Author Archives: lassesen

Unknown's avatar lassesen 4:04 am on November 20, 2017  

uBiome result for a sample “left on shelf”

A reader wrote:

“I “pushed” smartgut into ubiome explorer and downloaded the CSV. Based on your comments, I am suspicious of how low things are. I am concerned that this is the result of degradation. It took them almost 5 months to run the sample, I actually had to contact them to ask them what the hell was going on. “

Several people have done smartgut (the professional version — which is focused on known and accepted microbiome shifts). I am not qualified to comment on degradation aspect – I understand that the techniques used is similar to recovering DNA, so gut feeling is that there may not be significant changes because of the techniques being used.

Reader Summary

11/5/2015 I woke up feeling like I was hit with mono overnight.

By 12/1/2015 I was on FMLA bed rest. Lots of pain, shaking, sweating, fever, exhaustion.

By mid December I was so run down that I could only shower every other day. The act of showering forced me back into bed. By the end of December the leg pain and muscle spasms started. I thought it was relapse remitting multiple sclerosis.

At the University Hospital an infectious disease specialist saw me twice and ran a lot of bloodwork, a large portion of which had to be completed at the Mayo labs at Rochester, MN. He concluded that I was not dealing with anything infectious and the department notified me that they would not schedule me for another appointment. (I was dismissed).

I saw a neurologist 5/2016 who said “sorry, its not MS, its CFS.” Which was the equivalent of telling me nothing at the time.
I woke up suddenly on 7/5/2016 with massive abdominal pain at 3am. I began voiding enormous amounts of fluid into the toilet from my GI tract. It was like my small intestine just stopped absorbing water and dumped it out. I struggled to get this under control for 6 weeks and did end up in the ER due to dehydration in the middle of the summer.
Following that episode, I demanded a screen of my ANA, which was positive. I was referred to rheumatology and a workup found positive anti phospholipid antibodies.
I was sent to digestive diseases and pressured into having an upper and lower endscopy, which found nothing. I tried, really tried, to explain that it was probably part of the hallmark “IBS” portion of CFS. The procedure left me with three herniated discs in my neck, which is just stacking disability onto disability at this point.
I’ve had two tests for mycoplasma. Unfortunately they both came back in the equivocal range. I do have antibodies against CMV, but they are the “old” ones, not the “recent” ones. The levels were off the scale of the lab test.
In 4/2017 my ANA was rechecked and it had “gone away,” which only frustrated my situation.
Since 8/2016 I have been having susceptible stap infections on my face, neck, torso. I shower with chlorhexidine and use mupirocin to treat it topically when it occurs. The primary literature suggests that this is cutaneous anergy, which is part of CFIDS.
Since 1/2017 I have had “rug burn” like rashes on my eyelids. They wax and wane unless I use an expensive topical steroid for around the eyes.
Also, my spleen is very large and often uncomfortable.
I am on the very long wait list to be seen at Stanford because no one here at Iowa wants to even see me, much less treat me.

Standard Items:

  • No Probiotics genus thus: no Lactobacillus or bifidobacterium.
  • No Akkermansia reported

Typical CFS profile

High Bacteria

Bacteria
Ratio
Acidaminococcus: 7.11 X
Succinivibrio: 5.01 X
Catenibacterium: 4.38 X
Phascolarctobacterium 4.19 X
Haemophilus:  4.13 X
Peptoclostridium: 1.71 X
Sutterella: 1.70 X

References:

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

  • Bacillus natto (likely all bacillus)
  • Berberine
  • BIO-THREE
  • BPA bottles
  • Cashews
  • Enterococcus faecium
  • Ginkgo
  • Glutamate
  • Lactobacillus acidophilus
  • Lactobacillus rhamnosus
  • Navy bean (Cooked)
  • Partial Sleep Deprivation [parent]
  • Polydextrose
  • Proton-pump inhibitors (PPI)
  • Soluble corn fiber
  • Thiamine supplements
  • Xylans

Take

  • Acarbose
  • Cinnamon bark oil
  • Coriander oil
  • Cranberry bean flour [parent]
  • Flaxseed
  • Fructooligosaccharides (FOS)
  • Fumarate
  • Galactooligosaccharides (GOS)
  • High-protein, low-carbohydrate diet
  • Lactobacillus Casei
  • Lactobacillus kefiri
  • Lactobacillus paracasei
  • Lactobacillus plantarum
  • Lavender (spike) oil
  • Lemongrass oil
  • Peppermint oil
  • Perilla oil
  • Resistant starch (type II)
  • Saccharomyces boulardi
  • Sodium chloride (Table Salt)
  • Thyme oil
  • Vitamin D

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 9:32 pm on November 19, 2017  

