A SIBO patient shared with me their uBiome results. Before I look at them I will state a question that I have:

• Is SIBO substantially the same dysfunction but the person’s DNA can handle it without CFS or FM symptoms? We know that many symptoms are associated with specific SNP for both syndromes….

Patient Background

“After a bad case of food poisoning, I ended up with SIBO. The food poisoning was from campylobacter which produces the cdtb toxin…In my case of SIBO, it was caused by an autoimmune response. Taking probiotics triggers SIBO symptoms but I know I need to fix this imbalance. I would love to hear your thoughts or you can wait until I get my second results (unless you have some probiotics to try before retesting).”

Basic Criteria for CFS/FM

Lowish  E.Coli

• Not directly reported, but it parent is: Enterobacteriaceae  which is 13% of the reference group

What seems different from the usual CFS profile is that the Firmicutes/Bacteroidetes ration is effectively normal — a significant difference.

• Diversity: 59%ile – usually CFS is very high (95+%ile)

Overgrowth of Bacteria Genus

My criteria is to look at only those that are 1.5x or higher. We have only 2, a lot less than those seen in CFS/FM.

Rare Bacteria

Analysis of Over Growth

As usual, I head to datapunk.net to speed analysis (and allow folks to check or extend my research).

1. Dielma (genus)
2. Erysipelatoclostridium (genus)
3. Slackia (genus)  – no info
4. Holdemania (genus) 
5. Anaerotruncus (genus) 
6. Flavonifractor (genus) 
7. Blautia (genus)  High
8. Salmonella (genus) Rare
9. Vagococcus (genus) Rare
10. Delftia (genus)  Rare no info
11. Citrobacter (genus) Rare

The numbers above are used below

NUTRIENTS/ SUBSTRATES

• D-Glucose – 4, 6, 9
• L-Lysine – 8
• Iron supplements  – 8,11
• Acetoin – 8, 11
• L-Tryptophan – 5

INHIBITED BY

• Flaxseed – 1,2, 4, 7
• Walnuts – 5, 7
• Curcuma longa – 8
• Aloe vera – 8
• Plantain bananas – 8
• Garlic (allicin) – 8
• Pomegranate ellagitannins –  8, 11
• Sarcodiotheca gaudichaudii (red seaweed) – 8
• Hyocyamine – 8
• Butyrate -5
• Acetic acid – 5
• Proton-pump inhibitors  – 4

ENHANCED BY

• Partial Sleep Deprivation  – 1,2, 4
• Aspartame – 11
• Berberine – 7
• Cholic acid – 7
• Resistant starch (type IV) -7
• Walnuts – 5, 7
• Resistant starch (type II) -7
• Saccharomyces boulardii  – 7
• Gallate – 5
• Chemotherapy – 4

INHIBITS

• Bifidobacterium –  1, 4, 5, 7, 8, 11

Bottom-Line

This SIBO person has a uBiome very close to CFS/FM patients but with one, possibly critical, difference: Firmicutes/Bacteroidetes is normal. Also the diversity is normal.

While this is a single uBiome from SIBO without CFS, it suggests that the transition from SIBO to CFS may be caused by the Firmicutes/Bacteroidetes being lost; with this lost the equilibrium is gone and a ton of other bacteria genus can move in — pushing diversity to the top.

Suggestions for the patient to discuss with their medical professional:

• Having flaxseed with porridge daily
• Taking butyrate supplements, possibly taking the Miyarisan (Clostridium butyricum) probiotic.
• The Partial Sleep Deprivation suggests melatonin supplements
• I would not recommend Proton-pump inhibitors because so many of the bacteria seen in CFS are enhanced with PPIs.
• Reducing glucose in the diet. This is a specific type of sugar — regular sugar is converted to glucose which makes these high bacteria dependent on other bacteria. Having glucose in foods eliminates this dependency and allows more rapid growth.
  • This means going to NutritionData.Self.com listing high glucose foods and reducing them.  This is not a low sugar diet suggestion, but a low glucose diet (a specific type of sugar).

