Category Archives: Conditions

Unknown's avatar lassesen 6:22 pm on November 18, 2017  

Reducing Peptoclostridium Genus

For updated information see Microbiome Prescription

Includes Clostridium difficile (Peptoclostridium difficile)

DataPunk.Net Data

INHIBITED BY

PubMed Data

There are 10+ studies on PubMed

Disease

Diet

Prebiotics

Probiotics

Antibiotics

Bottom Line

Avoid

Take

Unknown's avatar lassesen 3:14 pm on November 18, 2017  

Enhanced analysis of a skinny CFS patient

Symptoms:

Extreme fatigue,brain fog,adrenal fatigue/low cortisol,high th2,constipation alternating to loose stools,bloating,depression,underweight. High levels of klebsiella pneumoniae found in stool test. All of the the typical CFS symptoms.

Standard Elements

  •  Lactobacillus 0x
  • Bifidobacterium 0x
  • Diversity:  2%  (unusually low)

Overgrowths of Bacteria Genus

Bacteria
Ratio
Alistipes:  2.95 X
Bacteroides:  2.71 X
Parabacteroides:  2.52 X
Sutterella: 2.02 X
Barnesiella: 1.70 X

Reference Deep Dives

Rare Bacteria Genus

Nothing below 5%

Bottom Line

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
  • Aspirin (other NSAID’s are fine)
  • Bacillus probiotics
  • Bacillus subtilis
  • Bifidobacterium Animalis subsp. Lactis BB-12
  • BPA bottles
  • Broad beans  and lupin seeds
  • Canole Oil
  • Cranberry
  • Fructo-oligosaccharides
  • Gallic acid
  • Glutten
  • Gum arabic
  • High meat diet
  • Lactobacillus casei
  • Lactobacillus acidophilus La-5
  • Lactobacillus Fermentum
  • Lactobacillus paracasei
  • Lactobacillus rhamnosus GG
  • Lactobacillus plantarum
  • L-citrulline
  • Lingonberries
  • Low fat diets
  • Melatonin
  • Oligofructose
  • Pea Fibre
  • Proton-pump inhibitors (PPI)
  • Red wine, Grape Seed Extract
  • Resistant starch (type IV)
  • Resveratrol (Grapes, wine)
  • Rhubarb
  • Saccharin
  • Stevia
  • Tannic acid

Take

  • Bacillus licheniformis
  • Bacillus subtilis natto (or nattokinease supplements)
  • Bifidobacterum Bifidum
  • Bifidobacterum Infantis
  • Bifidobacterum Longum
  • Bile supplements
  • Capsaicin  (chili peppers)
  • Dairy Products
  • Faecalibacterium prausnitzii
  • Garlic
  • High Fat diet
  • Lactobacillus kefiri LKF01
  • Metronidazole antibiotics
  • Polymannuronic acid
  • Sucralose (Splenda)
  • Tannin and Gallate   — green tea see this web page.
  • Walnuts
  • Whole-grain barley
  • Xylitol
  • β-Glucan

The Compounded Probiotic Dilemma!

The reader asked about taking Megaspore (which he just received). Checking my post for Bacillus probiotics that I know about, we find that it is the only one containing

  • Bacillus licheniformis [TAKE]

But it also contain

  • Bacillus subtilis [AVOID]

This leaves us with a dilemma which people will resolve different ways. Being aware of patients financials and that probiotic potency decreases over time, I would proceed for myself as follows:

  • Use the Megaspore but do not reorder. Keep one week supply for a re-trial later.
  • While not doing other changes, slowly ramp up and see if it has any impact

Once exhausted (except for the one week retrial amount) stay off it for at least 6 weeks and see if there are any changes from stopping it.  Do a retrial of it for a week and see if the earlier changes repeat or not. Re-evaluate based on your actual experience.

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

Unknown's avatar lassesen 3:35 am on November 15, 2017  

Revisiting old Ubiome’s “B”

A year ago, several readers shared their ubiome for me and I did a series of post looking for patterns. See this post on the Genus Numbers.

It is time that I do deep dives for these early sharers.

Results B

  • Sure, I got sick with ME after an infection I probably picked up on the airplane back from Asia. Probably lived in mold a few years prior to that that probably took my immune system down too, before the final straw with the infection. Major symptoms: fatigue, unable to do much physically, brainfog, get tired of concentrating too much and being social, my head “shuts down”, joint pain, muscle pain, headaches, swollen lymph nodes, feeling like a flu is coming on very frequently, everything is made worse by too much exertion I do not think I did much probiotics before the sample was done actually…
    • 4/12/2014
Genus B
Intestinimonas 4.45
Thalassospira 4.32
Alistipes 4.01
Bilophila 3.93
Oscillospira 3.93
Acetitomaculum 3.22
Butyricimonas 2.8
Clostridium 2.51
Lachnospira 1.81
Blautia 1.79
Sarcina 1.76
Collinsella 1.7
Dialister 1.7
Erysipelatoclostridium 1.68

Deep Dive References

 

Bottom Line Suggestions

The items from each of the deep dives aligned very nicely for this microbiome, for example, Inulin was listed many times.