Another Ubiome from a Spanish Reader

Reader Summary

  • Woman, 52 years old, Spain,
  • When I took the sample for Ubiome my situation was remission by 80-90%. I was asymptomatic and could lead an almost normal life.
  • I am now working to lower my bacteria over and I think I am walking backwards, I no longer feel with the energy and the spirit that I had. My intestinal problems keep well. It seems that some of these over bacteria are good for me.
  • And that my ubiome could represent in my case a marker very close to being
    healthy for me.
  • I have been ill for 12 years, diagnosed with breast cancer 7 years ago, Multiple Chemical Sensitivity severe degree three years ago
  • In the almost two years that I follow your blog I have improved up to almost 90%.
  • I have taken the following PROBIOTICS:
    • Lactobacillus plantarum (positive)
    • Presscrip Assist (unchanged) much anxiety
    • Symbioflor 2 (very positive)
    • Simbioflor 1 and 2 (positive)
    • Align (very positive)
    • Reuteri protectis and Prodentis (positive)
    • Culturelle (positive)
    • Lactobacillus fermentum M03 (excellent) Herx low doses to avoid progressive increased.
    • Others without significant results …..
  • I have taken the following Herbs:
    • Neem (positive)
    • Tulsi (unchanged)
    • Oregano (positive)
    • Thyme (positive)
    • Ashwaghanda (very positive)
    • Curcuma (positive)
      Others without apparent results ….
  • SUPPLEMENTS: (All recommended on your blog)
    • Vitamin D (very positive) taking a lot of sun.
      Other supplements (positive)

Standard Measures

  • Biodiversity: 82%ile
  • Bifidobacterium: 1.73x
  • Lactobacillus 0.02x
  • Firmicutes:Bacteroidetes ratio: 1.2 : 1 (normal 2.1:1)
  • Akkermansia: .48x (half the usual)

The microbiome appears to reflect the severity that is described above. If appears that Bifiobacterium and Akkermansia have managed to get established. On the opposite side, the Firmicutes:Bacteroidetes ratio being low suggests that we have not stabilized, that is “one set of demons have been tossed out of the house, but some new ones may start appearing!”

Overgrowth Bacteria Order

Erysipelotrichales: 2.17 X
Desulfovibrionales: 1.65 X
Bacteroidales:  1.26 X
Burkholderiales:  1.15 X
Bifidobacteriales: 1.09 X

Overgrowth Bacteria Genus

Oscillospira:  5.23 X
Adlercreutzia: 5.21 X
Butyricimonas: 4.02 X
Anaerotruncus: 3.45 X
Erysipelatoclostridium: 2.84 X
Parabacteroides:  2.75 X
Pseudoflavonifractor: 2.27 X
Bilophila: 2.02 X
Marvinbryantia: 1.92 X
Faecalibacterium:  1.89 X

Rare Bacteria Genus

Olsenella genus 4.2%

Reference

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

  • Amoxicillin-Clavulanate antibiotics
  • Barley
  • Berberine
  • Bifidobacterium adolescentis  Probiotics
  • Bifidobacterium animalis subsp.  lactis  B-12®) [See PDF where it was found to increase it 3 fold]
  • Bifidobacterium longum
  • Bifidobacterium pseudocatenulatum
  • Bile
  • Canola Oil
  • Clostridium butyricum (i.e. Miyarisan) probiotics
  • CVS Maximum Strength Probiotic
  • Dairy
  • Enterococcus probiotics
  • Fructooligosaccharides
  • Getting Cold
  • High Fiber Diet
  • Isoniazid-
  • Jerusalem artichoke, Inulin, Chicory
  • Lactobacillus fermentum
  • Lactobacillus paracasei
  • Lingonberries
  • Milk-derived saturated fat
  • Minocycline
  • Penicillin
  • Phosphorus containing food
  • Pyrazinamide
  • red wine (or grape seed extract or reservatol)
  • Resistant Starch
  • Resveratrol (Grapes, wine)
  • Rhubarb
  • Rifampin
  • Saccharomyces boulardii
  • Sleepless nights
  • VSL#3 Probiotics
  • Walnuts

Take

  • Bacilus Coagulans probiotics
  • Bile salts
  • Capsaicin (chili peppers)
  • Chicory
  • Chitosans
  • E.Coli Probioitics
  • Flaxseed
  • Gallate – Green Tea is highest
  • gluten-free diet
  • Grapes (table) – likely grape seed extract will help
  • High-fat diet
  • Iron supplements
  • Ketogenic diet
  • Lactobacillus Casei
  • Lactobacillus kefiri
  • Lactobacillus plantarum
  • Lactobacillus reuteri
  • Lactobacillus salivarius
  • Low fiber diet
  • Metronidazole antibiotics
  • Navy bean (Cooked)
  • Omega 3 fatty acids (600 mg of omega-3 daily for 14 days cited in studies )
  • Polymannuronic acid
  • Resistant starch (type II & IV)
  • Tea
  • Thyme
  • Vitamin K2

Comment on the above

  • It was interesting that all of the specific strains of Bifidobacterium were on the Avoid list — given that there is a high(173%) amount of Bifidobacterium, that makes sense. Genus that may be encouraged by the Bifidobacterium are in the high list, and those discouraged have already dropped to normal or below.
  •  No Dairy (i.e. no yogurt, cheese etc) seems indicated as well as No gluten.  Start looking for recipes with Thyme, Chili Peppers.

