Category Archives: Conditions

Unknown's avatar lassesen 9:10 pm on November 5, 2017  

Another enhanced uBiome Analysis

I have been slowly working on this analysis for almost a month because it has a large number of high bacteria genus. Many of which needed deep dive.  When I got to the bottom line, I was delighted that there was few common Avoid/Take items.

Standard Items

The items below follow the high level patterns of all other CFS readers.

Usual major shift of ratios

ah3

Unlike most CFS readers (where at least one is at 0x, we have both > 0, just very low)

ah2

Enterobacteriaceae (Parent of E.Coli)  0.01X (low or no E.Coli is standard)

Biodiversity:  94%ile (very high — typical for CFS readers using uBiome)

Uncommon Bacteria

ah4

I will do an addendum later for these rate bacteria.

High Bacteria Genus

We have 14 genus >= 1.5, a new record!

ah1

Bacteria “Hit List”

Bottom Line Suggestions

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

  • Aspirin (other NSAID’s are fine)
  • Bacillus subtilis
  • Barley
  • Berberine
  • Bifidobacterium animalis
  • BPA bottles
  • Chemotherapy
  • Gluten
  • High protein diet
  • Iron supplements
  • Kombucha
  • Lactobacillus Fermentum
  • Lactobacillus Reuteri
  • Oligofructose
  • Pomegranate
  • Proton-pump inhibitors (PPI)
  • Resistant starch (type I & III)
  • Saccharomyces boulardii
  • Sodium Butyrate
  • Walnuts
  • β-Glucan

Take

  • Bacillus licheniformis
  • Bifidobacterium Breve
  • Bile supplements
  • Cellobiose
  • Chitosan supplements
  • Chocolate!
  • Coconut Oil, Monolaurin (Lauric Acid)
  • Cranberry bean flour
  • Enterococcus  faecalis probiotics
  • Fennel
  • Flaxseed
  • Gallate – Tea
  • Gluten free diet
  • High Fat diet
  • High resistance starch
  • Inulin
  • Lactobacillus Casei
  • Lactobacillus kefiri LKF01
  • Lactobacillus plantarum probiotics
  • Lactobacillus rhamnosus probiotics
  • Lactobacillus acidophilus
  • L-glutamine
  • lychee, rambutan, guarana, korlan, pitomba, Spanish lime and ackee. [fam-Sapindaceae]
  • Navy bean (Cooked)
  • palm kernel meal
  • Polymannuronic acid
  • Prescript Assist
  • Resistant starch (type II & IV)
  • Smoking (!?!)
  • Streptococcus Probiotics
  • Trametes versicolor
  • Xylitol
  • Xylooligosaccharide

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 8:53 pm on November 5, 2017  

Decreasing Desulfovibrio Genus

For updated information see Microbiome Prescription

DataPunk.Net Data

ENHANCED BY

PubMed Data

There are 3000+ studies on PubMed.

Disease

Diet

  • “a high-fat, very low-carbohydrate normocaloric diet …a statistically significant increase in Desulfovibrio spp. (p = 0.025), a bacterial group supposed to be involved in the exacerbation of the inflammatory condition of the gut mucosa associated to the consumption of fats of animal origin.” [2017]

Prebiotics

Probiotics

  • “the relative abundance of Alistipes, Odoribacter, Ruminococcus, Blautia and Desulfovibrio were higher after Bacillus subtilis, while the potential pathogens such as Staphylococcus and Escherichia-Shigella were lower than those of control.”
  • “Lactobacillus plantarum P-8 …other beneficial bacteria, whereas Desulfovibrio (P < 0.05) and other opportunistic pathogens decreased after taking Lp-8 for 4 wk. ” [2014]

Antibiotics

Bottom Line

Avoid

Take

Unknown's avatar lassesen 8:35 pm on November 5, 2017  

Reducing Terrisporobacter Genus

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

PubMed Data

There are 6+  studies on PubMed.

Disease

Diet

  • ” Terrisporobacter and Clostridium were decreased in the  palm kernel meal  groups compared to the control. ” [2016]

Prebiotic

Probiotic

Antibiotic

  • “The patient received an 8-week course of moxifloxacin and metronidazole with an excellent clinical response at 12 months’ follow-up.” [2016]

Bottom Line

Avoid

Take

Unknown's avatar lassesen 8:26 pm on November 5, 2017  

Reducing Hespellia Genus

This is the sparsest deep dive — if you find anything, please comment

For updated information see Microbiome Prescription

DataPunk.net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 3+ studies on PubMed

Disease

Diet

Prebiotic

Probiotic

Antibiotic

Bottom Line

Avoid

Take

Unknown's avatar lassesen 8:13 pm on November 5, 2017  

Reducing Dialister Genus

For updated information see Microbiome Prescription

DataPunk.net Data

Nothing

PubMed Data

There are 180+ studies on PubMed.

