Author Archives: lassesen

Unknown's avatar lassesen 10:56 pm on October 21, 2017  

Decreasing Cronobacter genus

This is a rare bacteria occurring in only 4.2% of all uBiome samples. Any bacteria genus < 5% I view as a probable overgrowth that should be reduced as a secondary target.

“Cronobacter spp. were isolated from:

  • 15% of 33 spice and herb samples and
  • 3% of 36 taste foods,
  •  fresh vegetables were detected in 12% of field vegetables and 13% of hydroponic vegetables.
  • shredded vegetables were detected from 44% of 9 samples,” [2017]

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 750+ studies on PubMed. Many studies deal with contaminated milk formula in China. This dive is not fully done yet.

  • Disease:
  • Diet:
    • “Ketogenic diet poses a significant effect on imbalanced gut microbiota… decreases” [2017]
    • ” tea polyphenols  had an effective bactericidal effect against C. sakazakii,” [2016]
    • “. Both strains were susceptible to thymol, carvacrol, thymoquinone, p-cymene, linalool, camphor, citral, eugenol, and trans-cinnamaldehyde as well as cinnamon, lemongrass, oregano, clove, and laurel essential oils; their minimum inhibitory concentrations varied between 0.1 and 2.0 mg/mL” [2014]
    • “, combinations of commercial Nisaplin and the food additive citric acid reduced C. sakazakii numbers markedly in infant formula within the same 3 h period. ” [2017]
    • “Citral (lemon oil) substantially reduced the adhesion and invasion of C. sakazakii to Caco-2 cells and decreased bacterial survival and replication ” [2017]
  • Probiotics:
  • Antibiotics:
    • “Cronobacter strains identified in this study were not susceptible to third-generation cephalosporins, aminoglycoside, and/or trimethoprim-sulfamethoxazole. ” [2017]
    • “showed very high resistance to ampicillin, amoxicillin, tetracycline, chloramphenicol and sulfamethoxazole/trimethoprim.” [2015]

Bottom Line

Avoid

  • shredded vegetables

Take

  • Vitamin C
  • Lactobacillus plantarum
  •  Bifidobacterium bifidum ,
  • Lactobacillus rhamnosus
  • Nisaplin (from  Lactococcus lactis )
  • Ketogenic diet
  • Tea
  • Cinnamon,
  • Lemongrass,
  • Oregano,
  • Clove
Unknown's avatar lassesen 9:55 pm on October 21, 2017  

Logic for selecting what to act on or ignore on uBiome results

I started this blog taking as gospel (well, being a mathematician by training, a postulate) the results of a 1998 study from Australia. “Faecal Microbial Growth Inhibition in Chronic Fatigue/Pain Patients”  The key items were simple:

  • Low or no Lactobacillus
  • Low or no Bifidobacterium
  • Low or no E.Coli

With overgrowth in other bacteria including Enterococcus. Working from this and PubMed studies, I found that the antibiotics that I had been given in my last two sessions with CFS were appropriate to address overgrowth and undergrowth. Recently, I found that heparin which was prescribe for hyper-coagulation (thick bl0od), also “increased Lactobacillus spp. and decreased Enterococcus sp” [2013]. In short, my remission could be ascribed with my correcting the reported dysfunction of the microbiome — not mycoplasma infection, chronic EBV, richettsia infection, chronic lyme etc. The third time around, I added E.Coli probiotics, Bifidobacteria etc to the fix and made a very fast recovery.

Current Reasoning

In examining many CFS/IBS/MCS uBiomes, I constantly see the same three low or no bacteria in the results — not just from uBiome, but from other tests kits. In examining the highs (which vary greatly from one uBiome to the next – which is why results vary so much from one patient to the next), I found that they are all listed on DataPunk.Net as inhibiting Lactobacillus, Bifidobacterium and/or E.Coli.   You want to get rid of these thugs, these killers as an early step.

“But can’t you just take probiotics instead?” is a common question. “Well, your own lactobacillus, bifidobacterium and E.Coli already went to war with them —- and lost badly!”

What about trying to build up the low ones? Conceptually sounds reasonable — but the problem is that you have a bunch of bullies in the class room of your gut. As long as the bullies are not constrained, all of the shy bacteria will keep getting pushed down.

Battle Plan

  • Supplement what was being produced by missing bacteria to reduce symptoms (see this post)
  • Use your uBiome results and my deep dives on each genus (see the same post for links to all that I have done so far) to reduce all high genus
    • Emphasis taking specific probiotics listed in the deep dive when practical
  • When the high bacteria genus are shown to be eliminated or greatly reduced on a repeat of uBiome, work on increasing the low genus associated with being anti-inflammatory.
    • My hope is that once the thugs are eliminated, everything will auto-correct.

 

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

Bifidobacterium INHIBITED BY 

 

 

Unknown's avatar lassesen 7:42 pm on October 21, 2017  

Decreasing Actinobaculum genus

This is a rare bacteria occurring in only 1.7% of all uBiome samples. Any bacteria genus < 5% I view as a probable overgrowth that should be reduced as a secondary target.

For updated information see Microbiome Prescription

DataPunk.Net Data

No Data

PubMed Data

There are 80+ studies on PubMed. Most studies deal with it in soil.

