I do not have a protocol. I do not have a treatment. I have a model of what causes CFS from which individual patients (with their medical professionals) must find their own path. I do post general suggestions, like my Updated Model and Treatment Suggestions. Some suggestions will work for many and be adverse to others. The model — a shift of bacteria — is in agreement with this. Your gut bacteria is unique before you got CFS/IBS/etc. How it shifts is also unique.

A lot of my suggestions are theoretical. This appears to be a good idea based upon available data. For example, taking an E.Coli probiotic because low or no E.Coli is seen consistently in the lab reports. Whether a specific E.Coli probiotic is right is one best answered by practical experience reported from people trying them. The two reports below both had problems with Symbioflor-2 (which is the easiest to obtain). Mutaflor (E.Coli Nissle 1917) and E.Coli Leve 1931 are two alternatives. E.Coli Leve 1931 is not sold as a living bacteria, but the metabolities from this bacteria (so no risk of taking up residence).

Your contribution to surveys help others and yourself. See this summary page with links to surveys.

A long term reader update report

Even though I have been out of touch I am still reading your blog and appreciating it greatly, and have shared it with others.

I wanted to give you another update….the last time I wrote you, I had just tried Symbioflor II, which really didn’t work for me, and I also asked you about how you defined “remission” and I followed your advice and got a really undemanding part-time temp job which lasted couple of months and which I enjoyed a lot but which let me know I didn’t have as much stamina as I thought I did because I got sick the first week in and then was back to sleeping whenever I wasn’t at work. There was also a lot of family upheaval ….

Anyway, all that is background to the fact that I am actually doing pretty well in many ways, much thanks to you, plus a couple of other things that I have started doing that seem to be shoring up my results. I would say that I am at 60 – 70 percent energy most days, with that being pretty steady. In other words, without the energy surges and crashes I used to have before I got sick. I’m not taking naps, and all in all I’d say I have enough energy to get by on except the one deficit I really still have is in drive and motivation and the ability to concentrate (I sort of think of those three combined as one thing)

Here’s what I am doing:

1. Using the CFS Remission model – I will send you a detailed list of what I am taking in a day or two. I made changes based on your suggestion that I alternate between Prescript Assist and Equilibrium, which worked well. I also tweaked my herbs based on the results of your reader survey, and added in D-Ribose at the suggestion of a friend with fibromyalgia (and then I saw that you had written about it though I somehow missed it).

2. I finally saw a naturopath in October who said the CFS/ME diagnosis was pretty obvious…She did look at my supplement list, though, and gave it the thumbs up. She also made some diet recommendations…What I noticed about food lists for me is that many of the foods were those I had already been avoiding from the histamine restricted diet. Also, I had noticed that I felt a lot better when I ate beef, which according to the BTD is probably the best source of protein for me. It also recommended against grain (which you have also) and dairy. So I just chose to interpret her recommendation primarily as keep avoiding histamines, keep eating beef, and cut out milk and most grains, and of course most sugar and that seems to be working for me. I would say it has made the difference between having steadier energy vs. surges and crashes, which I was still having up until I started eating this way. I have also lost a little bit of weight, which I am happy about though I wasn’t really trying to do that.

3. I have gradually started exercising again. As you know it’s hard to exercise with CFS, not to mention contraindicated, so I had cut way back and was pretty inactive and deconditioned as a result of basically sleeping a whole year, and then when I got whooping cough you basically can’t exercise without triggering a fit that makes you feel like you are going to die. I literally once turned blue from doing the kind of yoga where you do nothing but lay on floor and breathe; it was terrifying. So despite the fact that exercise has always been my go-to for managing my depression, I was scared to start exercising again. I started with walking (since I have a dog) and using Audible, and I am enjoying it immensely, averaging about 8,000 steps a day, and sometimes a lot more – I got lost when I visited my husband (working away from home) and walked 11.5 miles and expected a crash afterwards, but none came. Yay! I have also started swimming twice a week (deliberately doing it *much* less strenuously and with less duration than I used to, because I think over-swimming was part of what triggered my CFS or mono or whatever my initiating event was) and rather than having to nap after a workout I feel energized. I want to do yoga again but the turning blue scare is still holding me back a bit even though I know I am recovered from whooping cough…if my heath holds up I will ease my way into that too.