Disease

  • “Subjects with ultrasound evidence of enthesitis were enriched in Campylobacter, while subjects with uveitis and radiographic sacroiliitis were respectively enriched in Erwinia and unclassified Ruminococcaceae, and both enriched in Dialister. ” [2017]
  • “observed the declined abundance of Prevotella_9 and Dialister,in  Hypothyroid Hashimoto’s thyroiditis ” [2017]
  • “In IBS, Dialister spp. and then Faecalibacterium prausnitzii were the most representative species. ” [2018]
  • “The genera Haemophilus (log2 fold change -2.15, P=.003), Dialister (log2 fold change -2.22, P=.009), Dorea (log2 fold change -1.65, P=.02), and Clostridium (log2 fold change -1.47, P=.002) were underrepresented among subjects with food sensitization. ” [2017]
  • Brief Report: Dialister as a Microbial Marker of Disease Activity in Spondyloarthritis [2017].
    • “abundance of the genus Dialister was found to be positively correlated with the Ankylosing Spondylitis Disease Activity Score “
  • “At the genus level, we observed a decrease in the relative abundance of Alistipes, Bilophila, Dialister, Parabacteroides, and Veillonella in the Autism spectrum disorders  cohort, while Collinsella, Corynebacterium, Dorea, and Lactobacillus were significantly increased.” [2017]
  • ” Genera Rhodococcus, Eggerthella, Klebsiella, Prevotella, Eubacterium, Flavonifractor and Incertae sedis were significantly enriched, while genera Dialister and Pseudobutyrivibrio were significantly depleted in Systemic lupus erythematosus  patients.” [2016]
  • “At the genus level, the composition of Blautia was increased in T1DM group than control group whereas the composition of Haemophilus, Lachnospira, Dialister, and Acidaminococcus was decreased” [2016]

Diet

  • “48 OTUs increased by 12.8-fold, including Lactobacillaceae (8 of 9 belonging to Lactobacillus), Ruminococcaceae (6 of 11 belonging to Faecalibacterium), and Veillonellaceae (8 of 15 belonging to Dialister) from taking  α-glucosidase inhibitor acarbose “
  • ” At the genus level, Dialister, Dorea, Pseudobutyrivibrio, and Veillonella, belonging to the Firmicutes phylum, had statistically significant reduction with oral supplementation with L-glutamine” [2015]
  • “The inclusion of whole-grain barley enriched the genera Roseburia, Bifidobacterium and Dialister, and the species Eubacterium rectale, Roseburia faecis and Roseburia intestinalis. ” [2013]

Prebiotics

Probiotics

  • “Reutericyclin producing L. reuteri increased the abundance of Dialister spp. and Mitsuokella spp. (P < 0.05) ” [2015]
  • “[Lactobacillus acidophilus NCFM (10(9) CFU) and cellobiose (5 g)] ..The synbiotic increased levels of Lactobacillus spp. and relative abundances of the genera Bifidobacterium, Collinsella, and Eubacterium while the genus Dialister was decreased (P < 0.05). [2014]
  • “In addition, the Enterococcus faecium NCIMB 11181  probiotic-fed group featured elevated levels of Lactobacillus, Enterococcus, Oscillibacter, Succinivibro, and Clostridium genera and decreased levels of Escherichia and Dialister genera, compared with the control group. ” [2015]

Antibiotics

  • ” The end of ciprofloxacin treatment correlated with a reduced proportion of Bifidobacterium (Actinobacteria), Alistipes (Bacteroidetes) and four genera from the phylum Firmicutes (Faecalibacterium, Oscillospira, Ruminococcus and Dialister) and an increased relative abundance of Bacteroides (Bacteroidetes) and the Firmicutes genera Blautia, Eubacterium and Roseburia. ” [2015]

Bottom Line

Avoid

  • Lactobacillus Reuteri
  • Barley

Take

  • L-glutamine
  • Lactobacillus acidophilus
  • Cellobiose