Reader Notes

Crohn’s + Severe CFS here, among other issues. We would expect an atypical microbiome for CFS/IBS because of the Crohn’s — we were not disappointed!

Standard Items:

• Lactobacillus: 0x
• Bifidobacterium: 0.47x
• Akkermansia:  0x
• Diversity:  7%ile
• Firmicutes to Bacteroidetes:  833:1 (Normal 2.1:1)
  • Bacteroidets — 0.06 %  Firmicutes: 50%

Uncommon Bacteria

High Bacteria

Reference

Because of the extreme shift of Firmicutes to Bacteroidetes, I called out the new bacterial genus that I had to do deep dives on.

• Parasutterella: https://cfsremission.wordpress.com/2017/10/19/decreasing-parasutterella-genus/
• [NEW] Anaerosinus: https://cfsremission.wordpress.com/2017/11/29/reducing-anaerosinus-genus/
• [NEW] Veillonella: https://cfsremission.wordpress.com/2017/11/29/reducing-veillonella-genus/
• Flavonifractor: https://cfsremission.wordpress.com/2017/11/05/reducing-flavonifractor-genus/
• Dorea :  https://cfsremission.wordpress.com/2017/10/18/reducing-dorea-genus/
• Clostridium :  https://cfsremission.wordpress.com/2017/10/07/decreasing-clostridium-genus/
• [NEW] Lactonifactor: https://cfsremission.wordpress.com/2017/11/29/reducing-lactonifactor-genus/
• Kluyvera: https://cfsremission.wordpress.com/2017/10/31/reducing-kluyvera-genus/
•  Lachnospira: https://cfsremission.wordpress.com/2017/11/03/reducing-lachnospira-genus/
• Also: https://atomic-temporary-42474220.wpcomstaging.com/2017/05/26/firmicutesbacteroidetes-ratio/It is interesting to note that this was the first ubiome I encountered with high Lactonifactor, although a Norwegian study found it was high with CFS patients![2013].

Bottom Line Suggestions

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.

Also: https://atomic-temporary-42474220.wpcomstaging.com/2017/05/26/firmicutesbacteroidetes-ratio/  because we want the ratio decreased.

Avoid

• Aspartame (Nutrasweet)
• Berbine
• Bifidobacterium catenulatum
• Bifidobacterium pseudocatenulatum
• Bifidobacterium animalis
• Gluten
• L-Glutamic acid ( monosodium glutamate– MSG) and possibly gluten
• L-Proline
• L-Serine
• Metformin
• Proton-pump inhibitors (PPI)
• Saccharomyces boulardii
• Soy
• Vegetables
• Vitamin K2
• Walnuts

Take

• Alcohol
• Bacillus licheniformis (it does produce histamines, see this post)
• Bifidobacterium longum and Bifidobacterium Breve
• Chitosan supplements
• Cranberry [2017]
• Enzymatically modified resistant starch
• Flaxseed
• Have Chocolate!
• Inulin
• Lactobacillus casei
• Lactobacillus Fermentum [2017]
• Lactobacillus kefiri
• Lactobacillus kefiri LKF01
• Lactobacillus reuteri
• Lactobacillus rhamnosus probiotics
• L-Phenylalanine (Good sources of phenylalanine are eggs, chicken, liver, beef, milk, and soybeans.[5])
• Low calories High protein diet
• Melatonin [2017]
• Pea Fibre [2017]
• Pomegranate ellagitannins
• Prescript Assist
• Resveratrol [2014]
• Streptococcus Probiotics
• Thiamine
• Vitamin D

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

For updated information see Microbiome Prescription

DataPunk.Net Data

Nothing

PubMed Data

There are 3+ studies on PubMed

Disease

Diet

Prebiotic

Probiotic

Antibiotic

Bottom Line

Absolutely nothing!

