For updated information see Microbiome Prescription

uBiome’s Smart Gut associate low levels with various conditions. Most of the studies deal with rumens (cows etc)

DataPub.Net

Firmicutes -> Clostridia -> Clostridiales -> Lachnospiraceae -> Butyrivibrio -> Butyrivibrio crossotus

For grand parent we have:

INHIBITED BY

• Flaxseed
• Quercetin w. Resveratrol 

ENHANCED BY

• Walnuts 
• Saccharomyces boulardii 

PubMed etc

We have 6+ studies for Butyrivibrio Crossotus, and  470+ studies for Butyrivibrio

Disease

Diet

• “There was also a correlation between Lactobacillus ruminis and sialidase, as well as Butyrivibrio crossotus and xylanase/xylosidase.” [2017]
• “Supplementation with marine[fish and algae] oils decreased the numbers of Butyrivibrio producers” [2017]

Prebiotic

Probiotic

Antibiotics

Bottom Line

Avoid

• Flaxseed
• Quercetin w. Resveratrol 
• Fish Oil

Take

• Walnuts 
• Saccharomyces boulardii 
• xylanase/xylosidase.

A reader asked for any recommendations of a microbiome savvy/understanding physician in Germany. Actually, the same applies to almost every country…. If you have suggestions, post them here as comments.

For updated information see Microbiome Prescription

Doctor’s Data tests will reports on C. Freundii and this is a summary of what can be done to reduce it. Citrobacter (genus) material is included.

DataPub.Net

Gammaproteobacteria -> Enterobacteriales -> Enterobacteriaceae -> Citrobacter -> Citrobacter freundii 

Nothing

PubMed etc

“our lab showed that exposure to the prolonged-restraint stressor prior to a challenge with C. rodentium alters the intestinal microbiota community structure, including a reduction of beneficial genera such as Lactobacillus, which may contribute to stressor-enhanced C. rodentium-induced infectious colitis”  [2013]

Disease

• “Urinary tract infections… abnormal inflammatory changes in the intestine, sometimes even resulting in necrotic changes….linked to neonatal meningitis” [edu]

Diet

• Dietary Chitosan Supplementation Increases Microbial Diversity and Attenuates the Severity of Citrobacter rodentium Infection in Mice[2016].
• “data indicated that the consumption of dietary fiber-rich diets ameliorates the effects of C. rodentium-induced enteritis ” [2016]
• “Dietary fiber deprivation, together with a fiber-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium.” [2016]
• “they find that a fiber-free diet promotes mucus-degrading bacteria and susceptibility to Citrobacter rodentium infection.” [2016]
• “Dietary vitamin D3 deficiency alters intestinal mucosal defense and increases susceptibility to Citrobacter rodentium-induced colitis. [2015]”
• “We also demonstrate the potential importance of vitamin B12 in controlling susceptibility to bacterial pathogens such as C. rodentium and S Typhimurium.” [2016]
• “After 5 weeks of dietary intervention, mice were challenged with Citrobacterrodentium, and pathological responses were assessed. Olive oil diets resulted in little colonic pathology associated with intestinal alkaline phosphatase…Fish oil combined with milk fat, unlike unsaturated lipid diets, had a protective effect ” [2016]
• White button mushrooms increase microbial diversity and accelerate the resolution of Citrobacterrodentium infection in mice [2013].
• Long-term selenium deficiency increases the pathogenicity of a Citrobacter rodentium infection in mice [2011].
• The pathogenicity of an enteric Citrobacter rodentium Infection is enhanced by deficiencies in the antioxidants selenium and vitamin E [2011].
• “A band corresponding to Citrobacter freundii (98% identity) was observed in almost all pigs from thymol groups, and only in 4 samples from pigs fed no thymol in the diet. ” [2008]

Prebiotic

• “Mice with pretreatment of L acidophilus, inulin, and both show reduced intestinal inflammation following Cr infection compared with controls” [2012]

Probiotic

• “Preadministration and coadministration of a probiotic mixture containing Lactobacillus helveticus and Lactobacillus rhamnosus  ameliorated C. rodentium” [2012]
• “While L. reuteri treatment did not reduce all aspects of stressor-enhanced infectious colitis, it did significantly reduce pathogen translocation from the colon to the spleen.”[2013]
• “. The results showed that administration of a combination of probiotics including Lactobacillus rhamnosus ATCC 53103, Lactobacillus acidophilus ATCC 4356 and Lactobacillus plantarum A significantly increased the production of CD11c⁺ dendritic cells in the spleen (3.62% vs phosphate buffered saline (PBS)-treated control, P<0.01) and mesenteric lymph nodes (MLNs)… for  a model of Citrobacter rodentium-induced colitis” [2016]

