lassesen 4:54 am on November 30, 2017  

A mother and daughter Microbiome Analysis

My understanding is that microbiome is partially inherited. A reader has CFS as well as her mother. I am curious to see how similar or dissimilar they are.

Reader Notes

Our medical histories are complicated.
My mother had a childhood infection that kept her bedridden and on antibiotics for years. Medical care was subpar – they weren’t sure she would survive. She emerged with permanently reduced kidney function. She was sick a bit more than usual for most of her life.
In 2005-2007 her CFS began to surface. She had to leave work. She can still walk around the block regularly, but there is a toll. She also has a history of acid reflux and taking PPIs, which may account for that streptococcal overgrowth. She had surgery to take care of that, so is no longer on the PPI. She is vegetarian.
My CFS started around 1997 or so. It seemed to be after a mono-like illness. It started suddenly, but progressed gradually. I was once an athlete, but I cannot walk much now – I’m often housebound. I also enjoyed studying, but that takes a large toll. My PEM is much worse than my mother’s. I am not vegetarian, but I eat far more vegetables than average.
General symptoms: severe fatigue, PEM, orthostatic intolerance / dizziness, sensitivity to light/sound, plaque psoriasis and psoriatic arthritis (plaque since 2000, arthritis since about 2010), poor sleep, and a lot of other recurrent annoyances.

Standard Items:

Firmicutes to Bacteroidetes:  Normal 2.1:1

Measure Daughter Mother
Diversity 6%ile 16%ile
Firmicutes to Bacteroidetes: 1420 :1 1.2:1
Akkermansia 0x 0x
Bifidobacterium 1x (Normal) 4.13x
Lactobacillus 0.02x < 0.01x

Uncommon Bacteria

It is interesting to note that the other extreme 822:1 ratio also included: Anaerosinus

Bacteria name Rank Daughter Mother
Anaerosinus Genus 0.3% 0.3%
 Proteiniphilum Genus  – 0.7%
Paraeggerthella Genus 0.5% –
Dysgonomonas Genus 0.7% –
Proteus Genus 1.1% –
Pediococcus Genus 2.6% –
Actinobaculum Genus – 1.8%
Anaerobacter Genus – 3.0

High Bacteria

Bacteria
 Daughter Mother
Candidatus Stoquefichus: 4.88 X –
Moryella: 4.32 X 0.01 X
Dorea: 4.06 X 1.26x
Lachnospira: 2.92 X 1.05
Haemophilus:  2.82 X < 0.01 X
Faecalibacterium:  2.64 X < 0.01 X
Eggerthella: 2.59 X 2.82 X
Sutterella: 2.58 X –
Fusicatenibacter: 2.12 X –
Roseburia:  1.88 X 0.60 X
Pseudobutyrivibrio: 1.52 X 1.06 X
Streptococcus:  0.99 X 10.39 X
Bilophila: – 3.43 X
Flavonifractor: 1.27 X 3.37 X
–
Bifidobacterium:  0.63 X 2.59 X
Erysipelatoclostridium: 0.88 X 2.09 X
Blautia:  1.39 X 1.81 X
Bacteroides:  – 1.73 X
Clostridium:  0.67 X 1.66 X
Anaerostipes: 1.29 X 1.62 X
Lactonifactor: 0.71 X 1.53 X

Reference

Both mother and daughter has long lists of overgrown genus

Daughter

Because of the extreme shift of Firmicutes to Bacteroidetes, I called out the new bacterial genus that I had to do a deep dive on.

Mother

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.

Daughter

I have done x # after items that are connected to multiple genus

Avoid

  • Animal-based diet
  • Arabinoxylans
  • Arginine supplements
  • Bacillus probiotics
  • Barley x 2
  • Berberine
  • Bifidobacterium adolescentis  Probiotics
  • Bifidobacterium pseudocatenulatum
  • Black Tea
  • BPA bottles
  • Chili pepers
  • Dietary fiber
  • Dopamine
  • Enterococcus probiotics
  • Grape seed extract, wine, Resveratrol
  • Helminth infections
  • High Fiber Diet
  • Jerusalem artichoke, Inulin, Chicory x 3
  • Lactobacillus paracasei
  • Lactobacillus salivarius
  • N-Acetyl-D-glucosamine
  • Polymannuronic acid
  • Proton-pump inhibitors (PPI) x 2
  • red wine (or grape seed extract or reservatol)
  • Resistant starch (type II)
  • Rifaximin
  • Saccharomyces boulardii  x 7
  • Sleeplessness
  • Stress
  • Vegetables
  • VSL#3 Probiotics
  • Walnuts x 8