Probiotics:  I would suggest trying at least one from each of the following two groups, I suspect the patients have done just the usual lactobacillus ones.

• Soil Based Organisms
  • General Biotic Equilibrium
  • Prescript Assist
• E-Coli Probiotics
  • Mutaflor
  • Symbioflor-2

As always — for educational purpose only.

Hypothesis

SIBO is the lost of Bifido, Lactobacillus, E.Coli without a loss of the Firmicutes/Bacteroidetes balance and without the blossoming of additional species (i.e. normal diversity)

CFS is the lost of Bifido, Lactobacillus, E.Coli with a loss of the Firmicutes/Bacteroidetes balance and with the blossoming of additional species (i.e. high diversity)

Metronidazole/Flagyl is reported to have 75% of CFS patients improving according to some surveys. I was asked what is the best dosage…  that is for your MD to determine.

See this post to understand how it may be helping CFS — probably not how you think!.

MDs are busy people and often do not have time to check the recent literature. I’m busy too, but made time for this. My results (for educational purposes) are below

• Metronidazole relieves symptoms in irritable bowel syndrome: the confusion with so-called ‘chronic amebiasis'[1997].
  • metronidazole (400 mg tid X 10 days)
• Systematic review and meta-analysis: triple therapy combining a proton-pump inhibitor, amoxicillin and metronidazole for Helicobacter pylori first-line treatment[2016].
  • “Use of 14 day, thrice daily and high-metronidazole-dose PAM treatments markedly increased the cure rate.”
• Secnidazole Treatment of Bacterial Vaginosis: A Randomized Controlled Trial [2017].
  • Secnidzaole is a variation of metronidazole. 2 grams/day performed better than 1 gram/day
• Improving malodour management in advanced cancer: a 10-year retrospective study of topical, oral and maintenance metronidazole.
  • “High-risk patients should start with 400 mg thrice daily ×7 days and continue 200 mg once daily.”
• Randomized, double-blind, comparative study of oral metronidazole and tinidazole in treatment of bacterial vaginosis [2016].
  • “tablet metronidazole 500 mg twice daily for 5 days”
• Variability in Antibiotic Regimens for Surgical Necrotizing Enterocolitis Highlights the Need for New Guidelines.
  • ” The most common pre-operative regimen was … metronidazole for 14 d.  The most common post-operative regimen was … and metronidazole for two days. No regimen or duration proved superior.”

From Drugs.com with more details on Medscape.

Do any MDs use it for CFS?

There are no dosage studies or guidance for CFS/ME. From the above, I would conclude the following as a reasonable plan:

• 400-500 mg three times a day for 14 days, followed by 200 mg/daily for at least 2 months.

NOTE: this applies to other antibiotics also
“Metronidazole can have cerebellar toxicity that manifests clinically with varying degrees of limb and gait ataxia and dysarthria (Table 2). Symptoms are accompanied by characteristic T2 high signal lesions on brain MRI in the cerebellum and brainstem. Neurotoxicity was seen after prolonged use of metronidazole with clinical symptoms resolving within 3–7 days of discontinuation of the medication, while follow-up MRIs also show resolution of cerebellar lesions [111]. While the precise mechanism for neurotoxicity is not entirely clear, one hypothesis is that it occurs via axonal swelling secondary to metronidazole-induced vasogenic oedema [112]. Peripheral neuropathy is another recognized potentially neurotoxic effect with use of metronidazole. One report describes a 53-year-old who developed encephalopathy, dysarthria, ataxia and a length-dependent peripheral neuropathy in the context of prolonged metronidazole therapy (a cumulative dose of 146 g over 88 days). Multiple skin biopsies confirmed evidence of a small fibre sensory neuropathy [113]. In another case reporting the rapid development of peripheral neuropathy related to metronidazole with electrophysiologic studies demonstrating prolonged distal motor latencies, mildly decreased compound muscle action potential and decreased sensory nerve action potentials involving the posterior tibial and peroneal nerves to varying degrees were noted [114]. Optic neuropathy, as well as autonomic neuropathy, have also been described in association with metronidazole use [115, 116]. Other neurological adverse effects ascribed to metronidazole include dizziness, headache and confusion [117].” 2011

Again, not medical advise, just a summary of the literature and conclusions from the literature for educational purposes. Applicability to individuals need to be done by a qualified medical professional who knows your medical history.