4. This is something that I haven’t mentioned before, I don’t think….I have had depression on an off since adolescence, sometimes acute, sometimes low-grade, and have been off and on antidepressants since my twenties. Most recently, I was on them for about 10 years, and at the time I got whooping cough I had three prescriptions going. While acutely ill with whooping cough, I was too sick to take them and thus went off them without intending to. I didn’t want to start them again without talking to my prescriber, but, meanwhile, between the herbs and probiotics etc., which I did restart when I was able,  my mood problems diminished drastically. I never did go see my prescriber and now have been off for almost a year, and feel better than I did when I was taking the meds (even though they helped and I am not an anti-med person at all). Often, if I go through a patch of getting tearful easily, adding in or increasing the Miyarisan takes care of it within 24 hours.

Anyhow….I wanted to let you know I am still around and still “working the program” and very grateful to you.

Happy Thanksgiving!!

 

Another Reader

I found your post today very interesting. I took Symbioflor 2 in February and unlike
your other reader has a dreadful reaction – very bad burning throughout my entire digestion
system. It made a bad situation even worse and I have not yet recovered. This would tally
with the significant survival time of the bacteria.

On a different note, as I mentioned I am currently in the middle of a very bad
period of digestion pain. So in desperation I tried my remaining Prescript Assist.
I find they only have an effect if taken at 2 or 3 times the dose.

2 days later I can feel my bowel inflammation lower

Comment: The remedy for adverse reaction to E.Coli probiotic is to take Lactobacillus probiotics. These suppresses E.Coli.   Lactobaccillus Gasseri is the preferred one.

I have intentionally avoid dealing with prebiotics in the past. Instead, I have advocated ‘raw appropriate seasonal food’. The microbiome has evolved with seasons, and having fresh strawberries or blueberries in January may contribute to microbiome dysfunctions (speculation). A reader forwarded a study that changed my perspective because the results of one specific prebiotic was very desirable!

• “To explain why some E. coli mutants do not grow as well on mucus in vitro as their wild type parents yet are better colonizers, we postulate that each one resides in a distinct “Restaurant” where it is served different nutrients because it interacts physically and metabolically with different species of anaerobes.” [2015]
• “When E. coli Nissle 1917 is the only E. coli strain in the streptomycin-treated mouse intestine, it appears to use arabinose, fucose, galactose, gluconate, mannose, N-acetylgalactosamine, and sialic acid to colonize (Table 2 and (58)). In contrast, E. coli Nissle 1917 does not appear to use ribose to colonize (Table 2).” [2015]
  • Dr Myhill states the same here and advises “Eat figs, hazelnuts, chickpeas!”

Below is what I could find on various types of prebiotics. For example, for mannan oligosaccharide – I could not find any suitable studies.

For most prebiotics, the results were less than ideal – increasing Bifidobacterium with a decrease of other bacteria.

Xylooligosaccharides and/or Pectin

“Purified xylooligosaccharides from Miscanthus × giganteus (M×G XOS) were used in an in vitro fermentation experiment inoculated with human fecal microbiota. A commercial XOS product and pectin were used as controls. Decreases in pH by 2.3, 2.4, and 2.0 units and production of short-chain fatty acids (SCFA; acetic acid, 7764.2, 6664.1, and 6387.9 μmol/g; propionic acid, 1006.7, 1089.5, and 661.5 μmol/g; and butyric acid, 955.5, 1252.9, and 917.7 μmol/g) were observed in M×G XOS, commercial XOS, and pectin medium after 12 h of fermentation, respectively. Titers of Bifidobacterium spp., Lactobacillus spp., and Escherichia coli increased when fed all three substrates as monitored by qPCR.” [2016]

Pectin is from fruit. Apple Pectin capsules are available from Now, Solgar etc. or buy in bulk and make your own capsules ($15 for 2 lbs on Amazon)

One source of Xylooligosaccharides.