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

  • Clostridium butyricum
  • Bacillus subtilis
  • Barley
  • Berberine
  • Bifidobacterium longum
  • Bifidobacterium animalis
  • Brown rice
  • Cholic acid
  • Dairy
  • Flavone
  • Fluoroquinolone
  • Generic Bacillus probiotics
  • High animal protein/meat diet
  • High grain diet
  • Isoniazid-
  • Lactobacillus fermentum
  • Lactobacillus plantarum
  • Lactobacillus Reuteri
  • Lysine supplements and foods
  • Metformin
  • Milk-derived saturated fat
  • omega-3
  • Pyrazinamide
  • Rifampin-
  • Rosemary
  • Saccharomyces boulardii
  • Safflower oil
  • Sleepless nights
  • Sodium butyrate
  • Starch
  • Vegetables
  • Walnuts
  • Wheat breads

Take

  • Bacillus licheniformis
  • Bifidobacterium Breve
  • Bifidobacterum Bifidum
  • Bifidobacterum Infantis
  • Cellobiose
  • Chicory
  • Chitosan supplements
  • Cranberry bean flour (or fresh cranberries)
  • Coli Probioitics
  • Enterococcus  faecalis probiotics
  • Faecalibacterium prausnitzii
  • Fennel
  • Flaxseed
  • Gluten free diet
  • Grape seed polyphenols,/ Wine
  • Green or black tea
  • Chocolate
  • High resistance starch
  • Inulin
  • Ketogenic diet
  • Lactobacillus Casei
  • Lactobacillus acidophilus
  • Lactobacillus paracasei (24 BCFU)
  • Low calories High protein diet
  • L-glutamine
  • lychee, rambutan, guarana, korlan, pitomba, Spanish lime and ackee. [fam-Sapindaceae]
  • NSAIDs (see list here), I prefer aspirin as first choice.
  • oral iron supplements
  • Oranges (pectin/flavanones)
  • Polymannuronic acid
  • pomegranate (walnuts is likely helpful too)
  • Prescript Assist
  • Streptococcus Probiotics
  • Sunflower seeds and oil
  • Thiamine

Vitamin D3

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

Unknown's avatar lassesen 5:20 am on November 14, 2017  

Decreasing Erysipelatoclostridium genus

For updated information see Microbiome Prescription

Most studies were done with cattle.

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 3+ studies on PubMed

Disease

  • Gout ..being up-regulation of opportunistic pathogens, such as Bacteroides, Porphyromonadaceae Rhodococcus, Erysipelatoclostridium and Anaerolineaceae. [2017]
  • “Our data also showed that Erysipelatoclostridium, Gemella, Granulicatella,
    Mogibacterium, Rothia, and Streptococcus increased dramatically in Crohn’s Disease patients,” [2017]
  • “Erysipelatoclostridium (0.77% vs 2.04% in the healthy infants, q-value < 0.05) ..in

    bronchiolitis” [2017]

  • “Whereas in individuals with other neurological diseases, increase of bacterium Erysipelatoclostridium ramosum”[2016]

Diet

  • “Dairy intake was positively associated with the Firmicutes:Bacteroidetes ratio, and in particular Erysipelatoclostridium spp.,” [2016]
  • “ketogenic diet exposure also induced a decrease in Erysipelatoclostridium (by 8.67% ..)” [2017]
  • “

Prebiotic

Probiotics

Antibiotics

  • “Interestingly, increases (as opposed to decreases) in bacterial taxa due to isoniazid-rifampin-pyrazinamide treatment were limited to genus Erysipelatoclostridium (and genus Eggerthia in the naïve versus TB + HRZ comparison).” [2017]

Bottom Line

Avoid

  • Sleepless nights
  • Isoniazid-
  • Rifampin-
  • Pyrazinamide
  • Dairy

Take

  • Flaxseed
  • Ketogenic diet
Unknown's avatar lassesen 5:02 am on November 14, 2017  

Decreasing Acetitomaculum genus

For updated information see Microbiome Prescription

Most studies were done with cattle.

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 10+ studies on PubMed

Disease

Diet

  • “Sunflower Oil addition decreased the relative abundance of Rikenellaceae_RC9 and Acetitomaculum. Starch increases” [2013]
  • Xylan increases [1994]

Prebiotic

Probiotics

Antibiotics

Bottom Line

Avoid

Take

  • Flaxseed
  • Sunflower seeds and oil