A reader wrote with some specific questions and shared her BioScreen report. I will first do my standard review and then address the questions. Remember, I am not a medical professional — more a librarian who knows how to lookup things, read things (ex-technical writer) and apply logic.

Basics Criteria

And as usual, their automated comments on each, for example:

• Low E.coli – as expected
• Low Lactobacillus – as expected
• Normal Bifidobacteria — BUT only one species.. i.e. all of the other species are missing!

Analysis of Over Growth

As usual, I head to datapunk.net to speed analysis (and allow folks to check or extend my research).

1. Bifidobacterium pseudocatenulatum (species) Note: I deem this to be an overgrowth, because it is the only bifidobacterium!
2. Streptococcus parasanguinis (species) 
3. Collinsella aerofaciens (species) 
4. Propionibacterium acnes (species)  I included this because it was there with no reference levels — i.e. unexpected growth!

Note: [Parent] below indicates that it applies to bifidobacterium and not this specific species (which we know nothing specific about)

NUTRIENTS/ SUBSTRATES

• Ellagic acid [parent]  -1
• D-Glucose [parent]  -1, 2, 3
• Raffinose [parent]  -1
• Stachyose (soy oligosaccharide) [parent]  -1
• Lecithin – 4

INHIBITED BY

• Laminaria hyperborea (curvie) [parent]  -1
• Chemotherapy [parent]  -1
• Magnesium-deficient diet [parent]  -1
• Low carbohydrate diet [parent]  -1
• Glyphosphate [parent]  -1
• High fat diet [parent]  -1
• Ascophyllum nodosum (rockweed) [parent]  -1
• Berberine [parent]  -1
• Sucralose (Splenda) [parent]  -1
• Low FODMAP diet [parent]  -1
• Thyme oil -2
• Peppermint oil -2
• Lemongrass oil -2
• Navy bean (Cooked) -2, 3
• Garlic (allicin) -2
• Resistant starch (type IV) -2
• Cinnamon bark oil -2
• Aloe vera -2
• Stevia -2
• Hyocyamine -2
• Berberine -2
• Stigmastanol -3
• β-sitosterol -3 

ENHANCED BY

• Proton-pump inhibitors (PPI) -2
• Sesame cake/meal [parent]  -1
• Almonds/ almond skins [parent]  -1
• Jerusalem artichoke [parent]  -1
• Green tea [parent]  -1
• Red wine [parent]  -1
• Navy bean (Cooked) [parent]  -1
• Fructo-oligosaccharides [parent]  -1
• Chicory [parent]  -1
• Resistant starch (type III) [parent]  -1
• Magnesium [parent]  -1
• Arabinoxylans [parent]  -1
• Chondrus crispus (red seaweed) [parent] -1
• Inulin [parent] -1
• Daesiho-tang (DSHT) [parent] -1
• Resveratrol [parent] -1

INHIBITS

• Bifidobacterium -1, 2, 3

Questions and attempted answers

Q:  My main overgrowth is Streptococcus Parasanguinis, I believe this lives in the mouth and is normally killed by the stomach acid. Does this automatically mean that  I have low stomach acid, and if so, this problem can not be repaired until the stomach acid issue it cleared. Or could it be that the strain I have has somehow adapted to with stand the acid in the stomach. I have also read somewhere that people with CFS can not produce enough stomach acid due to the high amount of energy required to do so, what are your thoughts. Is this strain of Strep overgrowth common?

