Reducing Citrobacter Freundii

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

 

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

Change of formula for Prescript Assist

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

PS1.jpg

New Formula

PS2.jpg

Comparison

From original post with documentation links to benefits

Only in New

Bottom Line

The current Prescript Assist product cannot be recommended for IBS based on studies.

None of the genus appear to be on the list of known overgrowth seen with CFS (See this post), HOWEVER some of the recommendations from deep-dive cites AVOID Bacillus probiotics. This has multiple families of bacillus probiotics, some of which are known histamine producers.

It is suggested that you know your Firmicutes-to-Bacteroidetes ratio before deciding to take or avoid this new formulation.

A microbiome caused by a C.Difficile cousin?

 

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

Bacteria name Rank % of Samples
Leptotrichia Genus 1.5%
Anaerovorax Genus 3.2%
Aggregatibacter Genus 4.7%

High Bacteria

Bacteria
Ratio
Romboutsia: 6.10 X
Erysipelatoclostridium: 3.11 X
Parabacteroides:  2.13 X
Pseudobutyrivibrio: 1.94 X
Dorea: 1.88 X

Romboutsia is a new genus to show up.

References

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.

Reducing Romboutsia genus

This is a rare one to be seen with CFS

DataPunk.Net

INHIBITED BY

 

PubMed Data

There are 8+ studies  on PubMed, many dealing with fish.

Disease

Diet

  • “DiCQAs (from ku ding cha tea) increased the relative abundances of Alistipes, Bacteroides, Bifidobacterium, Butyricimonas, Clostridium sensu stricto, Escherichia/Shigella, Parasutterella, Romboutsia, Oscillibacter, Veillonella, Phascolarctobacterium, Lachnospiracea incertae sedis, Gemmiger, Streptococcus, and Haemophilus and decreased the relative abundances of Ruminococcus, Anaerostipes, Dialister, Megasphaera, Megamonas, and Prevotella. ” [2017]

Prebiotic

Probiotics

Antibiotics

BottomLine

Avoid

  • Teas

Take

For a limited time, free…

For a limited time, free uBiome kits for the nose.
https://shop.ubiome.com/pages/sniffle-ome

Reader’s improvement and microbiome shift after 3 months

I had done an analysis of his original before doing deep-dives in this Aug, 2017 post and a followup post later that month.

Reminder: This is all based on a model, a hypothesis that appears to match the known studies. The model purpose is to increase the odds of getting improvements. There are many factors that may influence what works and does not work – DNA, specific strains of some bacteria. We do not have enough knowledge to know what will work for any individual — we can make suggestions that appear to be far more probable to work.

Reader Notes

First, Thank you for all the work you do that so benefits this community.

Using your guidelines for changing my biome I went vegan, except 4oz of kefir in the AM.
The space of time is a little over 2 and half months. There are some remarkable changes.
For one my mood has most definitely stabilized, I’m much calmer. Energy is a little better, hyper-sensitivity seem to be lessened.
I’m far from well but am really pleased with the progress.
Within this time frame I did a short course of amoxicillin for dental work.
I realize the time involved and the number of request you receive, but would love your input on my latest uBiome. 
As mentioned I went vegan except for a small amount kefir about 4 oz, part of a breakfast with Trader Joe’s ancient grains cereal, a lot of blueberries, whey, ground flax seed, inulin, almonds, prescript assist and Bimuno.
I added a few of the probiotics but felt they caused more issues, so I stayed with only Prescript assist. 
Along with these I ate 100% rye with a table spoon or 2 of avocado oil, also included bakers !00% chocolate. 
Everything else was lots of beans and vegetables. 
PS, I’ve regained bowel function! (chronic constipation) 

Standard Items:

  • Lactobacillus: 0.04x ( 0.04 Prior)
  • Bifidobacterium: < 0.01 (< 0.01 Prior)
  • Akkermansia:  1.98x (7.36x prior)
  • Diversity:  68%ile (95%ile prior)
  • Firmicutes to Bacteroidetes:  1.0:1 (Normal 2.1:1)
    • 1.1:1 prior
    • Bacteroidetes 1.25 –> 1.5
    • Firmicutes  0.64 –> 0.7

Historic Trends

We can see there are significant shifts of some phylums

Untitled

Uncommon Bacteria

Proteiniphilum Genus 0.7%
Caldicoprobacter Genus 3.1%  (was in Prior)
Parasporobacterium Genus 3.5%
Parvibacter Genus 4.1% (was in Prior)
Christensenella Genus 4.5%

High Bacteria

Bacteria
Ratio
Oscillospira:  4.19 X (2.42x prior)
Alistipes:  3.54 X (4.53x prior)
Parasutterella: 2.50 X (2.98x prior)
Coprobacter: 2.15 X
Intestinimonas: 2.14 X  (2.00x prior)
Butyricimonas: 2.05 X (1.92 prior)
Thalassospira: 1.90 X
Flavonifractor: 1.60 X
Pseudobutyrivibrio: 1.55 X

Following have dropped below 1.5x

Akkermansia (was 5.26x –> down to 1.42): , Intestinibacter (was 5.0x –> down to 0.24x): 

References

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

  • Barley and oat
  • Bifidobacterium animalis subsp.  lactis  B-12®
  • Bifidobacterium catenulatum
  • Bifidobacterium pseudocatenulatum
  • Black Tea
  • Clostridium butyricum (i.e. Miyarisan) probiotics
  • Generic Bacillus probiotics
  • Lactobacillus fermentum
  • Lysine supplements and foods
  • Metformin
  • Saccharomyces boulardii
  • Vitamin K2
  • Walnuts

Take

  • Alchohol
  • Bacillus subtilis natto
  • Bifidobacterum Bifidum
  • Bifidobacterum Infantis
  • Cranberry bean flour (or fresh cranberries)
  • E.Coli Probioitics
  • Enzymatically modified resistant starch
  • Faecalibacterium prausnitzii
  • Flaxseed
  • Gallate – Green Tea
  • Inulin
  • Lactobacillus Casei
  • Lactobacillus kefiri LKF01
  • Lactobacillus paracasei
  • Lactobacillus salivarius
  • L-glutamine
  • Polymannuronic acid
  • Resistant starch (type II & IV)
  • Tannin and Gallate   — green tea see this web page.

Personal Comments

It is interesting that Black Tea is a to avoid, while Green tea is a to take.

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.

Reducing Flavobacterium genus

DataPunk.Net

Nothing

PubMed Data

There are 3400+ studies on PubMed, many dealing with fish.

Disease

Diet

Prebiotic

Probiotics

Antibiotics

BottomLine

Avoid

Take