Fructooligosaccharides (FOS)

“Fructooligosaccharides (FOS) are one of the most studied prebiotics, selectively stimulating the growth of health-promoting bacteria in the host. However, there is increasing evidence that commensal gut bacteria, such as Bacteroides fragilis, Clostridium butyricum, Enterobacter cloacae, and even the pathogenic Escherichia coli BEN2908, are also able to metabolize FOS in vitro, and in some cases, FOS displayed adverse effects.” [2015]

Inulin

“By stimulating bifidobacteria, …. These potential beneficial effects have been largely studied in animals but have not really been proven in humans.”[1999]

“All inulin-type prebiotics are bifidogenic – stimulating the growth of Bifidobacteria species. The effects they have on other gut organisms are less consistent….intra-individual response to an identical dose of the same inulin-type prebiotic, in terms of stimulation of total number of Bifidobacteria and individual Bifidobacteria species, can be variable.” [2008]

• Inulin is typically made from chicory.

Galactooligosaccharides and Maltodextrins.

“a higher proportion of bifidobacteria (25.77%) was seen in the total bacterial population after cultivation on a prebiotic mixture than on the control medium (7.94%). The gram-negative anaerobe count significantly decreased …and the Escherichia coli count decreased” [2015]

“the galacto-oligosaccharide product was more bifidogenic(… much of this growth was attributed to growth of B. longum. …)  and potent in inhibiting E. coli than the other products tested.” [2014]

Almonds and Almond skins

“Significant increases in the populations of Bifidobacterium spp. and Lactobacillus spp. were observed in fecal samples as a consequence of almond or almond skin supplementation. However, the populations of Escherichia coli did not change significantly,” [2014]

 

The uniqueness of each person’s microbiome means that some probiotics may take up residency in one person and not the other. If the probiotic comes from a fish or an algae, it is unlikely that a compatible support community of friendly bacteria will be found in a human. Below are studies finding that a probiotic took up residency in at least some people in a study. Residency is defined as being found 7 days after last administration. The studies must be on humans.

• Enterogermina – Four Bacillus clausii Strains
  • “Bacillus clausii was found alive in faeces for up to 12 days. In some volunteers, the recovered amount of OC, NR or SIN was higher than the number of administered spores.” [2015]
• Symbioflor®2
  • “Stool analysis showed that the probiotic E. coli had colonised all five persons for a period of 10 to 30 weeks (mean: 18.7 weeks, median: 25.7 weeks). In two individuals there was evidence of competition between host E. coli and probiotic E. coli, while in two others total E. coli levels increased persistently with at least a factor of 10 as a result of the received dose.” [2014]
• Probiotic preparation inVag(®) – women only
  • “Molecular typing revealed the presence of Lactobacillus strains originating from inVag in 82% of women taking the drug at visit III (21 days), and 47.5% at visit IV. (28 days)” [2015]
  • “opical application of an ointment containing Lactobacillus gasseri LN40, L. fermentum LN99 and L. rhamnosus LN113…Topical application of a probiotic ointment is feasible to achieve persistence of lactobacilli for at least 10 days.” [2016]
• Lactobacillus rhamnosus GG (Culturelle)
  • “GG was also recovered in the faecal sample taken at the start of the intervention and at the time of the tissue sample collection, which indicates more persistent adherence of the probiotic” [2013]
• L. rhamnosus CNCM I-4036 (Human origin)
  • “was identified after the intervention (t₂) in fecal samples of volunteers that received this bacterial strain. This finding does not necessarily imply successful colonization but rather persistence of the strain at this time period. Detection of L. rhamnosus CNCM I-4036 for a much longer period would be needed to determine whether the strain does in fact colonize the gastrointestinal tract. [2013]
• Lactobacillus rhamnosus (573L/1-3)
  • ” The examined strains were detected in 37/46 (80.43%) patients after 5 days and in 19/46 (41.3%) patients after 14 days since the start of the treatment. L. rhamnosus 573L/1 strain colonised the G.I. tract more persistently.” [2006]
• L. plantarum  MF1298, DC13 (But not MF1291)
  • ” MF1298 and DC13 persisted in the same volunteer after ended intake, suggesting host-specific persistence behaviour.” [2006]