A: DataPunk cites ” The presence of S. parasanguinis in the oral cavity is associated with a healthy microflora. Identified as a constituent of the oral microbiome by Human Oral Microbiome Database. Identified as constituent of vaginal microbiome. [PMID:23282177]”

There are a large number of potential cooking items listed above that should suppress it in the gut. These include:

• Thyme oil
• Peppermint oil
• Lemongrass oil
• Navy bean (Cooked) 
• Garlic (allicin) 
• Cinnamon bark oil
• Aloe vera
• Stevia

Q: Do you recommend antibiotics, rather than herbs for my situation, if so which ones.

A: I always prefer non-antibiotics as the first choice. Antibiotics tend to have cascading side effects (‘casting out a demon from the house, and a dozen more takes it place’ syndrome). If you go the antibiotic route — make sure that you are not given an antibiotic that worked when your MD went to Medical School and is ineffectual now (See this search)

Q:  I also have a parasite (Blastocystis) which I believe this is very difficult to get rid off and requires multiple antibiotics. My thoughts are to ignore this for now until the bacteria is in a better place and then readdress it. What would your advise be?

A: I checked PubMed and found some studies of interest

• In vivo antiprotozoan effects of garlic (Allium sativum) and ginger (Zingiber officinale) extracts on experimentally infected mice with Blastocystis spp[2015].
  • “We conclude that using ginger and garlic for treatment of blastocystosis is beneficial.”
• In vitro effect of some Egyptian herbal extracts against Blastocystis hominis [2015].
  • Ginger treatment significantly (P < 0.002) lowered the number of the parasite after 48 hr. (mean, 335 ± 7.07)/ml.
  • Moreover, garlic treatment also significantly (P < 0.002) lowered the number of the parasite after 48 hr. (mean, 382.5 ± 10.60)/ml.
  • The reduction rates after 48 hr. in these treated samples compared to phosphate buffered saline were 92.98% and 92.44% respectively.
  • However, onion, and turmeric treatments insignificantly lowered the number of the parasite after 48 hr. (P < 0.15 & < 0.22 respectively).
  • You may wish to read “Blastocystis: how do specific diets and human gut microbiota affect its development and pathogenicity? [2017]” [Full Text]

Q:  I have had a bad herx from Prescription assist (dizziness, spaciness, bloating) however by the time I finished the 1st bottle I as able to take two caps per day and was feeling much better (no herx.)

A: Thank you for sharing! A herx can happen — my two worst were from Mutaflor and Lactobacillus Fermentum ME-3. As with you, the herx disappeared and I felt a lot better afterwards!

Q: I have just started on symbio 2. I started on one drop and by day three was up to the standard dose as I had no herx & felt a huge improvement in all my symptoms and energy (the best I’ve felt for months). Can you confirm that we need to take both Symbio 2 and Mutaflor or just one or the other? 

A: My own opinion is that if there is not an economic issue, do both. Symbioflor-2 standard dose is much less than Mutaflor standard dose (which is why I like suggesting using Symbioflor-2 to start). They are different strains.

Q: . I took a low dose of thyme and rosemary oil as an antibiotic, Interestingly my blood pressure dropped and I experienced POTS. These are CFS symptoms I have not experience for a few years since I started drinking liquorice tea daily in order to increase my blood pressure (which it did). I  wonder if bacteria affects blood pressure and causes POTS which a very common symptom in CFS.

A: There is a recent article that may answer that question:
The Microbiome and Blood Pressure : Can Microbes Regulate Our Blood Pressure? [2017]  “Studies have described how dysbiosis may modulate blood pressure and contribute to CVD. ”

As always, consult with your knowledgeable medical professional before any changes — I do not know your medical history and not qualified to give medical advice. The above is educational only.

I had done a detail post on Saccharomyces boulardii in 2016 and concluded Do not explicitly take this probiotic. Looking at the overgrowth of several bacteria genus in uBiome samples from CFS patients, I keep finding this listed as enhancing the overgrowth bacteria.  Almost all of these overgrowth bacteria suppresses bifidobacteria and thus appear to contribute to keeping supporting the CFS microbiome state.