  • Disease:
  • Diet:
    • “Actinobaculum sp. HOT 183 was detected at 5.6% in the low-sugar group and at 6.9% in the reference group.” [2017]
    • ” randomized controlled trial of 91 adults with moderate gingivitis was designed with two anti-gingivitis regimens: the brush-alone treatment and the brush-plus-rinse treatment. and dental scaling…Only Actinobaculum, TM7 and Leptotrichia were consistently reduced by all the three treatments, ” [2016]
  • Antibiotics:
    • “The identification of this uropathogen is all the more important because it is resistant to trimethoprim/sulfamethoxazole and second-generation quinolones that are widely used in the treatment of UTIs. Antimicrobial therapy using β-lactams prolonged for up to 2 weeks is the most efficient treatment and should be recommended.” [2016]
    • “When an infection caused by A. schaalii is suspected, there is a risk of clinical failure by treating with ciprofloxacin or co-trimoxazole, and β-lactams should be preferred. In addition, acquired resistance to fluoroquinolones more active against Gram-positive bacteria is possible.” [2010]

Bottom Line

Avoid

  • Drinking urine (which appears to be high in it)

Take

  • Good dental care
  • Low sugar diet
Unknown's avatar lassesen 7:20 pm on October 21, 2017  

Decreasing Planomicrobium genus

This is a rare bacteria occurring in only 1.5% of all uBiome samples. Any bacteria genus < 5% I view as a probable overgrowth that should be reduced as a secondary target. It is found in Korean traditional fermented seafood, Jeotgal [src].

For updated information see Microbiome Prescription

DataPunk.Net Data

No Data

PubMed Data

There are 40+ studies on PubMed. Most studies deal with it in soil.

  • Growing conditions:
    • “The optimal medium was composed of soluble starch 0.73%,peptone 0.68%,yeast extract 0.15%,FePO40.01%in sea water with the initial pH value of 8.0.” [2014]
    • Chitosan appears to inhibit it. [2016]

Almost nothing found was applicable — not unexpected given it’s rarity.

Bottom Line

Avoid

  • Jeotgal

Take

  • Chitosan
Unknown's avatar lassesen 4:41 am on October 20, 2017  

Decreasing Bacteroides genus

“Bacteroides induce higher IgA production than Lactobacillus by increasing activation-induced cytidine deaminase expression in B cells in murine Peyer’s patches.[2009]”

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

ANTIBIOTIC RESISTANCE

PubMed Data

There are 650+ studies on PubMed. This page is still incomplete, more work to do.

  • Disease
    • “rheumatoid arthritis (RA) is in article presented. The signs of III degree dysbiosis, by reducing the concentration of Bacteroides spp.,” [2014]
    • inflammatory bowel disease …  increased significantly,  [2013]
  • Diet
    • “Grape seed extract..increased levels of … Bacteroides . [2013]
    • “Garlic (Allium sativum) … a rapid killing effect of between 1 and 3 log CFU/ml reduction in cell numbers was observed with Bacteroides ovatus, Bifidobacterium longum ” [2012]
    • “Bacteroides were significantly higher for gum arabic than for inulin.” [2008]
    • “Broad beans (Vicia faba) and lupin seeds (Lupinus albus)  ..the microbial groups that increased significantly (P < 0.05) were … Bacteroides-Pretovella [2015]
    • “There was a decrease in the population of staphylococci, bacteroides, Escherichia coli, and total coliforms in most bowel regions with the L. casei ASCC 292, fructooligosaccharide, and maltodextrin  diet ” [2006]
    • “Genistein[soy] reduced growth rate of Bacteroides fragilis” [2017] – slows, did not reduce.
  • Prebiotics
    • ” polydextrose (PDX) and galactooligosaccharide (GOS) …no difference was seen in … Bacteroides” [2011]
  • Probiotics
    • “Lactobacillus acidophilus La-5 and Bifidobacterium
      BB-12 …Bacteroides were significantly increased” [2015]
    • ” bacteroides were significantly increased following Lactobacillus plantarum LP‑Onlly  administration. ” [2017]
    • ” L. casei CCFM419 dramatically increased the abundance of Bacteroidetes” [2017]
    • “Lactobacillus casei strain Shirota (LcS)-…a significant decline in the Bacteroides fragilis group, ” [2017]
    • “Lactobacillus kefiri LKF01 ..Bacteroides…. were significantly reduced ” [2017]
    • “Bacillus licheniformis-B. subtilis mixture …attenuated E. coli-induced expansion of Bacteroides uniformis” [2017]
    • “Bifidobacterium infantis 1222 highly inhibited the growth of B. vulgatus in the coculture ” [2003]
    • ” Lactobacillus salivarius ssp. salivarius UCC118….. no effect” [2001]
    • “VSL-3… while enterococci, coliforms, Bacteroides and Clostridium perfringens did not change significantly. ” [2001]
    • “Bacillus subtilis CSL2 …Bacteroidetes were more highly abundant ” [2017]
    • “The probiotica containing live combined Bifidobacterium, Lactobacillus and Enterococcus could increase bifidobacterium count (P<0.01) and lactobacillus count (P<0.05); decrease bacteroides count “[2006] – species behind pay wall 😦
    • ” Intake of yogurt with Bifidobacterium longum BB536 reduced the enterotoxigenic B. fragilis.” [2012]
  • adhesion inhibition (a good thing to reduce – does not mean kill): [2007]
    adh

Bottom Line

Avoid

Take