Does not Persist

• “Lactobacillus casei strain Shirota (Yakult) was undetectable with culture after 2 weeks of ceasing its consumption.” [2013]
• VSL#3
  • “Streptococcal population was detected after 3 days of administration and persisted for 6 days after the treatment suspension.” [2003] — did not make it to 7 days.

And the rest…

Assuming they do not take up residency is usually correct unless then are human sourced.

I think the easiest way to start a discussion is to look at what is in Swanson Ultra Dynamic Balance Blend Soil-Based Organisms.

What! Those are “normal” probiotics!  What is going on???? If you go over to Primal Defence probiotics you see a similar list of probiotics with the comment “homeostatic soil organisms”.

The harsh reality is that most probiotics are obtained from non-human sources. A few life Mutaflor (E.Coli Nissle 1917), Colibiogen (E.Coli Laves 1931)  and BioGala L. Reuteri come from a human sources. If the manufacturer does not clearly state that it is human sourced,  it is soil, animal, marine or some other environment source. There is a big marketing value to have a human source.

The diagram below shows the various strains for L.Reuteri. Note that almost all of the human L.Reuteri produces histamine — other species do not.

Why is the source important? Bacteria is like blood transfusion or organ transplants — foreigners will be rejected. For a commercial probiotic company — that makes economical sense! You want the customer to keep coming back. In reading many PubMed articles, I found that detecting any of a probiotic in stools after a week of consumption is a challenge resulting is different types of protection around the probiotic — while a suitable probiotic in water (Symbioflor-2) had no problem surviving (and taking up long term residence).

You can usually assume that 99% of probiotics that you buy are not from human sources. Most safety studies that I have seen filed with the FDA or EU’s equivalent, emphasis that the probiotic does not take up residence.

What is the use of taking probiotics then?

While these foreign bacteria are in your system, they are producing chemicals (metabolites) that favor your own missing bacteria reviving. This is the rationalize for  Colibiogen (E.Coli Laves 1931). The problem is that there are a large number of cross supporting interactions between both the good and the bad bacteria. It  unlikely that a single strain of any bacteria will be successful in correcting matters. A single strain may cause a dramatic result, but it’s ability to persist is fragile.

What can happen is a change, a new cross-supporting population – as illustrated by this report:

• “Re-colonization of E. faecium after simultaneous probiotic plus vancomycin intake occurs mainly with strains without close genetic relationship to the strains harboured before treatment or to the ingested E. faecium strain.” [2002]

A reader wrote:

Hi Ken i Have report after using Symbioflor-2

I took it for nearly one and half week. Changes were awesome, colour of stool changed from yellow and loose(which I guess is from lactate excess) to well formed and brown. My sleep change from very little and disturbed to quiet and deep sleep

It looks like that the E.coli could be displacing the Enterococcus. I toke 20 drops, 3 times at day (with GOS and Fucoidan)

I stopped it for 4 days, and symptoms came back (even more aggressive)… I guess because bacterial resistance?. My point now is to get fucose (looks like fucoidan powder doesn’t have in it) to get the E.coli established after a period of several weeks.

I eat carbs with my meals(which is sued as fuel for lactate) and quite high amounts of GHEE (maybe overloading lactic acid as well)

I think that the only way to get E.coli stablished for sure is to feed it in high amounts. D-ribose, Fucose and Galactose (Gos prebiotic, Ribose and seaweed?).. What points more would you mark to proper feed this e.coli (i guess also the time of feeding and taking it matters).

