Enhanced uBiome analysis of a UK reader

Patient History

“…began a gradual decline in health nearly 6years ago, root issue is unknown, was living with someone that had EBV at one point but never had it confirmed on herself, plenty of other potential causes around the time.  Daily at least from the outside reader does very well, reader has never been bedridden and can actually do quite a lot, nothing like her former self but maybe 50% in terms of energy. However, reader’s extremely headstrong which means reader can push through tough times at the expense of her future self. Current symptoms that are most prominent are night sweats, difficulty regulating body temperature, daily headaches which can progress to migraines if not caught with self-medication (migraleve.) Has had POTS confirmed by doctors, tends to get a sore spine and general ‘bone ache’ as reader describes it, this with night sweats and temperature difficulties can make sleep an issue (tends to wake frequently.) Extremely prone to sore throats and generating lots of mucus in this area, reader had her tonsils removed as a child after repeat throat infections, there was heavy antibiotic use at this time, first major illness. Has major issues around her menstrual cycle, incidence of headaches and likelihood of a migraine increase three-fold at this time, tends to feel very bloated and sore around the abdomen at this time. Investigated lots with endocrine and though they saw plenty of bizarre readings (i.e. prolactin 4 times normal reading), they were unwilling to do much. Has issues with constipation sometimes, digests fatty food poorly, diary and beans. Consuming these foods can result in painful bloating and diarrhoea. Regularly, reader will complain of what feels like something sitting on her chest and also random sharp pains in the same area.”

Standard Items

uk1

Biodiveristy:  92%ile (what seems to be the most common value for CFS patients)

Level of all Probiotics Explorer:  0% (none)

Firmicutes to Bacteroidetes ratio: 1.3: 1 (Normal is 2.1 to 1)

Note: The description in patient history and the relatively high bifidobacterium and less extreme Firmicutes to Bacteroidetes ratio than normally seen, suggests that this reader is in the least effective 10% — both from their history and their microbiome results.

High Bacteria Genus

UK2

Rare Bacteria Genus

uk3

I will revisit the rare bacteria in a later revision.

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

  • Aspartame (Nutrasweet)
  • Berberine
  • Bifidobacterium longum
  • Fructooligosaccharides
  • High Fat Diet
  • Lactobacillus fermentum
  • L-Glutamic acid ( monosodium glutamate – MSG) and possibly gluten
  • L-Proline
  • L-Serine
  • Lysine supplements and foods
  • Minocycline
  • Penicillin
  • Saccharomyces boulardii
  • Walnuts

Take

  • Enterococcus  faecalis probiotics
  • Fennel
  • Flaxseed
  • Gallate – Tea
  • Gluten free diet
  • High resistance starch
  • Inulin
  • Lactobacillus Casei
  • Lactobacillus kefiri LKF01
  • L-Phenylalanine (Good sources of phenylalanine are eggs, chicken, liver, beef, milk, and soybeans.[5])
  • lychee, rambutan, guarana, korlan, pitomba, Spanish lime and ackee. [fam-Sapindaceae]
  • Polymannuronic acid
  • Resistant starch (type II & IV)

Based on Symptoms:

 

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.

Decreasing Coprobacter Genus

This is the first genus with zero information, so far. There were hints of material behind paywalls.

For updated information see Microbiome Prescription

DataPunk.Net Data

Nothing

PubMed Data

There are 4+ studies on PubMed.

Disease

Diet

Prebiotic

Probiotic

Antibiotic

Bottom Line

Avoid

Take

Decreasing Marvinbryantia Genus

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 8+ studies on PubMed.

Disease

  • ” The relative abundances of the bacterial genera Marvinbryantia, Corynebacterium, Psychrobacter, Christensenella, Lactobacillus, Peptostreptococcaceae incertae sedis, Anaerovorax, Clostridiales incertae sedis and Coprococcus were significantly decreased, whereas Candidatus Arthromitus and Oscillibacter were markedly increased in model rats compared with normal controls for depresison” [2017]
  • “The total bacterial count of Marvinbryantia genus was significantly lower in upper motor neuron  bowel dysfunction group when compared to the lower motor neuron group. [Spinal Cord Injury]” [2016]

Diet

  • “The relative proportions of Blautia, Bryantella, Collinsella, Lactobacillus, Marvinbryantia, Turicibacter, Barnesiella, and Parabacteroides were significantly correlated with weight loss induced by tea extracts. ” [2017]
  • “dietary resistant starch diet caused significant shifts in microbial composition/diversity, with increases in Parabacteroides, Barnesiella, Ruminococcus, Marvinbryantia and Bifidobacterium as primary contributors to the shift. ” [2016]
  • “raw potato starch ( increased the relative abundance of Turicibacter, Blautia, Ruminococcus, Coprococcus, Marvinbryantia, and Ruminococcus bromii-related OTUs in colonic digesta and mucosa” [2015]

Prebiotics

  • “Fructooligosaccharides …. were identified to be FOS-metabolizing, of which Cronobacter sakazakii, Marvinbryantia formatexigens, Ruminococcus gnavus, and Weissella paramesenteroides are reported here for the first time. ” [2015]

Probiotic

Antibiotic

  • ” the key alteration caused by 2-week low-dose penicillin treatment was a decrease of Enterohadus, Lactobacillus, streptococcus, Candidatus Arthromitus, Allobaculum, and Turicibacter; and an increase in Bacteroides, staphylococcus, Marvinbryantia, Roseburia, Peptococcus, Oscillibacter, Escherichia-Shigella and Stenotrophomonas. ” [2017]
  • “the enrichment of Akkermansia, Bacteroides, Enterorhabdus, and Marvinbryantia in the Ang II+minocycline–treated group.” [2015]

Bottom Line

Avoid

Take

Decreasing Papillibacter Genus

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 17+ studies on PubMed.

Disease

  • “Parkinson’s disease reduced content of Dorea, Bacteroides, Prevotella, Faecalibacterium, Bacteroides massiliensis, Stoquefichus massiliensis, Bacteroides coprocola, Blautia glucerasea, Dorea longicatena, Bacteroides dorei, Bacteroides plebeus, Prevotella copri, Coprococcus eutactus, and Ruminococcus callidus, and increased content of Christensenella, Catabacter, Lactobacillus, Oscillospira, Bifidobacterium, Christensenella minuta, Catabacter hongkongensis, Lactobacillus mucosae, Ruminococcus bromii, and Papillibactercinnamivorans. ” [2017] [2016]
  • ” two genera belonging to the Clostridium leptum subgroup, Faecalibacteria and Papillibacter, display consistent patterns with respect to disease status and may thus serve as reliable ‘microbiomarkers’ for IBD. [2016]

Diet

Prebiotics

Probiotics

Antibiotics

  • “In general, the community changes induced by the three β-lactam antibiotics showed consistency in inhibiting Papillibacter, Prevotella and Alistipes while inducing massive growth of Clostridium” [2015]

Bottom Line

Avoid

Take

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.