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 

 

 

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.

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

 

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].

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

 

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]

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 Bfragilis.” [2012]
  • adhesion inhibition (a good thing to reduce – does not mean kill): [2007]
    adh

Bottom Line

Avoid

Take

 

 

Decreasing Odoribacter genus

DataPunk.Net Data

No data

PubMed Data

There are 35+ studies on PubMed.

  • Diet:
    • “Low Vitamin D…Odoribacter were depleted” [2015]
    • “pomegranate juice…positively correlated with Odoribacter genus.” [2015]
    • “the number of Odoribacter_f was increased in doenjang-treated mice (a fermented Korean soybean paste)” [2014]
    • “stress significantly increased the relative abundance of Odoribacter,” [2015]
    • “the animal-based diet caused a significant increase in the relative abundance of Bilophila, Odoribacter,”
    • “the levels of Odoribacter were significantly increased by 3.3 fold at the time point of 24 h after allergen challenge
  • Prebiotics:
    • “oligosaccharide treatment increased the levels of Lactobacillus and Bifidobacterium and decreased the levels of Odoribacter, ” [2017]
  •  Probiotics:
    • “Bacillus subtilis CGMCC 1.1086 …the relative abundance of Alistipes, Odoribacter, Ruminococcus, Blautia and Desulfovibrio were higher, ” [2016]
    • “edible bifidobacteria (Bifidobacterium longum, B. infantis, B. animalis, B. bifidum, B. adolescentis or B. breve) .. decreasing the abundance of Alistipes, Odoribacter and Clostridium. ” [2017]
    • “Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10, .. attenuated the D-GalN-induced Odoribacter depletion.”[2017]  – increased that is

Bottom Line

Avoid

  • Allergens
  • Bifidobacterium pseudocatenulatum
  • Bifidobacterium catenulatum
  • pomegranate juice
  • fermented Korean soybean paste
  • stress
  • animal-based diet

Take

  • Bifidobacterium longum, B. infantis, B. animalis, B. bifidum, B. adolescentis or B. breve — study only dealt with mixture 😦
  • Oligosaccharide prebiotics

Decreasing Eggerthella genus

” the gut bacterium Eggerthella lenta modifies the cardiac drug digoxin, and renders it inactive …implicated a role for arginine in regulating the growth of the organism”[2013]

DataPunk.Net Data

ENHANCED BY

ANTIBIOTIC RESISTANCE

PubMed Data

There are 120+ studies on PubMed.

  • Disease:
  • Diet:
    • Low Vitamin D… Eggerthella was enriched.[2015]
    • “the daily consumption of red wine polyphenol…significantly increased the number of … Eggerthella lenta, ” [2012]
    • The tea tree oil was the most active to Eggerthella” [2016]
  • Probiotics:
  •  Antibiotics:
    • “all were susceptible to amoxicillin-clavulanate, cefoxitin, metronidazole, piperacillin-tazobactam, ertapenem, and meropenem, 91% were susceptible to clindamycin, 74% were susceptible to moxifloxacin, and 39% were susceptible to penicillin.” [2015]

Bottom Line

Avoid

  • Grape seed extract, wine, Resveratrol
  • Arginine supplements

Take

  • Vitamin D
  • Tea Tree Oil

 

 

Decreasing Parasutterella Genus

DataPunk.Net Data

No Information

PubMed Data

There are 15+ studies on PubMed.

  • Disease:
    • “Crohn’s disease … as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp.” [2015]
    • “Hypothyroid Hashimoto’s thyroiditis …elevated genera of the diseased group included Escherichia-Shigella and Parasutterella. ” [2017]
    • “increase with food allergy” [2016]
    • “high in autism disorder [2013]
  • Diet:
    • “enzymatically modified resistant starch ….decreased abundance of Ruminococcus, Parasutterella, ” [2015]
    • “alchohol …indicated that a reduction of Porphyromonadaceae and Parasutterella” [2017]
    • “Vitamin K2 .. significantly enriched ” [2017]
    • High Fat diet reduces [2017]
    • ” both berberine and metformin … significantly increased Parasutterella” [2015]
    • “Glucevia®, a Fraxinus angustifolia Vahl samara extract… enrichment of different taxonomic groups (Burkholderiales, Sutterellacae, Parasutterella, ” [2017]
  • Probiotics:
    • “Bifidobacterium pseudocatenulatum LI09 and Bifidobacterium catenulatum LI10… enrichment of the opportunistic pathogen Parasutterella” [2017]
    • “Lactobacillus paracasei subsp. paracasei NTU 101  … no effect” [2017]
  •  Antibiotics:
    • “florfenicol and azithromycin…here were declines in Alistipes, Desulfovibrio, Parasutterella and Rikenella in both the antibiotic groups. ” [2017]

Bottom Line

Avoid

  • Berbine
  • Metformin
  • Vitamin K2
  • Bifidobacterium pseudocatenulatum
  • Bifidobacterium catenulatum

Take

  • Alchohol
  • Enzymatically modified resistant starch