Antibiotics

• “usually treated with antibiotics like fluoroquinolones, carbapenems and cephalosporins. The treatment plan depends up on the vulnerability of the microbe to the antibiotics and the site of the infection. Conversely, there is a growing alarm over the levels of resistance of C. freundii to a number of antibiotics. Supportive treatment is given as well to hasten cure. ” [edu]
• Further details.

Bottom Line

Avoid

• Thymol

Take

• Fiber
• Fish Oil with Milk Fat
• Inulin
• Lactobacillus plantarum
• Lactobacillus rhamnosus
• Lactobacillus acidophilus
• Lactobacillus Reuteri
• Lactobacillus helveticus
• Selenium
• Vitamin E
• Vitamin D
• Vitamin B12
• White button mushrooms

NOTICE: THIS POST HAS BEEN ALTERED DUE TO THREAT OF LEGAL ACTION. See communications received in comments.

There has been a change of formula for Prescript Assist.  This makes the existing documentation on the benefit of Prescript Assist for IBS questionable.

Prior Page with links to studies.

• Over half of the prior species have been removed
• The number of Firmicutes has increased significantly
  • If you have a Firmicutes to Bacteroidetes ratio < 1.6:1 on a uBiome test, it may be of benefit
  • If you have a Firmicutes to Bacteroidetes ratio > 2.5:1 on a uBiome test, it may make things worse

Old Formula

New Formula

Comparison

From original post with documentation links to benefits

• Actinobacteria -> Actinobacteria -> Micrococcales 
  • Brevibacteriaceae -> Brevibacterium
    • Brevibacterium lipolyticum,
    • Brevibacterium stationis,
  • -> Micrococcaceae -> Arthrobacter 
    • Arthrobacter agilis (species) ,
    • Arthrobacter citreus,
    • Arthrobacter globiformis – New
    • Arthrobacter luteus,
    • Arthrobacter simplex,
  • > Streptomycetales -> Streptomycetaceae -> Streptomyces 
    • Streptomyces fradiae,
    • Streptomyces celluslosae,
    • Streptomyces griseoflavus (species)  – New
• Proteobacteria
  •  -> Gammaproteobacteria -> Pseudomonadales 
    • > Moraxellaceae -> Acinetobacter 
      • Acinetobacter calcoaceticus,
    • -> Pseudomonadaceae 
      • -> Azotobacter group -> Azotobacter -> 
        • Azotobacter chroococcum – New
        • Azotobacter paspali – New
      • -> Pseudomonas
        • Pseudomonas dentrificans,
        • Pseudomonas flourescens – New
        • Pseudomonas glathei,
• Alphaproteobacteria -> Rhodospirillales -> Rhodospirillaceae  –> Azospirillum
  • Azospirillum brasiliense – New
  • Azospirillum lipoferum – New
• Firmicutes -> Bacilli -> Bacillales -> Bacillaceae -> Bacillus 
  • Bacillus brevis,
  • Bacillus marcerans,
  • Bacillus pumilis – New
  • Bacillus polymyxa,
  • Bacillus subtilis – New
  • Bacteroides lipolyticum
• Bacteroidetes
  • Bacteriodes succinogenes,
• Coryneform
  • Kurtha zopfil – New
• Clostridiales Family XI Incertae Sedis
  • Myrothecium verrucaria,
• Polyporales
  • Phanerochaete chrysosporium,

Only in New

• Proteobacteria -> Gammaproteobacteria -> Pseudomonadales -> Pseudomonadaceae -> Azotobacter group -> Azotobacter
  • Azotobacter vinelandii (species) 
• -> Bacilli -> Bacillales
  •  -> Bacillaceae
    •  -> Lentibacillus 
      • (Lenti)Bacillus amyloliquefaciens
    •  -> Bacillus 
      • Bacillus  atrophaeus related to bacillus anthracis and developed for US Military uses
      • Bacillus licheniformis
      • Bacillus megaterium (species) 
      • Bacillus firmus
      • -> Bacillus cereus group
        • Bacillus thuringiensis (species) 
• • -> Paenibacillaceae -> Brevibacillus 
    • Brevibacillus brevis (species) 
• Actinobacteria -> Actinobacteria 
  • > Streptomycetales -> Streptomycetaceae -> Streptomyces 
    • Streptomyces griseus group (species subgroup) 
    • Streptomyces venezuelae (species) 