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 8:37 pm on November 19, 2017  

Reducing Pseudoflavonifractor Genus

For updated information see Microbiome Prescription

Was reported high in Ian Lipkin study (see this post).

  • “This genus [Pseudoflavonifractor] is one of the most prominent butyrate producers, providing energy to the colonic mucosa and known to regulate gene expression, inflammation, differentiation, and apoptosis in host cells (Luo et al., 2013).”

DataPunk.Net Data

Nothing

PubMed Data

There are 10+ studies on PubMed.

Disease

  • “We also performed species classifications and found Holdemania filiformis and Pseudoflavonifractor capillosus to be increased and decreased in the PPI cohort, respectively.” [2016]

Diet

  • Phosphorus in diet increases [2016]

Prebiotics

Probiotics

Antibiotics

Bottom Line

Avoid

  • Phosphorus containing food

Take

  • Proton pump inhibitor
Unknown's avatar lassesen 8:21 pm on November 19, 2017  

Reducing Anaerotruncus Genus

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 32+ studies on PubMed.

Disease

  • “Genus Anaerotruncuswas increased in children of gestational diabetes mellitus  women ” [2017]
  • “Anaerotruncus and several Bacteroides spp., and correlated with nonmotor symptoms.. Parkinson’s disease” [2017]
  • “The genera Anaerotruncus and Oscillibacter as well as Ruminococcus torques and Eubacterium ventriosum were relatively enriched in patients with age-related macular degeneration ,” [2017]
  • “Several taxa were found to be significantly enriched in samples belonging to the endometrial cancer cohort: Firmicutes (Anaerostipes, ph2, Dialister, Peptoniphilus, 1-68, Ruminococcus, and Anaerotruncus), Spirochaetes (Treponema), Actinobacteria (Atopobium), Bacteroidetes (Bacteroides and Porphyromonas), and Proteobacteria (Arthrospira). ” [2016]
  • “Notably, the increased bacteria included Bifidobacterium spp. and various representatives of Clostridium clusters IV and XIVa, such as Clostridium leptum, Oscillospira guillermondii, Sporobacter termitidis, Anaerotruncus colihominis, Ruminococcus callidus, R. bromii, Lachnospira pectinoschiza, and C. colinum, which are presumed to be anti-inflammatory.. after a fecal transpant” [2014]
  • “Depression correlated inversely with Lachnospiraceae family (rho =-0.58, FDR_p = 0.018), anxiety with genus Anaerotruncus (rho = 0.65, FDR_p = 0.001), and IBS severity with genera Ruminococcus (rho = 0.62, FDR_p = 0.005) and Coprococcus (rho = 0.59, FDR_p = 0.013). ” [2017]

Diet

  • “Walnuts increased the abundance of Firmicutes and reduced the abundance of Bacteriodetes. Walnuts enriched the microbiota for probiotic-type bacteria including Lactobacillus, Ruminococcaceae, and Roseburia while significantly reducing Bacteroides and Anaerotruncus. ” [2017]

Prebiotics

Probiotics

  • “Lactobacillus salivarius SMXD51 ..Anaerotruncus sp. decrease and Subdoligranulum sp. increase.” [2017]
  • ” In particular, during the recovery phase the [L. rhamnosus A 191, Lactobacillus acidophilus, Bifidobacterium breve, Bifidobacterium longum (CVS Maximum Strength Probiotic)] probiotic caused a suppression of Enterobacteriaceae outgrowth (Shigella and Escherichia) while promoting a blooming of Firmicutes, particularly from the Anaerotruncus genus. ” [2016]

Antibiotics

Bottom Line

Avoid

Take

Unknown's avatar lassesen 7:45 pm on November 19, 2017  

Reducing Haemophilus Genus

For updated information see Microbiome Prescription

“the metabolism of Staphylococcus produces the necessary blood factor byproducts required for Haemophilus growth.” [wikipedia]

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

ANTIBIOTIC RESISTANCE

  • Cephalosporin
  • Chloramphenicol
  • Lincosamide
  • Macrolide
  • Penicillin
  • Streptogramin b
  • Tetracycline

PubMed Data

There are 28077+ study on PubMed

Disease

  • ” both of Moraxella and Haemophilus colonization are associated with higher risk of lower respiratory infection ” [2015]

Diet

  • “Vitamin D… Haemophilus and Veillonella were less abundant  in the subset with the highest vitamin D intake ” [2017]

Prebiotic

Probiotic

  • “at species level, a higher abundance of Blautia producta, Blautia wexlerae and Haemophilus ducrey was observed, together with a reduction of Holdemania filiformis, Escherichia vulneris, Gemmiger formicilis and Streptococcus sinensis abundance.. from Lactobacillus rhamnosus HN001 and Bifidobacterium longum BB536 .” [2017]
  • “after the end of Lactobacillus kefiri LKF01 DSM32079 (LKEF) probiotic administration Bacteroides, Barnesiella, Butyricicomonas, Clostridium, Haemophilus, Oscillibacter, Salmonella, Streptococcus, Subdoligranolum, and Veillonella were significantly reduced if compared to baseline samples.” [2017]

Antibiotic

Bottom Line

Avoid

Take