Avoid

Take

For updated information see Microbiome Prescription

“Bifidobacterium and Veillonella are commensal anaerobes which reside in gastrointestinal tract and help deconjugate bile acids. ” [2010]

DataPunk.Net Data

INHIBITED BY

• Chemotherapy

ENHANCED BY

• Proton-pump inhibitors (PPI)

PubMed Data

There are 1500+ studies on PubMed

Disease

•  “Microbial diversity and relative abundance of Streptococcus , Prevotella and Veillonella were inversely associated with airway inflammation in cystic fibrosis . ” [2017]
• ” decreased abundance of genus Akkermansia but increased abundance of Veillonella was found in children with food allergy in comparison with healthy control children.” [2017]
• “IBS microbiota is different from that of healthy individuals due to an unbalance in a number of commensal species, with an increase in relative abundance of lactobacilli, B. cereus and B. clausii, bifidobacteria, Clostridium cluster IX and E. rectale, and a decrease in abundance of Bacteroides/Prevotella group and Veillonella genus. ” [2012]
• In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia, and Fusobacteria were significantly increased, whereas Bacteroidetes and Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium, Streptococcus, Sutterella and Veillonella were increased, ” [2017]
• “Molecular techniques revealed Prevotella and Veillonella as potentially pathogenic anaerobic species with bronchiectasis ” [2017]

Diet

• “alterations of the microbiota in the oral carriage microbiome along with bacterial overgrowth (Streptococcus) and decreases in distinct bacterial species (Neisseria, Veillonella) were observed with proton pump inhibitors (PPIs)” [2017]
• “Veillonella. dispar DNA bands were markedly inhibited after washing with chlorhexidine mouthwash”. [2017]
• “However, lipopolysaccharides increased with the reduction of 25(OH)D (p-trend <0.05). Prevotella was more abundant (log2FC 1.67, p<0.01), while Haemophilus and Veillonella were less abundant (log2FC -2.92 and -1.46, p<0.01, respectively) in the subset with the highest vitamin D intake” [2017]
• “An Italian-style gluten-free diet caused increases in the abundance of Granulicatella, Porphyromonas and Neisseria and decreases in Clostridium, Prevotella and Veillonella,” [2015]

Prebiotic

Probiotic

• “Fecal calprotectin decreased rapidly in both groups. In the infants with dominant fecal gram negatives (Klebsiella, Proteus, and Veillonella), resolution of colic was associated with marked decreases in these organisms with Lactobacillus reuteri ” [2017]
• ” After one month of Lactobacillus kefiri LKF01 DSM32079 (LKEF)  probiotic oral intake we observed a reduction of Bilophila, Butyricicomonas, Flavonifractor, Oscillibacter and Prevotella. Interestingly, after the end of probiotic administration Bacteroides, Barnesiella, Butyricicomonas, Clostridium, Haemophilus, Oscillibacter, Salmonella, Streptococcus, Subdoligranolum, and Veillonella were significantly reduced if compared to baseline samples.”
• “there were greater proportions of Actinomyces and Streptococcus-like species and lower proportions of Veillonella parvula, Capnocytophaga sputigena, Eikenella corrodens, and Prevotella intermedia-like species with Bifidobacterium animalis subsp. lactis ” [2017]
• ” In addition, populations of Escherichia coli, Veillonella spp. and Bacteroides vulgatus were decreased, while populations of Bifidobacterium genus and Lactobacillus spp. were increased with Lactobacillus reuteri” [2014]

Antibiotic

Bottom Line

Avoid

• Proton-pump inhibitors (PPI)
• Gluten

Take

• proton pump inhibitors
• Lactobacillus reuteri
• Lactobacillus kefiri
• Vitamin D

For updated information see Microbiome Prescription

DataPunk.Net Data

Nothing

PubMed Data

There are 5+ studies on PubMed

Disease

• “A highly significant separation could be achieved between Norwegian controls and Norwegian myalgic encephalomyelitis/chronic fatigue syndrome patients: patients presented increased proportions of Lactonifactor and Alistipes, as well as a decrease in several Firmicutes populations.” [2013]
• ” Parabacteroides, Eubacterium, Anaerotruncus,
  Lactonifactor and Coprobacillus were more abundant in subjects in long-term care ” [2014]

Diet

• Soy “increases were seen in the intensity of specific DGGE bands corresponding to microorganisms known to be involved in the metabolism of dietary phytoestrogens (Lactonifactor longoviformis, Faecalibacterium prausnitzii, Bifidobacterium sp., Ruminococcus sp.). ” [2015]

Prebiotic

Probiotic

Antibiotic

Bottom Line

Avoid

• Soy

Take

Reader Notes

I’ve been debilitated with CFS since taking Levaquin in 2005. A few weeks ago I actually thought I was on the verge of some improvement but I found out how wrong I was. Last week I was given gentamicin ear drops for a minor ear infection caused by impacted wax. After just 3 doses I had to stop taking it because I started urinating extremely frequently. A day later I developed horrible intestinal burning sensations and, while in some ways I actually felt better, other symptoms became much more intense.