Molecular Monitoring of the Fecal Microbiota of Healthy Human Subjects during Administration of Lactulose and Saccharomyces boulardii [2006] found no impact on bifidobacteria but reading the study we read “”None of the subjects had a history of gastrointestinal or metabolic disease” as well as  “it cannot be excluded that subtle changes in less predominant species or groups of species may remain undetected by this approach.” On both of these grounds, their conclusions likely do not apply to dysfunction when rare bacteria take over; bacteria that are our overgrowth.

What should be considered as alternatives?

• Coconut oil /monolaurin Post
  • “we showed that adding coconut oil to the diet could become the first drug-free way to reduce Candida albicans in the gut.” [2015]
• Lactobacillus Fermentum Post
  • ““All Lactobacillus fermentum strains tested, namely LF5, LF09, LF10, and LF11, have the ability to significantly inhibit the growth of the five species of Candida of at least 4 logarithms (10000x). Furthermore, the best result obtained with miconazole on C. parapsilosis is still 2 logarithms lower.(100)” [2016]
• Mutaflor Post
  • “Orally administered E. coli strain Nissle 1917 [Mutaflor] reduced Listeria monocyto-genes and Candida albicans in a dose-dependent manner. Treatment with 10(9) cfu of E. coli bacteria led to a reduction of Listeria counts to 7.4% in spleen and 2.4% in liver. A more than 10-fold decrease of viable Candida albicans (residual parasitaemia 6.8%) in the kidneys of the infected animals was also achieved by this E. coli concentration.” [1997]
• L. Reuteri, L. Rhamnosus, L. Plantarum
  • Probiotic Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 exhibit strong antifungal effects against vulvovaginal candidiasis-causing Candida glabrata isolates [2015].
  • “Prophylactic L. reuteri supplementation is as effective as nystatin, and more effective in reducing the incidence of proven sepsis in addition to its favorable effect on feeding intolerance.” [2015]
  • Lactobacillus plantarum P17630 for preventing Candida vaginitis recurrence: a retrospective comparative study[2014].
    • ” A total of 65 patients were randomly assigned to receive oral local antifungal agents alone (gargle 2% sodium bicarbonate solution for 30 s, wait 10 min and then apply 2% nystatin paste) or these agents plus local probiotics (the mixture of Bifidobacterium longum, Lactobacillus bulgaricus and Streptococcus thermophilus) three times per day for 4 weeks… The detection rate of Candida spp. decreased (P = 0.000) in both groups and was significantly lower in the probiotic group than the control group (P = 0.038). ” [2014]
  • Probiotic interference of Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 with the opportunistic fungal pathogen Candida albicans [2012].
• Curcumin as a promising anticandidal of clinical interest[2011].
  • “In conclusion, curcumin is found to be active against all tested clinical and standard strains but is less effective than fluconazole. “
• Antifungal activity of turmeric oil extracted from Curcuma longa (Zingiberaceae)[1995].

Bottom Line

Many things work against candida. Some researcher are happy to publish positive results that it reduces candida by 50% (1/2). When actual numbers are given, we want the one(s) with the best numbers. The clear winner is: Lactobacillus Fermentum reducing to 1/10000. This is available on Amazon.com in 6 BCFU capsules.The next one with numbers is Mutaflor, just reducing candida to 1/10.

Another reader shared their results and a little history. Two dominant symptoms matches the bacteria genus overgrowths.

Patient Summary

• Gradual onset starting at 18, 10 years now
  • Suspected cause allergy vaccines
• Symptoms
  • Severe insomnia,
  • Acute stress in all situations.
  • Candida, bloating, can not eat fiber or starches.
  • All smells make me really really stress, and lack of thinking orientation etc.
  • Low energy, muscle loss. From 84 to 66 kg.
  • Hair loss… need mask for in to a shops etc and in polluted areas
• Tested positive for Epstein Barr (EBV) and Cytomegalovirus (CMV).
• I feel some relief with berberine and neem.
• Sacharomyces boulardii makes me anxious but after a while seems to help.

