patients carrying this allele. A recent study using Lewis rats transgenic for HLA-B27 and human β2-microglobulin demonstrated differences in the caecal microbiota in comparison to wild-type Lewis rats. Bacteroides vulgatus and Paraprevotella were abundant in transgenic rat caeca (Lin et al., 2014).

In addition to this unusual overgrowth was a marked lack of diversity. Two genera, bacteroides and paraprevotella, account for ~70% of total bacteria. Furthermore my PCR did not detect any lactobacilli, bifidobacteria, escherichia, butyrivibrio, veillonella, streptococcus, peptococcus or even prevotella. There are possibly other genera absent that I am not familiar with. The test is sensitive to genera accounting for >0.01%. My gut is radically different to both patients and controls in existing research on the gut microbiome in CFS/ME.

I have a CFS-friend with this Ubiome-test-result: firmicutes and bacteroides relatively normal (about 59 % to 40 %, very low actinos, very low proteos. She responded very well to pre- and prebiotics. After starting the methylation supps (active B12 and B9, she took higher dosages) she had severe inflammation, she stopped the methylation supps. Inflammation did not stop, and the next Ubiome test showed 85% bacteroides, 14 % firmicutes. She went to a FMT-clinic. The doctor told her, that it´s not so easy. There are certain conditions, that respond well to FMT (C. diff., colitis ulcerosa). But other conditions like MS, morbus crohn (where the small intestine is inflamed, too) tend to respond with much more inflammation. Chris Kresser describes the pros and contras here.

My friend could not tolerate any prebiotics with the high bacteroides. She took high dosages probiotics (several kinds), and the latest Ubiome-test show, that firmicutes are on the rise, and also inflammation decreases, my friend ist better.

Now she will start with GOS, and with time build up more prebiotics, and then start again with tiny tiny dosages of methylation supps.

I hope, this helps. But if you are sceptic against FMT: bacterial shift with diet is possible, too.

Best regards, jepps

 

[Cheesus]

@jepps

Thanks for the response. I've had a lot of inflammation while on the methylation protocol, but fortunately I started low and went really slow. I'm 2 months in and not up to the full dose yet.

I saw a small trial of FMT in ME which was quite successful. It's a long way down the road yet though as I am completely bedridden.

I've seen a study suggesting paraprevotella links to RA, so you must be right about indole. I've had joint pain since doing methylation but never before that. My clostridia do not seem to be doing too badly which could be because of plentiful indole.

If you put paraprevotella into pubmed you only get 7 hits, and most of those aren't really about paraprevotella. You get a few more on google scholar as you get high paraprevotela in the hindgut of ruminants. If all else fails maybe I can just go live in a barn.

 

[Cheesus]

@alicec

I have attached the complete profile of my gut. You'll notice phascolarctobacterium is elevated. This is a response to high paraprevotella as it produces succinate and phascolarctobacterium ferments only succinate. Interestingly a NutrEval test showed I have no succinate in my blood, which is very suspicious (succinate is a key player in the Krebs cycle). I wonder if this is an autoimmune component.

The genera you mentioned seem to be significantly depleted! It's quite incredible I have no GI symptoms.

 

[Cheesus]

@PDXhausted

I just noticed you mentioned you had elevated liver enzymes. The gut microbiome is popping up time and again in the hepatology literature as a cause of liver disease. The pieces of the puzzle are falling into place!

 

[PDXhausted]

@Cheesus have you ever tried taking a binder like charcoal or clay? I'm curious if that would help you feel better by binding out bacterial toxin.

For my case, whatever toxin and/or immune complex is clogging up my liver and system, I was able to bind out with charcoal and it gave me some relief.

Binders are something to be careful with though- they can be constipating and for whatever reason seemed to allow bacterial overgrowth in my upper gut after taking daily for about 3-4 months. If I could do it over, I would have done the charcoal like every other day or one week on, one off, or something like that. The gains were worth it in my case, but I'm still not 100% sure what exactly I have.

 

[Sushi]

My plan is to have a Fecal Microbial Transplant at the Taymount Clinic, but I am not nearly well enough at the minute. I am seeing some green shoots of improvement 2 months into a methylation protocol after 18 months of no change.
What do you all think?

I had a huge Prevotella overgrowth. My doctor prescribed 7 day pulses of Xifaxin (first 7 days of the month for 3 months with strong probiotics the rest of the month). I also had no "gut symptoms," but all my other symptoms improved dramatically with Xifaxin. Not for everyone, but on my next microbiome test the prevotella was normal.

 

[IreneF]

I always tell people to try natto, but I don't think anyone else has used it. For one thing, you have to get it in a Japanese market, and for another, most non-Japanese think it tastes disgusting.

It's a gluey bean dish made by fermenting soybeans with a common soil bacterium, Bacillus subtilis ssp. natto, which is also present in the human gut. This bacillus has been used as a remedy for dysentary. Because it forms spores it survives digestion.

It's not a miracle food, but it might help.

Oh yeah--it contains a ton of vitamin K, and there is some evidence that it protects against osteoporosis.

 

[Gondwanaland]

I've also had foamy saliva and drooling when taking phosphatidylcholine.

PC can cause B2 deficiency

 

[alicec]

I was very tired when I posted last night so just wanted to convey the basics.