It seems that the ear drops likely caused something in my gut to bloom. I tried Miyarisan and VSL3 to see if they could mitigate the intestinal symptoms and both seem to help a bit, with the VSL3 working better, but the symptoms are only lessened for a few hours. I’ve also noticed round white spots, about a half inch in diamater, in my stools the last two days, which I’ve never seen before. I have a sample at ubiome now but I only sent it off two weeks ago and of course it was before I took the gentamicin so that sample may not provide insight, and I can’t wait six weeks or so for new sample results. Something is very, very wrong in my gut. Do you know of any other labs that have a quick turnaround that are trustworthy and provide a report that is actionable? The delay in getting results is so frustrating.

Anyway, it seems like my gut microbiome must have been very fragile to respond so horribly to just 3 doses of ear drops.

Standard Items:

• Lactobacillus: 0.0x
• Bifidobacterium: 0.36x
• Akkermansia:  4.5x
• Diversity:  13%ile
• Firmicutes to Bacteroidetes: 1.2:1 (Normal 2.1:1) – shift probably caused by antibiotic

Uncommon Bacteria

High Bacteria

Reference

• Akkermansia: https://cfsremission.wordpress.com/2017/10/14/decreasing-akkermansia-genus/
• Flavonifractor: https://cfsremission.wordpress.com/2017/11/05/reducing-flavonifractor-genus/
• Bacteroides: https://cfsremission.wordpress.com/2017/10/20/decreasing-bacteroides-genus/

Bottom Line Suggestions

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.

Avoid

• Bacillus subtilis
• Bifidobacterium Animalis subsp. Lactis
• Broad beans  and lupin seeds
• Cranberry bean flour
• Cranberry polyphenols
• Daesiho-tang (DSHT)
• Fasting
• Fructo-oligosaccharides
• Gallic acid
• Grapes (table)
• Green tea
• gum arabic
• Heme
• High meat diet
• High protein diet
• Lactobacillus acidophilus
• Lactobacillus plantarum
• L-citrulline
• Lingonberries
• Low fat diets
• Low processed foods diet
• Melatonin
• Metformin
• Pomegranate ellagitannins
• Resveratrol, Red wine, Grape Seed Extract
• Rhubarb
• Saccharin
• Stevia
• Tannic acid

Take

• Bacillus licheniformis
• Bifidobacterium longum
• Flaxseed
• Garlic
• High fat diet
• Inulin
• Lactobacillus kefiri LKF01
• Lactobacilluscasei strain Shirota (Yakult brand only)
• Omega 3 fatty acids
• Polymannuronic acid
• Sucralose (Splenda)
• Walnuts
• Whole-grain barley
• β-Glucan

To the above, dairy should be added to increase the Firmicutes to Bacteroidetes ratio (see this post)

Comments on Antibiotics

The onset was due to Levofloxacin a member of the fluoroquinolones  family

• “At the phylum level, both types of antibiotics (β-lactams and fluoroquinolones) tested caused a decrease of Firmicutes and increase of Bacteroidetes (p<0.001; FDR = 0.002) ” [2012] – agrees with the ratio above.
  • “Like all fluoroquinolones tested, levofloxacin did not cause a clear increase of the microbial load. However, it significantly affected 14 bacterial taxa, out of which 10 unknown Bacteroides and 1 unknown Coproccocus were 3 to 56-fold increased and 1 unknown Blautia was 2-fold decreased (p<0.01; FDR<0.09) “

Gentamicin

• “As for the gut microbiome, after the 4 days of antibiotics, total anaerobic bacterial count decreased from 8.5 log10CFU/g to 6.2 log10 CFU/g. Enterococci, coliforms and bifidobacteria decreased significantly as well. ” [2015]
• “Gentamicin resistance, as assessed by the Stokes method, occurred in less than 2% of isolates of Escherichia coli, about 10–25% of most other enterobacteria, about 40% of Acinetobacter spp. and about 25% of Pseudomonas aeruginosa. This finding of relatively low rates of gentamicin in Enterobacteriaceae was surprising in view of the unregulated use of antibiotics until recent years.” [1989]
  • In other words, bye bye E.Coli, and many other families

You should insist on antibiotics that shifts your ratio closer to normal.,i.e. increase of Firmicutes and decrease of Bacteroidetes — your MD may need to do some research!

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of any condition. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.