Basics Criteria

• As is very often seen with CFS uBiomes– Diversity at the top of the scale – 98%,
  • statistically too often to be random.
• Bifidobacterium: 0
• Lactobacillus: 0
• Akkermansia:  1% of reference
• Low or no E.Coli
  • Not directly reported, but it parent is: Enterobacteriaceae  which is 2% of the reference group

Analysis of Over Growth by Bacteria Genus

1. Erysipelatoclostridium (genus) 
2. Butyricimonas (genus) 
3. Adlercreutzia (genus) 
4. Sutterella (genus) 
5. Anaerosporobacter (genus) 
6. Oscillibacter (genus) 
7. Slackia (genus) 
8. Marvinbryantia (genus) 

NUTRIENTS/ SUBSTRATES

• D-Glucose -2

INHIBITED BY

• Flaxseed -1, 5, 8
• Polymannuronic acid -4

ENHANCED BY

• Partial Sleep Deprivation -1
• Berberine -2
• Chemotherapy – 4
• High protein diet – 4
• Walnuts – 5, 8
• Saccharomyces boulardii  – 5, 8
• Resistant starch (type III) – 6
• Resistant starch (type II) – 6
• Resistant starch (type I) – 6

INHIBITS

• Bifidobacterium– 1,2,3, 5, 8

The amount of information that we have about these 8 high bacteria genus is not much.  The “Partial Sleep Deprivation” hints that melatonin may be helpful (not just for sleep, but chemically) – but this is speculation. This overgrowth does agree with your symptom of severe insomnia.

“can not eat fiber or starches” — well, we see above that those enhances the over growths! Microbiome matches symptoms!

Very Elusive Bacteria

Given the thin data above, I moved on to this set of data

1. Scardovia (genus) 
2. Oribacterium (genus) 
3. Neisseria (genus) 

NUTRIENTS/ SUBSTRATES

• Dextran

INHIBITED BY

• Iron supplements -1
• High fat diet -1
• Flaxseed -2

ENHANCED BY

• Proton-pump inhibitors (PPI) -1, 2
• Walnuts – 2
• Saccharomyces boulardii  -2

INHIBITS

• Bifidobacterium – 2

Bottom Line

Make sure that flaxseed is a regular part of your diet, avoid walnuts, avoid dairy products and supplements containing Saccharomyces boulardii.

You may wish to stop berberine — have you tried Tulsi or Rosehip teas?

Continue or start with the usual supplements.. see:

• A Frugal List of Supplements — if cost constrained.
• Survey of Supplements — other CFS patients experiences

For “Acute stress in all situations” try Ashwagandha – I will research what else may help that and do a post later this week.

For hair loss, I have had informal reports that biotin (vitamin H) helps. Literature:

• Intestinal Dysbiosis and Biotin Deprivation Induce Alopecia through Overgrowth of Lactobacillus murinus in Mice.[2017]
• Serum Biotin Levels in Women Complaining of Hair Loss [2016].
  • “Biotin deficiency was found in 38% of women complaining of hair loss. “
• “To date, there have been no clinical trials conducted to investigate the efficacy of biotin supplementation for the treatment of alopecia of any kind, nor has there been any randomized controlled trial to study its effect on hair quality and quantity in human subjects. ” [2017]

Reflection on Common Conventional Treatments

I have notices that Proton-pump inhibitors (PPI)  and Saccharomyces boulardii  (typically used as antifungal/anti-candida) keeps showing up in enhancers of the overgrowth. This raises the nasty question: “Have conventional treatments contributed to your CFS?“

Last — I will be researching a replacement for Saccharomyces boulardii treatment for candida and hopefully can produce a useful post.