While I agree that FMT might be the best option for you, it doesn't mean I think there is nothing else you can do in the meantime, though being bedridden does make it very hard.

Straightaway I thought about Xifaxin. I have never used it myself and know little about it, but as @Sushi says it has been used very successfully for some cases of dysbiosis.

If you have a helpful doctor, it could be worth considering soon. It might even make the FMT redundant.

This leads to probiotics, since these are usually part of the Xifaxin schedule.

I have a lot of experience with VSL3 (now called VivoMixx), one of the most potent around. It's not going to colonise and turn your gut around (it doesn't have the right species among other things) but it can be helpful for two reasons. It can prevent something really nasty from taking up residence (a bit late for you now, but it could be important if you take Xifaxin) and it can stimulate your own immune system as it transits through your gut.

I took it consistently when I took very nasty antibiotics for a long time and when I had a uBiome test afterwards (unfortunately no before - that was before the test became available) I was pleasantly surprised that my gut wasn't in worse shape. It is not great I must say, but could be much worse.

I can't prove that VSL3 did the trick but I do know that some time later I got tired of taking the probiotic and stopped for a while. During that time, I had a massive overgrowth of Kluyvera, one of the gamma Proteobacteria (fortunately not one of the really nasty ones). Reintroduction of VSL3 soon got it under control.

Now I just take VSL3 every day, just in case!

As @jepps says, diet, prebiotics and probiotics can be very helpful. She and I are veterans of the long resistant starch thread which canvassed every prebiotic known to humankind I think (as well as various probiotics) and eventually petered out when there was little left to say. The experience of her friend being very sensitive to prebiotics was not uncommon. I was too. I just concentrated on what I could tolerate - probiotics and as wide a selection of prebiotic foods as possible. More recently I have had another go at concentrated prebiotics and find my tolerance has increased considerably. I have introduced a wide variety in small amounts - much like we experience with a varied diet, just boosted a bit. I am eagerly awaiting uBiome results to see what has happened.

I'll look at your results closely when I have time later.

There is a uBiome thread that may be of some interest.

 

[Cheesus]

I had a huge Prevotella overgrowth. My doctor prescribed 7 day pulses of Xifaxin (first 7 days of the month for 3 months with strong probiotics the rest of the month). I also had no "gut symptoms," but all my other symptoms improved dramatically with Xifaxin. Not for everyone, but on my next microbiome test the prevotella was normal.

I will definitely keep that option in mind. My real challenge is going to be finding a doctor to prescribe it, though I may be able to get a prescription online.

I have a catch 22 here that is pertinent to many of the responses I have just received. A psychiatrist gave me pregabalin 18 months back and it caused me strange auditory hallucinations (not voices). I stopped taking it when the penny dropped it was that (I was so dopey from it I barely knew what was happening), but the hallucinations have not gone away.

I tried taking some straight butyrate recently and the hallucinations immediately became absolutely horrendous. They were so loud I was being woken up at night by them and struggled to hear things. Probiotics also worsen the hallucinations no doubt due to the butyrate, but they do seem to now follow the fluctuations of my ME making me think they will get better as I do. The challenge is figuring out how to improve sufficiently for the brain injury caused by the pregabalin to heal prior to boosting butyrate. Methylation seems to help so maybe that will carry me far enough.

@IreneF
I quite like kefir, which is my fermented food of choice. I was thinking of trying water kefir and sauerkraut too. You don't manage to make natto sound very appealing

@alicec
Thanks for this info. The vsl is waiting for me I'm the fridge, along with some kefir. The problem is as outlined above: how can I heal my gut without worsening the damage caused by the pregabalin. I would just put up with the hallucinations if the probiotics immediately helped me feel better, but as they seem to worsen me whilst the methylation is helping it's a trade-off that doesn't seem to be worth making at the moment. I eat quite a lot of ferment able fibres from starchy veg like sweet potato, but I've been doing that for years. What do you think of trying the opposite method and starving everything out with something like SCD?

@PDXhausted
I was taking chlorella for quite a while and improved notably during that time. I then tried to increase the dose but it turned out more was definitely not better. For some reason I stopped taking it altogether after that. In hindsight the sensible option would have been just to decrease the dose! I can't remember why I did that.

I am concerned with charcoal and clay that I would prevent the uptake of nutrients. I will start on the chlorella again though as that doesn't seem to interfere with nutrition or supplements.

 

[PDXhausted]

@Cheesus that's great that the chlorella helped some-- it doesn't seem to do much for me, although I haven't stuck with it consistently enough probably. I think I will try it again.

Totally understand your concern about charcoal and you definitely need to do whatever is right for you. FWIW, in my personal experience I found that the toxic load ostensibly increased my need for vitamins more than the charcoal did. I.e. I felt much healthier and felt less of a need for vitamins while on the charcoal, whereas when I am off it my system is so overloaded trying to clear this junk out of my body that I feel more dependent on vitamins. I did my vitamins/supps in the morning and at lunch time, and the charcoal at night.

 

[brenda]

@Cheesus

Thanks for the link - I ordered a test today.

I had the Metametrix stool analysis done but it was 6 years ago so I don't know if it is worth mentioning the results, besides I am on one of the paleo diets so that will have changed things. I am not yet on probiotics but have been eating umboshi plums.

I would not take charcoal daily - I only take when I am herxing from Lyme or once a week otherwise.