I look at the above report in several ways:

1. Probiotics can do a dynamic change of symptoms
2. Establishing a persistent change is the challenge

So what would be some suggestions for this reader? First, we appear to have a bad enterococcus overgrowth according to the report. This post looks at this specific issue: vancomycin antibiotic is one route, or non-prescription monolaurin and/or neem (Azadirachta indica) would be suggested before trying E.Coli probiotic again.  Possibly between these, taking some Bioflorin – Enterococcus faecium SF 68 ( NCIMB10415)  probiotics in the hope that it would out complete the bad enterococcus. Another enterococcus probiotic Enterococcus faecalis TH10 is available in Dr.Ohhira’s Probiotics Original Formula. This probiotic is reviewed on John Brisson’s site “Fix  Your Gut”

Dr. Ohhita’s probiotics contain:
• Bifidobacterium breve ss. breve
• Bifidobacterium infantis ss. infantis
• Bifidobacterium longum
• Enterococcus faecalis TH10
• Lactobacillus brevis
• Lactobacillus acidophilus
• Lactobacillus bulgaricus
• Lactobacillus casei ss. casei
• Lactobacillus fermentum
• Lactobacillus helveticus ss. jagurti
• Lactobacillus plantarum
• Streptococcus thermophilus

This is not recommended for long term use because of the Lactobacillus in it — but it may be useful for clearing out the bad enterococcus.

Bottom Line

“Snogging healthy young humans” may actually be the best way of getting bacteria that may persist into you! If you are married, that creates problems….

In my next post I will be digging thru PubMed to identify which probiotics are known to take up some residence (i.e. detectable after 7 or more days).

 

Update:

• “B. subtilis and CEBS supplementation caused a significant increase in the numbers of Lactobacillus and Bifidobacterium in the caecum, whereas the numbers of Escherichia coli and Staphylococcus decreased significantly compared with the control.” [2016]

Bacillus probiotics are now in my “use with caution” list.

ImmunoIn a recent post I suggested MegaSporeBiotic because it is full of different bacillus species [but only if you do not have histamine issues]. A reader pointed me at John Brisson’s blog on megaspore. He raises a valid question in his post “Why I Do Not Recommend MegaSporeBiotic or My Issues With Bacillus licheniformis”.

I reviewed this in a year ago with a do not take if you have histamine issues.

A reader tried it for two weeks and reported:

I will not be trying them again.

The Bacillus licheniformis strain is not identified nor it’s safety is unknown. John writes:

“Bacillus licheniformis is one of the worst offending soil based “probiotics” and is known to cause food poisoning, ⁸ septicemia, ^{9 10 11} peritonitis, ¹² and ophthalmitis. ¹³ Bacillus licheniformis is not native human flora but appears to be native flora in birds. ¹⁴ Bacillus licheniformis is a ubiquitous organism and likely enters the human digestive system many times a day. While data regarding its ability to survive in the human gastrointestinal tract is sparse, it is likely that the spores pass without activating. ^15“

John was kind enough to send me a followup draft. The manufacturer has launched a different version, Just Thrice, unfortunately it contains histamine producers still. A reader forwarded me a link to a Crohn’s Disease targeted probiot, Perfect Pass, which I have also added to the table below.

	Histamines Producers	Just Thrive	MegaSpore Biotic	Perfect Pass	Restorflora	Prescript Assist	Enterogermina
Bacillus Indicus HU36 Human sourced		X	X
Bacillus Coagulans	X	X	X	X
Bacillus Clausii		X	X	X	X		X
Bacillus Subtilis	X
Bacillus Subtilis HU58 Human Sourced		X	X	X	X	X
Bacillus Licheniformis	X		X
Bacillus Brevis	unknown					X
Bacillus Marcerans	unknown					X
Bacillus Pumilus	weak [2009]					X
Bacillus Polymyxa	unknown					X
Saccharomyces Boulardii	?????				X

As a FYI, Bacillus Indicus HU36 was obtained from the ocean [2015] but marketing literature cites human source. While Bacillus Subtilis HU58 was from humans  [2012].  Enterogermina contains 4 strains of Bacillus Clausii only.