Take

  • Bifidobacterium longum
  • Bacilus Coagulans
  • Bile salts
  • Chitosans
  • Cinnamon bark oil
  • Coriander oil
  • Epinephrine
  • Flaxseed x 7
  • Fructo-oligosaccharides
  • Galactooligosaccharides
  • Gluten-free diet
  • Green Tea (Gallate)
  • High animal protein diet
  • High Fat diet
  • High fat/ animal protein diet
  • High meat diet
  • Iron supplements
  • Lactobacillus kefiri
  • Lactobacillus plantarum probiotics
  • Lavender (spike) oil
  • Lemongrass oil
  • L-glutamine x 2
  • Low carbohydrate diet
  • Low calories High protein diet
  • Low fiber diet
  • Navy bean (Cooked)
  • Oral Iron Supplements
  • Peppermint oil
  • Perilla oil
  • Polymannuronic acid
  • Resveratrol (grape seed extract)
  • Tea Tree Oil
  • Thiamine
  • Thyme x 2
  • Vitamin D x 3

Mother

Avoid

  • Arabinoxylans
  • Bacillus subtilis x2
  • Barley x 2
  • Bifidobacterium adolescentis
  • Bifidobacterium animalis Lactis x 2
  • Broad beans  and lupin seeds
  • brown rice
  • Butyrate producing probiotics
  • Chicory root
  • Cholic acid
  • Dairy
  • flavone
  • Fluoroquinolone
  • Fructo-oligosaccharides
  • Gallic acid
  • Glucose foods (fructose [fruit sugar] appears to be fine)
  • Gum arabic
  • High animal protein/meat diet
  • High grain diet
  • High meat diet
  • Hospital Food
  • Isoniazid-
  • Lactobacillus acidophilus
  • L-citrulline
  • Low fat diets
  • L-sorbose
  • Metformin
  • Milk-derived saturated fat
  • Omega-3
  • Proton-pump inhibitors (PPI)
  • Pyrazinamide
  • Raspberries
  • Rifampin-
  • Rosemary
  • Saccharin
  • Saccharomyces boulardii
  • Safflower oil
  • Sleepless nights
  • Sodium butyrate
  • Soy
  • Stevia
  • Tannic acid
  • Xylitol

Take

  • Aloe vera
  • Bacillus clausii
  • Bacillus licheniformis x 2
  • Berberine
  • Black cumin Seed
  • Chinese Ginger, Fresh Ginger
  • Chitosan supplements
  • Chocolate
  • Cinnamon bark oil
  • Coleus forskohlii, Plectranthus barbatus, Indian Coleus
  • Coptis chinensis, Chinese gold thread
  • Eucalyptus globulus, Tasmanian bluegum
  • Figs
  • Flaxseed x 3
  • Garlic (allicin) x 2
  • Gooseberry
  • Green Tea
  • Hyocyamine
  • Inulin (Chicory) x 3
  • Ketogenic diet
  • Lactobacillus casei x 4
  • Lactobacillus kefiri x 3
  • Lactobacillus paracasei x 3
  • Lactobacillus Reuteri
  • Larreatridentata, chaparral, gobemadora, greasewood, creosote bush
  • Lemongrass oil
  • Licorice
  • Magnolia Bark
  • Mutaflor (E.Coli Nissle 1917)
  • Navy bean (Cooked)
  • Olive Leaf
  • Oranges (pectin/flavanones)
  • Peppermint oil
  • Polymannuronic acid
  • Prescript Assist
  • Propionibacterium freudenreichii
  • Salvia officinalis, Common Sage
  • Stevia
  • Streptococcus Probiotics x 2
  • Sucralose (Splenda)
  • Thyme
  • Triphala
  • Turmeric
  • Turnera diffusa, Damiana
  • Vitamin D x 2
  • Walnuts
  • Withania somnifera (Ashwangdha)
  • β-Glucan

What is in common?

Vitamin D, Flaxseed. Thyme, Chitosan, Cinnamon etc. no Saccharomyces boulardii, no Bifidobacterium adolescentis

IMHO, a lot of spicy food (“South Indian Spicy menu” – I love the spicy food in Hyderabad and Chennai when I worked there )

Both having Anaerosinus (probability is very very low, 1:100,000) and the other extreme F:B ratio also having it also — grabs my attention!

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