    -> Corynebacteriales -> Nocardiaceae -> Rhodococcus 

    • Rhodococcus rhodochrous (species) 
  • -> Micrococcales 
    • -> Cellulomonadaceae -> Cellulomonas
      • Cellulomonas fimi (species) 
    •  -> Micrococcaceae 
      • -> Micrococcus 
        • Micrococcus luteus (species) 
      • -> Arthrobacter
        • Nocardioides simplex (Arthrobacter simplex)
•  Proteobacteria 
  • -> Gammaproteobacteria 
    • -> Pseudomonadales -> Pseudomonadaceae 
      • -> Azotobacter group -> Azotobacter
        • Azotobacter vinelandii (species) 
      • -> Pseudomonas
        • Pseudomonas putida group (species group) 
    • • Rhodobacter sphaeroides (species) 
      • Rhodococcus rhodochrous (species) 
• Alphaproteobacteria 
  • -> Rhodobacterales -> Rhodobacteraceae -> Rhodobacter
    • Rhodobacter sphaeroides (species) 
    • Rhodococcus rhodochrous (species) 
  • -> Rhodospirillales -> Rhodospirillaceae -> Rhodospirillum
    • Rhodospirillum rubrum (species) 

Bottom Line

Revised: There are at this point of time there are not studies on PubMed dealing with the ingredients listed on the current bottles of this product.

Reader Notes

Standard Items:

• Lactobacillus: 0x
• Bifidobacterium: 2.09x – identified by species
  • Bifidobacterium adolescentis
  • Bifidobacterium longum
• Akkermansia:  0x
• Diversity:  40%ile
• Firmicutes to Bacteroidetes:  2.2:1 (Normal 2.1:1)

This does not feel like a normal CFS microbiome… and a first cousin to C. difficile may be the root cause of symptoms.

Uncommon Bacteria

High Bacteria

Romboutsia is a new genus to show up.

References

• Romboutsia: https://cfsremission.wordpress.com/2017/12/09/reducing-romboutsia-genus/
• Erysipelatoclostridium: https://cfsremission.wordpress.com/2017/11/14/decreasing-erysipelatoclostridium-genus/
• Parabacteroides: https://cfsremission.wordpress.com/2017/10/17/decreasing-parabacteroides-genus/
• Pseudobutyrivibrio: https://cfsremission.wordpress.com/2017/10/15/decreasing-pseudobutyrivibrio-genus/
• Dorea :  https://cfsremission.wordpress.com/2017/10/18/reducing-dorea-genus/

Bottom Line Suggestions For New Ones

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

• Amoxicillin-Clavulanate antibiotics
• Animal-based diet
• Barley
• Bifidobacterium longum
• Black Tea
• Canole Oil
• Dairy
• Helminth infections
• Inulin (common in many probiotics)
• Isoniazid-
• Lactobacillus casei
• Lactobacillus paracasei
• Lactobacillus rhamnosus
• Lingonberries
• Pomegranates
• Proton-pump inhibitors (PPI)
• Pyrazinamide
• Resistant Starch
• Resveratrol (Grapes, wine)
• Rhubarb
• Rifampin-
• Saccharomyces boulardii
• Sleepless nights
• Stress
• Teas *
• Walnuts

Take

Items with * are specific to Romboutsia, and should be a high priority.

• Bile salts *
• Capsaicin(chili peppers)
• Cranberry *
• Flaxseed
• Galactooligosaccharides
• high-fat diet
• Ketogenic diet
• Lactobacillus reuteri
• L-glutamine
• Metronidazole antibiotics
• Oral Iron Supplements
• Plantain bananas *
• Polymannuronic acid
• Vitamin D3
• β-glucan

Personal Comments

It is interesting to note all of the items rich in  polyphenols are on the avoid list except for cranberries. At the species level we found Bifidobacterium longum which is on the avoid list.

Second, this does not feel like a typicla CFS microbiome. The dominant, unusual genus, Romboutsia, being a first cousin to  C. difficile  [2014] may be the cause of the CFS-like symptoms.

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.