Immunosuppressed Patients

A reader wrote “Is it true that bacillus coagulans should not be taken by individuals immunosuppressed? I wanted to start with this probiotic for my child with ankylosing spondylitis and as you are taking immunomodulating wouldn’t know if its status would be compromised.”

I cannot give medical advise, I can provide education on what has been published else where (and the reader and their knowledgeable medical profession can draw their own conclusion).

• Nothing found searching for immunosuppress bacillus on PubMed
• A 1998 study on rare bacillus infections (not from taking probiotics) states: “Moreover, our finding of six B. cereus, three B. licheniformis, and two B. pumilus infections [in cancer patients] suggests that these species may be more pathogenic in immunosuppressed hosts than are other common species, such as B. subtilis or B. megaterium. ” [1987]
  • “Two cases of Bacillus cereus meningitis in immunocompromised children [in cancer patients] at our hospital within a 2-month period prompted us to review B. cereus-related invasive disease.” [2001], again — not from probiotics
• “Despite the widespread distribution of Bacillus organisms they are rarely implicated with actual infections and are more frequently isolated as a culture contaminant.” [Antimicrobe.org]
• “Live combined Bacillus subtilis and Enterococcus faecium ameliorate murine experimental colitis by immunosuppression manifested by downregulation of TLRs, macrophages, Th1, and Th2 but upregulation of Tregs.” [2014] So it appears to actually helps!
• Recurrent septicemia in an immunocompromised patient due to probiotic strains of Bacillus subtilis [1998]. [Full Text] Patient was “73-year-old male with chronic lymphocytic leukemia”
  • “We conclude that, even if the septicemia due to the probiotic strains of B. subtilis could not be related directly to the patient’s death, high numbers of viable microorganisms (especially if polyantibiotic resistant) should not be given to any patient with severe immunodeficiency.”
  • Probiotic was “. Each dose contains a mixture of 10⁹ spores of four distinct antibiotic-resistant derivatives of ATCC 9799 (Enterogermina; distributed by Sanofi Winthrop, Milan, Italy) (1, 4) per vial.”
  • “Moreover, probiotic products containing Bacillus species have been in the market for at least 50 years with the Italian product known as Enterogermina® registered in 1958 in Italy as an OTC medicinal supplement (Cutting, 2011). ” [2012]

So we have had one death reported associated with this in almost 60 years of OTC use.

Lactobacillus bacteremia (Lactobacillus infection) was found, very often — most of the reports below are within the last year! [80 reports for Lactobacillus bacteremia probiotic vs 5 for bacillus bacteremia probiotic ]

• “LB was observed in 38 patients (0.34% of all positive blood cultures). Cancer (40%), immunosuppression (37%), and use of central venous devices (29%) were frequently associated with LB.” [2017]
• Liver abscess and bacteremia caused by lactobacillus: role of probiotics? Case report and review of the literature [2016].
• Remote transient Lactobacillus animalis bacteremia causing prosthetic hip joint infection: a case report [2016].
• The potential risks of probiotics among HIV-infected persons: Bacteraemia due to Lactobacillus acidophilus and review of the literature [2016].
• Incidence and outcomes of bloodstream infections among hematopoietic cell transplant recipients from species commonly reported to be in over-the-counter probiotic formulations[2016].
• Importance of Molecular Methods to Determine Whether a Probiotic is the Source of LactobacillusBacteremia [2016].

If you want to play it safe, then definitely no yogurt or any fermented foods of any type. IMHO, the apparent risk is very very small.

Bottom Line

John raises valid questions about safety with the assumption of no major illnesses [Future link to his updated post will be here]. In dealing with patients with CFS, we have two major choices

• Avoid — and just accept CFS indefinitely
• Try — knowing that there is likely a low risk of the issues that he is concerned about, and a major risk of a beneficial shift and thus improvement.
  • If there is a concern or adverse effect, then stop
  • Ideally, use a lower risk item if available and the cost is acceptable, for example Enterogermina